Science.gov

Sample records for population association analysis

  1. Accounting for linkage disequilibrium in association analysis of diverse populations.

    PubMed

    Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

    2014-04-01

    The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases.

  2. [Analysis of population stratification using random SNPs in genome-wide association studies].

    PubMed

    Cao, Zong-Fu; Ma, Chuan-Xiang; Wang, Lei; Cai, Bin

    2010-09-01

    Since population genetic STRUCTURE can increase false-positive rate in genome-wide association studies (GWAS) for complex diseases, the effect of population stratification should be taken into account in GWAS. However, the effect of randomly selected SNPs in population stratification analysis is underdetermined. In this study, based on the genotype data generated on Genome-Wide Human SNP Array 6.0 from unrelated individuals of HapMap Phase2, we randomly selected SNPs that were evenly distributed across the whole-genome, and acquired Ancestry Informative Markers (AIMs) by the method of f value and allelic Fisher exact test. F-statistics and STRUCTURE analysis based on the select different sets of SNPs were used to evaluate the effect of distinguishing the populations from HapMap Phase3. We found that randomly selected SNPs that were evenly distributed across the whole-genome were able to be used to identify the population structure. This study further indicated that more than 3 000 randomly selected SNPs that were evenly distributed across the whole-genome were substituted for AIMs in population stratification analysis, when there were no available AIMs for spe-cific populations.

  3. Variants in multiple genes polymorphism association analysis of COPD in the Chinese Li population

    PubMed Central

    Ding, Yipeng; Yang, Danlei; Zhou, Long; Xu, Junxu; Chen, Yu; He, Ping; Yao, Jinjian; Chen, Jiannan; Niu, Huan; Sun, Pei; Jin, Tianbo

    2015-01-01

    Background It is known that the contribution of risk alleles to chronic obstructive pulmonary disease (COPD) may vary between populations. Further, previous studies involving various ethnic groups have revealed associations between COPD and genetic polymorphisms in families with sequence similarity 13, member A (FAM13A), micro-RNA 2054 (MIR2054), SET domain containing protein 7 (SETD7), ring finger protein 150 (RNF150), hedgehog interacting protein (HHIP), and vascular endothelial growth factor A (VEGFA). Our objective was to explore the association between these gene polymorphism and COPD in members of Chinese Li minority population. Materials and methods The Chinese Li population case–control study was conducted to assess genetic associations with COPD risk. Seven single nucleotide polymorphisms (SNPs) located on chromosome 4, including FAM13A, MIR2054, SETD7, RNF150, and HHIP, and nine SNPs in the VEGFA gene were genotyped among 234 cases and 240 controls using Sequenom Mass-ARRAY® platform. Linkage disequilibrium (LD) analysis was performed using Haploview software and the associations of the SNP frequencies with COPD were analyzed using chi-square (χ2) tests, genetic models analysis, and haplotype analysis. Results By χ2 we found the minor allele “G” of rs17050782 was with increased COPD risk in allele model. In genetic models, we found the minor allele of rs7671167 (P=0.028 by dominant model) and rs17050782 (P=0.008 by recessive model) was associated with the increased risk of COPD disease. Likewise, an increased risk of developing COPD was associated with the “GGCGC” haplotype of VEGFA (odds ratio =1.48, 95% confidence interval =1.02–2.12, P=0.037). Conclusion Our results were the first time to reveal that SNPs from FAM13A (rs7671167), SETD7 (rs17050782), and a haplotype of VEGFA (“GGCGC”) are potential susceptibility loci associated with increased COPD risk in Chinese Li minority population. PMID:26251585

  4. Adjustment for population stratification via principal components in association analysis of rare variants.

    PubMed

    Zhang, Yiwei; Guan, Weihua; Pan, Wei

    2013-01-01

    For unrelated samples, principal component (PC) analysis has been established as a simple and effective approach to adjusting for population stratification in association analysis of common variants (CVs, with minor allele frequencies MAF > 5%). However, it is less clear how it would perform in analysis of low-frequency variants (LFVs, MAF between 1% and 5%), or of rare variants (RVs, MAF < 5%). Furthermore, with next-generation sequencing data, it is unknown whether PCs should be constructed based on CVs, LFVs, or RVs. In this study, we used the 1000 Genomes Project sequence data to explore the construction of PCs and their use in association analysis of LFVs or RVs for unrelated samples. It is shown that a few top PCs based on either CVs or LFVs could separate two continental groups, European and African samples, but those based on only RVs performed less well. When applied to several association tests in simulated data with population stratification, using PCs based on either CVs or LFVs was effective in controlling Type I error rates, while nonadjustment led to inflated Type I error rates. Perhaps the most interesting observation is that, although the PCs based on LFVs could better separate the two continental groups than those based on CVs, the use of the former could lead to overadjustment in the sense of substantial power loss in the absence of population stratification; in contrast, we did not see any problem with the use of the PCs based on CVs in all our examples.

  5. Population structure analysis and association mapping of blast resistance in indica rice (Oryza sativa L.) landraces.

    PubMed

    Wu, Y Y; He, J B; Li, A H; Fang, N Y; He, W W; Dang, L L; Zeng, G Y; Huang, J; Bao, Y M; Zhang, H S

    2016-08-12

    Rice blast caused by Magnaporthe oryzae is one of the most devastating rice diseases worldwide. To understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (SSR) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. This population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. The genetic diversity and association of the population with resistance were analyzed by examining the phenotype for 160 SSR markers distributed on 12 rice chromosomes. The 276 accessions were classified into seven groups using model- and distance-based cluster analyses. Associations between SSR markers and blast resistance showed that 26 SSR markers were significantly associated with blast resistance in 2012 and 2013 (P < 0.01) and that the phenotypic variation ranged from 2.68 to 13.11%. Nineteen of the markers associated with blast resistance were located in regions where genes or quantitative trait loci (QTLs) have been previously reported, and seven were newly identified in this study. These results indicate that marker-trait association has potential advantages over classical linkage analysis and QTL mapping, and that these markers could be used for marker-assisted selection in rice blast-resistance-breeding programs.

  6. Association analysis of ANK3 gene variants with schizophrenia in a northern Chinese Han population

    PubMed Central

    Guo, Xiaojuan; Zhang, Yani; Du, Jieli; Yang, Hua; Ma, Yini; Li, Jingjie; Yan, Mengdan; Jin, Tianbo; Liu, Xianyang

    2016-01-01

    Schizophrenia is a chronic, severely debilitating mental disorder. Many studies have suggested that genetic factors play an important role in the onset and development of schizophrenia. In our study, we conducted a case-control study in a northern Chinese Han population of 499 schizophrenia patients and 500 controls to investigate the effect of variant genotypes of 13 SNPs in ANK3 on schizophrenia risk. Odds ratios (OR) and 95% confidence intervals (CI) were estimated using the chi-squared test, genetic model analysis, and haplotype analysis. Four ANK3 SNPs were associated with schizophrenia risk. The minor allele of rs958852 in ANK3 was associated with a 0.75-fold reduction in schizophrenia risk in an allelic model. In the genetic model, rs958852 was associated with a reduced schizophrenia risk, and rs10994336, rs10994338 and rs4948418 were associated with an increased schizophrenia risk (rs10994336, OR = 2.00, 95%CI: 1.01–3.94, p = 0.047; rs10994338, OR = 1.99, 95%CI: 1.01–3.93, p = 0.047; rs4948418, OR = 2.00, 95%CI: 1.01–3.94, p = 0.047). In addition, haplotype “TTC” of ANK3 was associated with a 0.73-fold reduced schizophrenia risk (95%CI: 0.54–0.99; p = 0.044). To our knowledge, this is the first to report of an association between ANK3 rs10994336, rs10994338, rs4948418 and rs958852 and schizophrenia risk in a northern Chinese Han population. PMID:27811378

  7. Association of carotid atherosclerosis and recurrent cerebral infarction in the Chinese population: a meta-analysis

    PubMed Central

    Liu, Jianping; Zhu, Yun; Wu, Yuhuai; Liu, Yan; Teng, Zhaowei; Hao, Yinglu

    2017-01-01

    Stroke, when poor blood flow to the brain results in cell death, is the third leading cause of disability and mortality worldwide, and appears as an unequal distribution in the global population. The cumulative risk of recurrence varies greatly up to 10 years after the first stroke. Carotid atherosclerosis is a major risk factor for stroke. The aim of this study was to investigate and estimate the relationship between carotid atherosclerosis and risk of stroke recurrence in the Chinese population. We performed a systematic review and meta-analysis of randomized controlled trials published from 2000 to 2013, using the following databases: PubMed, Embase, Medline, Wanfang, and the China National Knowledge Infrastructure. The odds ratios with 95% confidence intervals were calculated to examine this strength. A total of 22 studies, including 3,912 patients, 2,506 first-ever cases, and 1,406 recurrent cases, were pooled in this meta-analysis. Our results showed that the frequency of carotid atherosclerosis is higher in recurrent cases than that in the first-ever controls (78.88% vs 59.38%), and the statistical analysis demonstrated significant positive association between carotid atherosclerosis and recurrent cerebral infarction (odds ratio: 2.87; 95% confidence interval: 2.42–3.37; P<0.00001) in a fixed-effect model. No significant heterogeneity was observed across all studies. In conclusion, our results showed that carotid atherosclerosis was associated with increased risk of recurrent stroke. However, further well-designed research with large sample sizes is still needed to identify the clear mechanism. PMID:28260898

  8. Exome-Wide Association Analysis of Coronary Artery Disease in the Kingdom of Saudi Arabia Population

    PubMed Central

    de Kovel, Carolien G.; Mulder, Flip; van Setten, Jessica; van ‘t Slot, Ruben; Al-Rubaish, Abdullah; Alshehri, Abdullah M.; Al Faraidy, Khalid; Al-Ali, Abdullah; Al-Madan, Mohammed; Al Aqaili, Issa; Larbi, Emmanuel; Al-Ali, Rudaynah; Alzahrani, Alhusain; Asselbergs, Folkert W.; Koeleman, Bobby P. C.; Al-Ali, Amein

    2016-01-01

    Coronary Artery Disease (CAD) remains the leading cause of mortality worldwide. Mortality rates associated with CAD have shown an exceptional increase particularly in fast developing economies like the Kingdom of Saudi Arabia (KSA). Over the past twenty years, CAD has become the leading cause of death in KSA and has reached epidemic proportions. This rise is undoubtedly caused by fast urbanization that is associated with a life-style that promotes CAD. However, the question remains whether genetics play a significant role and whether genetic susceptibility is increased in KSA compared to the well-studied Western European populations. Therefore, we performed an Exome-wide association study (EWAS) in 832 patients and 1,076 controls of Saudi Arabian origin to test whether population specific, strong genetic risk factors for CAD exist, or whether the polygenic risk score for known genetic risk factors for CAD, lipids, and Type 2 Diabetes show evidence for an enriched genetic burden. Our results do not show significant associations for a single genetic locus. However, the heritability estimate for CAD for this population was high (h2 = 0.53, S.E. = 0.1, p = 4e-12) and we observed a significant association of the polygenic risk score for CAD that demonstrates that the population of KSA, at least in part, shares the genetic risk associated to CAD in Western populations. PMID:26849363

  9. A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

    PubMed

    Huyghe, Jeroen R; Fransen, Erik; Hannula, Samuli; Van Laer, Lut; Van Eyken, Els; Mäki-Torkko, Elina; Aikio, Pekka; Sorri, Martti; Huentelman, Matthew J; Van Camp, Guy

    2011-03-01

    The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise F(ST) statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, F(ST) was smallest for the comparison with the Russians (F(ST)=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

  10. A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies

    PubMed Central

    Huyghe, Jeroen R; Fransen, Erik; Hannula, Samuli; Van Laer, Lut; Van Eyken, Els; Mäki-Torkko, Elina; Aikio, Pekka; Sorri, Martti; Huentelman, Matthew J; Camp, Guy Van

    2011-01-01

    The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations. PMID:21150888

  11. Association analysis of the RGS4 gene in Han Chinese and Scottish populations with schizophrenia.

    PubMed

    Zhang, F; St Clair, D; Liu, X; Sun, X; Sham, P C; Crombie, C; Ma, X; Wang, Q; Meng, H; Deng, W; Yates, P; Hu, X; Walker, N; Murray, R M; Collier, D A; Li, T

    2005-10-01

    We investigated the RGS4 as a susceptibility gene for schizophrenia in Chinese Han (184 trios and 138 sibling pairs, a total of 322 families) and Scottish (580 cases and 620 controls) populations using both a family trio and case-control design. Both the samples had statistical power greater than 70% to detect a heterozygote genotype relative risk of >1.2 for frequent RGS4-risk alleles. We genotyped four single nucleotide polymorphisms (SNPs) which have previously been associated with schizophrenia as either individually or part of haplotypes. Allele frequencies and linkage disequilibrium between the SNPs was similar in the two populations. In the Chinese sample, no individual SNPs or any of their haplotypes were associated with schizophrenia. In the Scottish population, one SNP (SNP7) was significantly over-represented in the cases compared with the controls (0.44 vs. 0.38; A allele; chi(2) 7.08, P = 0.011 after correction for correlation between markers by permutation testing). One two-marker haplotype, composed of alleles T and A of SNP4 and SNP7, respectively, showed individual significance after correction by permutation testing (chi(2) 6.8; P = 0.04). None of the full four-marker haplotypes showed association, including the G-G-G-G haplotype previously associated with schizophrenia in more than one sample and the A-T-A-A haplotype. Thus, our data do not directly replicate previous associations of RGS4, but association with SNP 7 in the Scottish population provides some support for a role in schizophrenia susceptibility. We cannot conclusively exclude RGS4, as associated haplotypes are likely to be surrogates for unknown causative alleles, whose relationship with overlying haplotypes may differ between the population groups. Differences in the association seen across the two populations could result from methodological factors such as diagnostic differences but most likely result from ethnic differences in haplotype structures within RGS4.

  12. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  13. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    PubMed

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  14. Analysis of the genetic association between IL27 variants and coronary artery disease in a Chinese Han population

    PubMed Central

    Fan, Qian; Nie, Shaofang; Li, Sihui; Liao, Yuhua; Zhang, Hongsong; Zha, Lingfeng; Wang, Fan; Tang, Tingting; Xia, Ni; Xu, Chengqi; Wang, Pengyun; Xie, Tian; Xie, Jiangjiao; Lu, Qiulun; Li, Qingxian; Qian, Jin; Li, Bin; Wu, Gang; Wu, Yanxia; Yang, Yan; Wang, Qing K.; Tu, Xin; Cheng, Xiang

    2016-01-01

    Interleukin-27 (IL-27) is an important cytokine in inflammatory diseases, including coronary artery disease (CAD). To explore the precise role of IL-27 in CAD, we investigated the genetic association between IL27 and CAD in the GeneID Chinese Han population. A two-stage case control association analysis was performed for 3075 CAD cases and 2802 controls. Logistic regression analysis was used to adjust the traditional risk factors for CAD. Results showed that a promoter variant, rs153109, tended to be marginally associated with CAD in the discovery population (Padj = 0.028, OR = 1.27, 95%CI: 1.03–1.58). However, this association was not replicated in the validation stage (Padj = 0.559, OR = 1.04, 95%CI: 0.90–1.21). In addition, when we classified the combined population into two subgroups according to the age at disease onset or disease state, we again obtained no significant associations. Finally, we estimated the severity of coronary stenosis using the Gensini Scoring system and determined that the rs153109 genotypes were still not associated with the Gensini scores of the CAD patients. In conclusion, our study failed to find an association between common variants in the functional region of IL27 and CAD in a Chinese Han population, which indicated that IL-27 might only be an inflammatory marker during the development of CAD. PMID:27174010

  15. Genetic association of RIT2 rs12456492 polymorphism and Parkinson's disease susceptibility in Asian populations: a meta-analysis.

    PubMed

    Lu, Yanjun; Liu, Wei; Tan, Kun; Peng, Jing; Zhu, Yaowu; Wang, Xiong

    2015-09-03

    Recent studies investigating the association of the Ras-like without CAAX 2 (RIT2) polymorphism, rs12456492, with Parkinson's disease (PD) are controversial. We performed a meta-analysis to study the association between rs12456492 and PD susceptibility in Asian populations. Literature searches of PubMed and Embase were performed up to June 3, 2015, and the strength of the association between rs12456492 and PD was evaluated by odds ratios (OR) and 95% confidence intervals (CI). Four studies conducted between 2013 and 2015, comprising 2017 PD cases and 2010 controls, were included in the meta-analysis. Significant association of rs12456492 with PD was found in the dominant (GG + AG vs. AA: OR = 1.26, 95% CI = 1.20-1.44, P = 0.00) and additive models (GG vs. AA: OR = 1.38, 95% CI = 1.03-1.83, P = 0.030). Although sensitivity analysis found that the overall result was stable only in the dominant genetic model, a publication bias was also detected. Therefore, the results should be treated with caution. The current meta-analysis suggested that rs12456492 might be associated with increased PD risk in Asian populations, but studies using larger sample sizes and different ethnic populations will be needed to further confirm this association.

  16. Association analysis of GWAS and candidate gene loci in a Pakistani population with psoriasis.

    PubMed

    Munir, Saeeda; ber Rahman, Simeen; Rehman, Sadia; Saba, Nusrat; Ahmad, Wasim; Nilsson, Staffan; Mazhar, Kehkashan; Naluai, Åsa Torinsson

    2015-03-01

    Psoriasis is a common inflammatory and hyper proliferative condition of the skin and a serious chronic systemic autoimmune disease. We undertook an association study to investigate the genetic etiology of psoriasis in a Pakistani population by genotyping single-nucleotide polymorphisms (SNPs) previously reported to be associated in genome-wide association (GWAS) or in candidate gene studies of psoriasis. Fifty seven single-nucleotide polymorphisms (SNPs) from 42 loci were genotyped in 533 psoriasis patients and 373 controls. Our results showed genome wide significant association of the MHC region (rs1265181 being the most significant from five SNPs used with overall OR=3.38; p=2.97E-18), as well as nominally significant associations at ten other loci (p<0.05) in the Pakistani population (LCE3B, REL, IL13/IL4, TNIP1, IL12B, TRAF3IP2, ZC3H12C, NOS2 and RNF114 from GWAS and PRR9 from a previous candidate gene study). Overall, only nine SNPs out of the 42 GWAS loci, displayed an odds ratio in the opposite allelic direction and only three did not reach similar odds ratio within 95% confidence interval as previously reported (SLC45A1/TNFRSF9, ELMO1 and IL28RA). This indicates similar genetic risk factors and molecular mechanisms behind disease in Pakistani psoriasis patients as in other populations. In addition, we show that the MHC and TNIP1 regions are significantly different in patients with psoriasis onset before the age of 40 (type I) compared to after 40 years of age (type II). MHC being associated mainly with type I while TNIP1 with type II patients.

  17. Genetic Association Analysis of Common Variants in FOXO3 Related to Longevity in a Chinese Population

    PubMed Central

    Yan, Dongjing; Liao, Xiaoping; Wang, Xianshou; Fu, Yunxin; Cai, Wangwei

    2016-01-01

    Recent studies suggested that forkhead box class O3 (FOXO3) functions as a key regulator for the insulin/insulin-like growth factor-1signaling pathway that influence aging and longevity. This study aimed to comprehensively elucidate the association of common genetic variants in FOXO3 with human longevity in a Chinese population. Eighteen single-nucleotide polymorphisms (SNPs) in FOXO3 were successfully genotyped in 616 unrelated long-lived individuals and 846 younger controls. No nominally significant effects were found. However, when stratifying by gender, four SNPs (rs10499051, rs7762395, rs4946933 and rs3800230) previously reported to be associated with longevity and one novel SNP (rs4945815) showed significant association with male longevity (P-values: 0.007–0.032), but all SNPs were not associated with female longevity. Correspondingly, males carrying the G-G-T-G haplotype of rs10499051, rs7762395, rs4945815 and rs3800230 tended to have longer lifespan than those carrying the most common haplotype A-G-C-T (odds ratio = 2.36, 95% confidence interval = 1.20–4.63, P = 0.013). However, none of the associated SNPs and haplotype remained significant after Bonferroni correction. In conclusion, our findings revealed that the FOXO3 variants we tested in our population of Chinese men and women were associated with longevity in men only. None of these associations passed Bonferroni correction. Bonferroni correction is very stringent for association studies. We therefore believe the effects of these nominally significant variants on human longevity will be confirmed by future studies. PMID:27936216

  18. Association between the interleukin-1β C-511T polymorphism and periodontitis: a meta-analysis in the Chinese population.

    PubMed

    Wang, H F; He, F Q; Xu, C J; Li, D M; Sun, X J; Chi, Y T; Guo, W

    2017-02-23

    The association between the interleukin-1 beta (IL-1β) C-511T (or rs16944) polymorphism and periodontitis remains inconclusive, even though there have been previous studies on this association. To assess the effects of IL-1β C-511T variants on the risk of development of periodontitis, a meta-analysis was performed in a single ethnic population. Studies, published up to December 2015, were selected for the meta-analysis from PubMed and Chinese databases. The associations were assessed with pooled OR and 95%CI. This meta-analysis identified 8 studies, including 1276 periodontitis cases and 1558 controls. Overall, a significant association between the IL-1β C-511T polymorphism and periodontitis was found in the Chinese population (TT vs CC: OR = 1.48, 95%CI = 1.19-1.85; TT + CT vs CC: OR = 1.50, 95%CI = 1.25-1.81; T vs C: OR = 1.33, 95%CI = 1.06-1.68). In the subgroup analyses based on geographical area(s), source of controls, and type of periodontitis, significant results were obtained for the association between IL-1β C-511T variants and periodontitis. Our meta-analysis indicated that the IL-1β C-511T polymorphism may be a genetic susceptibility factor for periodontitis in the Chinese population. This marker could be used to identify Chinese individuals at a high risk for periodontitis.

  19. An epigenome-wide association analysis of cardiac autonomic responses among a population of welders

    PubMed Central

    Zhang, Jinming; Liu, Zhonghua; Umukoro, Peter E.; Cavallari, Jennifer M.; Fang, Shona C.; Weisskopf, Marc G.; Lin, Xihong; Mittleman, Murray A.

    2017-01-01

    ABSTRACT DNA methylation is one of the potential epigenetic mechanisms associated with various adverse cardiovascular effects; however, its association with cardiac autonomic dysfunction, in particular, is unknown. In the current study, we aimed to identify epigenetic variants associated with alterations in cardiac autonomic responses. Cardiac autonomic responses were measured with two novel markers: acceleration capacity (AC) and deceleration capacity (DC). We examined DNA methylation levels at more than 472,506 CpG probes through the Illumina Infinium HumanMethylation450 BeadChip assay. We conducted separate linear mixed models to examine associations of DNA methylation levels at each CpG with AC and DC. One CpG (cg26829071) located in the GPR133 gene was negatively associated with DC values after multiple testing corrections through false discovery rate. Our study suggests the potential functional importance of methylation in cardiac autonomic responses. Findings from the current study need to be replicated in future studies in a larger population. PMID:28075199

  20. Genetic distribution and association analysis of DRD2 gene polymorphisms with major depressive disorder in the Chinese Han population.

    PubMed

    He, Mei; Yan, Hong; Duan, Zhao-Xia; Qu, Wei; Gong, Hai-Yan; Fan, Zheng-Li; Kang, Jian-Yi; Li, Bing-Cang; Wang, Jian-Min

    2013-01-01

    Dopamine D2 receptor is involved in reward-mediating mesocorticolimbic pathways. It plays an important role in major depressive disorder (MDD). Three gene polymorphisms Taq1A, C957T and -141C ins/del, were identified in the DRD2 gene among the Western population. These variants in the DRD2 gene might be associated with the susceptibility of MDD patients through affecting the bioeffects of endogenous dopamine neurotransmission. However, little is known about their occurrence in Chinese population and their association with the susceptibility of patients with major depressive disorder. In this study, a total of 338 unrelated adult Chinese Han population, including 224 healthy volunteers and 114 patients with major depressive disorder, were recruited. DRD2 polymorphisms (Taq1A and -141C ins/del) were detected using restriction fragment length polymorphism (RFLP) analysis and the C957T were detected by sequencing directly. As a result, three polymorphisms were identified in Chinese Han population and all were common SNP. However, we could detect no evidence of genetic association between 3 markers in DRD2 and major depressive disorder in the Chinese Han population. To conclude, this result suggests that Taq1A, C957T and -141C ins/del of DRD2 gene may not be associated with major depressive disorder, also may be the sample sizes too small to allow a meaningful test.

  1. Analysis of genetic polymorphisms associated with leukoaraiosis in the southern Chinese population

    PubMed Central

    Huang, Wen-Qing; Ye, Hui-Ming; Li, Fang-Fang; Yi, Ke-Hui; Zhang, Ya; Cai, Liang-Liang; Lin, Hui-Nuan; Lin, Qing; Tzeng, Chi-Meng

    2016-01-01

    Abstract Leukoaraiosis (LA) is a frequent neuroimaging finding commonly observed on brain MRIs of elderly people with prevalence ranging from 50% to 100%. Multiple susceptibility genes or genetic risk factors for LA have been identified in subjects of European descent. Here, we report the first replication study on several common and novel genetic variations in the Chinese population. In this study, a total of 244 subjects (201 LA patients and 43 controls) were enrolled according to our new and strict definition for LA. Subsequently, 6 genetic variants at 5 genes, rs3744028 in TRIM65, rs1055129 in TRIM47, rs1135889 in FBF1, rs1052053 in PMF1, and rs1801133 (C677T) and rs1801131(A1298C) in MTHFR, were selected for genotyping using polymerase chain reaction (PCR)-based pyrosequencing and restriction fragment length polymorphism (RFLP) together with capillary electrophoresis (CE) and agarose gel electrophoresis. Finally, Pearson's χ2 and multivariate logistic regression tests were used to examine the associations between the genotypes and LA. Among these candidate polymorphisms, except for rs1052053 and rs1801131, rs1135889 (P = 0.012) showed significant associations with LA in the dominant model, and the other 3 SNPs, rs3744028 (P = 0.043), rs1055129 (P = 0.038), and rs1801133 (P = 0.027), showed significant associations with LA in the recessive model. However, these differences no longer remained significant after adjusting for age, gender, hypertension, and diabetes mellitus and applying Bonferroni correction or Sidak correction for multiple testing. These results suggest that the above-mentioned genetic variants are not associated with LA risk. In summary, the study did not replicate the susceptibility of rs3744028, rs1055129, and rs1135889 at the Chr17q25 locus for LA nor did it find any other significant results for rs1052053, rs1801133, and rs1801131 in the Chinese population. It strongly indicated the ethnic differences in the genetics of LA

  2. Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure.

    PubMed

    Crossa, José; Burgueño, Juan; Dreisigacker, Susanne; Vargas, Mateo; Herrera-Foessel, Sybil A; Lillemo, Morten; Singh, Ravi P; Trethowan, Richard; Warburton, Marilyn; Franco, Jorge; Reynolds, Matthew; Crouch, Jonathan H; Ortiz, Rodomiro

    2007-11-01

    Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype x environment interaction, thereby making possible the identification of markers contributing to both additive and additive x additive interaction effects of traits.

  3. Association between MTHFR C677T polymorphism and depression: a meta-analysis in the Chinese population.

    PubMed

    Jiang, Wei; Xu, Jun; Lu, Xiao-Jie; Sun, Yang

    2016-09-01

    Depression is a worldwide public health issue, and its prevalence increases each year. Although a number of studies have been conducted on the association between MTHFR C677T polymorphism and depression in China, this association remains elusive and controversial. To clarify the impact of MTHFR C677T polymorphism on the risk of depression, a meta-analysis was performed in the Chinese population. Relevant studies were identified using PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure and Chinese Biology Medicine through May 5, 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the associations. A total of 13 case-control studies including 1895 patients and 1913 controls were involved in this meta-analysis. Overall, T variant of MTHFR C677T gene polymorphism was significantly associated with an increased risk of depression in the Chinese population (T vs. C: OR = 1.52, 95% CI = 1.24-1.85; TT + CT vs. CC: OR = 1.64, 95% CI = 1.16-2.30; TT vs. CC: OR = 2.19, 95% CI = 1.49-3.24; TT vs. CC + CT: OR = 1.80, 95% CI = 1.31-2.46). In subgroup analyses stratified by geographic area and source of controls, the significant results were found in population-based studies, in hospital-based studies, in North and South China. The risk conferred by MTHFR C677T polymorphism is higher in North China than in South China. In conclusion, this meta-analysis suggests that MTHFR C677T polymorphism is associated with depression in the Chinese population, but these associations vary in different geographic locations.

  4. Analysis of population genetic structure from Bucaramanga (Colombia) based on gene polymorphisms associated with the regulation of blood pressure

    PubMed Central

    Rondón, Fernando; Vargas, Clara Inés; Oróstegui, Myriam; Bautista, Leonelo; Serrano, Norma Cecilia; Páez, María c; Castillo, Adriana

    2012-01-01

    Introduction: In spite of nearly 40% of variability in blood pressure being explained by genetic factors, the identification of genes associated with essential high blood pressure is difficult to determine in populations where individuals have different genetic backgrounds. In these circumstances it is necessary to determinate whether the population is sub-structured because this can bias studies associated with this disease. Objective: To determine the genetic structure of the population in Bucaramanga from genetic polymorphisms associated with the regulation of blood pressure: 448G>T, 679C>T y 1711C>T from the gene kinase 4 of the dopaminergic receptor linked to the protein G and Glu298Asp, -786T>C and the VNTR of the intron 4 of the gene of endothelial nitric oxide. Methods: A sample of 552 unrelated individuals was studied through analysis of restriction fragment length polymorphism. The allelic, haplotypic and genotypic frequencies were calculated, the Hardy-Weinberg equilibrium was determined and a molecular analysis of variance was performed to determine the genetic structure. Results: Thirty-eight (38) Haplotypes were identified with GCCTG4b being the most frequent (21.2%). The most diverse polymorphism was 448G>T with a frequency of 49.9% for heterozygous. The six polymorphisms were found in genetic equilibrium and a genetic structure of populations was not evidenced (FST= 0.0038). Conclusion: The population studied does not present a genetic sub-structure and the polymorphisms analyzed were found in genetic equilibrium. This indicates that the population mixes randomly and there are no sub-groups capable of affecting the results of the association studies. PMID:24893057

  5. Analysis of HLA-DP association with beryllium disease susceptibility in pooled exposed populations

    SciTech Connect

    Cesare Saltini, Massimo Amicosante

    2009-12-19

    in each immunogenetic study. In this context, the populations of the study already performed in this field by the University of Modena and Rome (by Prof. C. Saltini) and the University of Pennsylvania (by Prof. M. Rossman) have been evaluated by using similar HLA molecular typing methodologies and that both populations have now been followed up for a period of 4 to 7 years. The general objective of this study has to generate a larger data base comprising the two population with which analyze gene disease association with greater statistical power and ascertain the effect of lesser common gener variants which may be missed when analyzing associations on small populations. In particular addressing the role suggested in previous study such as: (1) the role of HLA-DP rare alleles and polymorphisms, and (2) the role of the HLA markers in disease progression from sensitization. The two populations from the already published studies (Saltini et al Eur Respir J. 2001 18:677-84; Rossman et al Am J Respir Crit Care Med. 2002 165:788-94) present similar aspects about: ethnicity, type and length of exposure to Be dust, a broadly similar association between beryllium related abnormalities and HLA. The two population have been pooled and evaluated using common criteria of diagnosis (Sensitized subject: at least 2 positive BeLPT tests each with 2 positive wells; CBD-affected subject: identification of well formed non-caseating granulomas on biopsy), follow up and HLA typing technique (complete HLA-DRB, DQB, DPB high resolution typing using amplification with sequence specific primers or sequence based typing). The two populations included 137 subjects with Beryllium hypersensitized (BH) and 155 Be-exposed controls. Inclusion criteria were met by one hundred and six subjects with Be-hypersensitivity of whom 55 were affected by CBD (age 52 {+-} 11 years; 50 caucasians, 2 African-Americans 2 Hispanics and 1 Asian; 46 males and 9 females; mean duration of Be-exposure 15 {+-} 9 years

  6. Is Statin Use Associated With Tendon Rupture? A Population-Based Retrospective Cohort Analysis.

    PubMed

    Contractor, Tahmeed; Beri, Abhimanyu; Gardiner, Joseph C; Tang, Xiaoqin; Dwamena, Francesca C

    2015-01-01

    Previous case reports and small studies have suggested that 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors (HMG-CoA-Is) may increase the risk of tendon rupture. We conducted a population-based retrospective cohort evaluation to better assess this relationship. From approximately 800,000 enrollees of a private insurance database, those who were aged ≤64 years with at least 1 year of continuous enrollment were selected. Exposure was defined as initiation of HMG-CoA-I after the beginning of the study period. Each exposed person was matched with 2 controls of similar age and gender. Baseline characteristics, including known risk factors for tendon rupture, were compared between exposed and control cohorts with fidelity to the study's matched design. After adjusting for differences in follow-up and baseline characteristics, incidence rate ratios for tendon rupture was assessed in HMG-CoA-I users and nonusers. A total of 34,749 exposed patients were matched with 69,498 controls. There was no difference in the occurrence of tendon ruptures in HMG-CoA-I users versus nonusers. The results remained unchanged after adjustment for age and gender. In conclusion, this population-based retrospective cohort evaluation suggests that use of HMG-CoA-Is as a group are not associated with tendon rupture.

  7. The association between HDAC9 gene polymorphisms and stroke risk in the Chinese population: A meta-analysis

    PubMed Central

    Zhou, Xin; Guan, Tangming; Li, Shuyuan; Jiao, Zinan; Lu, Xiaoshuang; Huang, Xiaodi; Ji, Yuhua; Ji, Qiuhong

    2017-01-01

    Several recent genome-wide association studies (GWASs) have suggested that the histone deacetylase 9 (HDAC9) gene is associated with stroke, but the reliability of these findings remains controversial, particularly for the data derived from different ethnicities and geographical locations. Therefore, we performed a meta-analysis to explore the associations between HDAC9 polymorphisms and the risk of stroke in the Chinese population. All eligible case-control studies that met the search criteria were retrieved from multiple databases, and six case-control studies with a total of 2,356 stroke patients and 3,420 healthy controls were included. The pooled odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated to assess the strengths of the associations of 3 HDAC9 gene polymorphisms with stroke risk. Our results revealed statistically significant associations of the rs2107595 (T/C) polymorphism with an increased risk of stroke in the allele, codominant and dominant models. Additionally, the rs2389995 (G/A) polymorphism was found to be significantly associated with a decreased risk of stroke in all genetic models. In conclusion, this meta-analysis suggested that the T allele of rs2107595 in HDAC9 increases the risk of stroke but that the G allele of rs2389995 decreases the risk of stroke in the Chinese population. PMID:28145521

  8. Statistical analysis of submarine fault populations associated with oceanic transform boundaries

    NASA Astrophysics Data System (ADS)

    Morrow, T. A.; Mittelstaedt, E. L.; Harpp, K.; Soule, S. A.

    2012-12-01

    Oceanic transform boundaries exhibit fault populations with strikingly different morphologies. Statistical analysis of these fault populations is a useful tool for investigating crustal strain, fault growth, and the regional stress field of the lithosphere (i.e., transpressional, transtensional, or strike slip). Achieving reliable statistics, however, requires the identification of numerous fault traces followed by accurate and precise measurements of the length, throw, and heave along each member of the fault set. Current methodologies for fault measurement from bathymetric data often require picking the tops and bottoms of digitized fault scarps by hand. This method is time-consuming for large fault populations and may be subject to expectation bias in measurements; consequently, it is difficult to make consistent interpretations of fault lineaments, particularly when dealing with large fault populations. Another method for gathering fault statistics from the seafloor uses binarized sidescan sonar data to identify fault traces and to measure fault heave. Fault throw is then calculated using a regional average fault dip, assuming that local variations in fault geometries are small. Sidescan methods are limited by the instrument's look direction, which can place fault scarps in shadow, producing significant variability in the apparent heave. We present a new computational method that measures observable fault heave and throw from high-resolution multibeam bathymetric data. The code first constructs a series of linear bathymetric transects orthogonal to fault strike. The top and bottom of each fault scarp are defined along these transects as the nearest local minima in the absolute value of the bathymetric gradient. Finally, a median filter is applied to the locations of the resulting fault bounding points to remove noise and erroneous values. Our method improves on previous techniques by allowing an automated, unbiased measure of heave and throw along every

  9. Modeling association among demographic parameters in analysis of open population capture-recapture data

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2005-01-01

    We present a hierarchical extension of the Cormack–Jolly–Seber (CJS) model for open population capture–recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis–Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.

  10. Pathway Analysis for Genome-Wide Association Study of Lung Cancer in Han Chinese Population

    PubMed Central

    Wu, Chen; Jin, Guangfu; Dai, Juncheng; Wang, Cheng; Hu, Lingmin; Gou, Jianwei; Qian, Chen; Bai, Jianling; Wu, Tangchun; Hu, Zhibin; Lin, Dongxin; Shen, Hongbing; Chen, Feng

    2013-01-01

    Genome-wide association studies (GWAS) have identified a number of genetic variants associated with lung cancer risk. However, these loci explain only a small fraction of lung cancer hereditability and other variants with weak effect may be lost in the GWAS approach due to the stringent significance level after multiple comparison correction. In this study, in order to identify important pathways involving the lung carcinogenesis, we performed a two-stage pathway analysis in GWAS of lung cancer in Han Chinese using gene set enrichment analysis (GSEA) method. Predefined pathways by BioCarta and KEGG databases were systematically evaluated on Nanjing study (Discovery stage: 1,473 cases and 1,962 controls) and the suggestive pathways were further to be validated in Beijing study (Replication stage: 858 cases and 1,115 controls). We found that four pathways (achPathway, metPathway, At1rPathway and rac1Pathway) were consistently significant in both studies and the P values for combined dataset were 0.012, 0.010, 0.022 and 0.005 respectively. These results were stable after sensitivity analysis based on gene definition and gene overlaps between pathways. These findings may provide new insights into the etiology of lung cancer. PMID:23469231

  11. Association and meta-analysis of HLA and non-obstructive azoospermia in the Han Chinese population.

    PubMed

    Zou, S; Song, P; Meng, H; Chen, T; Chen, J; Wen, Z; Li, Z; Li, Z; Shi, Y; Hu, H

    2017-03-01

    The exact aetiology and pathogenesis of most non-obstructive azoospermia (NOA) are still unknown. The previous two genomewide association studies (GWASs) have identified three different loci within the HLA region for NOA in the Han Chinese population, including rs3129878, rs498422 and rs7194. To further validate the risk of three GWAS-linked loci for NOA, we conducted a case-control study of these three risk loci in an independent Han Chinese male population, with 603 NOA patients and 610 controls. Furthermore, we also performed a meta-analysis of five studies on these three NOA-risk loci. The case-control study strongly suggested a significant association between loci rs3129878, rs498422 and rs7194 and NOA (P = 6.75 × 10(-21) (OR = 2.2586), P = 0.0060 (OR = 1.4013) and P = 0.0128 (OR = 1.2626) respectively). Our meta-analyses also supported the susceptibility of these three risk loci to NOA (P < 0.01). The risk variants within the HLA region potentially have a strong effect on males at risk of NOA, and may serve as diagnostic markers for male infertility. However, considering genetic difference between different populations, future validating studies in larger independent samples and animal experiments are suggested.

  12. A population structure and genome-wide association analysis on the USDA soybean germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genotype-phenotype associations within the soybean (Glycine max) germplasm collection could provide valuable information on the frequency and distribution of alleles affecting economically important traits. Here we performed a genome-wide association study (GWAS) for seed protein and oil content in ...

  13. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.

    PubMed

    Sabatti, Chiara; Service, Susan K; Hartikainen, Anna-Liisa; Pouta, Anneli; Ripatti, Samuli; Brodsky, Jae; Jones, Chris G; Zaitlen, Noah A; Varilo, Teppo; Kaakinen, Marika; Sovio, Ulla; Ruokonen, Aimo; Laitinen, Jaana; Jakkula, Eveliina; Coin, Lachlan; Hoggart, Clive; Collins, Andrew; Turunen, Hannu; Gabriel, Stacey; Elliot, Paul; McCarthy, Mark I; Daly, Mark J; Järvelin, Marjo-Riitta; Freimer, Nelson B; Peltonen, Leena

    2009-01-01

    Genome-wide association studies (GWAS) of longitudinal birth cohorts enable joint investigation of environmental and genetic influences on complex traits. We report GWAS results for nine quantitative metabolic traits (triglycerides, high-density lipoprotein, low-density lipoprotein, glucose, insulin, C-reactive protein, body mass index, and systolic and diastolic blood pressure) in the Northern Finland Birth Cohort 1966 (NFBC1966), drawn from the most genetically isolated Finnish regions. We replicate most previously reported associations for these traits and identify nine new associations, several of which highlight genes with metabolic functions: high-density lipoprotein with NR1H3 (LXRA), low-density lipoprotein with AR and FADS1-FADS2, glucose with MTNR1B, and insulin with PANK1. Two of these new associations emerged after adjustment of results for body mass index. Gene-environment interaction analyses suggested additional associations, which will require validation in larger samples. The currently identified loci, together with quantified environmental exposures, explain little of the trait variation in NFBC1966. The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci.

  14. Association analysis revealed one susceptibility locus for vitiligo with immune-related diseases in the Chinese Han population.

    PubMed

    Li, Shu; Yao, Weiyi; Pan, Qian; Tang, Xianfa; Zhao, Suli; Wang, Wenjun; Zhu, Zhengwei; Gao, Jinping; Sheng, Yujun; Zhou, Fusheng; Zheng, Xiaodong; Zuo, Xianbo; Sun, Liangdan; Zhang, Anping

    2015-07-01

    Generalized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair, and is associated with an elevated risk of other immune-related diseases. However, there is no reported study on the associations between immune susceptibility polymorphisms and the risk of vitiligo with immune-related diseases. The aim of this study was to evaluate the potential influence of 10 single-nucleotide polymorphisms (SNPs) at 18q21.31 (rs10503019), 4p16.1 (rs11940117), 3q28 (rs1464510), 14q12 (rs2273844), 12q13.2 (rs2456973), 16q12.2 (rs3213758), 10q25.3 (rs4353229), 3q13.33 (rs59374417), and 10p15.1 (rs706779 and rs7090530) on vitiligo with immune-related diseases in the Chinese Han population. All SNPs were genotyped in 552 patients with vitiligo-associated immune-related diseases and 1656 controls using the Sequenom MassArray system. Data were analyzed with PLINK 1.07 software. The C allele of rs2456973 at 12q13.2 was observed to be significantly associated with vitiligo-associated immune-related diseases (autoimmune diseases and allergic diseases) (P = 0.0028, odds ratio (OR) = 1.27). In subphenotype analysis, the rs2456973 C allele was also significantly associated with early-onset vitiligo by comparing with controls (P = 0.0001) and in the case-only analysis (P = 0.0114). We confirmed that 12q13.2 was an important candidate locus for vitiligo with immune-related diseases (autoimmune diseases and allergic diseases) and affected disease phenotypes with early onset.

  15. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.

    PubMed

    Okada, Yukinori; Sim, Xueling; Go, Min Jin; Wu, Jer-Yuarn; Gu, Dongfeng; Takeuchi, Fumihiko; Takahashi, Atsushi; Maeda, Shiro; Tsunoda, Tatsuhiko; Chen, Peng; Lim, Su-Chi; Wong, Tien-Yin; Liu, Jianjun; Young, Terri L; Aung, Tin; Seielstad, Mark; Teo, Yik-Ying; Kim, Young Jin; Lee, Jong-Young; Han, Bok-Ghee; Kang, Daehee; Chen, Chien-Hsiun; Tsai, Fuu-Jen; Chang, Li-Ching; Fann, S-J Cathy; Mei, Hao; Rao, Dabeeru C; Hixson, James E; Chen, Shufeng; Katsuya, Tomohiro; Isono, Masato; Ogihara, Toshio; Chambers, John C; Zhang, Weihua; Kooner, Jaspal S; Albrecht, Eva; Yamamoto, Kazuhiko; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki; Kato, Norihiro; He, Jiang; Chen, Yuan-Tsong; Cho, Yoon Shin; Tai, E-Shyong; Tanaka, Toshihiro

    2012-07-15

    Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

  16. Comparative analysis of the frequency, distribution and population sizes of yeasts associated with canine seborrheic dermatitis and healthy skin.

    PubMed

    Yurayart, Chompoonek; Chindamporn, Ariya; Suradhat, Sanipa; Tummaruk, Padet; Kajiwara, Susumu; Prapasarakul, Nuvee

    2011-03-24

    The purpose of this study was to investigate the diversity of yeast associated with the degree of canine seborrheic dermatitis (SD) by anatomical sites. Fifty-seven samples were divided as 17 healthy skin, 20 with primary seborrheic dermatitis (PSD), and 20 with secondary seborrheic dermatitis (SSD). Yeast isolation and characterization were carried out based on microscopical features and biochemical properties. DNA analysis at the internal transcribed spacer I of 26S rDNA region was utilized for species confirmation. Four species of yeast consisting Malassezia pachydermatis, Malassezia furfur, Candida parapsilosis and Candida tropicalis recovered from examined dogs. M. pachydermatis and C. parapsilosis were isolated from all dogs, but C. tropicalis and M. furfur were recovered from 3 healthy dogs and one diseased dog, respectively. The number of M. pachydermatis and C. parapsilosis in diseased dogs was higher than that of healthy specimens (P<0.01). High frequency and population size of C. parapsilosis were closely associated to PSD, while those of M. pachydermatis were associated with both PSD and SSD (P<0.01). C. parapsilosis were predominant at the perianal area. This study demonstrated the co-colonization of M. pachydermatis and C. parapsilosis in large amounts and frequency associated with stage of disease and anatomical site.

  17. Meta-Analysis of Rare Variant Association Tests in Multiethnic Populations.

    PubMed

    Mensah-Ablorh, Akweley; Lindstrom, Sara; Haiman, Christopher A; Henderson, Brian E; Marchand, Loic Le; Lee, Seunngeun; Stram, Daniel O; Eliassen, A Heather; Price, Alkes; Kraft, Peter

    2016-01-01

    Several methods have been proposed to increase power in rare variant association testing by aggregating information from individual rare variants (MAF < 0.005). However, how to best combine rare variants across multiple ethnicities and the relative performance of designs using different ethnic sampling fractions remains unknown. In this study, we compare the performance of several statistical approaches for assessing rare variant associations across multiple ethnicities. We also explore how different ethnic sampling fractions perform, including single-ethnicity studies and studies that sample up to four ethnicities. We conducted simulations based on targeted sequencing data from 4,611 women in four ethnicities (African, European, Japanese American, and Latina). As with single-ethnicity studies, burden tests had greater power when all causal rare variants were deleterious, and variance component-based tests had greater power when some causal rare variants were deleterious and some were protective. Multiethnic studies had greater power than single-ethnicity studies at many loci, with inclusion of African Americans providing the largest impact. On average, studies including African Americans had as much as 20% greater power than equivalently sized studies without African Americans. This suggests that association studies between rare variants and complex disease should consider including subjects from multiple ethnicities, with preference given to genetically diverse groups.

  18. Dermal digital ridge density of a penal population: Analysis of association and individualization.

    PubMed

    Kaur, Maninder; Sharma, Krishan

    2016-11-01

    The present study is an attempt to analyze an association between dermal digital ridge density and explosive personality based on the study of 100 male prisoners and 50 controls. The control group had higher ridge density than the prisoners. Bilateral differences revealed higher ridge density on left hand than right hand in both the groups, but differences between two groups for directional asymmetry were not significant. Surface area is not correlated with ridge density in all the digits. About 50% of the variation in ridge density may be explained by a single factor which in all probability is the genetic component of variation. Ridge density cannot be used as a marker for assessing individual's height. Individuals having ridge density less than 12 ridges and higher than 15 ridges, i.e. placed on the two extremes were more likely than not to have more explosive personality.

  19. Molecular analysis and conventional cytology: association between HPV and bacterial vaginosis in the cervical abnormalities of a Brazilian population.

    PubMed

    Peres, A L; Camarotti, J R S L; Cartaxo, M; Alencar, N; Stocco, R C; Beçak, W; Pontes-Filho, N T; Araújo, R F F; Lima-Filho, J L; Martins, D B G

    2015-08-14

    We investigated the association between bacterial vaginosis (BV) and human papillomavirus (HPV) infection in Papanicolaou smears in a Brazilian population. Cross-sectional analysis was performed on 673 samples collected from women attending public health centers in Olinda (PE, Brazil) by conventional cytology methodology and molecular analysis, PCR tests (GP5+/6+ and MY09/11). Cytological abnormalities, BV, and HPV-DNA were detected in 23 (3.4%) samples, 189 samples (28.1%), and 210 samples (31.2%), respectively. GP5+/6+ primers resulted in higher detection performance than MY09/11 primers, with 81% concordance between both primers (P < 0.0001). The occurrence of HPV-DNA and BV had ORs of 8.59 (P < 0.0001) and 2.91 (P = 0.0089) for abnormal cytology, respectively, whereas the concomitant presence of both infections showed an OR equal to 3.82 (P = 0.0054). Therefore, we observed an association between abnormal cervical cytology and HPV infection, BV, or both HPV infection and BV. These results highlight the necessity of monitoring patients presenting not only HPV, but also BV, as risk factors for cervical lesion development.

  20. The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations.

    PubMed

    Derks, E M; Zwinderman, A H; Gamazon, E R

    2017-02-10

    Population divergence impacts the degree of population stratification in Genome Wide Association Studies. We aim to: (i) investigate type-I error rate as a function of population divergence (FST) in multi-ethnic (admixed) populations; (ii) evaluate the statistical power and effect size estimates; and (iii) investigate the impact of population stratification on the results of gene-based analyses. Quantitative phenotypes were simulated. Type-I error rate was investigated for Single Nucleotide Polymorphisms (SNPs) with varying levels of FST between the ancestral European and African populations. Type-II error rate was investigated for a SNP characterized by a high value of FST. In all tests, genomic MDS components were included to correct for population stratification. Type-I and type-II error rate was adequately controlled in a population that included two distinct ethnic populations but not in admixed samples. Statistical power was reduced in the admixed samples. Gene-based tests showed no residual inflation in type-I error rate.

  1. Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp.) Evaluated by SSR Markers.

    PubMed

    Zhang, Liwu; Yuan, Minhang; Tao, Aifen; Xu, Jiantang; Lin, Lihui; Fang, Pingping; Qi, Jianmin

    2015-01-01

    Population structure and relationship analysis is of great importance in the germplasm utilization and association mapping. Jute, comprised of white jute (C. capsularis L) and dark jute (C. olitorius L), is second to cotton in its commercial significance in the world. Here, we assessed the genetic structure and relationship in a panel of 159 jute accessions from 11 countries and regions using 63 SSRs. The structure analysis divided the 159 jute accessions from white and dark jute into Co and Cc group, further into Co1, Co2, Cc1 and Cc2 subgroups. Out of Cc1 subgroup, 81 accessions were from China and the remaining 10 accessions were from India (2), Japan (5), Thailand, Vietnam (2) and Pakistan (1). Out of Cc2 subgroup, 35 accessions were from China, and the remaining 3 accessions were from India, Pakistan and Thailand respectively. It can be inferred that the genetic background of these jute accessions was not always correlative with their geographical regions. Similar results were found in Co1 and Co2 subgroups. Analysis of molecular variance revealed 81% molecular variation between groups but it was low (19%) within subgroups, which further confirmed the genetic differentiation between the two groups. The genetic relationship analysis showed that the most diverse genotypes were Maliyeshengchangguo and Changguozhongyueyin in dark jute, BZ-2-2, Aidianyehuangma, Yangjuchiyuanguo, Zijinhuangma and Jute 179 in white jute, which could be used as the potential parents in breeding programs for jute improvement. These results would be very useful for association studies and breeding in jute.

  2. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population.

    PubMed

    Ogut, F; Bian, Y; Bradbury, P J; Holland, J B

    2015-06-01

    Quantitative trait locus (QTL) mapping has been used to dissect the genetic architecture of complex traits and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an alternative approach to QTL mapping with a wider scope of inference. Joint-multiple population analysis should have higher power to detect QTL shared among multiple families, but may have lower power to detect rare QTL. We compared prediction ability of single-family and joint-family QTL analysis methods with fivefold cross-validation for 6 diverse traits using the maize nested association mapping population, which comprises 25 biparental recombinant inbred families. Joint-family QTL analysis had higher mean prediction abilities than single-family QTL analysis for all traits at most significance thresholds, and was always better at more stringent significance thresholds. Most robust QTL (detected in >50% of data samples) were restricted to one family and were often not detected at high frequency by joint-family analysis, implying substantial genetic heterogeneity among families for complex traits in maize. The superior predictive ability of joint-family QTL models despite important genetic differences among families suggests that joint-family models capture sufficient smaller effect QTL that are shared across families to compensate for missing some rare large-effect QTL.

  3. The association and interaction analysis of hypertension and diabetes mellitus on diastolic heart failure in a high-risk population

    PubMed Central

    Meng, Xiang-Ying; Zhou, Yong; Zhang, Jin; Tang, Zi-Hui

    2015-01-01

    Objective: The purpose of this study was to evaluate the extent to which hypertension (HT) interacts with diabetes mellitus (DM) to affect diastolic heart failure (DHF) in a high-risk population. Methods: We conducted a hospital-based case-control study to investigate the relationship between HT or DM and DHF in 251 patients (case: 133 patients with DHF; control: 118 patients without DHF). Echocardiography was used to assess left ventricular (LV) diastolic function. The association between HT or DM and DHF was assessed by multivariate logistic regression (MLR) analysis controlling for confounders. The effect of the interaction between HT and DM on DHF was assessed in MLR models. Interaction on an additive scale can be calculated by using the relative excess risk due to interaction (RERI), the proportion attributable to interaction (AP), and the synergy index (S). Results: The MLR analyses showed that HT and DM were independent predictors of DHF after adjustment for potential confounders (OR = 2.35-3.14, P<0.05 for all models). DHF was affected by the interaction between HT and DM (ORInt = 3.11-4.31, P Int<0.1, RETI = 2.13-2.69, AP = 0.38-0.49 and S = 4.11-6.80). Conclusion: The findings provide evidence that HT and DM are independent predictors of DHF and that both risk factors act synergistically to influence DHF in a Chinese high-risk population. PMID:26885071

  4. Genome Wide Association Analysis of a Founder Population Identified TAF3 as a Gene for MCHC in Humans

    PubMed Central

    Pistis, Giorgio; Okonkwo, Shawntel U.; Traglia, Michela; Sala, Cinzia; Shin, So-Youn; Masciullo, Corrado; Buetti, Iwan; Massacane, Roberto; Mangino, Massimo; Thein, Swee-Lay; Spector, Timothy D.; Ganesh, Santhi; Pirastu, Nicola; Gasparini, Paolo; Soranzo, Nicole; Camaschella, Clara; Hart, Daniel; Green, Michael R.; Toniolo, Daniela

    2013-01-01

    The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5–10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approaches alternative to large meta analysis. GWAS (Genome Wide Association Study) for red blood cell traits in a founder population cohort from Northern Italy identified a new locus for mean corpuscular hemoglobin concentration (MCHC) in the TAF3 gene. The association was replicated in two cohorts (rs1887582, P = 4.25E–09). TAF3 encodes a transcription cofactor that participates in core promoter recognition complex, and is involved in zebrafish and mouse erythropoiesis. We show here that TAF3 is required for transcription of the SPTA1 gene, encoding alpha spectrin, one of the proteins that link the plasma membrane to the actin cytoskeleton. Mutations in SPTA1 are responsible for hereditary spherocytosis, a monogenic disorder of MCHC, as well as for the normal MCHC level. Based on our results, we propose that TAF3 is required for normal erythropoiesis in human and that it might have a role in controlling the ratio between hemoglobin (Hb) and cell volume and in the dynamics of RBC maturation in healthy individuals. Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane. PMID:23935956

  5. Genome-wide association analysis on five isolated populations identifies variants of the HLA-DOA gene associated with white wine liking

    PubMed Central

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; Amin, Najaf; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia M; Toniolo, Daniela; Gasparini, Paolo

    2015-01-01

    Wine is the most popular alcoholic beverage around the world and because of its importance in society has been widely studied. Understanding what drives its flavor has been a quest for decades but much is still unknown and will be determined at least in part by individual taste preferences. Recently studies in the genetics of taste have uncovered the role of different genes in the determination of food preferences giving new insight on its physiology. In this context we have performed a genome-wide association study on red and white wine liking using three isolated populations collected in Italy, and replicated our results on two additional populations coming from the Netherland and Central Asia for a total of 3885 samples. We have found a significant association (P=2.1 × 10−8) between white wine liking and rs9276975:C>T a polymorphism in the HLA-DOA gene encoding a non-canonical MHC II molecule, which regulates other MHC II molecules. The same association was also found with red wine liking (P=8.3 × 10−6). Sex-separated analysis have also revealed that the effect of HLA-DOA is twice as large in women as compared to men suggesting an interaction between this polymorphism and gender. Our results are one of the first examples of genome-wide association between liking of a commonly consumed food and gene variants. Moreover, our results suggest a role of the MHC system in the determination of food preferences opening new insight in this field in general. PMID:25758996

  6. Genome-wide association analysis on five isolated populations identifies variants of the HLA-DOA gene associated with white wine liking.

    PubMed

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; Amin, Najaf; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia M; Toniolo, Daniela; Gasparini, Paolo

    2015-12-01

    Wine is the most popular alcoholic beverage around the world and because of its importance in society has been widely studied. Understanding what drives its flavor has been a quest for decades but much is still unknown and will be determined at least in part by individual taste preferences. Recently studies in the genetics of taste have uncovered the role of different genes in the determination of food preferences giving new insight on its physiology. In this context we have performed a genome-wide association study on red and white wine liking using three isolated populations collected in Italy, and replicated our results on two additional populations coming from the Netherland and Central Asia for a total of 3885 samples. We have found a significant association (P=2.1 × 10(-8)) between white wine liking and rs9276975:C>T a polymorphism in the HLA-DOA gene encoding a non-canonical MHC II molecule, which regulates other MHC II molecules. The same association was also found with red wine liking (P=8.3 × 10(-6)). Sex-separated analysis have also revealed that the effect of HLA-DOA is twice as large in women as compared to men suggesting an interaction between this polymorphism and gender. Our results are one of the first examples of genome-wide association between liking of a commonly consumed food and gene variants. Moreover, our results suggest a role of the MHC system in the determination of food preferences opening new insight in this field in general.

  7. Association studies in consanguineous populations

    SciTech Connect

    Genin, E.; Clerget-Darpous, F.

    1996-04-01

    To study the genetic determinism of multifactorial diseases in large panmictic populations, a strategy consists in looking for an association with markers closely linked to candidate genes. A distribution of marker genotypes different in patients and controls may indicate that the candidate gene is involved in the disease. In panmictic populations, the power to detect the role of a candidate gene depends on the gametic disequilibrium with the marker locus. In consanguineous populations, we show that it depends on the inbreeding coefficient F as well. Inbreeding increases the power to detect the role of a recessive or quasi-recessive disease-susceptibility factor. The gain in power turns out to be greater for small values of the gametic disequilibrium. Moreover, even in the absence of gametic disequilibrium, the presence of inbreeding may allow to detect the role of a recessive factor. Ignoring inbreeding when it exists may lead to reject falsely a recessive model if the mode of inheritance is inferred on the distribution of genotypes among patients. 5 refs., 6 figs., 1 tab.

  8. Common variant of PDZ domain containing 1 (PDZK1) gene is associated with gout susceptibility: A replication study and meta-analysis in Japanese population.

    PubMed

    Higashino, Toshihide; Matsuo, Hirotaka; Sakiyama, Masayuki; Nakayama, Akiyoshi; Nakamura, Takahiro; Takada, Tappei; Ogata, Hiraku; Kawamura, Yusuke; Kawaguchi, Makoto; Naito, Mariko; Kawai, Sayo; Takada, Yuzo; Ooyama, Hiroshi; Suzuki, Hiroshi; Shinomiya, Nariyoshi

    2016-12-01

    PDZ domain containing 1 (PDZK1) is a scaffold protein that organizes a transportsome and regulates several transporters' functions including urate and drug transporters. Therefore, PDZK1 in renal proximal tubules may affect serum uric acid levels through PDZK1-binding renal urate transporters. Two previous studies in Japanese male population reported that a PDZK1 single nucleotide polymorphism (SNP), rs12129861, was not associated with gout. In the present study, we performed a further association analysis between gout and rs12129861 in a different large-scale Japanese male population and a meta-analysis with previous Japanese population studies. We genotyped rs12129861 in 1210 gout cases and 1224 controls of a Japanese male population by TaqMan assay. As a result, we showed that rs12129861 was significantly associated with gout susceptibility (P = 0.016, odds ratio [OR] = 0.80, 95% confidence interval [CI] 0.67-0.96). The result of the meta-analysis among Japanese populations also showed a significant association (P = 0.013, OR = 0.85, 95%CI 0.75-0.97). Our findings show the significant association between gout susceptibility and common variant of PDZK1 which reportedly regulates the functions of urate transporters in the urate transportsome.

  9. [Spatial pattern analysis and associations of Quercus aquifolioides population at different growth stages in Southeast Tibet, China].

    PubMed

    Shen, Zhi-qiang; Hua, Min; Dan, Qu; Lu, Jie; Fang, Jiang-ping

    2016-02-01

    This article analyzed the spatial pattern and its correlation of Quercus aquifolioides, Southeast Tibet at different growing stages by using Ripley' s L function in the method of point pattern, analysis. The results showed the diameter structure of Q. aquifolioides population in Southeast Tibet followed a 'single peak' shape and the saplings and medium trees predominated in number in the whole population. The population had a high regeneration rate and was of increase type. In the growth process of Q. aquifolioides from saplings to large trees, saplings and medium trees showed aggregation distribution at.small scale, while large trees showed basically random distribution at whole scale. There was significant correlation between saplings with medium or large trees at small scale, however, there was no correlation between medium and large trees. In the growth process of Q. aquifolioides population from saplings, medium trees to large trees, its spatial pattern developed from aggregative distribution to random distribution. The natural regeneration of Q. aquifolioides population was affected not only by interspecific competition, but also by intraspecific competition. In the similar natural environment, the most important factors affecting the spatial pattern of Q. aquifoioides population were its own biological and ecological characteristics.

  10. Association of Climatic Variability, Vector Population and Malarial Disease in District of Visakhapatnam, India: A Modeling and Prediction Analysis

    PubMed Central

    Srimath-Tirumula-Peddinti, Ravi Chandra Pavan Kumar; Neelapu, Nageswara Rao Reddy; Sidagam, Naresh

    2015-01-01

    Background Malarial incidence, severity, dynamics and distribution of malaria are strongly determined by climatic factors, i.e., temperature, precipitation, and relative humidity. The objectives of the current study were to analyse and model the relationships among climate, vector and malaria disease in district of Visakhapatnam, India to understand malaria transmission mechanism (MTM). Methodology Epidemiological, vector and climate data were analysed for the years 2005 to 2011 in Visakhapatnam to understand the magnitude, trends and seasonal patterns of the malarial disease. Statistical software MINITAB ver. 14 was used for performing correlation, linear and multiple regression analysis. Results/Findings Perennial malaria disease incidence and mosquito population was observed in the district of Visakhapatnam with peaks in seasons. All the climatic variables have a significant influence on disease incidence as well as on mosquito populations. Correlation coefficient analysis, seasonal index and seasonal analysis demonstrated significant relationships among climatic factors, mosquito population and malaria disease incidence in the district of Visakhapatnam, India. Multiple regression and ARIMA (I) models are best suited models for modeling and prediction of disease incidences and mosquito population. Predicted values of average temperature, mosquito population and malarial cases increased along with the year. Developed MTM algorithm observed a major MTM cycle following the June to August rains and occurring between June to September and minor MTM cycles following March to April rains and occurring between March to April in the district of Visakhapatnam. Fluctuations in climatic factors favored an increase in mosquito populations and thereby increasing the number of malarial cases. Rainfall, temperatures (20°C to 33°C) and humidity (66% to 81%) maintained a warmer, wetter climate for mosquito growth, parasite development and malaria transmission. Conclusions

  11. Genetic diversity, population structure and genome-wide marker-trait association analysis of the USDA pea (Pisum sativum L.) core collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity, population structure and genome-wide marker-trait association analysis was conducted for the USDA pea (Pisum sativum L.) core collection. The core collection contained 285 accessions with diverse phenotypes and geographic origins. The 137 DNA markers included 102 polymorphic fra...

  12. Identifying associated factors with social capital using path analysis: A population-based survey in Tehran, Iran (Urban HEART-2).

    PubMed

    Asadi-Lari, Mohsen; Hassanzadeh, Jafar; Torabinia, Mansour; Vaez-Mahdavi, Mohammad Reza; Montazeri, Ali; Ghaem, Haleh; Menati, Rostam; Niazi, Mohsen; Kassani, Aziz

    2016-01-01

    Background: Social capital has been defined as norms, networks, and social links that facilitate collective actions. Social capital is related to a number of main social and public health variables. Therefore, the present study aimed to determine the factors associated with social capital among the residents of Tehran, Iran. Methods: In this large cross-sectional population-based study, 31531 residents aged 20 years and above were selected through multi-stage sampling method from 22 districts of Tehran in 2011. The social capital questionnaire, 28-item General Health Questionnaire (GHQ-28), and Short-Form Health Survey (SF-12) were used. Hypothetical causal models were designed to identify the pathways through which different variables influenced the components of social capital. Then, path analysis was conducted for identifying the determinants of social capital. Results: The most influential variables in 'individual trust' were job status (β=0.37, p=0.02), marital status (β=0.32, p=0.01), Physical Component Summary (PCS) (β=0.37, p=0.02), and age (β=0.34, p=0.03). On the other hand, education level (β=0.34, p=0.01), age (β=0.33, p=0.02), marital status (β=0.33, p=0.01), and job status (β=0.32, p=0.01) were effective in 'cohesion and social support'. Additionally, age (β=0.18, p=0.02), PCS (β=0.36, p=0.01), house ownership (β=0.23, p=0.03), and mental health (β=0.26, p=0.01) were influential in 'social trust/collective relations'. Conclusion: Social capital can be improved in communities by planning to improve education and occupation status, paying more attention to strengthening family bonds, and provision of local facilities and neighborhood bonds to reduce migration within the city.

  13. Identifying associated factors with social capital using path analysis: A population-based survey in Tehran, Iran (Urban HEART-2)

    PubMed Central

    Asadi-Lari, Mohsen; Hassanzadeh, Jafar; Torabinia, Mansour; Vaez-Mahdavi, Mohammad Reza; Montazeri, Ali; Ghaem, Haleh; Menati, Rostam; Niazi, Mohsen; Kassani, Aziz

    2016-01-01

    Background: Social capital has been defined as norms, networks, and social links that facilitate collective actions. Social capital is related to a number of main social and public health variables. Therefore, the present study aimed to determine the factors associated with social capital among the residents of Tehran, Iran. Methods: In this large cross-sectional population-based study, 31531 residents aged 20 years and above were selected through multi-stage sampling method from 22 districts of Tehran in 2011. The social capital questionnaire, 28-item General Health Questionnaire (GHQ-28), and Short-Form Health Survey (SF-12) were used. Hypothetical causal models were designed to identify the pathways through which different variables influenced the components of social capital. Then, path analysis was conducted for identifying the determinants of social capital. Results: The most influential variables in ‘individual trust’ were job status (β=0.37, p=0.02), marital status (β=0.32, p=0.01), Physical Component Summary (PCS) (β=0.37, p=0.02), and age (β=0.34, p=0.03). On the other hand, education level (β=0.34, p=0.01), age (β=0.33, p=0.02), marital status (β=0.33, p=0.01), and job status (β=0.32, p=0.01) were effective in ‘cohesion and social support’. Additionally, age (β=0.18, p=0.02), PCS (β=0.36, p=0.01), house ownership (β=0.23, p=0.03), and mental health (β=0.26, p=0.01) were influential in ‘social trust/collective relations’. Conclusion: Social capital can be improved in communities by planning to improve education and occupation status, paying more attention to strengthening family bonds, and provision of local facilities and neighborhood bonds to reduce migration within the city. PMID:28210579

  14. MicroRNA Genetic Variation: From Population Analysis to Functional Implications of Three Allele Variants Associated with Cancer.

    PubMed

    Torruella-Loran, Ignasi; Laayouni, Hafid; Dobon, Begoña; Gallego, Alicia; Balcells, Ingrid; Garcia-Ramallo, Eva; Espinosa-Parrilla, Yolanda

    2016-10-01

    Nucleotide variants in microRNA regions have been associated with disease; nevertheless, few studies still have addressed the allele-dependent effect of these changes. We studied microRNA genetic variation in human populations and found that while low-frequency variants accumulate indistinctly in microRNA regions, the mature and seed regions tend to be depleted of high-frequency variants, probably as a result of purifying selection. Comparison of pairwise population fixation indexes among regions showed that the seed had higher population fixation indexes than the other regions, suggesting the existence of local adaptation in the seed region. We further performed functional studies of three microRNA variants associated with cancer (rs2910164:C > G in MIR146A, rs11614913:C > T in MIR196A2, and rs3746444:A > G in both MIR499A and MIR499B). We found differences in the expression between alleles and in the regulation of several genes involved in cancer, such as TP53, KIT, CDH1, CLH, and TERT, which may result in changes in regulatory networks related to tumorigenesis. Furthermore, luciferase-based assays showed that MIR499A could be regulating the cadherin CDH1 and the cell adhesion molecule CLH1 in an allele-dependent fashion. A better understanding of the effect of microRNA variants associated with disease could be key in our way to a more personalized medicine.

  15. Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.

    PubMed

    Saad, Mohamad; Wijsman, Ellen M

    2014-11-01

    In the last two decades, complex traits have become the main focus of genetic studies. The hypothesis that both rare and common variants are associated with complex traits is increasingly being discussed. Family-based association studies using relatively large pedigrees are suitable for both rare and common variant identification. Because of the high cost of sequencing technologies, imputation methods are important for increasing the amount of information at low cost. A recent family-based imputation method, Genotype Imputation Given Inheritance (GIGI), is able to handle large pedigrees and accurately impute rare variants, but does less well for common variants where population-based methods perform better. Here, we propose a flexible approach to combine imputation data from both family- and population-based methods. We also extend the Sequence Kernel Association Test for Rare and Common variants (SKAT-RC), originally proposed for data from unrelated subjects, to family data in order to make use of such imputed data. We call this extension "famSKAT-RC." We compare the performance of famSKAT-RC and several other existing burden and kernel association tests. In simulated pedigree sequence data, our results show an increase of imputation accuracy from use of our combining approach. Also, they show an increase of power of the association tests with this approach over the use of either family- or population-based imputation methods alone, in the context of rare and common variants. Moreover, our results show better performance of famSKAT-RC compared to the other considered tests, in most scenarios investigated here.

  16. Polymorphism analysis in estrogen receptors alpha and beta genes and their association with infertile population in Pakistan

    PubMed Central

    Liaqat, Sinha; Hasnain, Shahida; Muzammil, Saima; Hayat, Sumreen

    2015-01-01

    Studies on polymorphism of estrogen receptor (ESR) alpha and beta genes have been mostly implicated in infertility, but the results have been controversial due to lack of comprehensive data. The present study focused on association of ESR genes with both male and female infertility. In ESRα, PvuII (rs2234693) and XbaI (rs9340799) were studied while in ESRβ gene, risk of infertility was determined for silent G/A RsaI (rs1256049) polymorphism. Total 124 subjects (74 cases and 50 controls) were part of this study having primary infertility. Restriction fragment length polymorphism (RFLP) was performed with PvuII, XbaI and RsaI to determine polymorphism. Correlation between age and follicle stimulating hormone (FSH) of cases and controls was determined and no association was found between infertility and FSH hormone. Heterozygous AG genotype of XbaI polymorphism (P= 2.505e-06) and heterozygous TC genotype (P= 0.00003) in PvuII polymorphism were strongly associated with risk of infertility. In ESRβ gene, there was lack of polymorphism for RsaI in our population as all subjects were homozygous (GG). Haplotype frequencies showed that XbaI and PvuII polymorphisms are in strong linkage disequilibrium. This study shows that in our population XbaI and PvuII polymorphisms of ESRα are associated with risk of infertility. PMID:27065769

  17. Genetic association of COL1A1 polymorphisms with high myopia in Asian population: a Meta-analysis

    PubMed Central

    Gong, Bo; Qu, Chao; Huang, Xiao-Fang; Ye, Zi-Meng; Zhang, Ding-Ding; Shi, Yi; Chen, Rong; Liu, Yu-Ping; Shuai, Ping

    2016-01-01

    AIM To comprehensively evaluate the potential association of COL1A1 polymorphisms with high myopia by a systematic review and Meta-analysis. METHODS All association studies on COL1A1 and high myopia reported up to June 10, 2014 in PubMed, Embase, Web of Science, and the Chinese Biomedical Database were retrieved. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were analyzed for single-nucleotide polymorphisms (SNPs) using fixed- and random- effects models according to between-study heterogeneity. Publication bias analyses were conducted by Egger's test. RESULTS A total of four studies from reported papers were included in this analysis. The Meta-analyses for COL1A1 rs2075555, composed of 2304 high myopia patients and 2272 controls, failed to detect any significant association with high myopia. A total of 971 cases and 649 controls were tested for COL1A1 rs2269336. The association of COL1A1 rs2269336 with high myopia was observed in recessive model (CC vs CG+GG, P=0.03) and in heterozygous model (CG vs GG, P=0.04), but not in other models. CONCLUSION This Meta-analysis shows that COL1A1 rs2269336 (CC vs CG+GG) affects individual susceptibility to high myopia, whereas there is no association detected between SNPs rs2075555 and high myopia. Given the limited sample size, further investigations including more ethnic groups are required to validate the association. PMID:27588274

  18. Analysis of the association between the LUM rs3759223 variant and high myopia in a Japanese population

    PubMed Central

    Okui, Shintaro; Meguro, Akira; Takeuchi, Masaki; Yamane, Takahiro; Okada, Eiichi; Iijima, Yasuhito; Mizuki, Nobuhisa

    2016-01-01

    Purpose Many studies have investigated the relationship of the lumican gene (LUM) rs3759223 variant with the risk of high myopia, but the results have been inconsistent and inconclusive. In this study, we investigated whether LUM rs3759223 is associated with high myopia in a Japanese population. Methods We recruited 1,585 Japanese patients with high myopia (spherical equivalent [SE] <−9.00 diopters [D]) and 1,011 Japanese healthy controls (SE ≥−1.00 D). The rs3759223 variant was genotyped using the TaqMan assay, and the allelic and genotypic diversity among cases and controls was analyzed according to the SE level. Results In the allelic tests, the odds ratio (OR) for the T allele of rs3759223 tended to increase with the progression of SE, and the highest OR (1.56) was found in patients with SE <−15 D in both eyes. The OR of the T allele tended to increase with the progression of SE in the additive, dominant, and recessive inheritance models. However, we found no significant associations for any of the alleles or genotype models. Conclusion These data support the possibility that the LUM rs3759223 T allele accelerates the progression of SE in the Japanese population, although no significant associations were observed in this study. Additional genetic studies with larger samples that take into account the degree of SE are needed to clarify the contribution of rs3759223 to the risk of high myopia. PMID:27826181

  19. Rank-based genome-wide analysis reveals the association of Ryanodine receptor-2 gene variants with childhood asthma among human populations

    PubMed Central

    2013-01-01

    Background The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in DNA sequence information, allele frequencies, effect sizes, and linkage disequilibrium patterns, SNP association using a uniform stringent threshold on p values may not be reproducible across populations. Here, we developed rank-based methods to investigate shared or population-specific loci and pathways for childhood asthma across individuals of diverse ancestry. We performed genome-wide association studies on 859,790 SNPs genotyped in 527 affected offspring trios of European, African, and Hispanic ancestry using publically available asthma database in the Genotypes and Phenotypes database. Results Rank-based analyses showed that there are shared genetic factors for asthma across populations, more at the gene and pathway levels than at the SNP level. Although the top 1,000 SNPs were not shared, 11 genes (RYR2, PDE4D, CSMD1, CDH13, ROBO2, RBFOX1, PTPRD, NPAS3, PDE1C, SEMA5A, and CTNNA2) mapped by these SNPs were shared across populations. Ryanodine receptor 2 (RYR2, a statin response-related gene) showed the strongest association in European (p value = 2.55 × 10−7) and was replicated in African (2.57 × 10−4) and Hispanic (1.18 × 10−3) Americans. Imputation analyses based on the 1000 Genomes Project uncovered additional RYR2 variants associated with asthma. Network and functional ontology analyses revealed that RYR2 is an integral part of dermatological or allergic disorder biological networks, specifically in the functional classes involving inflammatory, eosinophilic, and respiratory diseases. Conclusion Our rank-based genome-wide analysis revealed for the first time an association of RYR2 variants with asthma and replicated previously discovered PDE4D asthma gene across human populations. The replication of top

  20. Gene-wide association study between the methylenetetrahydrofolate reductase gene (MTHFR) and schizophrenia in the Japanese population, with an updated meta-analysis on currently available data.

    PubMed

    Yoshimi, Akira; Aleksic, Branko; Kawamura, Yukiko; Takahashi, Nagahide; Yamada, Shinnosuke; Usui, Hinako; Saito, Shinichi; Ito, Yoshihito; Iwata, Nakao; Inada, Toshiya; Noda, Yukihiro; Yamada, Kiyofumi; Ozaki, Norio

    2010-12-01

    Methylenetetrahydrofolate reductase (MTHFR) is a critical molecule for single-carbon transfer reactions. Recent evidence suggests that polymorphisms of MTHFR are related to neural tube deficits and the pathogenesis of schizophrenia. While several studies have demonstrated associations between the gene encoding the MTHFR (MTHFR) polymorphisms and schizophrenia, these studies lack consistency. Therefore, we conducted a gene-wide association study (patients with schizophrenia = 696, control subjects = 747) and performed imputation analysis. Additionally, we performed meta-analysis on currently available data from 18 studies for two common functional polymorphisms (rs1801131 and rs1801133). There were no significant associations with schizophrenia in the single marker analysis for the seven tagging SNPs of MTHFR. In the haplotypic analysis, a nominally significant association was observed between the haplotypes, which included four SNPs (rs1801133, rs17421511, rs17037396, and rs9651118) and the schizophrenic patients. Additionally, the imputation analysis demonstrated there were several associated markers on the MTHFR chromosomal region. However, confirmatory analyses of three tagging SNPs (rs1801133, rs17037396, and rs9651118) and the top SNP (rs17421511) for the imputation results (patients with schizophrenia = 797, control subjects = 1025) failed to replicate the haplotypic analysis and the imputation results. These findings suggest that MTHFR polymorphisms are unlikely to be related to the development of schizophrenia in the Japanese population. However, since our meta-analysis results demonstrated strong support for association of rs1801133 with schizophrenia, further replication studies based on a gene-wide approach need to be considered.

  1. Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.

    PubMed

    Ouvrard, Pierre; Hicks, Damien M; Mouland, Molly; Nicholls, James A; Baldock, Katherine C R; Goddard, Mark A; Kunin, William E; Potts, Simon G; Thieme, Thomas; Veromann, Eve; Stone, Graham N

    2016-12-01

    Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

  2. Association between chronic osteomyelitis and deep-vein thrombosis. Analysis of a nationwide population-based registry.

    PubMed

    Lin, T-Y; Chen, Y-G; Huang, W-Y; Lin, C-L; Peng, C-L; Sung, F-C; Kao, C-H

    2014-09-02

    Studies on the association between chronic osteomyelitis and deep vein thrombosis (DVT) and pulmonary thromboembolism (PE) are scarce. The aim of this study was to analyse a nationwide population-based database for association between DVT or PE after a diagnosis of chronic osteomyelitis. This nationwide population-based cohort study was based on data obtained from the Taiwan National Health Insurance Database from 1998 to 2008, with a follow-up period extending to the end of 2010. We identified patients with chronic osteomyelitis using International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes. The patients with chronic osteomyelitis and comparison controls were selected by 1:1 matching on a propensity score. The propensity score was calculated by a logistic regression to estimate the probability of the treatment assignment given the baseline variables including age, sex, and Charlson comorbidity index score. We analysed the risks of DVT and PE by using Cox proportional hazards regression models, including sex, age, and comorbidities. In total, 24,335 chronic osteomyelitis patients and 24,335 controls were enrolled in the study. The risk of developing DVT was 2.49-fold in patients with chronic osteomyelitis compared with the comparison cohort, after adjusting for age, sex, and comorbidities. The multiplicative increased risks of DVT were also significant in patients with chronic osteomyelitis with any comorbidity. In conclusion, physicians should consider chronic osteomyelitis in their evaluation of risk factors for DVT.

  3. Association of Sjögrens Syndrome in Patients with Chronic Hepatitis Virus Infection: A Population-Based Analysis

    PubMed Central

    Yeh, Chih-Ching; Wang, Wen-Chang; Wu, Chien-Sheng; Sung, Fung-Chang; Su, Chien-Tien; Shieh, Ying-Hua; Chang, Shih-Ni; Su, Fu-Hsiung

    2016-01-01

    Objective The association between Sjögren’s syndrome (SS) and chronic hepatitis virus infection is inconclusive. Hepatitis B (HBV) and hepatitis C virus (HCV) infections are highly prevalent in Taiwan. We used a population-based case-control study to evaluate the associations between SS and HBV and HCV infections. Materials and Methods We identified 9,629 SS patients without other concomitant autoimmune diseases and 38,516 sex- and age-matched controls without SS from the Taiwan National Health Insurance claims data between 2000 and 2011. We utilized multivariate logistic regression to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) of the associations between SS and HBV and HCV infections. Sex- and age-specific (<55 and ≥55 years) risks of SS were evaluated. Results The risk of SS was higher in patients with HCV than in those without chronic viral hepatitis (OR = 2.49, 95% CI = 2.16–2.86). Conversely, HBV infection was not associated with SS (OR = 1.10, 95% CI = 0.98–1.24). Younger HCV patients were at a higher risk for SS (<55 years: OR = 3.37, 95% CI = 2.62–4.35; ≥55 years: OR = 2.20, 95% CI = 1.84–2.62). Men with HCV were at a greater risk for SS (women: OR = 2.26, 95% CI = 1.94–2.63; men: OR = 4.22, 95% CI = 2.90–6.16). Only men with chronic HBV exhibited a higher risk of SS (OR = 1.61, 95% CI = 1.21–2.14). Conclusion HCV infection was associated with SS; however, HBV only associated with SS in men. PMID:27560377

  4. Association of lncRNA H19 rs217727 polymorphism and cancer risk in the Chinese population: a meta-analysis

    PubMed Central

    Shen, Na; Peng, Jing; Wang, Chunyu; Zhu, Yaowu; Wang, Xiong

    2016-01-01

    Reports on the relationship between the lncRNA H19 rs217727 polymorphism and the risk of cancer in the Chinese population have been inconsistent. Therefore, we performed a meta-analysis to evaluate this association, by searching the Embase, PubMed, Web of Science, Wanfang, and CNKI databases. Four case-control studies with 3,157 cases and 3,564 controls were selected for this meta-analysis. The odds ratios with 95% confidence intervals were examined using the random effect model. Allelic (A vs. G), dominant (AA + GA vs. GG), recessive (AA vs. GA + GG), and additive (AA vs. GG) genetic models were used to determine the association. Overall, no significant association was observed between the rs217727 polymorphism and cancer susceptibility in any of the four genetic models. Sensitivity analysis revealed that the results were stable in the allelic and dominant genetic models, but those from the recessive and additive models were unstable, which should be treated with caution. Our meta-analysis suggests that the lncRNA H19 rs217727 polymorphism might not be associated with overall cancer risk. However, well-designed, large-scale studies with different ethnic populations need to be conducted in the future to elucidate the potential association. PMID:27486980

  5. Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis

    PubMed Central

    Zhu, Hong; Xia, Wei; Mo, Xing-Bo; Lin, Xiang; Qiu, Ying-Hua; Yi, Neng-Jun; Zhang, Yong-Hong; Deng, Fei-Yan; Lei, Shu-Feng

    2016-01-01

    Objective Rheumatoid arthritis (RA) is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations. Methods Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects). For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected ‘highly verified’ genes were measured by ELISA among our in-house RA cases and controls. Results A total of 221 RA-associated genes were newly identified by gene-based association study, including 71‘overlapped’, 76 ‘European-specific’ and 74 ‘Asian-specific’ genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 ‘overlapped’ (ABCF1, FLOT1, HLA-F, IER3, TUBB, ZKSCAN4, BTN3A3, HSP90AB1, CUTA, BRD2, HLA-DMA), 5 ‘European-specific’ (PHTF1, RPS18, BAK1, TNFRSF14, SUOX) and 4 ‘Asian-specific’ (RNASET2, HFE, BTN2A2, MAPK13) genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes FLOT1 (P value = 1.70E-02) and HLA-DMA (P value = 4.70E-02) in plasma were significantly different in our in-house samples. Conclusion Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and

  6. Exploring causal associations of alcohol with cardiovascular and metabolic risk factors in a Chinese population using Mendelian randomization analysis.

    PubMed

    Taylor, Amy E; Lu, Feng; Carslake, David; Hu, Zhibin; Qian, Yun; Liu, Sijun; Chen, Jiaping; Shen, Hongbing; Smith, George Davey

    2015-09-14

    Observational studies suggest that moderate alcohol consumption may be protective for cardiovascular disease, but results may be biased by confounding and reverse causality. Mendelian randomization, which uses genetic variants as proxies for exposures, can minimise these biases and therefore strengthen causal inference. Using a genetic variant in the ALDH2 gene associated with alcohol consumption, rs671, we performed a Mendelian randomization analysis in 1,712 diabetes cases and 2,076 controls from Nantong, China. Analyses were performed using linear and logistic regression, stratified by sex and diabetes status. The A allele of rs671 was strongly associated with reduced odds of being an alcohol drinker in all groups, but prevalence of alcohol consumption amongst females was very low. The A allele was associated with reduced systolic and diastolic blood pressure and decreased total and HDL cholesterol in males. The A allele was also associated with decreased triglyceride levels, but only robustly in diabetic males. There was no strong evidence for associations between rs671 and any outcomes in females. Our results suggest that associations of alcohol consumption with blood pressure and HDL-cholesterol are causal. Alcohol also appeared to have adverse effects on triglyceride levels, although this may be restricted to diabetics.

  7. Exploring causal associations of alcohol with cardiovascular and metabolic risk factors in a Chinese population using Mendelian randomization analysis

    PubMed Central

    Taylor, Amy E.; Lu, Feng; Carslake, David; Hu, Zhibin; Qian, Yun; Liu, Sijun; Chen, Jiaping; Shen, Hongbing; Smith, George Davey

    2015-01-01

    Observational studies suggest that moderate alcohol consumption may be protective for cardiovascular disease, but results may be biased by confounding and reverse causality. Mendelian randomization, which uses genetic variants as proxies for exposures, can minimise these biases and therefore strengthen causal inference. Using a genetic variant in the ALDH2 gene associated with alcohol consumption, rs671, we performed a Mendelian randomization analysis in 1,712 diabetes cases and 2,076 controls from Nantong, China. Analyses were performed using linear and logistic regression, stratified by sex and diabetes status. The A allele of rs671 was strongly associated with reduced odds of being an alcohol drinker in all groups, but prevalence of alcohol consumption amongst females was very low. The A allele was associated with reduced systolic and diastolic blood pressure and decreased total and HDL cholesterol in males. The A allele was also associated with decreased triglyceride levels, but only robustly in diabetic males. There was no strong evidence for associations between rs671 and any outcomes in females. Our results suggest that associations of alcohol consumption with blood pressure and HDL-cholesterol are causal. Alcohol also appeared to have adverse effects on triglyceride levels, although this may be restricted to diabetics. PMID:26364564

  8. The association analysis of hOGG1 genetic variants and gastric cancer risk in a Chinese population

    PubMed Central

    Ma, Gaoxiang; Ge, Yuqiu; Zhang, Qiang; Chu, Haiyan; Tong, Na; Wang, Meilin; Qiu, Jinrong; Zhang, Zhengdong

    2016-01-01

    Human 8-oxoguanine DNA glycosylase (hOGG1) is known to play an important role in the prevention of carcinogenesis, including gastric cancer (GC). We performed a case-control study to investigate whether single nucleotide polymorphisms (SNPs) of hOGG1 are associated with GC risk in a Chinese population. Two potential functional tagSNPs (rs159153 and rs1052133) and a previously reported risk SNP (rs125701) were genotyped in 1,275 GC patients and 1,436 controls. We found that SNP rs125701 G > A was significantly associated with the increased GC risk [adjusted odds ratio (OR) = 1.38, 95% confidence interval (CI) = 1.05-1.79 in additive model]. Besides, the functional studies demonstrated that the minor A allele of rs125701 significantly reduced the transcriptional activity of hOGG1 promoter and enhanced the methylation level of CpG site of cg15357639. In conclusion, our results suggested that the SNP rs125701 in hOGG1 promoter was associated with the elevated GC risk, which could act as a new potential biomarker for GC susceptibility. Further functional verification of rs125701 in GC pathogenesis is warranted. PMID:27603140

  9. ERAP1 variants are associated with ankylosing spondylitis in East Asian population: a new Chinese case-control study and meta-analysis of published series.

    PubMed

    Chen, C; Zhang, X

    2015-06-01

    Endoplasmic reticulum aminopeptidase 1 (ERAP1) has been confirmed to be associated with ankylosing spondylitis (AS) in Caucasian. However, whether they are associated with AS in East Asian population remains unidentified. We investigated this relationship by a new Chinese case-control study and a meta-analysis of published series. 368 cases and 460 controls were recruited in the Chinese case-control study. Genotyping was completed using the chip-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Allelic associations were analysed using contingency tables. In the meta-analysis, up to 2748 cases and 2774 controls from seven different studies and the new Chinese study were combined using Review Manager software version 5.1.1. Mantel-Haenszel or Inverse Variance test was used to calculate fixed or random-effects pooled ORs. In the new Chinese study, strong association with AS was observed for marker rs10050860, rs27434 and rs1065407 at P value of <0.001. Moderate association was observed for rs30187 at P value of <0.01, while no association was observed for rs27044 (P = 0.37) and rs2287987 (P = 0.23). The meta-analysis showed that rs27037 and rs30187 were strongly associated with AS (P < 0.00001). Significant association was also observed for rs27434 (P = 0.001). No association was shown for rs27044 (P = 0.70). We concluded that ERAP1 variants are associated with AS in East Asian population, indicating a common pathogenic mechanism for AS in East Asians and Caucasians.

  10. Confirmatory factor analysis of the Adult Asperger Assessment: the association of symptom domains within a clinical population.

    PubMed

    Kuenssberg, Renate; McKenzie, Karen

    2011-01-01

    Autism Spectrum Disorder (ASD) is a behaviourally defined disorder characterised by impairments in three domains of social interaction, communication, and repetitive, stereotyped behaviours and activities. Proposed changes to diagnostic criteria suggest that the diagnostic triad may no longer fit as the best way to conceptualise ASD, and that social and communication impairments should be considered as a single domain. The aim of this study was to examine the structure of symptom domains within the Adult Asperger Assessment (AAA; Baron-Cohen, Wheelwright, Robinson, & Woodbury-Smith, 2005), a diagnostic tool for high functioning adults. As theoretical models already exist, confirmatory factor analysis was used to examine data from a clinical population of adults (n = 153) diagnosed with Asperger Syndrome (AS) and High Functioning Autism (HFA). Confirmatory factor analysis was used to fit different models based on the structure proposed by the authors of the AAA, the traditional triad and the newly proposed diagnostic dyad. Analysis suggested that none of the tested models were a good fit on the AAA dataset. However, it did highlight very high correlations between social and communication factors (r > 0.9) within unmodified models. The results of the analysis provide tentative support for the move towards considering ASD as a dyad of 'social-communication' impairments and repetitive/restricted interests behaviours and activities, rather than the traditional triad.

  11. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

    PubMed Central

    Taravella, Angela M.; Bustamante, Carlos D.; Sikora, Martin

    2017-01-01

    The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34–49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011–0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48–65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause. PMID:28282382

  12. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.

    PubMed

    Wen, Wanqing; Zheng, Wei; Okada, Yukinori; Takeuchi, Fumihiko; Tabara, Yasuharu; Hwang, Joo-Yeon; Dorajoo, Rajkumar; Li, Huaixing; Tsai, Fuu-Jen; Yang, Xiaobo; He, Jiang; Wu, Ying; He, Meian; Zhang, Yi; Liang, Jun; Guo, Xiuqing; Sheu, Wayne Huey-Herng; Delahanty, Ryan; Guo, Xingyi; Kubo, Michiaki; Yamamoto, Ken; Ohkubo, Takayoshi; Go, Min Jin; Liu, Jian Jun; Gan, Wei; Chen, Ching-Chu; Gao, Yong; Li, Shengxu; Lee, Nanette R; Wu, Chen; Zhou, Xueya; Song, Huaidong; Yao, Jie; Lee, I-Te; Long, Jirong; Tsunoda, Tatsuhiko; Akiyama, Koichi; Takashima, Naoyuki; Cho, Yoon Shin; Ong, Rick Th; Lu, Ling; Chen, Chien-Hsiun; Tan, Aihua; Rice, Treva K; Adair, Linda S; Gui, Lixuan; Allison, Matthew; Lee, Wen-Jane; Cai, Qiuyin; Isomura, Minoru; Umemura, Satoshi; Kim, Young Jin; Seielstad, Mark; Hixson, James; Xiang, Yong-Bing; Isono, Masato; Kim, Bong-Jo; Sim, Xueling; Lu, Wei; Nabika, Toru; Lee, Juyoung; Lim, Wei-Yen; Gao, Yu-Tang; Takayanagi, Ryoichi; Kang, Dae-Hee; Wong, Tien Yin; Hsiung, Chao Agnes; Wu, I-Chien; Juang, Jyh-Ming Jimmy; Shi, Jiajun; Choi, Bo Youl; Aung, Tin; Hu, Frank; Kim, Mi Kyung; Lim, Wei Yen; Wang, Tzung-Dao; Shin, Min-Ho; Lee, Jeannette; Ji, Bu-Tian; Lee, Young-Hoon; Young, Terri L; Shin, Dong Hoon; Chun, Byung-Yeol; Cho, Myeong-Chan; Han, Bok-Ghee; Hwu, Chii-Min; Assimes, Themistocles L; Absher, Devin; Yan, Xiaofei; Kim, Eric; Kuo, Jane Z; Kwon, Soonil; Taylor, Kent D; Chen, Yii-Der I; Rotter, Jerome I; Qi, Lu; Zhu, Dingliang; Wu, Tangchun; Mohlke, Karen L; Gu, Dongfeng; Mo, Zengnan; Wu, Jer-Yuarn; Lin, Xu; Miki, Tetsuro; Tai, E Shyong; Lee, Jong-Young; Kato, Norihiro; Shu, Xiao-Ou; Tanaka, Toshihiro

    2014-10-15

    Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488-47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10(-13)), ALDH2/MYL2 (rs671, P = 3.40 × 10(-11); rs12229654, P = 4.56 × 10(-9)), ITIH4 (rs2535633, P = 1.77 × 10(-10)) and NT5C2 (rs11191580, P = 3.83 × 10(-8)) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10(-8)) and an additional 14 at P < 1.0 × 10(-3) with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity.

  13. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

    PubMed Central

    Wen, Wanqing; Zheng, Wei; Okada, Yukinori; Takeuchi, Fumihiko; Tabara, Yasuharu; Hwang, Joo-Yeon; Dorajoo, Rajkumar; Li, Huaixing; Tsai, Fuu-Jen; Yang, Xiaobo; He, Jiang; Wu, Ying; He, Meian; Zhang, Yi; Liang, Jun; Guo, Xiuqing; Sheu, Wayne Huey-Herng; Delahanty, Ryan; Guo, Xingyi; Kubo, Michiaki; Yamamoto, Ken; Ohkubo, Takayoshi; Go, Min Jin; Liu, Jian Jun; Gan, Wei; Chen, Ching-Chu; Gao, Yong; Li, Shengxu; Lee, Nanette R.; Wu, Chen; Zhou, Xueya; Song, Huaidong; Yao, Jie; Lee, I-Te; Long, Jirong; Tsunoda, Tatsuhiko; Akiyama, Koichi; Takashima, Naoyuki; Cho, Yoon Shin; Ong, Rick TH; Lu, Ling; Chen, Chien-Hsiun; Tan, Aihua; Rice, Treva K; Adair, Linda S.; Gui, Lixuan; Allison, Matthew; Lee, Wen-Jane; Cai, Qiuyin; Isomura, Minoru; Umemura, Satoshi; Kim, Young Jin; Seielstad, Mark; Hixson, James; Xiang, Yong-Bing; Isono, Masato; Kim, Bong-Jo; Sim, Xueling; Lu, Wei; Nabika, Toru; Lee, Juyoung; Lim, Wei-Yen; Gao, Yu-Tang; Takayanagi, Ryoichi; Kang, Dae-Hee; Wong, Tien Yin; Hsiung, Chao Agnes; Wu, I-Chien; Juang, Jyh-Ming Jimmy; Shi, Jiajun; Choi, Bo Youl; Aung, Tin; Hu, Frank; Kim, Mi Kyung; Lim, Wei Yen; Wang, Tzung-Dao; Shin, Min-Ho; Lee, Jeannette; Ji, Bu-Tian; Lee, Young-Hoon; Young, Terri L.; Shin, Dong Hoon; Chun, Byung-Yeol; Cho, Myeong-Chan; Han, Bok-Ghee; Hwu, Chii-Min; Assimes, Themistocles L.; Absher, Devin; Yan, Xiaofei; Kim, Eric; Kuo, Jane Z.; Kwon, Soonil; Taylor, Kent D.; Chen, Yii-Der I.; Rotter, Jerome I.; Qi, Lu; Zhu, Dingliang; Wu, Tangchun; Mohlke, Karen L.; Gu, Dongfeng; Mo, Zengnan; Wu, Jer-Yuarn; Lin, Xu; Miki, Tetsuro; Tai, E. Shyong; Lee, Jong-Young; Kato, Norihiro; Shu, Xiao-Ou; Tanaka, Toshihiro

    2014-01-01

    Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488–47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10−13), ALDH2/MYL2 (rs671, P = 3.40 × 10−11; rs12229654, P = 4.56 × 10−9), ITIH4 (rs2535633, P = 1.77 × 10−10) and NT5C2 (rs11191580, P = 3.83 × 10−8) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10−8) and an additional 14 at P < 1.0 × 10−3 with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity. PMID:24861553

  14. Association of GSTT1 and GSTM1 polymorphisms with early pregnancy loss in an Indian population and a meta-analysis.

    PubMed

    Nair, Rohini R; Khanna, Anuradha; Singh, Kiran

    2013-04-01

    Glutathione S-transferase theta 1 (GSTT1) and glutathione S-transferase Mu 1 (GSTM1) enzymes of the glutathione detoxification pathway protect the embryo from oxidative stress. This study investigated GSTT1 and GSTM1 in relation to their role in conferring genetic susceptibility to pregnancy loss. In a case-control study, 174 early pregnancy loss (EPL) patients, of which 130 were recurrent pregnancy loss (RPL) patients, and 180 healthy controls were investigated. Null genotypes of GSTT1 and GSTM1 were identified in duplex PCR reaction systems. Age-adjusted odds ratios (aOR) were calculated by logistic regression analysis. A meta-analysis was also conducted. The GSTT1 null genotype was significantly associated with EPL (aOR 4.47, P=0.004) and RPL (aOR 4.39, P=0.006). No significant association of the GSTM1 null genotype was found with RPL. In a meta-analysis study, the presence of the GSTM1 null genotype was shown to be a risk for RPL. The GSTT1 null genotype was not found to be a risk factor for pregnancy loss in the pooled population but its association with RPL was found in the Indian population. This study suggests that women carriers of GSTT1 and GSTM1 null genotypes are more often at genetic risk of pregnancy loss. Glutathione S-transferase theta 1 (GSTT1) and glutathione S-transferase mu 1 (GSTM1), enzymes of detoxification pathway, protect the embryo from oxidative stress. In the present study we have investigated GSTT1 and GSTM1 in relation to their role in conferring genetic susceptibility for early pregnancy loss (EPL) and recurrent pregnancy loss (RPL). Meta-analysis on the polymorphisms was conducted to support our findings that the presence of mutant genotypes at this site increases the risk of pregnancy loss. The GSTT1 null genotype was significantly associated with both EPL and RPL. In the meta-analysis, the overall result showed that the association between GSTM1 null genotype and risk for RPL was statistically significant. On comparing the GSTT1

  15. Volatility and Growth in Populations of Rural Associations

    ERIC Educational Resources Information Center

    Wollebaek, Dag

    2010-01-01

    This article uses unique community-level data aggregated from censuses of associations to analyze growth and volatility in rural populations of grassroots associations. A qualitative comparative analysis (QCA) shows that the two main paths to growth were (1) centralization in polycephalous (multicentered) municipalities and (2) population growth…

  16. Genome-wide analysis of CNV (copy number variation) and their associations with narcolepsy in a Japanese population.

    PubMed

    Yamasaki, Maria; Miyagawa, Taku; Toyoda, Hiromi; Khor, Seik-Soon; Koike, Asako; Nitta, Aino; Akiyama, Kumi; Sasaki, Tsukasa; Honda, Yutaka; Honda, Makoto; Tokunaga, Katsushi

    2014-05-01

    In humans, narcolepsy with cataplexy (narcolepsy) is a sleep disorder that is characterized by sleepiness, cataplexy and rapid eye movement (REM) sleep abnormalities. Narcolepsy is caused by a reduction in the number of neurons that produce hypocretin (orexin) neuropeptide. Both genetic and environmental factors contribute to the development of narcolepsy.Rare and large copy number variations (CNVs) reportedly play a role in the etiology of a number of neuropsychiatric disorders. Narcolepsy is considered a neurological disorder; therefore, we sought to investigate any possible association between rare and large CNVs and human narcolepsy. We used DNA microarray data and a CNV detection software application, PennCNV-Affy, to detect CNVs in 426 Japanese narcoleptic patients and 562 healthy individuals. Overall, we found a significant enrichment of rare and large CNVs (frequency ≤1%, size ≥100 kb) in the patients (case-control ratio of CNV count=1.54, P=5.00 × 10(-4)). Next, we extended a region-based association analysis by including CNVs with its size ≥30 kb. Rare and large CNVs in PARK2 region showed a significant association with narcolepsy. Four patients were assessed to carry duplications of the gene region, whereas no controls carried the duplication, which was further confirmed by quantitative PCR assay. This duplication was also found in 2 essential hypersomnia (EHS) patients out of 171 patients. Furthermore, a pathway analysis revealed enrichments of gene disruptions by rare and large CNVs in immune response, acetyltransferase activity, cell cycle regulation and regulation of cell development. This study constitutes the first report on the risk association between multiple rare and large CNVs and the pathogenesis of narcolepsy. In the future, replication studies are needed to confirm the associations.

  17. Mutational analysis in podocin-associated hereditary nephrotic syndrome in Polish patients: founder effect in the Kashubian population.

    PubMed

    Lipska, Beata S; Balasz-Chmielewska, Irena; Morzuch, Lucyna; Wasielewski, Kacper; Vetter, Dominika; Borzecka, Halina; Drozdz, Dorota; Firszt-Adamczyk, Agnieszka; Gacka, Ewa; Jarmolinski, Tomasz; Ksiazek, Joanna; Kuzma-Mroczkowska, Elzbieta; Litwin, Mieczyslaw; Medynska, Anna; Silska, Magdalena; Szczepanska, Maria; Tkaczyk, Marcin; Wasilewska, Anna; Schaefer, Franz; Zurowska, Aleksandra; Limon, Janusz

    2013-08-01

    Hereditary nephrotic syndrome is caused by mutations in a number of different genes, the most common being NPHS2. The aim of the study was to identify the spectrum of NPHS2 mutations in Polish patients with the disease. A total of 141 children with steroid-resistant nephrotic syndrome (SRNS) were enrolled in the study. Mutational analysis included the entire coding sequence and intron boundaries of the NPHS2 gene. Restriction fragment length polymorphism (RFLP) and TaqMan genotyping assay were applied to detect selected NPHS2 sequence variants in 575 population-matched controls. Twenty patients (14 %) had homozygous or compound heterozygous NPHS2 mutations, the most frequent being c.1032delT found in 11 children and p.R138Q found in four patients. Carriers of the c.1032delT allele were exclusively found in the Pomeranian (Kashubian) region, suggesting a founder effect origin. The 14 % NPHS2 gene mutation detection rate is similar to that observed in other populations. The heterogeneity of mutations detected in the studied group confirms the requirement of genetic testing the entire NPHS2 coding sequence in Polish patients, with the exception of Kashubs, who should be initially screened for the c.1032delT deletion.

  18. Diversity of Pea-Associated F. proliferatum and F. verticillioides Populations Revealed by FUM1 Sequence Analysis and Fumonisin Biosynthesis

    PubMed Central

    Waśkiewicz, Agnieszka; Stępień, Łukasz; Wilman, Karolina; Kachlicki, Piotr

    2013-01-01

    Fusarium proliferatum and F. verticillioides are considered as minor pathogens of pea (Pisum sativum L.). Both species can survive in seed material without visible disease symptoms, but still contaminating it with fumonisins. Two populations of pea-derived F. proliferatum and F. verticillioides strains were subjected to FUM1 sequence divergence analysis, forming a distinct group when compared to the collection strains originating from different host species. Furthermore, the mycotoxigenic abilities of those strains were evaluated on the basis of in planta and in vitro fumonisin biosynthesis. No differences were observed in fumonisin B (FB) levels measured in pea seeds (maximum level reached 1.5 μg g−1); however, in rice cultures, the majority of F. proliferatum genotypes produced higher amounts of FB1–FB3 than F. verticillioides strains. PMID:23470545

  19. Association between HTR2A T102C polymorphism and major depressive disorder: a meta-analysis in the Chinese population.

    PubMed

    Lin, Chun-Xia; Hu, Zhe; Yan, Ze-Ming; Li, Wen; Chen, Yu-Sen; Zhao, Jiang-Hao; Zhang, Liang-Qing; Zhao, Bin; Zhong, Wang-Tao; Feng, Du

    2015-01-01

    Although a number of studies have been conducted on the association between HTR2A T102C polymorphism and major depressive disorder (MDD) in Chinese, this association remains elusive and controversial. To clarify the effects of HTR2A T102C polymorphism on the risk of MDD, a meta-analysis was performed in the Chinese population. Related studies were identified from PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) till 5 May 2015. The odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the strength of the associations. Statistical analyses were conducted with Version 10.0 STATA statistical software. A total of 12 case-control studies including 1444 MDD cases and 1445 controls were involved in this meta-analysis. Overall, no significant association with MDD risk was provided in the Chinese population (C vs. T: OR=0.97, 95% CI: 0.81-1.17, 95%; CC vs. TT: OR=0.95, 95% CI: 0.65-1.37; CC+TC vs. TT: OR=0.96, 95% CI: 0.75-1.12; CC vs. TT+TC: OR=0.94, 95% CI: 0.78-1.12). In subgroup analyses stratified by geographic area and source of controls, no significant association was found in any of the subgroups. In conclusion, this meta-analysis indicate that the HTR2A T102C polymorphism is not associated with susceptibility to MDD in Chinese population.

  20. Association between HTR2A T102C polymorphism and major depressive disorder: a meta-analysis in the Chinese population

    PubMed Central

    Lin, Chun-Xia; Hu, Zhe; Yan, Ze-Ming; Li, Wen; Chen, Yu-Sen; Zhao, Jiang-Hao; Zhang, Liang-Qing; Zhao, Bin; Zhong, Wang-Tao; Feng, Du

    2015-01-01

    Although a number of studies have been conducted on the association between HTR2A T102C polymorphism and major depressive disorder (MDD) in Chinese, this association remains elusive and controversial. To clarify the effects of HTR2A T102C polymorphism on the risk of MDD, a meta-analysis was performed in the Chinese population. Related studies were identified from PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) till 5 May 2015. The odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the strength of the associations. Statistical analyses were conducted with Version 10.0 STATA statistical software. A total of 12 case-control studies including 1444 MDD cases and 1445 controls were involved in this meta-analysis. Overall, no significant association with MDD risk was provided in the Chinese population (C vs. T: OR=0.97, 95% CI: 0.81-1.17, 95%; CC vs. TT: OR=0.95, 95% CI: 0.65-1.37; CC+TC vs. TT: OR=0.96, 95% CI: 0.75-1.12; CC vs. TT+TC: OR=0.94, 95% CI: 0.78-1.12). In subgroup analyses stratified by geographic area and source of controls, no significant association was found in any of the subgroups. In conclusion, this meta-analysis indicate that the HTR2A T102C polymorphism is not associated with susceptibility to MDD in Chinese population. PMID:26885016

  1. Association analysis between 12 genetic variants of ten genes and personality traits in a young chinese Han population.

    PubMed

    Gong, Pingyuan; Zheng, Anyun; Zhang, Kejin; Lei, Xu; Li, Fengchao; Chen, Dongmei; Chi, Wanyu; Tong, Xueli; Zheng, Zijian; Gao, Xiaocai; Zhang, Fuchang

    2010-09-01

    Some genes involved in neurotransmission synthesis and transmission have been hypothesized to affect personality traits. To investigate the possible roles of these genes in personality traits of 16 Personality Factor Questionnaire, we performed a population-based study in a young Chinese Han cohort. In the study, we selected some functional variations in ten candidate genes (COMT, DBH, DRD(2), DRD(3), DAT, MAOA, GRM(1), GRIN2B, 5-TH(2A), and 5-TH(6)) encoding components in dopamine, glutamate, and 5-hydroxytryptamine pathways. The results showed the T102C in 5-TH(2A) was associated with X3 (emotional and quiet alertness) and B (reasoning) (F = 4.71 and 6.23; p = 0.009 and 0.002), Val158Met in COMT with E (dominance) (F = 7.01; p = 0.0009), while the variations in DBH, DRD(2), DRD(3), MAOA, GRM(1), GRIN2B, and 5-TH(6) were not associated with any of the personality traits. This finding suggests that T102C in 5-TH(2A) and Val158Met in COMT play roles in some human personality traits.

  2. Iron deficiency is associated with increased levels of blood cadmium in the Korean general population: Analysis of 2008-2009 Korean National Health and Nutrition Examination Survey data

    SciTech Connect

    Lee, Byung-Kook; Kim, Yangho

    2012-01-15

    Introduction: We present data from the Korean National Health and Nutrition Examination Survey 2008-2009 on the distribution of blood cadmium levels and their association with iron deficiency in a representative sample of the adult Korean population. Methods: Serum ferritin was categorized into three levels: low (serum ferritin <15.0 {mu}g/L), low normal (15.0-30.0 {mu}g/L for women and 15.0-50.0 for men), and normal ({>=}30.0 {mu}g/L for women and {>=}50.0 for men), and its association with blood cadmium level was assessed after adjustment for various demographic and lifestyle factors. Results: Geometric means of blood cadmium in the low serum ferritin group in women, men, and all participants were significantly higher than in the normal group. Additionally, multiple regression analysis after adjusting for various covariates showed that blood cadmium was significantly higher in the low-ferritin group in women, men, and all participants compared with the normal group. We also found an association between serum ferritin and blood cadmium among never-smoking participants. Discussion: We found, similar to other recent population-based studies, an association between iron deficiency and increased blood cadmium in men and women, independent of smoking status. The results of the present study show that iron deficiency is associated with increased levels of blood cadmium in the general population.

  3. Association between monoamine oxidase B A644G polymorphism and Parkinson's disease risk: a meta-analysis in the Chinese population.

    PubMed

    Liu, J J; Wang, W; Meng, M; Liang, C S; Zhang, J W

    2016-07-14

    Although various individual studies have evaluated the correlation between monoamine oxidase B (MAOB), polymorphism, and Parkinson's disease (PD), the results remain inconclusive. Therefore, we performed a meta-analysis in the Chinese population to provide comprehensive data on the association between the MAOB polymorphism and PD. Eligible studies were identified via databases such as PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure, and Chinese Biology Medicine, throughout November 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strengths of these associations. Eight studies documenting a total of 1385 cases of PD and 1426 controls were included in this meta-analysis. Overall, no significant association was found between the MAOB A644G polymorphism and PD risk in the Chinese population. However, in subgroup analyses, where results were stratified by geographical areas and source of controls, increased risk for PD in Northern China was observed (allele A vs G: OR = 1.33, 95%CI = 1.11-1.58; AA vs GG: OR = 1.46, 95%CI = 1.09-1.97; AA + AG vs GG: OR = 1.42, 95%CI = 1.06-1.90). Similarly, population-based studies also showed significant association between the MAOB A644G polymorphism and PD risk among different populations (allele A vs G: OR = 1.29, 95%CI = 1.11-1.51; AA vs GG: OR = 1.41, 95%CI = 1.09-1.82; AA + AG vs GG: OR = 1.34, 95%CI = 1.04- 1.71). In conclusion, this meta-analysis provided evidence that the MAOB A644G polymorphism may contribute to PD development in Northern China. Further studies conducted in other ethnic groups are required for definite conclusions.

  4. Association between the PADI4 -94G/A polymorphism and rheumatoid arthritis: a meta-analysis in the Chinese population.

    PubMed

    Chang, H X

    2016-03-31

    Although a number of studies have been conducted on the association between the peptidylarginine deiminase (PADI4) -94G/A polymorphism and rheumatoid arthritis (RA) in the Chinese population, the association remains elusive and controversial. To clarify the impact of the PADI4 -94G/A polymorphism on the risk of RA, a meta-analysis was performed in the Chinese population. Related studies were identified from databases such as, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) up to May 21, 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of associations. A total of 10 studies with 2783 RA cases and 2887 controls were included in this meta-analysis. Overall, a significantly elevated risk of RA was associated with all variants of PADI4 -94G/A (A vs G: OR = 1.24, 95%CI = 1.15-1.34; AA + GA vs GG: OR = 1.45, 95%CI = 1.29-1.62; AA vs GG: OR = 1.49, 95%CI = 1.28-1.73; AA vs GG + GA: OR = 1.19, 95%CI = 1.04-1.35). Subgroup analyses stratified by geographic areas and source of controls revealed significant results in the population-based studies in North and South China. In conclusion, this meta-analysis showed that the PADI4 -94G/A variants may influence RA risk in the Chinese population. However, further studies with gene-gene and gene-environment interactions are required for definite conclusions.

  5. Assessment of association between common variants at 17q12 and prostate cancer risk-evidence from Serbian population and meta--analysis.

    PubMed

    Nikolić, Zorana Z; Branković, Ana S; Savić-Pavićević, Dušanka L J; Preković, Stefan M; Vukotić, Vinka D; Cerović, Snežana J; Filipović, Nataša N; Tomović, Saša M; Romac, Stanka P; Brajušković, Goran N

    2014-08-01

    This study aimed to evaluate possible association between genotypes and alleles of two 17q12 polymorphisms (rs3760511 and rs7501939) and prostate cancer (PCa) risk and progression. Two hundred seventy-one patients with PCa, 261 patients with benign prostatic hyperplasia (BPH), and 171 controls were included in the study. Single nucleotide polymorphisms (SNPs) were genotyped by using PCR followed by restriction fragment length (PCR-RFLP) analysis. We conducted meta-analysis of published studies regarding association of these SNPs with PCa risk. Evidence of positive association between the AC genotype of the SNP rs3760511 and BPH risk for the best-fitting overdominant model of association (BPH vs. controls comparison, p = 0.026; odds ratio [OR] = 1.58; 95% confidence interval [95%CI] 1.05-2.36) were obtained. The association between T allele of rs7501939 and PCa risk was determined in PCa versus controls comparison (p = 0.0032; OR = 0.66, 95%CI 0.50-0.87) with the best-fitting model of inheritance being log-additive. This variant was also found to be associated with the risk of BPH (p = 0.0023; OR = 0.65, 95%CI 0.49-0.86). We found no association between parameters of PCa progression and the analyzed SNPs. Meta-analysis showed strong association between these variants and PCa risk. Our study shows association between SNPs at locus 17q12 and the risk of prostatic diseases in Serbian population. At the same time, results of meta-analysis suggest the association of these SNPs with PCa risk.

  6. Replication Study in a Japanese Population of Six Susceptibility Loci for Type 2 Diabetes Originally Identified by a Transethnic Meta-Analysis of Genome-Wide Association Studies

    PubMed Central

    Matsuba, Ren; Imamura, Minako; Tanaka, Yasushi; Iwata, Minoru; Hirose, Hiroshi; Kaku, Kohei; Maegawa, Hiroshi; Watada, Hirotaka; Tobe, Kazuyuki; Kashiwagi, Atsunori; Kawamori, Ryuzo; Maeda, Shiro

    2016-01-01

    Aim We performed a replication study in a Japanese population to evaluate the association between type 2 diabetes and six susceptibility loci (TMEM154, SSR1, FAF1, POU5F1, ARL15, and MPHOSPH9) originally identified by a transethnic meta-analysis of genome-wide association studies (GWAS) in 2014. Methods We genotyped 7,620 Japanese participants (5,817 type 2 diabetes patients and 1,803 controls) for each of the single nucleotide polymorphisms (SNPs) using a multiplex polymerase chain reaction invader assay. The association of each SNP locus with the disease was evaluated using logistic regression analysis. Results Of the six SNPs examined in this study, four (rs6813195 near TMEM154, rs17106184 in FAF1, rs3130501 in POU5F1 and rs4275659 near MPHOSPH9) had the same direction of effect as in the original reports, but two (rs9505118 in SSR1 and rs702634 in ARL15) had the opposite direction of effect. Among these loci, rs3130501 and rs4275659 were nominally associated with type 2 diabetes (rs3130501; p = 0.017, odds ratio [OR] = 1.113, 95% confidence interval [CI] 1.019–1.215, rs4275659; p = 0.012, OR = 1.127, 95% CI 1.026–1.238, adjusted for sex, age and body mass index), but we did not observe a significant association with type 2 diabetes for any of the six evaluated SNP loci in our Japanese population. Conclusions Our results indicate that effects of the six SNP loci identified in the transethnic GWAS meta-analysis are not major among the Japanese, although SNPs in POU5F1 and MPHOSPH9 loci may have some effect on susceptibility to type 2 diabetes in this population. PMID:27115357

  7. The association and predictive value analysis of metabolic syndrome combined with resting heart rate on cardiovascular autonomic neuropathy in the general Chinese population

    PubMed Central

    2013-01-01

    Background The purpose of this study was to explore the extent of associations of cardiovascular autonomic neuropathy (CAN) with metabolic syndrome (MetS) and resting heart reate (HR), and to evaluate the predictive value of MetS combined with HR on CAN in a large sample derived from a Chinese population. Materials and methods We conducted a large-scale, population-based, cross-sectional study to explore the relationships of CAN with MetS and resting HR. This study included 2092 participants aged 30–80 years, and a total of 387 subjects were diagnosed with CAN in our dataset. The associations of CAN with MetS and resting HR were assessed by a multivariate logistic regression (MLR) analysis (using subjects without CAN as a reference group) after controlling for potential confounding factors. The predictive performance of resting HR and MetS was evaluated using the area under the receiver-operating characteristic curve (AUC). Results A tendency toward increased CAN prevalence with increasing resting HR was reported (p for trend < 0.001). MLR analysis showed that MetS and resting HR were very significantly and independently associated with CAN (β = 0.495 for MetS and β = 0.952 for HR, P < 0.001 for both). Resting HR alone and combined with MetS (MetS-HR) strongly predicted CAN (AUC = 0.719, P < 0.001 for resting HR and AUC = 0.735, P < 0.001 for MetS-HR). Conclusion Our findings signify that MetS and resting HR were very significantly and independently associated with CAN in the general Chinese population. Resting HR and MetS-HR both have a high value in predicting CAN in the general population. PMID:24238358

  8. Association between fluid intake and kidney function, and survival outcomes analysis: a nationwide population-based study

    PubMed Central

    Wu, Li-Wei; Chen, Wei-Liang; Liaw, Fang-Yih; Sun, Yu-Shan; Yang, Hui-Fang; Wang, Chung-Ching; Lin, Chien-Ming; Tsao, Yu-Tzu

    2016-01-01

    Objectives Fluid intake, one of the most common daily activities, has not been well studied in chronic kidney disease (CKD) populations, and clinical outcomes are rarely addressed. The aim of this nationwide study is to explore the influence of daily fluid intake on cardiovascular and all-cause mortality and its association with renal function. Design Observational cohort study. Participants In all, 2182 participants aged more than 20 years participated in the Third National Health and Nutrition Examination Survey (1988–1994). Main outcome measures Survival outcomes in patients with or without CKD, using multiple variable adjusted Cox proportional hazard models. Results In a longitudinal survey with a median follow-up length of 15.4 years, 1080 participants died and 473 cardiovascular deaths were recorded. For all-cause mortality in the CKD group, individuals in the highest quartile of fluid intake (≧3.576 L/day) had better survival outcomes than those in the lowest quartile of fluid intake (≤2.147 L/day) (p=0.029) after adjustment of several pertinent variables. Conclusions Although the interpretation of this observational study was limited by the failure to identify the compositions of ingested fluids, adequate hydration may offer some advantages in patients with CKD. However, the underlying pathophysiological mechanisms of the responses of normal and injured kidneys to chronic changes in fluid consumption warrant further investigation. PMID:27173809

  9. Association of ApoE gene with type 2 diabetic nephropathy in a Chinese population: a meta-analysis of case-control studies.

    PubMed

    Zhang, Cheng; Li, Shengbing; Zhang, Xianxiang; Liu, Hua; Luo, Yong

    2015-10-01

    Studies based on Chinese populations reported that inconsistent results were found on the association of ApoE gene polymorphisms with type 2 diabetic nephropathy (T2DN). Therefore, we performed this meta-analysis to provide a reliable evaluation of the associations between ApoE gene polymorphisms and T2DN. MEDLINE, EMBASE, Chinese Wanfang database and Chinese VIP database were searched for studies that reported the associations of ApoE gene polymorphisms with type 2 diabetic nephropathy in a Chinese population up to Dec 2013. A meta-analysis was performed to assess heterogeneity and combine results by using software RevMan 4.3.1. Sensitivity analysis and publication bias were conducted. Data from 16 published studies involving 4320 individuals were eligible for inclusion. After heterogeneity test in each analysis, corresponding effect models were applied to quantitatively syntheses data. The ApoE allele e2 and genotype e2/e3 occurred more frequently in T2DN than in T2DNN and NC group. Their ORs and 95%CIs in T2DN were 1.75 (1.27-2.42) and 1.68 (1.20-2.38) when compared with T2DNN, respectively (P<0.05); 2.59 (1.74-3.85) and 2.43 (1.61-3.65) when compared with NC, respectively (P<0.05). The publication bias diagnostics test and sensitivity analysis confirmed the reliability and stability of this meta-analysis. These findings support the significant association between ApoE gene polymorphisms and T2DN. It was revealed that allele e2 and genotype e2/e3 were risk factors for T2DN and allele e3 and genotype e3/e3 played a protective role in T2DN. Further studies will be needed to confirm the conclusion.

  10. Associations of All-Cause Mortality with Census-Based Neighbourhood Deprivation and Population Density in Japan: A Multilevel Survival Analysis

    PubMed Central

    Nakaya, Tomoki; Honjo, Kaori; Hanibuchi, Tomoya; Ikeda, Ai; Iso, Hiroyasu; Inoue, Manami; Sawada, Norie; Tsugane, Shoichiro

    2014-01-01

    Background Despite evidence that neighbourhood conditions affect residents' health, no prospective studies of the association between neighbourhood socio-demographic factors and all-cause mortality have been conducted in non-Western societies. Thus, we examined the effects of areal deprivation and population density on all-cause mortality in Japan. Methods We employed census and survival data from the Japan Public Health Center-based Prospective Study, Cohort I (n = 37,455), consisting of middle-aged residents (40 to 59 years at the baseline in 1990) living in four public health centre districts. Data spanned between 1990 and 2010. A multilevel parametric proportional-hazard regression model was applied to estimate the hazard ratios (HRs) of all-cause mortality by two census-based areal variables —areal deprivation index and population density—as well as individualistic variables such as socioeconomic status and various risk factors. Results We found that areal deprivation and population density had moderate associations with all-cause mortality at the neighbourhood level based on the survival data with 21 years of follow-ups. Even when controlling for individualistic socio-economic status and behavioural factors, the HRs of the two areal factors (using quartile categorical variables) significantly predicted mortality. Further, this analysis indicated an interaction effect of the two factors: areal deprivation prominently affects the health of residents in neighbourhoods with high population density. Conclusions We confirmed that neighbourhood socio-demographic factors are significant predictors of all-cause death in Japanese non-metropolitan settings. Although further study is needed to clarify the cause-effect relationship of this association, the present findings suggest that health promotion policies should consider health disparities between neighbourhoods and possibly direct interventions towards reducing mortality in densely populated and highly

  11. Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) mapping has been used to dissect the genetic architecture of a trait and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an ...

  12. GIS Early-Warning System for Vectors of Rift Valley Fever: Anomaly Analysis of Climate-Population Associations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A critical component of predicting the risk of transmission of mosquito-borne viruses is knowing the status of vector populations. Mosquito control agencies have good systems for measuring mosquito populations at county or district levels, but these data are not synthesized to regional or national ...

  13. A Genome-Wide Association Meta-Analysis of Attention-Deficit/Hyperactivity Disorder Symptoms in Population-Based Paediatric Cohorts

    PubMed Central

    Groen-Blokhuis, Maria M.; Pourcain, Beate St.; Greven, Corina U.; Pappa, Irene; Tiesler, Carla M.T.; Ang, Wei; Nolte, Ilja M.; Vilor-Tejedor, Natalia; Bacelis, Jonas; Ebejer, Jane L.; Zhao, Huiying; Davies, Gareth E.; Ehli, Erik A.; Evans, David M.; Fedko, Iryna O.; Guxens, Mònica; Hottenga, Jouke-Jan; Hudziak, James J.; Jugessur, Astanand; Kemp, John P.; Krapohl, Eva; Martin, Nicholas G.; Murcia, Mario; Myhre, Ronny; Ormel, Johan; Ring, Susan M.; Standl, Marie; Stergiakouli, Evie; Stoltenberg, Camilla; Thiering, Elisabeth; Timpson, Nicholas J.; Trzaskowski, Maciej; van der Most, Peter J.; Wang, Carol; Nyholt, Dale R.; Medland, Sarah E.; Neale, Benjamin; Jacobsson, Bo; Sunyer, Jordi; Hartman, Catharina A.; Whitehouse, Andrew J.O.; Pennell, Craig E.; Heinrich, Joachim; Plomin, Robert; Smith, George Davey; Tiemeier, Henning; Posthuma, Danielle; Boomsma, Dorret I.

    2016-01-01

    Objective To elucidate the influence of common genetic variants on childhood attention-deficit/hyperactivity disorder (ADHD) symptoms, to identify genetic variants that explain its high heritability, and to investigate the genetic overlap of ADHD symptom scores with ADHD diagnosis. Method Within the EArly Genetics and Lifecourse Epidemiology (EAGLE) consortium, genome-wide single nucleotide polymorphisms (SNPs) and ADHD symptom scores were available for 17,666 children (< 13 years) from nine population-based cohorts. SNP-based heritability was estimated in data from the three largest cohorts. Meta-analysis based on genome-wide association (GWA) analyses with SNPs was followed by gene-based association tests, and the overlap in results with a meta-analysis in the Psychiatric Genomics Consortium (PGC) case-control ADHD study was investigated. Results SNP-based heritability ranged from 5% to 34%, indicating that variation in common genetic variants influences ADHD symptom scores. The meta-analysis did not detect genome-wide significant SNPs, but three genes, lying close to each other with SNPs in high linkage disequilibrium (LD), showed a gene-wide significant association (p values between 1.46×10-6 and 2.66×10-6). One gene, WASL, is involved in neuronal development. Both SNP- and gene-based analyses indicated overlap with the PGC meta-analysis results with the genetic correlation estimated at 0.96. Conclusion The SNP-based heritability for ADHD symptom scores indicates a polygenic architecture and genes involved in neurite outgrowth are possibly involved. Continuous and dichotomous measures of ADHD appear to assess a genetically common phenotype. A next step is to combine data from population-based and case-control cohorts in genetic association studies to increase sample size and improve statistical power for identifying genetic variants. PMID:27663945

  14. Population Analysis: Communicating in Context

    NASA Technical Reports Server (NTRS)

    Rajulu, Sudhakar; Thaxton, Sherry

    2008-01-01

    Providing accommodation to a widely varying user population presents a challenge to engineers and designers. It is often even difficult to quantify who is accommodated and who is not accommodated by designs, especially for equipment with multiple critical anthropometric dimensions. An approach to communicating levels of accommodation referred to as population analysis applies existing human factors techniques in novel ways. This paper discusses the definition of population analysis as well as major applications and case studies. The major applications of population analysis consist of providing accommodation information for multivariate problems and enhancing the value of feedback from human-in-the-loop testing. The results of these analyses range from the provision of specific accommodation percentages of the user population to recommendations of design specifications based on quantitative data. Such feedback is invaluable to designers and results in the design of products that accommodate the intended user population.

  15. SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis.

    PubMed

    Valdisser, Paula Arielle M R; Pappas, Georgios J; de Menezes, Ivandilson P P; Müller, Bárbara S F; Pereira, Wendell J; Narciso, Marcelo G; Brondani, Claudio; Souza, Thiago L P O; Borba, Tereza C O; Vianello, Rosana P

    2016-06-01

    Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00 %) and non-coding (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6 %, showing 73 % of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A slightly increased He (0.161, n = 21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype patterns spanning 310 Mb of the genome (60 %) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel

  16. Random amplified polymorphic DNA analysis of kinship within host-associated populations of the symbiotic water mite Unionicola foili (Acari: Unionicolidae).

    PubMed

    Edwards, Dale D; Deatherage, Daniel E; Ernsting, Brian R

    2004-01-01

    Kinship relations within populations of unionicolid water mites are not well known, owing to their complex life cycles and the fact that interactions between active and resting stages for some species are transitory. A number of species of unionicolid water mites are, however, obligate symbionts of freshwater mussels and spend most of their life cycle in association with these hosts. Among these species of mites, parents and offspring are more likely to co-occur and thus provide opportunities to address questions related to the structure of the mating system. The present study employs random amplified polymorphic DNA (RAPD) analysis to address kinship within populations of Unionicola foili living in symbiotic association with the host mussel Utterbackia imbecillis. DNA was amplified from adult mites and a representative number of eggs or larvae (n = 20-30) that were removed from mussels collected on three separate occasions (July, November, and March) over a 12-month period. Parsimony analyses of the molecular data for adults and progeny collected from mussels during July, November, and March revealed distinct groupings, that for the most part, corresponded to mites collected from each of the sampling periods. Many of the genetic markers obtained for male and female U. foili were not evident among the larvae or eggs, suggesting that adults obtained from a host mussel at the time of collection were not the parents of a majority of the progeny. However, female mites and eggs collected from mussels during March and November shared more markers than did females and progeny examined during July. Furthermore, many offspring in the July sampling period were found to have one or more parents absent from the sampled population. Overall, RAPD profiling appears to have limited usage in determining kinship within populations of U. foili, due to its recruitment patterns, and the relatively large number of adults and progeny per mussel. It may, however, prove to be a useful

  17. Association of interleukin 1 receptor antagonist (IL1RN) gene polymorphism with recurrent pregnancy loss risk in the North Indian Population and a meta-analysis.

    PubMed

    Nair, Rohini Ravindran; Khanna, Anuradha; Singh, Kiran

    2014-09-01

    An appropriate ratio of interleukin 1 beta to interleukin 1 receptor antagonist (IL1Ra) is required for successful pregnancy. Our objective was to study the genetic association between IL1RN variable numbers of tandem repeat (VNTR) polymorphism and recurrent pregnancy loss (RPL). To analyze the association between IL1RN VNTR allele and RPL, we investigated the IL1RN VNTR polymorphism in 136 RPL patients and in 200 healthy control women. Meta-analysis on this polymorphism was conducted to support our findings. PCR based approach was used to analyze IL1RN VNTR polymorphism and it was further confirmed by sequencing. Systematic review and meta-analysis was done using electronic database (Pub-Med, Google Scholar and Ovid) up to February 27, 2013. This meta-analysis was assessed by comprehensive meta-analysis software version 2. For meta-analysis 549 cases and 1,450 controls were included. The frequency of IL1RN genotype 2/2 was significantly higher in RPL compared to control group (AORs 3.10, 95 % CI 1.58-6.11, p = 0.001). The presence of rare allele also increased the risk of RPL significantly (ORs 1.63, 95 % CI 1.16-2.29, p = 0.004). The meta-analysis stratified by ethnicity showed that individuals with allele 2 had increased risk of RPL (OR 1.29, 95 % CI 1.04-1.61, p = 0.01), in Asians population by using fixed model. However the data of the present study clearly suggests that IL1RN VNTR polymorphism is a genetic risk factor for pregnancy loss in the study population.

  18. A Colorectal Cancer Susceptibility New Variant at 4q26 in the Spanish Population Identified by Genome-Wide Association Analysis

    PubMed Central

    Real, Luis M.; Ruiz, Agustín; Gayán, Javier; González-Pérez, Antonio; Sáez, María E.; Ramírez-Lorca, Reposo; Morón, Francisco J.; Velasco, Juan; Marginet-Flinch, Ruth; Musulén, Eva; Carrasco, José M.; Moreno-Rey, Concha; Vázquez, Enrique; Chaves-Conde, Manuel; Moreno-Nogueira, Jose A.; Hidalgo-Pascual, Manuel; Ferrero-Herrero, Eduardo; Castellví-Bel, Sergi; Castells, Antoni; Fernandez-Rozadilla, Ceres; Ruiz-Ponte, Clara; Carracedo, Angel; González, Beatriz; Alonso, Sergio; Perucho, Manuel

    2014-01-01

    Background Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome–wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population. Results A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNP)s from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10−8), and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10−11). Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599), 8q24 (rs10505477), 8q24.21(rs6983267), 11q13.4 (rs3824999) and 14q22.2 (rs4444235). Conclusions Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses. PMID:24978480

  19. Significant association between Let-7-KRAS rs712 G > T polymorphism and cancer risk in the Chinese population: a meta-analysis.

    PubMed

    Du, Xin-Ya; Hu, Yuan-Yuan; Xie, Chun; Deng, Chun-Yan; Liu, Cai-Yun; Luo, Zhi-Guo; Niu, Yu-Ming; Shen, Ming

    2017-01-16

    Association between let-7-KRAS rs712 polymorphism and cancer risk was inconsistent. We therefore conducted this meta-analysis to clarify the association between let-7-KRAS rs712 polymorphism and cancer risk with STATA 14.0 software. A systemic literature search in online databases (PubMed, Embase, CNKI and Wanfang database) was preformed to obtain relevant articles. A total of 13 case-control studies involving 3,453 patients and 4,470 controls were identified up to May 16, 2015. The pooled results indicated that significantly increased risk were observed in Chinese population in T vs. G (OR = 1.21, 95% CI = 1.03-1.42) and TT vs. GG + GT genetic models (OR = 1.69, 95% CI = 1.17-2.42). Sensitivity analysis was conducted and the result without heterogeneity showed significant associations in all five genetic models. Subgroup analyses of cancer type indicated a similar result in digestive cancer (for T vs. G: OR = 1.41, 95% CI = 1.26-1.57; GT vs. GG: OR = 1.24, 95% CI = 1.07-1.43; TT vs. GG: OR = 2.53, 95% CI = 1.86-3.44; GT + TT vs. GG: OR = 1.36, 95% CI = 1.19-1.56; TT vs. GG + GT: OR = 2.35, 95% CI = 1.73-3.19). In summary, these evidences demonstrate that let-7-KRAS rs712 G > T polymorphism might be associated with digestive system cancer risk in the Chinese population.

  20. Associations of body mass index with cancer incidence among populations, genders, and menopausal status: A systematic review and meta-analysis.

    PubMed

    Wang, Jun; Yang, Dong-Lin; Chen, Zhong-Zhu; Gou, Ben-Fu

    2016-06-01

    In order to further reveal the differences of association between body mass index (BMI) and cancer incidence across populations, genders, and menopausal status, we performed comprehensive meta-analysis with eligible citations. The risk ratio (RR) of incidence at 10 different cancer sites (per 5kg/m(2) increase in BMI) were quantified separately by employing generalized least-squares to estimate trends, and combined by meta-analyses. We observed significantly stronger association between increased BMI and breast cancer incidence in the Asia-Pacific group (RR 1.18:1.11-1.26) than in European-Australian (1.05:1.00-1.09) and North-American group (1.06:1.03-1.08) (meta-regression p<0.05). No association between increased BMI and pancreatic cancer incidence (0.94:0.71-1.24) was shown in the Asia-Pacific group (meta-regression p<0.05), whereas positive associations were found in other two groups. A significantly higher RR in men was found for colorectal cancer in comparison with women (meta-regression p<0.05). Compared with postmenopausal women, premenopausal women displayed significantly higher RR for ovarian cancer (pre- vs. post-=1.10 vs. 1.01, meta-regression p<0.05), but lower RR for breast cancer (pre- vs. post-=0.99 vs. 1.11, meta-regression p<0.0001). Our results indicate that overweight or obesity is a strong risk factor of cancer incidence at several cancer sites. Genders, populations, and menopausal status are important factors effecting the association between obesity and cancer incidence for certain cancer types.

  1. Genetic analysis and identification of SSR markers associated with rice blast disease in a BC2F1 backcross population.

    PubMed

    Hasan, N; Rafii, M Y; Abdul Rahim, H; Nusaibah, S A; Mazlan, N; Abdullah, S

    2017-01-23

    Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC2F1), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC2F1 population. The 195 BC2F1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.

  2. Analysis of Intervention Strategies for Inhalation Exposure to Polycyclic Aromatic Hydrocarbons and Associated Lung Cancer Risk Based on a Monte Carlo Population Exposure Assessment Model

    PubMed Central

    Zhou, Bin; Zhao, Bin

    2014-01-01

    It is difficult to evaluate and compare interventions for reducing exposure to air pollutants, including polycyclic aromatic hydrocarbons (PAHs), a widely found air pollutant in both indoor and outdoor air. This study presents the first application of the Monte Carlo population exposure assessment model to quantify the effects of different intervention strategies on inhalation exposure to PAHs and the associated lung cancer risk. The method was applied to the population in Beijing, China, in the year 2006. Several intervention strategies were designed and studied, including atmospheric cleaning, smoking prohibition indoors, use of clean fuel for cooking, enhancing ventilation while cooking and use of indoor cleaners. Their performances were quantified by population attributable fraction (PAF) and potential impact fraction (PIF) of lung cancer risk, and the changes in indoor PAH concentrations and annual inhalation doses were also calculated and compared. The results showed that atmospheric cleaning and use of indoor cleaners were the two most effective interventions. The sensitivity analysis showed that several input parameters had major influence on the modeled PAH inhalation exposure and the rankings of different interventions. The ranking was reasonably robust for the remaining majority of parameters. The method itself can be extended to other pollutants and in different places. It enables the quantitative comparison of different intervention strategies and would benefit intervention design and relevant policy making. PMID:24416436

  3. Variance associated with the use of relative velocity for force platform gait analysis in a heterogeneous population of clinically normal dogs.

    PubMed

    Volstad, Nicola; Nemke, Brett; Muir, Peter

    2016-01-01

    Factors that contribute to variance in ground reaction forces (GRFs) include dog morphology, velocity, and trial repetition. Narrow velocity ranges are recommended to minimize variance. In a heterogeneous population, it may be preferable to minimize data variance and efficiently perform force platform gait analysis by evaluation of each individual dog at its preferred velocity, such that dogs are studied at a similar relative velocity (V*). Data from 27 normal dogs were obtained including withers and shoulder height. Each dog was trotted across a force platform at its preferred velocity, with controlled acceleration (±0.5 m/s(2)). V* ranges were created for withers and shoulder height. Variance effects from 12 trotting velocity ranges and associated V* ranges were examined using repeated-measures analysis-of-covariance. Mean bodyweight was 24.4 ± 7.4 kg. Individual dog, velocity, and V* significantly influenced GRF (P <0.001). Trial number significantly influenced thoracic limb peak vertical force (PVF) (P <0.001). Limb effects were not significant. The magnitude of variance effects was greatest for the dog effect. Withers height V* was associated with small GRF variance. Narrow velocity ranges typically captured a smaller percentage of trials and were not consistently associated with lower variance. The withers height V* range of 0.6-1.05 captured the largest proportion of trials (95.9 ± 5.9%) with no significant effects on PVF and vertical impulse. The use of individual velocity ranges derived from a withers height V* range of 0.6-1.05 will account for population heterogeneity while minimizing exacerbation of lameness in clinical trials studying lame dogs by efficient capture of valid trials.

  4. Prediabetes Is Associated with HNF-4α P2 Promoter Polymorphism rs1884613: A Case-Control Study in Han Chinese Population and an Updated Meta-Analysis

    PubMed Central

    Wang, Changyi; Chen, Sihan; Zhang, Tao; Chen, Zhongwei; Liu, Shengyuan; Peng, Xiaolin; Ma, Jianping; Zhong, Xiaohong; Yan, Yanqiong; Tang, Linlin; Mai, Yifeng; Han, Liyuan

    2014-01-01

    Background. Controversy remains for the association between hepatocyte nuclear factor 4α (HNF-4α) P2 promoter polymorphism rs1884613 and type 2 diabetes (T2D). There was no association test of this polymorphism with prediabetes and T2D in the Chinese population. Moreover, an updated meta-analysis in various ethnic groups is needed to establish the contribution of rs1884613 to T2D risk. Methods. Using the Sequenom MassARRAY platform approach, we genotyped rs1884613 of HNF-4α in the P2 promoter region among 490 T2D patients, 471 individuals with prediabetes, and 575 healthy controls. All the individuals were recruited from 16 community health service centers in Nanshan district in Shenzhen province. Using STATA 11.0 software, meta-analysis was performed to summarize the overall contribution of rs1884613 to T2D risk. Results. Polymorphism rs1884613 was associated with genetic susceptibility to prediabetes in the whole samples (OR = 1.40, 95% CI = 1.16–1.68, P = 0.0001) and the female subgrouped samples (OR = 1.48, 95% CI = 1.14–1.92, P = 0.003) after adjusting for age and body mass index (BMI). In contrast, there was no association of rs1884613 with T2D in the whole samples and male in our case-control study and meta-analysis. Conclusions. Our results suggest that rs1884613 contributes to susceptibility to prediabetes, whereas this polymorphism may not play an important role in the development of T2D. PMID:25400315

  5. Short-term population-based non-linear concentration-response associations between fine particulate matter and respiratory diseases in Taipei (Taiwan): a spatiotemporal analysis.

    PubMed

    Yu, Hwa-Lung; Chien, Lung-Chang

    2016-01-01

    Fine particulate matter <2.5 μm (PM2.5) has been associated with human health issues; however, findings regarding the influence of PM2.5 on respiratory disease remain inconsistent. The short-term, population-based association between the respiratory clinic visits of children and PM2.5 exposure levels were investigated by considering both the spatiotemporal distributions of ambient pollution and clinic visit data. We applied a spatiotemporal structured additive regression model to examine the concentration-response (C-R) association between children's respiratory clinic visits and PM2.5 concentrations. This analysis was separately performed on three respiratory disease categories that were selected from the Taiwanese National Health Insurance database, which includes 41 districts in the Taipei area of Taiwan from 2005 to 2007. The findings reveal a non-linear C-R pattern of PM2.5, particularly in acute respiratory infections. However, a PM2.5 increase at relatively lower levels can elevate the same-day respiratory health risks of both preschool children (<6 years old) and schoolchildren (6-14 years old). In preschool children, same-day health risks rise when concentrations increase from 0.76 to 7.44 μg/m(3), and in schoolchildren, same-day health risks rise when concentrations increase from 0.76 to 7.52 μg/m(3). Changes in PM2.5 levels generally exhibited no significant association with same-day respiratory risks, except in instances where PM2.5 levels are extremely high, and these occurrences do exhibit a significant positive influence on respiratory health that is especially notable in schoolchildren. A significant high relative rate of respiratory clinic visits are concentrated in highly populated areas. We highlight the non-linearity of the respiratory health effects of PM2.5 on children to investigate this population-based association. The C-R relationship in this study can provide a highly valuable alternative for assessing the effects of ambient air

  6. Analysis of Association between Norepinephrine Transporter Gene Polymorphisms and Personality Traits of NEO-FFI in a Japanese Population

    PubMed Central

    Narita, Shin; Nagahori, Kenta; Numajiri, Maki; Yoshihara, Eiji; Ohtani, Nobuyo; Ishigooka, Jun

    2015-01-01

    Objective Norepinephrine is an important chemical messenger that is involved in mood and stress in humans, and is reabsorbed by the norepinephrine transporter (NET). According to Cloninger's theory, the noradrenergic system mediates the personality trait of reward dependence. Thus far, although association studies on NET gene polymorphisms and Cloninger's personality traits have been reported, they yielded inconsistent results. Therefore, in the present study we investigated whether or not the 1287G/A, -182T/C and -3081A/T polymorphisms of the NET gene (SLC6A2) are associated with reward dependence-related traits, as assessed by the five-factor model. Methods After written informed consent was obtained from participants, the three NET gene polymorphisms were analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP), and personality was assessed by the Neuroticism Extraversion Openness-Five Factor Inventory (NEO-FFI) in 270 Japanese university students. Results A significant relation was found between the -3081A/T functional promoter polymorphism and NEO-FFI scores: those with the T allele exhibited a lower extraversion (E) score than those without the T allele (Mann-Whitney U-test: z=-3.861, p<0.001). However, there was no correlation between the other NET gene polymorphisms and E score, and no association with other dimensions and these three polymorphisms. Conclusion We conclude that the -3081A/T functional polymorphism in the NET gene may affect the extraversion of reward dependence-related traits, as measured by NEO-FFI. However, we used only the shortened version of NEO-PI-R in this study. Further investigations are necessary using the full version of self-rating personality questionnaires. PMID:26207133

  7. Analysis of the association between polymorphisms in the vitamin D receptor (VDR) gene and dental caries in a Chinese population.

    PubMed

    Hu, X P; Li, Z Q; Zhou, J Y; Yu, Z H; Zhang, J M; Guo, M L

    2015-09-28

    Environmental influences on the development and progression of dental caries are well known; however, there is little evidence of a genetic component imparting susceptibility to dental caries. The aim of this study was to investigate the relationship between a single nucleotide polymorphism in the vitamin D receptor TaqI locus and dental caries susceptibility in a Chinese population. This case-control study was conducted with a case group (264 patients with dental caries from northwestern China) and a control group (219 individuals without dental caries or systemic disease from the same area). DNA was extracted from the peripheral venous blood of the study participants; the distribution of TaqI locus genotypes and allele frequencies was determined via polymerase chain reaction-restriction fragment length polymorphism. The data obtained were statistically analyzed using the Hardy-Weinberg equilibrium and Chi-square test. The frequency of the Tt genotype in the case group (14.0%) was significantly higher than that in the control group (4.3%), as determined using the genotype TT as the reference. The risk of dental caries was increased 3.8-fold in individuals with the heterozygous Tt genotype compared to that in the individuals with the TT genotype. The proportion of the 't' allele in the case group (7.0%) and the control group (2.1%) was observed to be significantly different [P = 0.0003; OR = 3.592, confidence interval 95% (1.790-7.208)]. Our results therefore suggested that the allele 't' might be a genetic factor determining dental caries susceptibility in individuals from the northwest of China.

  8. The SNP rs402710 in 5p15.33 Is Associated with Lung Cancer Risk: A Replication Study in Chinese Population and a Meta-Analysis

    PubMed Central

    Zhu, Yaowu; Zou, Li; Li, Huijun; Zhu, Beibei; Xiong, Zhigang; Chen, Wei; Deng, Lingyan; Lou, Jiao; Wang, Xianxiu; Zhang, Yu; Wang, Zhenling; Miao, Xiaoping; Cheng, Liming

    2013-01-01

    Background Lung cancer is the most commonly diagnosed cancer and leading cause of cancer mortality in the world. A single nucleotide polymorphism (SNP), rs402710, located in 5p15.33, was firstly identified to be associated with the lung cancer risk in a genome-wide association study. However, some following replication studies yielded inconsistent results. Methodology and Findings A case-control study of 611 cases and 1062 controls in a Chinese population was conducted, and then a meta-analysis integrating the current and previously published studies with a total 31811 cases and 36333 controls was performed to explore the real effect of rs402710 on lung cancer susceptibility. Significant associations between the SNP rs402710 and lung cancer risk were observed in both case-control study and meta-analysis, with ORs equal to 0.77 (95%CI = 0.63–0.95) and 0.83 (95%CI = 0.81–0.86) in dominant model, respectively. By stratified analysis of our case-control study, the associations were also observed in never smoker group and non-small cell lung cancer(NSCLC) group with ORs equal to 0.71 (95%CI = 0.53–0.95) and 0.69 (95%CI = 0.55–0.87), which was remarkable that larger effect of the minor allele T was seen in the two groups than that in overall lung cancer. Besides, the sensitive and cumulative analysis indicated the robust stability of the current results of meta-analysis. Conclusion The results from our replication study and the meta-analysis provided firm evidence that rs402710 T allele significantly contributed to decreased lung cancer risk, and the case-control study implied that the variant may yield stronger effect on NSCLC and never smokers. However, the mechanism underlying the polymorphism conferring susceptibility to lung cancer is warranted to clarify in the follow-up studies. PMID:24194831

  9. Risk of autism associated with general anesthesia during cesarean delivery: a population-based birth-cohort analysis.

    PubMed

    Chien, Li-Nien; Lin, Hsiu-Chen; Shao, Yu-Hsuan Joni; Chiou, Shu-Ti; Chiou, Hung-Yi

    2015-04-01

    The rates of Cesarean delivery (C-section) have risen to >30% in numerous countries. Increased risk of autism has been shown in neonates delivered by C-section. This study examined the incidence of autism in neonates delivered vaginally, by C-section with regional anesthesia (RA), and by C-section with general anesthesia (GA) to evaluate the risk of autism associated with C-section and obstetric anesthesia. During a mean follow-up of 4.3 years, the incidence of autism was higher in neonates delivered by C-section with GA than in neonates delivered vaginally, with an adjusted risk of 1.52 (95% confidence interval 1.18-1.94). However, the adjusted risk of autism in neonates delivered by C-section with RA and in neonates delivered vaginally was nonsignificantly different.

  10. Direct analysis of unphased SNP genotype data in population-based association studies via Bayesian partition modelling of haplotypes.

    PubMed

    Morris, Andrew P

    2005-09-01

    We describe a novel method for assessing the strength of disease association with single nucleotide polymorphisms (SNPs) in a candidate gene or small candidate region, and for estimating the corresponding haplotype relative risks of disease, using unphased genotype data directly. We begin by estimating the relative frequencies of haplotypes consistent with observed SNP genotypes. Under the Bayesian partition model, we specify cluster centres from this set of consistent SNP haplotypes. The remaining haplotypes are then assigned to the cluster with the "nearest" centre, where distance is defined in terms of SNP allele matches. Within a logistic regression modelling framework, each haplotype within a cluster is assigned the same disease risk, reducing the number of parameters required. Uncertainty in phase assignment is addressed by considering all possible haplotype configurations consistent with each unphased genotype, weighted in the logistic regression likelihood by their probabilities, calculated according to the estimated relative haplotype frequencies. We develop a Markov chain Monte Carlo algorithm to sample over the space of haplotype clusters and corresponding disease risks, allowing for covariates that might include environmental risk factors or polygenic effects. Application of the algorithm to SNP genotype data in an 890-kb region flanking the CYP2D6 gene illustrates that we can identify clusters of haplotypes with similar risk of poor drug metaboliser (PDM) phenotype, and can distinguish PDM cases carrying different high-risk variants. Further, the results of a detailed simulation study suggest that we can identify positive evidence of association for moderate relative disease risks with a sample of 1,000 cases and 1,000 controls.

  11. [Association between CDH23 gene polymorphisms and susceptibility to noise-induced hearing loss in the Chinese population: a meta-analysis].

    PubMed

    Yu, J N; Wu, S S; He, C H; Zhang, C Y; Mu, H X; Ma, W S; Liu, B; Zhang, Y; Yu, S F

    2016-12-20

    Objective: To investigate the association between cadherin-23 (CDH23) gene polymorphisms and susceptibility to noise-induced hearing loss (NIHL) in the Chinese population through a meta-analysis. Methods: In June 2016, CNKI, VIP, Wanfang Data, and PubMed were searched for studies on the association between CDH23 gene polymorphisms and susceptibility to NIHL in the Chinese population. The articles were screened according to inclusion and exclusion criteria and related data were extracted. RevMan 5.3 was used for the meta-analysis. Results: A total of three Chinese articles were included. For CDH23-rs1227049, the risk of NIHL in people with C allele was 0.82 times (95%CI 0.39-1.73) that in people with G allele, the risk of NIHL in people with CG+CC genotype in the dominant model was 0.70 times (95%CI 0.34-1.43) that in people with GG genotype, the risk of NIHL in people with CC genotype in the recessive model was 1.23 times (95%CI 0.28-5.43) that in people with CG+GG genotype, and the risk of NIHL in people with CC genotype in the additive model was 1.05 times (95%CI 0.20-5.44) that in people with GG genotype (all P>0.05) . For CDH23-rs1227051, the risk of NIHL in people with T allele was 0.98 times (95%CI 0.71-1.37) that in people with C allele, and the risk of NIHL in people with CT+CC genotype in the dominant model was 1.09 times (95%CI 0.75-1.57) that in patients with TT genotype (both P>0.05) . Conclusion: There is still no enough evidence for the determination of CDH23-rs1227049 and CDH23-rs1227051 to be the susceptibility gene loci of NIHL.

  12. Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers

    PubMed Central

    Anandan, Annamalai; Anumalla, Mahender; Pradhan, Sharat Kumar; Ali, Jauhar

    2016-01-01

    Early seedling vigor (ESV) is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS). It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA) and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR) markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC) value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM) and mixed linear model (MLM) approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection. PMID:27031620

  13. A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations

    PubMed Central

    Zhang, Han; Wheeler, William; Hyland, Paula L.; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

    2016-01-01

    Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs. PMID:27362418

  14. Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials

    PubMed Central

    Holmes, Michael V; Newcombe, Paul; Hubacek, Jaroslav A; Sofat, Reecha; Ricketts, Sally L; Cooper, Jackie; Breteler, Monique MB; Bautista, Leonelo E; Sharma, Pankaj; Whittaker, John C; Smeeth, Liam; Fowkes, F Gerald R; Algra, Ale; Shmeleva, Veronika; Szolnoki, Zoltan; Roest, Mark; Linnebank, Michael; Zacho, Jeppe; Nalls, Michael A; Singleton, Andrew B; Ferrucci, Luigi; Hardy, John; Worrall, Bradford B; Rich, Stephen S; Matarin, Mar; Norman, Paul E; Flicker, Leon; Almeida, Osvaldo P; van Bockxmeer, Frank M; Shimokata, Hiroshi; Khaw, Kay-Tee; Wareham, Nicholas J; Bobak, Martin; Sterne, Jonathan AC; Smith, George Davey; Talmud, Philippa J; van Duijn, Cornelia; Humphries, Steve E; Price, Jackie F; Ebrahim, Shah; Lawlor, Debbie A; Hankey, Graeme J; Meschia, James F; Sandhu, Manjinder S; Hingorani, Aroon D; Casas, Juan P

    2011-01-01

    Summary Background The MTHFR 677C→T polymorphism has been associated with raised homocysteine concentration and increased risk of stroke. A previous overview showed that the effects were greatest in regions with low dietary folate consumption, but differentiation between the effect of folate and small-study bias was difficult. A meta-analysis of randomised trials of homocysteine-lowering interventions showed no reduction in coronary heart disease events or stroke, but the trials were generally set in populations with high folate consumption. We aimed to reduce the effect of small-study bias and investigate whether folate status modifies the association between MTHFR 677C→T and stroke in a genetic analysis and meta-analysis of randomised controlled trials. Methods We established a collaboration of genetic studies consisting of 237 datasets including 59 995 individuals with data for homocysteine and 20 885 stroke events. We compared the genetic findings with a meta-analysis of 13 randomised trials of homocysteine-lowering treatments and stroke risk (45 549 individuals, 2314 stroke events, 269 transient ischaemic attacks). Findings The effect of the MTHFR 677C→T variant on homocysteine concentration was larger in low folate regions (Asia; difference between individuals with TT versus CC genotype, 3·12 μmol/L, 95% CI 2·23 to 4·01) than in areas with folate fortification (America, Australia, and New Zealand, high; 0·13 μmol/L, −0·85 to 1·11). The odds ratio (OR) for stroke was also higher in Asia (1·68, 95% CI 1·44 to 1·97) than in America, Australia, and New Zealand, high (1·03, 0·84 to 1·25). Most randomised trials took place in regions with high or increasing population folate concentrations. The summary relative risk (RR) of stroke in trials of homocysteine-lowering interventions (0·94, 95% CI 0·85 to 1·04) was similar to that predicted for the same extent of homocysteine reduction in large genetic studies in populations with similar

  15. Lower estimated glomerular filtration rate and higher albuminuria are associated with all-cause and cardiovascular mortality. A collaborative meta-analysis of high-risk population cohorts.

    PubMed

    van der Velde, Marije; Matsushita, Kunihiro; Coresh, Josef; Astor, Brad C; Woodward, Mark; Levey, Andrew; de Jong, Paul; Gansevoort, Ron T; van der Velde, Marije; Matsushita, Kunihiro; Coresh, Josef; Astor, Brad C; Woodward, Mark; Levey, Andrew S; de Jong, Paul E; Gansevoort, Ron T; Levey, Andrew; El-Nahas, Meguid; Eckardt, Kai-Uwe; Kasiske, Bertram L; Ninomiya, Toshiharu; Chalmers, John; Macmahon, Stephen; Tonelli, Marcello; Hemmelgarn, Brenda; Sacks, Frank; Curhan, Gary; Collins, Allan J; Li, Suying; Chen, Shu-Cheng; Hawaii Cohort, K P; Lee, Brian J; Ishani, Areef; Neaton, James; Svendsen, Ken; Mann, Johannes F E; Yusuf, Salim; Teo, Koon K; Gao, Peggy; Nelson, Robert G; Knowler, William C; Bilo, Henk J; Joosten, Hanneke; Kleefstra, Nanno; Groenier, K H; Auguste, Priscilla; Veldhuis, Kasper; Wang, Yaping; Camarata, Laura; Thomas, Beverly; Manley, Tom

    2011-06-01

    Screening for chronic kidney disease is recommended in people at high risk, but data on the independent and combined associations of estimated glomerular filtration rate (eGFR) and albuminuria with all-cause and cardiovascular mortality are limited. To clarify this, we performed a collaborative meta-analysis of 10 cohorts with 266,975 patients selected because of increased risk for chronic kidney disease, defined as a history of hypertension, diabetes, or cardiovascular disease. Risk for all-cause mortality was not associated with eGFR between 60-105 ml/min per 1.73 m², but increased at lower levels. Hazard ratios at eGFRs of 60, 45, and 15 ml/min per 1.73 m² were 1.03, 1.38 and 3.11, respectively, compared to an eGFR of 95, after adjustment for albuminuria and cardiovascular risk factors. Log albuminuria was linearly associated with log risk for all-cause mortality without thresholds. Adjusted hazard ratios at albumin-to-creatinine ratios of 10, 30 and 300 mg/g were 1.08, 1.38, and 2.16, respectively compared to a ratio of five. Albuminuria and eGFR were multiplicatively associated with all-cause mortality, without evidence for interaction. Similar associations were observed for cardiovascular mortality. Findings in cohorts with dipstick data were generally comparable to those in cohorts measuring albumin-to-creatinine ratios. Thus, lower eGFR and higher albuminuria are risk factors for all-cause and cardiovascular mortality in high-risk populations, independent of each other and of cardiovascular risk factors.

  16. Association of Change of Anthropometric Measurements With Incident Type 2 Diabetes Mellitus: A Pooled Analysis of the Prospective Population-Based CARLA and SHIP Cohort Studies.

    PubMed

    Hartwig, Saskia; Greiser, Karin Halina; Medenwald, Daniel; Tiller, Daniel; Herzog, Beatrice; Schipf, Sabine; Ittermann, Till; Völzke, Henry; Müller, Grit; Haerting, Johannes; Kluttig, Alexander

    2015-08-01

    Our objective was to investigate the association of change of anthropometric measurements and the incidence of type 2 diabetes mellitus (T2DM) within a pooled sample of 2 population-based cohorts.A final sample of 1324 women and 1278 men aged 31 to 83 years from 2 prospective cohorts in Germany, the CARLA (Cardiovascular Disease - Living and Ageing in Halle) and the SHIP study (Study of Health in Pomerania), were pooled. The association of change of body weight and waist circumference (WC) with incidence of T2DM was assessed by calculating sex-specific hazard ratios (HRs). We investigated the absolute change of markers of obesity as well as change relative to the baseline value and estimated crude and adjusted HRs. Furthermore, we conducted the analyses stratified by obesity status and age (<60 vs ≥60 years) at baseline.Associations were found for both change of body weight and WC and incidence of T2DM in the crude and adjusted analyses. In the stratified study sample, those participants with a body mass index of <30 kg/m at baseline showed considerably lower HRs compared with obese women and men for both weight and WC. In the age-stratified analysis, we still found associations between change of weight and WC and incident T2DM with only marginal differences between the age groups.Our study showed associations of change of weight and WC as markers of obesity with incidence of T2DM. Keeping a healthy and primarily stable weight should be the goal for preventing the development of T2DM.

  17. Analysis of Grapevine rupestris stem pitting-associated virus in Slovakia Reveals Differences in Intra-Host Population Diversity and Naturally Occurring Recombination Events.

    PubMed

    Glasa, Miroslav; Predajňa, Lukáš; Šoltys, Katarína; Sihelská, Nina; Nagyová, Alžbeta; Wetzel, Thierry; Sabanadzovic, Sead

    2017-02-01

    Grapevine rupestris stem pitting-associated virus (GRSPaV) is a worldwide-distributed pathogen in grapevines with a high genetic variability. Our study revealed differences in the complexity of GRSPaV population in a single host. A single-variant GRSPaV infection was detected from the SK30 grapevine plant. On the contrary, SK704 grapevine was infected by three different GRSPaV variants. Variant-specific RT-PCR detection protocols have been developed in this work to study distribution of the three different variants in the same plant during the season. This study showed their randomized distribution in the infected SK704 grapevine plant. Comparative analysis of fulllength genome sequences of four Slovak GRSPaV isolates determined in this work and 14 database sequences showed that population of the virus cluster into four major phylogenetic lineages. Moreover, our analyses suggest that genetic recombination along with point mutations could play a significant role in shaping evolutionary history of GRSPaV and contributed to its extant genetic diversification.

  18. Analysis of Grapevine rupestris stem pitting-associated virus in Slovakia Reveals Differences in Intra-Host Population Diversity and Naturally Occurring Recombination Events

    PubMed Central

    Glasa, Miroslav; Predajňa, Lukáš; Šoltys, Katarína; Sihelská, Nina; Nagyová, Alžbeta; Wetzel, Thierry; Sabanadzovic, Sead

    2017-01-01

    Grapevine rupestris stem pitting-associated virus (GRSPaV) is a worldwide-distributed pathogen in grapevines with a high genetic variability. Our study revealed differences in the complexity of GRSPaV population in a single host. A single-variant GRSPaV infection was detected from the SK30 grapevine plant. On the contrary, SK704 grapevine was infected by three different GRSPaV variants. Variant-specific RT-PCR detection protocols have been developed in this work to study distribution of the three different variants in the same plant during the season. This study showed their randomized distribution in the infected SK704 grapevine plant. Comparative analysis of fulllength genome sequences of four Slovak GRSPaV isolates determined in this work and 14 database sequences showed that population of the virus cluster into four major phylogenetic lineages. Moreover, our analyses suggest that genetic recombination along with point mutations could play a significant role in shaping evolutionary history of GRSPaV and contributed to its extant genetic diversification. PMID:28167886

  19. Population-based case-control association studies.

    PubMed

    Hancock, Dana B; Scott, William K

    2012-07-01

    This unit provides an overview of the design and analysis of population-based case-control studies of genetic risk factors for complex disease. Considerations specific to genetic studies are emphasized. The unit reviews basic study designs differentiating case-control studies from others, presents different genetic association strategies (candidate gene, genome-wide association, and high-throughput sequencing), introduces basic methods of statistical analysis for case-control data and approaches to combining case-control studies, and discusses measures of association and impact. Admixed populations, controlling for confounding (including population stratification), consideration of multiple loci and environmental risk factors, and complementary analyses of haplotypes, genes, and pathways are briefly discussed. Readers are referred to basic texts on epidemiology for more details on general conduct of case-control studies.

  20. Association between population prevalence of smoking and incidence of meningococcal disease in Norway, Sweden, Denmark and the Netherlands between 1975 and 2009: a population-based time series analysis

    PubMed Central

    Norheim, Gunnstein; Sadarangani, Manish; Omar, Omar; Yu, Ly-Mee; Mølbak, Kåre; Howitz, Michael; Olcén, Per; Haglund, Margaretha; van der Ende, Arie; Pollard, Andrew J

    2014-01-01

    Objective To investigate the relationship between the prevalence of smoking in the population and incidence of invasive meningococcal disease (IMD) among children under 5 years of age. Design Retrospective, longitudinal, observational study. Poisson regression controlled for confounding factors. Setting Norway, Sweden, Denmark and the Netherlands between 1975 and 2009. Population Total population of approximately 35 million people in these four countries. Data sources Data were collected from the Ministries of Health, National Statistics Bureaus and other relevant national institutes. Results In Norway, there was a significant positive relationship between the annual prevalence of daily smokers among individuals aged 25–49 years and the incidence of IMD in children under 5 years of age, unadjusted (RR=1.04–1.06, 95% CI 1.02 to 1.07, p<0.001) and after adjustment for time of year (quarter), incidence of influenza-like illness and household crowding (RR=1.05–1.07, 95% CI 1.03 to 1.09, p<0.001). Depending on age group, the risk of IMD increased by 5.2–6.9% per 1% increase in smoking prevalence among individuals aged 25–49 years in adjusted analyses. Using limited datasets from the three other countries, unadjusted analysis showed positive associations between IMD in children related to older smokers in Sweden and the Netherlands and negative associations related to younger smokers in Sweden. However, there were no demonstrable associations between incidence of IMD and prevalence of smoking, after adjustment for the same confounding variables. Conclusions The reduced incidence of IMD in Norway between 1975 and 2009 may partly be explained by the reduced prevalence of smoking during this period. High-quality surveillance data are required to confirm this in other countries. Strong efforts to reduce smoking in the whole population including targeted campaigns to reduce smoking among adults may have a role to play in the prevention of IMD in children

  1. Associations of pregnancy-associated plasma protein-A level with essential hypertension and hypertensive disorders in pregnancy in Chinese population: a meta-analysis of 20 research studies involving 3332 individuals

    PubMed Central

    Cai, Gaojun; Zhang, Bifeng; Weng, Weijin; Yang, Liping; Shi, Ganwei; Xue, Sheliang; Fu, Xingli

    2015-01-01

    Objective To explore the associations between serum pregnancy-associated plasma protein-A (PAPP-A) level, and essential hypertension (EH) and hypertensive disorders in pregnancy (HDP) in Chinese population. Methods Pertinent studies were independently searched in PubMed, Embase, Cochrane Library, Chinese Biomedical Database (CBM), Wanfang databases and China National Knowledge Infrastructure (CNKI). The standardised mean difference (SMD) with 95% CIs was used to estimate the size of the effect. The subgroup analyses and meta-regression analysis were performed to identify the sources of heterogeneity among studies. Sensitivity analysis was conducted to assess the stability of the results. The publication bias between studies was examined by using Begg's funnel plots and Egger's test. Results A total of 20 studies involving 1493 patients and 1839 controls were included in the current meta-analysis. The PAPP-A level was significantly higher in EH patients than in controls (SMD=1.960, 95% CI 1.305 to 2.615, p<0.001), and significant associations were observed in all subgroups. The PAPP-A level was also significantly higher in HDP patients than in healthy pregnant women (SMD=2.249; 95% CI 1.324 to 3.173, p<0.001). The positive association between PAPP-A level and the risk of HDP was consistently observed in all subgroups except the subgroup with low NOS score. Conclusions The present meta-analysis suggests that an elevated PAPP-A level may be associated with susceptibilities to EH and HDP. PMID:26416511

  2. Next generation semiconductor based sequencing of bitter taste receptor genes in different pig populations and association analysis using a selective DNA pool-seq approach.

    PubMed

    Ribani, A; Bertolini, F; Schiavo, G; Scotti, E; Utzeri, V J; Dall'Olio, S; Trevisi, P; Bosi, P; Fontanesi, L

    2017-02-01

    Taste perception in animals affects feed intake and may influence production traits. In particular, bitter is sensed by receptors encoded by the family of TAS2R genes. In this research, using a DNA pool-seq approach coupled with next generation semiconductor based target resequencing, we analysed nine porcine TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R38 and TAS2R39) to identify variability and, at the same time, estimate single nucleotide polymorphism (SNP) allele frequencies in several populations and testing differences in an association analysis. Equimolar DNA pools were prepared for five pig breeds (Italian Duroc, Italian Landrace, Pietrain, Meishan and Casertana) and wild boars (5-10 individuals each) and for two groups of Italian Large White pigs with extreme and divergent back fat thickness (50 + 50 pigs). About 1.8 million reads were obtained by sequencing amplicons generated from these pools. A total of 125 SNPs were identified, of which 37 were missense mutations. Three of them (p.Ile53Phe and p.Trp85Leu in TAS2R4; p.Leu37Ser in TAS2R39) could have important effects on the function of these bitter taste receptors, based on in silico predictions. Variability in wild boars seems lower than that in domestic breeds potentially as a result of selective pressure in the wild towards defensive bitter taste perception. Three SNPs in TAS2R38 and TAS2R39 were significantly associated with back fat thickness. These results may be important to understand the complexity of taste perception and their associated effects that could be useful to develop nutrigenetic approaches in pig breeding and nutrition.

  3. Association of serum ferritin levels with smoking and lung function in the Korean adult population: analysis of the fourth and fifth Korean National Health and Nutrition Examination Survey

    PubMed Central

    Lee, Chan Ho; Goag, Eun Kyung; Lee, Su Hwan; Chung, Kyung Soo; Jung, Ji Ye; Park, Moo Suk; Kim, Young Sam; Kim, Se Kyu; Chang, Joon; Song, Joo Han

    2016-01-01

    Background Iron-catalyzed oxidative stress contributes to lung injury after exposure to various toxins, including cigarette smoke. An oxidant/antioxidant imbalance is considered to play a critical role in the pathogenesis of COPD. Ferritin is a key protein in iron homeostasis, and its capacity to oxidize and sequester the metal preventing iron prooxidant activity implicates its possible role in the alteration of antioxidant imbalance. We investigated the relationship among cigarette smoking, lung function, and serum ferritin concentration in a large cohort representative of the Korean adult population. Materials and methods Among 50,405 participants of the Korean National Health and Nutrition Examination Survey from 2010 to 2014, 15,239 adult subjects older than 40 years with serum ferritin levels and spirometric data were selected for this study. Results The mean age was 56.5 years for men (43%) and 56.9 years for women (57%). The prevalence of airway obstruction was 13.4%, which was significantly higher in men than in women, and increased in former or current smokers. The median levels of serum ferritin were highest in the airway obstruction group, followed by the restrictive pattern group, and lowest in the normal lung function group. The median ferritin levels were increased by smoking status and amounts in each spirometric subgroup. In multivariable regression analysis, serum ferritin was positively associated with forced expiratory volume in 1 second and forced expiratory volume in 1 second/forced vital capacity, whereas the smoking amount was negatively associated with the adjustment with age, sex, height, and weight. Conclusion Serum ferritin levels were increased in former or current smokers and were increased with smoking amount in all subgroups of participants categorized according to spirometric results. The result was also evident in the subgroups divided by obstructive severity. While smoking amount was inversely related to lung function, higher

  4. A Comparative Analysis of the Validity of US State- and County-Level Social Capital Measures and Their Associations with Population Health

    ERIC Educational Resources Information Center

    Lee, Chul-Joo; Kim, Daniel

    2013-01-01

    The goals of this study were to validate a number of available collective social capital measures at the US state and county levels, and to examine the relative extent to which these social capital measures are associated with population health outcomes. Measures of social capital at the US state level included aggregate indices based on the…

  5. Analysis of Polymorphisms in Genes (AGT, MTHFR, GPIIIa, and GSTP1) Associated with Hypertension, Thrombophilia and Oxidative Stress in Mestizo and Amerindian Populations of México

    PubMed Central

    Juárez-Velázquez, Rocio; Canto, Patricia; Canto-Cetina, Thelma; Rangel-Villalobos, Hector; Rosas-Vargas, Haydee; Rodríguez, Maricela; Canizales-Quinteros, Samuel; Velázquez Wong, Ana Claudia; Ordoñez-Razo, Rosa María; Vilchis-Dorantes, Guadalupe; Coral-Vázquez, Ramón Mauricio

    2010-01-01

    Several polymorphisms related to hypertension, thrombophilia, and oxidative stress has been associated with the development of cardiovascular disease. We analyzed the frequency of M235T angiotensinogen (AGT), A222V 5,10 methylenete-trahydrofolate reductase (MTHFR), L33P glycoprotein IIIa (GPIIIa), and I105V glutathione S-transferase P1 (GSTP1) polymorphisms in 285 individuals belonging to Mexican-Mestizo and five Amerindian population from México, by real time PCR allelic discrimination. Allele and genotype frequencies were compared using χ2 tests. All populations followed the Hardy Weinberg equilibrium for assay markers with the exception of the Triki, whose were in Hardy Weinberg dysequilibrium for the glutathione S-transferase P1 polymorphism. Interestingly, according to all the analyzed single nucleotide polymorphisms (SNPs), the Triki population was the most differentiated and homogeneous group of the six populations analyzed. A comparison of our data with those previously published for some Caucasian, Asian and Black populations showed quite significant differences. These differences were remarkable with all the Mexican populations having a lower frequency of the 105V allele of the glutathione S-transferase P1 and reduced occurrence of the 222A allele of the 5,10 methylenetetrahydrofolate reductase. Our results show the genetic diversity among different Mexican populations and with other racial groups. PMID:20592457

  6. Association between mRNA expression of chemotherapy-related genes and clinicopathological features in colorectal cancer: A large-scale population analysis

    PubMed Central

    SHIMAMOTO, YUJI; NUKATSUKA, MAMORU; TAKECHI, TEIJI; FUKUSHIMA, MASAKAZU

    2016-01-01

    To establish the individualized treatment of patients with colorectal cancer, factors associated with chemotherapeutic effects should be identified. However, to the best of our knowledge, few studies are available on this topic, although it is known that the prognosis of patients and sensitivity to chemotherapy depend on the location of the tumor and that the tumor location is important for individualized treatment. In this study, primary tumors obtained from 1,129 patients with colorectal cancer were used to measure the mRNA expression levels of the following genes associated with the effects of standard chemotherapy for colorectal cancer: 5-fluorouracil (5-FU)-related thymidylate synthase (TYMS), dihydropyrimidine dehydrogenase (DPYD) and thymidine phosphorylase (TYMP); folate-related dihydrofolate reductase (DHFR), folylpolyglutamate synthase (FPGS) and gamma-glutamyl hydrolase (GGH); irinotecan-related topoisomerase I (TOP1); oxaliplatin-related excision repair cross-complementing 1 (ERCC1); biologic agent-related vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR). Large-scale population analysis was performed to determine the association of gene expression with the clinicopathological features, in particular, the location of the colorectal cancer. From the results of our analysis of the mRNA expression of these 10 genes, we noted the strongest correlation between DPYD and TYMP, followed by TYMS and DHFR. The location of the colorectal cancer was classified into 4 regions (the right- and left-sided colon, rectosigmoid and rectum) and was compared with gene expression. A significant difference in all genes, apart from VEGF, was noted. Of the remaining 9 genes, the highest expression of TYMS and DPYD was observed in the right-sided colon; the highest expression of GGH and EGFR was noted in the left-sided colon; the highest expression of DHFR, FPGS, TOP1 and ERCC1 was noted in the rectosigmoid, whereas TYMP expression was

  7. Psychotropic Medication Burden and Factors Associated with Antipsychotic Use: An Analysis of a Population-Based Sample of Community-Dwelling Older Persons with Dementia

    PubMed Central

    Rhee, YongJoo; Csernansky, John G.; Emanuel, Linda L.; Chang, Chang-Gok; Shega, Joseph W.

    2011-01-01

    Objectives To estimate the proportion of community dwelling older adults with dementia being prescribed a psychotropic and identify patient and caregiver factors associated with antipsychotics use. Methods Retrospective cohort study of The Aging, Demographics, and Memory Study (ADAMS) from 2002 to 2004 designed to assess dementia severity and service use among community-dwelling older adults. The frequency of psychotropic medication (antipsychotics, antidepressants, anticonvulsants and benzodiazepines) use was tabulated and weighted to the US population by dementia diagnosis. Logistic regression analysis identified factors associated with antipsychotic use. Results The 307 participants of ADAMS had the following dementia diagnosis: Alzheimer’s disease (69.29%), vascular dementia (17.74%) and other dementia (12.39%). The proportion of participants prescribed a psychotropic medication broken down by therapeutic class was as 19.07% antipsychotics, 29.08% antidepressants, 9.84% benzodiazepines, and 8.85% anticonvulsants. Older adults with dementia were significantly more likely to receive an antipsychotic if they had moderate dementia (OR =7.4, p<0.05), or severe dementia (OR=5.80, p<0.05), compared to mild dementia or were diagnosed with Alzheimer (OR =6.7, p<0.05) dementia compared to vascular dementia. Older adults with dementia who lived with their caregivers in were significantly less likely to be medicated with antipsychotics (OR= 0.19, p<0.05) compared to those who lived alone. Also, persons with dementia were significantly less likely to be prescribed an antipsychotic if the caregivers were clinically depressed (OR=0.03, p<0.05) compared to those who were not depressed. Conclusion We found psychotropic medication use is common among community-dwelling older adults with dementia. Caregivers appear to have a substantial impact on whether or not an antipsychotic is prescribed, which adds additional complexity to conversations discussing the risk-benefit ratio of

  8. Variance associated with subject velocity and trial repetition during force platform gait analysis in a heterogeneous population of clinically normal dogs.

    PubMed

    Hans, Eric C; Zwarthoed, Berdien; Seliski, Joseph; Nemke, Brett; Muir, Peter

    2014-12-01

    Factors that contribute to variance in ground reaction forces (GRF) include dog morphology, velocity, and trial repetition. Narrow velocity ranges are recommended to minimize variance. In a heterogeneous population of clinically normal dogs, it was hypothesized that the dog subject effect would account for the majority of variance in peak vertical force (PVF) and vertical impulse (VI) at a trotting gait, and that narrow velocity ranges would be associated with less variance. Data from 20 normal dogs were obtained. Each dog was trotted across a force platform at its habitual velocity, with controlled acceleration (±0.5 m/s(2)). Variance effects from 12 trotting velocity ranges were examined using repeated-measures analysis-of-covariance. Significance was set at P <0.05. Mean dog bodyweight was 28.4 ± 7.4 kg. Individual dog and velocity significantly affected PVF and VI for thoracic and pelvic limbs (P <0.001). Trial number significantly affected thoracic limb PVF (P <0.001). Limb (left or right) significantly affected thoracic limb VI (P = 0.02). The magnitude of variance effects from largest to smallest was dog, velocity, trial repetition, and limb. Velocity ranges of 1.5-2.0 m/s, 1.8-2.2 m/s, and 1.9-2.2 m/s were associated with low variance and no significant effects on thoracic or pelvic limb PVF and VI. A combination of these ranges, 1.5-2.2 m/s, captured a large percentage of trials per dog (84.2 ± 21.4%) with no significant effects on thoracic or pelvic limb PVF or VI. It was concluded that wider velocity ranges facilitate capture of valid trials with little to no effect on GRF in normal trotting dogs. This concept is important for clinical trial design.

  9. Bacterial Populations Associated with Smokeless Tobacco Products

    PubMed Central

    Han, Jing; Sanad, Yasser M.; Deck, Joanna; Sutherland, John B.; Li, Zhong; Walters, Matthew J.; Duran, Norma; Holman, Matthew R.

    2016-01-01

    ABSTRACT There are an estimated 8 million users of smokeless tobacco products (STPs) in the United States, and yet limited data on microbial populations within these products exist. To better understand the potential microbiological risks associated with STP use, a study was conducted to provide a baseline microbiological profile of STPs. A total of 90 samples, representing 15 common STPs, were purchased in metropolitan areas in Little Rock, AR, and Washington, DC, in November 2012, March 2013, and July 2013. Bacterial populations were evaluated using culture, pyrosequencing, and denaturing gradient gel electrophoresis (DGGE). Moist-snuff products exhibited higher levels of bacteria (average of 1.05 × 106 CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 101 CFU/g STP) and some chewing tobacco products (average of 2.54 × 105 CFU/g STP). The most common species identified by culturing were Bacillus pumilus, B. licheniformis, B. safensis, and B. subtilis, followed by members of the genera Oceanobacillus, Staphylococcus, and Tetragenococcus. Pyrosequencing analyses of the 16S rRNA genes identified the genera Tetragenococcus, Carnobacterium, Lactobacillus, Geobacillus, Bacillus, and Staphylococcus as the predominant taxa. Several species identified are of possible concern due to their potential to cause opportunistic infections and reported abilities to reduce nitrates to nitrites, which may be an important step in the formation of carcinogenic tobacco-specific N′-nitrosamines. This report provides a microbiological baseline to help fill knowledge gaps associated with microbiological risks of STPs and to inform potential regulations regarding manufacture and testing of STPs. IMPORTANCE It is estimated that there 8 million users of smokeless tobacco products (STPs) in the United States; however, there are limited data on microbial populations that exist within these products. The current study was undertaken to better understand the

  10. Mosquito populations dynamics associated with climate variations.

    PubMed

    Wilke, André Barretto Bruno; Medeiros-Sousa, Antônio Ralph; Ceretti-Junior, Walter; Marrelli, Mauro Toledo

    2017-02-01

    Mosquitoes are responsible for the transmission of numerous serious pathogens. Members of the Aedes and Culex genera, which include many important vectors of mosquito-borne diseases, are highly invasive and adapted to man-made environments. They are spread around the world involuntarily by humans and are highly adapted to urbanized environments, where they are exposed to climate-related abundance drivers. We investigated Culicidae fauna in two urban parks in the city of São Paulo to analyze the correlations between climatic variables and the population dynamics of mosquitoes in these urban areas. Mosquitoes were collected monthly over one year, and sampling sufficiency was evaluated after morphological identification of the specimens. The average monthly temperature and accumulated rainfall for the collection month and previous month were used to explain climate-related abundance drivers for the six most abundant species (Aedes aegypti, Aedes albopictus, Aedes fluviatilis, Aedes scapularis, Culex nigripalpus and Culex quinquefasciatus) and then analyzed using generalized linear statistical models and the Akaike Information Criteria corrected for small samples (AICc). The strength of evidence in favor of each model was evaluated using Akaike weights, and the explanatory model power was measured by McFadden's Pseudo-R(2). Associations between climate and mosquito abundance were found in both parks, indicating that predictive models based on climate variables can provide important information on mosquito population dynamics. We also found that this association is species-dependent. Urbanization processes increase the abundance of a few mosquito species that are well adapted to man-made environments and some of which are important vectors of pathogens. Predictive models for abundance based on climate variables may help elucidate the population dynamics of urban mosquitoes and their impact on the risk of disease transmission, allowing better predictive scenarios to be

  11. Correlation of population parameters leading to power differences in association studies with population stratification.

    PubMed

    He, Y; Jiang, R; Fu, W; Bergen, A W; Swan, G E; Jin, L

    2008-11-01

    The power of statistical tests to measure effect sizes in the presence of population stratification is an important issue for the design and analysis of population-based association studies. Comparisons of statistical tests have shown that the power of different statistical approaches varies in different genetic scenarios. However, the impact of stratified population parameters on statistical power is not yet understood in a general statistical framework, particularly the impact of correlated population parameters. To investigate such impact in detail, we implemented a genetic model for population-based association studies with stratified samples and evaluated the impact on power with different genetic scenarios. The investigation shows that correlation between disease prevalence and risk allele frequency among subpopulations impacts statistical power. In a model with five subpopulations and moderate population divergence (Fst= 0.01), the correlation accounts for more than 85% of power difference. Our results also show that the estimation of genetic effect for candidate loci is biased by population divergence. Beneficial alleles could be wrongly characterized as risk alleles when prevalence differences and divergences of risk loci are large among subpopulations.

  12. Association between MTHFR C677T polymorphism and diabetic nephropathy in the Chinese population: An updated meta-analysis and review.

    PubMed

    Xiong, Xuan; Lin, Xiao-Kun; Xiao, Xiao; Qin, Dan-Ping; Zhou, Dao-Yuan; Hu, Jian-Guang; Liu, Yan; Zhong, Xiao-Shi

    2016-01-01

    To clarify the effects of MTHFR C677T polymorphism on the risk of diabetic nephropathy (DN) in the Chinese population, an updated meta-analysis was performed. Related studies were identified from PubMed, Springer Link, Ovid and Chinese Databases up to 24 February 2015. A total of 15 studies including 1227 DN cases, 586 healthy controls and 1277 diabetes mellitus (DM) controls were involved in this meta-analysis. Overall, a significantly elevated risk of DN was associated with all variants of MTHFR C677T when compared with the healthy group (T vs C, odds ratio (OR) = 2.22, 95% confidence interval (CI) = 1.88-2.61; TT vs CC, OR = 4.22, 95% CI = 3.02-5.90; TT + CT vs CC, OR = 2.62, 95% CI = 2.07-3.31; TT vs CC + CT, OR = 2.81, 95% CI = 2.08-3.81) or DM (T vs C, OR = 1.78, 95% CI = 1.59-2.00; TT vs CC, OR = 2.95, 95% CI = 2.33-3.73; TT + CT vs CC, OR = 1.93, 95% CI = 1.63-2.29; TT vs CC + CT, OR = 2.31, 95% CI = 1.87-2.84). In subgroup analyses stratified by ethnicity and geographic areas, it revealed the significant results in Chinese Han, in North and South China. The risk conferred by MTHFR C677T polymorphism is higher in North China than in South China. This meta-analysis showed that the MTHFR C677T variants may influence DN risk in Chinese, and further studies with gene-gene and gene-environment interactions are required for definite conclusions.

  13. Population pharmacokinetic analysis of bisoprolol.

    PubMed

    Grevel, J; Thomas, P; Whiting, B

    1989-07-01

    The technique of population pharmacokinetic analysis was employed to study the variability in the dose concentration relationship of bisoprolol during its clinical development. The influence of demographic factors on the variability of clearance was investigated in 3 different populations: group I, patients (including an elderly group) with essential hypertension receiving multiple oral doses of bisoprolol 10 or 20mg for 3 months; group II, patients with different degrees of renal impairment and healthy controls; and group III, patients with different types of hepatic impairment and healthy controls. Patients and controls in groups II and III received only a single oral dose of bisoprolol 10mg. The 3 data sets were analysed separately, using a non-linear mixed effects model (the NONMEM program). A 2-compartment pharmacokinetic model with first-order absorption described the data adequately. The typical values of volume of central compartment, volume of distribution at steady-state and the absorption rate constant for the 3 populations were: for group I, 68L, 235L, and 0.7h-1; for group II, 28L, 179L, and 0.3h-1; and for group III, 55L, 256L, and 0.4h-1, respectively. Plasma clearance was related to age in group I, to serum creatinine in group II and to aspartate transaminase activity in group III. The 68% confidence limits for clearance and elimination half-life were 8.2 to 21.5 L/h and 7.6 to 19.7h, respectively, for 50-year-old patients in group I. The analysis predicted that progressive increases in serum creatinine or aspartate transaminase activity will result in only a 50% reduction of clearance.

  14. Association between unemployment, income, education level, population size and air pollution in Czech cities: evidence for environmental inequality? A pilot national scale analysis.

    PubMed

    Branis, Martin; Linhartova, Martina

    2012-09-01

    We analyzed differentials in exposure to SO(2), PM(10) and NO(2) among Czech urban populations categorized according to education level, unemployment rate, population size and average annual salary. Altogether 39 cities were included in the analysis. The principal component analysis revealed two factors explaining 72.8% of the data variability. The first factor explaining 44.7% of the data variability included SO(2), PM(10), low education level and high unemployment, documenting that inhabitants with unfavorable socioeconomic status mainly reside in smaller cities with higher concentration levels of combustion-related air pollutants. The second factor explaining 28.1% of the data variability included NO(2), high salary, high education level and large population, suggesting that large cities with residents with higher socioeconomic status are exposed to higher levels of traffic-related air pollution. We conclude that, after more than a decade of free-market economy, the Czech Republic, a former Soviet satellite with a centrally planned economy, displays signs of a certain kind of environmental inequality, since environmental hazards are unevenly distributed among the Czech urban populations.

  15. Characterization of the metabolic profile associated with serum 25-hydroxyvitamin D: a cross-sectional analysis in population-based data

    PubMed Central

    Vogt, Susanne; Wahl, Simone; Kettunen, Johannes; Breitner, Susanne; Kastenmüller, Gabi; Gieger, Christian; Suhre, Karsten; Waldenberger, Melanie; Kratzsch, Jürgen; Perola, Markus; Salomaa, Veikko; Blankenberg, Stefan; Zeller, Tanja; Soininen, Pasi; Kangas, Antti J; Peters, Annette; Grallert, Harald; Ala-Korpela, Mika; Thorand, Barbara

    2016-01-01

    Background: Numerous observational studies have observed associations between vitamin D deficiency and cardiometabolic diseases, but these findings might be confounded by obesity. A characterization of the metabolic profile associated with serum 25-hydroxyvitamin D [25(OH)D] levels, in general and stratified by abdominal obesity, may help to untangle the relationship between vitamin D, obesity and cardiometabolic health. Methods: Serum metabolomics measurements were obtained from a nuclear magnetic resonance spectroscopy (NMR)- and a mass spectrometry (MS)-based platform. The discovery was conducted in 1726 participants of the population-based KORA-F4 study, in which the associations of the concentrations of 415 metabolites with 25(OH)D levels were assessed in linear models. The results were replicated in 6759 participants (NMR) and 609 (MS) participants, respectively, of the population-based FINRISK 1997 study. Results: Mean [standard deviation (SD)] 25(OH)D levels were 15.2 (7.5) ng/ml in KORA F4 and 13.8 (5.9) ng/ml in FINRISK 1997; 37 metabolites were associated with 25(OH)D in KORA F4 at P < 0.05/415. Of these, 30 associations were replicated in FINRISK 1997 at P < 0.05/37. Among these were constituents of (very) large very-low-density lipoprotein and small low-density lipoprotein subclasses and related measures like serum triglycerides as well as fatty acids and measures reflecting the degree of fatty acid saturation. The observed associations were independent of waist circumference and generally similar in abdominally obese and non-obese participants. Conclusions: Independently of abdominal obesity, higher 25(OH)D levels were associated with a metabolite profile characterized by lower concentrations of atherogenic lipids and a higher degree of fatty acid polyunsaturation. These results indicate that the relationship between vitamin D deficiency and cardiometabolic diseases is unlikely to merely reflect obesity-related pathomechanisms. PMID:27605587

  16. HLA-B*15:02 association with carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis in an Indian population: a pooled-data analysis and meta-analysis.

    PubMed

    Khor, Amy Hui-Ping; Lim, Kheng-Seang; Tan, Chong-Tin; Wong, Su-Ming; Ng, Ching-Ching

    2014-11-01

    This study aimed to investigate the prevalence and association of HLA-B*15:02 with carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis (CBZ-SJS/TEN) in the Indian population in Malaysia, which mostly originated from Southern India. HLA-B alleles in five Indian case patients with CBZ-SJS/TEN and 52 CBZ-tolerant controls, and followed by a pooled sample of seven cases from two centers in Malaysia were analyzed. Positive association for HLA-B*15:02 with CBZ-SJS/TEN was detected in Indians (40% [2/5] vs. 3.8% [2/52], odds ratio [OR] 16.7, p = 0.0349), of which 80% (4/5) of the Indian patients originated from Southern India. A pooled sample of seven cases showed stronger association between HLA-B*15:02 and CBZ-SJS/TEN (57.1% [4/7] vs. 3.8% [2/52], OR 33.3, 95% confidence interval [CI] 4.25-162.21, p = 1.05 × 10(-3)). Subsequent meta-analysis on Indians from Malaysia and India further demonstrated a significant and strong association between HLA-B*15:02 and CBZ-SJS/TEN (OR 38.54; 95% CI 6.83-217.34, p < 1.0 × 10(-4)). Our study is the first on Indians predominantly from Southern India that demonstrated HLA-B*15:02 as a strong risk factor for CBZ-SJS/TEN despite a low population allele frequency. This stressed the importance of testing for HLA-B*15:02, irrespective of the ancestral background, including populations with low allele frequency.

  17. Bone fracture risk is not associated with the use of glucagon-like peptide-1 receptor agonists: a population-based cohort analysis.

    PubMed

    Driessen, Johanna H M; Henry, Ronald M A; van Onzenoort, Hein A W; Lalmohamed, Arief; Burden, Andrea M; Prieto-Alhambra, Daniel; Neef, Cees; Leufkens, Hubert G M; de Vries, Frank

    2015-08-01

    Glucagon-like Peptide-1 receptor agonists (GLP1-ra) are a relatively new class of anti-hyperglycemic drugs which may positively affect bone metabolism and thereby decrease (osteoporotic) bone fracture risk. Data on the effect of GLP1-ra on fracture risk are scarce and limited to clinical trial data only. The aim of this study was to investigate, in a population-based cohort, the association between the use of GLP1-ra and bone fracture risk. We conducted a population-based cohort study, with the use of data from the Clinical Practice Research Datalink (CPRD) database (2007-2012). The study population (N = 216,816) consisted of all individuals with type 2 diabetes patients with at least one prescription for a non-insulin anti-diabetic drug and were over 18 years of age. Cox proportional hazards models were used to estimate the hazard ratio of fracture in GLP1-ra users versus never-GLP1-ra users. Time-dependent adjustments were made for age, sex, lifestyle, comorbidity and the use of other drugs. There was no decreased risk of fracture with current use of GLP1-ra compared to never-GLP1-ra use (adjusted HR 0.99, 95 % CI 0.82-1.19). Osteoporotic fracture risk was also not decreased by current GLP1-ra use (adjusted HR 0.97; 95 % CI 0.72-1.32). In addition, stratification according to cumulative dose did not show a decreased bone fracture risk with increasing cumulative GLP1-ra dose. We showed in a population-based cohort study that GLP1-ra use is not associated with a decreased bone fracture risk compared to users of other anti-hyperglycemic drugs. Future research is needed to elucidate the potential working mechanisms of GLP1-ra on bone.

  18. On association analysis of rare variants under population substructure: an approach for the detection of subjects that can cause bias in the analysis--T opt: an outlier detection method.

    PubMed

    Qiao, Dandi; Mattheisen, Manuel; Lange, Christoph

    2013-07-01

    For the analysis of rare-variant data in population-based designs, we propose a method to detect study subjects that may create population substructure in the study sample. Our approach is computationally fast and simple, permitting applications to whole-genome sequencing studies. The method does not require the variants to be in linkage equilibrium and can be applied to all the genetic loci that are available in the study. For both rare and common variants, we assess the performance of our approach by its application to the 1000 Genome Project data, and in simulation studies. The results are compared to the commonly used outlier detection algorithm based on principal component analysis (PCA). The statistical power of both approaches to detect outliers are comparable in most of the scenarios, but the power of PCA to detect outliers is lower than the novel approach in the presence of linkage disequilibrium and for subpopulations that are genetically similar. The data analysis and the simulation studies suggest that the number of false-positive results appears to be different for the two approaches. Our approach maintains the type I error rate while the outlier detection approach based on PCA does not. Taking additionally into account the minimal computational requirements of our approach and the ability to incorporate all the marker information, the proposed method will have important application in sequencing studies and genome-wide association studies.

  19. Association of volunteering with mental well-being: a lifecourse analysis of a national population-based longitudinal study in the UK

    PubMed Central

    Tabassum, Faiza; Mohan, John; Smith, Peter

    2016-01-01

    Objectives The association of volunteering with well-being has been found in previous research, but mostly among older people. The aim of this study was to examine the association of volunteering with mental well-being among the British population across the life course. Design British Household Panel Survey, a population-based longitudinal study. Setting UK. Participants 66 343 observations (person-years). Main outcome measures Mental well-being was measured by using the General Health Questionnaire (GHQ-12 or GHQ); high values denote high mental disorder. Four groups of volunteering participation were created: frequent (once a week), infrequent (once a month/several times a year), rare (once or less a year) and never. Multilevel linear models were used to analyse variations in mental well-being over the life course by levels of volunteering. Results When not considering age, those who engaged in volunteering regularly appeared to experience higher levels of mental well-being than those who never volunteered. To explore the association of volunteering with the GHQ across the life course, interaction terms were fitted between age and volunteering. The interactions were significant, demonstrating that these associations vary by age. The association between volunteering and well-being did not emerge during early adulthood to mid-adulthood, instead becoming apparent above the age of 40 years and continuing up to old age. Moreover, in early adulthood, the absence of engagement in voluntary activity was not related to mental well-being, but GHQ scores for this group increased sharply with age, levelling off after the age of 40 and then increasing again above the age of 70 years. The study also indicates variation in GHQ scores (65%) within individuals across time, suggesting evidence of lifecourse effects. Conclusions We conclude that volunteering may be more meaningful for mental well-being at some points of time in the life course. PMID:27503861

  20. The association between the rs11196218A/G polymorphism of the TCF7L2 gene and type 2 diabetes in the Chinese Han population: a meta-analysis

    PubMed Central

    Ma, Enting; Wang, Huili; Guo, Jing; Tian, Ruirui; Wei, Li

    2015-01-01

    Transcription factor 7-like 2 has been shown to be associated with type 2 diabetes mellitus in multiple ethnic groups in recent years. In the Chinese Han population in particular, numerous studies have evaluated the association between the rs11196218A/G polymorphism of the transcription factor 7-like 2 gene and type 2 diabetes mellitus. However, the results have been inconsistent, so we performed a meta-analysis to assess the association. Odds ratio and 95% confidence interval values were calculated using a random-effects model or a fixed-effects model based on heterogeneity analysis. The quality of the included studies was evaluated using the Newcastle-Ottawa Scale. Subgroup analyses were conducted based on conformity with Hardy-Weinberg equilibrium in the control group as well as on other variables, such as age, sex and body mass index. Sensitivity analysis was also performed to detect heterogeneity and to assess the stability of the results. In total, 10 case-control studies comprising 7,491 cases and 12,968 controls were included in this meta-analysis. The combined analysis indicated that the rs11196218A/G polymorphism was not associated with type 2 diabetes mellitus (G vs. A, OR=1.04, 95% CI=0.97-1.13, p=0.28). The subgroup analyses also did not show any association between the rs11196218A/G polymorphism and the risk of type 2 diabetes mellitus. Furthermore, the results of the subgroup analyses indicated that the absence of an association was not influenced by age, sex or body mass index. The results of the sensitivity analysis verified the reliability and stability of this meta-analysis. In conclusion, this study indicated that there is no significant association between the rs11196218A/G polymorphism and the risk of type 2 diabetes mellitus in the Chinese Han population. PMID:26247673

  1. Association analysis of DACT1 genetic variants and gastric cancer risk in a Chinese Han population: a case–control study

    PubMed Central

    Huang, Chi; Wang, Younan; Fan, Hao; Ma, Xiang; Tang, Ran; Huan, Xiangkun; Zhu, Yi; Xu, Zekuan; Xu, Hao; Yang, Li

    2016-01-01

    Purpose Disheveled-binding antagonist of beta-catenin 1 (DACT1) is involved in tumorigenesis through influencing cell apoptosis and proliferation. We aimed to investigate the effect of three tag single-nucleotide polymorphisms (SNPs) in DACT1 (rs863091 C>T, rs17832998 C>T, and rs167481 C>T) on the occurrence of gastric cancer (GC), their association with specific clinical characteristics, and consideration of the functional relevance of GC-related SNPs. Subjects and methods In this hospital-based case–control study, the genotypes were acquired using the TaqMan-MGB method consisting of 602 cases and 602 controls. DACT1 messenger RNA level was evaluated in 76 paired tumoral and normal tissues using quantitative reverse transcription–polymerase chain reaction. Logistic regression was used to evaluate the associations among the DACT1 SNPs and GC. Results We found a significant association between the variant genotypes of rs863091 and decreased risk of GC (TT vs CC: P=0.009, adjusted odds ratio =0.34, 95% confidence interval =0.15–0.77; CT + TT vs CC: P=0.030, adjusted odds ratio =0.74, 95% confidence interval =0.57–0.97). In further stratified analyses, rs863091 variant genotypes were associated with a reduced risk of GC in younger individuals (<60 years) and males. No overall significant association with GC risk was observed in SNP rs17832998 or rs167481. Additionally, we assessed DACT1 messenger RNA levels in GC and found that DACT1 expressions of individuals carrying CT and TT genotypes were much higher than those with CC genotype. Conclusion Our findings suggest that the DACT1 rs863091 C>T polymorphism may be associated with a decreased risk of GC in the Chinese Han population and influence DACT1 expression. PMID:27729806

  2. Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes.

    PubMed

    Millman, Kim; Black, Carolyn M; Stamm, Walter E; Jones, Robert B; Hook, Edward W; Martin, David H; Bolan, Gail; Tavaré, Simon; Dean, Deborah

    2006-03-01

    Chlamydia trachomatis is the leading cause of bacterial sexually transmitted diseases worldwide. Urogenital strains are classified into serotypes and genotypes based on the major outer membrane protein and its gene, ompA, respectively. Studies of the association of serotypes with clinical signs and symptoms have produced conflicting results while no studies have evaluated associations with ompA polymorphisms. We designed a population-based cross-sectional study of 344 men and women with urogenital chlamydial infections (excluding co-pathogen infections) presenting to clinics serving five U.S. cities from 1995 to 1997. Signs, symptoms and sequelae of chlamydial infection (mucopurulent cervicitis, vaginal or urethral discharge; dysuria; lower abdominal pain; abnormal vaginal bleeding; and pelvic inflammatory disease) were analyzed for associations with serotype and ompA polymorphisms. One hundred and fifty-three (44.5%) of 344 patients had symptoms consistent with urogenital chlamydial infection. Gender, reason for visit and city were significant independent predictors of symptom status. Men were 2.2 times more likely than women to report any symptoms (P=0.03) and 2.8 times more likely to report a urethral discharge than women were to report a vaginal discharge in adjusted analyses (P=0.007). Differences in serotype or ompA were not predictive except for an association between serotype F and pelvic inflammatory disease (P=0.046); however, the number of these cases was small. While there was no clinically prognostic value associated with serotype or ompA polymorphism for urogenital chlamydial infections except for serotype F, future studies might utilize multilocus genomic typing to identify chlamydial strains associated with clinical phenotypes.

  3. Genetic Association Analysis of Fasting and 1- and 2-Hour Glucose Tolerance Test Data Using a Generalized Index of Dissimilarity Measure for the Korean Population

    PubMed Central

    Yee, Jaeyong; Kim, Yongkang; Park, Taesung

    2016-01-01

    Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait. PMID:28154509

  4. Associations of Steroid Sex Hormones and Sex Hormone-Binding Globulin With the Risk of Type 2 Diabetes in Women: A Population-Based Cohort Study and Meta-analysis.

    PubMed

    Muka, Taulant; Nano, Jana; Jaspers, Loes; Meun, Cindy; Bramer, Wichor M; Hofman, Albert; Dehghan, Abbas; Kavousi, Maryam; Laven, Joop S E; Franco, Oscar H

    2017-03-01

    It remains unclear whether endogenous sex hormones (ESH) are associated with risk of type 2 diabetes (T2D) in women. Data of 3,117 postmenopausal women participants of the Rotterdam Study were analyzed to examine whether ESH and sex hormone-binding globulin (SHBG) were associated with the risk of incident T2D. Additionally, we performed a systematic review and meta-analysis of studies assessing the prospective association of ESH and SHBG with T2D in women. During a median follow-up of 11.1 years, we identified 384 incident cases of T2D in the Rotterdam Study. No association was observed between total testosterone (TT) or bioavailable testosterone (BT) with T2D. SHBG was inversely associated with the risk of T2D, whereas total estradiol (TE) was associated with increased risk of T2D. Similarly, in the meta-analysis of 13 population-based prospective studies involving more than 1,912 incident T2D cases, low levels of SHBG and high levels of TE were associated with increased risk of T2D, whereas no associations were found for other hormones. The association of SHBG with T2D did not change by menopause status, whereas the associations of ESH and T2D were based only in postmenopausal women. SHBG and TE are independent risk factors for the development of T2D in women.

  5. Population dynamics of Vibrio spp. associated with marine sponge microcosms.

    PubMed

    Hoffmann, Maria; Fischer, Markus; Ottesen, Andrea; McCarthy, Peter J; Lopez, Jose V; Brown, Eric W; Monday, Steven R

    2010-12-01

    Vibrio is a diverse genus of marine-associated bacteria with at least 74 species and more expected as additional marine ecospheres are interrogated. This report describes a phylogenetic reconstruction of Vibrio isolates derived from one such unique ecosystem, marine sponges (Phylum Porifera) collected from depths of 150 to 1242 feet. 16S rRNA gene sequencing along with molecular typing of 16S-23S rRNA intergenic spacer regions clustered many sponge-associated Vibrio (spp) with current known species. That is, several benthic Vibrio species commensal with Porifera sponges seemed genetically linked to vibrios associated with coastal or shallow-water communities, signalling a panmictic population structure among seemingly ecologically disparate strains. Conversely, phylogenetic analysis provided evidence for at least two novel Vibrio speciation events within this specific sponge microcosm. Collectively, these findings earmark this still relatively unknown environment as a bastion of taxonomic and phylogenetic variability for the genus and probably other bacterial taxa.

  6. Multilocus family-based association analysis of seven candidate polymorphisms with essential hypertension in an african-derived semi-isolated brazilian population.

    PubMed

    Kimura, L; Angeli, C B; Auricchio, M T B M; Fernandes, G R; Pereira, A C; Vicente, J P; Pereira, T V; Mingroni-Netto, R C

    2012-01-01

    Background. It has been widely suggested that analyses considering multilocus effects would be crucial to characterize the relationship between gene variability and essential hypertension (EH). Objective. To test for the presence of multilocus effects between/among seven polymorphisms (six genes) on blood pressure-related traits in African-derived semi-isolated Brazilian populations (quilombos). Methods. Analyses were carried out using a family-based design in a sample of 652 participants (97 families). Seven variants were investigated: ACE (rs1799752), AGT (rs669), ADD2 (rs3755351), NOS3 (rs1799983), GNB3 (rs5441 and rs5443), and GRK4 (rs1801058). Sensitivity analyses were further performed under a case-control design with unrelated participants only. Results. None of the investigated variants were associated individually with both systolic and diastolic BP levels (SBP and DBP, respectively) or EH (as a binary outcome). Multifactor dimensionality reduction-based techniques revealed a marginal association of the combined effect of both GNB3 variants on DBP levels in a family-based design (P = 0.040), whereas a putative NOS3-GRK4 interaction also in relation to DBP levels was observed in the case-control design only (P = 0.004). Conclusion. Our results provide limited support for the hypothesis of multilocus effects between/among the studied variants on blood pressure in quilombos. Further larger studies are needed to validate our findings.

  7. Multilocus Family-Based Association Analysis of Seven Candidate Polymorphisms with Essential Hypertension in an African-Derived Semi-Isolated Brazilian Population

    PubMed Central

    Kimura, L.; Angeli, C. B.; Auricchio, M. T. B. M.; Fernandes, G. R.; Pereira, A. C.; Vicente, J. P.; Pereira, T. V.; Mingroni-Netto, R. C.

    2012-01-01

    Background. It has been widely suggested that analyses considering multilocus effects would be crucial to characterize the relationship between gene variability and essential hypertension (EH). Objective. To test for the presence of multilocus effects between/among seven polymorphisms (six genes) on blood pressure-related traits in African-derived semi-isolated Brazilian populations (quilombos). Methods. Analyses were carried out using a family-based design in a sample of 652 participants (97 families). Seven variants were investigated: ACE (rs1799752), AGT (rs669), ADD2 (rs3755351), NOS3 (rs1799983), GNB3 (rs5441 and rs5443), and GRK4 (rs1801058). Sensitivity analyses were further performed under a case-control design with unrelated participants only. Results. None of the investigated variants were associated individually with both systolic and diastolic BP levels (SBP and DBP, respectively) or EH (as a binary outcome). Multifactor dimensionality reduction-based techniques revealed a marginal association of the combined effect of both GNB3 variants on DBP levels in a family-based design (P = 0.040), whereas a putative NOS3-GRK4 interaction also in relation to DBP levels was observed in the case-control design only (P = 0.004). Conclusion. Our results provide limited support for the hypothesis of multilocus effects between/among the studied variants on blood pressure in quilombos. Further larger studies are needed to validate our findings. PMID:23056922

  8. Association of XPC Gene Polymorphisms with Colorectal Cancer Risk in a Southern Chinese Population: A Case-Control Study and Meta-Analysis

    PubMed Central

    Hua, Rui-Xi; Zhu, Jinhong; Jiang, Dan-Hua; Zhang, Shao-Dan; Zhang, Jiang-Bo; Xue, Wen-Qiong; Li, Xi-Zhao; Zhang, Pei-Fen; He, Jing; Jia, Wei-Hua

    2016-01-01

    Xeroderma pigmentosum group C (XPC) is a key component of the nucleotide excision repair (NER) pathway. Dysfunctional XPC protein may impair NER-mediated DNA repair capacity and further lead to genomic instability and carcinogenesis. Two common nonsynonymous polymorphisms in the XPC gene, Lys939Gln (rs2228001 A > C) and Ala499Val (rs2228000 C > T), have been investigated in various types of cancer. We genotyped these two polymorphisms in 1141 cases with histologically confirmed colorectal cancer (CRC) and 1173 healthy controls to explore their causative association with CRC susceptibility. Overall, no association was observed between these two variants and the risk of CRC. Our meta-analysis also confirmed a lack of overall association. Stratified analyses were performed by age, gender, smoking status, pack-year, drinking status, tumor sites, and Duke’s stages. We found that XPC Lys939Gln polymorphism was significantly associated with an increased CRC risk in subjects at 57 years of age or younger (adjusted odds ratio (OR) = 1.37, 95% confidence interval (CI) = 1.004–1.86, p = 0.047) and non-drinkers (adjusted OR = 1.53, 95% CI = 1.10–2.12, p = 0.011). Our results indicated that XPC Lys939Gln may be a low-penetrance CRC susceptibility polymorphism. Our findings warrant further validation. PMID:27669310

  9. Microsatellite data analysis for population genetics.

    PubMed

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  10. Association study between genetic variations in Axin2 gene and lung cancer risk in North Indian population: A multiple interaction analysis.

    PubMed

    Bahl, Charu; Sharma, Siddharth; Singh, Navneet; Behera, Digamber

    2017-04-01

    Wnt pathway has been implicated in the process of human carcinogenesis. Axis inhibition protein2 ( Axin2), a major scaffold protein is an antagonist of Wnt pathway and is potent to act as a tumor suppressor gene in various human cancers. Therefore, the seven polymorphic sites of Axin2 gene were analyzed, in relation to lung cancer susceptibility in North Indians. A total of 608 subjects were genotyped using PCR-RFLP technique for each polymorphic site including 303 cases and 305 controls. Further association analysis was carried out using logistic regression approach to obtain adjusted odds ratio and statistical significance. MDR and CART analysis were applied to evaluate high order interactions between the SNP's. Three out of seven studied polymorphic sites showed a strong protective effect in subjects having mutant genotype for Axin2 148 C >T and heterozygous genotype for 1365 G > A and 1712 + 19 G > T towards lung cancer risk. The other important finding was the significant association of Axin2 148 C >T in SQCC patients having variant (TT) genotype. Axin2 1712 + 19 G >T showed a decreased risk for all the histological subtypes in patients with heterozygous (GT) genotype. MDR analysis predicted a best interaction model ( Axin2 148, Axin2 2062 and Axin2 1712 +19) with maximum CVC (10/10) and minimum prediction error (0.38) along with significant permutation p-value. CART analysis gave a wide spectrum of interactive combinations which exhibited a major contribution in modulating lung cancer susceptibility. Axin2 148 and Axin2 1712 + 19 were found to play a major role in modulating lung cancer risk.

  11. Association analysis of bitter receptor genes in five isolated populations identifies a significant correlation between TAS2R43 variants and coffee liking.

    PubMed

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; d'Adamo, Pio; Amin, Najaf; d'Eustacchio, Angela; Navarini, Luciano; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

    2014-01-01

    Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people's health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics.

  12. Effects of circadian clock genes and health-related behavior on metabolic syndrome in a Taiwanese population: Evidence from association and interaction analysis

    PubMed Central

    Lin, Eugene; Kuo, Po-Hsiu; Liu, Yu-Li; Yang, Albert C.; Kao, Chung-Feng; Tsai, Shih-Jen

    2017-01-01

    Increased risk of developing metabolic syndrome (MetS) has been associated with the circadian clock genes. In this study, we assessed whether 29 circadian clock-related genes (including ADCYAP1, ARNTL, ARNTL2, BHLHE40, CLOCK, CRY1, CRY2, CSNK1D, CSNK1E, GSK3B, HCRTR2, KLF10, NFIL3, NPAS2, NR1D1, NR1D2, PER1, PER2, PER3, REV1, RORA, RORB, RORC, SENP3, SERPINE1, TIMELESS, TIPIN, VIP, and VIPR2) are associated with MetS and its individual components independently and/or through complex interactions in a Taiwanese population. We also analyzed the interactions between environmental factors and these genes in influencing MetS and its individual components. A total of 3,000 Taiwanese subjects from the Taiwan Biobank were assessed in this study. Metabolic traits such as waist circumference, triglyceride, high-density lipoprotein cholesterol, systolic and diastolic blood pressure, and fasting glucose were measured. Our data showed a nominal association of MetS with several single nucleotide polymorphisms (SNPs) in five key circadian clock genes including ARNTL, GSK3B, PER3, RORA, and RORB; but none of these SNPs persisted significantly after performing Bonferroni correction. Moreover, we identified the effect of GSK3B rs2199503 on high fasting glucose (P = 0.0002). Additionally, we found interactions among the ARNTL rs10832020, GSK3B rs2199503, PER3 rs10746473, RORA rs8034880, and RORB rs972902 SNPs influenced MetS (P < 0.001 ~ P = 0.002). Finally, we investigated the influence of interactions between ARNTL rs10832020, GSK3B rs2199503, PER3 rs10746473, and RORB rs972902 with environmental factors such as alcohol consumption, smoking status, and physical activity on MetS and its individual components (P < 0.001 ~ P = 0.002). Our study indicates that circadian clock genes such as ARNTL, GSK3B, PER3, RORA, and RORB genes may contribute to the risk of MetS independently as well as through gene-gene and gene-environment interactions. PMID:28296937

  13. Association Analysis of Bitter Receptor Genes in Five Isolated Populations Identifies a Significant Correlation between TAS2R43 Variants and Coffee Liking

    PubMed Central

    Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M.; Pistis, Giorgio; d’Adamo, Pio; Amin, Najaf; d’Eustacchio, Angela; Navarini, Luciano; Sala, Cinzia; Karssen, Lennart C.; van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

    2014-01-01

    Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people’s health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics. PMID:24647340

  14. How Does Neighborhood Quality Moderate the Association Between Online Video Game Play and Depression? A Population-Level Analysis of Korean Students.

    PubMed

    Kim, Harris Hyun-Soo; Ahn, Sun Joo Grace

    2016-10-01

    The main objective of our study is to assess the relationship between playing online video games and mental wellbeing of adolescents based on a nationally representative sample. Data come from the Korean Children and Youth Panel Survey (KCYPS), a government-funded multiyear research project. Through a secondary analysis of W2 and W3 of data collected in 2011 and 2012, we examine the extent to which time spent playing online games is related to depression, as measured by a battery of items modeled after the abridged version of Center for Epidemiologic Studies Depression Scale Revised (CESD-R). For proper temporal ordering, the outcome variable is drawn from the latter wave (W3), whereas all time-lagged covariates are taken from the earlier wave (W2). Multilevel regression models show that more game playing is associated with greater depression. Findings also indicate that, net of individual-level variables (e.g., gender, health, family background), living in a community with more divorced families adds to adolescent depression. Finally, a cross-level interaction is observed: the positive association between game playing and depression is more pronounced in an area characterized by a lower aggregate divorce rate.

  15. Socio-Economic Differences in the Association between Self-Reported and Clinically Present Diabetes and Hypertension: Secondary Analysis of a Population-Based Cross-Sectional Study

    PubMed Central

    Tompkins, Gerald; Forrest, Lynne F.; Adams, Jean

    2015-01-01

    Background Diabetes and hypertension are key risk factors for coronary heart disease. Prevalence of both conditions is socio-economically patterned. Awareness of presence of the conditions may influence risk behaviour and use of preventative services. Our aim was to examine whether there were socio-economic differences in awareness of hypertension and diabetes in a UK population. Method Data from the Scottish Health Survey was used to compare self-reported awareness of hypertension and diabetes amongst those found on examination to have these conditions, by socioeconomic position (SEP) (measured by occupation, education and income). Odds ratios of self-reported awareness against presence, and the sensitivity, specificity and predictive value of self-reporting as a measure of the presence of the condition, were calculated. Results Presence and self-reported awareness of both conditions increased as SEP decreased, on most measures. There was only one significant difference in awareness by SEP once other factors had been taken into account. Sensitivity showed that those in the most disadvantaged groups were most likely to self-report awareness of their hypertension, and specificity showed that those in the least disadvantaged groups were most likely to self-report awareness of its absence. There were few differences of note for diabetes. Conclusion We found no consistent pattern in the associations between SEP and the presence and self-reported awareness of hypertension and diabetes amongst those with these conditions. Without evidence of differences, it is important that universal approaches continue to be applied to the identification and management of those at risk of these and other conditions that underpin cardiovascular disease. PMID:26466384

  16. Discovering potential serological biomarker for chronic Hepatitis B Virus-related hepatocellular carcinoma in Chinese population by MAL-associated serum glycoproteomics analysis

    PubMed Central

    Liu, Tianhua; Liu, Denghe; Liu, Riqiang; Jiang, Hucong; Yan, Guoquan; Li, Wei; Sun, Lu; Zhang, Shu; Liu, Yinkun; Guo, Kun

    2017-01-01

    The accuracy of current biomarkers for the diagnosis of hepatocellular carcinoma (HCC), especially chronic Hepatitis B Virus (HBV)-related HCC, is limited. Recent progress in glycoproteomics has provided a novel platform for screening novel serological biomarkers of HCC. In this study, lectin affinity chromatography by Maackia amurensis lectin (MAL) and iTRAQ combined with mass spectrometric analysis were performed to enrich and identify the glycoprotein fractions in serum samples from HBV-related HCC patients and from healthy controls. Seventeen differential MAL-associated glycoproteins were identified. Among them, Galectin 3 binding protein (Gal-3BP) was selected for further evaluated by ELISA analysis and showed a high diagnostic potential of HBV-related HCC, with the AUC of 0.898 and a sensitivity, specificity and accuracy of 80.00%, 93.75% and 86.88%, respectively. Moreover, we constructed a predictive model through the combined use of serum Gal-3BP and Alpha Fetoprotein (AFP), which improved the sensitivity (from 87.5% to 95%), specificity (from 93.75% to 95%) and accuracy (from 90.63% to 95%) of diagnosing early HCC. These data suggested serum Gal-3BP level is a promising biomarker to identify HBV-related HCC and the combined use of serum Gal-3BP and AFP improves the diagnostic potential of HBV-HCC compared with AFP alone in current clinical practice. PMID:28079114

  17. A mixed model reduces spurious genetic associations produced by population stratification in genome-wide association studies.

    PubMed

    Shin, Jimin; Lee, Chaeyoung

    2015-04-01

    Population stratification can produce spurious genetic associations in genome-wide association studies (GWASs). Mixed model methodology has been regarded useful for correcting population stratification. This study explored statistical power and false discovery rate (FDR) with the data simulated for dichotomous traits. Empirical FDRs and powers were estimated using fixed models with and without genomic control and using mixed models with and without reflecting loci linked to the candidate marker in genetic relationships. Population stratification with admixture degree ranged from 1% to 10% resulted in inflated FDRs from the fixed model analysis without genomic control and decreased power from the fixed model analysis with genomic control (P<0.05). Meanwhile, population stratification could not change FDR and power estimates from the mixed model analyses (P>0.05). We suggest that the mixed model methodology was useful to reduce spurious genetic associations produced by population stratification in GWAS, even with a high degree of admixture (10%).

  18. The association forecasting of 13 variants within seven asthma susceptibility genes on 3 serum IgE groups in Taiwanese population by integrating of adaptive neuro-fuzzy inference system (ANFIS) and classification analysis methods.

    PubMed

    Wang, Cheng-Hang; Liu, Baw-Jhiune; Wu, Lawrence Shih-Hsin

    2012-02-01

    Asthma is one of the most common chronic diseases in children. It is caused by complicated coactions between various genetic factors and environmental allergens. The study aims to integrate the concept of implementing adaptive neuro-fuzzy inference system (ANFIS) and classification analysis methods for forecasting the association of asthma susceptibility genes on 3 serum IgE groups. The ANFIS model was trained and tested with data sets obtained from 425 asthmatic subjects and 483 non-asthma subjects from the Taiwanese population. We assessed 13 single-nucleotide polymorphisms (SNPs) in seven well-known asthma susceptibility genes; firstly, the proposed ANFIS model learned to reduce input features from the 13 SNPs. And secondly, the classification will be used to classify the serum IgE groups from the simulated SNPs results. The performance of the ANFIS model, classification accuracies and the results confirmed that the integration of ANFIS and classified analysis has potential in association discovery.

  19. Association between Impulsivity and Weight Status in a General Population

    PubMed Central

    Bénard, Marc; Camilleri, Géraldine M.; Etilé, Fabrice; Méjean, Caroline; Bellisle, France; Reach, Gérard; Hercberg, Serge; Péneau, Sandrine

    2017-01-01

    The objective of this study is to examine the association between impulsivity and weight status in a large sample of the adult general population in France, and the influence of gender on this relationship. A total of 11,929 men and 39,114 women participating in the NutriNet-Santé cohort were selected in this cross-sectional analysis. The Barratt Impulsiveness Scale (BIS-11) was used to assess impulsivity. Weight and height were self-reported. The association between impulsivity and BMI was estimated using logistic regressions adjusted for socio-demographic and lifestyle factors. Individuals with high impulsivity levels (BIS-11 total score >71) were more likely to be obese (Odds Ratio (OR) = 1.80, 95% Confidence Interval (CI): 1.39, 2.33 in men; OR = 1.30, 95% CI: 1.15, 1.48 in women) compared to individuals in the average range of impulsivity. The strongest associations between impulsivity and obesity were observed in men, where highly impulsive participants were more likely to be class III obese (BMI > 40 kg/m2) (OR = 3.57, 95% CI: 1.86, 6.85). This large sample analysis supports the existence of a relationship between impulsivity and weight status and the importance of psychological factors in the prevention of obesity. PMID:28257032

  20. Microsatellite data analysis for population genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  1. Association of lymphocytic colitis and lactase deficiency in pediatric population.

    PubMed

    Sun, Jihong; Lin, Jingmei; Parashette, Kalayan; Zhang, Jianjun; Fan, Rong

    2015-02-01

    Characterized by colonic mucosa intraepithelial lymphocytosis, lymphocytic colitis is primarily an entity presented in the middle-aged to elderly patient population. Very few large series of lymphocytic colitis of childhood occurrence are available in the medical literature. Ten cases each of lymphocytic colitis and of colonic lymphocytosis of other diagnosis, all with duodenal disaccharidases analysis data, were collected from the files of our institution. The electronic medical records were reviewed and multiple variables were analyzed. The ten patients with lymphocytic colitis presented with diarrhea. Of these, three had abdominal pain. The age range was 2-18 years. Nearly all patients were Caucasian (90%) and 70% were female. Endoscopically, most had normal appearing colonic mucosa. Significant past medical history, family medical history and associated comorbidities included celiac disease, Down syndrome, juvenile arthritis and other autoimmune diseases. Interestingly, the most revealing observation was that the majority of cases (80%) were associated with lactase deficiency and, for the most part, gastrointestinal symptoms improved simply by treatment with Lactaid or avoidance of dairy products. This association is statistically significant. Our clinicopathological study indicates that the typical pediatric patient is a female Caucasian. A large of portion of the patients had associated lactase deficiency and improved on Lactaid supplement alone.

  2. Genome-Wide Association Study of Schizophrenia in Japanese Population

    PubMed Central

    Yamada, Kazuo; Iwayama, Yoshimi; Hattori, Eiji; Iwamoto, Kazuya; Toyota, Tomoko; Ohnishi, Tetsuo; Ohba, Hisako; Maekawa, Motoko; Kato, Tadafumi; Yoshikawa, Takeo

    2011-01-01

    Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits. Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS) is a potentially powerful tool for identifying the risk variants that underlie the disease. Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach. Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs) in 120 patient-parents trio samples from Japanese schizophrenia pedigrees. In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p<0.01 and 473 SNPs of p<0.05 that located in previously reported linkage regions). The second sample consisted of 1,012 case-control samples of Japanese origin. The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila)-like 2] gene located on 9p21.3 (p = 0.00087). In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals) of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026). The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology. PMID:21674006

  3. Population Analysis: Communicating About Anthropometry in Context

    NASA Technical Reports Server (NTRS)

    Thaxton, Sherry; Rajulu, Sudhakar

    2009-01-01

    This slide presentation reviews the importance of communications about anthropometry and population analysis in particular for the design of aerospace systems. The difficulty of providing anthropometric accomodation an entire range of the population is reviewed, and the importance of communication of the issues with human system integration is emphasized, and the analysis of population as it applies to existing human factors methodologies is a novel way to assist with the communication. The issues of space suit design and anthropometry is reviewed as an example.

  4. Unbiased methods for population-based association studies.

    PubMed

    Devlin, B; Roeder, K; Bacanu, S A

    2001-12-01

    Large, population-based samples and large-scale genotyping are being used to evaluate disease/gene associations. A substantial drawback to such samples is the fact that population substructure can induce spurious associations between genes and disease. We review two methods, called genomic control (GC) and structured association (SA), that obviate many of the concerns about population substructure by using the features of the genomes present in the sample to correct for stratification. The GC approach exploits the fact that population substructure generates "over dispersion" of statistics used to assess association. By testing multiple polymorphisms throughout the genome, only some of which are pertinent to the disease of interest, the degree of overdispersion generated by population substructure can be estimated and taken into account. The SA approach assumes that the sampled population, although heterogeneous, is composed of subpopulations that are themselves homogeneous. By using multiple polymorphisms throughout the genome, this "latent class method" estimates the probability sampled individuals derive from each of these latent subpopulations. GC has the advantage of robustness, simplicity, and wide applicability, even to experimental designs such as DNA pooling. SA is a bit more complicated but has the advantage of greater power in some realistic settings, such as admixed populations or when association varies widely across subpopulations. It, too, is widely applicable. Both also have weaknesses, as elaborated in our review.

  5. An association analysis of HLA-DQB1 with narcolepsy without cataplexy and idiopathic hypersomnia with/without long sleep time in a Japanese population

    PubMed Central

    Miyagawa, Taku; Toyoda, Hiromi; Kanbayashi, Takashi; Imanishi, Aya; Sagawa, Yohei; Kotorii, Nozomu; Kotorii, Tatayu; Hashizume, Yuji; Ogi, Kimihiro; Hiejima, Hiroshi; Kamei, Yuichi; Hida, Akiko; Miyamoto, Masayuki; Ikegami, Azusa; Wada, Yamato; Takami, Masanori; Fujimura, Yota; Tamura, Yoshiyuki; Omata, Naoto; Masuya, Yasuhiro; Kondo, Hideaki; Moriya, Shunpei; Furuya, Hirokazu; Kato, Mitsuhiro; Kojima, Hiroto; Kashiwase, Koichi; Saji, Hiroh; Khor, Seik-Soon; Yamasaki, Maria; Ishigooka, Jun; Wada, Yuji; Chiba, Shigeru; Yamada, Naoto; Okawa, Masako; Kuroda, Kenji; Kume, Kazuhiko; Hirata, Koichi; Uchimura, Naohisa; Shimizu, Tetsuo; Inoue, Yuichi; Honda, Yutaka; Mishima, Kazuo; Honda, Makoto; Tokunaga, Katsushi

    2015-01-01

    Narcolepsy without cataplexy (NA w/o CA) (narcolepsy type 2) is a lifelong disorder characterized by excessive daytime sleepiness and rapid eye movement (REM) sleep abnormalities, but no cataplexy. In the present study, we examined the human leukocyte antigen HLA-DQB1 in 160 Japanese patients with NA w/o CA and 1,418 control subjects. Frequencies of DQB1*06:02 were significantly higher in patients with NA w/o CA compared with controls (allele frequency: 16.6 vs. 7.8%, P=1.1×10−7, odds ratio (OR)=2.36; carrier frequency: 31.3 vs. 14.7%, P=7.6×10−8, OR=2.64). Distributions of HLA-DQB1 alleles other than DQB1*06:02 were compared between NA w/o CA and narcolepsy with cataplexy (NA-CA) to assess whether the genetic backgrounds of the two diseases have similarities. The distribution of the HLA-DQB1 alleles in DQB1*06:02-negative NA w/o CA was significantly different from that in NA-CA (P=5.8×10−7). On the other hand, the patterns of the HLA-DQB1 alleles were similar between DQB1*06:02-positive NA w/o CA and NA-CA. HLA-DQB1 analysis was also performed in 186 Japanese patients with idiopathic hypersomnia (IHS) with/without long sleep time, but no significant associations were observed. PMID:27081540

  6. An association analysis of HLA-DQB1 with narcolepsy without cataplexy and idiopathic hypersomnia with/without long sleep time in a Japanese population.

    PubMed

    Miyagawa, Taku; Toyoda, Hiromi; Kanbayashi, Takashi; Imanishi, Aya; Sagawa, Yohei; Kotorii, Nozomu; Kotorii, Tatayu; Hashizume, Yuji; Ogi, Kimihiro; Hiejima, Hiroshi; Kamei, Yuichi; Hida, Akiko; Miyamoto, Masayuki; Ikegami, Azusa; Wada, Yamato; Takami, Masanori; Fujimura, Yota; Tamura, Yoshiyuki; Omata, Naoto; Masuya, Yasuhiro; Kondo, Hideaki; Moriya, Shunpei; Furuya, Hirokazu; Kato, Mitsuhiro; Kojima, Hiroto; Kashiwase, Koichi; Saji, Hiroh; Khor, Seik-Soon; Yamasaki, Maria; Ishigooka, Jun; Wada, Yuji; Chiba, Shigeru; Yamada, Naoto; Okawa, Masako; Kuroda, Kenji; Kume, Kazuhiko; Hirata, Koichi; Uchimura, Naohisa; Shimizu, Tetsuo; Inoue, Yuichi; Honda, Yutaka; Mishima, Kazuo; Honda, Makoto; Tokunaga, Katsushi

    2015-01-01

    Narcolepsy without cataplexy (NA w/o CA) (narcolepsy type 2) is a lifelong disorder characterized by excessive daytime sleepiness and rapid eye movement (REM) sleep abnormalities, but no cataplexy. In the present study, we examined the human leukocyte antigen HLA-DQB1 in 160 Japanese patients with NA w/o CA and 1,418 control subjects. Frequencies of DQB1*06:02 were significantly higher in patients with NA w/o CA compared with controls (allele frequency: 16.6 vs. 7.8%, P=1.1×10(-7), odds ratio (OR)=2.36; carrier frequency: 31.3 vs. 14.7%, P=7.6×10(-8), OR=2.64). Distributions of HLA-DQB1 alleles other than DQB1*06:02 were compared between NA w/o CA and narcolepsy with cataplexy (NA-CA) to assess whether the genetic backgrounds of the two diseases have similarities. The distribution of the HLA-DQB1 alleles in DQB1*06:02-negative NA w/o CA was significantly different from that in NA-CA (P=5.8×10(-7)). On the other hand, the patterns of the HLA-DQB1 alleles were similar between DQB1*06:02-positive NA w/o CA and NA-CA. HLA-DQB1 analysis was also performed in 186 Japanese patients with idiopathic hypersomnia (IHS) with/without long sleep time, but no significant associations were observed.

  7. Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cowpea (Vigna unguiculata (L) Walp.) is an important legume and the antioxidants in cowpea seeds have been recognized as health-promoting compounds for human. The objectives of this study were to analyze the population structure of cowpea collections using single nucleotide polymorphism (SNP) and to...

  8. -141C insertion/deletion polymorphism of the dopamine D2 receptor gene is associated with schizophrenia in Chinese Han population: Evidence from an ethnic group-specific meta-analysis.

    PubMed

    Zhao, Xiaofeng; Huang, Yinglin; Chen, Kaiyuan; Li, Duolu; Han, Chao; Kan, Quancheng

    2016-09-01

    Accumulate evidence has implicated dopamine D2 receptor gene polymorphisms in the etiology of schizophrenia. A single nucleotide polymorphism, -141C insertion/deletion (Ins/Del) (rs1799732), in the promoter region of the dopamine D2 receptor gene has been linked to schizophrenia; however, the data are inconclusive. This study investigated whether the -141C polymorphism is associated with the risk of schizophrenia in different ethnic groups by performing a meta-analysis. A total of 24 case-control studies examining the association between -141C Ins/Del polymorphism and schizophrenia were identified according to established inclusion criteria. Significant association was revealed between -141C Ins/Del polymorphism and schizophrenia risk in dominant genetic model (Ins/Ins + Ins/Del versus Del/Del) (odds ratio = 0.33, 95% confidence interval = 0.14-0.81, z = 2.41, P = 0.02) in Chinese Han but not in Caucasian, Japanese or India populations. Our results indicate that -141C Ins/Del polymorphism might be a susceptibility factor for schizophrenia in Chinese Han population.

  9. Eating Behaviour in the General Population: An Analysis of the Factor Structure of the German Version of the Three-Factor-Eating-Questionnaire (TFEQ) and Its Association with the Body Mass Index.

    PubMed

    Löffler, Antje; Luck, Tobias; Then, Francisca S; Sikorski, Claudia; Kovacs, Peter; Böttcher, Yvonne; Breitfeld, Jana; Tönjes, Anke; Horstmann, Annette; Löffler, Markus; Engel, Christoph; Thiery, Joachim; Villringer, Arno; Stumvoll, Michael; Riedel-Heller, Steffi G

    2015-01-01

    The Three-Factor-Eating-Questionnaire (TFEQ) is an established instrument to assess eating behaviour. Analysis of the TFEQ-factor structure was based on selected, convenient and clinical samples so far. Aims of this study were (I) to analyse the factor structure of the German version of the TFEQ and (II)--based on the refined factor structure--to examine the association between eating behaviour and the body mass index (BMI) in a general population sample of 3,144 middle-aged and older participants (40-79 years) of the ongoing population based cohort study of the Leipzig Research Center for Civilization Diseases (LIFE Health Study). The factor structure was examined in a split-half analysis with both explorative and confirmatory factor analysis. Associations between TFEQ-scores and BMI values were tested with multiple regression analyses controlled for age, gender, and education. We found a three factor solution for the TFEQ with an 'uncontrolled eating', a 'cognitive restraint' and an 'emotional eating' domain including 29 of the original 51 TFEQ-items. Scores of the 'uncontrolled eating domain' showed the strongest correlation with BMI values (partial r = 0.26). Subjects with scores above the median in both 'uncontrolled eating' and 'emotional eating' showed the highest BMI values (mean = 29.41 kg/m²), subjects with scores below the median in all three domains showed the lowest BMI values (mean = 25.68 kg/m²; F = 72.074, p<0.001). Our findings suggest that the TFEQ is suitable to identify subjects with specific patterns of eating behaviour that are associated with higher BMI values. Such information may help health care professionals to develop and implement more tailored interventions for overweight and obese individuals.

  10. Mapping asthma-associated variants in admixed populations

    PubMed Central

    Mersha, Tesfaye B.

    2015-01-01

    Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease–associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges

  11. Analysis of the mycotoxigenic fungi associated with southeastern U.S. winegrapes reveals a large population of Fusarium fujikuroi isolates producing high levels of fumonisins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycotoxins pose a serious challenge to a consistently safe food supply worldwide, and their threat is only expected to worsen with our changing climate. Species of Fusarium produce one or more of several mycotoxins, including tricothecenes, zearalenone, and fumonisins, which have been associated wi...

  12. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

    PubMed Central

    Buck, Moritz; Nilsson, Louise K. J.; Brunius, Carl; Dabiré, Roch K.; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

  13. Association mapping in an elite maize breeding population.

    PubMed

    Liu, Wenxin; Gowda, Manje; Steinhoff, Jana; Maurer, Hans Peter; Würschum, Tobias; Longin, Carl Friedrich Horst; Cossic, Frédéric; Reif, Jochen Christoph

    2011-09-01

    Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.

  14. Associations of Serum Manganese Levels with Prediabetes and Diabetes among ≥60-Year-Old Chinese Adults: A Population-Based Cross-Sectional Analysis.

    PubMed

    Wang, Xuan; Zhang, Mingyue; Lui, Guang; Chang, Hong; Zhang, Meilin; Liu, Wei; Li, Ziwei; Liu, Yixin; Huang, Guowei

    2016-08-13

    Older adults can experience glucose metabolism dysfunction, and although manganese may help regulate glucose metabolism, there is little information regarding this association among older people. This cross-sectional study included 2402 Chinese adults who were ≥60 years old in 2013 (Tianjin, China), and evaluated the associations of serum manganese with prediabetes and diabetes. Serum manganese levels were measured using inductively coupled plasma mass spectrometry. Multivariable logistic regression models were used to evaluate the sex-specific associations of manganese levels with diabetes and prediabetes after adjusting for confounding factors (age, sex, life style factors, and health status). Based on the WHO criteria, prediabetes was observed in 15.1% of men and 13.4% of women, while diabetes was observed in 30.0% of men and 34.4% of women. In the final model, the odds ratios (95% confidence interval) for prediabetes according to manganese quartile were 1.000, 0.463 (0.269-0.798), 0.639 (0.383-1.065), and 0.614 (0.365-1.031) among men and 1.000, 0.773 (0.498-1.200), 0.602 (0.382-0.947), and 0.603 (0.381-0.953) among women (p for trend = 0.134 and 0.015, respectively). The lowest prevalence of diabetes among men occurred at a moderate range of serum manganese (p < 0.05). Therefore, appropriate serum manganese levels may help prevent and control prediabetes and diabetes.

  15. [Population and environment. Requests for interdisciplinary analysis].

    PubMed

    Tudela, F

    1991-01-01

    Serious difficulties impede interdisciplinary research involving demographers, ecologists, and other students of the environment. The 1st problem concerns definitions of the different subject areas. Demographers have focused on the dynamics of some indicators that reflect complex and heterogeneous population processes. The relative autonomy of demography as a discipline was gained through an empirical orientation reflected in the statistical treatment of causality. But the traditional demographic paradigm is insufficient for untangling the causal mechanisms underlying population dynamics. Environmental disciplines on the other hand face methodologic difficulties in transcending a strictly biological focus to incorporate aspects of cultural and social influence on ecological processes. "Human ecology", a possible meeting ground for ecological and demographic studies, is more of an ambitious program of transdisciplinary research than an independent discipline. Relations between the environment and development processes, including population aspects, are of increasing international concern. A conceptual base has developed in Latin America which emphasizes the global and structural aspects of the environment and of development styles. It has been extremely difficult to apply the entire conceptualization to the concrete environmental problems that are of current interest to both civil society and governments. It may be time to replace the umbrella term "environment", defining it in more specific, systemic, and operational terms. It is time to delimit study topics in terms of concrete problems. A good example would be the situation of Lake Chapala, the largest lake in Mexico. Damage caused to it cannot be assessed by referring to the "population explosion" or an "overall development style". Environmental, economic, and sociodemographic aspects will however necessarily enter the analysis. Fragile and unstable situations are of special interest in the study of relations

  16. An inbreeding model of associative overdominance during a population bottleneck.

    PubMed Central

    Bierne, N; Tsitrone, A; David, P

    2000-01-01

    Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect. PMID:10924490

  17. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

    PubMed Central

    Fischer, Martin C; Rellstab, Christian; Tedder, Andrew; Zoller, Stefan; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex

    2013-01-01

    Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST-based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment. PMID:24102711

  18. Associations of Serum Manganese Levels with Prediabetes and Diabetes among ≥60-Year-Old Chinese Adults: A Population-Based Cross-Sectional Analysis

    PubMed Central

    Wang, Xuan; Zhang, Mingyue; Lui, Guang; Chang, Hong; Zhang, Meilin; Liu, Wei; Li, Ziwei; Liu, Yixin; Huang, Guowei

    2016-01-01

    Older adults can experience glucose metabolism dysfunction, and although manganese may help regulate glucose metabolism, there is little information regarding this association among older people. This cross-sectional study included 2402 Chinese adults who were ≥60 years old in 2013 (Tianjin, China), and evaluated the associations of serum manganese with prediabetes and diabetes. Serum manganese levels were measured using inductively coupled plasma mass spectrometry. Multivariable logistic regression models were used to evaluate the sex-specific associations of manganese levels with diabetes and prediabetes after adjusting for confounding factors (age, sex, life style factors, and health status). Based on the WHO criteria, prediabetes was observed in 15.1% of men and 13.4% of women, while diabetes was observed in 30.0% of men and 34.4% of women. In the final model, the odds ratios (95% confidence interval) for prediabetes according to manganese quartile were 1.000, 0.463 (0.269–0.798), 0.639 (0.383–1.065), and 0.614 (0.365–1.031) among men and 1.000, 0.773 (0.498–1.200), 0.602 (0.382–0.947), and 0.603 (0.381–0.953) among women (p for trend = 0.134 and 0.015, respectively). The lowest prevalence of diabetes among men occurred at a moderate range of serum manganese (p < 0.05). Therefore, appropriate serum manganese levels may help prevent and control prediabetes and diabetes. PMID:27529280

  19. Assessing the Causality Factors in the Association between (Abdominal) Obesity and Physical Activity among the Newfoundland Population-A Mendelian Randomization Analysis.

    PubMed

    Barning, Frank; Abarin, Taraneh

    2016-01-01

    A total of 1,263 adults from Newfoundland and Labrador were studied in the research. Body mass index (BMI) and percent trunk fat (PTF) were analyzed as biomarkers for obesity. The Mendelian randomization (MR) approach with two single-nucleotide polymorphisms in the fat-mass and obesity (FTO) gene as instruments was employed to assess the causal effect. In both genders, increasing physical activity significantly reduced BMI and PTF when adjusted for age and the FTO gene. The effect of physical activity was stronger on PTF than BMI. Direct observational analyses showed significant increase in BMI/PTF when physical activity decreased. A similar association in MR analyses was not significant. The association between physical activity and BMI/PTF could be due to reversed causality or common confounding factors. Our study provides insights into the causal contributions of obesity to physical activity in adults. Health intervention strategies to increase physical activity among adults should include some other plans such as improving diet for reducing obesity.

  20. Associations of blood lead, cadmium, and mercury with estimated glomerular filtration rate in the Korean general population: Analysis of 2008-2010 Korean National Health and Nutrition Examination Survey data

    SciTech Connect

    Kim, Yangho; Lee, Byung-Kook

    2012-10-15

    Introduction: The objective of this study was to evaluate associations between blood lead, cadmium, and mercury levels with estimated glomerular filtration rate in a general population of South Korean adults. Methods: This was a cross-sectional study based on data obtained in the Korean National Health and Nutrition Examination Survey (KNHANES) (2008-2010). The final analytical sample consisted of 5924 participants. Estimated glomerular filtration rate (eGFR) was calculated using the MDRD Study equation as an indicator of glomerular function. Results: In multiple linear regression analysis of log2-transformed blood lead as a continuous variable on eGFR, after adjusting for covariates including cadmium and mercury, the difference in eGFR levels associated with doubling of blood lead were -2.624 mL/min per 1.73 m Superscript-Two (95% CI: -3.803 to -1.445). In multiple linear regression analysis using quartiles of blood lead as the independent variable, the difference in eGFR levels comparing participants in the highest versus the lowest quartiles of blood lead was -3.835 mL/min per 1.73 m Superscript-Two (95% CI: -5.730 to -1.939). In a multiple linear regression analysis using blood cadmium and mercury, as continuous or categorical variables, as independent variables, neither metal was a significant predictor of eGFR. Odds ratios (ORs) and 95% CI values for reduced eGFR calculated for log2-transformed blood metals and quartiles of the three metals showed similar trends after adjustment for covariates. Discussion: In this large, representative sample of South Korean adults, elevated blood lead level was consistently associated with lower eGFR levels and with the prevalence of reduced eGFR even in blood lead levels below 10 {mu}g/dL. In conclusion, elevated blood lead level was associated with lower eGFR in a Korean general population, supporting the role of lead as a risk factor for chronic kidney disease.

  1. An association analysis between mitochondrial DNA content, G10398A polymorphism, HPV infection, and the prognosis of cervical cancer in the Chinese Han population.

    PubMed

    Feng, Dali; Xu, Hui; Li, Xin; Wei, Yuehua; Jiang, Huangang; Xu, Hong; Luo, Aihua; Zhou, Fuxiang

    2016-04-01

    The aim was to analyze quantitative (mitochondrial DNA (mtDNA) content) and qualitative (G10398A polymorphism) mtDNA alterations as well as human papillomavirus (HPV) infection in cervical cancer prognosis. One hundred and twenty-two cases of formalin-fixed paraffin-embedded cervical carcinoma specimens were collected from the Yichang Tumor Hospital and Zhongnan Hospital of Wuhan University in the recent 10 years together with medical records. A quantitative real-time PCR (RT-PCR) was used to determine the copy number of the mitochondrial DNA and HPV expression levels. G10398A polymorphism was determined by PCR-RFLP assay. The overall survival of patients with higher mtDNA content was significantly reduced compared with lower mtDNA content patients (P = 0.029). But there was no difference of prognosis between the mtDNA 10398 A allele and G allele. However, the Kaplan-Meier survival curve illustrated a significantly reduced overall survival in the patients with 10398A plus high mtDNA copy number compared with the other groups (P < 0.05). Although no association between HPV expression level and cervical cancer prognosis was observed, 10398A got increased mtDNA content compared with 10398G (P < 0.05) and 10398G displayed an increased HPV-positive rate compared with 10398A. Furthermore, HPV-18 and mtDNA content were positively related in the younger subgroup (≤45 years) (correlation coefficient = 0.456, P = 0.022). This study indicated that mtDNA content and HPV infection status are associated with cervical cancer prognosis. High mitochondrial DNA content plus 10398 A may be a marker of poor prognosis in cervical cancer. And mtDNA variation may potentially influence the predisposition to HPV infection and cervical carcinogenesis.

  2. Physiogenomic analysis of the Puerto Rican population

    PubMed Central

    Ruaño, Gualberto; Duconge, Jorge; Windemuth, Andreas; Cadilla, Carmen L; Kocherla, Mohan; Villagra, David; Renta, Jessica; Holford, Theodore; Santiago-Borrero, Pedro J

    2009-01-01

    Aims Admixture in the population of the island of Puerto Rico is of general interest with regards to pharmacogenetics to develop comprehensive strategies for personalized healthcare in Latin Americans. This research was aimed at determining the frequencies of SNPs in key physiological, pharmacological and biochemical genes to infer population structure and ancestry in the Puerto Rican population. Materials & methods A noninterventional, cross-sectional, retrospective study design was implemented following a controlled, stratified-by-region, random sampling protocol. The sample was based on birthrates in each region of the island of Puerto Rico, according to the 2004 National Birth Registry. Genomic DNA samples from 100 newborns were obtained from the Puerto Rico Newborn Screening Program in dried-blood spot cards. Genotyping using a physiogenomic array was performed for 332 SNPs from 196 cardiometabolic and neuroendocrine genes. Population structure was examined using a Bayesian clustering approach as well as by allelic dissimilarity as a measure of allele sharing. Results The Puerto Rican sample was found to be broadly heterogeneous. We observed three main clusters in the population, which we hypothesize to reflect the historical admixture in the Puerto Rican population from Amerindian, African and European ancestors. We present evidence for this interpretation by comparing allele frequencies for the three clusters with those for the same SNPs available from the International HapMap project for Asian, African and European populations. Conclusion Our results demonstrate that population analysis can be performed with a physiogenomic array of cardiometabolic and neuroendocrine genes to facilitate the translation of genome diversity into personalized medicine. PMID:19374515

  3. A Nonparametric Regression Approach to Control for Population Stratification in Rare Variant Association Studies

    PubMed Central

    Sha, Qiuying; Zhang, Kui; Zhang, Shuanglin

    2016-01-01

    Recently, there is increasing interest to detect associations between rare variants and complex traits. Rare variant association studies usually need large sample sizes due to the rarity of the variants, and large sample sizes typically require combining information from different geographic locations within and across countries. Although several statistical methods have been developed to control for population stratification in common variant association studies, these methods are not necessarily controlling for population stratification in rare variant association studies. Thus, new statistical methods that can control for population stratification in rare variant association studies are needed. In this article, we propose a principal component based nonparametric regression (PC-nonp) approach to control for population stratification in rare variant association studies. Our simulations show that the proposed PC-nonp can control for population stratification well in all scenarios, while existing methods cannot control for population stratification at least in some scenarios. Simulations also show that PC-nonp’s robustness to population stratification will not reduce power. Furthermore, we illustrate our proposed method by using whole genome sequencing data from genetic analysis workshop 18 (GAW18). PMID:27857226

  4. A Nonparametric Regression Approach to Control for Population Stratification in Rare Variant Association Studies.

    PubMed

    Sha, Qiuying; Zhang, Kui; Zhang, Shuanglin

    2016-11-18

    Recently, there is increasing interest to detect associations between rare variants and complex traits. Rare variant association studies usually need large sample sizes due to the rarity of the variants, and large sample sizes typically require combining information from different geographic locations within and across countries. Although several statistical methods have been developed to control for population stratification in common variant association studies, these methods are not necessarily controlling for population stratification in rare variant association studies. Thus, new statistical methods that can control for population stratification in rare variant association studies are needed. In this article, we propose a principal component based nonparametric regression (PC-nonp) approach to control for population stratification in rare variant association studies. Our simulations show that the proposed PC-nonp can control for population stratification well in all scenarios, while existing methods cannot control for population stratification at least in some scenarios. Simulations also show that PC-nonp's robustness to population stratification will not reduce power. Furthermore, we illustrate our proposed method by using whole genome sequencing data from genetic analysis workshop 18 (GAW18).

  5. A non-exercise testing method for estimating cardiorespiratory fitness: associations with all-cause and cardiovascular mortality in a pooled analysis of eight population-based cohorts

    PubMed Central

    Stamatakis, Emmanuel; Hamer, Mark; O'Donovan, Gary; Batty, George David; Kivimaki, Mika

    2013-01-01

    Aims Cardiorespiratory fitness (CRF) is a key predictor of chronic disease, particularly cardiovascular disease (CVD), but its assessment usually requires exercise testing which is impractical and costly in most health-care settings. Non-exercise testing cardiorespiratory fitness (NET-F)-estimating methods are a less resource-demanding alternative, but their predictive capacity for CVD and total mortality has yet to be tested. The objective of this study is to examine the association of a validated NET-F algorithm with all-cause and CVD mortality. Methods and results The participants were 32 319 adults (14 650 men) aged 35–70 years who took part in eight Health Survey for England and Scottish Health Survey studies between 1994 and 2003. Non-exercise testing cardiorespiratory fitness (a metabolic equivalent of VO2max) was calculated using age, sex, body mass index (BMI), resting heart rate, and self-reported physical activity. We followed participants for mortality until 2008. Two thousand one hundred and sixty-five participants died (460 cardiovascular deaths) during a mean 9.0 [standard deviation (SD) = 3.6] year follow-up. After adjusting for potential confounders including diabetes, hypertension, smoking, social class, alcohol, and depression, a higher fitness score according to the NET-F was associated with a lower risk of mortality from all-causes (hazard ratio per SD increase in NET-F 0.85, 95% confidence interval: 0.78–0.93 in men; 0.88, 0.80–0.98 in women) and CVD (men: 0.75, 0.63–0.90; women: 0.73, 0.60–0.92). Non-exercise testing cardiorespiratory fitness had a better discriminative ability than any of its components (CVD mortality c-statistic: NET-F = 0.70–0.74; BMI = 0.45–0.59; physical activity = 0.60–0.64; resting heart rate = 0.57–0.61). The sensitivity of the NET-F algorithm to predict events occurring in the highest risk quintile was better for CVD (0.49 in both sexes) than all-cause mortality (0.44 and 0.40 for men and women

  6. Phenotypic assessments of peanut nested association mapping (NAM) populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping (NAM) is a valuable innovation and multi-parental mapping population strategy in peanut genetics which increases the power to map quantitative trait loci and assists in extending the gene pool of elite peanut lines. In the peanut research community, two structured mapping ...

  7. There are Two Populations of Energetic Electrons Associated with CMEs

    NASA Astrophysics Data System (ADS)

    Haggerty, D. K.; Roelof, E. C.

    2001-05-01

    The time histories of electron impulsive beam events (40-300 keV, 0.4associated with such electron events [Simnett, Roelof, and Haggerty, this Conference]. We have performed a detailed statistical analysis of the timing between the electron injection [{it Roelof and Haggerty}, this Conference] and the peak emission of type III bursts measured by WIND/WAVES at 14 MHz and 2 MHz (corresponding to solar radii of ~2.5 and ~5, respectively). We almost always found a type III burst closely associated with the electron beams. However, the average time difference between type III maxima at 14 MHz and 2 MHz was ~90 s. Since a 1 keV electron travels 1 Rs in 37s, the time difference of 90s for transit over ~2.5 Rs implies that 1 keV is the mean energy of the exciter beam in the high corona. However, we find that the 40-300keV beam electrons at ACE are injected on average about 11 min after the typeIII burst at 14 MHz. We almost never see 40-300 keV electron injections simultaneous with the solar type III bursts. Therefore the ~1 keV electron populations generating the solar type III bursts must have a low intensity and/or a very soft spectrum compared to the 40-300 keV electron events, and the near-relativistic electrons must be accelerated/injected on average some 11 min later. We note that a shock moving at 1000 km/s moves one solar radius in 12 minutes. Hence, if the prompt type III emission is associated with the launch of a shock, it is reasonable that the near-relativistic electrons could be accelerated by such a shock moving out through the corona. This is also consistent with the associations found with CMEs [Simnett, Roelof, and Haggerty

  8. Prevalence of Diabetes and Associated Factors in the Uyghur and Han Population in Xinjiang, China

    PubMed Central

    Gong, Haiying; Pa, Lize; Wang, Ke; Mu, Hebuli; Dong, Fen; Ya, Shengjiang; Xu, Guodong; Tao, Ning; Pan, Li; Wang, Bin; Shan, Guangliang

    2015-01-01

    Objective: To estimate the prevalence of diabetes and identify risk factors in the Uyghur and Han population in Xinjiang, China. Methods: A cross-sectional study in urban and rural areas in Xinjiang, including 2863 members of the Uyghur population and 3060 of the Han population aged 20 to 80 years, was conducted from June 2013 to August 2013. Data on fasting plasma glucose (FPG) and personal history of diabetes were used to estimate the prevalence of diabetes. Data on demographic characteristics, lifestyle risk factors, and lipid profiles were collected to identify risks factors using the multivariate logistic regression model. Results: In urban areas, the age- and gender-standardized prevalence of diabetes was 8.21%, and the age- and gender-standardized prevalence of diabetes was higher in the Uyghur population (10.47%) than in the Han population (7.36%). In rural areas, the age- and gender-standardized prevalence of diabetes was 6.08%, and it did not differ significantly between the Uyghur population (5.71%) and the Han population (6.59%). The results of the multivariate logistic regression analysis showed that older age, obesity, high triglycerides (TG), and hypertension were all associated with an increased risk of diabetes in the Uyghur and Han population. Urban residence and low high-density lipoprotein cholesterol (HDL-C) were associated with an increased risk of diabetes in the Uyghur population. Being an ex-drinker was associated with an increased risk of diabetes and heavy physical activity was associated with a decreased risk of diabetes in the Han population. Conclusions: Our study indicates that diabetes is more prevalent in the Uyghur population compared with the Han population in urban areas. Strategies aimed at the prevention of diabetes require ethnic targeting. PMID:26473908

  9. The association between ALS and population density: A population based study.

    PubMed

    Scott, Kirsten M; Abhinav, Kumar; Wijesekera, Lokesh; Ganesalingam, Jeban; Goldstein, Laura H; Janssen, Anna; Dougherty, Andrew; Willey, Emma; Stanton, Biba R; Turner, Martin R; Ampong, Mary-Ann; Sakel, Mohammed; Orrell, Richard; Howard, Robin; Shaw, Christopher E; Nigel Leigh, P; Al-Chalabi, Ammar

    2010-10-01

    We aimed to assess whether rural residence is associated with amyotrophic lateral sclerosis in the south-east of England using a population based register. Previous studies in different populations have produced contradictory findings. Residence defined by London borough or non-metropolitan district at time of diagnosis was recorded for each incident case in the South-East England ALS Register between 1995 and 2005. Each of the 26 boroughs or districts of the catchment area of the register was classified according to population density. Age- and sex-adjusted incidence of ALS was calculated for each region and the relationship with population density tested by linear regression, thereby controlling for the underlying population structure. We found that population density in region of residence at diagnosis explained 25% of the variance in ALS rates (r = 0.5, p < 0.01). Thus, in this cohort in the south-east of England, people with ALS were more likely to be resident in areas of high population density at diagnosis.

  10. Population Cancer Risks Associated with Coal Mining: A Systematic Review

    PubMed Central

    Jenkins, Wiley D.; Christian, W. Jay; Mueller, Georgia; Robbins, K. Thomas

    2013-01-01

    Background Coal is produced across 25 states and provides 42% of US energy. With production expected to increase 7.6% by 2035, proximate populations remain at risk of exposure to carcinogenic coal products such as silica dust and organic compounds. It is unclear if population exposure is associated with increased risk, or even which cancers have been studied in this regard. Methods We performed a systematic review of English-language manuscripts published since 1980 to determine if coal mining exposure was associated with increased cancer risk (incidence and mortality). Results Of 34 studies identified, 27 studied coal mining as an occupational exposure (coal miner cohort or as a retrospective risk factor) but only seven explored health effects in surrounding populations. Overall, risk assessments were reported for 20 cancer site categories, but their results and frequency varied considerably. Incidence and mortality risk assessments were: negative (no increase) for 12 sites; positive for 1 site; and discordant for 7 sites (e.g. lung, gastric). However, 10 sites had only a single study reporting incidence risk (4 sites had none), and 11 sites had only a single study reporting mortality risk (2 sites had none). The ecological study data were particularly meager, reporting assessments for only 9 sites. While mortality assessments were reported for each, 6 had only a single report and only 2 sites had reported incidence assessments. Conclusions The reported assessments are too meager, and at times contradictory, to make definitive conclusions about population cancer risk due to coal mining. However, the preponderance of this and other data support many of Hill’s criteria for causation. The paucity of data regarding population exposure and risk, the widespread geographical extent of coal mining activity, and the continuing importance of coal for US energy, warrant further studies of population exposure and risk. PMID:23977014

  11. ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure.

    PubMed

    Thornton, Timothy; McPeek, Mary Sara

    2010-02-12

    Genome-wide association studies are routinely conducted to identify genetic variants that influence complex disorders. It is well known that failure to properly account for population or pedigree structure can lead to spurious association as well as reduced power. We propose a method, ROADTRIPS, for case-control association testing in samples with partially or completely unknown population and pedigree structure. ROADTRIPS uses a covariance matrix estimated from genome-screen data to correct for unknown population and pedigree structure while maintaining high power by taking advantage of known pedigree information when it is available. ROADTRIPS can incorporate data on arbitrary combinations of related and unrelated individuals and is computationally feasible for the analysis of genetic studies with millions of markers. In simulations with related individuals and population structure, including admixture, we demonstrate that ROADTRIPS provides a substantial improvement over existing methods in terms of power and type 1 error. The ROADTRIPS method can be used across a variety of study designs, ranging from studies that have a combination of unrelated individuals and small pedigrees to studies of isolated founder populations with partially known or completely unknown pedigrees. We apply the method to analyze two data sets: a study of rheumatoid arthritis in small UK pedigrees, from Genetic Analysis Workshop 15, and data from the Collaborative Study of the Genetics of Alcoholism on alcohol dependence in a sample of moderate-size pedigrees of European descent, from Genetic Analysis Workshop 14. We detect genome-wide significant association, after Bonferroni correction, in both studies.

  12. SIRT1 gene, schizophrenia and bipolar disorder in the Japanese population: an association study.

    PubMed

    Kishi, T; Fukuo, Y; Kitajima, T; Okochi, T; Yamanouchi, Y; Kinoshita, Y; Kawashima, K; Inada, T; Kunugi, H; Kato, T; Yoshikawa, T; Ujike, H; Ozaki, N; Iwata, N

    2011-04-01

    Several lines of evidence suggest that alterations in circadian rhythms might be associated with the pathophysiology of psychiatric disorders such as schizophrenia and bipolar disorder (BP). A recent study reported that SIRT1 is a molecule that plays an important role in the circadian clock system. Therefore, to evaluate the association among the SIRT1 gene, schizophrenia and BP, we conducted a case-control study of Japanese population samples (1158 schizophrenia patients, 1008 BP patients and 2127 controls) with four tagging SNPs (rs12778366, rs2273773, rs4746720 and rs10997875) in the SIRT1 gene. Marker-trait association analysis was used to evaluate the allele and the genotype association with the χ(2) test, and haplotype association analysis was evaluated with a likelihood ratio test. We showed an association between rs4746720 in the SIRT1 gene and schizophrenia in the allele and the genotype analysis. However, the significance of these associations did not survive after Bonferroni's correction for multiple testing. On the other hand, the SIRT1 gene was associated with Japanese schizophrenia in a haplotype-wise analysis (global P(all markers) = 4.89 × 10(-15)). Also, four tagging SNPs in the SIRT1 gene were not associated with BP. In conclusion, the SIRT1 gene may play an important role in the pathophysiology of schizophrenia in the Japanese population.

  13. Association of serine racemase gene variants with type 2 diabetes in the Chinese Han population.

    PubMed

    Zhang, Simin; Xiao, Jianzhong; Ren, Qian; Han, Xueyao; Tang, Yong; Yang, Wenying; Zhou, Xianghai; Ji, Linong

    2014-05-04

    A genome-wide association study in the Chinese Han population has identified several novel genetic variants of the serine racemase (SRR) gene in type 2 diabetes. Our purpose was to systematically evaluate the contribution of SRR variants in the Chinese Han population. rs391300 and rs4523957 in SRR were genotyped respectively in the two independent populations. A meta-analysis was used to estimate the effects of SRR in 21,305 Chinese Han individuals. Associations between single-nucleotide polymorphisms and diabetes-related phenotypes were analyzed among 2,615 newly diagnosed type 2 diabetes patients and 5,029 controls. Neither rs391300 nor rs4523957 were associated with type 2 diabetes in populations. Furthermore, meta-analysis did not confirm an association between type 2 diabetes and SRR. In the controls, rs391300-A and rs4523957-G were associated with higher 30-min plasma glucose in an oral glucose tolerance test. The present study did not confirm that SRR was associated with type 2 diabetes.

  14. Population-specific association of genes for telomere-associated proteins with longevity in an Italian population.

    PubMed

    Crocco, Paolina; Barale, Roberto; Rose, Giuseppina; Rizzato, Cosmeri; Santoro, Aurelia; De Rango, Francesco; Carrai, Maura; Fogar, Paola; Monti, Daniela; Biondi, Fiammetta; Bucci, Laura; Ostan, Rita; Tallaro, Federica; Montesanto, Alberto; Zambon, Carlo-Federico; Franceschi, Claudio; Canzian, Federico; Passarino, Giuseppe; Campa, Daniele

    2015-06-01

    Leukocyte telomere length (LTL) has been observed to be hereditable and correlated with longevity. However, contrasting results have been reported in different populations on the value of LTL heritability and on how biology of telomeres influences longevity. We investigated whether the variability of genes correlated to telomere maintenance is associated with telomere length and affects longevity in a population from Southern Italy (20-106 years). For this purpose we analyzed thirty-one polymorphisms in eight telomerase-associated genes of which twelve in the genes coding for the core enzyme (TERT and TERC) and the remaining in genes coding for components of the telomerase complex (TERF1, TERF2, TERF2IP, TNKS, TNKS2 and TEP1). We did not observe (after correcting for multiple testing) statistically significant associations between SNPs and LTL, possibly suggesting a low genetic influence of the variability of these genes on LTL in the elderly. On the other hand, we found that the variability of genes encoding for TERF1 and TNKS2, not directly involved in LTL, but important for keeping the integrity of the structure, shows a significant association with longevity. This suggests that the maintenance of these chromosomal structures may be critically important for preventing, or delaying, senescence and aging. Such a correlation was not observed in a population from northern Italy that we used as an independent replication set. This discrepancy is in line with previous reports regarding both the population specificity of results on telomere biology and the differences of aging in northern and southern Italy.

  15. Population Viability Analysis of Riverine Fishes

    SciTech Connect

    Bates, P.; Chandler, J.; Jager, H.I.; Lepla, K.; Van Winkle, W.

    1999-04-12

    Many utilities face conflkts between two goals: cost-efficient hydropower generation and protecting riverine fishes. Research to develop ecological simulation tools that can evaluate alternative mitigation strategies in terms of their benefits to fish populations is vital to informed decision-making. In this paper, we describe our approach to population viability analysis of riverine fishes in general and Snake River white sturgeon in particular. We are finding that the individual-based modeling approach used in previous in-stream flow applications is well suited to addressing questions about the viability of species of concern for several reasons. Chief among these are: (1) the abiIity to represent the effects of individual variation in life history characteristics on predicted population viabili~, (2) the flexibili~ needed to quanti~ the ecological benefits of alternative flow management options by representing spatial and temporal variation in flow and temperaturty and (3) the flexibility needed to quantifi the ecological benefits of non-flow related manipulations (i.e., passage, screening and hatchery supplementation).

  16. [APOE gene polymorphisms associated with Down syndrome in Colombian populations].

    PubMed

    Rengifo, Lucero; Gaviria, Duverney; Serrano, Herman

    2012-06-01

    Introduction.Gene APOEε4 allele polymorphisms have been examined in Down syndrome because of the relationship between (a) the E4 isoform and (b) the type of Alzheimer's dementia that appears in individuals with Down syndrome. This isoform is considered a risk factor for Alzheimer's disease development and has been associated with early death in Down syndrome. Objectives. The polymorphisms in the APOE gene were characterized for Down syndrome individuals and their parents, in order to detect associations between the APOE polymorphisms and Down syndrome. Materials and methods. APOE gene polymorphisms were detected by RFLP-PCR and analyzed in 134 young individuals with Down syndrome, 87 mothers and 54 fathers, residents of the departments of Quindío and Risaralda, Colombia. The controls were 525 healthy individuals. Results. The APOEε3 allele and ε3/ε3 genotype were most frequent in all the populations (83-90% and 70-78%). The allelic frequency of APOEε2 was very low and ε2/ε2 (3-7%) was absent in Down syndrome and their parents. The allele APOEε4 was more frequent (11% vs. 9%) in Down syndrome individuals than in the controls. Comparing the allelic and genotypic frequencies between the populations with Down syndrome and their parents with the controls using Pearson c2 test and Fisher's exact test odds ratio, no statistically significant differences were found. Conclusions. No statistically significant association was found between the polymorphisms of the APOE gene and Down syndrome. Sample size or ethnic influences may have affected these results. More studies are necessary with other Colombian populations to determine possible associations in other genes related to Alzheimer's disease.

  17. Identification of loci affecting teat number by genome-wide association studies on three pig populations

    PubMed Central

    Tang, Jianhong; Zhang, Zhiyan; Yang, Bin; Guo, Yuanmei; Ai, Huashui; Long, Yi; Su, Ying; Cui, Leilei; Zhou, Liyu; Wang, Xiaopeng; Zhang, Hui; Wang, Chengbin; Ren, Jun; Huang, Lusheng; Ding, Nengshui

    2017-01-01

    Objective Three genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number. Methods We performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc×Erhualian F2 resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383). Results We detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome-wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the F2 resource population, corresponding to four loci for pig teat number. We highlighted vertnin (VRTN) and lysine demethylase 6B (KDM6B) as two interesting candidate genes at the loci on SSC7 and SSC12. No significant associated SNPs were identified in the meta-analysis of GWAS. Conclusion The results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three populations PMID:27165028

  18. Association study in three different populations between the GPR88 gene and major psychoses

    PubMed Central

    Del Zompo, Maria; Deleuze, Jean-François; Chillotti, Caterina; Cousin, Emmanuelle; Niehaus, Dana; Ebstein, Richard P; Ardau, Raffaella; Macé, Sandrine; Warnich, Louise; Mujahed, Mustafa; Severino, Giovanni; Dib, Colette; Jordaan, Esme; Murad, Ibrahim; Soubigou, Stéphane; Koen, Liezl; Bannoura, Issam; Rocher, Corinne; Laurent, Claudine; Derock, Murielle; Faucon Biguet, Nicole; Mallet, Jacques; Meloni, Rolando

    2014-01-01

    GPR88, coding for a G protein-coupled orphan receptor that is highly represented in the striatum, is a strong functional candidate gene for neuropsychiatric disorders and is located at 1p22-p21, a chromosomal region that we have previously linked to bipolar disorder (BD) in the Sardinian population. In order to ascertain the relevance of GPR88 as a risk factor for psychiatric diseases, we performed a genetic association analysis between GPR88 and BD in a sample of triads (patient and both parents) recruited in the Sardinian and the Palestinian population as well as between GPR88 and schizophrenia (SZ) in triads from the Xhosa population in South Africa. We found a positive association between GPR88 and BD in the Sardinian and Palestinian triads. Moreover, we found a positive association between GPR88 and SZ in triads from the Xhosa population in South Africa. When these results were corrected for multiple testing, the association between GPR88 and BD was maintained in the Palestinian population. Thus, these results suggest that GPR88 deserves consideration as a candidate gene for psychiatric diseases and requires to be further investigated in other populations. PMID:24689078

  19. Population Analysis: A Methodology for Understanding Populations in COIN Environments

    DTIC Science & Technology

    2008-12-01

    predict cause and effect of human 30 behavior. In the late 19th century, Wilhelm Wundt founded the first psychology department at the University of...on the application of power with respect to managing people, organizations, markets, and populations. Philosophers and authors such as Friedrich ... Nietzsche , Jeffery Pfeffer, Bertram Raven, and John French have each laid out models by which power, and its implementation can be better understood

  20. Single-strand conformational polymorphism analysis of a common single nucleotide variation in WRAP53 gene, rs2287499, and evaluating its association in relation to breast cancer risk and prognosis among Iranian-Azeri population.

    PubMed

    Sedaie Bonab, Aida; Pouladi, Nasser; Hosseinpourfeizi, Mohammad Ali; Ravanbakhsh Gavgani, Reyhaneh; Dehghan, Roghayeh; Azarfam, Parvin; Montazeri, Vahid; Fakhrjou, Ashraf

    2014-09-01

    The WRAP53 (WD40-encoding RNA antisense to p53) gene encodes an antisense RNA, essential for p53 stabilization and induction upon DNA damage. Single nucleotide polymorphisms (SNPs) in WRAP53 have been associated with risk of cancer, which strengthens the role of WRAP53 in the pathogenesis of human malignancies. In fact, WRAP53 has been considered as a candidate cancer susceptibility gene. Accordingly, we performed a study to examine the association of a frequent genetic variation in WRAP53, rs2287499 (C/G), with breast cancer risk and prognosis among Iranian-Azeri population. A case-control association study, including 206 cases and 203 controls from Iranian-Azeri population, was conducted. Genomic DNA was extracted from peripheral blood and tumor samples by salting-out method. SNP genotyping was carried out by polymerase chain reaction-based single-strand conformational polymorphism (PCR-SSCP) technique. The sequence variation of SSCP banding patterns was determined by sequencing. The collected data were analyzed through statistical package for the social sciences software, using Chi-square (χ (2)) or Fisher's exact tests, with a significance level of 0.05. No significant differences in the allele and genotype frequencies between cases and controls were detected. Similarly, no significant associations between genotypes and clinicopathological data were observed. Concisely, no significant overall associations between rs2287499 and breast cancer risk and prognosis were detected in the studied population. The rs2287499 SNP is not associated with breast cancer predisposition in Iranian-Azeri women; it also cannot be used as a molecular biomarker to predict breast cancer prognosis in Iranian-Azeri population.

  1. Fine-scale patterns of population stratification confound rare variant association tests.

    PubMed

    O'Connor, Timothy D; Kiezun, Adam; Bamshad, Michael; Rich, Stephen S; Smith, Joshua D; Turner, Emily; Leal, Suzanne M; Akey, Joshua M

    2013-01-01

    Advances in next-generation sequencing technology have enabled systematic exploration of the contribution of rare variation to Mendelian and complex diseases. Although it is well known that population stratification can generate spurious associations with common alleles, its impact on rare variant association methods remains poorly understood. Here, we performed exhaustive coalescent simulations with demographic parameters calibrated from exome sequence data to evaluate the performance of nine rare variant association methods in the presence of fine-scale population structure. We find that all methods have an inflated spurious association rate for parameter values that are consistent with levels of differentiation typical of European populations. For example, at a nominal significance level of 5%, some test statistics have a spurious association rate as high as 40%. Finally, we empirically assess the impact of population stratification in a large data set of 4,298 European American exomes. Our results have important implications for the design, analysis, and interpretation of rare variant genome-wide association studies.

  2. GST polymorphisms are associated with hepatocellular carcinoma risk in Chinese population

    PubMed Central

    Yu, Lei; Wang, Chun-Yu; Xi, Bo; Sun, Lei; Wang, Ruo-Qi; Yan, Yin-Kun; Zhu, Li-Ying

    2011-01-01

    AIM: To investigate the association between GSTM1 and GSTT1 polymorphisms and the risk of hepatocellular carcinoma (HCC) in Chinese population. METHODS: Literature databases including PubMed, ISI web of science and other databases were searched. Pooled odds ratio (OR) and 95% CI were calculated using random- or fixed- effects model. Subgroup analysis and sensitivity analysis were also performed. RESULTS: Nineteen studies of GSTM1 (2660 cases and 4017 controls) and 16 studies of GSTT1 (2410 cases and 3669 controls) were included. The GSTM1/GSTT1 null genotypes were associated with increased risk of HCC in Chinese population (for GSTM1, OR = 1.487, 95% CI: 1.159 to 1.908, P = 0.002; for GSTT1, OR = 1.510, 95% CI: 1.236 to 1.845, P = 0.000). No publication bias was detected. In subgroup analysis, glutathione S-transferases polymorphisms were significantly associated with HCC risk among the subjects living in high-incidence areas, but not among the subjects living in low-incidence areas. CONCLUSION: The present meta-analysis suggests that GSTM1/GSTT1 null genotypes are associated with increased risk of HCC in Chinese population. PMID:21912475

  3. Characterization of population exposure to organochlorines: a cluster analysis application.

    PubMed

    Guimarães, Raphael Mendonça; Asmus, Carmen Ildes Rodrigues Fróes; Burdorf, Alex

    2013-06-01

    This study aimed to show the results from a cluster analysis application in the characterization of population exposure to organochlorines through variables related to time and exposure dose. Characteristics of 354 subjects in a population exposed to organochlorine pesticides residues related to time and exposure dose were subjected to cluster analysis to separate them into subgroups. We performed hierarchical cluster analysis. To evaluate the classification accuracy, compared to intra-group and inter-group variability by ANOVA for each dimension. The aggregation strategy was accomplished by the method of Ward. It was, for the creation of clusters, variables associated with exposure and routes of contamination. The information on the estimated intake doses of compound were used to weight the values of exposure time at each of the routes, so as to obtain values proxy exposure intensity. The results showed three clusters: cluster 1 (n = 45), characteristics of greatest exposure, the cluster 2 (n = 103), intermediate exposure, and cluster 3 (n = 206), less exposure. The bivariate analyzes performed with groups that are groups showed a statistically significant difference. This study demonstrated the applicability of cluster analysis to categorize populations exposed to organochlorines and also points to the relevance of typological studies that may contribute to a better classification of subjects exposed to chemical agents, which is typical of environmental epidemiology studies to a wider understanding of etiological, preventive and therapeutic contamination.

  4. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping.

    PubMed

    Jin, Liang; Lu, Yan; Xiao, Peng; Sun, Mei; Corke, Harold; Bao, Jinsong

    2010-08-01

    Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify

  5. Population ecology of Aspergillus flavus associated with Mississippi Delta soils.

    PubMed

    Zablotowicz, R M; Abbas, H K; Locke, M A

    2007-10-01

    Understanding the source of Aspergillus flavus is required to manage aflatoxin contamination of maize (Zea mays L.). Studies assessed A. flavus propagules, Fusarium spp., and total fungi associated with Mississippi Delta soils. Soils from 12 and 15 sites were collected in 2000 and 2001, respectively. The propagule density of A. flavus ranged from log(10) 2.0 to 4.3 colony-forming units (cfu) g(-1) soil, while total fusaria ranged from log(10) 3.0 to 5.4 cfu g(-1) soil. The highest populations of A. flavus were associated with soils containing higher organic matter, especially in sites under a no-tillage management. The frequency of aflatoxin production in isolates ranged from 13 to 81% depending on soil. In 2001, there was a highly significant correlation between A. flavus and the history of maize cultivation. Soil fertility factors such as organic matter content, nitrate and extractable phosphorus correlated with the density of Aspergillus, Fusarium spp., and total fungi. The relationship between soil parameters and Aspergillus populations may be useful in predicting the contribution of soil microflora to aflatoxin contamination.

  6. Microbial Population of Feedlot Waste and Associated Sites

    PubMed Central

    Rhodes, R. A.; Hrubant, G. R.

    1972-01-01

    A quantitative determination was made every 2 months for a year of the microflora of beef cattle waste and runoff at a medium-sized midwestern feedlot. Counts were obtained for selected groups of organisms in waste taken from paved areas of pens cleaned daily and, therefore, reflect the flora of raw waste. Overall, in terms of viable count per gram dry weight, the feedlot waste contained 1010 total organisms, 109 anaerobes, 108 gram-negative bacteria, 107 coliforms, 106 sporeformers, and 105 yeasts, fungi, and streptomycetes. The specific numbers and pattern of these groups of organisms varied only slightly during the study in spite of a wide variation in weather. Data indicate that little microbial growth occurs in the waste as it exists in the feedlot. Runoff from the pens contained the same general population pattern but with greater variation attributable to volume of liquid. Comparable determinations of an associated field disposal area (before and after cropping), stockpiled waste, and elevated dirt areas in the pens indicate that fungi, and especially streptomycetes, are the aerobic organisms most associated with final stabilization of the waste. Yeasts, which are the dominant type of organism in the ensiled corn fed the cattle, do not occur in large numbers in the animal waste. Large ditches receiving runoff and subsurface water from the fields have a population similar to the runoff but with fewer coliforms. PMID:16349931

  7. Association between gout and vertigo in a Taiwanese population.

    PubMed

    Lin, Yu-Ting; Lin, Hui-Wen; Huang, Yu-Chen; Ho, Wen-Tsao; Li, Yu-Chuan; Chen, Ting-Jui

    2013-06-01

    There are reports of an association between benign paroxysmal positional vertigo and hyperuricemia. We sought to determine the risk of vertigo among patients with gout compared with the general population, using a nationwide Taiwanese population-based claims database. Our study cohort consisted of patients with a diagnosis of gout disorders in 2004 (N = 18773). Four age- and gender-matched controls for every patient in the study cohort were selected using random sampling as the comparison cohort (N = 75092). All subjects were followed from the date of cohort entry until they developed vertigo or to the end of 2006. Cox proportional hazard regressions were performed to evaluate the 3-year vertigo-free survival rates. Of the total sample, 2563 (incidence, 10.09 per 1000 person-years) had vertigo during the 3-year follow-up period: 570 (incidence, 11.78 per 1000 person-years) from the study cohort and 1993 (incidence, 9.69 per 1000 person-years) from the comparison cohort. The adjusted hazard ratios (HR) of peripheral and central vertigo in patients with gout compared with controls during the 2-3-year follow-up were 1.17 (95% confidence interval [CI] = 1.05-1.29, p = 0.003) and 1.08 (95% CI = 0.86-1.36, p = 0.53), respectively. This is the first population-based study performed to suggest that patients with gout may have an increased risk of peripheral vertigo but not central vertigo. Benign paroxysmal positional vertigo may be the reason for the observed association; however, future studies are required to further ascertain the relationship between gout and the various causes of peripheral vertigo.

  8. Assessing population exposure for landslide risk analysis using dasymetric cartography

    NASA Astrophysics Data System (ADS)

    Garcia, Ricardo A. C.; Oliveira, Sérgio C.; Zêzere, José L.

    2016-12-01

    Assessing the number and locations of exposed people is a crucial step in landslide risk management and emergency planning. The available population statistical data frequently have insufficient detail for an accurate assessment of potentially exposed people to hazardous events, mainly when they occur at the local scale, such as with landslides. The present study aims to apply dasymetric cartography to improving population spatial resolution and to assess the potentially exposed population. An additional objective is to compare the results with those obtained with a more common approach that uses, as spatial units, basic census units, which are the best spatial data disaggregation and detailed information available for regional studies in Portugal. Considering the Portuguese census data and a layer of residential building footprint, which was used as ancillary information, the number of exposed inhabitants differs significantly according to the approach used. When the census unit approach is used, considering the three highest landslide susceptible classes, the number of exposed inhabitants is in general overestimated. Despite the associated uncertainties of a general cost-benefit analysis, the presented methodology seems to be a reliable approach for gaining a first approximation of a more detailed estimation of exposed people. The approach based on dasymetric cartography allows the spatial resolution of population over large areas to be increased and enables the use of detailed landslide susceptibility maps, which are valuable for improving the exposed population assessment.

  9. Association of Microalbuminuria with Metabolic Syndrome among Aged Population.

    PubMed

    Li, Xiao-Hong; Lin, Hai-Yan; Wang, Shu-Hua; Guan, Li-Ying; Wang, Yi-Bing

    2016-01-01

    Background. The impact of the various components of metabolic syndrome (MetS) on chronic kidney disease has been conflicting. We aim to investigate the association between MetS and microalbuminuria and identify the major contributing components of MetS that result in microalbuminuria in the Chinese aged population. Methods. A total of 674 adults aged 55-98 years (males: 266; mean age: 66.5 ± 7.5 years) were studied. MetS was defined by the 2004 Chinese Diabetes Society criteria and microalbuminuria by urine albumin-creatinine ratio (UACR) ≥3 mg/mmoL. Results. The prevalence of microalbuminuria was gradually increased with increasing number of MetS components (P < 0.05). In multivariate regression, after adjusting for age and sex, MetS was the strongest correlate of microalbuminuria (OR = 1.781, 95% CI = 1.226-2.587; P < 0.05) followed by the fasting plasma glucose (FPG) (OR = 1.217, 95% CI = 1.044-1.092; P < 0.05), systolic blood pressure (SBP) (OR = 1.011, 95% CI = 1.107-1.338; P < 0.05), and high-density lipoprotein cholesterol (HDL-C) (OR = 0.576, 95% CI = 0.348-0.953; P < 0.05). Conclusions. MetS is independently associated with microalbuminuria in the Chinese aged population. Elevated FPG is the most predominant component of metabolic syndrome associated with microalbuminuria followed by elevated SBP and reduced HDL-C.

  10. Allelic diversity associated with aridity gradient in wild emmer wheat populations.

    PubMed

    Peleg, Zvi; Saranga, Yehoshua; Krugman, Tamar; Abbo, Shahal; Nevo, Eviatar; Fahima, Tzion

    2008-01-01

    The association between allelic diversity and ecogeographical variables was studied in natural populations of wild emmer wheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell.], the tetraploid progenitor of cultivated wheat. Patterns of allelic diversity in 54 microsatellite loci were analyzed in a collection of 145 wild emmer wheat accessions representing 25 populations that were sampled across naturally occurring aridity gradient in Israel and surrounding regions. The obtained results revealed that 56% of the genetic variation resided among accessions within populations, while only 44% of the variation resided between populations. An unweighted pair-group method analysis (UPGMA) tree constructed based on the microsatellite allelic diversity divided the 25 populations into six major groups. Several groups were comprised of populations that were collected in ecologically similar but geographically remote habitats. Furthermore, genetic differentiation between populations was independent of the geographical distances. An interesting evolutionary phenomenon is highlighted by the unimodal relationship between allelic diversity and annual rainfall (r = 0.74, P < 0.0002), indicating higher allelic diversity in populations originated from habitats with intermediate environmental stress (i.e. rainfall 350-550 mm year(-1)). These results show for the first time that the 'intermediate-disturbance hypothesis', explaining biological diversity at the ecosystem level, also dominates the genetic diversity within a single species, the lowest hierarchical element of the biological diversity.

  11. Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.).

    PubMed

    Stich, Benjamin; Melchinger, Albrecht E; Heckenberger, Martin; Möhring, Jens; Schechert, Axel; Piepho, Hans-Peter

    2008-11-01

    Association mapping in multiple segregating populations (AMMSP) combines high power to detect QTL in genome-wide approaches of linkage mapping with high mapping resolution of association mapping. The main objectives of this study were to (1) examine the applicability of AMMSP in a plant breeding context based on segregating populations of various size of sugar beet (Beta vulgaris L.), (2) compare different biometric approaches for AMMSP, and (3) detect markers with significant main effect across locations for nine traits in sugar beet. We used 768 F(n) (n = 2, 3, 4) sugar beet genotypes which were randomly derived from 19 crosses among diploid elite sugar beet clones. For all nine traits, the genotypic and genotype x location interaction variances were highly significant (P < 0.01). Using a one-step AMMSP approach, the total number of significant (P < 0.05) marker-phenotype associations was 44. The identification of genome regions associated with the traits under consideration indicated that not only segregating populations derived from crosses of parental genotypes in a systematic manner could be used for AMMSP but also populations routinely derived in plant breeding programs from multiple, related crosses. Furthermore, our results suggest that data sets, whose size does not permit analysis by the one-step AMMSP approach, might be analyzed using the two-step approach based on adjusted entry means for each location without losing too much power for detection of marker-phenotype associations.

  12. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  13. GABRB2 Haplotype Association with Heroin Dependence in Chinese Population

    PubMed Central

    Kim, Yung Su; Yang, Mei; Mat, Wai-Kin; Tsang, Shui-Ying; Su, Zhonghua; Jiang, Xianfei; Ng, Siu-Kin; Liu, Siyu; Hu, Taobo; Pun, Frank; Liao, Yanhui; Tang, Jinsong; Chen, Xiaogang; Hao, Wei; Xue, Hong

    2015-01-01

    Substance dependence is a frequently observed comorbid disorder in schizophrenia, but little is known about genetic factors possibly shared between the two psychotic disorders. GABRB2, a schizophrenia candidate gene coding for GABAA receptor β2 subunit, is examined for possible association with heroin dependence in Han Chinese population. Four single nucleotide polymorphisms (SNPs) in GABRB2, namely rs6556547 (S1), rs1816071 (S3), rs18016072 (S5), and rs187269 (S29), previously associated with schizophrenia, were examined for their association with heroin dependence. Two additional SNPs, rs10051667 (S31) and rs967771 (S32), previously associated with alcohol dependence and bipolar disorder respectively, were also analyzed. The six SNPs were genotyped by direct sequencing of PCR amplicons of target regions for 564 heroin dependent individuals and 498 controls of Han Chinese origin. Interestingly, it was found that recombination between the haplotypes of all-derived-allele (H1; OR = 1.00) and all-ancestral-allele (H2; OR = 0.74) at S5-S29 junction generated two recombinants H3 (OR = 8.51) and H4 (OR = 5.58), both conferring high susceptibility to heroin dependence. Additional recombination between H2 and H3 haplotypes at S1-S3 junction resulted in a risk-conferring haplotype H5 (OR = 1.94x109). In contrast, recombination between H1 and H2 haplotypes at S3-S5 junction rescued the risk-conferring effect of recombination at S5-S29 junction, giving rise to the protective haplotype H6 (OR = 0.68). Risk-conferring effects of S1-S3 and S5-S29 crossovers and protective effects of S3-S5 crossover were seen in both pure heroin dependent and multiple substance dependence subgroups. In conclusion, significant association was found with haplotypes of the S1-S29 segment in GABRB2 for heroin dependence in Han Chinese population. Local recombination was an important determining factor for switching haplotypes between risk-conferring and protective statuses. The present study

  14. Mitochondrial DNA polymorphisms associated with longevity in the Turkish population.

    PubMed

    Guney, Ozgur; Ak, Handan; Atay, Sevcan; Ozkaya, Ali Burak; Aydin, Hikmet Hakan

    2014-07-01

    The accumulation of mutations in mitochondrial DNA is a widely recognized mechanism for aging and age related diseases. However, studies indicate that some mutations could be beneficial to longevity by slowing down the function of the electron transport chain, reducing free radical production. In this study, we re-sequenced the entire mitochondrial DNA from 50 individuals and examined aging-related variations in the Turkish population. We evaluated sequence data by comparing whole SNP frequencies, individual SNP frequencies, the effect of SNPs, SNP accumulation in certain mtDNA regions and haplotype profiles between elderly and control groups. The frequency of total mitochondrial SNPs was significantly higher in nonagenarians than controls (p=0.0094). Furthermore, non-coding, synonymous and tRNA mutations were more prevalent in the 90+ group compared to controls (p=0.0001, p<0.001, p=0.0096, respectively). A73G and C152T polymorphisms were significantly associated with longevity in the Turkish population (p=0.0086 and p=0.004, respectively). Additionally, C150T was specific to the 90+ group, but the difference failed to reach statistical significance (p=0.053). We also detected a novel transversion in the ATPase6 gene (C8899A) that was negatively associated with longevity (p=0.0016). Examining the distribution of SNPs among genes and functionally associated gene regions revealed a significant accumulation of mutations in the D-loop region and genes encoding Complex I subunits (ND1-6) (p<0.0001, p=0.0302, respectively). Moreover, there was an increase in the non-synonymous mutation frequency of Complex I genes in aged subjects (p<0.0001). Haplotype H was also significantly increased in the control group (p=0.0405). Overall, our findings support a role for mitochondrial genome variations and the functionality of oxidative phosphorylation in longevity. In this report, we sequenced the whole mtDNA of the Turkish population for the first time.

  15. Factors Associated with Gastrointestinal Parasitic Infections among Young Population in Northeast Brazil

    PubMed Central

    da Silva, Juliana Vasconcelos Lyra; Fontes, Gilberto; dos Santos, Célia Dias; dos Santos, Rafael Vital

    2016-01-01

    Background. Intestinal parasitic infections constitute a major public health problem that is frequently associated with poverty, inadequate sanitation, and the nutritional status of the population. Objective. The aim of the present study is to investigate the possible association of parasitic infections, sanitary conditions, hygiene practices, and the nutritional and socioeconomic status of a poor youth population. Methods. A cross-sectional study was conducted with 367 children and adolescents inhabiting a substandard settlement in the urban area of Maceió (Alagoas State, Brazil). Data collection included socioeconomic status, anthropometric measurements, fecal sample examinations, and laboratory blood analysis. The identification of factors associated with gastrointestinal parasitic infections was undertaken through bi- and multivariate analyses. Results. Stool sample analysis obtained from 300 individuals revealed that 204 (68%) were infected with at least one parasite species and of these 130 (63.7%) were polyparasitized. No significant associations were identified between low height for age (stunted), parasitic infections, and polyparasitism. There was also no association between family income and parasitosis. However, low socioeconomic status proved to be a potential risk factor for parasitic infections. Conclusion. Actions must be taken to improve sanitation, housing, and environmental conditions in order to eliminate the risk factors for parasitic infections, and thereby guarantee a better quality of life for this population. PMID:27528878

  16. Association analysis of food allergens.

    PubMed

    Kanagawa, Yoshiyuki; Matsumoto, Shinya; Koike, Soichi; Imamura, Tomoaki

    2009-06-01

    Food allergy patients are known to present with allergic reactions to multiple allergens, but extrapolating these associations is difficult. Data mining, a procedure that analyzes characteristic combinations among large amounts of information, is often used to analyze and predict consumer purchasing behaviour. We applied this technique to the extrapolation of food allergen associations in allergy patients. We sent 1510 families our 'Questionnaire survey for the prevention of food allergies'. Responses noting 6549 allergens came from 878 families with 1383 patients, including 402 with anaphylaxis. Some results of the survey have already been published and here we presented the results of our association analysis of combinations of food allergens. Egg, milk, wheat, peanuts, and buckwheat are the most common food allergens. The most common simultaneous combinations of these allergens were 'egg-milk', 'egg-wheat', and 'milk-wheat'. The occurrence probability of a combination (i.e. one person suffering from a certain allergen also suffers from another) is called 'confidence'. Confidence was higher for 'chicken-egg', 'abalone-salmon eggs', and 'matsutake mushroom-milk'. As well, the combinations of 'crab-shrimp', 'squid-shrimp', and 'squid-crab' also indicated higher values in a statistical examination of the occurrence probabilities of these allergen combinations (Z-score). From the results of the association analysis, we speculated that some food allergens, such as abalone, orange, salmon, chicken, pork, matsutake mushroom, peach and apple did not independently induce food allergies. We also found that combinations, such as 'crab-shrimp', 'squid-shrimp', 'squid-crab', 'chicken-beef', and 'salmon-mackerel' had strong associations.

  17. Association of Vitamin D Receptor Gene Polymorphisms with Colorectal Cancer in a Saudi Arabian Population

    PubMed Central

    Alkhayal, Khayal A.; Awadalia, Zainab H.; Vaali-Mohammed, Mansoor-Ali; Al Obeed, Omar A.; Al Wesaimer, Alanoud; Halwani, Rabih; Zubaidi, Ahmed M.

    2016-01-01

    Background Vitamin D, causally implicated in bone diseases and human malignancies, exerts its effects through binding to the vitamin D receptor (VDR). VDR is a transcription factor modulating the expression of several genes in different pathways. Genetic variants in the VDR gene have been associated with several cancers in different population including colorectal cancer. Objective To assess the association of VDR gene polymorphisms in relation with colorectal cancer (CRC) in a Saudi population. Methods The polymorphisms of VDR gene (BsmI, FokI, ApaI and TaqI) were analyzed by the polymerase chain reaction amplification of segments of interest followed by Sanger sequencing. One hundred diagnosed CRC patients and 100 healthy control subjects that were age and gender matched were recruited. Results We did not observe significant association of any of the four VDR polymorphisms with colorectal cancer risk in the overall analysis. Although not statistically significant, the AA genotype of BsmI conferred about two-fold protection against CRCs compared to the GG genotype. Stratification of the study subjects based on age and gender suggests statistically significant association of CRC with the ‘C’ allele of ApaI in patients >57 years of age at disease diagnosis and BsmI polymorphism in females. In addition, statistically significant differences were observed for the genotypic distributions of VDR-BsmI, ApaI and TaqI SNPs between Saudi Arabian population and several of the International HapMap project populations. Conclusion Despite the absence of correlation of the examined VDR polymorphisms with CRCs in the combined analysis, ApaI and BsmI loci are statistically significantly associated with CRC in elderly and female patients, respectively. These findings need further validation in larger cohorts prior to utilizing these SNPs as potential screening markers for colorectal cancers in Saudi population. PMID:27309378

  18. Association Analysis in Rice: From Application to Utilization

    PubMed Central

    Zhang, Peng; Zhong, Kaizhen; Shahid, Muhammad Qasim; Tong, Hanhua

    2016-01-01

    Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding. PMID:27582745

  19. Automated analysis of a diverse synapse population.

    PubMed

    Busse, Brad; Smith, Stephen

    2013-01-01

    Synapses of the mammalian central nervous system are highly diverse in function and molecular composition. Synapse diversity per se may be critical to brain function, since memory and homeostatic mechanisms are thought to be rooted primarily in activity-dependent plastic changes in specific subsets of individual synapses. Unfortunately, the measurement of synapse diversity has been restricted by the limitations of methods capable of measuring synapse properties at the level of individual synapses. Array tomography is a new high-resolution, high-throughput proteomic imaging method that has the potential to advance the measurement of unit-level synapse diversity across large and diverse synapse populations. Here we present an automated feature extraction and classification algorithm designed to quantify synapses from high-dimensional array tomographic data too voluminous for manual analysis. We demonstrate the use of this method to quantify laminar distributions of synapses in mouse somatosensory cortex and validate the classification process by detecting the presence of known but uncommon proteomic profiles. Such classification and quantification will be highly useful in identifying specific subpopulations of synapses exhibiting plasticity in response to perturbations from the environment or the sensory periphery.

  20. Genome-wide association study reveals regions associated with gestation length in two pig populations.

    PubMed

    Hidalgo, A M; Lopes, M S; Harlizius, B; Bastiaansen, J W M

    2016-04-01

    Reproduction traits, such as gestation length (GLE), play an important role in dam line breeding in pigs. The objective of our study was to identify single nucleotide polymorphisms (SNPs) that are associated with GLE in two pig populations. Genotypes and deregressed breeding values were available for 2081 Dutch Landrace-based (DL) and 2301 Large White-based (LW) pigs. We identified two QTL regions for GLE, one in each population. For DL, three associated SNPs were detected in one QTL region spanning 0.52 Mbp on Sus scrofa chromosome (SSC) 2. For LW, four associated SNPs were detected in one region of 0.14 Mbp on SSC5. The region on SSC2 contains the heparin-binding EGF-like growth factor (HBEGF) gene, which promotes embryo implantation and has been described to be involved in embryo survival throughout gestation. The associated SNP can be used for marker-assisted selection in the studied populations, and further studies of the HBEGF gene are warranted to investigate its role in GLE.

  1. Support for the Microgenderome: Associations in a Human Clinical Population

    PubMed Central

    Wallis, Amy; Butt, Henry; Ball, Michelle; Lewis, Donald P.; Bruck, Dorothy

    2016-01-01

    The ‘microgenderome’ provides a paradigm shift that highlights the role of sex differences in the host-microbiota interaction relevant for autoimmune and neuro-immune conditions. Analysis of cross-sectional self-report and faecal microbial data from 274 patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) suggests that commensal gut microorganisms may play both protective and deleterious roles in symptom expression. Results revealed significant sex-specific interactions between Firmicutes (Clostridium, Streptococcus, Lactobacillus and Enterococcus) and ME/CFS symptoms (including neurological, immune and mood symptoms), regardless of compositional similarity in microbial levels across the sexes. Extending animal studies, we provide support for the microgenderome in a human clinical population. Applied and mechanistic research needs to consider sex-interactions when examining the composition and function of human microbiota. PMID:26757840

  2. Sexual dimorphism is associated with population fitness in the seed beetle Callosobruchus maculatus.

    PubMed

    Rankin, Daniel J; Arnqvist, Göran

    2008-03-01

    The population consequences of sexual selection remain empirically unexplored. Comparative studies, involving extinction risk, have yielded different results as to the effect of sexual selection on population densities make contrasting predictions. Here, we investigate the relationship between sexual dimorphism (SD) and population productivity in the seed beetle Callosobruchus maculatus, using 13 populations that have evolved in isolation. Geometric morphometric methods and image analysis are employed to form integrative measures of sexual dimorphism, composed of variation in weight, size, body shape, and pigmentation. We found a positive relationship between SD and adult fitness (net adult offspring production) across our study populations, but failed to find any association between SD and juvenile fitness (egg-to-adult survival). Several mechanisms may have contributed to the pattern found, and variance in sexual selection regimes across populations, either in female choice for "good genes" or in the magnitude of direct benefits provided by their mates, would tend to produce the pattern seen. However, our results suggest that evolutionary constraints in the form of intralocus sexual conflict may have been the major generator of the relationship seen between SD and population fitness.

  3. Detailed analysis of Japanese population substructure with a focus on the southwest islands of Japan.

    PubMed

    Nishiyama, Takeshi; Kishino, Hirohisa; Suzuki, Sadao; Ando, Ryosuke; Niimura, Hideshi; Uemura, Hirokazu; Horita, Mikako; Ohnaka, Keizo; Kuriyama, Nagato; Mikami, Haruo; Takashima, Naoyuki; Mastuo, Keitaro; Guang, Yin; Wakai, Kenji; Hamajima, Nobuyuki; Tanaka, Hideo

    2012-01-01

    Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating F(ST) among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study.

  4. Genetic variants in RELN are associated with otosclerosis in a non-European population from Tunisia.

    PubMed

    Khalfallah, Ayda; Schrauwen, Isabelle; Mnaja, Malek; Fransen, Erik; Lahmar, Imed; Ealy, Megan; Dhouib, Leila; Ayadi, Hammadi; Charfedine, Ilhem; Driss, Nabil; Ghorbel, Abdelmonem; Smith, Richard J H; Masmoudi, Saber; Van Camp, Guy

    2010-09-01

    Otosclerosis is a common form of conductive hearing loss, caused by an abnormal bone remodelling in the otic capsule. Both environmental and genetic factors have been implicated in the etiology of this disease. A recent genome wide association study identified two regions associated with otosclerosis, one on chr7q22.1, located in the RELN gene, and one on chr11q13.1. A second study in four European populations has replicated the association of the RELN gene with otosclerosis. To investigate the association of these loci with otosclerosis in a non-European population, we tested 11 SNPs from the two regions in 149 unrelated Tunisian patients and 152 controls. Four SNPs were significantly associated with otosclerosis. Three SNPs are located in the RELN region and the last one is located in the region on chromosome 11. We also observed a significant interaction with gender for rs3914132. This suggests an influence of sex on the association of RELN with otosclerosis. A meta-analysis showed that the disease-associated alleles in the Tunisian sample are the same as in all previously reported associations. Our study provides additional evidence implicating RELN in the development of otosclerosis. Additional functional studies should determine the role of RELN in the physiopathology of this disease.

  5. Associations of childhood eczema severity: A US population based study

    PubMed Central

    Silverberg, Jonathan I.; Simpson, Eric L.

    2014-01-01

    Little is known about predictors of eczema severity in the US population. We sought to determine the distribution and associations of childhood eczema severity in the US. We analyzed data from the 2007 National Survey of Children's Health, a prospective questionnaire-based study of a nationally representative sample of 91,642 children (0-17yr). The prevalence of childhood eczema was 12.97% (95% confidence interval [95% CI]=12.42–13.53); 67.0% (95% CI: 64.8–69.2) had mild, 26.0% (95% CI: 23.9–28.1) moderate and 7.0% (95% CI: 5.8–8.3) severe disease. There was significant statewide-variation of the distribution of eczema severity (Rao-Scott chi square, P=0.004), with highest rates of severe disease in Northeastern and Midwestern states. In univariate models, eczema severity was increased with older age, African-American and Hispanic race/ethnicity, lower household income, oldest child in the family, home with a single mother, lower paternal/maternal education level, maternal general health, maternal/paternal emotional health, dilapidated housing and garbage on the streets. In multivariate survey logistic regression models using stepwise and backward selection, moderate–severe eczema was associated with older age, lower household income and fair or poor maternal health, but inversely associated with birthplace outside the US. These data indicate that environmental and/or lifestyle factors play an important role in eczema severity. PMID:24819283

  6. Lack of Associations between XPC Gene Polymorphisms and Neuroblastoma Susceptibility in a Chinese Population

    PubMed Central

    Zheng, Jintao; Zhang, Ruizhong; Zhu, Jinhong; Wang, Fenghua; Yang, Tianyou

    2016-01-01

    Neuroblastoma is one of the most malignant solid tumors in infants and young children. No more than 40% of neuroblastoma patients can survive for longer than five years after it has been diagnosed. XPC protein is a pivotal factor that recognizes DNA damage and starts up the nucleotide excision repair (NER) in mammalian cells. This makes up the first group to defend against the cancer. Previous studies have identified that XPC gene polymorphisms were associated with various types of cancer. However, the associations between XPC gene polymorphisms and neuroblastoma risk have not yet been studied. We investigated the associations between three XPC gene polymorphisms (rs2228001 A>C, rs2228000 C>T, and rs2229090 G>C) and neuroblastoma risk with 256 neuroblastoma patients and 531 healthy controls in a Chinese Han population. Odds ratios and 95% confidence intervals were used to access the association between these three polymorphisms and neuroblastoma risk. No significant association was detected between these three polymorphisms and neuroblastoma risk in the overall analysis as well as in the stratification analysis. These results suggest that none of these three polymorphisms may be associated with the risk of neuroblastoma in the Chinese Han population. PMID:27847809

  7. Lack of Associations between XPC Gene Polymorphisms and Neuroblastoma Susceptibility in a Chinese Population.

    PubMed

    Zheng, Jintao; Zhang, Ruizhong; Zhu, Jinhong; Wang, Fenghua; Yang, Tianyou; He, Jing; Xia, Huimin

    2016-01-01

    Neuroblastoma is one of the most malignant solid tumors in infants and young children. No more than 40% of neuroblastoma patients can survive for longer than five years after it has been diagnosed. XPC protein is a pivotal factor that recognizes DNA damage and starts up the nucleotide excision repair (NER) in mammalian cells. This makes up the first group to defend against the cancer. Previous studies have identified that XPC gene polymorphisms were associated with various types of cancer. However, the associations between XPC gene polymorphisms and neuroblastoma risk have not yet been studied. We investigated the associations between three XPC gene polymorphisms (rs2228001 A>C, rs2228000 C>T, and rs2229090 G>C) and neuroblastoma risk with 256 neuroblastoma patients and 531 healthy controls in a Chinese Han population. Odds ratios and 95% confidence intervals were used to access the association between these three polymorphisms and neuroblastoma risk. No significant association was detected between these three polymorphisms and neuroblastoma risk in the overall analysis as well as in the stratification analysis. These results suggest that none of these three polymorphisms may be associated with the risk of neuroblastoma in the Chinese Han population.

  8. Association of STAT4 polymorphisms with hepatitis B virus infection and clearance in Chinese Han population.

    PubMed

    Jiang, Xianzhong; Su, Kunkai; Tao, Jingjing; Fan, Rongli; Xu, Yi; Han, Haijun; Li, Lanjuan; Li, Ming D

    2016-11-01

    Genome-wide association study indicates that STAT4 is a plausible candidate for an association study with HBV-related liver diseases. We aimed to examine the roles of STAT4 polymorphisms on HBV-related liver diseases in a Chinese Han population. We selected 13 SNPs in STAT4 based on the HapMap database to investigate their associations in 3,033 participants. SNP rs7574865 was significantly associated with HBV infection [odds ratio (OR) 1.15; 95 % confidence interval (CI) 1.00, 1.31; P = 0.046] and clearance (OR 1.17; 95 % CI 1.02, 1.33; P = 0.028). Further, haplotype-based association analysis indicated that the haplotype CTCTT, formed by SNPs rs8179673, rs7574865, rs4274624, rs11889341, and rs10168266, was significantly associated with HBV infection (OR 0.87; 95 % CI 0.76, 0.99; P = 0.022) and clearance (OR 0.86; 95 % CI 0.75, 0.99; P = 0.018). Bioinformatics analysis of these SNPs predicted that they participate in transcriptional regulation. Taken together, our findings demonstrate that variants in STAT4 play a critical role in HBV infection and clearance in the Chinese Han population.

  9. Genetic variants in TERT are associated with risk of gastric cancer in a Chinese Han population

    PubMed Central

    Duan, Xianglong; Cao, Wei; Wang, Lijie; Liu, Sida; Liu, Zhao; Zhang, Bolun; Yang, Hua; Feng, Tian; Zhang, Jiayi; Zhang, Xiyang; Long, Yanbin; Jin, Tianbo

    2016-01-01

    Telomerase reverse transcriptase (TERT) is a gene within the cancer susceptibility region located at Chr5p15.33, which is associated with multiple cancer types. In this study, we validated the association between TERT polymorphisms and gastric cancer (GC) risk with a case-control study in a Chinese Han population. A total of 302 GC patients and 300 control individuals were recruited. We identified three single nucleotide polymorphisms (SNPs) in TERT that were associated with GC. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in logistic regression models after adjusting for age and gender to assess the association. The minor alleles of three SNPs were associated with increased GC risk inallelic model analysis. For two of the SNPs, rs10069690 and rs2853676,, the dominant and additive model frequencies were higher in GC cases compared to controls. Further haplotype analysis revealed a protective effect of haplotype “CG” of the TERT gene, while the haplotype “TA” increased GC risk.Our resultsprovide new evidence for the association between TERT and GC susceptibility in the Chinese Han population. PMID:27825130

  10. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    PubMed

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier.inra.fr/CBGP/software/baypass/.

  11. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

    PubMed Central

    Gautier, Mathieu

    2015-01-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier

  12. Identification of a novel locus associated with skin colour in African-admixed populations

    PubMed Central

    Hernandez-Pacheco, Natalia; Flores, Carlos; Alonso, Santos; Eng, Celeste; Mak, Angel C. Y.; Hunstman, Scott; Hu, Donglei; White, Marquitta J.; Oh, Sam S.; Meade, Kelley; Farber, Harold J.; Avila, Pedro C.; Serebrisky, Denise; Thyne, Shannon M.; Brigino-Buenaventura, Emerita; Rodriguez-Cintron, William; Sen, Saunak; Kumar, Rajesh; Lenoir, Michael; Rodriguez-Santana, Jose R.; Burchard, Esteban G.; Pino-Yanes, Maria

    2017-01-01

    Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10−5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10−14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10−10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10−9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation. PMID:28300201

  13. Extinction-effective population index: incorporating life-history variations in population viability analysis.

    PubMed

    Fujiwara, Masami

    2007-09-01

    Viability status of populations is a commonly used measure for decision-making in the management of populations. One of the challenges faced by managers is the need to consistently allocate management effort among populations. This allocation should in part be based on comparison of extinction risks among populations. Unfortunately, common criteria that use minimum viable population size or count-based population viability analysis (PVA) often do not provide results that are comparable among populations, primarily because they lack consistency in determining population size measures and threshold levels of population size (e.g., minimum viable population size and quasi-extinction threshold). Here I introduce a new index called the "extinction-effective population index," which accounts for differential effects of demographic stochasticity among organisms with different life-history strategies and among individuals in different life stages. This index is expected to become a new way of determining minimum viable population size criteria and also complement the count-based PVA. The index accounts for the difference in life-history strategies of organisms, which are modeled using matrix population models. The extinction-effective population index, sensitivity, and elasticity are demonstrated in three species of Pacific salmonids. The interpretation of the index is also provided by comparing them with existing demographic indices. Finally, a measure of life-history-specific effect of demographic stochasticity is derived.

  14. Variants and Haplotypes in Angiotensinogen Gene Are Associated With Plasmatic Angiotensinogen Level in Mexican Population

    PubMed Central

    Balam-Ortiz, Eros; Esquivel-Villarreal, Adolfo; Alfaro-Ruiz, Luis; Carrillo, Karol; Elizalde, Adela; Gil, Trinidad; Urushihara, Maki; Kobori, Hiroyuki; Jimenez-Sanchez, Gerardo

    2011-01-01

    Introduction The plasmatic angiotensinogen (AGT) level has been associated with essential hypertension. Linkage analysis has found a relationship between the AGT gene locus and hypertension in the Mexican-American population, but studies have failed to identify genetic variants associated with hypertension or plasma AGT levels. This study analyzes the relationship between polymorphisms in the AGT gene and plasmatic AGT levels in Mexican population. Methods Nine polymorphisms in AGT gene were genotyped, and plasma AGT level was determined by enzyme-linked immunosorbent assay. Results Differences in AGT plasma levels were associated with 2 polymorphisms: T-20G, TT = 25.3 ± 8.3 versus TG + GG = 21.6 ± 8.8 μg/mL; P = 0.008 and C3389T (T174M), CC = 25.8 ± 9.9 versus TC + TT = 20.5 ± 5.4 μg/mL; P = 0.0002. Haplotype 2 was associated with low plasma AGT (−5.1 μg/mL [95% confidence interval: −8.6 to −1.6], P = 0.004) and Haplotype 8 was associated with high plasma AGT (6.5 μg/mL [95% confidence interval: 2.5 to 10.6], P = 0.001). This association remained after adjustment for covariates. A Likelihood Ratio Test for haplotype-phenotype association adjusted for covariates resulted in χ2 = 38.9, P = 0.0005. The total effect of the haplotypes on plasma AGT level variance was 19.5%. No association was identified between haplotypes and quantitative traits of blood pressure. Conclusions Two polymorphisms (T-20G and C3389T) and 2 haplotypes (H2 and H8) showed an association with plasma AGT levels in Mexican population. PMID:21629041

  15. Dissection of the HLA association with multiple sclerosis in the founder isolated population of Sardinia.

    PubMed

    Marrosu, M G; Murru, R; Murru, M R; Costa, G; Zavattari, P; Whalen, M; Cocco, E; Mancosu, C; Schirru, L; Solla, E; Fadda, E; Melis, C; Porru, I; Rolesu, M; Cucca, F

    2001-12-01

    Several studies have indicated that multiple sclerosis (MS) is associated and linked to the major histocompatibility complex (MHC)/human leukocyte antigen (HLA) region of chromosome 6p21.3, but the exact location and nature of the primarily associated locus within the HLA complex is still controversial and largely presumptive. By linkage disequilibrium mapping, we have systematically investigated this chromosome region in the founder population of Sardinia to determine the relative associations of the various loci with MS. An overall 11.4 Mb region, which encompasses the whole HLA complex, was scanned with 19 microsatellite markers and with single nucleotide polymorphisms within 12 functional candidate genes and assessed for MS association using the extended transmission disequilibrium test (ETDT). A peak of association represented by the three adjacent DRB1, -DQA1 and -DQB1 loci was detected in the class II region. Two additional less significant areas of association were detected, respectively, in the centromeric side of the class II region at the DPB1 locus and, telomeric of the classically defined class I loci, at the D6S1683 microsatellite. Conditional ETDT analysis indicated that these regions of association could be independent of each other. Within the main peak of association, DRB1 and DQB1 contribute to the disease association independently of each other whereas DQA1 had no detectable primary genetic effects. We evaluated the haplotype distribution at the region showing the strongest association and found five DQB1-DRB1 haplotypes positively associated with MS in Sardinia. These consistently included all the haplotypes previously found associated with MS in the various human populations, thus supporting a primary effect of the products of these loci in MS. Overall these results are consistent with a multilocus model of the MHC encoded susceptibility to MS.

  16. The growth hormone receptor gene is associated with mandibular height in a Chinese population.

    PubMed

    Zhou, J; Lu, Y; Gao, X H; Chen, Y C; Lu, J J; Bai, Y X; Shen, Y; Wang, B K

    2005-11-01

    Genetic influences are important in the determination of mandibular morphology, and growth hormone receptor (GHR) is believed to have an important influence on the growth of craniofacial bone. In this study, we used quantitative trait locus methods to evaluate the relationship between craniofacial morphology and single-nucleotide polymorphisms (SNPs) in GHR in an unselected healthy Chinese population. We systematically screened the 10 exons and nearby introns of GHR and identified 6 SNPs. Using 4 SNPs as markers, we studied the relationships between genotypes and craniofacial linear measurements. Individuals with the genotype CC of polymorphism I526L had a significantly greater mandibular ramus length (condylion-gonion/ articulare-gonion) than those with genotype AC or AA. Haplotype analysis showed that there were also significant differences between the long and short mandibular height groups in an extreme population. Our results indicate that the GHR gene polymorphism I526L is associated with mandibular height in the Chinese population.

  17. Population structure and marker-trait association of salt tolerance in barley (Hordeum vulgare L.).

    PubMed

    Elakhdar, Ammar; El-Sattar, Mohamed Abd; Amer, Khairy; Rady, Assma; Kumamaru, Toshihiro

    Association mapping is becoming an important tool for identifying alleles and loci responsible for dissecting highly complex traits in barley. This study describes the population structure and marker-trait association using general linear model (GLM) analysis on a site of 60 barley genotypes, evaluated in six salinity environments. Ninety-eight SSR and SNP alleles were employed for the construction of a framework genetic map. The genetic structure analysis of the collection turned out to consist of two major sub-populations, mainly comprising hulled and naked types. LD significantly varied among the barley chromosomes, suggesting that this factor may affect the resolution of association mapping for QTL located on different chromosomes. Numerous significant marker traits were associated in different regions of the barley genome controlling salt tolerance and related traits; among them, 46 QTLs were detected on 14 associated traits over the two years, with a major QTL controlling salt tolerance on 1H, 2H, 4H and 7H, which are important factors in improving barley's salt tolerance.

  18. Point mutations associated with Leber hereditary optic neuropathy in a Latvian population

    PubMed Central

    Baumane, Kristine; Zalite, Solveiga; Ranka, Renate; Zole, Egija; Pole, Ilva; Sepetiene, Svetlana; Laganovska, Guna; Baumanis, Viesturs; Pliss, Liana

    2013-01-01

    Purpose To study mutations associated with Leber hereditary optic neuropathy (LHON) in patients suspected of having this mitochondrial disorder in a Latvian population. Additional aims were to determine the heteroplasmy status of all non-synonymous polymorphisms identified in the current study and to identify the mitochondrial haplogroups of the studied participants because these factors may contribute to the manifestation of LHON. Methods Twelve patients, including patients in two families, were enrolled in the current study. LHON was suspected based on the findings of ophthalmologic examinations. In clinically affected individuals, the presence of all previously reported LHON-associated mutations was assessed with sequencing analysis. Additionally, the SURVEYOR endonuclease assay was used to detect heteroplasmy. The mitochondrial haplogroups were identified with restriction analysis and the sequencing of hypervariable segment 1. Results In one family (mother and son), there was one primary LHON-associated mutation, G11778A. In addition, one rare previously reported LHON-associated polymorphism, A13637G, was detected in two unrelated patients. A non-synonymous polymorphism at T6253C was found in one individual. This mutation was reported in the background of the 3460 mutation among LHON patients in a Chinese population. No non-synonymous point mutations in mitochondrial DNA were found in five of the study participants. Conclusions Molecular analysis of 12 patients with suspected LHON confirmed the diagnosis in four patients and allowed the use of appropriate prophylactic measures and treatment. Further investigations and additional studies of different populations are necessary to confirm the role of the non-synonymous polymorphisms A13637G and T6253C in the manifestation of LHON and the associations of these polymorphisms with mitochondrial haplogroups and heteroplasmy. PMID:24319328

  19. Arterial stiffness is not associated with bone parameters in an elderly hyperhomocysteinemic population.

    PubMed

    van Dijk, S C; de Jongh, R T; Enneman, A W; Ham, A C; Swart, K M A; van Wijngaarden, J P; van der Zwaluw, N L; Brouwer-Brolsma, E M; van Schoor, N M; Dhonukshe-Rutten, R A M; Lips, P; de Groot, C P G M; Smulders, Y M; Blom, H J; Feskens, E J; Geleijnse, J M; van den Meiracker, A H; Mattace Raso, F U S; Uitterlinden, A G; Zillikens, M C; van der Velde, N

    2016-01-01

    Several studies have observed positive associations between bone disease and cardiovascular disease. A potential common pathway is hyperhomocysteinemia; however, to date, there is a lack of data regarding hyperhomocysteinemic populations. Therefore, we examined both cross-sectionally and longitudinally, whether there is an association between bone parameters and arterial stiffness in a hyperhomocysteinemic population, and investigated the potential common role of homocysteine (hcy) level on these associations. Cross-sectional and longitudinal data of the B-PROOF study were used (n = 519). At both baseline and 2-year follow-up we determined bone measures-incident fractures and history of fractures, bone-mineral density (BMD) and quantitative ultrasound (QUS) measurement. We also measured arterial stiffness parameters at baseline-pulse wave velocity, augmentation index and aortic pulse pressure levels with applanation tonometry. Linear regression analysis was used to examine these associations and we tested for potential interaction of hcy level. The mean age of the study population was 72.3 years and 44.3 % were female. Both cross-sectionally and longitudinally there was no association between arterial stiffness measures and BMD or QUS measurements or with incident fractures (n = 16) within the 2-3 years of follow-up. Hcy level did not modify the associations and adjustment for hcy did not change the results. Arterial stiffness was not associated with bone parameters and fractures, and hcy neither acted as a pleiotropic factor nor as a mediator. The potential association between bone and arterial stiffness is therefore not likely to be driven by hyperhomocysteinemia.

  20. Population description and its role in the interpretation of genetic association

    PubMed Central

    Yu, Joon-Ho; Crouch, Julia; Fryer-Edwards, Kelly; Burke, Wylie

    2010-01-01

    Despite calls for greater clarity and precision of population description, studies have documented persistent ambiguity in the use of race/ethnicity terms in genetic research. It is unclear why investigators tolerate such ambiguity, or what effect these practices have on the evaluation of reported associations. To explore the way that population description is used to replicate and/or extend previously reported genetic observations, we examined articles describing the association of the peroxisome proliferator-activated receptor-gamma-γ Pro12Ala polymorphism with type 2 diabetes mellitus and related phenotypes, published between 1997 and 2005. The 80 articles identified were subjected to a detailed content analysis to determine (1) how sampled populations were described, (2) whether and how the choice of sample was explained, and (3) how the allele frequency and genetic association findings identified were contextualized and interpreted. In common with previous reports, we observed a variety of sample descriptions and little explanation for the choice of population investigated. Samples of European origin were typically described with greater specificity than samples of other origin. However, findings from European samples were nearly always compared to samples described as “Caucasian” and sometimes generalized to all Caucasians or to all humans. These findings suggest that care with population description, while important, may not fully address analytical concerns regarding the interpretation of variable study outcomes or ethical concerns regarding the attribution of genetic observations to broad social groups. Instead, criteria which help investigators better distinguish justified and unjustified forms of population generalization may be required. PMID:20157827

  1. PRDM9 gene polymorphism may not be associated with defective spermatogenesis in the Chinese Han population.

    PubMed

    He, Xiao-Jin; Ruan, Jian; Du, Wei-Dong; Cao, Yun-Xia; Chen, Gang; Zuo, Xian-Bo; Peng, Yu-Wan; Wu, Huan; Song, Bing; Zhang, Xue-Jun

    2013-02-01

    PRDM9 is essential for the progression through early meiotic prophase, including double strand break repair, homologous chromosome pairing, and sex body formation during spermatogenesis. In order to evaluate the association of the PRDM9 gene variants with defective spermatogenesis in the Chinese Han population, we assessed two single nucleotide polymorphisms (SNPs) in the PRDM9 gene (rs1874165 and rs2973631) using Sequenom iplex technology in 309 cases of severely defective spermatogenesis (199 cases with non-obstructive azoospermia and 110 cases with severe oligozoospermia) and 377 controls. The allele frequencies of the SNPs were not statistically different between the study groups and the controls (P = 0.95 in rs1874165 and P = 0.80 in rs2973631, respectively). The genetic model analysis of the two SNPs indicated that these SNPs variants may not be associated with defective spermatogenesis in the Chinese Han population.

  2. Factors associated with psychological distress or common mental disorders in migrant populations across the world.

    PubMed

    Jurado, Dolores; Alarcón, Renato D; Martínez-Ortega, José M; Mendieta-Marichal, Yaiza; Gutiérrez-Rojas, Luis; Gurpegui, Manuel

    We systematically review factors associated with the presence of psychological distress or common mental disorders in migrant populations. Articles published between January 2000 and December 2014 were reviewed and 85 applying multivariate statistical analysis were selected. Common mental disorders were significantly associated with socio-demographic and psychological characteristics, as observed in large epidemiological studies on general populations. The probability of common mental disorders occurrence differs significantly among migrant groups according to their region of origin. Moreover, traumatic events prior to migration, forced, unplanned, poorly planned or illegal migration, low level of acculturation, living alone or separated from family in the host country, lack of social support, perceived discrimination, and the length of migrants' residence in the host country all increase the likelihood of CMD. In contrast, language proficiency, family reunification, and perceived social support reduce such probability. Factors related with the risk of psychiatric morbidity among migrants should be taken into account to design preventive strategies.

  3. Propionibacterium acnes strain populations in the human skin microbiome associated with acne.

    PubMed

    Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying

    2013-09-01

    The human skin microbiome has important roles in skin health and disease. However, bacterial population structure and diversity at the strain level is poorly understood. We compared the skin microbiome at the strain level and genome level of Propionibacterium acnes, a dominant skin commensal, between 49 acne patients and 52 healthy individuals by sampling the pilosebaceous units on their noses. Metagenomic analysis demonstrated that although the relative abundances of P. acnes were similar, the strain population structures were significantly different in the two cohorts. Certain strains were highly associated with acne, and other strains were enriched in healthy skin. By sequencing 66 previously unreported P. acnes strains and comparing 71 P. acnes genomes, we identified potential genetic determinants of various P. acnes strains in association with acne or health. Our analysis suggests that acquired DNA sequences and bacterial immune elements may have roles in determining virulence properties of P. acnes strains, and some could be future targets for therapeutic interventions. This study demonstrates a previously unreported paradigm of commensal strain populations that could explain the pathogenesis of human diseases. It underscores the importance of strain-level analysis of the human microbiome to define the role of commensals in health and disease.

  4. Population dynamics and associated factors of cereal aphids and armyworms under global change.

    PubMed

    Wang, Leyun; Hui, Cang; Sandhu, Hardev S; Li, Zhihong; Zhao, Zihua

    2015-12-22

    Studying the impacts of global change, which comprises largely climate and landscape changes, on agricultural pests is crucial for developing sustainable pest management. This research is focused on understanding the factors associated with population dynamics of cereal aphids and armyworms feeding on wheat in Henan province in China from 1987 to 2010. Association between changes in climate (temperature, precipitation, and relative humidity) and agricultural characteristics (wheat proportion, crop diversity, fertilizer input, and wheat yield per unit area) and damage from cereal aphids and armyworms were examined. Cereal aphid damage has been rising, while armyworm damage had no obvious trends, but with strong year-to-year fluctuations. The analysis indicates that the factors most strongly associated with the population dynamics of cereal aphids are fertilizer input and mean temperature in February, while the population dynamics of armyworms is significantly related to precipitation in May. By comparing the characteristics of these two agricultural pests, we identify possible reasons for the disparity between their associated factors, which are related to the differences in their foraging behaviour, host range, migration capacity, and life history. These results may contribute to developing ecologically based pest management for cereal aphids and armyworms under global change.

  5. The CAPN10 Gene Is Associated with Insulin Resistance Phenotypes in the Spanish Population

    PubMed Central

    Sáez, María E.; González-Sánchez, José L.; Ramírez-Lorca, Reposo; Martínez-Larrad, María T.; Zabena, Carina; González, Alejandro; Morón, Francisco J.; Ruiz, Agustín; Serrano-Ríos, Manuel

    2008-01-01

    Cardiovascular disease is the leading cause of morbidity and mortality in the industrialized world. Familial aggregation of cardiovascular risk factors is a frequent finding, but genetic factors affecting its presentation are still poorly understood. The calpain 10 gene (CAPN10) has been associated with type 2 diabetes (T2DM), a complex metabolic disorder with increased risk of cardiovascular disease. Moreover, the CAPN10 gene has been associated with the presence of metabolic syndrome (MS) in T2DM and in polycystic ovary syndrome (PCOS). In this work, we have analysed whether the polymorphisms UCSNP44, -43, -19 and -63 are related to several cardiovascular risk factors in the context of MS. Molecular analysis of CAPN10 gene was performed in 899 individuals randomly chosen from a cross-sectional population-based epidemiological survey. We have found that CAPN10 gene in our population is mainly associated with two indicators of the presence of insulin resistance: glucose levels two hours after a 75-g oral glucose tolerance test (OGTT) and HOMA values, although cholesterol levels and blood pressure values are also influenced by CAPN10 variants. In addition, the 1221/1121 haplogenotype is under-represented in individuals that fulfil the International Diabetes Federation (IDF) diagnostic criteria for MS. Our results suggest that CAPN10 gene is associated with insulin resistance phenotypes in the Spanish population. PMID:18698425

  6. The Association between the LPA Gene Polymorphism and Coronary Artery Disease in Chinese Han Population

    PubMed Central

    Song, Zi-Kai; Wu, Hai-Di; Cao, Hong-Yan

    2014-01-01

    Lp(a) has been well known as an independent risk factor for coronary artery disease (CAD). The LPA gene, as it encodes apo(a) of the Lp(a) lipoprotein particle, was associated with increased risk of CAD. The purpose of this study was to analyze the relationship between the polymorphisms of LPA gene and CAD in Chinese Han population. Five SNPs (rs1367211, rs3127596, rs6415085, rs9347438, and rs9364559) in the LPA gene were genotyped using Sequenom MassARRAY time-of-flight mass spectrometer (TOF) in 560 CAD patients as case group and 531 non-CAD subjects as control group. The numbers of these two groups were from Chinese Han ancestry. The results showed that allele (P = 0.046) and genotype (P = 0.026) of rs9364559 in the LPA gene was associated with CAD. The frequency of rs9364559 minor allele (G) in case group was obviously higher than that in control group. Results of haplotype analysis showed that 4 haplotypes which contained rs9364559-G were associated with increased risk of CAD in this population. This study explored rs9364559 in the LPA gene may be associated with the pathogenesis of CAD; and the risk of CAD might be higher in the population carrying 4 haplotypes of different blocks in the LPA gene. PMID:24790998

  7. Association of methionine synthase gene polymorphisms with wool production and quality traits in Chinese Merino population.

    PubMed

    Rong, E G; Yang, H; Zhang, Z W; Wang, Z P; Yan, X H; Li, H; Wang, N

    2015-10-01

    Methionine synthase (MTR) plays a crucial role in maintaining homeostasis of intracellular methionine, folate, and homocysteine, and its activity correlates with DNA methylation in many mammalian tissues. Our previous genomewide association study identified that 1 SNP located in the gene was associated with several wool production and quality traits in Chinese Merino. To confirm the potential involvement of the gene in sheep wool production and quality traits, we performed sheep tissue expression profiling, SNP detection, and association analysis with sheep wool production and quality traits. The semiquantitative reverse transcription PCR analysis showed that the gene was differentially expressed in skin from Merino and Kazak sheep. The sequencing analysis identified a total of 13 SNP in the gene from Chinese Merino sheep. Comparison of the allele frequencies revealed that these 13 identified SNP were significantly different among the 6 tested Chinese Merino strains ( < 0.001). Linkage disequilibrium analysis showed that SNP 3 to 11 were strongly linked in a single haplotype block in the tested population. Association analysis showed that SNP 2 to 11 were significantly associated with the average wool fiber diameter and the fineness SD and that SNP 4 to 11 were significantly associated with the CV of fiber diameter trait ( < 0.05). Single nucleotide polymorphism 2 and SNP 5 to 12 were weakly associated with wool crimp. Similarly, the haplotypes derived from these 13 identified SNP were also significantly associated with the average wool fiber diameter, fineness SD, and the CV of fiber diameter ( < 0.05). Our results suggest that is a candidate gene for sheep wool production and quality traits, and the identified SNP might be used in sheep breeding.

  8. Genetic polymorphisms in ALDH2 are associated with drug addiction in a Chinese Han population.

    PubMed

    Zhang, Chan; Ding, Heng; Cheng, Yujing; Chen, Wanlu; Li, Qi; Li, Qing; Dai, Run; Luo, Manlin

    2017-01-31

    We investigated the association between single nucleotide polymorphisms (SNPs) in ALDH2, which has been associated with alcohol dependence and several types of diseases, and the risk of drug addiction in a Chinese Han population. In a case-control study that included 692 cases and 700 healthy controls, eight SNPs in ALDH2 were selected and genotyped using the Sequenom MassARRAY platform. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression after adjusting for age and gender. We determined that rs671 is significantly associated with a 1.551-fold increased drug addiction risk (95% CI = 1.263-1.903; p < 0.001). In the genetic model analysis, we found that rs671 is associated with an increased risk of drug addiction under additive, dominant and recessive models (p < 0.001), while rs886205, rs441 and rs4646778 displayed a decreased drug addiction risk under additive and recessive model, respectively (p < 0.05). SNP rs671 remained significant after Bonferroni correction (p<0.00125). Additionally, we observed that haplotype "GTCAC" was associated with increased drug addiction risk (OR = 1.668; 95% CI, 1.328-2.094, p < 0.001); in contrast, "ATCGC" was a protective haplotype for drug addiction risk (OR = 0.444; 95% CI, 0.281-0.704, p < 0.001). Our findings showed that ALDH2 polymorphisms are significantly associated with the risk of drug addiction in the Chinese Han population.

  9. Vegetation changes associated with a population irruption by Roosevelt elk

    PubMed Central

    Starns, Heath D; Weckerly, Floyd W; Ricca, Mark A; Duarte, Adam

    2015-01-01

    Interactions between large herbivores and their food supply are central to the study of population dynamics. We assessed temporal and spatial patterns in meadow plant biomass over a 23-year period for meadow complexes that were spatially linked to three distinct populations of Roosevelt elk (Cervus elaphus roosevelti) in northwestern California. Our objectives were to determine whether the plant community exhibited a tolerant or resistant response when elk population growth became irruptive. Plant biomass for the three meadow complexes inhabited by the elk populations was measured using Normalized Difference Vegetation Index (NDVI), which was derived from Landsat 5 Thematic Mapper imagery. Elk populations exhibited different patterns of growth through the time series, whereby one population underwent a complete four-stage irruptive growth pattern while the other two did not. Temporal changes in NDVI for the meadow complex used by the irruptive population suggested a decline in forage biomass during the end of the dry season and a temporal decline in spatial variation of NDVI at the peak of plant biomass in May. Conversely, no such patterns were detected in the meadow complexes inhabited by the nonirruptive populations. Our findings suggest that the meadow complex used by the irruptive elk population may have undergone changes in plant community composition favoring plants that were resistant to elk grazing. PMID:25628868

  10. Vegetation changes associated with a population irruption by Roosevelt elk

    USGS Publications Warehouse

    Starns, H D; Weckerly, Floyd W.; Ricca, Mark; Duarte, Adam

    2015-01-01

    Interactions between large herbivores and their food supply are central to the study of population dynamics. We assessed temporal and spatial patterns in meadow plant biomass over a 23-year period for meadow complexes that were spatially linked to three distinct populations of Roosevelt elk (Cervus elaphus roosevelti) in northwestern California. Our objectives were to determine whether the plant community exhibited a tolerant or resistant response when elk population growth became irruptive. Plant biomass for the three meadow complexes inhabited by the elk populations was measured using Normalized Difference Vegetation Index (NDVI), which was derived from Landsat 5 Thematic Mapper imagery. Elk populations exhibited different patterns of growth through the time series, whereby one population underwent a complete four-stage irruptive growth pattern while the other two did not. Temporal changes in NDVI for the meadow complex used by the irruptive population suggested a decline in forage biomass during the end of the dry season and a temporal decline in spatial variation of NDVI at the peak of plant biomass in May. Conversely, no such patterns were detected in the meadow complexes inhabited by the nonirruptive populations. Our findings suggest that the meadow complex used by the irruptive elk population may have undergone changes in plant community composition favoring plants that were resistant to elk grazing.

  11. Vegetation changes associated with a population irruption by Roosevelt elk.

    PubMed

    Starns, Heath D; Weckerly, Floyd W; Ricca, Mark A; Duarte, Adam

    2015-01-01

    Interactions between large herbivores and their food supply are central to the study of population dynamics. We assessed temporal and spatial patterns in meadow plant biomass over a 23-year period for meadow complexes that were spatially linked to three distinct populations of Roosevelt elk (Cervus elaphus roosevelti) in northwestern California. Our objectives were to determine whether the plant community exhibited a tolerant or resistant response when elk population growth became irruptive. Plant biomass for the three meadow complexes inhabited by the elk populations was measured using Normalized Difference Vegetation Index (NDVI), which was derived from Landsat 5 Thematic Mapper imagery. Elk populations exhibited different patterns of growth through the time series, whereby one population underwent a complete four-stage irruptive growth pattern while the other two did not. Temporal changes in NDVI for the meadow complex used by the irruptive population suggested a decline in forage biomass during the end of the dry season and a temporal decline in spatial variation of NDVI at the peak of plant biomass in May. Conversely, no such patterns were detected in the meadow complexes inhabited by the nonirruptive populations. Our findings suggest that the meadow complex used by the irruptive elk population may have undergone changes in plant community composition favoring plants that were resistant to elk grazing.

  12. Using Christmas Bird Count data in analysis of population change

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.

    2002-01-01

    The scientific credibility of Christmas Bird Count (CBC) results depend on the development and implementation of appropriate methods of statistical analysis. The key to any successful analysis of CBC data is to begin with a careful review of how the limitations of the data are likely to influence the results of the analysis, then to choose methods of analysis that accommodate as much as possible the limitations of the survey. For our analyses of CBC data, we develop a flexible model for effort adjustment and use information from the data to guide the selection of the best model. We include geographic structuring to accommodate the regional variation in number of samples, use a model that allows for overdispersed poisson data appropriate for counts, and employ empirical Bayes procedures to accommodate differences in quality of information in regional summaries. This generalized linear model approach is very flexible, and can be applied to a variety of studies focused on factors influencing wintering bird populations. In particular, the model can be easily modified to contain covariates, allowing for assessment of associations between CBC counts and winter weather, disturbance, and a variety of other environmental factors. These new survey analysis methods have added value in that they provide insights into changes in survey design that can enhance the value of the information. The CBC has been extremely successful as a tool for increasing public interest in birding and bird conservation. Use of the information for bird conservation creates new demands on quality of information, and it is important to maintain a dialogue between users of the information, information needs for the analyses, and survey coordinators and participants. Our work as survey analysts emphasizes the value and limitations of existing data, and provides some indications of what features of the survey could be modified to make the survey a more reliable source of bird population data. Surveys

  13. Genome-Wide Association Study Identifies Variants in PMS1 Associated with Serum Ferritin in a Chinese Population

    PubMed Central

    Gao, Yong; Tan, Aihua; Wu, Chunlei; Lu, Zheng; Yang, Xiaobo; Zhang, Shijun; Hu, Yanlin; Qin, Xue; Li, Jianling; Chen, Gang; Xu, Jianfeng; Mo, Zengnan; Zhang, Haiying

    2014-01-01

    Only a small proportion of genetic variation in serum ferritin has been explained by variant genetic studies, and genome-wide association study (GWAS) for serum ferritin has not been investigated widely in Chinese population. We aimed at exploring the novel genetic susceptibility to serum ferritin, and performed this two stage GWAS in a healthy Chinese population of 3,495 men aged 20–69 y, including 1,999 unrelated subjects in the first stage and 1,496 independent individuals in the second stage. Serum ferritin was measured with electrochemiluminescence immunoassay, and DNA samples were collected for genotyping. A total of 1,940,243 SNPs were tested by using multivariate linear regression analysis. After adjusting for population stratification, age and BMI, the rs5742933 located in the 5′UTR region of PMS1 gene on chromosome 2 was the most significantly associated with ferritin concentrations (P-combined = 2.329×10−10) (β = −0.11, 95% CI: −0.14, −0.07). Moreover, this marker was about 200kb away from the candidate gene SLC40A1 which is responsible for iron export. PMS1 gene was the novel genetic susceptibility to serum ferritin in Chinese males and its relation to SLC40A1 needs further study. PMID:25162662

  14. Association between RTEL1 gene polymorphisms and COPD susceptibility in a Chinese Han population

    PubMed Central

    Ding, Yipeng; Xu, Heping; Yao, Jinjian; Xu, Dongchuan; He, Ping; Yi, Shengyang; Li, Quanni; Liu, Yuanshui; Wu, Cibing; Tian, Zhongjie

    2017-01-01

    Objective We investigated the association between single-nucleotide polymorphisms in regulation of telomere elongation helicase 1 (RTEL1), which has been associated with telomere length in several brain cancers and age-related diseases, and the risk of chronic obstructive pulmonary disease (COPD) in a Chinese Han population. Methods In a case–control study that included 279 COPD cases and 290 healthy controls, five single-nucleotide polymorphisms in RTEL1 were selected and genotyped using the Sequenom MassARRAY platform. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression after adjusting for age and gender. Results In the genotype model analysis, we determined that rs4809324 polymorphism had a decreased effect on the risk of COPD (CC versus TT: OR =0.28; 95% CI =0.10–0.82; P=0.02). In the genetic model analysis, we found that the “C/C” genotype of rs4809324 was associated with a decreased risk of COPD based on the codominant model (OR =0.33; 95% CI =0.13–0.86; P=0.022) and recessive model (OR =0.32; 95% CI =0.12–0.80; P=0.009). Conclusion Our data shed new light on the association between genetic polymorphisms of RTEL1 and COPD susceptibility in the Chinese Han population. PMID:28360516

  15. Genome-wide association of serum bilirubin levels in Korean population.

    PubMed

    Kang, Tae-Wook; Kim, Hee-Jin; Ju, Hyoungseok; Kim, Jeong-Hwan; Jeon, Yeo-Jin; Lee, Han-Chul; Kim, Ka-Kyung; Kim, Jong-Won; Lee, Siwoo; Kim, Jong Yeol; Kim, Seon-Young; Kim, Yong Sung

    2010-09-15

    A large-scale, genome-wide association study was performed to identify genetic variations influencing serum bilirubin levels using 8841 Korean individuals. Significant associations were observed at UGT1A1 (rs11891311, P = 4.78 x 10(-148)) and SLCO1B3 (rs2417940, P = 1.03 x 10(-17)), which are two previously identified loci. The two single-nucleotide polymorphisms (SNPs) were replicated (rs11891311, P = 3.18 x 10(-15)) or marginally significant (rs2417940, P = 8.56 x 10(-4)) in an independent cohort of 1096 individuals. In a conditional analysis adjusted for the top UGT1A1 variant (rs11891311), another variant in UGT1A1 (rs4148323, P = 1.22 x 10(-121)) remained significant; this suggests that in UGT1A1 at least two independent genetic variations influence the bilirubin levels in the Korean population. The protein coding variant rs4148323, which is monomorphic in European-derived populations, may be specifically associated with serum bilirubin levels in Asians (P = 2.56 x 10(-70)). The SLCO1B3 variant (rs2417940, P = 1.67 x 10(-18)) remained significant in a conditional analysis for the top UGT1A1 variant. Interestingly, there were significant differences in the associated variations of SLCO1B3 between Koreans and European-derived populations. While the variant rs2417940 at intron 7 of SLCO1B3 was more significantly associated in Koreans, variants rs17680137 (P = 0.584) and rs2117032 (P = 2.76 x 10(-5)), two of the top-ranked SNPs in European-derived populations, did not reach the genome-wide significance level. Also, variants in SLCO1B1 did not reach genome-wide significance in Koreans. Our result supports the idea that there are considerable ethnic differences in genetic association of bilirubin levels between Koreans and European-derived populations.

  16. Meta-analysis genomewide association of pork quality traits: ultimate pH and shear force

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is common practice to perform genome-wide association analysis (GWA) using a genomic evaluation model of a single population. Joint analysis of several populations is more difficult. An alternative to joint analysis could be the meta-analysis (MA) of several GWA from independent genomic evaluatio...

  17. Global Population Genetic Analysis of Aspergillus fumigatus

    PubMed Central

    Ashu, Eta Ebasi; Hagen, Ferry; Chowdhary, Anuradha

    2017-01-01

    ABSTRACT Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen capable of causing invasive aspergillosis, a globally distributed disease with a mortality rate of up to 90% in high-risk populations. Effective control and prevention of this disease require a thorough understanding of its epidemiology. However, despite significant efforts, the global molecular epidemiology of A. fumigatus remains poorly understood. In this study, we analyzed 2,026 A. fumigatus isolates from 13 countries in four continents using nine highly polymorphic microsatellite markers. Genetic cluster analyses suggest that our global sample of A. fumigatus isolates belonged to eight genetic clusters, with seven of the eight clusters showing broad geographic distributions. We found common signatures of sexual recombination within individual genetic clusters and clear evidence of hybridization between several clusters. Limited but statistically significant genetic differentiations were found among geographic and ecological populations. However, there was abundant evidence for gene flow at the local, regional, and global scales. Interestingly, the triazole-susceptible and triazole-resistant populations showed different population structures, consistent with antifungal drug pressure playing a significant role in local adaptation. Our results suggest that global populations of A. fumigatus are shaped by historical differentiation, contemporary gene flow, sexual reproduction, and the localized antifungal drug selection that is driving clonal expansion of genotypes resistant to multiple triazole drugs. IMPORTANCE The genetic diversity and geographic structure of the human fungal pathogen A. fumigatus have been the subject of many studies. However, most previous studies had relatively limited sample ranges and sizes and/or used genetic markers with low-level polymorphisms. In this paper, we characterize a global collection of strains of A. fumigatus using a panel of 9 highly

  18. Population viability analysis of the Endangered shortnose sturgeon

    SciTech Connect

    Jager, Yetta; Bevelhimer, Mark S; Peterson, Douglas L.

    2011-07-01

    This study used population viability analysis (PVA) to partition the influences of potential threats to the endangered shortnose sturgeon (Acipenser brevirostrum). A workshop brought together experts to help identify potential threats including groundwater withdrawal, poor water quality, saltwater intrusion, mercury effects, harvest as by-catch, and sedimentation of spawning habitat. During the course of the project, we eliminated some threats and added new ones. Groundwater withdrawal was dismissed after a study failed to identify connection with groundwater and the majority of pumping is from a confined aquifer. We also eliminated activities on Fort Stewart as influences on spawning habitat because any successful spawning must occur upstream of Fort Stewart. We added climate change to the list of threats based on our assessment of temperature effects and expectations of sea-level rise. Our study highlighted the role of populations in nearby rivers in providing metapopulation support, raising the concern that the population in the Ogeechee River acts as a demographic sink. As part of this study, we carried out a field sampling study to analyze effects of training activities on headwater streams. We developed a new methodology for sampling design as part of this effort and used a mixed-modeling approach to identify relationships between land cover-land use, including those associated with military training activity and water quality. We found that tank training was associated with higher suspended sediment and equipment training was associated with higher organic carbon) and water quality. We detected effects of training on suspended sediment and organic carbon. We also carried out a field sampling effort in the Canoochee and Ogeechee Rivers. In the Ogeechee River, we found that dissolved oxygen in 40% of measurements during summer were below 4 mg L-1. To evaluate mercury as a potential threat, we developed a mercury uptake model and analyzed mercury levels in

  19. A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil.

    PubMed

    Coelho, A V C; Moura, R R; Cavalcanti, C A J; Guimarães, R L; Sandrin-Garcia, P; Crovella, S; Brandão, L A C

    2015-03-31

    Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples' genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries. We tested the feasibility of a subset of the 12 most informative markers from a previously established study to estimate influence from three ancestral populations: European, African and Amerindian. The results showed that in a sample with a diverse ethnicity (N = 822) derived from 1000 Genomes database, the 12 AIMs had the same capacity to estimate ancestries when compared to the original set of 128 AIMs, since estimates from the two panels were closely correlated. Thus, these 12 SNPs were used to estimate ancestry in a new sample (N = 192) from an admixed population in Recife, Northeast Brazil. The ancestry estimates from Recife subjects were in accordance with previous studies, showing that Northeastern Brazilian populations show great influence from European ancestry (59.7%), followed by African (23.0%) and Amerindian (17.3%) ancestries. Ethnicity self-classification according to skin-color was confirmed to be a poor indicator of population substructure in Brazilians, since ancestry estimates overlapped between classifications. Thus, our streamlined panel of 12 markers may substitute panels with more markers, while retaining the capacity to control for population substructure and admixture, thereby reducing sample processing time.

  20. Projecting the success of plant restoration with population viability analysis

    USGS Publications Warehouse

    Bell, T.J.; Bowles, M.L.; McEachern, A.K.; Brigham, C.A.; Schwartz, M.W.

    2003-01-01

    Conserving viable populations of plant species requires that they have high probabilities of long-term persistence within natural habitats, such as a chance of extinction in 100 years of less than 5% (Menges 1991, 1998; Brown 1994; Pavlik 1994; Chap. 1, this Vol.). For endangered and threatened species that have been severely reduces in range and whose habitats have been fragmented, important species conservation strategies may include augmenting existing populations or restoring new viable populations (Bowles and Whelan 1994; Chap. 2, this Vol.). Restoration objectives may include increasing population numbers to reduce extinction probability, deterministic manipulations to develop a staged cohort structure, or more complex restoration of a desired genetic structure to allow outcrossing or increase effective population size (DeMauro 1993, 1994; Bowles et al. 1993, 1998; Pavlik 1994; Knapp and Dyer 1998; Chap. 2, this Vol.). These efforts may require translocation of propagules from existing (in situ) populations, or from ex situ botanic gardens or seed storage facilities (Falk et al. 1996; Guerrant and Pavlik 1998; Chap. 2, this Vol.). Population viability analysis (PVA) can provide a critical foundation for plant restoration, as it models demographic projections used to evaluate the probability of population persistence and links plant life history with restoration strategies. It is unknown how well artificially created populations will meet demographic modeling requirements (e.g., due to artificial cohort transitions) and few, if any, PVAs have been applied to restorations. To guide application of PVA to restored populations and to illustrate potential difficulties, we examine effects of planting different life stages, model initial population sizes needed to achieve population viability, and compare demographic characteristics between natural and restored populations. We develop and compare plant population restoration viability analysis (PRVA) case studies of

  1. The Disk Population of the Upper Scorpius Association

    NASA Astrophysics Data System (ADS)

    Luhman, K. L.; Mamajek, E. E.

    2012-10-01

    We present photometry at 3-24 μm for all known members of the Upper Scorpius association (τ ~ 11 Myr) based on all images of these objects obtained with the Spitzer Space Telescope and the Wide-field Infrared Survey Explorer. We have used these data to identify the members that exhibit excess emission from circumstellar disks and estimate the evolutionary stages of these disks. Through this analysis, we have found ~50 new candidates for transitional, evolved, and debris disks. The fraction of members harboring inner primordial disks is <~ 10% for B-G stars (M > 1.2 M ⊙) and increases with later types to a value of ~25% at gsimM5 (M <~ 0.2 M ⊙), in agreement with the results of previous disk surveys of smaller samples of Upper Sco members. These data indicate that the lifetimes of disks are longer at lower stellar masses and that a significant fraction of disks of low-mass stars survive for at least ~10 Myr. Finally, we demonstrate that the distribution of excess sizes in Upper Sco and the much younger Taurus star-forming region (τ ~ 1 Myr) is consistent with the same, brief timescale for clearing of inner disks.

  2. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    PubMed Central

    2011-01-01

    Background Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping

  3. Positive association between PPARD rs2016520 polymorphism and coronary heart disease in a Han Chinese population.

    PubMed

    Ye, H D; Li, Y R; Hong, Q X; Zhou, A N; Zhao, Q L; Xu, L M; Xu, M Q; Xu, X T; Tang, L L; Dai, D J; Jiang, D J; Huang, Y; Wang, D W; Duan, S W

    2015-06-11

    PPARD encodes peroxisome proliferator-activated re-ceptor delta, which has been shown to play an important role in control-ling lipid metabolism and atherosclerosis. In this case-control study, we explored the relationship between PPARD rs2016520 polymorphism and coronary heart disease (CHD) in a Han Chinese population. A to-tal of 657 CHD cases and 640 controls were included in the associa-tion study. rs2016520 polymorphism genotyping was performed using the melting temperature-shift polymerase chain reaction method. The PPARD rs2016520-G allele reduced CHD risk by 17.9% (χ(2) = 5.061, P = 0.025, OR = 0.821, 95%CI = 0.692-0.975). Furthermore, a signifi-cant difference in CHD risk was observed for the PPARD rs2016520 polymorphism in the dominant model (AG + GG vs AA: χ(2) = 4.751, degrees of freedom (df) = 1, P = 0.029, OR = 0.784, 95%CI = 0.631- 0.976). Analysis by age suggested that the G-allele decreased CHD risk by 14.8% in ages greater than 65 years (χ(2) = 4.446, P = 0.035, OR = 0.852, 95%CI = 0.684-1.060). In contrast, meta-analysis of PPARD rs2016520 among 3732 cases and 5042 controls revealed no associa-tion between PPARD rs2016520 and CHD (P = 0.19). We found that the PPARD rs2016520-GG genotype decreased CHD risk in a Han Chinese population. Moreover, we found an association between serum high-density lipoprotein cholesterol level and PPARD rs2016520 in senior individuals aged ≥ 65 years. The meta-analysis revealed no association between PPARD rs2016520 and CHD, suggesting ethnic differences in the association between the PPARD locus and CHD.

  4. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population

    PubMed Central

    Kornilov, Sergey A.; Rakhlin, Natalia; Koposov, Roman; Lee, Maria; Yrigollen, Carolyn; Caglayan, Ahmet Okay; Magnuson, James S.; Mane, Shrikant; Chang, Joseph T.

    2016-01-01

    BACKGROUND AND OBJECTIVE: Developmental language disorder (DLD) is a highly prevalent neurodevelopmental disorder associated with negative outcomes in different domains; the etiology of DLD is unknown. To investigate the genetic underpinnings of DLD, we performed genome-wide association and whole exome sequencing studies in a geographically isolated population with a substantially elevated prevalence of the disorder (ie, the AZ sample). METHODS: DNA samples were collected from 359 individuals for the genome-wide association study and from 12 severely affected individuals for whole exome sequencing. Multifaceted phenotypes, representing major domains of expressive language functioning, were derived from collected speech samples. RESULTS: Gene-based analyses revealed a significant association between SETBP1 and complexity of linguistic output (P = 5.47 × 10−7). The analysis of exome variants revealed coding sequence variants in 14 genes, most of which play a role in neural development. Targeted enrichment analysis implicated myocyte enhancer factor–2 (MEF2)-regulated genes in DLD in the AZ population. The main findings were successfully replicated in an independent cohort of children at risk for related disorders (n = 372). CONCLUSIONS: MEF2-regulated pathways were identified as potential candidate pathways in the etiology of DLD. Several genes (including the candidate SETBP1 and other MEF2-related genes) seem to jointly influence certain, but not all, facets of the DLD phenotype. Even when genetic and environmental diversity is reduced, DLD is best conceptualized as etiologically complex. Future research should establish whether the signals detected in the AZ population can be replicated in other samples and languages and provide further characterization of the identified pathway. PMID:27016271

  5. Association of ENPP1 gene polymorphisms with hand osteoarthritis in a Chuvasha population

    PubMed Central

    Suk, Eun-Kyung; Malkin, Ida; Dahm, Stefan; Kalichman, Leonid; Ruf, Nico; Kobyliansky, Eugene; Toliat, Mohammad; Rutsch, Frank; Nürnberg, Peter; Livshits, Gregory

    2005-01-01

    Periarticular calcification is a common attendant symptom of generalized arterial calcification of infancy, a rare Mendelian disorder caused by mutations of the gene coding for ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1). This prompted us to perform a family-based association study to test the hypothesis that genetic variation at the ENPP1 locus is involved in the etiology of osteoarthritis of the hand. The study population comprised 126 nuclear families with 574 adult individuals living in small villages in the Chuvasha and Bashkirostan autonomies of the Russian Federation. The extent of osteoarthritis was determined by analyzing plain hand radiographs. The outcome of a principal component analysis of osteoarthritis scores of a total of 28 joints of both hands was used as a primary phenotype in this study. Maximum likelihood estimates of the variance component analysis revealed a substantial contribution of genetic factors to the overall trait variance of about 25% in this homogeneous population. Three short tandem repeat (STR) polymorphisms – one intragenic and two flanking markers – and four single-nucleotide polymorphisms were tested. The markers tagged the ENPP1 locus at nearly equal intervals. We used three different transmission disequilibrium tests and obtained highly significant association signals. Alleles of the upstream microsatellite marker as well as several single-nucleotide polymorphism haplotypes consistently revealed the association. Thus, our data highlights variability of ENPP1 as an important genetic factor in the pathogenesis of idiopathic osteoarthritis. PMID:16207325

  6. No evidence for the association of DRD4 with ADHD in a Taiwanese population within-family study

    PubMed Central

    Brookes, Keeley-Joanne; Xu, Xiaohui; Chen, Chih-Ken; Huang, Yu-Shu; Wu, Yu-Yu; Asherson, Philip

    2005-01-01

    Background Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent and highly heritable childhood disorder. The dopamine D4 receptor (DRD4) gene has shown a genetic association with ADHD in Caucasian populations with meta-analysis indicating a small but significant effect across datasets. It remains uncertain whether this association can be generalised to non-Caucasian ethnic groups. Here we investigate two markers within the DRD4 gene in a Taiwanese population, the exon 3 variable number tandem repeat (VNTR) and a 5' 120 base-pair duplication. Methods Within-family transmission disequilibrium tests of association of the 5' 120 base-pair duplication, and exon 3 VNTR in a Taiwanese population. Results No evidence of association of ADHD with either polymorphism in this population was observed. Conclusion The DRD4 gene markers investigated were not found to be associated with ADHD in this Taiwanese sample. Further work in Taiwanese and other Asian populations will therefore be required to establish whether the reports of association of DRD4 genetic variants in Caucasian samples can be generalised to Asian populations. PMID:16143039

  7. PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population.

    PubMed

    Aslibekyan, Stella; Dashti, Hassan S; Tanaka, Toshiko; Sha, Jin; Ferrucci, Luigi; Zhi, Degui; Bandinelli, Stefania; Borecki, Ingrid B; Absher, Devin M; Arnett, Donna K; Ordovas, Jose M

    2014-11-01

    Sunlight exposure has been shown to alter DNA methylation patterns across several human cell-types, including T-lymphocytes. Since epigenetic changes establish gene expression profiles, changes in DNA methylation induced by sunlight exposure warrant investigation. The purpose of this study was to assess the effects of sunlight exposure on CD4+ T-cell methylation patterns on an epigenome-wide scale in a North American population of European origin (n=991). In addition, we investigated the genetic contribution to epigenetic variation (methylQTL). We used linear regression to test the associations between methylation scores at 461,281 cytosine-phosphate-guanine (CpG) sites and sunlight exposure, followed by a genome-wide association analysis (methylQTL) to test for associations between methylation at the top CpG locus and common genetic variants, assuming an additive genetic model. We observed an epigenome-wide significant association between sunlight exposure and methylation status at cg26930596 (p=9.2×10(-8)), a CpG site located in protein kinase C zeta (PRKCZ), a gene previously shown to be entrained by light. MethylQTL analysis resulted in significant associations between cg26930596 and two intergenic single nucleotide polymorphisms on chromosome 3, rs4574216 (p=1.5×10(-10)) and rs4405858 (p=1.9×10(-9)). These common genetic variants reside downstream of WWTR1, a transcriptional co-activator of PRKCZ. Associations observed in the North American population, however, did not replicate in an independent Mediterranean cohort. Our preliminary results support the role of sunlight exposure in epigenetic processes, and lay the groundwork for future studies of the molecular link between sunlight and physiologic processes such as tumorigenesis and metabolism.

  8. Evaluation of mixed-population flood-frequency analysis

    USGS Publications Warehouse

    Murphy, P.J.

    2001-01-01

    A mixed population of flood flows was shown to cause quality-of-fit problems if a single-population flood-frequency distribution was used to describe the flood data. The three populations in this mix were "ordinary," tropical cyclone, and ice-jam-release floods. Parametric descriptions of the single and separated flood populations were evaluated using probability-plot correlation-coefficient tests. These tests quantified how well the flood-probability distributions agreed with plotting-position descriptions of the data and quantified the differences due to the mixed-population analysis. High outliers caused the high skewness found in the single- population analyses. The tropical cyclone component was underestimated by single-population analyses at gauging stations in Massachusetts that had little data.

  9. Association between Apolipoprotein E genotype and cerebral palsy is not confirmed in a Caucasian population.

    PubMed

    McMichael, Gai L; Gibson, Catherine S; Goldwater, Paul N; Haan, Eric A; Priest, Kevin; Dekker, Gustaaf A; MacLennan, Alastair H

    2008-11-01

    Apolipoprotein E (APOE) plays a significant role in lipid metabolism and has been implicated in the growth and repair of injured neurons. Two small studies have suggested an association between APOE genotype and cerebral palsy. We investigated if APOE genotype is associated with an increased risk for cerebral palsy, influences the type of cerebral palsy or interacts with prenatal viral infection to influence risk of cerebral palsy. The population-based case-control study comprised newborn screening cards of 443 Caucasian patients with cerebral palsy and 883 Caucasian matched controls. APOE genotyping was performed on DNA extracted from dried blood spots. Allelic and genotypic frequencies did not differ between cases and controls and combined frequencies were 0.10 (epsilon2), 0.76 (epsilon3), 0.14 (epsilon4), 0.03 (epsilon2/epsilon2), 0.10 (epsilon2/epsilon3), 0.03 (epsilon2/epsilon4), 0.02 (epsilon4/epsilon4), 0.21 (epsilon3/epsilon4), 0.61 (epsilon3/epsilon3). APOE genotype was correlated with cerebral palsy, type of cerebral palsy, gestation at birth and the presence of viral nucleic acids detected in previous work. Analysis by gestational age (all gestational ages, >/=37, 32-36 and <32 weeks) and type of cerebral palsy (all types, diplegia, hemiplegia and quadriplegia) showed no association between APOE genotype and cerebral palsy in this Caucasian population. An association between prenatal viral infection, APOE genotype and cerebral palsy was not demonstrated. These results did not confirm an association between APOE genotype, cerebral palsy, type of cerebral palsy and prenatal infection in a Caucasian population. Given the low frequency of APOE epsilon2 and some of the heterozygote and homozygote combinations in this study, a larger study is assessing this further.

  10. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification.

    PubMed

    Zhang, Lei; Li, Jian; Pei, Yu-Fang; Liu, Yongjun; Deng, Hong-Wen

    2009-11-01

    Traditional transmission disequilibrium test (TDT) based methods for genetic association analyses are robust to population stratification at the cost of a substantial loss of power. We here describe a novel method for family-based association studies that corrects for population stratification with the use of an extension of principal component analysis (PCA). Specifically, we adopt PCA on unrelated parents in each family. We then infer principal components for children from those for their parents through a TDT-like strategy. Two test statistics within the variance-components model are proposed for association tests. Simulation results show that the proposed tests have correct type I error rates regardless of population stratification, and have greatly improved power over two popular TDT-based methods: QTDT and FBAT. The application to the Genetic Analysis Workshop 16 (GAW16) data sets attests to the feasibility of the proposed method.

  11. Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models

    PubMed Central

    Chen, Han; Wang, Chaolong; Conomos, Matthew P.; Stilp, Adrienne M.; Li, Zilin; Sofer, Tamar; Szpiro, Adam A.; Chen, Wei; Brehm, John M.; Celedón, Juan C.; Redline, Susan; Papanicolaou, George J.; Thornton, Timothy A.; Laurie, Cathy C.; Rice, Kenneth; Lin, Xihong

    2016-01-01

    Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM’s constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs. PMID:27018471

  12. Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models.

    PubMed

    Chen, Han; Wang, Chaolong; Conomos, Matthew P; Stilp, Adrienne M; Li, Zilin; Sofer, Tamar; Szpiro, Adam A; Chen, Wei; Brehm, John M; Celedón, Juan C; Redline, Susan; Papanicolaou, George J; Thornton, Timothy A; Laurie, Cathy C; Rice, Kenneth; Lin, Xihong

    2016-04-07

    Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM's constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs.

  13. Association of hypertension with coronary artery disease onset in the Lebanese population.

    PubMed

    Milane, Aline; Abdallah, Jad; Kanbar, Roy; Khazen, Georges; Ghassibe-Sabbagh, Michella; Salloum, Angelique K; Youhanna, Sonia; Saad, Aline; El Bayeh, Hamid; Chammas, Elie; Platt, Daniel E; Hager, Jörg; Gauguier, Dominique; Zalloua, Pierre; Abchee, Antoine

    2014-01-01

    The onset of coronary artery disease (CAD) is influenced by cardiovascular risk factors that often occur in clusters and may build on one another. The objective of this study is to examine the relationship between hypertension and CAD age of onset in the Lebanese population. This retrospective analysis was performed on data extracted from Lebanese patients (n = 3,753). Logistic regression examined the association of hypertension with the age at CAD diagnosis after controlling for other traditional risk factors. The effect of antihypertensive drugs and lifestyle changes on the onset of CAD was also investigated. Results showed that hypertension is associated with late onset CAD (OR=0.656, 95% CI=0.504-0.853, p=0.001). Use of antihypertensive drugs showed a similar association with delayed CAD onset. When comparing age of onset in CAD patients with traditional risk factors such as hypertension, diabetes, hyperlipidemia, obesity, smoking and family history of CAD, the age of onset was significantly higher for patients with hypertension compared to those with any of the other risk factors studied (p < 0.001). In conclusion, hypertension and its treatment are associated with late coronary atherosclerotic manifestations in Lebanese population. This observation is currently under investigation to clarify its genetic and/or environmental mechanisms.

  14. Association between PARP-1 V762A Polymorphism and Breast Cancer Susceptibility in Saudi Population

    PubMed Central

    Pathan, Akbar Ali Khan; Shaik, Jilani P.; Alabdulkarim, Huda A.; Semlali, Abdelhabib; Bazzi, Mohammad D.; Parine, Narasimha Reddy

    2013-01-01

    Genetic aberrations of DNA repair enzymes are known to be common events and to be associated with different cancer entities. Aim of the following study was to analyze the genetic association of rs1136410 (Val762Ala) in PARP1 gene with the risk of breast cancer using genotypic assays and insilico structural predictions. Genotypic analysis of individual locus showed statistically significant association of Val762Ala with increased susceptibility to breast cancer. Protein structural analysis was performed with Val762Ala variant allele and compared with the predicted native protein structure. Protein prediction analysis showed that this nsSNP may cause changes in the protein structure and it is associated with the disease. In addition to the native and mutant 3D structures of PARP1 were also analyzed using solvent accessibility models for further protein stability confirmation. Taken together, this the first study that confirmed Val762Ala variant has functional effect and structural impact on the PARP1 and may play an important role in breast cancer progression in Saudi population. PMID:24392019

  15. Association between PARP-1 V762A polymorphism and breast cancer susceptibility in Saudi population.

    PubMed

    Alanazi, Mohammad; Pathan, Akbar Ali Khan; Abduljaleel, Zainularifeen; Arifeen, Zainul; Shaik, Jilani P; Alabdulkarim, Huda A; Semlali, Abdelhabib; Bazzi, Mohammad D; Parine, Narasimha Reddy

    2013-01-01

    Genetic aberrations of DNA repair enzymes are known to be common events and to be associated with different cancer entities. Aim of the following study was to analyze the genetic association of rs1136410 (Val762Ala) in PARP1 gene with the risk of breast cancer using genotypic assays and insilico structural predictions. Genotypic analysis of individual locus showed statistically significant association of Val762Ala with increased susceptibility to breast cancer. Protein structural analysis was performed with Val762Ala variant allele and compared with the predicted native protein structure. Protein prediction analysis showed that this nsSNP may cause changes in the protein structure and it is associated with the disease. In addition to the native and mutant 3D structures of PARP1 were also analyzed using solvent accessibility models for further protein stability confirmation. Taken together, this the first study that confirmed Val762Ala variant has functional effect and structural impact on the PARP1 and may play an important role in breast cancer progression in Saudi population.

  16. Population and genomic lessons from genetic analysis of two Indian populations.

    PubMed

    Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

    2014-10-01

    Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

  17. Factors associated with spontaneous clearance of hepatitis C virus in Chinese population.

    PubMed

    Kong, Fei; Pan, Yu; Chi, Xiumei; Wang, Xiaomei; Chen, Linjiao; Lv, Juan; Sun, Haibo; Wu, Ruihong; Jin, Jinglan; Yu, Ge; Ma, Zhenhua; Wang, Yang; Huang, Xinxing; Li, Hua; Bai, Yang; Jia, Jing; Minuk, Gerald Y; Zhong, Jin; Sun, Bing; Jiang, Jing; Niu, Junqi

    2014-01-01

    Hepatitis C virus (HCV) infections spontaneously clear in approximately 15-45% of infected individuals. Factors which influence spontaneous HCV clearance remain to be identified. The purpose of the present study was to identify variables associated with spontaneous HCV clearance in a referred population of Chinese patients. The prevalence of host, viral, and environmental factors known to influence the outcome of HCV infections was compared in 92 HCV spontaneous clearance subjects and 318 HCV persistent infection subjects. Univariate and multivariate analyses were performed to identify those factors associated with spontaneous HCV clearance. In univariate analysis, female gender, a history of icteric hepatitis, serologic evidence of concurrent HBV infection, and rs12979860 CC genotype were positively associated with spontaneous HCV clearance, while alcohol consumption was negatively associated with clearance. In multivariate analysis, female gender, a history of icteric hepatitis, concurrent HBV infection, and rs12979860 CC genotype remained independent variables associated with spontaneous HCV clearance. Spontaneous HCV clearance is more likely to occur in females, subjects with a history of icteric hepatitis, HBV coinfections, and those with the rs12979860 CC genotype.

  18. Multiple genetic variants associated with primary biliary cirrhosis in a Han Chinese population.

    PubMed

    Dong, Ming; Li, Jinxin; Tang, Ruqi; Zhu, Ping; Qiu, Fang; Wang, Chan; Qiu, Jie; Wang, Lan; Dai, Yaping; Xu, Ping; Gao, Yueqiu; Han, Chongxu; Wang, Yongzhong; Wu, Jian; Wu, Xudong; Zhang, Kui; Dai, Na; Sun, Weihao; Zhou, Jianpo; Hu, Zhigang; Liu, Lei; Jiang, Yuzhang; Nie, Jinshan; Zhao, Yi; Gong, Yuhua; Tian, Ye; Ji, Hualiang; Jiao, Zhijun; Jiang, Po; Shi, Xingjuan; Jawed, Rohil; Zhang, Yu; Huang, Qinghai; Li, Enling; Wei, Yiran; Xie, Wei; Zhao, Weifeng; Liu, Xiang; Zhu, Xiang; Qiu, Hong; He, Gengsheng; Chen, Weichang; Seldin, Michael F; Gershwin, M Eric; Liu, Xiangdong; Ma, Xiong

    2015-06-01

    Multiple genome-wide association studies of primary biliary cirrhosis (PBC) in both European and Japanese ancestries have shown significant associations of many genetic loci contributing to the susceptibility to PBC. Major differences in susceptibility loci between these two population groups were observed. In this study, we examined whether the most significant loci observed in either European and/or Japanese cohorts are associated with PBC in a Han Chinese population. In 1070 PBC patients and 1198 controls, we observed highly significant associations at CD80 (rs2293370, P = 2.67 × 10(-8)) and TNFSF15 (rs4979462, P = 3.86 × 10(-8)) and significant associations at 17q12-21 (rs9303277), PDGFB (rs715505), NF-κB1 (rs7665090), IL12RB2 (rs11209050), and STAT4 (rs7574865; all corrected P values <0.01). However, no association was observed for POU2AF1 (rs4938534), IL12A (rs485499 and rs2366408), IL7R (rs6897932), CXCR5 (rs715412), SOCS1 (rs725613), and TNFRSF1A (rs1800693). STAT4 (rs7574865) was strongly associated after additional control samples were analyzed. Our study is the first large-scale genetic analysis in a Han Chinese PBC cohort. These results do not only reflect that Han Chinese PBC patients share common genetic susceptibility genes with both their Japanese and European counterparts but also suggest a distinctly different genetic susceptibility profile.

  19. Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study.

    PubMed

    Carlson, Christopher S; Matise, Tara C; North, Kari E; Haiman, Christopher A; Fesinmeyer, Megan D; Buyske, Steven; Schumacher, Fredrick R; Peters, Ulrike; Franceschini, Nora; Ritchie, Marylyn D; Duggan, David J; Spencer, Kylee L; Dumitrescu, Logan; Eaton, Charles B; Thomas, Fridtjof; Young, Alicia; Carty, Cara; Heiss, Gerardo; Le Marchand, Loic; Crawford, Dana C; Hindorff, Lucia A; Kooperberg, Charles L

    2013-09-01

    The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification

  20. A multi-marker association method for genome-wide association studies without the need for population structure correction.

    PubMed

    Klasen, Jonas R; Barbez, Elke; Meier, Lukas; Meinshausen, Nicolai; Bühlmann, Peter; Koornneef, Maarten; Busch, Wolfgang; Schneeberger, Korbinian

    2016-11-10

    All common genome-wide association (GWA) methods rely on population structure correction, to avoid false genotype-to-phenotype associations. However, population structure correction is a stringent penalization, which also impedes identification of real associations. Using recent statistical advances, we developed a new GWA method, called Quantitative Trait Cluster Association Test (QTCAT), enabling simultaneous multi-marker associations while considering correlations between markers. With this, QTCAT overcomes the need for population structure correction and also reflects the polygenic nature of complex traits better than single-marker methods. Using simulated data, we show that QTCAT clearly outperforms linear mixed model approaches. Moreover, using QTCAT to reanalyse public human, mouse and Arabidopsis GWA data revealed nearly all known and some previously undetected associations. Following up on the most significant novel association in the Arabidopsis data allowed us to identify a so far unknown component of root growth.

  1. A multi-marker association method for genome-wide association studies without the need for population structure correction

    PubMed Central

    Klasen, Jonas R.; Barbez, Elke; Meier, Lukas; Meinshausen, Nicolai; Bühlmann, Peter; Koornneef, Maarten; Busch, Wolfgang; Schneeberger, Korbinian

    2016-01-01

    All common genome-wide association (GWA) methods rely on population structure correction, to avoid false genotype-to-phenotype associations. However, population structure correction is a stringent penalization, which also impedes identification of real associations. Using recent statistical advances, we developed a new GWA method, called Quantitative Trait Cluster Association Test (QTCAT), enabling simultaneous multi-marker associations while considering correlations between markers. With this, QTCAT overcomes the need for population structure correction and also reflects the polygenic nature of complex traits better than single-marker methods. Using simulated data, we show that QTCAT clearly outperforms linear mixed model approaches. Moreover, using QTCAT to reanalyse public human, mouse and Arabidopsis GWA data revealed nearly all known and some previously undetected associations. Following up on the most significant novel association in the Arabidopsis data allowed us to identify a so far unknown component of root growth. PMID:27830750

  2. Differences in genetic variation in antigen-processing machinery components and association with cervical carcinoma risk in two Indonesian populations.

    PubMed

    Mehta, Akash M; Spaans, Vivian M; Mahendra, Nyoman Bayu; Osse, Elisabeth M; Vet, Jessica N I; Purwoto, Gatot; Surya, I G D; Cornian, Santoso; Peters, Alexander A; Fleuren, Gert J; Jordanova, Ekaterina S

    2015-06-01

    Genetic variation of antigen-processing machinery (APM) components has been shown to be associated with cervical carcinoma risk and outcome in a genetically homogeneous Dutch population. However, the role of APM component single nucleotide polymorphisms (SNPs) in genetically heterogeneous populations with different distributions of human papillomavirus (HPV) subtypes remains unclear. Eleven non-synonymous, coding SNPs in the TAP1, TAP2, LMP2, LMP7 and ERAP1 genes were genotyped in cervical carcinoma patients and healthy controls from two distinct Indonesian populations (Balinese and Javanese). Individual genotype and allele distributions were investigated using single-marker analysis, and combined SNP effects were assessed by haplotype construction and haplotype interaction analysis. Allele distribution patterns in Bali and Java differed in relation to cervical carcinoma risk, with four ERAP1 SNPs and one TAP2 SNP in the Javanese population showing significant association with cervical carcinoma risk, while in the Balinese population, only one TAP2 SNP showed this association. Multimarker analysis demonstrated that in the Javanese patients, one specific haplotype, consisting of the ERAP1-575 locus on chromosome 5 and the TAP2-379 and TAP2-651 loci on chromosome 6, was significantly associated with cervical carcinoma risk (global P = 0.008); no significant haplotype associations were found in the Balinese population. These data indicate not only that genetic variation in APM component genes is associated with cervical carcinoma risk in Indonesia but also that the patterns of association differ depending on background genetic composition and possibly on differences in HPV type distribution.

  3. Genome-Wide Association of Body Fat Distribution in African Ancestry Populations Suggests New Loci

    PubMed Central

    Lange, Leslie; Demerath, Ellen W.; Palmas, Walter; Wojczynski, Mary K.; Ellis, Jaclyn C.; Vitolins, Mara Z.; Liu, Simin; Papanicolaou, George J.; Irvin, Marguerite R.; Xue, Luting; Griffin, Paula J.; Nalls, Michael A.; Adeyemo, Adebowale; Liu, Jiankang; Li, Guo; Ruiz-Narvaez, Edward A.; Chen, Wei-Min; Chen, Fang; Henderson, Brian E.; Millikan, Robert C.; Ambrosone, Christine B.; Strom, Sara S.; Guo, Xiuqing; Andrews, Jeanette S.; Sun, Yan V.; Mosley, Thomas H.; Yanek, Lisa R.; Shriner, Daniel; Haritunians, Talin; Rotter, Jerome I.; Speliotes, Elizabeth K.; Smith, Megan; Rosenberg, Lynn; Mychaleckyj, Josyf; Nayak, Uma; Spruill, Ida; Garvey, W. Timothy; Pettaway, Curtis; Nyante, Sarah; Bandera, Elisa V.; Britton, Angela F.; Zonderman, Alan B.; Rasmussen-Torvik, Laura J.; Chen, Yii-Der Ida; Ding, Jingzhong; Lohman, Kurt; Kritchevsky, Stephen B.; Zhao, Wei; Peyser, Patricia A.; Kardia, Sharon L. R.; Kabagambe, Edmond; Broeckel, Ulrich; Chen, Guanjie; Zhou, Jie; Wassertheil-Smoller, Sylvia; Neuhouser, Marian L.; Rampersaud, Evadnie; Psaty, Bruce; Kooperberg, Charles; Manson, JoAnn E.; Kuller, Lewis H.; Ochs-Balcom, Heather M.; Johnson, Karen C.; Sucheston, Lara; Ordovas, Jose M.; Palmer, Julie R.; Haiman, Christopher A.; McKnight, Barbara; Howard, Barbara V.; Becker, Diane M.; Bielak, Lawrence F.; Liu, Yongmei; Allison, Matthew A.; Grant, Struan F. A.; Burke, Gregory L.; Patel, Sanjay R.; Schreiner, Pamela J.; Borecki, Ingrid B.; Evans, Michele K.; Taylor, Herman; Sale, Michele M.; Howard, Virginia; Carlson, Christopher S.; Rotimi, Charles N.; Cushman, Mary; Harris, Tamara B.; Reiner, Alexander P.; Cupples, L. Adrienne; North, Kari E.; Fox, Caroline S.

    2013-01-01

    Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0×10−6 were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10−8 for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10−8 for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5×10−8; RREB1: p = 5.7×10−8). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce

  4. Association of variants in FRAP1 and PDGFRA with corneal curvature in Asian populations from Singapore.

    PubMed

    Han, Siyu; Chen, Peng; Fan, Qiao; Khor, Chiea-Chuen; Sim, Xueling; Tay, Wan-Ting; Ong, Rick Twee-Hee; Suo, Chen; Goh, Liang-Kee; Lavanya, Raghavan; Zheng, Yingfeng; Wu, Renyi; Seielstad, Mark; Vithana, Eranga; Liu, Jianjun; Chia, Kee-Seng; Lee, Jeannette Jen-Mai; Tai, E-Shyong; Wong, Tien-Yin; Aung, Tin; Teo, Yik-Ying; Saw, Seang-Mei

    2011-09-15

    Corneal curvature (CC) is a key determinant of major eye diseases, such as keratoconus, myopia and corneal astigmatism. No prior studies have discovered the genes for CC. Here we report the findings from four genome-wide association studies of CC in 10 008 samples from three population groups in Singapore. Our discovery phase surveyed 2867 Chinese and 3072 Malays, allowing us to identify two loci that were associated with CC variation: FRAP1 on chromosome 1p36.2 and PDGFRA on chromosome 4q12. These findings were subsequently replicated in a validation study involving an additional 2953 Asian Indians and a further collection of 1116 Chinese children. The effect sizes of the identified variants were consistent across all four cohorts, with seven single nucleotide polymorphisms (SNPs) in FRAP1 (lead SNP: rs17036350, meta P-value = 4.06 × 10(-13)) and six SNPs in PDGFRA (lead SNP: rs2114039, meta P-value = 1.33 × 10(-9)) attaining genome-wide significance in the SNP-based meta-analysis of the four studies. This is the first genome-wide survey of CC variation and we have identified two implicated loci in three genetically diverse Asian populations, suggesting the presence of common genetic etiology across multiple populations.

  5. A practical guide to environmental association analysis in landscape genomics.

    PubMed

    Rellstab, Christian; Gugerli, Felix; Eckert, Andrew J; Hancock, Angela M; Holderegger, Rolf

    2015-09-01

    Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced-representation sequencing, candidate-gene approaches, linearity of allele-environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.

  6. Factors associated with cervical cancer screening in a safety net population

    PubMed Central

    Heberer, Meredith A; Komenaka, Ian K; Nodora, Jesse N; Hsu, Chiu-Hsieh; Gandhi, Sonal G; Welch, Lauren E; Bouton, Marcia E; Aristizabal, Paula; Weiss, Barry D; Martinez, Maria Elena

    2016-01-01

    AIM To identify factors associated with Papanicolaou-smear (Pap-smear) cervical cancer screening rates in a safety net population. METHODS From January 2012 to May 2013, the use of Pap-smear was determined for all patients seen at the breast clinic in a safety net hospital. Health literacy assessment was performed using the validated Newest Vital Sign. The records of patients were reviewed to determine if they had undergone Pap-smears for cervical cancer screening. Sociodemographic information was collected included age, education, monthly income, race/ethnicity, employment, insurance status, and primary care provider of the patient. Logistic regression analysis was then performed to determine factors associated with utilization of Pap-smears. Crude and adjusted odds ratios derived from multivariate logistic regression models were calculated as well as the associated 95%CIs and P-values. RESULTS Overall, 39% had Pap-smears in the prior 15 mo, 1377 consecutive women were seen during the study period and their records were reviewed. Significantly more patients with adequate health literacy underwent Pap-smears as compared to those with limited health literacy (59% vs 34%, P < 0.0001). In multivariate analysis, patients with adequate health literacy, younger patients, and those with later age of first live birth were more likely to undergo Pap-smears. Patients whose primary care providers were gynecologists were also significantly more likely to have Pap-smears compared to other specialties (P < 0.0001). Patients younger than 21 years or older than 65 years underwent screening less frequently (11% and 11%, respectively) than those 21-64 years (41%, P < 0.0001). Race, ethnicity, language, and insurance status were not associated with Pap-smear screening rates. CONCLUSION Patient health literacy and primary care physician were associated with Pap-smear utilization. Development of interventions to target low health literacy populations could improve cervical cancer

  7. Genome-wide Association Study of Autism Spectrum Disorder in the East Asian Populations.

    PubMed

    Liu, Xiaoxi; Shimada, Takafumi; Otowa, Takeshi; Wu, Yu-Yu; Kawamura, Yoshiya; Tochigi, Mamoru; Iwata, Yasuhide; Umekage, Tadashi; Toyota, Tomoko; Maekawa, Motoko; Iwayama, Yoshimi; Suzuki, Katsuaki; Kakiuchi, Chihiro; Kuwabara, Hitoshi; Kano, Yukiko; Nishida, Hisami; Sugiyama, Toshiro; Kato, Nobumasa; Chen, Chia-Hsiang; Mori, Norio; Yamada, Kazuo; Yoshikawa, Takeo; Kasai, Kiyoto; Tokunaga, Katsushi; Sasaki, Tsukasa; Gau, Susan Shur-Fen

    2016-03-01

    Autism spectrum disorder is a heterogeneous neurodevelopmental disorder with strong genetic basis. To identify common genetic variations conferring the risk of ASD, we performed a two-stage genome-wide association study using ASD family and healthy control samples obtained from East Asian populations. A total of 166 ASD families (n = 500) and 642 healthy controls from the Japanese population were used as the discovery cohort. Approximately 900,000 single nucleotide polymorphisms (SNPs) were genotyped using Affymetrix Genome-Wide Human SNP array 6.0 chips. In the replication stage, 205 Japanese ASD cases and 184 healthy controls, as well as 418 Chinese Han trios (n = 1,254), were genotyped by TaqMan platform. Case-control analysis, family based association test, and transmission/disequilibrium test (TDT) were then conducted to test the association. In the discovery stage, significant associations were suggested for 14 loci, including 5 known ASD candidate genes: GPC6, JARID2, YTHDC2, CNTN4, and CSMD1. In addition, significant associations were identified for several novel genes with intriguing functions, such as JPH3, PTPRD, CUX1, and RIT2. After a meta-analysis combining the Japanese replication samples, the strongest signal was found at rs16976358 (P = 6.04 × 10(-7)), which is located near the RIT2 gene. In summary, our results provide independent support to known ASD candidate genes and highlight a number of novel genes warranted to be further investigated in a larger sample set in an effort to improve our understanding of the genetic basis of ASD.

  8. Changes in size and trends of North American sea duck populations associated with North Pacific oceanic regime shifts

    USGS Publications Warehouse

    Flint, Paul L.

    2013-01-01

    Broad-scale multi-species declines in populations of North American sea ducks for unknown reasons is cause for management concern. Oceanic regime shifts have been associated with rapid changes in ecosystem structure of the North Pacific and Bering Sea. However, relatively little is known about potential effects of these changes in oceanic conditions on marine bird populations at broad scales. I examined changes in North American breeding populations of sea ducks from 1957 to 2011 in relation to potential oceanic regime shifts in the North Pacific in 1977, 1989, and 1998. There was strong support for population-level effects of regime shifts in 1977 and 1989, but little support for an effect of the 1998 shift. The continental-level effects of these regime shifts differed across species groups and time. Based on patterns of sea duck population dynamics associated with regime shifts, it is unclear if the mechanism of change relates to survival or reproduction. Results of this analysis support the hypothesis that population size and trends of North American sea ducks are strongly influenced by oceanic conditions. The perceived population declines appear to have halted >20 years ago, and populations have been relatively stable or increasing since that time. Given these results, we should reasonably expect dramatic changes in sea duck population status and trends with future oceanic regime shifts.

  9. Molecular characterization and population structure of blackberry vein banding associated virus, new Ampelovirus associated with yellow vein disease.

    PubMed

    Thekke-Veetil, Thanuja; Aboughanem-Sabanadzovic, Nina; Keller, Karen E; Martin, Robert R; Sabanadzovic, Sead; Tzanetakis, Ioannis E

    2013-12-26

    Blackberry yellow vein disease is the most important viral disease of blackberry in the United States. Experiments were conducted to characterize a new virus identified in symptomatic plants. Molecular analysis revealed a genome organization resembling Grapevine leafroll-associated virus 3, the type species of the genus Ampelovirus in the family Closteroviridae. The genome of the virus, provisionally named blackberry vein banding associated virus (BVBaV), consists of 18,643 nucleotides and contains 10 open reading frames (ORFs). These ORFs encode closterovirid signature replication-associated and quintuple gene block proteins, as well as four additional proteins of unknown function. Phylogenetic analyses of taxonomically relevant products consistently placed BVBaV in the same cluster with GLRaV-3 and other members of the subgroup I of the genus Ampelovirus. The virus population structure in the U.S. was studied using the replication associated polyprotein 1a, heat shock 70 homolog and minor coat proteins of 25 isolates. This study revealed significant intra-species variation without any clustering among isolates based on their geographic origin. Further analyses indicated that these proteins are under stringent purifying selections. High genetic variability and incongruent clustering of isolates suggested the possible involvement of recombination in the evolution of BVBaV.

  10. Variation in the checkpoint kinase 2 gene is associated with type 2 diabetes in multiple populations

    PubMed Central

    Franceschini, Nora; Avery, Christy L.; Baird, Lisa; Graff, Mariaelisa; Leppert, Mark; Chung, Jay H.; Zhang, Jinghui; Hanis, Craig; Boerwinkle, Eric; Volcik, Kelly A.; Grove, Megan L.; Mosley, Thomas H.; Gu, Charles; Heiss, Gerardo; Pankow, James S.; Couper, David J.; Ballantyne, Christie M.; Linda Kao, W. H.; Weder, Alan B.; Cooper, Richard S.; Ehret, Georg B.; O'Connor, Ashley A.; Chakravarti, Aravinda; Hunt, Steven C.

    2010-01-01

    Identification and characterization of the genetic variants underlying type 2 diabetes susceptibility can provide important understanding of the etiology and pathogenesis of type 2 diabetes. We previously identified strong evidence of linkage for type 2 diabetes on chromosome 22 among 3,383 Hypertension Genetic Epidemiology Network (HyperGEN) participants from 1,124 families. The checkpoint 2 (CHEK2) gene, an important mediator of cellular responses to DNA damage, is located 0.22 Mb from this linkage peak. In this study, we tested the hypothesis that the CHEK2 gene contains one or more polymorphic variants that are associated with type 2 diabetes in HyperGEN individuals. In addition, we replicated our findings in two other Family Blood Pressure Program (FBPP) populations and in the population-based Atherosclerosis Risk in Communities (ARIC) study. We genotyped 1,584 African-American and 1,531 white HyperGEN participants, 1,843 African-American and 1,569 white GENOA participants, 871 African-American and 1,009 white GenNet participants, and 4,266 African-American and 11,478 white ARIC participants for four single nucleotide polymorphisms (SNPs) in CHEK2. Using additive models, we evaluated the association of CHEK2 SNPs with type 2 diabetes in participants within each study population stratified by race, and in a meta-analysis, adjusting for age, age2, sex, sex-by-age interaction, study center, and relatedness. One CHEK2 variant, rs4035540, was associated with an increased risk of type 2 diabetes in HyperGEN participants, two replication samples, and in the meta-analysis. These results may suggest a new pathway in the pathogenesis of type 2 diabetes that involves pancreatic beta-cell damage and apoptosis. PMID:19855918

  11. Main visual symptoms associated to refractive errors and spectacle need in a Brazilian population

    PubMed Central

    Schellini, Silvana; Ferraz, Fabio; Opromolla, Paula; Oliveira, Laryssa; Padovani, Carlos

    2016-01-01

    AIM To determine the main visual symptoms in a Brazilian population sample, associated to refractive errors (REs) and spectacle need to suggest priorities in preventive programs. METHODS A cross-sectional study was conducted in nine counties of the southeast region of Brazil, using a systematic sampling of households, between March 2004 and July 2005. The population was defined as individuals aged between 1 and 96y, inhabitants of 3600 residences to be evaluated and 3012 households were included, corresponding to 8010 subjects considered for participation in the survey, of whom 7654 underwent ophthalmic examinations. The individuals were evaluated according their demographic data, eye complaints and eye examination including the RE and the need to prescribe spectacles according to age. Statistical analysis was performed using SPSS software package and descriptive analysis using 95% confidence intervals (P<0.05). RESULTS The main symptom detected was asthenopia, most frequent in the 2nd and 3rd decades of life, with a significant decline after the 4th decade. Astigmatism was the RE most associated with asthenopia. Reduced near vision sight was more frequent in those ≥40y with a progressive decline thereafter. Spectacles were most frequently required in subjects of ≥40 years of age. CONCLUSION The main symptom related to the vision was asthenopia and was associated to astigmatism. The greatest need for spectacles prescription occurred after 40's, mainly to correct near vision. Subjects of ≥40 years old were determined to be at high risk of uncorrected REs. These observations can guide intervention programs for the Brazilian population. PMID:27990372

  12. Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

    PubMed Central

    Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

    2015-01-01

    The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

  13. CAPL: a novel association test using case-control and family data and accounting for population stratification.

    PubMed

    Chung, Ren-Hua; Schmidt, Michael A; Morris, Richard W; Martin, Eden R

    2010-11-01

    The recent successes of GWAS based on large sample sizes motivate combining independent datasets to obtain larger sample sizes and thereby increase statistical power. Analysis methods that can accommodate different study designs, such as family-based and case-control designs, are of general interest. However, population stratification can cause spurious association for population-based association analyses. For family-based association analysis that infers missing parental genotypes based on the allele frequencies estimated in the entire sample, the parental mating-type probabilities may not be correctly estimated in the presence of population stratification. Therefore, any approach to combining family and case-control data should also properly account for population stratification. Although several methods have been proposed to accommodate family-based and case-control data, all have restrictions. Most of them require sampling a homogeneous population, which may not be a reasonable assumption for data from a large consortium. One of the methods, FamCC, can account for population stratification and uses nuclear families with arbitrary number of siblings but requires parental genotype data, which are often unavailable for late-onset diseases. We extended the family-based test, Association in the Presence of Linkage (APL), to combine family and case-control data (CAPL). CAPL can accommodate case-control data and families with multiple affected siblings and missing parents in the presence of population stratification. We used simulations to demonstrate that CAPL is a valid test either in a homogeneous population or in the presence of population stratification. We also showed that CAPL can have more power than other methods that combine family and case-control data.

  14. Graphic analysis of population structure on genome-wide rheumatoid arthritis data.

    PubMed

    Zhang, Jun; Weng, Chunhua; Niyogi, Partha

    2009-12-15

    Principal-component analysis (PCA) has been used for decades to summarize the human genetic variation across geographic regions and to infer population migration history. Reduction of spurious associations due to population structure is crucial for the success of disease association studies. Recently, PCA has also become a popular method for detecting population structure and correction of population stratification in disease association studies. Inspired by manifold learning, we propose a novel method based on spectral graph theory. Regarding each study subject as a node with suitably defined weights for its edges to close neighbors, one can form a weighted graph. We suggest using the spectrum of the associated graph Laplacian operator, namely, Laplacian eigenfunctions, to infer population structures instead of principal components (PCs). For the whole genome-wide association data for the North American Rheumatoid Arthritis Consortium (NARAC) provided by Genetic Workshop Analysis 16, Laplacian eigenfunctions revealed more meaningful structures of the underlying population than PCA. The proposed method has connection to PCA, and it naturally includes PCA as a special case. Our simple method is computationally fast and is suitable for disease studies at the genome-wide scale.

  15. Population-Specific Haplotype Association of the Postsynaptic Density Gene DLG4 with Schizophrenia, in Family-Based Association Studies

    PubMed Central

    Balan, Shabeesh; Yamada, Kazuo; Hattori, Eiji; Iwayama, Yoshimi; Toyota, Tomoko; Ohnishi, Tetsuo; Maekawa, Motoko; Toyoshima, Manabu; Iwata, Yasuhide; Suzuki, Katsuaki; Kikuchi, Mitsuru; Yoshikawa, Takeo

    2013-01-01

    The post-synaptic density (PSD) of glutamatergic synapses harbors a multitude of proteins critical for maintaining synaptic dynamics. Alteration of protein expression levels in this matrix is a marked phenomenon of neuropsychiatric disorders including schizophrenia, where cognitive functions are impaired. To investigate the genetic relationship of genes expressed in the PSD with schizophrenia, a family-based association analysis of genetic variants in PSD genes such as DLG4, DLG1, PICK1 and MDM2, was performed, using Japanese samples (124 pedigrees, n = 376 subjects). Results showed a significant association of the rs17203281 variant from the DLG4 gene, with preferential transmission of the C allele (p = 0.02), although significance disappeared after correction for multiple testing. Replication analysis of this variant, found no association in a Chinese schizophrenia cohort (293 pedigrees, n = 1163 subjects) or in a Japanese case-control sample (n = 4182 subjects). The DLG4 expression levels between postmortem brain samples from schizophrenia patients showed no significant changes from controls. Interestingly, a five marker haplotype in DLG4, involving rs2242449, rs17203281, rs390200, rs222853 and rs222837, was enriched in a population specific manner, where the sequences A-C-C-C-A and G-C-C-C-A accumulated in Japanese (p = 0.0009) and Chinese (p = 0.0007) schizophrenia pedigree samples, respectively. However, this could not be replicated in case-control samples. None of the variants in other examined candidate genes showed any significant association in these samples. The current study highlights a putative role for DLG4 in schizophrenia pathogenesis, evidenced by haplotype association, and warrants further dense screening for variants within these haplotypes. PMID:23936182

  16. Fast Genome-Wide QTL Association Mapping on Pedigree and Population Data.

    PubMed

    Zhou, Hua; Blangero, John; Dyer, Thomas D; Chan, Kei-Hang K; Lange, Kenneth; Sobel, Eric M

    2017-04-01

    Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even datasets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Pedigrees selected for extreme trait values often segregate a single gene with strong effect. Finally, many pedigrees are available as an important legacy from the era of linkage analysis. Unfortunately, pedigree likelihoods are notoriously hard to compute. In this paper, we reexamine the computational bottlenecks and implement ultra-fast pedigree-based GWAS analysis. Kinship coefficients can either be based on explicitly provided pedigrees or automatically estimated from dense markers. Our strategy (a) works for random sample data, pedigree data, or a mix of both; (b) entails no loss of power; (c) allows for any number of covariate adjustments, including correction for population stratification; (d) allows for testing SNPs under additive, dominant, and recessive models; and (e) accommodates both univariate and multivariate quantitative traits. On a typical personal computer (six CPU cores at 2.67 GHz), analyzing a univariate HDL (high-density lipoprotein) trait from the San Antonio Family Heart Study (935,392 SNPs on 1,388 individuals in 124 pedigrees) takes less than 2 min and 1.5 GB of memory. Complete multivariate QTL analysis of the three time-points of the longitudinal HDL multivariate trait takes less than 5 min and 1.5 GB of memory. The algorithm is implemented as the Ped-GWAS Analysis (Option 29) in the Mendel statistical genetics package, which is

  17. Sleep Apnea and Cancer: Analysis of a Nationwide Population Sample

    PubMed Central

    Gozal, David; Ham, Sandra A.; Mokhlesi, Babak

    2016-01-01

    Study Objectives: Epidemiological evidence from relatively small cohorts suggests that obstructive sleep apnea (OSA) is associated with higher cancer incidence and mortality. Here we aimed to determine whether cancer incidence for major cancer types and risk of metastases or mortality from cancer are increased in the presence of OSA. Methods: All OSA diagnoses included in an employee-sponsored health insurance database spanning the years 2003–2012 were identified and 1:1 matched demographically based on age, gender, and state of residence, or alternatively matched by comorbidities. The incidence of 12 types of cancer was assessed. In addition, another cohort of patients with a primary diagnosis of cancer was retrieved, and the risk of metastatic disease or cancer mortality was determined as a function of the presence or absence of OSA. Multivariate Cox proportional hazards regression models were fitted to assess the independent associations between OSA and outcomes of interest. Results: Based on a cohort of ∼5.6 million individuals, the incidence of all cancer diagnoses combined was similar in OSA and retrospectively matched cases. However, the adjusted risk of pancreatic and kidney cancer and melanoma were significantly higher in patients with OSA, while the risk of colorectal, breast, and prostate cancers appeared to be lower. Among individuals with a diagnosis of cancer, the presence of OSA was not associated with an increased risk for metastasis or death. Conclusions: In a large nationally representative health insurance database, OSA appears to increase the risk for only a very selective number of cancer types, and does not appear to be associated with an increased risk of metastatic cancer or cancer-related deaths. Citation: Gozal D, Ham SA, Mokhlesi B. Sleep apnea and cancer: analysis of a nationwide population sample. SLEEP 2016;39(8):1493–1500. PMID:27166241

  18. Single nucleotide polymorphisms of TNFAIP3 are associated with systemic lupus erythematosus in Han Chinese population.

    PubMed

    Han, J-W; Wang, Y; Li, H-B; Alateng, C; Bai, Y-H; Sun, Z-Q; Lv, X-X; Wu, R-N

    2016-04-01

    The polymorphisms of tumour necrosis factor alpha-induced protein 3 (TNFAIP3) have been found to associate with several autoimmune diseases. This study aimed to explore the association of single nucleotide polymorphisms (SNPs) of TNFAIP3 gene with systemic lupus erythematosus (SLE) in Han Chinese. Thirty-two SNPs were genotyped in 284 patients with SLE and 630 controls using the ligation detection reaction (LDR) method. The quality control steps and statistical analyses were performed using the PLINK 1.07 package and HAPLOVIEW software. We found that 13 SNPs in TNFAIP3 showed significant association with SLE (P < 1.85 × 10(-3)), and all of them were in high linkage disequilibrium (LD). After conditioning on the SNP rs2230926, other 12 SNPs did not show association (P > 0.27). All 13 SNPs showed most significant association in the dominant model. In haplotype analysis, a long risk SNP haplotype (GCCCGTGTCATGG) showed most significant association (P = 1.00 × 10(-4)). In conclusion, our data suggest that TNFAIP3 is a susceptible gene for SLE in the Han Chinese population.

  19. Association between Common Genetic Variants and Polycystic Ovary Syndrome Risk in a Chinese Han Population

    PubMed Central

    Sun, Ying; Yuan, Yi; Yang, Hua; Li, Jingjie; Feng, Tian; Ouyang, Yongri; Jin, Tianbo; Liu, Ming

    2016-01-01

    Objective: Polycystic ovary syndrome (PCOS) is one of the most common endocrinopathies affecting 5-7% of reproductive age women worldwide. The aim of our study was to explore the PCOS-related single nucleotide polymorphism (SNP) associations between common genetic variants and PCOS risk in a Han Chinese women population. Methods: In this case-control study, 285 Chinese Han women aged 28.50±6.858 years with PCOS and 299 controls of a mean age of 32.66±7.018 years were compared. We selected recently published genome-wide association studies (GWAS) which identified several genetic loci in PCOS. All the SNPs were genotyped by Sequenom Mass-ARRAY technology. Associations between the gene and the risk of PCOS were tested using various genetic models by Statistical Package for the Social Sciences and Plink. Results: We found that rs705702 in the RAB5B/SUOX was associated with PCOS (odds ratio=1.42; 95% confidence interval=1.08-1.87, p=0.011) and increased the PCOS risk. The genotypic model analysis also showed that rs705702 was associated with PCOS risk. Conclusion: Our results suggest that SNPs rs705702 in gene RAB5B/SUOX was associated with PCOS in Han Chinese women. PMID:27217259

  20. Bacterial populations and the volatilome associated to meat spoilage.

    PubMed

    Casaburi, Annalisa; Piombino, Paola; Nychas, George-John; Villani, Francesco; Ercolini, Danilo

    2015-02-01

    Microbial spoilage of meat is a complex event to which many different bacterial populations can contribute depending on the temperature of storage and packaging conditions. The spoilage can derive from microbial development and consumption of meat nutrients by bacteria with a consequent release of undesired metabolites. The volatile organic compounds (VOCs) that are generated during meat storage can have an olfactory impact and can lead to rejection of the product when their concentration increase significantly as a result of microbial development. The VOCs most commonly identified in meat during storage include alcohols, aldehydes, ketones, fatty acids, esters and sulfur compounds. In this review, the VOCs found in fresh meat during storage in specific conditions are described together with the possible bacterial populations responsible of their production. In addition, on the basis of the data available in the literature, the sensory impact of the VOCs and their dynamics during storage is discussed to highlight their possible contribution to the spoilage of meat.

  1. Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

    PubMed Central

    Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; Conway, David J.; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N.; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G.; Small, Kerrin S.; Teo, Yik Ying; Kwiatkowski, Dominic P.; Rockett, Kirk A.; Barrett, Jeffrey C.; Spencer, Chris C. A.

    2013-01-01

    Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles. PMID:23717212

  2. Aspirin Use Associated With Amyotrophic Lateral Sclerosis: a Total Population-Based Case-Control Study

    PubMed Central

    Tsai, Ching-Piao; Lin, Feng-Cheng; Lee, Johnny Kuang-Wu; Lee, Charles Tzu-Chi

    2015-01-01

    Background The association of aspirin use and nonsteroid anti-inflammatory drug (NSAID) use with amyotrophic lateral sclerosis (ALS) risk is unclear. This study determined whether use of any individual compound is associated with ALS risk by conducting a total population-based case-control study in Taiwan. Methods A total of 729 patients with newly diagnosed ALS who had a severely disabling disease certificate between January 1, 2002, and December 1, 2008, comprised the case group. These cases were compared with 7290 sex-, age-, residence-, and insurance premium-matched controls. Drug use by each Anatomical Therapeutic Chemical code was analyzed using conditional logistic regression models. False discovery rate (FDR)-adjusted P values were reported in order to avoid inflating false positives. Results Of the 1336 compounds, only the 266 with use cases exceeding 30 in our database were included in the screening analysis. Without controlling for steroid use, the analysis failed to reveal any compound that was inversely associated with ALS risk according to FDR criteria. After controlling for steroid use, we found use of the following compounds to be associated with ALS risk: aspirin, diphenhydramine (one of the antihistamines), and mefenamic acid (one of the NSAIDs). A multivariate analysis revealed that aspirin was independently inversely associated with ALS risk after controlling for diphenhydramine, mefenamic acid, and steroid use. The inverse association between aspirin and ALS was present predominately in patients older than 55 years. Conclusions The results of this study suggested that aspirin use might reduce the risk of ALS, and the benefit might be more prominent for older people. PMID:25721071

  3. TRPM8 genetic variations associated with COPD risk in the Chinese Han population

    PubMed Central

    Xiong, Mingmei; Wang, Jian; Guo, Meihua; Zhou, Qipeng; Lu, Wenju

    2016-01-01

    TRPM8 plays a key role in COPD. The development of pulmonary hypertension (PH) in COPD adversely affects survival and exercise capacity. Thus, the aim of this study was to evaluate the possible association between single nucleotide polymorphisms (SNPs) in TRPM8 and COPD or PH in COPD among the Chinese Han population. A total of 513 COPD patients and 506 controls were enrolled in the study. Six tag SNPs (tSNPs) were genotyped. The relationship between COPD or PH in COPD and the six tSNPs was evaluated using the χ2 test and genetic model analysis. In the rs9789398 polymorphism, the T/C genotype was associated with an increased risk for COPD (P=0.005). Under the assumption of models of inheritance, there was an association between the rs9789398 polymorphism and COPD. In the rs9789675 polymorphism, the G/A genotype was associated with an increased risk for COPD (P=0.021). Furthermore, by the χ2 test, we found that the minor allele “A” of rs9789675 (odds ratio [OR] =0.63, 95% confidence interval [CI], 0.42–0.97, P=0.034) and the minor allele “C” of rs9789398 (OR =1.59, 95% CI, 1.03–2.44, P=0.034) were associated with a decreased risk of PH in COPD in allele models. In genetic models, the genotypes “GA” and “AA” of rs9789675 were associated with a decreased risk of PH in COPD. The genotypes “TC” and “CC” of rs9789398 were associated with a decreased risk of PH in COPD. Moreover, “CG” of rs1004478 was significantly associated with a decreased risk of PH in COPD. There was a significant association between the five SNPs (rs2362290, rs9789675, rs9789398, rs1003540, and rs104478) in the TRPM8 gene and the risk of PH in COPD. Our findings indicated that rs9789398 in the TRPM8 gene was significantly associated with the risk of COPD in the Chinese Han population. Moreover, rs9789675, rs9789398, and rs1004478 were significantly associated with the risk of PH in COPD. This study provides a novel insight into COPD and PH in the development of COPD

  4. Demographics of reintroduced populations: estimation, modeling, and decision analysis

    USGS Publications Warehouse

    Converse, Sarah J.; Moore, Clinton T.; Armstrong, Doug P.

    2013-01-01

    Reintroduction can be necessary for recovering populations of threatened species. However, the success of reintroduction efforts has been poorer than many biologists and managers would hope. To increase the benefits gained from reintroduction, management decision making should be couched within formal decision-analytic frameworks. Decision analysis is a structured process for informing decision making that recognizes that all decisions have a set of components—objectives, alternative management actions, predictive models, and optimization methods—that can be decomposed, analyzed, and recomposed to facilitate optimal, transparent decisions. Because the outcome of interest in reintroduction efforts is typically population viability or related metrics, models used in decision analysis efforts for reintroductions will need to include population models. In this special section of the Journal of Wildlife Management, we highlight examples of the construction and use of models for informing management decisions in reintroduced populations. In this introductory contribution, we review concepts in decision analysis, population modeling for analysis of decisions in reintroduction settings, and future directions. Increased use of formal decision analysis, including adaptive management, has great potential to inform reintroduction efforts. Adopting these practices will require close collaboration among managers, decision analysts, population modelers, and field biologists.

  5. The association between emotions and eating behaviour in an obese population with binge eating disorder.

    PubMed

    Nicholls, W; Devonport, T J; Blake, M

    2016-01-01

    There is utility in understanding the antecedents of binge eating (BE), with a view to explaining poorer weight loss treatment responses in this subgroup. A systematic review was completed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines with the aim of exploring associations between emotions and eating behaviour in a population affected by obesity and binge eating disorder (BED). A comprehensive literature search of four electronic databases (2004-2014) yielded 15 studies for inclusion. Included studies performed poorly on data quality analysis with respect to controlling for confounding variables, and sample size. Included papers largely focused on negative emotions as antecedents of BE; depression was consistently associated with a BED-obese classification and BE. Negative mood, sadness, tension and instability of emotions were found to be antecedents of BE in an adult BED-obese sample. However, findings were mixed regarding the role of stress, anger and positive emotions within the BED-obese population. Recommendations are presented for the identification of BED, and ecologically valid experimental designs that further understanding of the complex and varied emotions that associate with BE. The implications of these and other limitations for both researchers and practitioners are discussed. The paper concludes with recommendations for future research alongside suggestions for practitioners. © 2015 World Obesity.

  6. VNTR alleles associated with the {alpha}-globin locus are haplotype and population related

    SciTech Connect

    Martinson, J.J.; Clegg, J.B.; Boyce, A.J.

    1994-09-01

    The human {alpha}-globin complex contains several polymorphic restriction-enzyme sites (i.e., RFLPs) linked to form haplotypes and is flanked by two hypervariable VNTR loci, the 5{prime} hypervariable region (HVR) and the more highly polymorphic 3{prime}HVR. Using a combination of RFLP analysis and PCR, the authors have characterized the 5{prime}HVR and 3{prime}HVR alleles associated with the {alpha}-globin haplotypes of 133 chromosomes, and they here show that specific {alpha}-globin haplotypes are each associated with discrete subsets of the alleles observed at these two VNTR loci. This statistically highly significant association is observed over a region spanning {approximately} 100 kb. With the exception of closely related haplotypes, different haplotypes do not share identically sized 3{prime}HVR alleles. Earlier studies have shown that {alpha}-globin haplotype distributions differ between populations; the current findings also reveal extensive population substructure in the repertoire of {alpha}-globin VNTRs. If similar features are characteristic of other VNTR loci, this will have important implications for forensic and anthropological studies. 42 refs., 5 figs., 5 tabs.

  7. IL-10 Genetic Polymorphisms Were Associated with Valvular Calcification in Han, Uygur and Kazak Populations in Xinjiang, China

    PubMed Central

    Ma, Yi-Tong; Wulasihan, Muhuyati; Huang, Ying; Adi, Dilare; Yang, Yi-Ning; Ma, Xiang; Li, Xiao-Mei; Xie, Xiang; Huang, Ding; Liu, Fen; Chen, Bang-Dang

    2015-01-01

    Objective Valvular calcification occurs via ongoing endothelial injury associated with inflammation. IL-10 is an anti-inflammatory cytokine and 75% of the variation in IL-10 production is genetically determined. However, the relationship between genetic polymorphisms of IL-10 and valvular calcification has not been studied. The objective of this study was to investigate the association between valvular calcification and IL-10 genetic polymorphisms in the Han, Uygur and Kazak populations in China. Patients and Methods All of the participants were selected from subjects participating in the Cardiovascular Risk Survey (CRS) study. The single nucleotide polymorphisms (SNPs) rs1800871 and rs1800872 of the IL-10 gene were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three independent case-control studies involving the Han population, the Uygur population and the Kazak population were used in the analysis. Results For the Han and Kazak populations, rs1800871 was found to be associated with valvular calcification in the recessive model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.031, respectively). For the Han, Uygur and Kazak populations, rs1800872 was found to be associated with valvular calcification in the dominant model, and the difference remained statistically significant following multivariate adjustment (p<0.001, p=0.009, and p=0.023,respectively) Conclusion Both rs1800871 and rs1800872 of the IL-10 gene are associated with valvular calcification in the Han and Kazak populations in China. Rs1800872 is also associated with valvular calcification in the Uygur population. PMID:26039365

  8. HLA Associations and Risk of Posttransplant Lymphoproliferative Disorder in a Danish Population-Based Cohort

    PubMed Central

    Vase, Maja Ølholm; Maksten, Eva Futtrup; Strandhave, Charlotte; Søndergaard, Esben; Bendix, Knud; Hamilton-Dutoit, Stephen; Andersen, Claus; Møller, Michael Boe; Sørensen, Søren Schwartz; Kampmann, Jan; Eiskjær, Hans; Iversen, Martin; Weinreich, Ilse Duus; Møller, Bjarne; Jespersen, Bente; d'Amore, Francesco

    2015-01-01

    Background Posttransplant lymphoproliferative disorder (PTLD) is a feared complication to organ transplantation, associated with substantial morbidity and inferior survival. Risk factors for PTLD include T cell–depleting induction therapy and primary infection or reactivation of Epstein-Barr virus. Possible associations between certain HLA types and the risk of developing PTLD have been reported by other investigators; however, results are conflicting. Methods We conducted a retrospective, population-based study on 4295 Danish solid organ transplant patients from the Scandiatransplant database. Having identified 93 PTLD patients in the cohort, we investigated the association of HLA types with PTLD, Epstein-Barr virus status and time to PTLD onset. The outcomes survival and PTLD were evaluated using Cox regression; mismatching, and the PTLD-specific mortality were evaluated in a competing risk analysis. Results Risk of PTLD was associated with male sex (odds ratio, 1.70; 95% confidence interval, 1.07-2.71), and, in women, HLA-DR13 conferred an increased risk (odds ratio, 3.22; 95% confidence interval, 1.41-7.31). In multivariate analysis, HLA-B45 and HLA-DR13 remained independent predictive factors of PTLD. Mismatching in the B locus was associated with a reduced risk of PTLD (P < 0.001). Overall survival was poor after a PTLD diagnosis and was significantly worse than that in the remaining transplant cohort (P < 0.001). Conclusions Our data indicate risk-modifying HLA associations, which can be clinically useful after transplantation in personalized monitoring schemes. Given the strong linkage disequilibrium in the HLA region, the associations must be interpreted carefully. The large size, virtually complete ascertainment of cases and no loss to follow-up remain important strengths of the study. PMID:27500227

  9. Declining scaup populations: A retrospective analysis of long-term population and harvest survey data

    USGS Publications Warehouse

    Afton, A.D.; Anderson, M.G.

    2001-01-01

    We examined long-term databases concerning population status of scaup (lesser [Aythya affinis] and greater scaup [A. marila] combined) and harvest statistics of lesser scaup to identify factors potentially limiting population growth. Specifically, we explored evidence for and against the general hypotheses that scaup populations have declined in association with declining recruitment and/or female survival. We examined geographic heterogeneity in scaup demographic patterns that could yield evidence about potential limiting factors. Several biases exist in survey methodology used to estimate scaup populations and harvest statistics; however, none of these biases likely accounted for our major findings that (1) the continental scaup breeding population has declined over the last 20 years, with widespread and consistent declines within surveyed areas of the Canadian western boreal forest where most lesser scaup breed; (2) sex ratios of lesser scaup in the U.S. harvest have increased (more males now relative to females); and (3) age ratios of lesser scaup in the U.S. harvest have declined (fewer immatures now relative to adults), especially in the midcontinent region. We interpreted these major findings as evidence that (1) recruitment of lesser scaup has declined over the last 20 years, particularly in the Canadian western boreal forest; and (2) survival of female lesser scaup has declined relative to that of males. We found little evidence that harvest was associated with the scaup population decline. Our findings underscore the need for both improvements and changes to population survey procedures and new research to discriminate among various hypotheses explaining the recent scaup population decline.

  10. Association Between KCNQ1 Genetic Variants and Type 2 Diabetes in the Uyghur Population

    PubMed Central

    Ma, Qi; Wang, Li; Wang, Ting-ting; Ma, Yan; Su, Yin-xia; Wang, Zhi-qiang; Zhu, Jun; Wang, Shu-xia; Zhang, Zhao-xia; Hou, Qin-qin; Cai, Ren; Gong, Xue-li

    2015-01-01

    Objective: To investigate the association between KCNQ1 gene polymorphisms and type 2 diabetes (T2D) in an admixed ethnic minority, Uyghur population, living in the Northwest region of China. Materials and Methods: We genotyped three tagging single-nucleotide polymorphisms rs2283171, rs11023485, and rs2283208 of the KCNQ1 gene in 1006 T2D participants and 1004 controls and conducted association analysis. Results: The frequencies of the AG and GG genotypes and the G allele of rs2283171 were higher in the control group (51.4%, 22%, and 47.7%, respectively) than in the case group (49%, 17.6%, and 42.1%, respectively). The minor G allele decreased the risk of T2D with a per-allele odds ratio of 0.79 (95% CI: 0.70–0.90) for the additive genetic model in univariate analysis (p = 0.0001). After adjustment for the covariates of age, gender, smoking, alcohol use, systolic blood pressure (SBP), diastolic blood pressure (DBP), body mass index (BMI), triglyceride (TG), and total cholesterol (TC), the diabetic protective effect of the rs2283171-G allele remained. No difference was observed in the frequency distributions of the rs11023485 and rs2283208 genotypes between the two groups. Conclusion: We identified a novel association between rs2283171 of KCNQ1 and T2D in the Uyghur population. Further association and functional studies are required to identify the causal functional variant that is in linkage disequilibrium with this polymorphism. PMID:26540651

  11. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    PubMed Central

    Kamvar, Zhian N.; Brooks, Jonah C.; Grünwald, Niklaus J.

    2015-01-01

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies. PMID:26113860

  12. Association between prothrombin gene polymorphisms and hereditary thrombophilia in Xinjiang Kazakhs population.

    PubMed

    Ge, Xiao-Hu; Zhu, Feng; Wang, Bing-Lin; Wang, Chang-Min; Zhu, Bing; Guan, Sheng; Ci, Hong-Bo; Sai, Li-Mu; Jiang, Xiao-Kui; Ren, Hao; Fang, Qing-Bo; Tian, Guang-Lei

    2014-03-01

    To assess the association between polymorphisms of prothrombin gene and hereditary thrombophilia in Xinjiang Kazakhs population. Through cross-sectional investigation, permanent Kazakh population of Ili Kazakh Autonomous Prefecture was selected as the study object to measure their antithrombin III (AT-III), protein C, protein S activity and activated C protein resistance value, thus defining the situation of the crowd's hereditary thrombophilia. Sequenom Massarray detection technology was used to conduct a genotype test of the six sites selected by the case and control groups. Haploview software was used to perform linkage disequilibrium analysis of the six sites, and the impact of the interaction between genetic variations and environment on hereditary thrombophilia was researched by the use of sum model. A total of 1005 Kazakh volunteers participated in the test (332 men and 673 women), average age (41.13 ± 11.50) years; the prevalence of hereditary thrombophilia in Xinjiang Kazakh population was 31.0%, and the prevalence of AT-III deficiency, protein C deficiency, protein S deficiency and activated protein C resistance was 16.4, 14.9, 20.6 and 7.8%, respectively. The difference in allele frequency of the hereditary thrombophilia patient group at rs3136447 and rs5896 sites was statistically significant (P = 0.0483 and P = 0.0302, respectively). rs5896 and rs2070852 had high linkage disequilibrium (r = 0.99), and constituted a single-domain block 1. The rs3136447 and the rs5896 polymorphisms located in the region of the prothrombin gene may be associated with hereditary thrombophilia in the Xinjiang Kazakhs population. There is additive interactive effect of rs5896 polymorphism (CT + TT) and smoke on hereditary thrombophilia.

  13. Gender-Specific Association of ATP2B1 Variants with Susceptibility to Essential Hypertension in the Han Chinese Population.

    PubMed

    Xu, Jin; Qian, Hai-xia; Hu, Su-pei; Liu, Li-ya; Zhou, Mi; Feng, Mei; Su, Jia; Ji, Lin-dan

    2016-01-01

    Previous genome-wide association studies (GWASs) found that several ATP2B1 variants are associated with essential hypertension (EHT). But the "genome-wide significant" ATP2B1 SNPs (rs2681472, rs2681492, rs17249754, and rs1105378) are in strong linkage disequilibrium (LD) and are located in the same LD block in Chinese populations. We asked whether there are other SNPs within the ATP2B1 gene associated with susceptibility to EHT in the Han Chinese population. Therefore, we performed a case-control study to investigate the association of seven tagSNPs within the ATP2B1 gene and EHT in the Han Chinese population, and we then analyzed the interaction among different SNPs and nongenetic risk factors for EHT. A total of 902 essential hypertensive cases and 902 normotensive controls were involved in the study. All 7 tagSNPs within the ATP2B1 gene were retrieved from HapMap, and genotyping was performed using the Tm-shift genotyping method. Chi-squared test, logistic regression, and propensity score analysis showed that rs17249754 was associated with EHT, particularly in females. The MDR analysis demonstrated that the interaction of rs2070759, rs17249754, TC, TG, and BMI increased the susceptibility to hypertension. Crossover analysis and stratified analysis indicated that BMI has a major effect on the development of hypertension, while ATP2B1 variants have a minor effect.

  14. No association between dietary patterns and depressive symptoms among a community-dwelling population in Japan

    PubMed Central

    2012-01-01

    Background Studies of the associations between diet and depression have primarily focused on single nutrients or foods. Recently, dietary patterns representing a combination of foods have attracted more interest than individual nutrient. The objective of this study was to examine the association between dietary patterns and depressive symptoms among a community-dwelling population in Japan. Methods We examined the association between dietary patterns and the risk of depression among 791 Japanese community-dwelling individuals. Diet was assessed with a validated brief-type self-administered diet history questionnaire (BDHQ). Dietary patterns from 52 predefined food groups [energy-adjusted food (g/d)] were extracted by principal component analysis. The Center for Epidemiologic Studies Depression Scale (CES-D) with a cut-off point of 16 was used to assess the prevalence of depression. Results A total of 97 subjects (12.3%) were classified as having depression. Four dietary patterns were identified: “Healthy”, “Western”, “Bread and confectionery”, and “Alcohol and accompanying” dietary patterns. After adjusting for potential confounders, the dietary patterns were not related to the risk of depression. Conclusions The present study failed to find associations between dietary patterns and the risk of depression. However, the interpretation of our results was hampered by the lack of certain data, including employment physical activity and longitudinal observations. Potential associations between dietary patterns and depressive symptoms were not completely ruled out. Future research exploring dietary patterns and depressive symptoms is warranted. PMID:23006931

  15. Association study of PARD3 gene polymorphisms with neural tube defects in a Chinese Han population.

    PubMed

    Gao, Yonghui; Chen, Xiaoli; Shangguan, Shaofang; Bao, Yihua; Lu, Xiaoli; Zou, Jizhen; Guo, Jin; Dai, Yaohua; Zhang, Ting

    2012-07-01

    Partitioning defective 3 homolog (PARD3) is an attractive candidate gene for screening neural tube defect (NTD) risk. To investigate the role of genetic variants in PARD3 on NTD risk, a case-control study was performed in a region of China with a high prevalence of NTDs. Total 53 single-nucleotide polymorphisms (SNPs) in PARD3 were genotyped in 224 fetuses with NTDs and in 253 normal fetuses. We found that 6 SNPs (rs2496720, rs2252655, rs3851068, rs118153230, rs10827337, and rs12218196) were statistically associated with NTDs (P < .05). After stratifying participants by NTD phenotypes, the significant association only existed in cases with anencephaly rather than spina bifida. Further haplotype analysis confirmed the association between PARD3 polymorphisms and NTD risk (global test P = 3.41e-008). Our results suggested that genetic variants in PARD3 were associated with susceptibility to NTDs in a Chinese Han population, and this association was affected by NTD phenotypes.

  16. Only severe COPD is associated with being underweight: results from a population survey.

    PubMed

    Eriksson, Berne; Backman, Helena; Bossios, Apostolos; Bjerg, Anders; Hedman, Linnea; Lindberg, Anne; Rönmark, Eva; Lundbäck, Bo

    2016-07-01

    Low body mass index (BMI) and malnutrition in chronic obstructive pulmonary disease (COPD) are associated with a poor prognosis. The prevalence of underweight, as well as overweight, in severity grades of COPD is sparsely investigated in studies of the general population and the associated patterns of risk factors are not well established. The aim of the present study was to determine the association between severity grades of airflow limitation in COPD, and both underweight and obesity when corrected for possible confounding factors. The study is based on pooled data from the OLIN (Obstructive Lung Disease in Northern Sweden) studies. Complete records with lung function, BMI and structured interview data were available from 3942 subjects (50.7% women and 49.3% men). COPD and severity grading were defined using the Global Initiative for Chronic Obstructive Lung Disease criteria. In sensitivity analyses, the lower limit of normal was used. The prevalence of underweight was 7.3% in severe COPD (grades 3 and 4) versus 2.0% in those with normal spirometry. The prevalence of obesity increased from 9.7% in grade 1, to 16.3% in grade 2 and 20.0% in severe COPD, versus 17.7% in those with normal spirometry. In adjusted analysis, of the COPD severity grades, only severe COPD was associated with underweight (OR 3.24, 95% CI 1.0004-10.5), while the COPD severity grades tended to be inversely associated with overweight.

  17. Only severe COPD is associated with being underweight: results from a population survey

    PubMed Central

    Backman, Helena; Bossios, Apostolos; Bjerg, Anders; Hedman, Linnea; Lindberg, Anne; Rönmark, Eva; Lundbäck, Bo

    2016-01-01

    Low body mass index (BMI) and malnutrition in chronic obstructive pulmonary disease (COPD) are associated with a poor prognosis. The prevalence of underweight, as well as overweight, in severity grades of COPD is sparsely investigated in studies of the general population and the associated patterns of risk factors are not well established. The aim of the present study was to determine the association between severity grades of airflow limitation in COPD, and both underweight and obesity when corrected for possible confounding factors. The study is based on pooled data from the OLIN (Obstructive Lung Disease in Northern Sweden) studies. Complete records with lung function, BMI and structured interview data were available from 3942 subjects (50.7% women and 49.3% men). COPD and severity grading were defined using the Global Initiative for Chronic Obstructive Lung Disease criteria. In sensitivity analyses, the lower limit of normal was used. The prevalence of underweight was 7.3% in severe COPD (grades 3 and 4) versus 2.0% in those with normal spirometry. The prevalence of obesity increased from 9.7% in grade 1, to 16.3% in grade 2 and 20.0% in severe COPD, versus 17.7% in those with normal spirometry. In adjusted analysis, of the COPD severity grades, only severe COPD was associated with underweight (OR 3.24, 95% CI 1.0004–10.5), while the COPD severity grades tended to be inversely associated with overweight. PMID:27730201

  18. Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping Population.

    PubMed

    Camargo, Anyela V; Mott, Richard; Gardner, Keith A; Mackay, Ian J; Corke, Fiona; Doonan, John H; Kim, Jan T; Bentley, Alison R

    2016-01-01

    The appropriate timing of developmental transitions is critical for adapting many crops to their local climatic conditions. Therefore, understanding the genetic basis of different aspects of phenology could be useful in highlighting mechanisms underpinning adaptation, with implications in breeding for climate change. For bread wheat (Triticum aestivum), the transition from vegetative to reproductive growth, the start and rate of leaf senescence and the relative timing of different stages of flowering and grain filling all contribute to plant performance. In this study we screened under Smart house conditions a large, multi-founder "NIAB elite MAGIC" wheat population, to evaluate the genetic elements that influence the timing of developmental stages in European elite varieties. This panel of recombinant inbred lines was derived from eight parents that are or recently have been grown commercially in the UK and Northern Europe. We undertook a detailed temporal phenotypic analysis under Smart house conditions of the population and its parents, to try to identify known or novel Quantitative Trait Loci associated with variation in the timing of key phenological stages in senescence. This analysis resulted in the detection of QTL interactions with novel traits such the time between "half of ear emergence above flag leaf ligule" and the onset of senescence at the flag leaf as well as traits associated with plant morphology such as stem height. In addition, strong correlations between several traits and the onset of senescence of the flag leaf were identified. This work establishes the value of systematically phenotyping genetically unstructured populations to reveal the genetic architecture underlying morphological variation in commercial wheat.

  19. Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping Population

    PubMed Central

    Camargo, Anyela V.; Mott, Richard; Gardner, Keith A.; Mackay, Ian J.; Corke, Fiona; Doonan, John H.; Kim, Jan T.; Bentley, Alison R.

    2016-01-01

    The appropriate timing of developmental transitions is critical for adapting many crops to their local climatic conditions. Therefore, understanding the genetic basis of different aspects of phenology could be useful in highlighting mechanisms underpinning adaptation, with implications in breeding for climate change. For bread wheat (Triticum aestivum), the transition from vegetative to reproductive growth, the start and rate of leaf senescence and the relative timing of different stages of flowering and grain filling all contribute to plant performance. In this study we screened under Smart house conditions a large, multi-founder “NIAB elite MAGIC” wheat population, to evaluate the genetic elements that influence the timing of developmental stages in European elite varieties. This panel of recombinant inbred lines was derived from eight parents that are or recently have been grown commercially in the UK and Northern Europe. We undertook a detailed temporal phenotypic analysis under Smart house conditions of the population and its parents, to try to identify known or novel Quantitative Trait Loci associated with variation in the timing of key phenological stages in senescence. This analysis resulted in the detection of QTL interactions with novel traits such the time between “half of ear emergence above flag leaf ligule” and the onset of senescence at the flag leaf as well as traits associated with plant morphology such as stem height. In addition, strong correlations between several traits and the onset of senescence of the flag leaf were identified. This work establishes the value of systematically phenotyping genetically unstructured populations to reveal the genetic architecture underlying morphological variation in commercial wheat. PMID:27822218

  20. Excessive interatrial adiposity is associated with left atrial remodeling, augmented contractile performance in asymptomatic population

    PubMed Central

    Lai, Yau-Huei; Yun, Chun-Ho; Su, Cheng-Huang; Yang, Fei-Shih; Yeh, Hung-I; Hou, Charles Jia-Yin; Wu, Tung-Hsin; Cury, Ricardo C; Bezerra, Hiram G

    2016-01-01

    Abstract Purpose Pericardial adipose tissue had been shown to exert local effects on adjacent cardiac structures. Data regarding the mechanistic link between such measures and left atrial (LA) structural/functional remodeling, a clinical hallmark of early stage heart failure (HF) and atrial fibrillation (AF) incidence, in asymptomatic population remain largely unexplored. Methods This retrospective analysis includes 356 subjects free from significant valvular disorders, atrial fibrillation, or clinical HF. Regional adipose tissue including pericardial and periaortic fat volumes, interatrial septal (IAS), and left atrioventricular groove (AVG) fat thickness were all measured by multidetector computed tomography (MDCT) (Aquarius 3D Workstation, TeraRecon, San Mateo, CA, USA). We measured LA volumes, booster performance, reservoir capacity as well as conduit function, and analyzed their association with adiposity measures. Results All four adiposity measures were positively associated with greater LA volumes (all P < 0.05), while IAS and AVG fat were also related to larger LA kinetic energy and worse reservoir capacity (both P < 0.01). In multivariate models, IAS fat thickness remained independently associated with larger LA volumes, increased LA kinetic energy and ejection force (β-coef: 0.17 & 0.15, both P < 0.05), and impaired LA reservoir and conduit function (β-coef: −0.20 & −0.12, both P < 0.05) after adjusting for clinical variables. Conclusion Accumulated visceral adiposity, especially interatrial fat depots, was associated with certain LA structural/functional remodeling characterized by impaired LA reservoir and conduit function though augmented kinetic energy and ejection performance. Our data suggested that interatrial fat burden may be associated with certain detrimental LA functions with compensatory LA adaptation in an asymptomatic population. PMID:27249809

  1. Association between interleukin-17 gene polymorphisms and the risk of laryngeal cancer in a Chinese population.

    PubMed

    Si, F Z; Feng, Y Q; Han, M

    2017-03-30

    IL-17 is associated with the occurrence and development of laryngeal cancer. However, no study has reported the association between IL-17 polymorphisms and laryngeal cancer susceptibility. Therefore, we analyzed the association of three polymorphism loci (rs2275913, 197 G/A; rs3748067, 383 A/G; and rs763780, 7488 T/C) of IL-17A and IL-17F with laryngeal cancer in the Chinese population. A case-control study was performed with 325 patients and 325 controls. Polymorphisms were detected by polymerase chain reaction and sequencing methods. SPSS17.0 software was used for statistical analysis. Allele and genotype frequencies of IL-17A rs2275913 were significantly different between patients and controls (P < 0.05). Frequencies of rs2275913 (197 G/A) AA and GA+AA genotypes compared to the GG genotype were significantly higher in patients than in controls, indicating the association of these genes with laryngeal cancer susceptibility; adjusted OR values were 2.54 (1.50-4.23) and 1.62 (1.19-2.17), respectively. Furthermore, individuals with the GA+AA genotype, compared to the GG genotype, aged ≤60 years, with smoking and alcohol consumption habits, and without a family history of cancer showed a higher cancer risk (OR = 2.74, 95%CI = 1.41-5.23; OR = 2.11, 95%CI = 1.21-3.55; OR = 1.91, 95%CI = 1.02-3.70; OR = 1.99, 95%CI = 1.08-3.39, respectively). In conclusion, the rs2275913 IL-17A (197 G/A) is associated with the incidence and development of laryngeal cancer in the Chinese population, and the AA and GA+AA genotypes harbor a high laryngeal cancer risk.

  2. Molecular characterization and population structure of Blueberry mosaic associated virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blueberry mosaic disease was first described in the 1950s but the causal agent has not been characterized to date. Next generation sequencing was employed in the identification of the causal agent and an undescribed ophiovirus, tentatively named as Blueberry mosaic associated virus (BlMaV), was dete...

  3. TMEM187-IRAK1 Polymorphisms Associated with Rheumatoid Arthritis Susceptibility in Tunisian and French Female Populations: Influence of Geographic Origin

    PubMed Central

    Lambert, Nathalie; Auger, Isabelle; Roudier, Jean; Sénéchal, Audrey; Geneviève, David; Lefranc, Gérard; Mrenda, Bakridine M'Madi; Benedito, Cécilia; Pardoux, Etienne; Gagez, Anne-Laure; Jorgensen, Christian; Mahjoub, Touhami

    2017-01-01

    Polymorphisms have been identified in the Xq28 locus as risk loci for rheumatoid arthritis (RA). Here, we investigated the association between three polymorphisms in the Xq28 region containing TMEM187 and IRAK1 (rs13397, rs1059703, and rs1059702) in two unstudied populations: Tunisian and French. The rs13397 G and rs1059703 T major alleles were significantly increased in RA patients (n = 408) compared with age-matched controls (n = 471) in both Tunisian and French women. These results were confirmed by a meta-analysis replication study including two independent Greek and Korean cohorts. The rs1059702 C major allele was significantly associated with RA, only with French women. In the French population, the GTC haplotype displayed a protective effect against RA, while the ATC, GCC, and GTT haplotypes conferred significant risk for RA. No association for these haplotypes was found in the Tunisian population. Our results replicated for the first time the association of the three Xq28 polymorphisms with RA risk in Tunisian and French populations and suggested that RA susceptibility is associated with TMEM187-IRAK1 polymorphisms in women. Our data further support the involvement of X chromosome in RA susceptibility and evidence ethnicities differences that might be explained by differences in the frequencies of SE HLA-DRB1 alleles between both populations. PMID:28271077

  4. An epidemiological analysis of potential associations between C-reactive protein, inflammation, and prostate cancer in the male US population using the 2009 - 2010 National Health and Nutrition Examination Survey (NHANES) data

    NASA Astrophysics Data System (ADS)

    St. Hill, Catherine; Lutfiyya, M. Nawal

    2015-08-01

    Prostate cancer is the second leading cause of cancer-related deaths in US males, yet much remains to be learned about the role of inflammation in its etiology. We hypothesized that preexisting exposure to chronic inflammatory conditions caused by infectious agents or inflammatory diseases increase the risk of prostate cancer. Using the 2009-2010 National Health and Nutrition Examination Survey, we examined the relationships between demographic variables, inflammation, infection, circulating plasma C-reactive protein (CRP), and the risk of occurrence of prostate cancer in US men over 18 years of age. Using IBM SPSS, we performed bivariate and logistic regression analyses using high CRP values as the dependent variable and five study covariates including prostate cancer status. From 2009 - 2010, an estimated 5,448,373 men reported having prostate cancer of which the majority were Caucasian (70.1%) and were aged 40 years and older (62.7%). Bivariate analyses demonstrated that high CRP was not associated with an increased risk of prostate cancer. Greater odds of having prostate cancer were revealed for men that had inflammation related to disease (OR = 1.029, CI 1.029-1.029) and those who were not taking drugs to control inflammation (OR = 1.330, CI 1.324-1.336). Men who did not have inflammation resulting from non-infectious diseases had greater odds of not having prostate cancer (OR = 1.031, CI 1.030-1.031). Logistic regression analysis yielded that men with the highest CRP values had greater odds of having higher household incomes and lower odds of having received higher education, being aged 40 years or older, being of a race or ethnicity different from other, and of having prostate cancer. Our results show that chronic inflammation of multiple etiologies is a risk factor for prostate cancer and that CRP is not associated with this increased risk. Further research is needed to elucidate the complex interactions between inflammation and prostate cancer.

  5. What affects response rates in primary healthcare-based programmes? An analysis of individual and unit-related factors associated with increased odds of non-response based on HCV screening in the general population in Poland

    PubMed Central

    Parda, Natalia; Stępień, Małgorzata; Zakrzewska, Karolina; Madaliński, Kazimierz; Kołakowska, Agnieszka; Godzik, Paulina; Rosińska, Magdalena

    2016-01-01

    Objectives Response rate in public health programmes may be a limiting factor. It is important to first consider their delivery and acceptability for the target. This study aimed at determining individual and unit-related factors associated with increased odds of non-response based on hepatitis C virus screening in primary healthcare. Design Primary healthcare units (PHCUs) were extracted from the Register of Health Care Centres. Each of the PHCUs was to enrol adult patients selected on a random basis. Data on the recruitment of PHCUs and patients were analysed. Multilevel modelling was applied to investigate individual and unit-related factors associated with non-response. Multilevel logistic model was developed with fixed effects and only a random intercept for the unit. Preliminary analysis included a random effect for unit and each of the individual or PHCU covariates separately. For each of the PHCU covariates, we applied a two-level model with individual covariates, unit random effect and a single fixed effect of this unit covariate. Setting This study was conducted in primary care units in selected provinces in Poland. Participants A total of 242 PHCUs and 24 480 adults were invited. Of them, 44 PHCUs and 20 939 patients agreed to participate. Both PHCUs and patients were randomly selected. Results Data on 44 PHCUs and 24 480 patients were analysed. PHCU-level factors and recruitment strategies were important predictors of non-response. Unit random effect was significant in all models. Larger and private units reported higher non-response rates, while for those with a history of running public health programmes the odds of non-response was lower. Proactive recruitment, more working hours devoted to the project and patient resulted in higher acceptance of the project. Higher number of personnel had no such effect. Conclusions Prior to the implementation of public health programme, several factors that could hinder its execution should be addressed. PMID

  6. Analysis of Population Substructure in Two Sympatric Populations of Gran Chaco, Argentina

    PubMed Central

    Sevini, Federica; Yao, Daniele Yang; Lomartire, Laura; Barbieri, Annalaura; Vianello, Dario; Ferri, Gianmarco; Moretti, Edgardo; Dasso, Maria Cristina; Garagnani, Paolo; Pettener, Davide; Franceschi, Claudio; Luiselli, Donata; Franceschi, Zelda Alice

    2013-01-01

    Sub-population structure and intricate kinship dynamics might introduce biases in molecular anthropology studies and could invalidate the efforts to understand diseases in highly admixed populations. In order to clarify the previously observed distribution pattern and morbidity of Chagas disease in Gran Chaco, Argentina, we studied two populations (Wichí and Criollos) recruited following an innovative bio-cultural model considering their complex cultural interactions. By reconstructing the genetic background and the structure of these two culturally different populations, the pattern of admixture, the correspondence between genealogical and genetic relationships, this integrated perspective had the power to validate data and to link the gap usually relying on a singular discipline. Although Wichí and Criollos share the same area, these sympatric populations are differentiated from the genetic point of view as revealed by Non Recombinant Y Chromosome genotyping resulting in significantly high Fst values and in a lower genetic variability in the Wichí population. Surprisingly, the Amerindian and the European components emerged with comparable amounts (20%) among Criollos and Wichí respectively. The detailed analysis of mitochondrial DNA showed that the two populations have as much as 87% of private haplotypes. Moreover, from the maternal perspective, despite a common Amerindian origin, an Andean and an Amazonian component emerged in Criollos and in Wichí respectively. Our approach allowed us to highlight that quite frequently there is a discrepancy between self-reported and genetic kinship. Indeed, if self-reported identity and kinship are usually utilized in population genetics as a reliable proxy for genetic identity and parental relationship, in our model populations appear to be the result not only and not simply of the genetic background but also of complex cultural determinants. This integrated approach paves the way to a rigorous reconstruction of

  7. Association between interleukin-18 variants and prostate cancer in Slovak population.

    PubMed

    Jurecekova, J; Babusikova, E; Kmetova Sivonova, M; Drobkova, H; Petras, M; Kliment, J; Halasova, E

    2017-01-01

    Interleukin-18 (IL-18), pro-inflammatory cytokine, plays important role in antitumor immunity. Polymorphisms in the IL-18 gene may lead to its altered production/activity and such modulate susceptibility to prostate cancer. The aim of this study was to evaluate the relationship between the -607 and +105 polymorphisms in the IL-18 gene and the risk of prostate cancer development and progression in Slovak population. The study was performed using 425 patients with prostate cancer, 270 patients with benign prostatic hyperplasia (BHP) and 263 healthy male controls. The statistically significant association of the -607 AC genotype (OR = 2.24; p < 0.001), CC genotype (OR = 1.86; p = 0.006), as well as C allele (OR = 1.27; p = 0.033) with the higher risk of prostate cancer development was observed. No association of the IL-18 -607 polymorphism and BHP was detected. The subset analysis revealed the significant association of the -607 AC genotype (OR = 2.01; p = 0.008) with development of higher-grade carcinomas (Gleason score ≥7) and the strong association of the -607 AC genotype (OR = 3.11; p < 0.001), CC genotype (OR = 2.96; p < 0.001) as well as C allele (OR = 1.51; p = 0.003) with the higher risk of prostate cancer development in the group of patients with PSA < 10 ng/ml. The -607 AC genotype was also connected with significantly higher IL-18 plasma concentrations. No association between the IL-18 +105 polymorphism and prostate cancer was observed. The analysis of the distribution of the -607 and +105 haplotypes showed significant association of the - 607 C/ + 105 A and - 607 C/ + 105 C haplotypes with the risk of prostate cancer. This study found that the IL-18 -607 promoter polymorphism could contribute to prostate cancer development in Slovak population. Its presence was also associated with development of higher-grade carcinomas and therefore may influences the prognosis and aggressiveness of the disease.

  8. The CLU gene rs11136000 variant is significantly associated with Alzheimer's disease in Caucasian and Asian populations.

    PubMed

    Liu, Guiyou; Wang, Haiyang; Liu, Jiafeng; Li, Jingbo; Li, Hali; Ma, Guoda; Jiang, Yongshuai; Chen, Zugen; Zhao, Bin; Li, Keshen

    2014-03-01

    Large-scale genomewide association studies have reported that the CLU rs11136000 polymorphism is significantly associated with Alzheimer's disease (AD) in people of Caucasian ancestry. Recently, this association was investigated in Asian populations (Chinese, Japanese, and Korean). However, these studies reported either a weak association or no association between the rs11136000 polymorphism and AD. We believe that this discrepancy may be caused by the relatively small sample size of the previous studies and the genetic heterogeneity of the rs11136000 polymorphism in AD among different populations. For this study, we searched the PubMed and AlzGene databases. We selected 18 independent studies (6 studies of Asian populations and 12 of populations of Caucasian ancestry) that evaluated the association between the rs11136000 polymorphism and AD using a case-control experimental design. We evaluated the genetic heterogeneity of the rs11136000 polymorphism in Caucasian and Asian populations. We then investigated the rs11136000 polymorphism by a meta-analysis in Asian populations using allele, dominant, and recessive models. We identified a significant association between rs11136000 and AD with the allele model (P = 2.00 × 10(-4)) and the dominant model (P = 5.00 × 10(-3)). Meanwhile, a similar genetic risk of the rs11136000 polymorphism in AD was observed in Asian and Caucasian populations. Further meta-analysis in pooled Asian and Caucasian populations indicated a more significant association with the allele (P = 8.30 × 10(-24)), dominant (P = 4.46 × 10(-17)), and recessive (P = 3.92 × 10(-12)) models. Collectively, our findings from this meta-analysis indicate that the effect of the CLU rs11136000 polymorphism on AD risk in Asian cohorts (Chinese, Japanese, and Korean) is consistent with the protective effect observed in Caucasian AD cohorts.

  9. Associations between Ionomic Profile and Metabolic Abnormalities in Human Population

    PubMed Central

    An, Peng; Yu, Danxia; Yu, Zhijie; Li, Huaixing; Sheng, Hongguang; Cai, Lu; Xue, Jun; Jing, Miao; Li, Yixue; Lin, Xu; Wang, Fudi

    2012-01-01

    Background Few studies assessed effects of individual and multiple ions simultaneously on metabolic outcomes, due to methodological limitation. Methodology/Principal Findings By combining advanced ionomics and mutual information, a quantifying measurement for mutual dependence between two random variables, we investigated associations of ion modules/networks with overweight/obesity, metabolic syndrome (MetS) and type 2 diabetes (T2DM) in 976 middle-aged Chinese men and women. Fasting plasma ions were measured by inductively coupled plasma mass spectroscopy. Significant ion modules were selected by mutual information to construct disease related ion networks. Plasma copper and phosphorus always ranked the first two among three specific ion networks associated with overweight/obesity, MetS and T2DM. Comparing the ranking of ion individually and in networks, three patterns were observed (1) “Individual ion,” such as potassium and chrome, which tends to work alone; (2) “Module ion,” such as iron in T2DM, which tends to act in modules/network; and (3) “Module-individual ion,” such as copper in overweight/obesity, which seems to work equivalently in either way. Conclusions In conclusion, by using the novel approach of the ionomics strategy and the information theory, we observed potential associations of ions individually or as modules/networks with metabolic disorders. Certainly, these findings need to be confirmed in future biological studies. PMID:22719963

  10. Evidence of Heterosis Associated with an Enzyme Locus in a Natural Population of Drosophila*

    PubMed Central

    Richmond, Rollin C.; Powell, Jeffrey R.

    1970-01-01

    A wild population of Drosophila paulistorum (Andean semispecies) was analyzed by starch gel electrophoresis for a sex-linked enzyme locus, Tetrazolium oxidase. The results of the analysis of F1 progenies from 106 single female lines from São José do Rio Prêto, Brazil, has allowed us to determine the genotype of 106 wild-collected females and 104 wild-collected males. The population is polymorphic for two alleles with frequencies of 0.56 and 0.44. The observed frequencies among the females of the two homozygotes were 0.23 and 0.13 and of the heterozygote 0.64. The deviation from the frequencies expected according to the Hardy-Weinberg formula is statistically significant (P < 0.005). There is a substantial excess of heterozygotes over the expected number. This observation is interpreted to mean that this polymorphism is maintained by heterosis. This is probably the first reported case of heterosis associated with an enzyme locus in a natural population of Drosophila. Images PMID:5274455

  11. Breeding bird populations and habitat associations within the Savannah River Site (SRS).

    SciTech Connect

    Gauthreaux, Sidney, A.; Steven J. Wagner.

    2005-06-29

    Gauthreaux, Sidney, A., and Steven J. Wagner. 2005. Breeding bird populations and habitat associations within the Savannah River Site (SRS). Final Report. USDA Forest Service, Savannah River, Aiken, SC. 48 pp. Abstract: During the 1970's and 1980's a dramatic decline occurred in the populations of Neotropical migratory birds, species that breed in North America and winter south of the border in Central and South America and in the Caribbean. In 1991 an international initiative was mounted by U. S. governmental land management agencies, nongovernmental conservation agencies, and the academic and lay ornithological communities to understand the decline of Neotropical migratory birds in the Americas. In cooperation with the USDA Forest Service - Savannah River (FS - SR) we began 1992 a project directed to monitoring population densities of breeding birds using the Breeding Bird Census (BBC) methodology in selected habitats within the Savannah River Site SRS. In addition we related point count data on the occurrence of breeding Neotropical migrants and other bird species to the habitat data gathered by the Forest Inventory and Analysis (FIA) program of the USDA Forest Service and data on habitat treatments within forest stands.

  12. Agriculture, population growth, and statistical analysis of the radiocarbon record.

    PubMed

    Zahid, H Jabran; Robinson, Erick; Kelly, Robert L

    2016-01-26

    The human population has grown significantly since the onset of the Holocene about 12,000 y ago. Despite decades of research, the factors determining prehistoric population growth remain uncertain. Here, we examine measurements of the rate of growth of the prehistoric human population based on statistical analysis of the radiocarbon record. We find that, during most of the Holocene, human populations worldwide grew at a long-term annual rate of 0.04%. Statistical analysis of the radiocarbon record shows that transitioning farming societies experienced the same rate of growth as contemporaneous foraging societies. The same rate of growth measured for populations dwelling in a range of environments and practicing a variety of subsistence strategies suggests that the global climate and/or endogenous biological factors, not adaptability to local environment or subsistence practices, regulated the long-term growth of the human population during most of the Holocene. Our results demonstrate that statistical analyses of large ensembles of radiocarbon dates are robust and valuable for quantitatively investigating the demography of prehistoric human populations worldwide.

  13. Agriculture, population growth, and statistical analysis of the radiocarbon record

    PubMed Central

    Zahid, H. Jabran; Robinson, Erick; Kelly, Robert L.

    2016-01-01

    The human population has grown significantly since the onset of the Holocene about 12,000 y ago. Despite decades of research, the factors determining prehistoric population growth remain uncertain. Here, we examine measurements of the rate of growth of the prehistoric human population based on statistical analysis of the radiocarbon record. We find that, during most of the Holocene, human populations worldwide grew at a long-term annual rate of 0.04%. Statistical analysis of the radiocarbon record shows that transitioning farming societies experienced the same rate of growth as contemporaneous foraging societies. The same rate of growth measured for populations dwelling in a range of environments and practicing a variety of subsistence strategies suggests that the global climate and/or endogenous biological factors, not adaptability to local environment or subsistence practices, regulated the long-term growth of the human population during most of the Holocene. Our results demonstrate that statistical analyses of large ensembles of radiocarbon dates are robust and valuable for quantitatively investigating the demography of prehistoric human populations worldwide. PMID:26699457

  14. IL10 Variant g.5311A Is Associated with Visceral Leishmaniasis in Indian Population

    PubMed Central

    Mishra, Anshuman; Nizamuddin, Sheikh; Arekatla, Geethika; Prakash, Satya; Dewangan, Hemlata; Dominic, Abishai; Mishra, Abhishek; Sudhakar, Digumarthi V. S.; Parine, Narasimha R.; Tupperwar, Nitin C.; Thangaraj, Kumarasamy

    2015-01-01

    Background Visceral leishmaniasis (VL) is a multifactorial disease, where the host genetics play a significant role in determining the disease outcome. The immunological role of anti-inflammatory cytokine, Interleukin 10 (IL10), has been well-documented in parasite infections and considered as a key regulatory cytokine for VL. Although VL patients in India display high level of IL10 in blood serum, no genetic study has been conducted to assess the VL susceptibility / resistance. Therefore, the aim of this study is to investigate the role of IL10 variations in Indian VL; and to estimate the distribution of disease associated allele in diverse Indian populations. Methodology All the exons and exon-intron boundaries of IL10 were sequenced in 184 VL patients along with 172 ethnically matched controls from VL endemic region of India. Result and Discussion Our analysis revealed four variations; rs1518111 (2195 A>G, intron), rs1554286 (2607 C>T, intron), rs3024496 (4976 T>C, 3’ UTR) and rs3024498 (5311 A>G, 3’ UTR). Of these, a variant g.5311A is significantly associated with VL (χ2=18.87; p =0.00001). In silico approaches have shown that a putative micro RNA binding site (miR-4321) is lost in rs3024498 mRNA. Further, analysis of the above four variations in 1138 individuals from 34 ethnic populations, representing different social and linguistic groups who are inhabited in different geographical regions of India, showed variable frequency. Interestingly, we have found, majority of the tribal populations have low frequency of VL (‘A’ of rs3024498); and high frequency of leprosy (‘T’ of rs1554286), and Behcet’s (‘A’ of rs1518111) associated alleles, whereas these were vice versa in castes. Our findings suggest that majority of tribal populations of India carry the protected / less severe allele against VL, while risk / more severe allele for leprosy and Behcet’s disease. This study has potential implications in counseling and management of VL and other

  15. Circulating irisin levels are associated with lipid and uric acid metabolism in a Chinese population.

    PubMed

    Tang, Shanshan; Zhang, Rong; Jiang, Feng; Wang, Jie; Chen, Miao; Peng, Danfeng; Yan, Jing; Wang, Shiyun; Bao, Yuqian; Hu, Cheng; Jia, Weiping

    2015-06-26

    Irisin is a novel hormone secreted by skeletal muscle after exercise, which may ameliorate insulin resistance. In this study, we aimed to explore the relationship between circulating irisin levels and type 2 diabetes (T2DM) as well as related metabolic traits in a Chinese population. A total of 203 subjects were recruited. Of these, 68 subjects with NGT, 63 subjects with IGR and 72 subjects with new-onset T2DM. Circulating irisin levels were measured by ELISA. Detailed clinical investigations and biochemistry measurements were carried out in all of the subjects. Multivariate linear regression analysis was performed to assess the association between irisin levels and related metabolic characteristics. All subjects were classified into normal weight and overweight/obese subgroups according to body mass index (BMI). No significant differences in circulating irisin levels were identified among the three groups (p=0.9741). After adjusting for covariates, multiple linear regression analysis revealed that serum irisin level was independently and significantly associated with total cholesterol (p=0.0005), low-density lipoprotein cholesterol (p=0.0014), fasting fatty acids (p=0.0402) and uric acid (p=0.0062). By dividing the serum irisin levels into three tertile group, the values of total cholesterol, low-density lipoprotein cholesterol, fasting fatty acids and uric acid were all increased significantly with the increase of irisin (p<0.05) . Moreover, serum irisin levels remain closely related to total cholesterol in both normal weight and overweight/obese subgroups. Our study suggests that circulating irisin concentrations are significantly associated with lipid and uric acid metabolism in a Chinese population. This article is protected by copyright. All rights reserved.

  16. High Vitamin D Consumption Is Inversely Associated with Cardiovascular Disease Risk in an Urban Mexican Population

    PubMed Central

    Flores, Mario; Salazar-Martínez, Eduardo

    2016-01-01

    Background Vitamin D deficiency is a major global public health problem. Recent epidemiological studies have assessed the relationship between vitamin D and multiple outcomes, including cardiovascular disease. However, this evidence is limited and inconclusive. Our purpose in this study was to evaluate the association between dietary vitamin D intake and cardiovascular disease risk in adult Mexican population. Methods We conducted a cross-sectional analysis with the baseline data from 6294 men and women aged 20–80 years participating in the Health Workers Cohort Study. Data on sociodemographic, lifestyle, and medical history factors were collected with a self-administered questionnaire. Dietary intake was evaluated by using a semi-quantitative food-frequency questionnaire. Cardiovascular disease risk was calculated using a recalibration of the Framingham heart disease prediction score. To evaluate the association between vitamin D intake and 10-year cardiovascular disease risk, odds ratios (OR) and 95% confidence intervals (95% CI) were calculated using multiple logistic regression analysis. Results A total of 6294 subjects (1820 men and 4474 women) with a mean age of 42 years, were included. Of these, subjects in the highest quintile of vitamin D intake presented lower levels of triglycerides 14.6 mg/dL (P for trend = 0.001); 2.0 cm less in waist circumference (P for trend = 0.001) and 0.8 points less in the Framingham cardiovascular disease risk score (P for trend = 0.002) compared with the subjects in the lower quintile of vitamin D intake. Additionally, participants in the highest quintile of vitamin D consumption were less likely to develop elevated 10-year cardiovascular disease risk, compared with those in the lowest quintile (OR = 0.51; 95%CI: 0.33, 0.77; P for trend = 0.007). Conclusion Our data suggest that higher consumption of vitamin D is associated with a reduced risk of cardiovascular disease in Mexican population. PMID:27893863

  17. Genetic analysis reveals demographic fragmentation of grizzly bears yielding vulnerably small populations.

    PubMed

    Proctor, Michael F; McLellan, Bruce N; Strobeck, Curtis; Barclay, Robert M R

    2005-11-22

    Ecosystem conservation requires the presence of native carnivores, yet in North America, the distributions of many larger carnivores have contracted. Large carnivores live at low densities and require large areas to thrive at the population level. Therefore, if human-dominated landscapes fragment remaining carnivore populations, small and demographically vulnerable populations may result. Grizzly bear range contraction in the conterminous USA has left four fragmented populations, three of which remain along the Canada-USA border. A tenet of grizzly bear conservation is that the viability of these populations requires demographic linkage (i.e. inter-population movement of both sexes) to Canadian bears. Using individual-based genetic analysis, our results suggest this demographic connection has been severed across their entire range in southern Canada by a highway and associated settlements, limiting female and reducing male movement. Two resulting populations are vulnerably small (< or =100 animals) and one of these is completely isolated. Our results suggest that these trans-border bear populations may be more threatened than previously thought and that conservation efforts must expand to include international connectivity management. They also demonstrate the ability of genetic analysis to detect gender-specific demographic population fragmentation in recently disturbed systems, a traditionally intractable yet increasingly important ecological measurement worldwide.

  18. Genetic analysis in the Collaborative Cross breeding population

    PubMed Central

    Philip, Vivek M.; Sokoloff, Greta; Ackert-Bicknell, Cheryl L.; Striz, Martin; Branstetter, Lisa; Beckmann, Melissa A.; Spence, Jason S.; Jackson, Barbara L.; Galloway, Leslie D.; Barker, Paul; Wymore, Ann M.; Hunsicker, Patricia R.; Durtschi, David C.; Shaw, Ginger S.; Shinpock, Sarah; Manly, Kenneth F.; Miller, Darla R.; Donohue, Kevin D.; Culiat, Cymbeline T.; Churchill, Gary A.; Lariviere, William R.; Palmer, Abraham A.; O'Hara, Bruce F.; Voy, Brynn H.; Chesler, Elissa J.

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. PMID:21734011

  19. Streamflow Flashiness in the Mid-Atlantic Region: A Historical Analysis of Flashiness and Population Density, Imperviousness and Urban Development

    EPA Science Inventory

    The relationship between stream flashiness and watershed-scale estimates of percent imperviousness, urban development, and population density were used in an historic landscape analysis at the individual watershed spatial scale. GIS technology was employed to spatially associate...

  20. Association between intermediate uveitis and toxocariasis in the Korean population

    PubMed Central

    Kwon, Jin-woo; Sim, Yoonseob; Jee, Donghyun

    2017-01-01

    Abstract The aim of the study was to investigate the characteristics of ocular toxocariasis (OT) presenting with intermediate uveitis in the Korean population. We studied intermediate uveitis patients using ocular and systemic evaluations and a Toxocara IgG serology test. Of 50 intermediate uveitis patients, 19 were seropositive for Toxocara IgG. Of the 19 OT patients, 4 presented with recurrence within 6 months and were significantly younger than nonrecurrence patients (P = 0.009). Thirteen patients had a history of eating raw cow liver. There were 14 males and 5 females in the OT group, and 11 males and 20 females in the non-OT group (P = 0.009). There was bilateral involvement in 7 out of 19 patients in the OT group, and 20 out of 31 patients in non-OT group (P = 0.033). Intermediate uveitis patients in OT were predominately male and had more unilateral presentation than non-OT patients. PMID:28151857

  1. Association between intermediate uveitis and toxocariasis in the Korean population.

    PubMed

    Kwon, Jin-Woo; Sim, Yoonseob; Jee, Donghyun

    2017-02-01

    The aim of the study was to investigate the characteristics of ocular toxocariasis (OT) presenting with intermediate uveitis in the Korean population.We studied intermediate uveitis patients using ocular and systemic evaluations and a Toxocara IgG serology test.Of 50 intermediate uveitis patients, 19 were seropositive for Toxocara IgG. Of the 19 OT patients, 4 presented with recurrence within 6 months and were significantly younger than nonrecurrence patients (P = 0.009). Thirteen patients had a history of eating raw cow liver.There were 14 males and 5 females in the OT group, and 11 males and 20 females in the non-OT group (P = 0.009). There was bilateral involvement in 7 out of 19 patients in the OT group, and 20 out of 31 patients in non-OT group (P = 0.033).Intermediate uveitis patients in OT were predominately male and had more unilateral presentation than non-OT patients.

  2. Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population.

    PubMed

    Dayo, G K; Gautier, M; Berthier, D; Poivey, J P; Sidibe, I; Bengaly, Z; Eggen, A; Boichard, D; Thevenon, S

    2012-04-01

    African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker.

  3. Association of ACE Gene I/D polymorphism with migraine in Kashmiri population

    PubMed Central

    Wani, Irfan Yousuf; Sheikh, Saleem; Shah, Zafar Amin; Pandith, Arshid A.; Wani, Mushtaq; Asimi, Ravouf; Wani, Maqbool; Sheikh, Shahnawaz; Mehraj, Iqra

    2016-01-01

    Introduction: Migraine is a complex, recurrent headache disorder that is one of the most common complaints in neurology practice. The role of various genes in its pathogenesis is being studied. We did this study to see whether an association exists between ACE gene I/D polymorphism and migraine in our region. Materials and Methods: The study included 100 patients diagnosed with migraine and 121 healthy controls. The study subject were age and gender matched. The analysis was based on Polymerase Chain Reaction (PCR) and included following steps: DNA extraction from blood, PCR and Restriction Fragment Length Polymorphism (RFLP). Results: Out of 100 cases, 69 were females and 31 were males. Fifty-seven were having migraine without aura and 43 had migraine with aura. 45 of the cases had II polymorphism, 40 had ID polymorphism and 15 had DD polymorphism in ACE gene. Conclusion: We were not able to find a statistically significant association between ACE gene I/D polymorphism with migraine. The reason for difference in results between our study and other studies could be because of different ethnicity in study populations. So a continuous research is needed in this regard in order to find the genes and different polymorphism that increase the susceptibility of Kashmiri population to migraine. PMID:27011636

  4. Exploratory Factor Analysis of Self-Reported Symptoms in a Large, Population-Based Military Cohort

    DTIC Science & Technology

    2010-10-15

    analysis suggests that it could be a manifestation of it or another condition associated with anxiety such as fibromyalgia [33]. Factor 3...military population. However, general muscle pain can accompany many other illnesses, such as infectious diseases, autoimmune disorders, fibromyalgia ...Rosenberg R, Bach FW, Jensen TS. Depression, anxiety, health-related quality of life and pain in patients with chronic fibromyalgia and neuropathic pain

  5. The association of adjuvant therapy with survival at the population level following pancreatic adenocarcinoma resection

    PubMed Central

    Kagedan, Daniel J.; Raju, Ravish S.; Dixon, Matthew E.; Shin, Elizabeth; Li, Qing; Liu, Ning; Elmi, Maryam; El-Sedfy, Abraham; Paszat, Lawrence; Kiss, Alexander; Earle, Craig C.; Mittmann, Nicole; Coburn, Natalie G.

    2016-01-01

    Background Using a retrospective observational cohort approach, the overall survival (OS) following curative-intent resection of pancreatic adenocarcinoma (PC) was defined at the population level according to adjuvant treatment, and predictors of OS were identified. Methods Patients undergoing resection of PC in the province of Ontario between 2005 and 2010 were identified using the provincial cancer registry, and linked to databases that include all treatments received and outcomes experienced in the province. Pathology reports were abstracted for staging and margin status. Patients were identified as having received chemotherapy (CT), chemoradiation therapy (CRT), or no adjuvant treatment (NAT). Kaplan–Meier survival analysis of patients surviving ≥6 months was performed, and predictors of OS identified by log-rank test. Cox multivariable analysis was used to define independent predictors of OS. Results Among the 473 patients undergoing PC resection, the median survival was 17.8 months; for the 397 who survived ≥6 months following surgery, the 5-year OS for the CT, CRT, and NAT groups was 21%, 16%, and 17%, respectively (p = 0.584). Lymph node-negative patients demonstrated improved OS associated with chemotherapy on multivariable analysis (HR = 2.20, 95% CI = 1.25–3.83 for NAT vs. CT). Conclusions Following PC resection, only patients with negative lymph nodes demonstrated improved OS associated with adjuvant chemotherapy. PMID:27037203

  6. Associations between Common Variants in Iron-Related Genes with Haematological Traits in Populations of African Ancestry

    PubMed Central

    Tanaka, Toshiko; Towers, G. Wayne; Verhoef, Hans; Veenemans, Jacobien; Talsma, Elise F.; Harryvan, Jan; Boekschoten, Mark V.; Feskens, Edith J.; Melse-Boonstra, Alida

    2016-01-01

    Background Large genome-wide association (GWA) studies of European ancestry individuals have identified multiple genetic variants influencing iron status. Studies on the generalizability of these associations to African ancestry populations have been limited. These studies are important given interethnic differences in iron status and the disproportionate burden of iron deficiency among African ancestry populations. Methods We tested the associations of 20 previously identified iron status-associated single nucleotide polymorphisms (SNPs) in 628 Kenyans, 609 Tanzanians, 608 South Africans and 228 African Americans. In each study, we examined the associations present between 20 SNPs with ferritin and haemoglobin, adjusting for age, sex and CRP levels. Results In the meta analysis including all 4 African ancestry cohorts, we replicated previously reported associations with lowered haemoglobin concentrations for rs2413450 (β = -0.19, P = 0.02) and rs4820268 (β = -0.16, P = 0.04) in TMPRSS6. An association with increased ferritin concentrations was also confirmed for rs1867504 in TF (β = 1.04, P = <0.0001) in the meta analysis including the African cohorts only. Conclusions In all meta analyses, we only replicated 4 of the 20 single nucleotide polymorphisms reported to be associated with iron status in large GWA studies of European ancestry individuals. While there is now evidence for the associations of a number of genetic variants with iron status in both European and African ancestry populations, the considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of iron status in ethnically diverse populations. PMID:27332551

  7. Association of methylenetetrahydrofolate reductase (MTHFR) gene polymorphism with ischemic stroke in the Eastern Chinese Han population.

    PubMed

    Lv, Q-Q; Lu, J; Sun, H; Zhang, J-S

    2015-04-27

    The association between the MTHFR genetic polymorphism and ischemic stroke has been reported by a number of investigators. However, the results have been controversial and conflicting. The aim of this study was to explore the association between the MTHFR variants C677T and A1298C and the risk of ischemic stroke in an Eastern Chinese Han population. A total of 199 patients with ischemic stroke and 241 controls were recruited. Genotyping of the MTHFR C677T and A1298C polymorphisms was carried out using the Taqman 7900HT Sequence Detection System. The overall estimates (odds ratio: OR) for the allele (C) and genotype (AC+CC) of the A1298C polymorphism were 1.57 [95% confidence interval (CI) = 1.16-2.10], and 2.36 (95%CI = 1.39-4.00), respectively, establishing significant association of the MTHFR A1298C polymorphism with ischemic stroke. In contrast, there were no statistically significant differences compared to controls between MTHFR C677T polymorphic variants in the association ischemic stroke risk. Furthermore, haplotype-based analysis demonstrated that compared with the C-677-A-1298 haplotype, the C-677-C-1298 and T-677-C-1298 haplotypes showed significant increased risk of ischemic stroke (OR = 1.56; 95%CI = 1.07- 2.2; P = 0.02; OR = 1.76; 95%CI = 1.17-2.65; P < 0.01, respectively). We concluded that the A1298C polymorphism and the haplotypes C-677-C-1298 and T-677-C-1298 in MTHFR might modulate the risk of ischemic stroke in the Eastern Chinese Han population.

  8. The Association Between Oxidative Stress and Depressive Symptom Scores in Elderly Population: A Repeated Panel Study

    PubMed Central

    2016-01-01

    Objectives Previous epidemiological studies about oxidative stress and depression are limited by hospital-based case-control design, single-time measurements of oxidative stress biomarkers, and the small number of study participants. Therefore, in this study, we analyzed the association between biomarker of oxidative stress and depressive symptom scores using repeatedly measured panel data from a community-dwelling elderly population. Methods From 2008 to 2010, a total of 478 elderly participants residing in Seoul, Korea, were evaluated three times. Participants underwent the Korean version of the Short Form Generic Depression Scale (SGDS-K) test for screening depression, and urinary malondialdehyde (MDA) levels were measured as an oxidative stress biomarker. We used a generalized estimating equation with a compound symmetry covariance structure to estimate the effects of oxidative stress on depressive symptom scores. Results A two-fold increase in urinary MDA concentration was significantly associated with a 33.88% (95% confidence interval [CI], 21.59% to 47.42%) increase in total SGDS-K scores. In subgroup analyses by gender, a two-fold increase in urinary MDA concentration was significantly associated with increased SGDS-K scores in both men and women (men: 30.88%; 95% CI, 10.24% to 55.37%; women: 34.77%; 95% CI, 20.09% to 51.25%). In bivariate analysis after an SGDS-K score ≥8 was defined as depression, the third and the fourth urinary MDA quartiles showed a significantly increased odds ratio(OR) of depression compared to the lowest urinary MDA quartile (third quartile OR, 6.51; 95% CI, 1.77 to 24.00; fourth quartile OR, 7.11; 95% CI, 1.99 to 25.42). Conclusions Our study suggests a significant association between oxidative stress and depressive symptoms in the elderly population. PMID:27744668

  9. Loss-of-function mutations in filaggrin gene associate with psoriasis vulgaris in Chinese population.

    PubMed

    Hu, Zhengmao; Xiong, Zhimin; Xu, Xiaojuan; Li, Fangfang; Lu, Lina; Li, Wei; Su, Juan; Liu, Yalan; Liu, Deyuan; Xie, Zhiguo; Peng, Yu; Kuang, Yehong; Wu, Lisha; Zhang, Jianglin; Pan, Qian; Tang, Beisha; Chen, Xiang; Xia, Kun

    2012-07-01

    Loss-of-function mutations in filaggrin gene (FLG; OMIM #135940) have been reported to cause the semi-dominant keratinizing disorders such as ichthyosis vulgaris (IV; OMIM #146700) and atopic dermatitis (AD; OMIM #605803). Recent linkage analysis and immunohistochemical studies suggest the possible contribution of FLG to psoriatic susceptibility. However, no susceptibility variant in FLG gene associated with psoriasis (OMIM #177900) has been identified. In this study, we identified a non-sense mutation of FLG (p.K4022X) in a Chinese psoriasis/IV coexisting family. The homozygous p.K4022X mutation was detected in a psoriasis patient, whereas the heterozygous p.K4022X mutation was identified in two IV patients and four apparently normal family members. We also genotyped p.K4022X variant in 441 sporadic Chinese psoriasis patients and found homozygous mutation in two patients, while no homozygous variant was found in 500 control individuals. After sequencing the entire coding region of FLG gene in 441 psoriasis patients, we identified another five mutations (p.R826X, p.W2583X, c.7945delA, c.3321delA and p.Q2417X). Although all six FLG mutations as a whole was not significantly associated with psoriasis (P = 0.105), mutation p.K4022X was significantly associated with psoriasis (P < 0.05). Our data thus indicates an association of FLG with psoriasis in Chinese population.

  10. Helicobacter pylori infection is associated with the presence of thyroid nodules in the euthyroid population.

    PubMed

    Shen, Zhe; Qin, Yu'e; Liu, Yi; Lu, Yi; Munker, Stefan; Chen, Lihua; Yu, Chaohui; Chen, Peng; Li, Youming

    2013-01-01

    Helicobacter pylori infection is associated with extragastric diseases. The thyroid may be one of the targets of chronic inflammation. Here, we sought to investigate whether H. pylori infections were associated with the presence of thyroid nodules. A total of 988 euthyroid subjects from China were included in this cross-sectional study. Four hundred thirty-five (44.0%) subjects were diagnosed as having thyroid nodules, and 486 (49.2%) were diagnosed with H. pylori infections. The thyroid nodules group had a higher proportion of H. pylori infections than the control group (P = 0.002). Free thyroxine (FT4) levels were lower and the prevalence of thyroid nodules was higher in patients with H. pylori infection compared to those without infection, even after adjustment for age, gender, and body mass index (BMI; all P < 0.05). The prevalence of H. pylori infection showed a decreasing trend as serum FT4 level increased (P(trend) = 0.020). Stepwise logistic regression analysis showed that H. pylori infection was significantly associated with the risk of thyroid nodules (odds ratio: 1.390, 95% confidence interval: 1.059-1.824, P = 0.018). Our results suggested that H. pylori infections were positively associated with the presence of thyroid nodules in the euthyroid population, whose thyroid functions were in the reference range.

  11. Association between oral malodour and periodontal disease-related parameters in a population of 71 Israelis.

    PubMed

    Stamou, E; Kozlovsky, A; Rosenberg, M

    2005-01-01

    The aim of the present study was to determine whether oral malodour and periodontal disease parameters are associated with one another in 71 Israeli subjects (mean age 36.2 +/- 18.4; ages ranging from 15 to 65). Parameters measured included whole mouth odour judge scoring, Halimeter, OK to Kiss test, gingival index, plaque index and probing depth. Odour judge scores were significantly associated with Halimeter (r = 0.55; P < 0.001), as well as the OK to Kiss test (r = 0.52; P < 0.001). However, neither gingival index, plaque index nor probing depth was significantly associated with odour judge scores or Halimeter scores. Logistic regression analysis showed that both Halimeter and OK to Kiss scores factored significantly (P = 0.005 and 0.018, respectively, odds ratios 14.9 and 2.7, respectively) in predicting the severity of oral malodour. Results suggest that in the population studied, periodontal health and oral malodour are not associated with one another.

  12. Association study of polymorphisms between the Radixin gene and rheumatoid arthritis in a Korean population.

    PubMed

    Kim, H-K; Joo, J-S; Lee, H-Y; Kwon, J-T; Sohn, D-R; Hong, S-J; Kim, H-J

    2014-05-09

    Radixin (RDX) is part of the ezrin-radixin-moesin (ERM) protein family. It functions as a membrane-cytoskeletal linker in actin-rich cell surface structures and is thought to be essential for cortical cytoskeleton organization, cell motility, adhesion, and proliferation. An increase in phosphorylated ERM in fibroblast-like synoviocytes contributes to rheumatoid arthritis (RA) synovial hyperplasia. We examined the genetic association between the RDX gene and RA in a Korean population. To identify the relationship between RDX gene polymorphisms and RA, we genotyped 2 single nucleotide polymorphisms (SNPs; rs11213326 and rs12575162) of RDX using a direct sequencing method in 296 RA patients and 493 control subjects. In this study, the 2 SNPs showed no association with RA disease susceptibility. However, further analysis based on clinical information of the RA patient group showed that the SNPs were associated with the erythrocyte sedimentation rate (ESR) in RA patients. These data suggest an association between RDX polymorphisms and the clinical features of RA patients, particularly the ESR.

  13. Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level

    PubMed Central

    Takemura, Alison F.; Chien, Diana M.; Polz, Martin F.

    2013-01-01

    The Vibrionaceae, which encompasses several potential pathogens, including V. cholerae, the causative agent of cholera, and V. vulnificus, the deadliest seafood-borne pathogen, are a well-studied family of marine bacteria that thrive in diverse habitats. To elucidate the environmental conditions under which vibrios proliferate, numerous studies have examined correlations with bulk environmental variables—e.g., temperature, salinity, nitrogen, and phosphate—and association with potential host organisms. However, how meaningful these environmental associations are remains unclear because data are fragmented across studies with variable sampling and analysis methods. Here, we synthesize findings about Vibrio correlations and physical associations using a framework of increasingly fine environmental and taxonomic scales, to better understand their dynamics in the wild. We first conduct a meta-analysis to determine trends with respect to bulk water environmental variables, and find that while temperature and salinity are generally strongly predictive correlates, other parameters are inconsistent and overall patterns depend on taxonomic resolution. Based on the hypothesis that dynamics may better correlate with more narrowly defined niches, we review evidence for specific association with plants, algae, zooplankton, and animals. We find that Vibrio are attached to many organisms, though evidence for enrichment compared to the water column is often lacking. Additionally, contrary to the notion that they flourish predominantly while attached, Vibrio can have, at least temporarily, a free-living lifestyle and even engage in massive blooms. Fine-scale sampling from the water column has enabled identification of such lifestyle preferences for ecologically cohesive populations, and future efforts will benefit from similar analysis at fine genetic and environmental sampling scales to describe the conditions, habitats, and resources shaping Vibrio dynamics. PMID:24575082

  14. Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

    PubMed

    Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

    2015-07-22

    Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

  15. Genome-wide association study with the risk of schizophrenia in a Korean population.

    PubMed

    Kim, Lyoung Hyo; Park, Byung Lae; Cheong, Hyun Sub; Namgoong, Suhg; Kim, Ji On; Kim, Jeong-Hyun; Shin, Joong-Gon; Park, Chul Soo; Kim, Bong-Jo; Kim, Jae Won; Choi, Ihn-Geun; Hwang, Jaeuk; Shin, Hyoung Doo; Woo, Sung-Il

    2016-03-01

    Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies.

  16. ZFAT gene variant association with multiple sclerosis in the Arabian Gulf population: A genetic basis for gender-associated susceptibility

    PubMed Central

    Bourguiba-Hachemi, Sonia; Ashkanani, Tebah K.; Kadhem, Fatema J.; Almawi, Wassim Y.; Alroughani, Raed; Fathallah, M. Dahmani

    2016-01-01

    Single nucleotide polymorphisms (SNPs) are useful genetic markers to investigate the onset of multiple sclerosis (MS). A genome wide association study identified 7 SNPs associated with interferon-β therapy response, however, not with MS risk in a Spanish population. To investigate these findings in a different cohort, the 7 SNPs were investigated in an Arabian Gulf population. The SNPs were analyzed in 268 subjects (156 patients and 112 healthy volunteers) from the Arabian Gulf region using restriction fragment length polymorphism-polymerase chain reaction (PCR) and KBioscience Competitive Allele Specific PCR genotyping methods. Associations between the SNPs and MS were investigated using logistic regression. The present study observed, for the first time, that in an Arabian Gulf population, the ZFAT rs733254 polymorphism (T>G) is a gender-specific risk marker for MS. ZFAT was associated with MS in women but not in men. The G variant was highly associated with the risk of MS [odds ratio (OR)=2.38 and 95% confidence interval (CI), 1.45–3.91); P=0.0014]. Whereas variant T was a significantly protective factor [OR=0.420 (95% CI, 0.25–0.69); P=0.0014, recessive model]. The findings of the present study provide a genetic basis for the gender-associated susceptibility to MS. In addition, this MS-associated rs733254 SNP may predict MS onset in females from the Arabian Gulf population. PMID:27572828

  17. Power comparison of admixture mapping and direct association analysis in genome-wide association studies.

    PubMed

    Qin, Huaizhen; Zhu, Xiaofeng

    2012-04-01

    When dense markers are available, one can interrogate almost every common variant across the genome via imputation and single nucleotide polymorphism (SNP) test, which has become a routine in current genome-wide association studies (GWASs). As a complement, admixture mapping exploits the long-range linkage disequilibrium (LD) generated by admixture between genetically distinct ancestral populations. It is then questionable whether admixture mapping analysis is still necessary in detecting the disease associated variants in admixed populations. We argue that admixture mapping is able to reduce the burden of massive comparisons in GWASs; it therefore can be a powerful tool to locate the disease variants with substantial allele frequency differences between ancestral populations. In this report we studied a two-stage approach, where candidate regions are defined by conducting admixture mapping at stage 1, and single SNP association tests are followed at stage 2 within the candidate regions defined at stage 1. We first established the genome-wide significance levels corresponding to the criteria to define the candidate regions at stage 1 by simulations. We next compared the power of the two-stage approach with direct association analysis. Our simulations suggest that the two-stage approach can be more powerful than the standard genome-wide association analysis when the allele frequency difference of a causal variant in ancestral populations, is larger than 0.4. Our conclusion is consistent with a theoretical prediction by Risch and Tang ([2006] Am J Hum Genet 79:S254). Surprisingly, our study also suggests that power can be improved when we use less strict criteria to define the candidate regions at stage 1.

  18. Important population viability analysis parameters for giant pandas (Aliuropoda melanoleuca).

    PubMed

    Gong, Minghao; Song, Yanling; Yang, Zhisong; Lin, Chen

    2012-06-01

    Population viability analysis (PVA) is a tool to evaluate the risk of extinction for endangered species and aid conservation decision-making. The quality of PVA output is dependent on parameters related to population dynamics and life-history; however, it has been difficult to collect this information for the giant panda (Aliuropoda melanoleuca), a rare and endangered mammal native to China, confined to some 30 fragmented habitat patches. Since giant pandas are long-lived, mature late, have lower reproductive rates, and show little sexual dimorphism, obtaining data to perform adequate PVA has been difficult. Here, we develop a parameter sensitivity index by modeling the dynamics of six giant panda populations in the Minshan Mountains, in order to determine the parameters most influential to giant panda populations. Our data shows that the giant panda populations are most sensitive to changes in four female parameters: initial breeding age, reproductive rate, mortality rate between age 0 and 1, and mortality rate of adults. The parameter sensitivity index strongly correlated with initial population size, as smaller populations were more sensitive to changes in these four variables. This model suggests that demographic parameters of females have more influence on the results of PVA, indicating that females may play a more important role in giant panda population dynamics than males. Consequently, reintroduction of female individuals to a small giant panda population should be a high priority for conservation efforts. Our findings form a technical basis for the coming program of giant panda reintroduction, and inform which parameters are crucial to successfully and feasibly monitoring wild giant panda populations.

  19. Genetic ancestry is associated with colorectal adenomas and adenocarcinomas in Latino populations.

    PubMed

    Hernandez-Suarez, Gustavo; Sanabria, Maria Carolina; Serrano, Marta; Herran, Oscar F; Perez, Jesus; Plata, Jose L; Zabaleta, Jovanny; Tenesa, Albert

    2014-10-01

    Colorectal cancer rates in Latin American countries are less than half of those observed in the United States. Latin Americans are the resultant of generations of an admixture of Native American, European, and African individuals. The potential role of genetic admixture in colorectal carcinogenesis has not been examined. We evaluate the association of genetic ancestry with colorectal neoplasms in 190 adenocarcinomas, 113 sporadic adenomas and 243 age- and sex-matched controls enrolled in a multicentric case-control study in Colombia. Individual ancestral genetic fractions were estimated using the STRUCTURE software, based on allele frequencies and assuming three distinct population origins. We used the Illumina Cancer Panel to genotype 1,421 sparse single-nucleotide polymorphisms (SNPs), and Northern and Western European ancestry, LWJ and Han Chinese in Beijing, China populations from the HapMap project as references. A total of 678 autosomal SNPs overlapped with the HapMap data set SNPs and were used for ancestry estimations. African mean ancestry fraction was higher in adenomas (0.13, 95% confidence interval (95% CI)=0.11-0.15) and cancer cases (0.14, 95% CI=0.12-0.16) compared with controls (0.11, 95% CI=0.10-0.12). Conditional logistic regression analysis, controlling for known risk factors, showed a positive association of African ancestry per 10% increase with both colorectal adenoma (odds ratio (OR)=1.12, 95% CI=0.97-1.30) and adenocarcinoma (OR=1.19, 95% CI=1.05-1.35). In conclusion, increased African ancestry (or variants linked to it) contributes to the increased susceptibility of colorectal cancer in admixed Latin American population.

  20. High dietary selenium intake is associated with less insulin resistance in the Newfoundland population.

    PubMed

    Wang, Yongbo; Lin, Meiju; Gao, Xiang; Pedram, Pardis; Du, Jianling; Vikram, Chandurkar; Gulliver, Wayne; Zhang, Hongwei; Sun, Guang

    2017-01-01

    As an essential nutrient, Selenium (Se) is involved in many metabolic activities including mimicking insulin function. Data on Se in various biological samples and insulin resistance are contradictory, moreover there is no large study available regarding the relationship of dietary Se intake with insulin resistance in the general population. To investigate the association between dietary Se intake and variation of insulin resistance in a large population based study, a total of 2420 subjects without diabetes from the CODING (Complex Diseases in the Newfoundland Population: Environment and Genetics) study were assessed. Dietary Se intake was evaluated from the Willett Food Frequency questionnaire. Fasting blood samples were used for the measurement of glucose and insulin. Insulin resistance was determined with the homeostasis model assessment (HOMA-IR). Body composition was measured using dual energy X-ray absorptiometry. Analysis of covariance showed that high HOMA-IR groups in both males and females had the lowest dietary Se intake (μg/kg/day) (p < 0.01), being 18% and 11% lower than low HOMA-IR groups respectively. Insulin resistance decreased with the increase of dietary Se intake in females but not in males after controlling for age, total calorie intake, physical activity level, serum calcium, serum magnesium, and body fat percentage (p < 0.01). Partial correlation analysis showed that dietary Se intake was negatively correlated with HOMA-IR after adjusting for the Se confounding factors in subjects whose dietary Se intake was below 1.6 μg/kg/day (r = -0.121 for males and -0.153 for females, p < 0.05). However, the negative correlation was no longer significant when dietary Se intake was above 1.6 μg/kg/day. Our findings suggest that higher dietary Se intake is beneficially correlated with lower insulin resistance when total dietary Se intake was below 1.6 μg/kg/day. Above this cutoff, this beneficial effect disappears.

  1. Association analysis for oxalate concentration in spinach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Screening and breeding low-oxalate germplasm is a major objective in spinach breeding. This research aims to conduct association analysis and identify SNP markers associated with oxalate concentration in spinach germplasm. A total of 310 spinach genotypes including 300 USDA germplasm accessions and ...

  2. Broader autism phenotype and nonverbal sensitivity: evidence for an association in the general population.

    PubMed

    Ingersoll, Brooke

    2010-05-01

    This study examined the relationship between characteristics of the Broader Autism Phenotype (BAP) and nonverbal sensitivity, the ability to interpret nonverbal aspects of communication, in a non-clinical sample of college students. One hundred and two participants completed a self-report measure of the BAP, the Autism Spectrum Quotient (AQ), and two tests of nonverbal sensitivity, the Test of Nonverbal Cue Knowledge (TONCK), and the Diagnostic Analysis of Nonverbal Accuracy 2 (DANVA2). AQ score was correlated with TONCK performance and number of errors on the adult faces subtest of the DANVA2, but not adult paralanguage or postures. These findings suggest that characteristics of ASD in the general population are associated with differences in both explicit and implicit knowledge of nonverbal cues.

  3. A combined linkage and association strategy identifies a variant near the GSTP1 gene associated with BMI in the Mexican population.

    PubMed

    Villamil-Ramírez, Hugo; León-Mimila, Paola; Macias-Kauffer, Luis R; Canizalez-Román, Adrián; Villalobos-Comparán, Marisela; León-Sicairos, Nidia; Vega-Badillo, Joel; Sánchez-Muñoz, Fausto; López-Contreras, Blanca; Morán-Ramos, Sofía; Villarreal-Molina, Teresa; Zurita, Luis C; Campos-Pérez, Francisco; Huertas-Vazquez, Adriana; Bojalil, Rafael; Romero-Hidalgo, Sandra; Aguilar-Salinas, Carlos A; Canizales-Quinteros, Samuel

    2017-03-01

    Obesity is a major public health concern in Mexico and worldwide. Although the estimated heritability is high, common variants identified by genome-wide association studies explain only a small proportion of this heritability. A combination of linkage and association strategies could be a more robust and powerful approach to identify other obesity-susceptibility variants. We thus sought to identify novel genetic variants associated with obesity-related traits in the Mexican population by combining these methods. We performed a genome-wide linkage scan for body mass index (BMI) and other obesity-related phenotypes in 16 Mexican families using the Sequential Oligogenic Linkage Analysis Routines Program. Associated single-nucleotide polymorphisms (SNPs) were tested for associations in an independent cohort. Two suggestive BMI-linkage peaks (logarithm of odds ⩾1.5) were observed at chromosomal regions 11q13 and 13q22. Only rs614080 in the 11q13 region was significantly associated with BMI and related traits in these families. This association was also significant in an independent cohort of Mexican adults. Moreover, this variant was significantly associated with GSTP1 gene expression levels in adipose tissue. In conclusion, the rs614080 SNP near the GSTP1 gene was significantly associated with BMI and GSTP1 expression levels in the Mexican population.

  4. Analysis of iris surface features in populations of diverse ancestry

    PubMed Central

    Edwards, Melissa; Cha, David; Krithika, S.; Johnson, Monique; Parra, Esteban J.

    2016-01-01

    There are many textural elements that can be found in the human eye, including Fuchs’ crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs’ crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs’ crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest. PMID:26909168

  5. Genetic association of rs1344706 in ZNF804A with bipolar disorder and schizophrenia susceptibility in Chinese populations

    PubMed Central

    Rao, Shuquan; Yao, Yao; Ryan, Joanne; Jin, Chunhui; Xu, Yong; Huang, Xinhe; Guo, Jianxiu; Wen, Yueqiang; Mao, Canquan; Meyre, David; Zhang, Fuquan

    2017-01-01

    Rs1344706 in the the zinc finger protein 804A (ZNF804A) gene has been identified to be associated with schizophrenia and bipolar disorder (BD) in Europeans. However, whether rs1344706 is associated with schizophrenia in Chinese populations remains inconclusive; furthermore, the association between rs1344706 and BD in Chinese populations has been rarely explored. To explore the association between rs1344706 and schizophrenia/BD in Chinese populations, we genotyped rs1344706 among 1128 Chinese subjects (537 patients with BD and 591 controls) and found that rs1344706 showed marginal allelic association with BD (P = 0.028) with T-allele being more prevalent in cases than that in controls (OR = 1.19, 95% CI 1.03–1.37). Meta-analysis of rs1344706 by pooling all available data showed that rs1344706 was significantly associated with BD (P = 0.001). Besides, positive association of rs1344706 with schizophrenia was observed in Northern Chinese (P = 0.005). Furthermore, ZNF804A is highly expressed in human and mouse brains, especially in prenatal stage. PMID:28120939

  6. AB111. Genetic variations rs11892031 and rs401681 are associated with bladder cancer risk in a Chinese population

    PubMed Central

    Zhang, Yu; Hu, Hailong; Tian, Dawei; Wu, Changli

    2016-01-01

    Objective Genome-wide association studies (GWAS) have identified a number of genetic variants associated with risk of bladder cancer in populations of European descent. Methods we assessed association of two of these variants, rs11892031 (2q37.1 region) and rs401681 (5p15.33 region) in a Chinese case-control study, which included 367 bladder cancer cases and 420 controls. Results We found that the AC genotype of rs11892031 was associated with remarkably decreased risk of bladder cancer [adjusted odds ratio (OR), 0.27; 95% confidence interval (CI), 0.09–0.81; P=0.019), compared with the AA genotype of rs11892031; and that CT/CC genotypes of rs401681 were associated with significantly increased risk of bladder cancer (adjusted OR, 1.79; 95% CI, 1.10–2.91; P=0.02), compared with the TT genotype of rs401681. We further conducted stratification analysis to examine the correlation between single nucleotide polymorphism (SNP) rs11892031/rs401681 and tumor grade/stage. Results showed that heterogeneity in ORs of tumor categories was not significant for either rs11892031 or rs401681 (P>0.05), indicating that the two SNPs seemingly do not associate with tumor grade and stage of bladder cancer in our study population. Conclusions The present study suggests that the SNPs rs11892031 and rs401681 are associated with bladder cancer risk in a Chinese population.

  7. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  8. Association of SNPs in the PPARγ gene and hypertension in a Mongolian population.

    PubMed

    Yang, L; Tian, R G; Chang, P Y; Yan, M R; Su, X L

    2015-12-29

    The association of single nucleotide polymorphisms (SNPs) in PPARγ with hypertension is controversial. The aim of the present study was to clarify the contributions of PPARγ genetic variants to hypertension through an association study. A total of 414 unrelated Mongolian herdsmen and 524 Han farmers were included in this study. Fourteen intronic SNPs were analyzed and genotyped using a polymerase chain reaction/ligase detection reaction assay. Prior to correction for multiple testing, the SNPs rs6802898 and rs12633551 were significantly associated with the prevalence of hypertension in the Han and Mongolian populations, respectively. The genetic association of each SNP with hypertension was individually tested using logistic regression. The SNP rs6802898 was associated with hypertension in both dominant (P = 0.033) and additive models (P = 0.026) in the Han population, whereas the SNP rs12633551 was associated with hypertension in both dominant (P = 0.014) and additive models (P = 0.0073) in the Mongolian population. Moreover, SNP rs12633551 had a significant effect on systolic and diastolic blood pressure response. However, none of these associations were statistically significant after Bonferroni correction for multiple testing, although there was a significant difference among the haplotypes in the Han and Mongolian populations. Interestingly, there was an association of the PPARγ haplotypes with hypertension even after Bonferroni correction. Thus, determination of the PPARγ haplotypes in different populations may prove informative for assessment of the genetic risk for hypertension.

  9. CYP7A1 genotypes and haplotypes associated with hypertension in an obese Han Chinese population.

    PubMed

    Fu, Lingyu; Zhao, Yanyan; Wu, Xiaomei; Liu, Hong; Shi, Jingpu; Lu, Jingyu; Zhou, Bo

    2011-06-01

    This study investigated the association between single-nucleotide polymorphisms (SNPs; rs3808607 and rs1125226) within the CYP7A1 promoter and hypertension susceptibility in a Han Chinese population. From 2003 through 2006, a population-based case-control study was performed in a cohort of 1187 randomly selected Han Chinese subjects. A sib-pair study for a transmission disequilibrium test analysis was carried out in 76 hypertensive (HT) families (n=312) from northeastern Liaoning province. SNPs were detected using real-time PCR. No significant differences were found in the genotype or allele frequencies of either SNP (P>0.05), with no excessive allele sharing. For rs3808607, the frequency of the AA genotype in obese hypertensive patients was 31.91%, significantly higher than in normotensive (NT) subjects (12.73%; odds ratio (OR)=3.21, 95% confidence interval (CI)=1.35-7.66). For rs3808607, the AA genotype frequency was significantly higher in obese male HT subjects (27.87%) than in matched NTs (7.41%; OR=4.83, 95% CI=1.03-22.65). After adjustment for environmental risk factors in obese participants, the AA genotype was associated with hypertension (OR=3.395, 95% CI=1.412-8.162). Among subjects with body mass index 28 kg m(-2), the HT and NT groups had significantly different frequencies of Hap I (C/C) and Hap IV (A/A). The frequencies of rs3808607 alleles in the CYP7A1 gene differed significantly between obese HT and NT men. Haplotypes I and IV were associated with hypertension in obese participants.

  10. Significant Association Between CAV1 Variant rs3807989 on 7p31 and Atrial Fibrillation in a Chinese Han Population

    PubMed Central

    Chen, Shanshan; Wang, Chuchu; Wang, Xiaojing; Xu, Chengqi; Wu, Manman; Wang, Pengxia; Tu, Xin; Wang, Qing K

    2015-01-01

    Background Recent genome-wide association studies (GWAS) in European ancestry populations revealed several genomic loci for atrial fibrillation (AF). We previously replicated the 4q25 locus (PITX2) and 16q22 locus (ZFHX3) in the Chinese population, but not the KCNN3 locus on 1q21. With single-nucleotide polymorphism rs3807989 in CAV1 encoding caveolin-1, however, controversial results were reported in 2 Chinese replication studies. Methods and Results Six remaining AF genetic loci from GWAS, including rs3807989/CAV1, rs593479/PRRX1, rs6479562/C9orf3, rs10824026/SYNPO2L, rs1152591/SYNE2, and rs7164883/HCN4, were analyzed in a Chinese Han population with 941 cases and 562 controls. Only rs3807989 showed significant association with AF (Padj=4.77×10−5), and the finding was replicated in 2 other independent populations with 709 cases and 2175 controls, 463 cases and 644 controls, and the combined population with a total of 2113 cases and 3381 controls (Padj=2.20×10−9; odds ratio [OR]=1.34 for major allele G). Meta-analysis, together with data from previous reports in Chinese and Japanese populations, also showed a significant association between rs3807989 and AF (P=3.40×10−4; OR=1.24 for allele G). We also found that rs3807989 showed a significant association with lone AF in 3 independent populations and in the combined population (Padj=3.85×10−8; OR=1.43 for major allele G). Conclusions The data in this study revealed a significant association between rs3807989 and AF in the Chinese Han population. Together with the findings that caveolin-1 interacts with potassium channels Kir2.1, KCNH2, and HCN4 and sodium channels Nav1.5 and Nav1.8, CAV1 becomes a strong candidate susceptibility gene for AF across different ethnic populations. This study is the first to show a significant association between rs3807989 and lone AF. PMID:25953654

  11. The association between Internet addiction and personality disorders in a general population-based sample

    PubMed Central

    Zadra, Sina; Bischof, Gallus; Besser, Bettina; Bischof, Anja; Meyer, Christian; John, Ulrich; Rumpf, Hans-Jürgen

    2016-01-01

    Background and aims Data on Internet addiction (IA) and its association with personality disorder are rare. Previous studies are largely restricted to clinical samples and insufficient measurement of IA. Methods Cross-sectional analysis data are based on a German sub-sample (n = 168; 86 males; 71 meeting criteria for IA) with increased levels of excessive Internet use derived from a general population sample (n = 15,023). IA was assessed with a comprehensive standardized interview using the structure of the Composite International Diagnostic Interview and the criteria of Internet Gaming Disorder as suggested in DSM-5. Impulsivity, attention deficit hyperactivity disorder, and self-esteem were assessed with the widely used questionnaires. Results Participants with IA showed higher frequencies of personality disorders (29.6%) compared to those without IA (9.3%; p < .001). In males with IA, Cluster C personality disorders were more prevalent than among non-addicted males. Compared to participants who had IA only, lower rates of remission of IA were found among participants with IA and additional cluster B personality disorder. Personality disorders were significantly associated with IA in multivariate analysis. Discussion and conclusion: Comorbidity of IA and personality disorders must be considered in prevention and treatment. PMID:28005417

  12. Prevalence, associated factors and management of insomnia in prison populations: An integrative review.

    PubMed

    Dewa, Lindsay H; Kyle, Simon D; Hassan, Lamiece; Shaw, Jenny; Senior, Jane

    2015-12-01

    Prisoners have many potential risk factors for insomnia including mental ill health and substance misuse. However, literature on prevalence, associated factors and management of insomnia in prison has yet to be systematically examined in this group. The paper objective was to synthesise and appraise the research that examines insomnia in a prison environment. An integrative literature review using thematic analysis was conducted to critically reflect on the current evidence base and outline a prospective research agenda. From the original 384 sourced papers, 33 met the inclusion criteria and were subsequently included for review. Definitions of insomnia and assessment tools used in studies varied considerably making the overall validity of findings uncertain. Notably, no studies used a recommended measure to assess insomnia disorder (ID). Thematic analysis yielded five themes: 1) the varied prevalence of insomnia; 2) the comorbidity of insomnia, psychiatric disorder and substance misuse; 3) the negative influence of prison-related situational and environmental factors on insomnia; 4) the role of hypnotic medication, and, 5) preliminary indications that non-pharmacological treatment can improve sleep. The methodological heterogeneity and variable quality across studies in the assessment of insomnia means conclusive data on prevalence, associated factors and management is lacking. Nonetheless, sleep problems are common and impairing in prison, are linked to comorbid conditions and negatively influenced by the prison environment, which routinely provides limited scope for effective management. Future research in prison populations is needed to reliably identify insomnia prevalence and determine how it can be managed effectively.

  13. Association of post stroke depression with social factors, insomnia, and neurological status in Chinese elderly population.

    PubMed

    Wang, Lingru; Tao, Yong; Chen, Yang; Wang, Hua; Zhou, Huadong; Fu, Xiaoyan

    2016-08-01

    The purpose of this study was to investigate the association of post stroke depression (PSD) with social factors, insomnia, and neurological status among elderly Chinese patients with ischemic stroke. Six hundred and eight patients over 60 years of age, who had suffered from a first episode of ischemic stroke within 7 days, were enrolled into the study. They were divided into PSD and non-PSD groups according to the Self-rating Depression Scale (SDS) scores. The association of PSD with social factors, insomnia, and neurological status was analyzed using multivariable logistic regression analysis. Compared with the patients who did not develop PSD, those with PSD reported adverse life events more frequently, and more subjects with PSD lived alone, had left carotid artery infarction and cortical infarction (P < 0.05), history of insomnia, and high National Institute of Health Stroke Scale (NIHSS) scores and low Barthel Index (BI) scores (P < 0.01). The multivariable logistic regression analysis showed that the occurrence of PSD was associated with a history of insomnia (HR = 1.59, 95 % CI 1.12-2.36, P < 0.01), NIHSS scores (HR = 2.45, 95 % CI 1.42-3.91, P < 0.01) and BI scores (HR = 2.56, 95 % CI 1.39-4.25, P < 0.01). Insomnia and the degree of neurological deficit were associated with PSD in an elderly population of Chinese people.

  14. Association between pterygium and obesity status in a South Korean population

    PubMed Central

    Nam, Ga Eun; Kim, Seonjoo; Paik, Ji-Sun; Kim, Hyun-Seung; Na, Kyung-Sun

    2016-01-01

    Abstract This study examined the association between pterygium and obesity status by examining a nationally representative sample of South Korean adults. This population-based, cross-sectional study comprised 16,234 adults (aged ≥19 years) who had participated in the fifth annual Korea National Health and Nutrition Examination Survey from 2010 to 2012. The enrolled subjects underwent interviews, clinical examinations, and laboratory investigations. We compared body mass index (BMI) and waist circumference (WC), according to the presence of pterygium. Multiple logistic regression analysis was conducted to examine the associations of each obesity parameter with pterygium after adjusting for age, smoking status, alcohol consumption, physical activities, educational levels, outdoor occupation, area of residence, and daily sun exposure duration. The prevalence rate of pterygium tended to increase as the BMI increased only in women, and both male and female subjects with higher WC were likely to have more pterygium in both sexes. In the multivariate analysis, overweight women had an odd ratio (OR) (95% confidence interval (CI)) of 1.16 (0.86–1.55) and obese women had an OR (95% CI) of 1.35 (1.02–1.77) compared to women with normal weight (P for trend for ORs = 0.04). Compared to women without abdominal obesity, abdominally obese women had an OR (95% CI) of 1.26 (1.01–1.58). There was no significant association between obesity and pterygium in men. The present study provides epidemiologic evidence of an association between obesity and pterygium in women. Further studies are needed to examine the sex difference in the pathogenesis of pterygium. PMID:27977614

  15. Association of Occupational and Leisure-Time Physical Activity with Aerobic Capacity in a Working Population

    PubMed Central

    Mundwiler, Jonas; Schüpbach, Ulla; Dieterle, Thomas; Leuppi, Jörg Daniel; Schmidt-Trucksäss, Arno; Wolfer, David Paul; Miedinger, David; Brighenti-Zogg, Stefanie

    2017-01-01

    Introduction Objective data on the association of maximal aerobic capacity (VO2max) with work related physical activity are sparse. Thus, it is not clear whether occupational physical activity (OPA) contributes to an increase of VO2max. This study examined the association of VO2max with work and non-work related physical activity in a Swiss working population. Methods In this cross-sectional study, a total of 337 healthy and full-time employed adults were recruited. Demographic data, height, weight and BMI were recorded in all subjects. Participants were classified into nine occupational categories (ISCO-88) and merged into three groups with low, moderate, and high OPA. Physical activity was objectively measured by the SenseWear Mini Armband on seven consecutive days (23 hours per day). Participants were regarded as sufficiently active when accumulating ≥30 min of moderate-to-vigorous physical activity per day. VO2max was evaluated using the multistage 20-meter shuttle run test. Results Data of 303 participants were considered for analysis (63% male, age 33 yrs, SD 12). Multiple linear regression analysis (adjusted R2 = 0.69) revealed significant positive associations of VO2max with leisure-time physical activity (LTPA) at vigorous intensity (β = 0.212) and sufficient moderate-to-vigorous physical activity (β = 0.100) on workdays. Female gender (β = -0.622), age (β = -0.264), BMI (β = -0.220), the ratio of maximum to resting heart rate (β = 0.192), occupational group (low vs. high OPA, β = -0.141), and smoking (β = -0.133) were also identified as independent predictors of VO2max. Conclusions The present results suggest that VO2max is positively associated with LTPA, but not with OPA on workdays. This finding emphasizes the need for employees to engage in sufficient high-intensity physical activity in recreation for maintaining or improving VO2max with regard to health benefits. PMID:28045939

  16. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders.

  17. Association of systemic lupus erythematosus clinical features with European population genetic substructure.

    PubMed

    Alonso-Perez, Elisa; Suarez-Gestal, Marian; Calaza, Manuel; Witte, Torsten; Papasteriades, Chryssa; Marchini, Maurizio; Migliaresi, Sergio; Kovacs, Attila; Ordi-Ros, Josep; Bijl, Marc; Santos, Maria Jose; Ruzickova, Sarka; Pullmann, Rudolf; Carreira, Patricia; Skopouli, Fotini N; D'Alfonso, Sandra; Sebastiani, Gian Domenico; Suarez, Ana; Blanco, Francisco J; Gomez-Reino, Juan J; Gonzalez, Antonio

    2011-01-01

    Systemic Lupus Erythematosus (SLE) is an autoimmune disease with a very varied spectrum of clinical manifestations that could be partly determined by genetic factors. We aimed to determine the relationship between prevalence of 11 clinical features and age of disease onset with European population genetic substructure. Data from 1413 patients of European ancestry recruited in nine countries was tested for association with genotypes of top ancestry informative markers. This analysis was done with logistic regression between phenotypes and genotypes or principal components extracted from them. We used a genetic additive model and adjusted for gender and disease duration. Three clinical features showed association with ancestry informative markers: autoantibody production defined as immunologic disorder (P = 6.8×10(-4)), oral ulcers (P = 6.9×10(-4)) and photosensitivity (P = 0.002). Immunologic disorder was associated with genotypes more common in Southern European ancestries, whereas the opposite trend was observed for photosensitivity. Oral ulcers were specifically more common in patients of Spanish and Portuguese self-reported ancestry. These results should be taken into account in future research and suggest new hypotheses and possible underlying mechanisms to be investigated. A first hypothesis linking photosensitivity with variation in skin pigmentation is suggested.

  18. Orthostatic hypotension: prevalence and associated risk factors among the ambulatory elderly in an Asian population

    PubMed Central

    Zhu, Qing Olivia; Tan, Choon Seng Gilbert; Tan, Hwee Leong; Wong, Ruining Geraldine; Joshi, Chinmaya Shrikant; Cuttilan, Ravi Amran; Sng, Gek Khim Judy; Tan, Ngiap Chuan

    2016-01-01

    INTRODUCTION The prevalence of orthostatic hypotension (OH) among the elderly population in Singapore, as defined by a decline in blood pressure upon a change in position, is not well-established. Studies associate OH with clinically significant outcomes such as falls. This study aims to determine the prevalence of OH among elderly patients attending a public primary care clinic (polyclinic) for chronic disease management, and examine the relationships between postulated risk factors and OH. METHODS Patients aged ≥ 65 years attending a typical polyclinic in Geylang were identified and targeted for recruitment at the study site. A questionnaire on symptoms and postulated risk factors was administered, followed by supine and standing blood pressure measurements. Cross-sectional analysis was performed with independent sample t-test for continuous data and chi-square test for categorical data. Prevalence rate ratios with 95% confidence interval were calculated for the latter. RESULTS A total of 364 multiethnic patients participated in the study. The prevalence of OH was 11.0%. Older age, comorbidities such as cardiac failure and kidney disease, being physically inactive at work, fatigue, self-reported dizziness in the past year, and the use of loop diuretics were found to be significantly associated with OH. CONCLUSION About one in ten elderly patients at a local polyclinic was affected by OH, which was associated with multiple factors. Some of these factors are modifiable and can be addressed to reduce the incidence of OH. PMID:27549316

  19. Association between Polymorphism of Exportin-5 and Susceptibility to Lead Poisoning in a Chinese Population

    PubMed Central

    Zhang, Hengdong; Xu, Ming; Zhao, Qiuni; Sun, Kai; Gong, Wei; Zhang, Qiaoyun; Zhu, Baoli; An, Yan

    2016-01-01

    Lead (Pb) is one of the major contaminants in many industries, and imposes hazardous effects on multiple human organs and systems. Studies have shown that lead is able to induce the alteration of microRNA (miRNA) expression in serum and organs. In this study we investigated whether polymorphisms in miRNA-regulating genes were associated with the risk of lead exposure. We genotyped seven single-nucleotide polymorphisms (SNPs) in 113 lead-sensitive and 113 lead-resistant lead-related Chinese workers by Taqman analysis. The lead-sensitive group showed a significantly higher blood lead level (BLL) than the resistant group based on unconditional logistic regression results. One SNP in XPO5 extron (rs2257082) was significantly associated with lead-poisoning (p = 0.022, odds rate (OR) = 1.63, 95% confidence interval (CI) = 1.07–2.47 in the C allele compared to the T allele). There were no significant associations between the other six SNPs and the blood lead levels. Therefore, polymorphism rs2257082 could be used to distinguish lead-resistant and lead-susceptible populations, and to develop more specific and accurate preventions. PMID:28042866

  20. Association between XRCC3 Thr241Met polymorphism and risk of osteosarcoma in a Chinese population.

    PubMed

    Guo, J; Lv, H C; Shi, R H; Liu, W L

    2015-12-09

    Osteosarcoma is one of the most common bone malignancies in adolescents, and hereditary factors may influence its susceptibility. We assessed the association between XRCC3 Thr241Met polymorphism and susceptibility to osteosarcoma in a Chinese population. Between May 2012 and May 2014, a total of 136 osteosarcoma patients and 136 healthy control subjects were included in our study. The XRCC3 Thr241Met polymorphism was analyzed using a polymerase chain reaction restriction fragment length polymorphism assay. By multiple logistic regression analysis, individuals carrying the Met/Met genotype of XRCC3 Thr241Met were at significantly increased risk of osteosarcoma when compared with the Thr/Thr (OR = 2.50, 95%CI = 1.13-5.66). The Thr/Met+Met/Met genotype of XRCC3 Thr241Met was furthermore found to be correlated with an elevated increased risk of osteosarcoma when compared with the Thr/Thr genotype (OR = 1.71, 95%CI = 1.03-2.87), and Met/Met genotype of XRCC3 Thr241Met was associated with an increased risk of osteosarcoma compared to the Thr/Thr (OR = 3.50, 95%CI = 1.51-8.79). In conclusion, our study firstly reports that XRCC3 Thr241Met gene polymorphism is associated with an elavated risk of osteosarcoma.

  1. Association of Lifetime Intellectual Enrichment with Cognitive Decline in the Older Population

    PubMed Central

    Vemuri, Prashanthi; Lesnick, Timothy G.; Przybelski, Scott A.; Machulda, Mary; Knopman, David S.; Mielke, Michelle M.; Roberts, Rosebud O.; Geda, Yonas E.; Rocca, Walter A.; Petersen, Ronald C.; Jack, Clifford R.

    2014-01-01

    IMPORTANCE Intellectual lifestyle enrichment throughout life is increasingly viewed as a protective strategy against commonly observed cognitive decline in the elderly. OBJECTIVE To investigate the association of lifetime intellectual enrichment with baseline cognitive performance and rate of cognitive decline in a non-demented elderly population and to estimate difference (in years) associated with lifetime intellectual enrichment to the onset of cognitive impairment. DESIGN, SETTING, PARTICIPANTS Prospective analysis of subjects enrolled in the Mayo Clinic Study of Aging (MCSA), a longitudinal population-based study of cognitive aging in Olmsted County, Minnesota. We studied 1995 non-demented (1718 cognitively normal, 277 MCI) participants in MCSA who completed intellectual lifestyle measures at baseline and underwent at least one follow-up visit. MAIN OUTCOMES AND MEASURES We studied the effect of lifetime intellectual enrichment by separating the variables into two non-overlapping principal components: education/occupation-score and mid/late-life cognitive activity measure based on self-report questionnaires. A global cognitive Z-score served as our summary cognition measure. We used linear mixed-effects models to investigate the associations of demographic and intellectual enrichment measures with global cognitive Z-score trajectories. RESULTS Baseline cognitive performance was lower in older subjects and in those with lower education/occupation, lower mid/late-life cognitive activity, apolipoprotein E4 (APOE) genotype, and in men. The interaction between the two intellectual enrichment measures was significant such that the beneficial effect of mid/late-life cognitive activity on baseline cognitive performance was reduced with increasing education/occupation. Only baseline age, mid/late-life cognitive activity, and APOE4 genotype were significantly associated with longitudinal change in cognitive performance from baseline. For APOE4 carriers with high

  2. Association between functional performance and executive cognitive functions in an elderly population including patients with low ankle–brachial index

    PubMed Central

    Ferreira, Naomi Vidal; Cunha, Paulo Jannuzzi; da Costa, Danielle Irigoyen; dos Santos, Fernando; Costa, Fernando Oliveira; Consolim-Colombo, Fernanda; Irigoyen, Maria Cláudia

    2015-01-01

    Introduction Peripheral arterial disease, as measured by the ankle–brachial index (ABI), is prevalent among the elderly, and is associated with functional performance, assessed by the 6-minute walk test (6MWT). Executive cognitive function (ECF) impairments are also prevalent in this population, but no existing study has investigated the association between ECF and functional performance in an elderly population including individuals with low ABI. Aim To investigate the association between functional performance, as measured by the 6MWT, and loss in ECF, in an elderly sample including individuals with low ABI. Method The ABI group was formed by 26 elderly individuals with low ABI (mean ABI: 0.63±0.19), and the control group was formed by 40 elderly individuals with normal ABI (mean ABI: 1.08±0.07). We analyzed functional performance using the 6MWT, global cognition using the Mini-Mental State Examination (MMSE), and ECF using the Digit Span for assessing attention span and working memory, the Stroop Color Word Test (SCWT) for assessing information processing speed and inhibitory control/impulsivity, and the Controlled Oral Word Association Test (COWAT) for assessing semantic verbal fluency and phonemic verbal fluency. We also used a factor analysis on all of the ECF tests (global ECF). Results Before adjustment, the ABI group performed worse on global cognition, attention span, working memory, inhibitory control/impulsivity, semantic verbal fluency, and phonemic verbal fluency. After adjustment, the ABI group performance remained worse for working memory and semantic verbal fluency. In a simple correlation analysis including all of the subjects, the 6MWT was associated with global cognition, attention span, working memory, information processing speed, inhibitory control/impulsivity, semantic verbal fluency, and global ECF. After adjustment, all the associations remained statistically significant. Conclusion This study found an independent association between

  3. Genetic analysis of CHCHD2 in a southern Spanish population.

    PubMed

    Tejera-Parrado, Cristina; Jesús, Silvia; Huertas-Fernández, Ismael; Bernal-Bernal, Inmaculada; Bonilla-Toribio, Marta; Córdoba-Tevar, Isabel; Abreu-Rodríguez, Irene; Carrillo, Fátima; Bernal-Escudero, Maravilla; Vargas-González, Laura; Carballo, Manuel; Gómez-Garre, Pilar; Mir, Pablo

    2017-02-01

    Researching genetic factors involved in Parkinson's disease (PD) is crucial to increase our knowledge about the pathophysiology of the disorder. A missense mutation has recently been reported within CHCHD2, a gene newly associated with autosomal dominant PD. Subsequent studies in different ethnic populations have not reached any conclusive result about the role of CHCHD2 in PD. Therefore, the aim of this study was to investigate the implication of this gene for a PD population from southern Spain (including 536 PD patients and 518 unrelated control subjects). We studied all 4 exons of CHCHD2 and their exon-intron boundary regions. Four variants were observed in non-coding regions. No significant differences were observed in the allele frequencies of these variants between patients and controls. Thus, our study suggests that CHCHD2 is probably not involved in the etiopathogenesis of PD in our population.

  4. Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

    PubMed Central

    Demers, Jill E.; Gugino, Beth K.

    2014-01-01

    The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates. PMID:25304514

  5. Genetic analysis in the Collaborative Cross breeding population

    SciTech Connect

    Philip, Vivek; Sokoloff, Greta; Ackert-Bicknell, Cheryl; Striz, Martin; Branstetter, Lisa R; Beckmann, Melissa; Spence, Jason S; Jackson, Barbara L; Galloway, Leslie D; Barker, Gene; Wymore, Ann M; Hunsicker, Patricia R; Durtschi, David W; Shaw, Ginger S; Shinpock, Sarah G; Manly, Kenneth F; Miller, Darla R; Donahue, Kevin; Culiat, Cymbeline T; Churchill, Gary A; Lariviere, William R; Palmer, Abraham; O'Hara, Bruce; Voy, Brynn H; Chesler, Elissa J

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  6. Associations of Moyamoya patients with HLA class I and class II alleles in the Korean population.

    PubMed Central

    Han, Hoon; Pyo, Chul-Woo; Yoo, Do-Sung; Huh, Pil-Woo; Cho, Kyung-Souk; Kim, Dal-Soo

    2003-01-01

    Moyamoya disease is characterized by progressive cerebrovascular occlusion at the peripheral internal carotid artery and development of abnormal collateral circulation at the cerebral basal region. Although abnormal thrombogenesis, inflammation and autoimmune process might be involved in the etiology, the genetic pathogenesis of Moyamoya disease is still unknown. To evaluate the association of Moyamoya disease with HLA alleles in the Korean population, we investigated HLA class I and class II alleles in 28 Moyamoya patients and 198 unrelated healthy controls. The frequency of HLA-B35 allele was significantly increased in the patients compared to the controls (32.1% vs. 10.1%, RR=4.2, p<0.008). Further analysis of HLA-B35 on onset age and sex showed that this allele was significantly increased compared to the controls in both late-onset and female group. Especially, HLA-B35 was the most significantly increased in female of late-onset group compared to the controls. These results suggest that HLA-B35 may be an useful genetic marker for Moyamoya disease, and particularly in females of late onset group in the Korean population. PMID:14676447

  7. Methods for the survey and genetic analysis of populations

    DOEpatents

    Ashby, Matthew

    2003-09-02

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  8. Population trends in northern spotted owls: Associations with climate in the Pacific Northwest

    USGS Publications Warehouse

    Glenn, E.M.; Anthony, R.G.; Forsman, E.D.

    2010-01-01

    We used reverse time capture-mark-recapture models to describe associations between rate of population change (??) and climate for northern spotted owls (Strix occidentalis caurina) at six long-term study areas in Washington and Oregon, USA. Populations in three of six areas showed strong evidence of declining populations, while populations in two additional areas were likely declining as well. At four areas, ?? was positively associated with wetter-than-normal conditions during the growing season, which likely affects prey availability. Lambda was also negatively associated with cold, wet winters and nesting seasons, and the number of hot summer days. The amount of annual variation in ?? accounted for by climate varied across study areas (3-85%). Rate of population change was more sensitive to adult survival than to recruitment; however, there was considerable variation among years and across study areas for all demographic rates. While annual survival was more closely related to regional climate conditions, recruitment was often associated with local weather. In addition to climate, declines in recruitment at four of six areas were associated with increased presence of barred owls. Climate change models predict warmer, wetter winters and hotter, drier summers for the Pacific Northwest in the first half of the 21st century. Our results indicate that these conditions have the potential to negatively affect annual survival, recruitment, and consequently population growth rates for northern spotted owls. ?? 2010 Elsevier Ltd.

  9. Analyses of a multi-parent population derived from two diverse alfalfa germplasms: testcross evaluations and phenotype-DNA associations.

    PubMed

    Maureira-Butler, I J; Udall, J A; Osborn, T C

    2007-10-01

    In a previous study, we showed that the genetic variation present in the Medicago sativa subsp. sativa Peruvian and M. sativa subsp. falcata WISFAL germplasms could be used to improve forage yields when favorable alleles were recombined and used in hybrid combination with cultivated alfalfa. In this paper, we present testcross forage yield and fall growth data for two seasons of a C0 population generated after intermating the Peruvian x WISFAL population for several generations. In addition, we conducted marker-trait association analysis as an attempt to identify Peruvian and WISFAL genomics regions affecting the targeted traits. Five and seven genomic regions were found significantly associated with forage yield and fall growth, respectively. In the case of fall growth, alleles from both accessions were positively associated with plant height. However, more alleles from WISFAL were positively associated with forage yield than from Peruvian. WISFAL is known for its winter hardiness and genomic regions with large effects on winter survival may have masked the effect of forage yield from Peruvian. The fact that most of the genomic regions discovered in this study have been previously associated with traits involved in winter hardiness validates our findings and suggests that associations between DNA fragments and agronomic traits can be detected without the necessity of developing bi-parental mapping populations.

  10. Association of CLCNKB haplotypes and hypertension in Mongolian and Han populations.

    PubMed

    Su, Xiulan; Chang, Peiye; Liu, Zhiyue; Yan, Meirong; Liu, Guirong; Cui, Hongwei

    2012-01-01

    We investigated a possible association between genetic variations in chloride channel Kb (CLCNKB) gene and essential hypertension (EH) in the Mongolian and Han populations in Inner Mongolia. Our study included 414 unrelated Mongolian herdsmen and 524 Han farmers. Two tagSNPs of CLCNKB (rs945393 and rs10803414) were identified from the Chinese HapMap database based on pairwise r(2) ≥ 0.5 and minor allele frequency ≥0.05. Genotyping was performed using the PCR/ligase detection reaction assay. There was significant difference in allele frequency of rs10803414 between the EH group (35%) and the control group (26%) in the Mongolian population (P < .05). Significant association was identified between rs10803414 and EH in the Mongolian population (P < .05) and rs945393 and EH in the Han population (P < .01). The frequency of haplotype CC in the EH group (9.4%) was significantly higher than in the control group (4.6%) in the Mongolian population; individuals who possessed the CC haplotype had a significantly higher risk of EH in the Mongolian population. There was no association between haplotype and EH in the Han population. After adjusting for age, sex, and other confounding risk factors, only rs10803414 was the risk factor of hypertension in Mongolians. Our results indicate that rs10803414 in CLCNKB confers a significant risk of EH in the Mongolian population and haplotype CC of CLCNKB is a genetic factor for EH in the Mongolian population. Our study expands the association between CLCNKB and EH to a non-European ancestry population and provides the first evidence of a cross-race susceptibility of EH locus.

  11. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico.

    PubMed

    Silva-Zolezzi, Irma; Hidalgo-Miranda, Alfredo; Estrada-Gil, Jesus; Fernandez-Lopez, Juan Carlos; Uribe-Figueroa, Laura; Contreras, Alejandra; Balam-Ortiz, Eros; del Bosque-Plata, Laura; Velazquez-Fernandez, David; Lara, Cesar; Goya, Rodrigo; Hernandez-Lemus, Enrique; Davila, Carlos; Barrientos, Eduardo; March, Santiago; Jimenez-Sanchez, Gerardo

    2009-05-26

    Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America.

  12. Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico

    PubMed Central

    Silva-Zolezzi, Irma; Hidalgo-Miranda, Alfredo; Estrada-Gil, Jesus; Fernandez-Lopez, Juan Carlos; Uribe-Figueroa, Laura; Contreras, Alejandra; Balam-Ortiz, Eros; del Bosque-Plata, Laura; Velazquez-Fernandez, David; Lara, Cesar; Goya, Rodrigo; Hernandez-Lemus, Enrique; Davila, Carlos; Barrientos, Eduardo; March, Santiago; Jimenez-Sanchez, Gerardo

    2009-01-01

    Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America. PMID:19433783

  13. Associations of moderate-to-vigorous-intensity physical activity and body mass index with glycated haemoglobin within the general population: a cross-sectional analysis of the 2008 Health Survey for England

    PubMed Central

    Bakrania, Kishan; Yates, Thomas; Edwardson, Charlotte L; Bodicoat, Danielle H; Esliger, Dale W; Gill, Jason M R; Kazi, Aadil; Velayudhan, Latha; Sinclair, Alan J; Sattar, Naveed; Biddle, Stuart J H; Hamer, Mark; Davies, Melanie J; Khunti, Kamlesh

    2017-01-01

    Objectives To investigate the associations of objectively measured moderate-to-vigorous-intensity physical activity (MVPA) and body mass index (BMI) with glycated haemoglobin (HbA1c) in a national sample of English adults. Methods The 2008 Health Survey for England data were used with 1109 participants aged ≥18 providing complete data. MVPA time was assessed using an accelerometer. Weighted linear regression models, adjusted for several confounders, quantified the associations between continuous measures of MVPA and BMI with HbA1c. Interaction analyses were implemented to observe whether the association of MVPA with HbA1c was modified by BMI or vice versa. Further weighted linear regression models examined the differences in HbA1c across four mutually exclusive categories of MVPA and BMI: (1) ‘physically active and non-obese’, (2) ‘physically active and obese’, (3) ‘physically inactive and non-obese’ and (4) ‘physically inactive and obese’. ‘Physically active’ was defined as: ≥150 min/week of MVPA. ‘Obese’ was defined as: BMI ≥30.0 kg/m2. A wide range of sensitivity analyses were also implemented. Results Every 30 min/day increment in MVPA was associated with a 0.7 mmol/mol (0.07% (p<0.001)) lower HbA1c level. Each 1 kg/m2 increment in BMI was associated with a 0.2 mmol/mol (0.02% (p<0.001)) higher HbA1c level. The association of MVPA with HbA1c was stronger in obese individuals (−1.5 mmol/mol (−0.13% (p<0.001))) than non-obese individuals (−0.7 mmol/mol (−0.06% (p<0.001))); p=0.004 for interaction. The association of BMI with HbA1c remained stable across MVPA categories. Compared with individuals categorised as ‘physically inactive and obese’, only those categorised as ‘physically active and obese’ or ‘physically active and non-obese’ had lower HbA1c levels by 2.1 mmol/mol (0.19% (p=0.005)) and 3.5 mmol/mol (0.32% (p<0.001)), respectively. Sensitivity analyses indicated robustness and stability

  14. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  15. Collection of pedigree data for genetic analysis in isolate populations.

    PubMed

    Williams-Blangero, Sarah; Blangero, John

    2006-02-01

    Pedigree data are useful for a wealth of research purposes in human population biology and genetics. The collection of extended pedigrees represents the most powerful sampling design for quantitative genetic and linkage studies of both normal and disease-related quantitative traits. In this paper we outline an approach for collecting pedigree data in stable isolate populations. As an example, the pedigree for the Jirel population, which was obtained using the methods presented, is described. The Jirel pedigree contains 2,000 study participants and more than 62,000 pairwise relationships that are informative for genetic analysis. Once such pedigrees are genetically characterized by a genome scan for a given trait, they become an invaluable resource for future genetic studies of any quantitative trait.

  16. Chromosome 11-q24 region in Tourette syndrome: association and linkage disequilibrium study in the French Canadian population.

    PubMed

    Díaz-Anzaldúa, Adriana; Rivière, Jean-Baptiste; Dubé, Marie-Pierre; Joober, Ridha; Saint-Onge, Judith; Dion, Yves; Lespérance, Paul; Richer, Francois; Chouinard, Sylvain; Rouleau, Guy Armand

    2005-10-15

    Previous studies have found association and linkage between Tourette syndrome (TS) and markers at the 11q24 region, mainly with markers D11S1377 and D11S933. In order to determine if these positive findings could be replicated in our sample, we undertook a family-based association study in 199 French Canadian TS nuclear families. We genotyped 572 individuals from 174 complete and 25 incomplete TS trios. TDT analysis failed to detect an association between TS and six markers from 11q24. Furthermore, no haplotype combining alleles from D11S1377, D11S933, or any of the other four markers was associated with the disorder. Linkage disequilibrium analysis showed evidence of historical recombination between every contiguous pair of markers, indicating that these genetic variants are probably in equilibrium in the French Canadian population. Further analysis in additional families, with different methodologies (linkage and association) will be required in order to determine if the 11q24 region harbors a susceptibility locus for TS. If it does, this defect may not be frequent in the French Canadian population due to locus heterogeneity.

  17. Association study of BCL9 gene polymorphism rs583583 with schizophrenia and negative symptoms in Japanese population

    PubMed Central

    Kimura, Hiroki; Tanaka, Satoshi; Kushima, Itaru; Koide, Takayoshi; Banno, Masahiro; Kikuchi, Tsutomu; Nakamura, Yukako; Shiino, Tomoko; Yoshimi, Akira; Oya-Ito, Tomoko; Xing, Jingrui; Wang, Chenyao; Takasaki, Yuto; Aleksic, Branko; Okada, Takashi; Ikeda, Masashi; Inada, Toshiya; Iidaka, Tetsuya; Iwata, Nakao; Ozaki, Norio

    2015-01-01

    B-cell CLL/lymphoma 9 (BCL9) is located within the schizophrenia (SCZ) suspected locus chr1q21.1. A recent study reported that a single nucleotide polyphormism (SNP) within BCL9 (rs583583) is associated with negative symptoms of Schizophrenia, as measured by the Positive and Negative Syndrome Scale (PANSS), in the Caucasian population. We therefore investigated genetic association of rs583583, and its effect on negative symptoms in the Japanese patients. For association analysis, we used a Japanese sample set comprising 1089 SCZ and 950 controls (CON). Analysis of the effect of rs586586 on negative symptoms as examined by PANSS was investigated using 280 SCZ. Furthermore, for analysis of cognitive performance, we investigated 90 SCZ and 51 CON using the Continuous Performance Test (CPT-IP) and the Wisconsin Card Sorting Test (WCST) Keio version. We did not detect association between rs583583 and SCZ. Furthermore, rs583583 was not associated with PANSS negative scores or with CPT-IT or WCST cognitive tests. Considering the results of our previous study, combined with the results of the current study of rs583583, we argue that BCL9 most likely does not harbor a common genetic variant that can increase the risk for SCZ in the Japanese population. PMID:26494551

  18. The single nucleotide polymorphism Rs12817488 is associated with Parkinson's disease in the Chinese population.

    PubMed

    Yu, Ri-li; Guo, Ji-feng; Wang, Ya-qin; Liu, Zhen-hua; Sun, Zhan-fang; Su, Li; Zhang, Yuan; Yan, Xin-xiang; Tang, Bei-sha

    2015-06-01

    A recent meta-analysis of datasets from five of the published Parkinson's disease (PD) genome-wide association studies implicated the single nucleotide polymorphism (SNP) rs12817488 in coiled-coil domain containing 62 (CCDC62)/huntingtin interacting protein 1 related (HIP1R) as a risk factor for PD. We conducted a case-control study to evaluate the possible association between rs12817488 and PD in Chinese people. All patients (515 PD patients and 518 age and sex-matched controls) were successfully genotyped using polymerase chain reaction restriction fragment length polymorphism analysis. We observed that the rs12817488 polymorphism is associated with PD (p=0.003) and that the genotype and allele frequencies showed a difference between late-onset PD patients and male controls (p=0.025 and p=0.007, respectively). However, there was no difference in the early-onset PD patients and controls. We found a difference in the genotype and allele frequencies between the male PD patients and the male controls (p=0.034 and p=0.017, respectively). However, there was no difference in females. Patients with the A allele were susceptible to PD in both dominant (GA+AA versus GG; odds ratio [OR] 1.365, 95% confidence interval [CI] 1.041-1.788) and recessive (AA versus GG+GA; OR 1.606, 95% CI 1.194-2.158) models. Therefore, our findings support the conclusion that the rs12817488 in CCDC62/HIP1R polymorphism may increase the risk of PD in the Chinese Han population.

  19. Genome-wide association study of carbon and nitrogen metabolism in the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and at the basis of yield and adaptation. We have applied high throughput metabolite analyses to over 12,000 diverse field grown samples from the maize nested association mapping population. This allowed us to identi...

  20. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nested association mapping (NAM) offers unprecedented power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5000 lines from 25 families representing the global diversity of maize, was evaluated for resistance to Southern leaf blight (SLB) diseas...

  1. Genetic analysis of three US population groups using an X-chromosomal STR decaplex.

    PubMed

    Gomes, Iva; Prinz, Mechthild; Pereira, Rui; Meyers, Carole; Mikulasovich, Rebecca S; Amorim, António; Carracedo, Angel; Gusmão, Leonor

    2007-05-01

    An X-chromosomal multiplex amplifying ten short tandem repeats (STRs) in one single PCR reaction was developed and optimized in this work. The X-STRs included were DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101, and DXS6789. Decaplex performance was tested on 377 male samples from three United States population groups, namely, 130 African Americans, 104 Asians, and 143 Hispanics. DXS8377 was the most polymorphic locus across all three populations, whereas DXS7423 was the least informative marker. Genetic distance analysis (R (ST) and F (ST)) performed for the three populations residing in New York showed significant genetic distances between population groups for most pairwise comparisons, except for HPRTB, DXS6809, and DXS7132. When testing linkage disequilibrium for all pairs of loci in the three groups, no significant association was found between any pair of the loci studied, after applying Bonferroni correction. The high values for the average probability of excluding a random man obtained in all three populations when both mother and daughter are tested or when father/daughter relationships are evaluated support the potential of this decaplex system in kinship analysis. Also, the overall high power of discrimination values for samples of female and male origin, confirms the usefulness of this decaplex system in identification analysis. As expected, results also support the use of independent databases comprising these ten X-linked loci for the three US populations evaluated.

  2. Association between single nucleotide polymorphisms in the TSPYL6 gene and breast cancer susceptibility in the Han Chinese population

    PubMed Central

    Guo, Wen; Zhang, Xiyang; Chen, Zhengshuai; Li, Jingjie; Yan, Mengdan; Chen, Chao; Jin, Tianbo

    2016-01-01

    We investigated the associations between single nucleotide polymorphisms (SNPs) in the testis-specific Y-encoded-like protein 6 (TSPYL6) gene and breast cancer (BC) susceptibility in the Han Chinese population. A total of 183 BC patients and 195 healthy women were included in the study. Six SNPs in TSPYL6 were genotyped and the association with BC risk analyzed. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using unconditional logistic regression analysis. Multivariate logistic regression analysis was used to identify SNPs that correlated with BC susceptibility. Rs11896604 was associated with a decreased risk of BC based on dominant and genotype models. Rs843706 was associated with an increased risk of BC based on a recessive model. Rs11125529 was associated with decreased BC susceptibility based on a genotype model. Finally, rs843711 inversely correlated with clinical stage III/IV BC. Our findings reveal a significant association between SNPs in the TSPYL6 gene and BC risk in a Han Chinese population. PMID:27458158

  3. A theoretical analysis of optimum consumer population and its control.

    PubMed

    Jiang, Z; Mao, Z; Wang, H

    1994-01-01

    consumption structure elasticity. This model was used in the correlation analysis of the coordinated healthy development of optimum consumer population and the economy.

  4. Population.

    ERIC Educational Resources Information Center

    King, Pat; Landahl, John

    This pamphlet has been prepared in response to a new problem, a rapidly increasing population, and a new need, population education. It is designed to help teachers provide their students with some basic population concepts with stress placed on the elements of decision making. In the first section of the pamphlet, some of the basic concepts of…

  5. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  6. Population genetic analysis and sub-structuring in Babesia bovis.

    PubMed

    Simuunza, Martin; Bilgic, Huseyin; Karagenc, Tulin; Syakalima, Michelo; Shiels, Brian; Tait, Andy; Weir, William

    2011-06-01

    The tick-borne protozoan parasite, Babesia bovis is one of the causes of bovine babesiosis, an economically important disease of cattle in tropical and sub-tropical countries. Using the recently published genome sequence of the parasite, we developed a panel of eight mini- and micro-satellite markers and used these to investigate the role of genetic exchange in the population structure and diversity of the parasite using isolates from Zambia and Turkey. This population genetic analysis showed that genetic exchange occurs and that there are high levels of genetic diversity, with geographical sub-structuring quantified using Wright's F Index. Linkage disequilibrium was observed when isolates from both countries were treated as one population, but when isolates from Zambia were analysed separately linkage equilibrium was observed. The Turkish isolates were sub-structured, containing two genetically distinct sub-groups, both of which appeared to be in linkage equilibrium. The results of the Zambian study suggest that a sub-set of the parasite population is responsible for the westward spread of babesiosis into the previously disease-free central region of the country. The Zambian isolates had a significantly higher number of genotypes per sample than those from Turkey and age was found to be a significant predictor of the multiplicity of infection. The high levels of diversity seen in the Zambian and Turkish B. bovis populations have implications in the development of subunit vaccines against the disease and the spread of dr