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1

Patterns of extensive genetic differentiation and variation among European harbor seals (Phoca vitulina vitulina) revealed using microsatellite DNA polymorphisms.  

PubMed

The harbor seal (Phoca vitulina) has the most extensive distribution of any phocid seal species. An analysis of population structure in this species across its European range was made using 7 phocid derived microsatellites in a sample of 1,029 individuals from 12 separate geographic areas. Despite the species potential for long-distance movement, significant genetic differentiation between areas was observed using an unbiased estimator of RST. Six distinct population units were identified: Ireland-Scotland, English east coast, Waddensea, western Scandinavia (Norway-Kattegat-Skagerrak-west Baltic), east Baltic, and Iceland. Little local substructuring is present along coastlines with a continuous distribution of breeding animals, but differentiation does increase with geographic distance. The degree of differentiation is greater over equivalent distances where the distribution is discontinuous, such as along coasts where breeding colonies are separated by large distances or by stretches of open sea. Patterns of population differentiation derived from microsatellites are very similar to those obtained from previous mitochondrial DNA analysis and suggest that philopatry in harbor seals operates over 300-500 km. In Europe, harbor seals have experienced a complex demographic history and patterns of population structure are likely to have been affected by natural environmental influences such as Pleistocene glaciations and epizootics. Comparison of Nm values from an unbiased estimator of RST, GST, and theta are consistent and, in some cases, may indicate populations where conditions deviate from the expectations of the RST model. PMID:9491609

Goodman, S J

1998-02-01

2

Genetics Home Reference: Floating-Harbor syndrome  

MedlinePLUS

... PubMed Recent literature OMIM Genetic disorder catalog Conditions > Floating-Harbor syndrome On this page: Description Genetic changes ... names Glossary definitions Reviewed December 2012 What is Floating-Harbor syndrome? Floating-Harbor syndrome is a disorder ...

3

Osteopontin: an early innate immune marker of Escherichia coli mastitis harbors genetic polymorphisms with possible links with resistance to mastitis  

PubMed Central

Background Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable alleles that support greater resistance to infection, thus reducing antibiotic use. This study aims to identify a key gene in the innate immune response to mastitis, led us to evaluate its genetic association with somatic cell score (SCS), which is an indicator of clinical mastitis, and to evaluate its impact on other traits related to milk production. Results The osteopontin transcript (SPP1) was identified in the somatic cells from cows experimentally infected with Escherichia coli. By selecting bulls with extreme estimated breeding values (EBVs) for SCS, which is an indicator of mammary gland health, four DNA polymorphisms in the SPP1 genomic sequence were found. Statistical analysis revealed that the SNP SPP1c.-1301G>A has an impact on EBV for SCS (P < 0.001) Using an allele substitution model, SPP1c.-1251C>T, SPP1c.-430G>A, and SPP1c.*40A>C have an impact on SCS whereas SPP1c.-1301G>A has an effect on the EBVs for milk yield (second and third lactations), fat and protein percentages (all three lactations). Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (P = 0.012), second (P < 0.001), and third (P < 0.001) lactations. Conclusion This study reports the link between DNA polymorphisms of SPP1, the number of milk immune cells and, potentially, the susceptibility to mastitis. These SNPs were identified by in silico search to be located in transcription factor recognition sites which factors are presumably involved in the Th1 immune response and in the Th2 regulation pathway. Indeed, one SNP abolished the SP1 recognition site, whereas another SNP affected the transcription binding factor IKAROS. All together, these findings support the genetic potential of these variants in terms of selection for the improvement of mastitis resistance in dairy cows. PMID:19765294

Alain, Karin; Karrow, Niel A; Thibault, Catherine; St-Pierre, Jessika; Lessard, Martin; Bissonnette, Nathalie

2009-01-01

4

Genetic Polymorphism in Evolving Population  

E-print Network

We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping diversity in the gene pool under abrupt environmental changes. The model provides reasonable estimates for the proportions of polymorphic and heterozygous loci and for the mutation rate, as observed in nature.

H. Y. Lee; D. Kim; M. Y. Choi

1998-01-09

5

GENETIC POLYMORPHISMS AND PERITONEAL MEMBRANE FUNCTION.  

PubMed

? Background: Outcomes for peritoneal dialysis (PD) patients are affected by the characteristics of the peritoneal membrane, which may be determined by genetic variants. We carried out a systematic review of the literature to identify studies which assessed the association between genetic polymorphisms, peritoneal membrane solute transport, and clinical outcomes for PD patients. ? Methods: The National Library of Medicine was searched using a variety of strategies. Studies which met our inclusion criteria were reviewed and data abstracted. Our outcomes of interest included: high transport status peritoneal membrane, risk for peritonitis, encapsulating peritoneal sclerosis (EPS), patient and technique survival. We combined data from studies which evaluated the same genetic polymorphism and the same outcome. ? Results: We evaluated 18 relevant studies. All studies used a candidate gene approach. Gene polymorphisms in the interleukin (IL)-6 gene were associated with peritoneal membrane solute transport in several studies in different ethnic populations. Associations with solute transport and polymorphisms in endothelial nitric oxide synthase and receptor for advanced glycation end product genes were also identified. There was evidence of a genetic predisposition for peritonitis found in 2 studies, and for EPS in 1 study. Survival was found to be associated with a polymorphism in vascular endothelial growth factor and technique failure was associated with a polymorphism in the IL-1 receptorantagonist. ? Conclusions: There is evidence that characteristics of the peritoneal membrane and clinical outcomes for PD patients have genetic determinants. The most consistent association was between IL-6 gene polymorphisms and peritoneal membrane solute transport. PMID:25395500

Siddique, Imad; Brimble, E Scott; Walkin, Louise; Summers, Angela; Brenchley, Paul; Herrick, Sarah; Margetts, Peter

2014-11-13

6

Migraine and genetic polymorphisms: an overview.  

PubMed

The relationship between genetic polymorphisms and migraine as a cause of an increased risk of thrombotic disorders development is still debated In this respect, factor V Leiden, factor V (H1299R), prothrombin G20210A, factor XIII (V34L), ?-fibrinogen, MTHFR (C677T), MTHFR (A1298C), APO E, PAI-1, HPA-1 and ACE I/D seem to play a determinant role in vascular diseases related to migraine. The present review analyzes both the incidence of the above genetic vascular mutations in migraineurs and the most re-cent developments related to genetic polymorphisms and migraine. PMID:22962564

Pizza, Vincenzo; Agresta, Anella; Agresta, Antonio; Lamaida, Eros; Lamaida, Norman; Infante, Francesco; Capasso, Anna

2012-01-01

7

Migraine and Genetic Polymorphisms: An Overview  

PubMed Central

The relationship between genetic polymorphisms and migraine as a cause of an increased risk of thrombotic disorders development is still debated In this respect, factor V Leiden, factor V (H1299R), prothrombin G20210A, factor XIII (V34L), ?-fibrinogen, MTHFR (C677T), MTHFR (A1298C), APO E, PAI-1, HPA-1 and ACE I/D seem to play a determinant role in vascular diseases related to migraine. The present review analyzes both the incidence of the above genetic vascular mutations in migraineurs and the most re-cent developments related to genetic polymorphisms and migraine. PMID:22962564

Pizza, Vincenzo; Agresta, Anella; Agresta, Antonio; Lamaida, Eros; Lamaida, Norman; Infante, Francesco; Capasso, Anna

2012-01-01

8

Digoxin pharmacokinetics and MDR1 genetic polymorphisms  

Microsoft Academic Search

Background. The effect of MDR1 C3435T single nucleotide polymorphism (SNP) in exon 26 on digoxin pharmacokinetics has recently been challenged. Objective. To clarify the relationships between MDR1 genetic polymorphisms in exon 26 (C3435T) and 21 (G2677T\\/A) and digoxin pharmacokinetics. Materials and methods. MDR1 genotypes for C3435T and G2677T\\/A SNPs were determined in 32 healthy subjects whose single oral dose digoxin

Céline Verstuyft; Mathias Schwab; Elke Schaeffeler; Reinhold Kerb; Ulrich Brinkmann; Patrice Jaillon; Christian Funck-Brentano; Laurent Becquemont

2003-01-01

9

Genetic polymorphisms in lung disease: bandwagon or breakthrough?  

PubMed Central

The study of genetic polymorphisms has touched every aspect of pulmonary and critical care medicine. We review recent progress made using genetic polymorphisms to define pathophysiology, to identify persons at risk for pulmonary disease and to predict treatment response. Several pitfalls are commonly encountered in studying genetic polymorphisms, and this article points out criteria that should be applied to design high-quality genetic polymorphism studies. PMID:11980584

Iannuzzi, Michael C; Maliarik, Mary; Rybicki, Benjamin

2002-01-01

10

GLIADINS OF COMMON WHEAT: POLYMORPHISMS & GENETICS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Wheat gliadins are a highly polymorphic group of seed storage proteins arising from a series of complex genetic loci found on several chromosome arms. Gliadin encoding alleles are numerous, and their frequency differs amongst countries, with wheat cultivars from different countries being easily dist...

11

Accessing genetic variation: genotyping single nucleotide polymorphisms  

Microsoft Academic Search

Understanding the relationship between genetic variation and biological function on a genomic scale is expected to provide fundamental new insights into the biology, evolution and pathophysiology of humans and other species. The hope that single nucleotide polymorphisms (SNPs) will allow genes that underlie complex disease to be identified, together with progress in identifying large sets of SNPs, are the driving

Ann-Christine Syvänen

2001-01-01

12

MUC7 gene expression and genetic polymorphism  

Microsoft Academic Search

This study examined differential expression of several mucin genes in the human submandibular gland and trachea, MUC7 tissue\\u000a and species specificity, and MUC7 genetic polymorphism. Mucin gene expression examined by RT-PCR indicated that MUC1, MUC4\\u000a and MUC7 are expressed in the human submandibular gland, while MUC1, MUC2, MUC4, MUC5 and MUC7 are expressed in the human\\u000a trachea. Northern blot analysis

Aaron R. Biesbrock; Libuse A. Bobek; Michael J. Levine

1997-01-01

13

Special considerations in prognostic research in cancer involving genetic polymorphisms.  

PubMed

Analysis of genetic polymorphisms may help identify putative prognostic markers and determine the biological basis of variable prognosis in patients. However, in contrast to other variables commonly used in the prognostic studies, there are special considerations when studying genetic polymorphisms. For example, variable inheritance patterns (recessive, dominant, codominant, and additive genetic models) need to be explored to identify the specific genotypes associated with the outcome. In addition, several characteristics of genetic polymorphisms, such as their minor allele frequency and linkage disequilibrium among multiple polymorphisms, and the population substructure of the cohort investigated need to be accounted for in the analyses. In addition, in cancer research due to the genomic differences between the tumor and non-tumor DNA, differences in the genetic information obtained using these tissues need to be carefully assessed in prognostic studies. In this article, we review these and other considerations specific to genetic polymorphism by focusing on genetic prognostic studies in cancer. PMID:23773794

Savas, Sevtap; Liu, Geoffrey; Xu, Wei

2013-01-01

14

Original article 789 Genetic polymorphisms and benzene metabolism in humans  

E-print Network

Original article 789 Genetic polymorphisms and benzene metabolism in humans exposed to a wide Range on levels of benzene metabolites in 250 benzene-exposed and 136 control workers in Tianjin, China (for all, catechol, and hydroquinone) and nine polymorphisms in seven genes coding for key enzymes in benzene

California at Berkeley, University of

15

Genome-wide association study to identify genetic variants present in Japanese patients harboring intracranial aneurysms  

Microsoft Academic Search

An intracranial aneurysm (IA), which results in a subarachnoid hemorrhage with a high mortality on rupture, is a major public health concern. To identify genetic susceptibility loci for IA, we carried out a multistage association study using genome-wide single nucleotide polymorphisms (SNPs) in Japanese case–control subjects. In this study, we assessed evidence for association in standard approaches, and additional tests

Koichi Akiyama; Akira Narita; Hirofumi Nakaoka; Tailin Cui; Tomoko Takahashi; Katsuhito Yasuno; Atsushi Tajima; Boris Krischek; Ken Yamamoto; Hidetoshi Kasuya; Akira Hata; Ituro Inoue

2010-01-01

16

Genetic polymorphism of blood proteins in a population of Shetland ponies  

Microsoft Academic Search

Genetic variation of proteins (protein polymorphism) is widespread among many animal species. The biological significance of protein polymorphism has been the subject of many studies. This variation has a supporting function for population genetic studies as a source of genetic markers. In farm animals it is used in population genetics and in parentage control, mostly together with blood group polymorphism.In

R. C. Buis

1976-01-01

17

Genetic Polymorphisms and Risk Assessment for Cancer Chemoprevention  

Microsoft Academic Search

Cancer risk carries wide interindividual variation; only a fraction of the population exposed to a known carcinogen develops\\u000a cancer. Genetic susceptibility is both inherited and acquired. Genes that affect cancer susceptibility can be found in those\\u000a controlling behavior, carcinogen metabolism, and cellular response to carcinogen exposure. Genetic traits affect DNA repair,\\u000a cell cycle control, and immune response. Polymorphic genetic variants

Sonia de Assis; Peter G. Shields

18

Genetic Polymorphisms and Sepsis in Premature Neonates  

PubMed Central

Identifying single nucleotide polymorphisms (SNPs) in the genes involved in sepsis may help to clarify the pathophysiology of neonatal sepsis. The aim of this study was to evaluate the relationships between sepsis in pre-term neonates and genes potentially involved in the response to invasion by infectious agents. The study involved 101 pre-term neonates born between June 2008 and May 2012 with a diagnosis of microbiologically confirmed sepsis, 98 pre-term neonates with clinical sepsis and 100 randomly selected, otherwise healthy pre-term neonates born during the study period. During the study, 47 SNPs in 18 candidate genes were genotyped on Guthrie cards using an ABI PRISM 7900 HT Fast real-time and MAssARRAY for nucleic acids instruments. Genotypes CT and TT of rs1143643 (the IL1? gene) and genotype GG of rs2664349GG (the MMP-16 gene) were associated with a significantly increased overall risk of developing sepsis (p?=?0.03, p?=?0.05 and p?=?0.03), whereas genotypes AG of rs4358188 (the BPI gene) and CT of rs1799946 (the DEF?1 gene) were associated with a significantly reduced risk of developing sepsis (p?=?0.05 for both). Among the patients with bacteriologically confirmed sepsis, only genotype GG of rs2664349 (the MMP-16 gene) showed a significant association with an increased risk (p?=?0.02). Genotypes GG of rs2569190 (the CD14 gene) and AT of rs4073 (the IL8 gene) were associated with a significantly increased risk of developing severe sepsis (p?=?0.05 and p?=?0.01). Genotype AG of rs1800629 (the LTA gene) and genotypes CC and CT of rs1341023 (the BPI gene) were associated with a significantly increased risk of developing Gram-negative sepsis (p?=?0.04, p?=?0.04 and p?=?0.03). These results show that genetic variability seems to play a role in sepsis in pre-term neonates by influencing susceptibility to and the severity of the disease, as well as the risk of having disease due to specific pathogens. PMID:25000179

Esposito, Susanna; Zampiero, Alberto; Pugni, Lorenza; Tabano, Silvia; Pelucchi, Claudio; Ghirardi, Beatrice; Terranova, Leonardo; Miozzo, Monica; Mosca, Fabio; Principi, Nicola

2014-01-01

19

GENETIC POLYMORPHISM IN HUMAN GLYCINE-RICH BETA-GLYCOPROTEIN*, {  

E-print Network

GENETIC POLYMORPHISM IN HUMAN GLYCINE-RICH BETA-GLYCOPROTEIN*, { BY CHESTER A. ALPER, THOMAS-glycoprotein (GBG) 1 (1) is a 6.2S globulin which, on storage of serum, slowly converts to two fragments. The more basic fragment, glycine- rich -r-glycoprotein (GGG) (2) is probably identical to/32-glycoprotein

Alper, Chester A.

20

Random amplified polymorphic DNA analysis of genetically modified organisms  

Microsoft Academic Search

Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45%

Cheah Yoke-Kqueen; Son Radu

2006-01-01

21

A polymorphic DNA marker genetically linked to Huntington's disease  

Microsoft Academic Search

Family studies show that the Huntington's disease gene is linked to a polymorphic DNA marker that maps to human chromosome 4. The chromosomal localization of the Huntington's disease gene is the first step in using recombinant DNA technology to identify the primary genetic defect in this disorder.

James F. Gusella; Nancy S. Wexler; P. Michael Conneally; Susan L. Naylor; Mary Anne Anderson; Rudolph E. Tanzi; Paul C. Watkins; Kathleen Ottina; Margaret R. Wallace; Alan Y. Sakaguchi; Anne B. Young; Ira Shoulson; Ernesto Bonilla; Joseph B. Martin

1983-01-01

22

Genetic polymorphisms in pakistani women with polycystic ovary syndrome.  

PubMed

Polycystic ovary syndrome (PCOS) is the major cause of anovulatory infertility. Although the genetic basis of PCOS is not well understood, it is a common metabolic and endocrine disorder. This study investigates the possible genomic variants associated with PCOS in Pakistani women from the Punjab region. DNA samples from 96 patients with genetically unrelated PCOS and 96 controls were analyzed by direct sequencing to determine the polymorphisms of different loci on follicle-stimulating hormone receptor (fshr), follicle-stimulating hormone ? (fshr?), luteinizing hormone chorionic gonadotropin (lhcgr), luteinizing hormone ? (lh?), estrogen receptor ? (esr1), and estrogen receptor ? (esr2) genes. Significant associations were observed within the genotype frequencies, allele frequencies, and multi-single-nucleotide polymorphism (SNP) haplotype analysis of most polymorphisms studied. This study identified new SNPs at positions 605+52 Del/T in lhcgr genes occurring in this particular subpopulation. The strong r (2) value suggests that polymorphisms in the fshr and esr1 genes were in linkage disequilibrium. Our study provides evidence of statistically significant associations between susceptibility to PCOS in Pakistani women and the gene polymorphisms mentioned earlier. This suggests that the susceptible loci for PCOS lie within or very close to the chromosomal regions spanning these genes. PMID:25100445

Liaqat, Irfana; Jahan, Nusrat; Krikun, Graciela; Taylor, Hugh S

2015-03-01

23

Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)  

PubMed Central

Background The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary. Methodology/Principal Findings Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 54–65% and 46–63% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses. Conclusions Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts. PMID:19582155

Kang, Hae Ji; Bennett, Shannon N.; Sumibcay, Laarni; Arai, Satoru; Hope, Andrew G.; Mocz, Gabor; Song, Jin-Won; Cook, Joseph A.; Yanagihara, Richard

2009-01-01

24

[Genetic polymorphism of bluegrass cultivars detected by RAPDs].  

PubMed

Kentucky bluegrass (Poa pratensis L.) is a hardy, persistent forage and turf grass adapted to a wide range of soils and climates. Its ever-increasing adoption in highly cared-for sports fields has attracted the attention of many seed companies. However in the past, the breeding of elite varieties was often hampered by the extreme complexity of the genome. The polymorphism is important for broading the genetic basis and may be exploited for application of heterosis. The genetic relationship of 16 bluegrass cultivars, including 15 accessions Kentucky bluegrass cultivars and 1 entries Canada bluegrass (Poa compressa L.) cultivar from different breeding company were analyzed using 25 RAPD markers. 25 RAPD primers generated 218 bands, of which 196 bands (89.91%) were polymorphism. It showed that the Canada Bluegrass was separated from other Kentucky Bluegrass and genetic polymorphism in the Kentucky Bluegrass cultivars was low, the genetic similarity among the cultivars fell between 66%-98%. Dendrogram obtained using these molecular markers were partly in agreement with their separated morphologic character. Cultivars from the same company were not clustered in one group. PMID:16120587

Ning, Ting-Ting; Zhang, Zai-Jun; Jin, Cheng-Zan; Zhu, Ying-Guo

2005-07-01

25

New source of genetic polymorphisms in Lepidoptera?  

PubMed

The variability level of the ISSR (inter-simple sequences repeat) primer (GACA)4 was examined in the three Lepidoptera families Pyralidae, Sphingidae and Pieridae. Our study shows that the tetra-repeat (GACA)n is evidently present in sufficient numbers in these butterflies to provide informative DNA fingerprints. The variability is mostly rather high, but within a comparable range to other ISSR studies. Although less polymorphisms may be encountered in some butterfly families, this study indicates that high variability of this marker may be a common characteristic of Lepidoptera genomes. An appeal for a minimal level of standardization of ISSR-PCR data analysis is formulated to enable an exact comparison between the groups of organisms studied with this fingerprint technique. PMID:16163839

Hundsdoerfer, Anna K; Wink, Michael

2005-01-01

26

Copyright 2001 by the Genetics Society of America Regions of Lower Crossing Over Harbor More Rare Variants in  

E-print Network

Copyright 2001 by the Genetics Society of America Regions of Lower Crossing Over Harbor More Rare Variants in African Populations of Drosophila melanogaster Peter Andolfatto* and Molly Przeworski scattered throughout the Drosophila melanogaster genome. We show that, in African populations, a summary

Andolfatto, Peter

27

Single nucleotide polymorphisms as tools in human genetics.  

PubMed

The development of detailed single nucleotide polymorphism (SNP) maps of the human genome coupled with high-throughput genotyping technologies may allow us to unravel complex genetic traits, such as multifactorial disease or drug response, over the next few years. Here we describe the current efforts to identify and characterize the large numbers of SNPs required and discuss the practicalities of association studies for the identification of genes involved in complex traits. PMID:11005795

Gray, I C; Campbell, D A; Spurr, N K

2000-10-01

28

Predisposition of genetic polymorphism with the risk of urolithiasis  

Microsoft Academic Search

Urolithiasis is a relevant clinical problem with a subsequent burden for health system. The aim of this review is to provide\\u000a recent progress made using genetic polymorphisms to define pathophysiology, to identify persons at risk for kidney stone disease\\u000a and to predict treatment response. Population case-control studies are useful both as an alternative and an adjunct as compared\\u000a to family

Rama D. Mittal; Hemant K. Bid; Parmeet K. Manchanda; Rakesh Kapoor

2008-01-01

29

Uridine 5?-diphosphoglucuronosyltransferase genetic polymorphisms and response to cancer chemotherapy  

PubMed Central

Pharmacogenetics aims to elucidate how genetic variation affects the efficacy and side effects of drugs, with the ultimate goal of personalizing medicine. Clinical studies of the genetic variation in the uridine 5?-diphosphoglucuronosyltransferase gene have demonstrated how reduced-function allele variants can predict the risk of severe toxicity and help identify cancer patients who could benefit from reduced-dose schedules or alternative chemotherapy. Candidate polymorphisms have also been identified in vitro, although the functional consequences of these variants still need to be tested in the clinical setting. Future approaches in uridine 5?-diphosphoglucuronosyltransferase pharmacogenetics include genetic testing prior to drug treatment, genotype-directed dose-escalation studies, study of genetic variation at the haplotype level and genome-wide studies. PMID:20373870

Ramírez, Jacqueline; Ratain, Mark J; Innocenti, Federico

2011-01-01

30

High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis  

SciTech Connect

The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

1994-09-01

31

Genetic polymorphism in the NRF2 gene as a prognosis marker for cancer chemotherapy  

PubMed Central

NF-E2-related factor 2 (NRF2) is a transcription factor that controls the expression of a variety of antioxidant and detoxification genes. Accumulating evidence strongly suggests that NRF2 mediates cancer cell proliferation and drug resistance, as well. Single nucleotide polymorphism (SNP) -617C > A in the anti-oxidant response element-like loci of the human NRF2 gene play a pivotal role in the positive feedback loop of transcriptional activation of the NRF2 gene. Since the SNP (-617A) reportedly decreases the binding affinity to the transcription factors of NRF2/small multiple alignment format (MafK), the homozygous -617A/A allele may attenuate the positive feedback loop of transcriptional activation of the NRF2 gene and reduce the NRF2 protein level. As the consequence, cancer cells are considered to become more sensitive to therapy and less aggressive than cancer cells harboring the -617C (WT) allele. Indeed, Japanese lung cancer patients carrying SNP homozygous alleles (c. -617A/A) exhibited remarkable survival over 1,700 days after surgical operation (log-rank p = 0.021). The genetic polymorphism in the human NRF2 gene is considered as one of prognosis markers for cancer therapy. PMID:25408701

Ishikawa, Toshihisa

2014-01-01

32

CD209 Genetic Polymorphism and Tuberculosis Disease  

PubMed Central

Background Tuberculosis causes significant morbidity and mortality worldwide, especially in sub-Saharan Africa. DC-SIGN, encoded by CD209, is a receptor capable of binding and internalizing Mycobacterium tuberculosis. Previous studies have reported that the CD209 promoter single nucleotide polymorphism (SNP)-336A/G exerts an effect on CD209 expression and is associated with human susceptibility to dengue, HIV-1 and tuberculosis in humans. The present study investigates the role of the CD209 -336A/G variant in susceptibility to tuberculosis in a large sample of individuals from sub-Saharan Africa. Methods and Findings A total of 2,176 individuals enrolled in tuberculosis case-control studies from four sub-Saharan Africa countries were genotyped for the CD209 -336A/G SNP (rs4804803). Significant overall protection against pulmonary tuberculosis was observed with the -336G allele when the study groups were combined (n?=?914 controls vs. 1262 cases, Mantel-Haenszel 2x2 ?2?=?7.47, P?=?0.006, odds ratio?=?0.86, 95%CI 0.77–0.96). In addition, the patients with -336GG were associated with a decreased risk of cavitory tuberculosis, a severe form of tuberculosis disease (n?=?557, Pearson's 2×2 ?2?=?17.34, P?=?0.00003, odds ratio?=?0.42, 95%CI 0.27–0.65). This direction of association is opposite to a previously observed result in a smaller study of susceptibility to tuberculosis in a South African Coloured population, but entirely in keeping with the previously observed protective effect of the -336G allele. Conclusion This study finds that the CD209 -336G variant allele is associated with significant protection against tuberculosis in individuals from sub-Saharan Africa and, furthermore, cases with -336GG were significantly less likely to develop tuberculosis-induced lung cavitation. Previous in vitro work demonstrated that the promoter variant -336G allele causes down-regulation of CD209 mRNA expression. Our present work suggests that decreased levels of the DC-SIGN receptor may therefore be protective against both clinical tuberculosis in general and cavitory tuberculosis disease in particular. This is consistent with evidence that Mycobacteria can utilize DC-SIGN binding to suppress the protective pro-inflammatory immune response. PMID:18167547

Vannberg, Fredrik O.; Tosh, Kerrie; Floyd, Sian; Jackson-Sillah, Dolly; Crampin, Amelia; Sichali, Lifted; Bah, Boubacar; Gustafson, Per; Aaby, Peter; McAdam, Keith P. W. J.; Bah-Sow, Oumou; Lienhardt, Christian; Sirugo, Giorgio; Fine, Paul; Hill, Adrian V. S.

2008-01-01

33

Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms.  

PubMed

Switchgrass (Panicum virgatum) is a perennial warm-season grass native to North America that has been identified as a dedicated cellulosic biofuel crop. We quantified genetic diversity in tetraploid switchgrass germplasm collected at Oklahoma State University and characterized genetic relatedness among the collections from distinct regions. Fifty-six tetraploid accessions, including seven upland and 49 lowland genotypes from throughout the US, were examined. The amplified fragment length polymorphism (AFLP) procedure was utilized to generate DNA profiling patterns that were scored visually. Sixteen selective AFLP primer combinations were used to amplify 452 polymorphic bands. The accessions' genetic similarity coefficients, UPGMA (unweighted pair-group method with arithmetic averaging) cluster analysis and principle coordinate analysis, were performed. The upland and lowland accessions clustered according to ecotypes, with one exception (TN104). Genetic similarity coefficients among the accessions ranged from 0.73 to 0.95. Analysis of molecular variance (AMOVA) was performed, showing significant differences between the upland and lowland genotypes. The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4). PMID:22180031

Todd, J; Wu, Y Q; Wang, Z; Samuels, T

2011-01-01

34

Genetic polymorphisms and associated susceptibility to asthma  

PubMed Central

As complex common diseases, asthma and allergic diseases are caused by the interaction of multiple genetic variants with a variety of environmental factors. Candidate-gene studies have examined the involvement of a very large list of genes in asthma and allergy, demonstrating a role for more than 100 loci. These studies have elucidated several themes in the biology and pathogenesis of these diseases. A small number of genes have been associated with asthma or allergy through traditional linkage analyses. The publication of the first asthma-focused genome-wide association (GWA) study in 2007 has been followed by nearly 30 reports of GWA studies targeting asthma, allergy, or associated phenotypes and quantitative traits. GWA studies have confirmed several candidate genes and have identified new, unsuspected, and occasionally uncharacterized genes as asthma susceptibility loci. Issues of results replication persist, complicating interpretation and making conclusions difficult to draw, and much of the heritability of these diseases remains undiscovered. In the coming years studies of complex diseases like asthma and allergy will probably involve the use of high-throughput next-generation sequencing, which will bring a tremendous influx of new information as well as new problems in dealing with vast datasets. PMID:23637549

March, Michael E; Sleiman, Patrick MA; Hakonarson, Hakon

2013-01-01

35

Evaluation of Genetic Polymorphisms in Patients with Multiple Chemical Sensitivity  

PubMed Central

Objective Multiple chemical sensitivity (MCS) is a chronic medical condition characterized by symptoms that the affect an individual’s response to low-level chemical exposure. In this study, we identified a chemical sensitive population (CSP) and investigated the effect of genetic polymorphisms on their risk of chemical sensitivity. Methods A quick environment exposure sensitivity (QEESI) questionnaire was used to survey 324 Japanese male workers whose DNA samples had been collected and stored. The following genes, which encode enzymes affecting the metabolic activation of a large number of xenobiotic compounds, were selected and analyzed in order to determine their influence on genetic predisposition to CSP: cytochrome P450 (CYP) 2E1, N-acetyl transferase (NAT) 2, glutathione S-transferase (GST) M1, GSTT1, GSTP1, low Km aldehyde dehydrogenase (ALDH2), and superoxide dismutase (SOD) 2. Results Significant case-control distributed differences were observed in SOD2 polymorphisms and allele frequency distribution in high chemical sensitive subjects. Both the significant adjusted OR of 4.30 (95% CI, 1.23–15.03) and 4.53 (95% CI, 1.52-13.51) were observed in SOD2 Ala/Ala and Val/Ala compared to Val/Val and in SOD2 Ala/Ala compared to Val/Ala compared to Val/Val genetic analysis in the high chemical sensitivity case-control study. Conclusions We observed that high chemical sensitive individuals diagnosed by using Japanese criteria as MCS patients were more significantly associated with SOD2 polymorphisms. PMID:23967348

Cui, Xiaoyi; Lu, Xi; Hiura, Mizue; Oda, Masako; Miyazaki, Wataru; Katoh, Takahiko

2013-01-01

36

From twins to genetic polymorphisms: behavioral genetic research in Poland.  

PubMed

Behavioral genetic research has been conducted at the University of Warsaw for the past 20 years. The work done at the University focuses primarily on the origins of individual differences in temperament and other personality traits. In particular, research is directed toward the traits postulated in the Regulative Theory of Temperament. We also focused on the heritability of socio-political attitudes, risk factors for human health, and post-traumatic stress disorder. The majority of the research that has been carried out is grounded in twin and family studies, although recent work based on molecular techniques has also been developed. This article reviews the most important directions and findings of behavioral genetics research at the University of Warsaw. PMID:25091033

Oniszczenko, W?odzimierz; Dragan, Wojciech ?ukasz

2014-10-01

37

Genetic polymorphism and interethnic variability of plasma paroxonase activity.  

PubMed Central

A method for determining plasma paroxonase activity using an auto-analyser is described. Frequency distributions for British and Indian subjects show bimodality. A study of 40 British families confirms the presence of a genetic polymorphism with regard to plasma paroxonase activity. Two phenotypes can be defined, controlled by two alleles at one autosomal locus. The frequency of the low activity phenotype is less in the Indian population than in the British population. Malay, Chinese, and African subjects fail to show obvious bimodality. PMID:1003443

Playfer, J R; Eze, L C; Bullen, M F; Evans, D A

1976-01-01

38

Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism  

Microsoft Academic Search

We report construction of an initial genetic linkage map for the black tiger shrimp, Penaeus monodon. Mapping was carried out using polymorphic markers derived from 23 Amplified Fragment Length Polymorphism (AFLP) primer pairs. These were analysed on three reference families of known pedigree. A total of 673 polymorphic AFLP loci that conformed to expected Mendelian segregation ratios were scored in

Kate Wilson; Yutao Li; Vicki Whan; Sigrid Lehnert; Keren Byrne; Stephen Moore; Siriporn Pongsomboon; Anchalee Tassanakajon; George Rosenberg; Elizabeth Ballment; Zahra Fayazi; Jennifer Swan; Matthew Kenway; John Benzie

2002-01-01

39

Genetic variation in cucumber (Cucumis sativus L.) as assessed by random amplified polymorphic DNA1  

Microsoft Academic Search

Isozyme and restriction fragment length polymorphisms (RFLPs) have been applied to studies of genetic relationships and germplasm management in cucumber (Cucumis sativus L.). However, isozymes identify relatively few polymorphisms, and RFLPs are technically complex, expensive, and not compatible for the high through-put required for rigorous assessment of this narrow-based germplasm. Since random amplified polymorphic DNA (RAPD) markers do not manifest

Thomas Horejsi; Jack E. Staub

1999-01-01

40

Genetic analysis of Tunisian fig ( Ficus carica L.) cultivars using amplified fragment length polymorphism (AFLP) markers  

Microsoft Academic Search

Genetic diversity of forty fig cultivars collected from five regions in Tunisia was investigated using amplified fragment length polymorphism (AFLP). A total of 342 reproducible bands amplified with six AFLP primer combinations were obtained. The high percentage of polymorphic bands (%PB) of 97.5 and the resolving power (Rp) collective rate value of 143 were scored. In addition, the polymorphism information

Ghada Baraket; Khaled Chatti; Olfa Saddoud; Messaoud Mars; Mohamed Marrakchi; Mokhtar Trifi; Amel Salhi-Hannachi

2009-01-01

41

Trypanosoma evansi: Genetic variability detected using amplified restriction fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analysis of Kenyan isolates  

Microsoft Academic Search

We compared two methods to generate polymorphic markers to investigate the population genetics of Trypanosoma evansi; random amplified polymorphic DNA (RAPD) and amplified restriction fragment length polymorphism (AFLP) analyses. AFLP accessed many more polymorphisms than RAPD. Cluster analysis of the AFLP data showed that 12 T.evansi isolates were very similar (‘type A’) whereas 2 isolates differed substantially (‘type B’). Type

Daniel K. Masiga; Kariuki Ndung’u; Alison Tweedie; Andrew Tait; C. Michael R. Turner

2006-01-01

42

Stability of genetic polymorphism in host–parasite interactions  

PubMed Central

Allelic diversity is common at host loci involved in parasite recognition, such as the major histocompatibility complex in vertebrates or gene-for-gene relationships in plants, and in corresponding loci encoding antigenic molecules in parasites. Diverse factors have been proposed in models to account for genetic polymorphism in host–parasite recognition. Here, a simple but general theory of host–parasite coevolution is developed. Coevolution implies the existence of indirect frequency-dependent selection (FDS), because natural selection on the host depends on the frequency of a parasite gene, and vice versa. It is shown that polymorphism can be maintained in both organisms only if there is negative, direct FDS, such that the strength of natural selection for the host resistance allele, the parasite virulence allele or both declines with increasing frequency of that allele itself. This condition may be fulfilled if the parasite has more than one generation in the same host individual, a feature which is common to most diseases. It is argued that the general theory encompasses almost all factors previously proposed to account for polymorphism at corresponding host and parasite loci, including those controlling gene-for-gene interactions. PMID:17251091

Tellier, Aurélien; Brown, James K.M

2006-01-01

43

Genetic polymorphism in pathogenesis of irritable bowel syndrome.  

PubMed

Irritable bowel syndrome (IBS) is a complex symptom-based disorder without established biomarkers or putative pathophysiology. IBS is a common functional gastrointestinal disorder which is defined as recurrent abdominal pain or discomfort that has at least two of the following symptoms for 3 d per month in the past 3 mo according to ROME III: relief by defecation, onset associated with a change in stool frequency or onset with change in appearance or form of stool. Recent discoveries revealed genetic polymorphisms in specific cytokines and neuropeptides may possibly influence the frequencies and severity of symptoms, as well as the therapeutic responses in treating IBS patients. This review gives new insights on how genetic determinations influence in clinical manifestations, treatment responses and potential biomarkers of IBS. PMID:25548468

Cheung, Cynthia K Y; Wu, Justin C Y

2014-12-21

44

Genetic polymorphism in pathogenesis of irritable bowel syndrome  

PubMed Central

Irritable bowel syndrome (IBS) is a complex symptom-based disorder without established biomarkers or putative pathophysiology. IBS is a common functional gastrointestinal disorder which is defined as recurrent abdominal pain or discomfort that has at least two of the following symptoms for 3 d per month in the past 3 mo according to ROME III: relief by defecation, onset associated with a change in stool frequency or onset with change in appearance or form of stool. Recent discoveries revealed genetic polymorphisms in specific cytokines and neuropeptides may possibly influence the frequencies and severity of symptoms, as well as the therapeutic responses in treating IBS patients. This review gives new insights on how genetic determinations influence in clinical manifestations, treatment responses and potential biomarkers of IBS. PMID:25548468

Cheung, Cynthia KY; Wu, Justin CY

2014-01-01

45

A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism  

Microsoft Academic Search

A genetic linkage map of tef was constructed with amplified fragment length polymorphism (AFLP) markers using F5 recombinant inbred lines (RILs) derived by single seed descent from the intraspecific cross of ’Kaye Murri’×’Fesho’. A total\\u000a of 192 EcoRI\\/MseI primer combinations were screened for parental polymorphism. Around three polymorphic fragments per primer combination were\\u000a detected, indicating a low polymorphism level in

G. Bai; H. Tefera; M. Ayele; H. T. Nguyen

1999-01-01

46

The role of genetic polymorphisms in environmental health.  

PubMed Central

Interest is increasing in the role of variations in the human genome (polymorphisms) in modifying the effect of exposures to environmental health hazards (often referred to as gene-environment interaction), which render some individuals or groups in the population more or less likely to develop disease after exposure. This review is intended for an audience of environmental health practitioners and students and is designed to raise awareness about this rapidly growing field of research by presenting established and novel examples of gene-environment interaction that illustrate the major theme of effect modification. Current data gaps are identified and discussed to illustrate limitations of past research and the need for the application of more robust methods in future research projects. Two primary benefits of incorporating genetics into the existing environmental health research framework are illustrated: a) the ability to detect different levels of risk within the population, and b) greater understanding of etiologic mechanisms. Both offer opportunities for developing new methods of disease prevention. Finally, we describe a basic framework for researchers interested in pursuing health effects research that incorporates genetic polymorphisms. PMID:12826477

Kelada, Samir N; Eaton, David L; Wang, Sophia S; Rothman, Nathaniel R; Khoury, Muin J

2003-01-01

47

Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs  

Microsoft Academic Search

Recently a new class of genetic polymorphism, restriction fragment length polymorphisms (RFLPs), has been uncovered by the use of restriction endonucleases which cleave DNA molecules at specific sites and cloned DNA probes which detect specific homologous DNA fragments. RFLPs promise to be exceedingly numerous and are expected to have genetic characteristics — lack of dominance, multiple allelic forms and absence

J. S. Beckmann; M. Soller

1983-01-01

48

High genetic polymorphism among Giardia duodenalis isolates from Sahrawi children.  

PubMed

Human giardiasis, the gastrointestinal infection caused by two genetically different groups (or assemblages) of Giardia duodenalis, is very common worldwide, and its prevalence is higher in developing countries. However, few surveys in these regions have been performed to include a genetic characterization of the parasite, which is necessary to unravel the complex epidemiology of the infection. In this work, we screened 120 faecal samples collected from Sahrawi children in 2003-2005, and found 41 (34.2%) of them to be positive, using immunofluorescent microscopy, for the presence of G. duodenalis cysts. Molecular characterization of the isolates was performed by RFLP and/or sequence analysis of the triose phosphate isomerase (tpi) and the glutamate dehydrogenase (gdh) genes. The results disclosed an unexpectedly high genetic polymorphism among isolates of both assemblages A and B, and a large percentage of the sequences (50% for the tpi gene, and 90% for the gdh gene) from assemblage B isolates characterized by the presence of overlapping nucleotide peaks at specific positions in the chromatograms, which can be attributed to mixed infections or to allelic sequence heterozygosity of single cysts. Notably, this phenomenon was not observed in sequences from assemblage A isolates. These results suggest that the genetic structure is different in isolates of assemblages A and B. PMID:19477474

Lalle, Marco; Bruschi, Fabrizio; Castagna, Barbara; Campa, Mario; Pozio, Edoardo; Cacciò, Simone M

2009-08-01

49

Genetic structure of Balearic honeybee populations based on microsatellite polymorphism  

PubMed Central

The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees. PMID:12729553

De la Rúa, Pilar; Galián, José; Serrano, José; Moritz, Robin FA

2003-01-01

50

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms  

E-print Network

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms Anne genetic control, respectively, showing that genetic modifiers contribute to persistence. These results-L, Nagarajan M, Veyrieras J-B, Bottin H, Steinmetz LM, et al. (2012) Genetic Modifiers of Chromatin Acetylation

Paris-Sud XI, Université de

51

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster  

SciTech Connect

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

2001-04-16

52

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster.  

PubMed

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that span the genome. Most of these markers are single nucleotide polymorphisms and sequences for these variants are provided in an accessible format. The average density of the new markers is one per 225 kb on the autosomes and one per megabase on the X chromosome. We include in this survey a set of P-element strains that provide additional use for high-resolution mapping. We show one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community. PMID:11381036

Hoskins, R A; Phan, A C; Naeemuddin, M; Mapa, F A; Ruddy, D A; Ryan, J J; Young, L M; Wells, T; Kopczynski, C; Ellis, M C

2001-06-01

53

Homocysteine and related genetic polymorphisms in Down's syndrome IQ  

PubMed Central

Objective: Down's syndrome (DS) is the most frequent genetic cause of Alzheimer-type dementia. Its metabolic phenotype involves an increased trans-sulphuration of homocysteine. The aim of the present study was to investigate the influence of homocysteinaemia (t-Hcys), folate, vitamin B12, and related polymorphisms on intelligence quotient (IQ) in DS. Methods: The IQ of 131 patients with trisomy 21 from a specialist centre in Sicily was determined and classified according to DMS-IV. The effects of age, folate, vitamin B12, t-Hcys, and genetic polymorphisms on IQ were evaluated separately and in combination using regression analyses. Results: IQ was significantly lower in DS patients with t-Hcys >7.5 µmol/l (median) and in those who were carriers of methylenetetrahydrofolate reductase (MTHFR) 677 T allele and of methylenetetrahydrofolate reductase 677 T and transcobalamin 776 G combined alleles (p = 0.0013, p = 0.0165, and p = 0.0074, respectively). The IQ correlated significantly with t-Hcys and folate in single and multiple regression analyses, independently of age. In addition, t-Hcys >9.6 µmol/l (upper quartile) was found to be associated with low IQ (<40, median of study group) with an odds ratio of 2.61 (p = 0.0203). The odds ratio was increased by threefold in carriers of MTHFR 677T allele. The MTHFR 677T allele/transcobalamin 776 G allele combination was associated with the risk of DS patients to have an IQ less that the median with an odds ratio of 2.68 (95% CI 1.26 to 5.70, p = 0.0104). Conclusion: This study found evidence of an association between t-Hcys and MTHFR 677 T and transcobalamin 776 G alleles with IQ in patients with DS. The association may be related to a defective remethylation of homocysteine, affecting IQ. PMID:15834031

Gueant, J; Anello, G; Bosco, P; Gueant-Rodriguez, R; Romano, A; Barone, C; Gerard, P; Romano, C

2005-01-01

54

Cryptogenic Stroke in Relation to Genetic Variation in Clotting Factors and Other Genetic Polymorphisms Among Young Men and Women  

Microsoft Academic Search

Background and Purpose—The purpose of the present study was to compare the prevalences of genetic polymorphisms in persons with cryptogenic stroke with those among stroke patients with evidence of large-artery occlusive disease or an unequivocal cardioembolic source (noncryptogenic stroke). Methods—We compared the prevalences of genetic polymorphisms thought to be related to thrombi formation in young stroke patients with evidence of

Harland Austin; Marc I. Chimowitz; Holly A. Hill; Seemant Chaturvedi; Lawrence R. Wechsler; Robert J. Wityk; Elizabeth Walz; Janet L. Wilterdink; Bruce Coull; Cathy A. Sila; Panos Mitsias; Bruce Evatt; W. Craig Hooper

2010-01-01

55

DNA repair gene polymorphisms and genetic predisposition to cutaneous melanoma.  

PubMed

The incidence of cutaneous melanoma is rising rapidly in a number of countries. The key environmental risk factor is exposure to the ultraviolet (UV) component in sunlight. The nucleotide excision repair (NER) pathway deals with the main forms of UV-induced DNA damage. We have investigated the hypothesis that polymorphisms in NER genes constitute genetic susceptibility factors for melanoma. However, not all melanomas arise on sun-exposed sites and so we investigated the hypothesis that genes involved in other pathways for the repair of oxidative DNA damage may also be involved in susceptibility to melanoma. Scotland, with its high incidence of melanoma and stable homogeneous population, was ideal for this case-control study, involving 596 Scottish melanoma patients and 441 population-based controls. Significant associations were found for the NER genes ERCC1 and XPF, with the strongest associations for melanoma cases aged 50 and under [ERCC1 odds ratio (OR) 1.59, P = 0.008; XPF OR 1.69, P = 0.003]. Although an XPD haplotype was associated with melanoma, it did not contain the variant 751 Gln allele, which has been associated with melanoma in some previous studies. No associations were found for the base excision repair and DNA damage response genes investigated. An association was also found for a polymorphism in the promoter of the vitamin D receptor gene, VDR (OR 1.88, P = 0.005). The products of the two NER genes, ERCC1 and XPF, where associations with melanoma were found, act together in a rate-limiting step in the repair pathway. PMID:17210993

Povey, Joanne E; Darakhshan, Fatemeh; Robertson, Karen; Bisset, Yvonne; Mekky, Magda; Rees, Jonathan; Doherty, Val; Kavanagh, Gina; Anderson, Niall; Campbell, Harry; MacKie, Rona M; Melton, David W

2007-05-01

56

Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines  

Microsoft Academic Search

Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of

W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

1995-01-01

57

The Genetic Basis of a Flower Color Polymorphism in the Common Morning  

E-print Network

The Genetic Basis of a Flower Color Polymorphism in the Common Morning Glory (Ipomoea purpurea) R) is highly polymorphic for flower color. Part of this phenotypic variation is due to allelic variation at the P locus. This locus determines whether flowers will be purple or pink, where purple is dominant

Rausher, Mark D.

58

Genetic polymorphisms and non-small-cell lung cancer: future paradigms.  

PubMed

This article addresses some current issues about genetic polymorphisms studied in the non-small-cell lung cancer translational field. Furthermore, it discusses about new potential biomarkers regarding lung cancer risk and prognosis. PMID:25410679

Mello, Ramon Andrade Bezerra de

2014-11-18

59

Influence of Multiple Genetic Polymorphisms on Genitourinary Morbidity After Carbon Ion Radiotherapy for Prostate Cancer  

SciTech Connect

Purpose: To investigate the genetic risk of late urinary morbidity after carbon ion radiotherapy in prostate cancer patients. Methods and Materials: A total of 197 prostate cancer patients who had undergone carbon ion radiotherapy were evaluated for urinary morbidity. The distribution of patients with dysuria was as follows: Grade 0, 165; Grade 1, 28; and Grade 2, 4 patients. The patients were divided (2:1) consecutively into the training and test sets and then categorized into control (Grade 0) and case (Grade 1 or greater) groups. First, 450 single nucleotide polymorphisms (SNPs) in 118 candidate genes were genotyped in the training set. The associations between the SNP genotypes and urinary morbidity were assessed using Fisher's exact test. Then, various combinations of the markers were tested for their ability to maximize the area under the receiver operating characteristics (AUC-ROC) curve analysis results. Finally, the test set was validated for the selected markers. Results: When the SNP markers in the SART1, ID3, EPDR1, PAH, and XRCC6 genes in the training set were subjected to AUC-ROC curve analysis, the AUC-ROC curve reached a maximum of 0.86. The AUC-ROC curve of these markers in the test set was 0.77. The SNPs in these five genes were defined as 'risk genotypes.' Approximately 90% of patients in the case group (Grade 1 or greater) had three or more risk genotypes. Conclusions: Our results have shown that patients with late urinary morbidity after carbon ion radiotherapy can be stratified according to the total number of risk genotypes they harbor.

Suga, Tomo; Iwakawa, Mayumi [RadGenomics Research Group, National Institute of Radiological Sciences, Chiba (Japan); Tsuji, Hiroshi; Ishikawa, Hitoshi [Research Center Hospital for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Oda, Eisei [Medical Toukei Corporation, Tokyo (Japan); Noda, Shuhei; Otsuka, Yoshimi; Ishikawa, Atsuko; Ishikawa, Ken-Ichi [RadGenomics Research Group, National Institute of Radiological Sciences, Chiba (Japan); Shimazaki, Jun [Research Center Hospital for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Department of Urology, Chiba University Graduate School of Medicine, Chiba (Japan); Mizoe, Jun-Etsu; Tsujii, Hirohiko [Research Center Hospital for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Imai, Takashi [RadGenomics Research Group, National Institute of Radiological Sciences, Chiba (Japan)], E-mail: imait@nirs.go.jp

2008-11-01

60

The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for  

E-print Network

many variants are found at low frequencies and only a minority of vari- ants are common. We conclude- bution of allele frequencies in the CC resembles that seen in natural populations like humans in which strains have been derived that harbor a tremendous amount of natural genetic variation (Beck et al. 2000

Wang, Wei

61

Genetic variation for an aphid wing polyphenism is genetically linked to a naturally occurring wing polymorphism  

PubMed Central

Many polyphenisms are examples of adaptive phenotypic plasticity where a single genotype produces distinct phenotypes in response to environmental cues. Such alternative phenotypes occur as winged and wingless parthenogenetic females in the pea aphid (Acyrthosiphon pisum). However, the proportion of winged females produced in response to a given environmental cue varies between clonal genotypes. Winged and wingless phenotypes also occur in males of the sexual generation. In contrast to parthenogenetic females, wing production in males is environmentally insensitive and controlled by the sex-linked, biallelic locus, aphicarus (api). Hence, environmental or genetic cues induce development of winged and wingless phenotypes at different stages of the pea aphid life cycle. We have tested whether allelic variation at the api locus explains genetic variation in the propensity to produce winged females. We assayed clones from an F2 cross that were heterozygous or homozygous for alternative api alleles for their propensity to produce winged offspring. We found that clones with different api genotypes differed in their propensity to produce winged offspring. The results indicate genetic linkage of factors controlling the female wing polyphenism and male wing polymorphism. This finding is consistent with the hypothesis that genotype by environment interaction at the api locus explains genetic variation in the environmentally cued wing polyphenism. PMID:15817441

Braendle, Christian; Friebe, Ilvy; Caillaud, Marina C; Stern, David L

2005-01-01

62

A Web-Based Genetic Polymorphism Learning Approach for High School Students and Science Teachers  

ERIC Educational Resources Information Center

Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using…

Amenkhienan, Ehichoya; Smith, Edward J.

2006-01-01

63

Genetic diversity of fringed brome ( Bromus ciliatus ) as determined by amplified fragment length polymorphism  

Microsoft Academic Search

Fringed brome (Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four

Yong-Bi Fu; Bruce E. Coulman; Yasas S. N. Ferdinandez; Jacques Cayouette; Paul M. Peterson

2005-01-01

64

Genetic diversity of Uapaca kirkiana Muel. Årg. populations as revealed by amplified fragment length polymorphisms (AFLPs)  

Microsoft Academic Search

Uapaca kirkiana is a priority fruit tree species for domestication in miombo woodlands of Southern Africa. Natural populations of U. kirkiana are declining through out the woodlands due to deforestation, forest fragmentation and wildfires. Knowledge of population structure and genetic diversity is prerequisite for development of conservation strategies. Amplified fragment length polymorphisms (AFLP) were used to assess the genetic diversity

Weston F. Mwase; Å. Bjørnstad; B. Stedje; J. M. Bokosi; M. B. Kwapata

2006-01-01

65

Genetic polymorphism of ?-lactoglobulin in sheep raised for milk production  

Microsoft Academic Search

To investigate ?-lactoglobulin polymorphism using polymerase chain reaction – restriction fragment length polymorphism in Polish Mountain, East Friesian, Polish Merino and Austrian Bergschaf sheep raised for milk production, three ?-LGB genotypes (AA, AB and BB) were found in all the groups, AB being the most frequent genotype in all the groups. The frequency of ?-LGB A genes was 0.66 in

Aldona Kawecka; Anna Radko

2011-01-01

66

Influence of GSTT1 Genetic Polymorphisms on Arsenic Metabolism  

PubMed Central

SUMMARY A repeated measures study was conducted in Pabna, Bangladesh to investigate factors that influence biomarkers of arsenic exposure. Drinking water arsenic concentrations were measured by inductively-coupled plasma mass spectrometry (ICP-MS) and urinary arsenic species [arsenite (As3), arsenate (As5), monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)] were detected using High Performance Liquid Chromatography (HPLC) and Hydride Generated Atomic Absorption Spectrometry (HGAAS). Linear mixed effects models with random intercepts were used to evaluate the effects of arsenic contaminated drinking water, genetic polymorphisms in glutathione-S-transferase (GSTT1 and GSTM1) on total urinary arsenic, primary methylation index [MMA/(As3+As5)], secondary methylation index (DMA/MMA), and total methylation index [(MMA+DMA)/(As3+As5)]. Drinking water arsenic concentrations were positively associated with total urinary arsenic concentrations and total methylation index. A significant gene-environment interaction was observed between urinary arsenic exposure in drinking water GSTT1 but not GSTM1 where GSTT1 null individuals had a slightly higher excretion rate of arsenic compared to GSTT1 wildtypes after adjusting for other factors. Additionally, individuals with GSTT1 null genotypes had a higher primary methylation index and lower secondary methylation index compared to GSTT1 wildtype after adjusting for other factors. This data suggests that GSTT1 contributes to the observed variability in arsenic metabolism. Since individuals with a higher primary methylation index and lower secondary methylation index are more susceptible to arsenic related disease, these results suggest that GSTT1 null individuals may be more susceptible to arsenic-related toxicity. No significant associations were observed between GSTM1 and any of the arsenic methylation indices. PMID:24511153

Kile, Molly L.; Houseman, E. Andres; Quamruzzaman, Quazi; Rahman, Mahmuder; Mahiuddin, Golam; Mostofa, Golam; Hsueh, Yu-Mei; Christiani, David C.

2014-01-01

67

Sensitivity of random amplified polymorphic DNA analysis to detect genetic change in sugarcane during tissue culture.  

PubMed

Random amplified polymorphic DNA (RAPD) analysis using 10-mer oligonucleotide primers efficiently differentiated sugarcane cultivars and proved suitable for detecting gross genetic change such as that which can occur in sugarcane subjected to prolonged tissue culture, for example in protoplast-derived callus. However, RAPD analysis was not sufficiently sensitive to detect smaller genetic changes that occur during sugarcane genetic transformation. The length of DNA scored for polymorphism per primer averaged 13.2 kb, or 0.0001% of the typical sugarcane genome size of 1.2 × 107 kb (2C). RAPD analysis of sugarcane plants regenerated from embryogenic callus revealed very few polymorphisms, indicating that gross genetic change is infrequent during this tissue culture procedure, although epigenetic effects result in transient morphological changes in regenerated plants. More sensitive variations on the RAPD technique may increase the practicality of DNA-based screening of regenerated plant lines to reveal somaclonal variants. PMID:24173080

Taylor, P W; Geijskes, J R; Ko, H L; Fraser, T A; Henry, R J; Birch, R G

1995-06-01

68

Meta-analysis of genetic polymorphisms and gastric cancer risk: variability in associations according to race.  

PubMed

The goal of this study was to consolidate information on genetic risk factors for gastric cancer. An additional aim was to investigate the influence of race on these genetic risk associations. Relevant studies were identified from PubMed and references of retrieved articles. Meta-analysis techniques were used to summarise associations between genetic polymorphisms and gastric cancer. A total of 203 relevant studies were identified, assessing 225 polymorphisms across 95 genes. Subgroup analysis indicated that Chinese, Japanese and Korean data were consistent and could be pooled. However, 6 of 13 polymorphisms (ACE I/D, CCND1 870G>A, CDH1 -160C>A, IL1B -511C>T, IL4 -590C>T, IL10 -592A>C) displayed conflicting effects between Asian and Caucasian populations, three of which (ACE I/D, CCND1 870G>A, IL1B -511C>T) had significantly different odds ratios between the two racial groups. In total, 37 polymorphisms across 27 genes were found to be significantly associated with gastric cancer in Asians, and 12 polymorphisms across 11 genes in Caucasians. Consolidated panels of polymorphisms associated with gastric cancer risk were identified in Asians and Caucasians. The results caution against the assumption that genetic risk factors are consistent between races. PMID:19375306

Loh, Marie; Koh, King Xin; Yeo, Boon Huat; Song, Chun Meng; Chia, Kee Seng; Zhu, Feng; Yeoh, Khay Guan; Hill, Jeffrey; Iacopetta, Barry; Soong, Richie

2009-09-01

69

Association of neonatal necrotizing enterocolitis with myeloid differentiation-2 and GM2 activator protein genetic polymorphisms.  

PubMed

The aim of the present study was to investigate the association of neonatal necrotizing enterocolitis (NEC) with myeloid differentiation?(MD?2) and GM2 activator protein (GM2A) genetic polymorphisms. Gene resequencing of the MD?2 and GM2A gene exons was performed on 42 neonates, diagnosed with NEC (NEC group), as well as in the rs11465996 locus, located in the MD?2 gene promoter region. The aim was to detect the genetic polymorphisms present in the neonates with NEC and compare the functional polymorphic loci with 83 neonates without NEC (control group), who had been born during the same period. A polymorphic locus with abnormal frequency was detected in the exon region of the MD?2 gene. In the NEC group, the frequency of genotypes carrying the low frequency allele (G) in the rs11465996 locus (MD?2 promoter region) was significantly higher compared with the control group (?2=4.388, P=0.036). Furthermore, the frequencies of genotypes carrying the low frequency A and C alleles in the rs1048719 (GM2A gene exon 1) and rs2075783 loci (GM2A intron), respectively, were significantly higher in the NEC group compared with the control group (?2=4.316, P=0.038; and ?2=13.717, P=0.000, respectively). In addition, the rs11465996 polymorphism in the MD?2 gene promoter region was found to be associated with the severity of NEC. Furthermore, the rs2075783 polymorphism in the GM2A gene exon 1 and the rs1048719 polymorphism in the intron region of this gene, were associated with the occurrence of NEC. The present study demonstrated that gene polymorphisms of MD?2 and GM2A were associated with the occurrence or severity of NEC; however, further in?depth exploration is required to clarify the associations between genetic predispositions to polymorphisms, and NEC. PMID:25816011

Zhou, Wei; Yuan, Weiming; Huang, Longguang; Wang, Ping; Rong, Xiao; Tang, Juan

2015-07-01

70

Genetic variability in yam cultivars from Guinea-Sudan of Benin assessed by random amplified polymorphic DNA  

Microsoft Academic Search

Yam (Dioscorea spp.) is an important food and cash crop in the Guinea-Sudan zone of Benin. The genetic diversity of about 70 cultivars of Dioscorea cayenensis\\/Dioscorea rotundata (Guinea yam) and about 20 cultivars of Dioscorea alata (water yam) was analysed using random amplified polymorphic DNA (RAPD). The amplified bands revealed high polymorphism. These polymorphic DNA fragments were used to construct

A. Zannou; E. Agbicodo; J. Zoundjihékpon; P. C. Struik; A. Ahanchédé; D. K. Kossou; A. Sanni

2009-01-01

71

Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm founder effect in  

E-print Network

1 Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear a founder effect during colonization of North America. Occurrence of polymorphism in the D America, i.e. individuals from their primary habitat; (ii) estimation of the polymorphism of North

Paris-Sud XI, Université de

72

Genetic polymorphisms of biotransformation enzymes in patients with Hodgkin's and non-Hodgkin's lymphomas  

Microsoft Academic Search

Objective. Considering the role in the metabolism of chemicals played by biotransformation enzymes, we aimed at determining whether any association exists between genetic polymorphisms in cytochromes P450 (CYP1A1 and CYP2E1), epoxide hydrolase (EPHX1), NAD(P)H: quinone oxidoreductase (NQO1), glutathione S-transferases (GSTs M1\\/P1\\/T1) and individual susceptibility to lymphomas. Methods. Genotyping assays based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were used

P. Soucek; J. Šarmanová; V. Kristensen; M. Apltauerová; I. Gut

2002-01-01

73

Genetic diversity among selected Argentinean garlic clones ( Allium sativum L.) using AFLP (Amplified Fragment Length Polymorphism)  

Microsoft Academic Search

Genetic diversity of eight selected Argentinean garlic clones (Allium sativum L.) were investigated at the DNA level with the amplified fragment length polymorphism DNA (AFLP) procedure. A total of 405\\u000a unambiguous bands were identified by six primer combinations of EcoR I +3 and Mse I +3, of those, 398 showed a clear polymorphism, representing 98% of the total bands. A

S. García Lampasona; L. Martínez; J. L. Burba

2003-01-01

74

A CD14 monocyte receptor polymorphism and genetic susceptibility to Parkinson's disease for females  

Microsoft Academic Search

Recent studies suggest that inflammation may play an important role in the pathogenesis of Parkinson's disease (PD). Because the C(?260)?T polymorphism in the promoter of the CD14 monocyte receptor gene (pCD14) could affect the predisposition to the inflammatory response, we conducted a case-control study to investigate a possible genetic susceptibility of the pCD14 polymorphism in patients with PD. This study

J. J. Lin; C. H. Chen; K. C. Yueh; C. Y. Chang; S. Z. Lin

2006-01-01

75

Genetic diversity of Rehmannia glutinosa cultivars based on sequence-related amplified polymorphism markers  

Microsoft Academic Search

SRAP analytic system was used to assess genetic diversity of Rehmnnia glutinosa. Twenty-three Rehmnnia glutinosa cultivars were screened with 288 primer combinations, of which 13 produced stable and reproducible amplification patterns in three repetitive experiments. Among a total of 338 amplified fragments, 306 (90.5%) were polymorphic, with an average of 23.5 fragments for each primer combination. The percentage of polymorphic

Yanqing Zhou; Fengping Gu; Chune Zhou; Huanling Yao; Hongying Duan; Fang Wang; Yanju Liu; Yanhao Xing; Suxia Chu

2010-01-01

76

Association of Polymorphism Harbored by Tumor Necrosis Factor Alpha Gene and Sex of Calf with Lactation Performance in Cattle  

PubMed Central

In a majority of mammals, male infants have heavier body mass and grow faster than female infants. Accordingly, male offspring nursing requires a much greater maternal energy contribution to lactation. It is possible that the maternal-fetal immunoendocrine dialog plays an important role in female preparation for lactation during pregnancy. Immune system genes are an integral part of gene regulatory networks in lactation and tumor necrosis factor alpha (TNF?) is a proinflammatory cytokine that also plays an important role in normal mammary gland development. The aim of this study was to evaluate the influence of the sex of calf and/or the -824A/G polymorphism in the promoter region of TNF? gene on milk performance traits in Black Pied cattle over the course of lactation. We also studied the allele frequency differences of -824A/G variants across several cattle breeds, which were bred in different climatic conditions. The G allele frequency decreased gradually over the course of lactation events in the Black Pied dairy cattle because of a higher culling rate of cows with the G/G genotype (p<0.001). In contrast to the genotypes A/A and A/G, cows with G/G genotype showed significant variability of milk and milk fat yield subject to sex of delivered calf. Milk yield and milk fat yield were significantly higher in the case of birth of a bull calf than with a heifer calf (p<0.03). The G allele frequency varies from 48% to 58% in Grey Ukrainian and Black Pied cattle to 77% in aboriginal Yakut cattle. Our results suggest that the TNF? -824A/G gene polymorphism may have an influence on the reproductive efforts of cows over the course of lactation events depending on the sex of progeny. Allocation of resources according to sex of the calf allows optimizing the energy cost of lactation. This may be a probable reason for high G allele frequency in Yakut cattle breeding in extreme environmental conditions. Similarly, the dramatic fall in milk production after birth of a heifer calf increases the probability of culling for the cows with the G/G genotype in animal husbandry. PMID:25049721

Yudin, N. S.; Aitnazarov, R. B.; Voevoda, M. I.; Gerlinskaya, L. A.; Moshkin, M. P.

2013-01-01

77

Rapid identification of genetic variation and pathotype of Leptosphaeria maculans by random amplified polymorphic DNA assay.  

PubMed Central

Canadian isolates of Leptosphaeria maculans, the causal agent of blackleg of crucifers, were examined for genetic relatedness by the random amplified polymorphic DNA assay. DNA polymorphisms amplified with random decamer primers were used to distinguish three groups of isolates. Group 1 contained all isolates of the virulent pathotype, group 2 contained isolates of the avirulent pathotype from western Canada, and group 3 contained avirulent pathotype isolates from Ontario. These results agreed with other reports which showed many genetic differences between pathotypes and were consistent with the hypothesis that the virulent pathotype was recently introduced into Canada and has diverged relatively little. In contrast, the avirulent pathotype has probably been present in Canada for a longer time and has diverged with geographic isolation. In addition to establishing genetic relationships, DNA fingerprints generated by the random amplified polymorphic DNA assay have potential applications in pathotype identification and blackleg disease management. Images PMID:1768121

Goodwin, P H; Annis, S L

1991-01-01

78

Use of multi-dose activated charcoal in phenytoin toxicity secondary to genetic polymorphism.  

PubMed

Abstract Introduction. Phenytoin is metabolised in the liver by cytochrome (CYP)2C9 and 2C19 enzymes. Due to saturation of enzyme capacity, the elimination half-life is prolonged at supratherapeutic levels. Genetic polymorphisms of CYP2C9 and 2C19 are reasonably common and further prolong the elimination of phenytoin. There are conflicting reports regarding whether multiple-dose activated charcoal (MDAC) significantly increases the clearance of phenytoin in poisoning. Case report. We present 3 patients with phenytoin toxicity and very slow elimination secondary to reduced CYP enzyme function from genetic polymorphisms. MDAC was used in two patients and led to rapid and large reductions in the measured elimination half-lives. This is contrasted with very prolonged elimination in a third patient who did not receive MDAC. Conclusion. MDAC may play a role in the management of chronic phenytoin toxicity, especially in those with very slow endogenous elimination secondary to genetic polymorphisms. PMID:25597548

Chan, Betty S H; Sellors, Kate; Chiew, Angela L; Buckley, Nicholas A

2015-02-01

79

[Genetic polymorphism of Gentiana lutea L. (Gentianaceae) populations from Chornohora Ridge of Ukrainian Carpathians].  

PubMed

The features of genetic structure and level of diversity were investigated for G. lutea populations from Chornohora Ridge of Ukrainian Carpathians using RAPD- and ISSR-PCR. We have shown a high level of genetic diversity for investigated populations. The differences between populations account for 59-72% of the total genetic variation, whereas intrapopulation polymorphism makes up 28-41%. The relationships among genetic variability level and ecological-geographical conditions as well as biological features of the species were assumed to be possible. The obtained results indicate the genetic isolation of G. lutea Chornohora populations from Ukrainian Carpathians. Pozhyzhevska agropopulation was characterized by a high level of polymorphism that means the possibility to use artificial plantings of the investigated species for its conservation. PMID:25536820

2014-01-01

80

Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat  

PubMed Central

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2013-01-01

81

Analysis of genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces using amplified fragment length polymorphism (AFLP) markers  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among 100 selected bambara groundnut (Vigna subterranea (L.) Verdc) landraces from a diverse geographic area of Tanzania. Eleven informative AFLP primer combinations generated a total of 49 scorable polymorphic amplification fragments across the bambara groundnut accessions. Genetic distances between all accessions based on Jaccard's variability index ranged from 0.1

Wazael H. Ntundu; Inga C. Bach; Jørgen L. Christiansen; Sven B. Andersen

82

The Genetic Basis of a Rare Flower Color Polymorphism in Mimulus lewisii Provides Insight into the Repeatability  

E-print Network

The Genetic Basis of a Rare Flower Color Polymorphism in Mimulus lewisii Provides Insight of a Rare Flower Color Polymorphism in Mimulus lewisii Provides Insight into the Repeatability of Evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within

Oregon, University of

83

Relationships of LDLR genetic polymorphisms with cerebral infarction: a meta-analysis.  

PubMed

This meta-analysis was undertaken to identify the relationships between genetic polymorphisms in the LDLR gene and the risk of cerebral infarction. The Web of Science (1945-2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966-2013), EMBASE (1980-2013), CINAHL (1982-2013) and the Chinese Biomedical Database (CBM) (1982-2013) were searched for relevant articles without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Crude odds ratios (OR) with their corresponding 95% confidence interval (CI) were calculated. Eight case-control studies with a total of 4,655 patients with cerebral infarction and 15,920 healthy control subjects were included in our meta-analysis. Five common polymorphisms in the LDLR gene were evaluated, including rs11669576 A > T, rs1433099 C > T, rs5925 C > T, rs688 C > T, rs1122608 T > G in the LDLR gene. The results of this meta-analysis revealed that cerebral infarction patients had a higher frequency of LDLR genetic polymorphisms than that of healthy controls (allele model: OR 1.17, 95% CI 1.05-1.30, P = 0.004; dominant model: OR 1.18, 95% CI 1.05-1.33, P = 0.007; homozygous model: OR 1.50, 95% CI 1.03-2.16, P = 0.032; respectively), especially for the rs11669576 A > T, rs1433099 C > T and rs5925 C > T polymorphisms. Among different ethnic subgroups, the results demonstrated positive correlations between LDLR genetic polymorphisms and an increased risk of cerebral infarction among both Asians and Caucasians under the allele and dominant models (all P < 0.05). Our findings indicate that LDLR genetic polymorphisms may be strongly involved in the pathogenesis of cerebral infarction, especially the rs11669576 A > T, rs1433099 C > T, rs5925 C > T polymorphisms. PMID:24595448

Yan, Hai-Cheng; Wang, Wei; Dou, Chang-Wu; Tian, Fu-Ming; Qi, Song-Tao

2014-07-01

84

Protein Polymorphisms, Segregation in Genetic Crosses and Genetic Distances among Fishes of the Genus Xiphophorus (Poeciliidae)  

PubMed Central

The products of 49 protein-coding loci were examined by starch gel electrophoresis for populational variation in six species of Xiphophorus fishes and/or segregation in intra- and interspecific backcross and intercross hybrids. Electrophoretic variation was observed for 29 of the 35 locus products in a survey of 42 population samples. The highest frequency of polymorphic loci observed in noninbred populations was 0.143. After ten or more generations of inbreeding, all loci studied were monomorphic. Inbred strains generally exhibited the commonest electrophoretic alleles of the population from which they were derived. An assessment of genetic distances among Xiphophorus populations reflected classical systematic relationships and suggested incipient subspeciation between X. maculatus from different drainages as well as several species groups. Thirty-three loci were analyzed with respect to segregation in hybrids. The goodness of fit of segregations to Mendelian expectations at all loci analyzed (except loci in linkage group I) is interpreted as evidence for high genetic compatibility of the genomes of Xiphophorus species. It is anticipated that these data will result in a rapid expansion of the assignment of protein-coding loci to linkage groups in these lower vertebrate species. PMID:7173606

Morizot, Don C.; Siciliano, Michael J.

1982-01-01

85

Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster  

Microsoft Academic Search

For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify

Roger A. Hoskins; Alexander C. Phan; Mohammed Naeemuddin; Felipa A. Mapa; David A. Ruddy; Jessica J. Ryan; Lynn M. Young; Trent Wells; Casey Kopczynski; Michael C. Ellis

2001-01-01

86

A Simplified Technique for Evaluating Human "CCR5" Genetic Polymorphism  

ERIC Educational Resources Information Center

To involve students in thinking about the problem of AIDS (which is important in the view of nondecreasing infection rates), we established a practical lab using a simplified adaptation of Thomas's (2004) method to determine the polymorphism of HIV co-receptor CCR5 from students' own epithelial cells. CCR5 is a receptor involved in…

Falteisek, Lukáš; Cerný, Jan; Janštová, Vanda

2013-01-01

87

GENETIC MAPPING PORCINE EST SEQUENCES USING LENGTH POLYMORPHISMS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The current priority of the MARC swine genome group is to identify and map SNPs (single nucleotide polymorphisms) associated with EST sequences to develop the comparative map and provide a large number of validated SNP markers for the porcine genome. Our approach is based on sequencing amplicons fr...

88

The Role of Genetic Polymorphisms in Environmental Health  

Microsoft Academic Search

Interest is increasing in the role of variations in the human genome (polymorphisms) in modifying the effect of exposures to environmental health hazards (often referred to as gene-environment inter- action), which render some individuals or groups in the population more or less likely to develop dis- ease after exposure. This review is intended for an audience of environmental health practitioners

Samir N. Kelada; David L. Eaton; Sophia S. Wang; Nathaniel R. Rothman; Muin J. Khoury

2003-01-01

89

Genetic polymorphisms in the vitamin D pathway in relation to lung cancer risk and survival  

PubMed Central

Studies have suggested that vitamin D may have protective effects against cancer development or tumor progression. To search for additional evidence, we investigated the role of genetic polymorphisms involved in the vitamin D pathway in non-small cell lung cancer (NSCLC). We evaluated common genetic polymorphisms associated with the vitamin D pathway in relation to NSCLC in a case-control study of 603 newly diagnosed NSCLC patients and 661 matched healthy controls. Seven single nucleotide polymorphisms (SNPs) were genotyped, the expression of CYP27B1 and CYP24A1 were measured in 153 tumor samples and their associations with genotypes and patient survival were also analyzed. In the case-control comparison, we found SNP rs3782130 (CYP27B1), rs7041 (GC), rs6068816 and rs4809957 (CYP24A1) associated with NSCLC risk. The risk of NSCLC was increased with the number of risk alleles. CYP27B1 and CYP24A1 expression were significantly different between tumor and normal tissues in NSCLC. High CYP27B1 expression was associated with better overall survival, and the expression was different by the rs3782130 genotype. The study suggests that some genetic polymorphisms involved in the vitamin D pathway may associate with NSCLC risk, and one of the polymorphisms (rs3782130) may affect gene expression and patient survival. PMID:25544771

Kong, Jinyu; Xu, Fangxiu; Qu, Jinli; Wang, Yu; Gao, Ming; Yu, Herbert; Qian, Biyun

2015-01-01

90

Genetic mapping of the human tryptophan hydroxylase gene on chromosome 11, using an intronic conformational polymorphism  

SciTech Connect

The identification of polymorphic alleles at loci coding for functional genes is crucial for genetic association and linkage studies. Since the tryptophan hydroxylase (TPH) gene codes for the rate-limiting enzyme in the biosynthesis of the neurotransmitter serotonin, it would be advantageous to identify a polymorphism in this gene. By examining introns of the human TPH gene by PCR amplification and analysis by the single-strand conformation polymorphism (SSCP) technique, an SSCP was revealed with two alleles that occur with frequencies of .40 and .60 in unrelated Caucasians. DNAs from 24 informative CEPH families were typed for the TPH intron polymorphism and analyzed with respect to 10 linked markers on chromosome 11, between p13 and p15, with the result that TPH was placed between D11S151 and D11S134. This region contains loci for several important genes, including those for Beckwith-Wiedemann syndrome and tyrosine hydroxylase. 37 refs., 2 figs., 1 tab.

Nielsen, D.A.; Goldman, D. (National Inst. on Alcohol Abuse and Alcoholism, Bethesda, MD (United States)); Dean, M. (National Cancer Inst., Frederick, MD (United States))

1992-12-01

91

Genetic Association Analysis of Dopamine DRD3 Ser9Gly Polymorphism and Schizophrenia in Malay Population  

PubMed Central

Background: Molecular components of the dopamine receptor (DRD3) play an important role in the pathophysiology of schizophrenia (SCZ). Previous studies have demonstrated an association between the DRD3 Ser9Gly polymorphism and SCZ but the results have been inconclusive. Method: In this study, we investigated this controversial association between the Ser9Gly (A/G) polymorphism and SCZ using Malay cases-control (261 cases/157 controls) samples. PCR-RFLP was performed to genotype the distribution of the DRD3 Ser9Gly polymorphism. Results: Both healthy control and SCHZ patient groups were in of Hardy-Weinberg equilibrium for the analyzed genetic variability. There was a significant association between the genotype distribution DRD3 polymorphisms and SCZ (?2= 9.359; df = 2; P = 0.009). Conclusion: We believe that further studies are required to examine the association between others dopamine-related genes and the behavioral phenotypes of SCZ. PMID:23113067

Tee, SF; Tang, PY; Loh, HC

2011-01-01

92

Identification of possible genetic polymorphisms involved in cancer cachexia: a systematic review  

Microsoft Academic Search

Cancer cachexia is a polygenic and complex syndrome. Genetic variations in regulation of the inflammatory response, muscle\\u000a and fat metabolic pathways, and pathways in appetite regulation are likely to contribute to the susceptibility or resistance\\u000a to developing cancer cachexia. A systematic search of Medline and EmBase databases, covering 1986–2008 was performed for potential\\u000a candidate genes\\/genetic polymorphisms relating to cancer cachexia.

BENJAMIN H. L. TAN; JAMES A. ROSS; STEIN KAASA; FRANK SKORPEN; KENNETH C. H. FEARON

2011-01-01

93

Estimating genetic diversity of Arabidopsis thaliana ecotypes with amplified fragment length polymorphisms (AFLP)  

Microsoft Academic Search

The extensive natural variation of Arabidopsis thaliana ecotypes is being increasingly exploited as a source of variants of genes which control (agronomically) important traits.\\u000a We have subjected 19 different Arabidopsis thaliana ecotypes to an analysis using the anplified fragment length polymorphism (AFLP) technique in order to estimate their genetic\\u000a diversity. The genetic diversity was estimated applying the method of Nei

S. Erschadi; G. Haberer; M. Schöniger; R. A. Torres-Ruiz

2000-01-01

94

[Exploring genetic diversity in Dioscorea zingiberensis by amplified fragment length polymorphism molecular markers].  

PubMed

Amplified fragment length polymorphism (AFLP) was used to study 30 individuals from 5 wild populations of Dioscorea zingiberensis for the first time. A total of 14 698 bands were detected with 9 pairs of AFLP primers and 12 686 of them were polymorphic. On the average each primer combination could be used to detect 230 polymorphic bands and account for 85.92% of total genetic diversity at species level. Shannonos index of diversity (I) was 0.3656-/+0.1721, and Nei's gene diversity (H) was 0.2322-/+0.2200 at the species level. The result of genetic variance analysis showed the coefficient of genetic differentiation (Gst) was 0.4827 at species level, it indicated there were certain degree of genetic differentiation in five Dioscorea zingiberensis populations. The gene flow (Nm) among populations of D. zingiberensis was 0.5358. The data were analyzed using unweighted pair group method, basing on arithmetic averages (UPGMA) bootstrap analysis. Cluster analyses were performed by using NTSYSpc version 2.11F and Popgene 1.32 software. The results showed that the genetic differentiation of 5 wild populations of D. zingiberensis was abundant, and 5 wild populations of D. zingiberensis could be clustered by the distance of the position basically. The AFLP molecular marker was used to identify the genetic differences of different populations of Dioscorea zingiberensis. PMID:17675758

Li, Yong-Hui; Li, Xiang-Min

2007-08-01

95

The impact of genetic polymorphisms on the protein composition of ruminant milks  

E-print Network

encoding b-lactoglobulin and as1- and as2-caseins, have been found, in cattle, to influence- nique have been designed and applied in selection and breeding programmes to improve milk protein quality. gene expression / milk protein / genetic polymorphism / ruminants Reprod. Nutr. Dev. 42 (2002

Paris-Sud XI, Université de

96

5-HTTLPR polymorphism impacts human cingulate-amygdala interactions: a genetic susceptibility mechanism for depression  

Microsoft Academic Search

Carriers of the short allele of a functional 5? promoter polymorphism of the serotonin transporter gene have increased anxiety-related temperamental traits, increased amygdala reactivity and elevated risk of depression. Here, we used multimodal neuroimaging in a large sample of healthy human subjects to elucidate neural mechanisms underlying this complex genetic association. Morphometrical analyses showed reduced gray matter volume in short-allele

Lukas Pezawas; Andreas Meyer-Lindenberg; Emily M Drabant; Beth A Verchinski; Karen E Munoz; Bhaskar S Kolachana; Michael F Egan; Venkata S Mattay; Ahmad R Hariri; Daniel R Weinberger

2005-01-01

97

Cystic Fibrosis Locus Defined by a Genetically Linked Polymorphic DNA Marker  

Microsoft Academic Search

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of

Lap-Chee Tsui; Manuel Buchwald; David Barker; Jeffrey C. Braman; Robert Knowlton; James W. Schumm; Hans Eiberg; Jan Mohr; Dara Kennedy; Natasa Plavsic; Martha Zsiga; Danuta Markiewicz; Gita Akots; Valerie Brown; Cynthia Helms; Thomas Gravius; Carol Parker; Kenneth Rediker; Helen Donis-Keller

1985-01-01

98

Random amplified polymorphic DNA (RAPD) markers for genetic analysis in micropropagated plants of Populus deltoides Marsh  

Microsoft Academic Search

RAPD markers were used to assess genetic fidelity of 23 micropropagated plants of a single clone (L34) of Populus deltoides. Eleven arbitrary 10-base primers were successfully used to amplify DNA from in vivo and in vitro material. Of these, 5 distinguished a total of 13 polymorphisms common across 6 micropropagated plants. Apart from these 6 plants, the amplification products were

Vijay Rani; Ajay Parida; S. N. Raina

1995-01-01

99

Genetic polymorphisms and the efficacy and toxicity of cisplatin-based chemotherapy in ovarian cancer patients  

Microsoft Academic Search

Platinum drugs are among the most active and widely used agents in the treatment of different cancers. However, the great individual variability in both outcome and toxicity of platinum chemotherapy requires the identification of genetic markers that can be used to screen patients before treatment. In this study, 21 polymorphisms in 10 genes, the protein activities of which may be

A V Khrunin; A Moisseev; V Gorbunova; S Limborska

2010-01-01

100

Effect of combined genetic polymorphisms on lung cancer risk in northern Thai women  

Microsoft Academic Search

Lung cancer is a major cause of cancer-related death in developed countries, and its incidence in developing countries is increasing. In Thailand, cancer incidences differ greatly from region to region, and lung cancer is the most common cancer in the northern Thai population. The polymorphic frequency of 10 genetic susceptibility genes and their association with lung cancer were examined in

Jaewwaew Klinchid; Busyamas Chewaskulyoung; Somchareon Saeteng; Nirush Lertprasertsuke; Watchara Kasinrerk; Ratchada Cressey

2009-01-01

101

Rapid and efficient detection of genetic polymorphism in wheat through amplification by polymerase chain reaction  

Microsoft Academic Search

The polymerase chain reaction (PCR) was used to amplify genomic DNA of several wheat genotypes. The oligonucleotides used as primers were the terminal sequences of a gamma-gliadin gene. The electrophoretic analysis of the PCR products showed specific bands which revealed both inter- and intra-specific genetic polymorphism among the examined genotypes. The technique is proposed as a very simple and efficient

R. D'Ovidio; O. A. Tanzarella; E. Porceddu

1990-01-01

102

Genetic polymorphism of LDLR (rs688) is associated with primary intracerebral hemorrhage.  

PubMed

Intracranial hemorrhage is the third most common cause of cerebrovascular disease. Some polymorphisms that affect clotting factors increase the risk of thrombosis. However, few reports have analyzed the effect of polymorphisms on the hemostatic state in bleeding disorders. The low-density lipoprotein receptor (LDLR) has been shown to contribute to factor VIII (FVIII) homeostasis, which represents a link between LDLR and hemostasis. FVIII plays a pivotal role in the coagulation cascade. Patients with high levels of FVIII are at an increased risk of arterial and venous thrombosis. On the other hand, patients with insufficient FVIII tend to bleed excessively, such as in hemophilia A. In a previous study, analysis of the genetic LDLR variant rs688 provided evidence suggesting that genetic polymorphisms of rs688 are associated with thrombotic cardiovascular diseases. The current study aimed to investigate the potential role of rs688 in primary intracerebral hemorrhage (PICH). This genetic association study was conducted within an isolated Taiwanese population (447 PICH patients and 430 controls). Genotypes C/C and C/T were used as the reference genotypes, and the genotype T/T was found to be associated with a 73% decreased risk of PICH. The preliminary evidence suggests that genetic polymorphisms of LDLR are associated with PICH. PMID:24295502

Lee, Jiann-Der; Hsiao, Kuang-Ming; Lee, Tsong-Hai; Kuo, Ya-Wen; Huang, Yen-Chu; Hsu, Huan-Lin; Lin, Ya-Hui; Wu, Chih-Ying; Huang, Ying-Chih; Lee, Meng; Yang, Hsin-Ta; Hsu, Chia-Yu; Pan, Yi-Ting

2014-02-01

103

Investigation of genetic polymorphisms and smoking in a bladder cancer casecontrol study in Argentina  

E-print Network

Investigation of genetic polymorphisms and smoking in a bladder cancer case­control study. Smitha,* a School of Public Health, Arsenic Health Effects Research Program, University of California controls. The strongest evidence was for an interaction between NQO1 genotype and smoking. For ever smoking

California at Berkeley, University of

104

Cell proliferation-related genetic polymorphisms and gastric cancer risk: systematic review and meta-analysis  

PubMed Central

Apart from Helicobacter pylori infection and lifestyle factors, host genetic susceptibility has been suggested to contribute to individual variation in gastric cancer risk as well. Aiming to evaluate the associations between host cell proliferation-related genetic polymorphisms and gastric cancer susceptibility, we reviewed the related studies published until 15 September 2008 and quantitatively summarized the associations of the most widely studied polymorphisms (TP53 Arg72Pro, L-myc EcoRI) using meta-analysis. Fifty-five eligible studies were included in this review. Twenty-three polymorphisms significantly related to gastric cancer risk in at least one study were identified. Polymorphisms determining higher levels of growth factors, which are important for tissue repair, were recently observed to be associated with reduced risk of gastric cancer. In the meta-analysis, TP53 72Pro was associated with increased risk of diffuse gastric cancer among Asians (OR, 1.44; 95% CI, 1.04–1.99), but decreased risk of intestinal gastric cancer among Caucasians (OR, 0.56; 95% CI, 0.36–0.89). This review suggests that cell proliferation-related genetic polymorphisms could be candidate biomarkers of gastric cancer risk, but current evidence for the use for risk stratification is still very limited. Modestly significant associations in meta-analyses stratified by population or type of gastric cancer may be observed by chance because of the limited number of studies and small sample size. Larger studies are warranted to clarify the effect of cell proliferation-related genetic polymorphisms on gastric carcinogenesis. PMID:19536170

Gao, Lei; Nieters, Alexandra; Brenner, Hermann

2009-01-01

105

Harbor lights  

PubMed

Illuminating Life: Selected Papers from Cold Spring Harbor (1903-1969) by J. Witkowski Cold Spring Harbor Laboratory Press (2000) pp. 383 + xvi. ISBN 0-87969-566-8 $25.00 If you are anywhere on the spectrum from frequent Cold Spring Harbor visitor to someone who barely knows that Symposia of that name were until recently published in maroon covers, and if you want to learn more of the history of this remarkable research centre, then this book is for you. At first sight, Illuminating Life looks like a coffee table book, but it is much more than that. Jan Witkowski has assembled a history of the Cold Spring Harbor Laboratories from their inception in 1890 through to 1968, illustrated by a selection of research papers from 1903 to 1969. Each one or two papers is preceded by an interpretative essay and a biographical note on the principal author(s), and the whole is introduced by an informative historical preface. At the end are three obituaries from the literature summarizing the lives of three key players, Davenport, Harris and Demerec. For a book of this size and compass, the essentials can be assimilated remarkably quickly, and at $25 the book is exceptional value for money. First read the preface. Then the essays. These are gems, and at two or three pages each there is no need to postpone them until later! Then dip into a few research papers. Then re-read the preface. Then you will know a lot about Cold Spring Harbor. If you read the obituaries you will know even more. Here are just a few impressions. On p. 364 there is a photograph of one of the early buildings, the James Laboratory. The laboratory was constructed for $12,000 in 1928 for biophysics research (p117). It looks tiny, but in the early years of the Symposia, which were then on biophysical topics, it housed a galaxy of summer visitors including Curtis and Cole (electrophysiology), J. Z. Young (nerve conduction), Davison and Danielli (need one say more?) and many others. If biophysics under Reginald Harris (1924-36) was what made Cold Spring Harbor Quantitative, then the quest for the genetic material and its properties is what has made it most widely famed. The book brings out the seminal contributions of Demerec, both as scientist and as director (1941-60) and of McClintock, Hershey, Cairns (director 1963-8) and others. The chosen research papers include many that are landmarks in science, from maize to bacteria and phage, and generally they are easy to read. They are largely devoid of the ponderous throat-clearing and innumerable citations that are so much a part of scientific literature today. Many examples could be given of such ease of style and freedom from excess verbage, but one will suffice here. 'Aggregation of DNA is often suspected but seldom studied. In phage &lgr; we found a DNA that can form characteristic and stable complexes. A first account of them is given here'. That is the entire introduction in Hershey, A. D., Burgi, E. and Ingraham, L. (1963), Cohesion of DNA molecules isolated from phage &lgr;. Proc. Nat. Acad. Sci. USA 49, 748-755. The paper by de Lucia and Cairns (1969) on 'Isolation of an E. coli strain with a mutation affecting DNA polymerase' is a fitting choice with which to conclude the compilation. In the late 1960s something seemed not quite right about the Kornberg enzyme as the putative engine of replication. Several suspicious inconsistencies were accumulating. How to test these suspicions? Random mutagenesis, a precise and rapid screening assay applicable to thousands of isolates. The rest is history. What of the last thirty years? The spine of the cover says, rather enigmatically, 'Volume 1'; the reviewer could find no statement elsewhere in the book that more is to follow. Perhaps we can look forward to Volume 2. Surely that volume will contain, among many other landmark papers, one called 'An amazing sequence arrangement at the 5 ends of Adenovirus 2 messenger RNA'. PMID:11069757

Maden

2000-12-01

106

Paraoxonase1 Genetic Polymorphisms in a Mixed Ancestry African Population  

PubMed Central

Paraoxonase 1 (PON1) activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4%) and 55M (82.6%). The Q192 was significantly associated with 5.8 units' increase in PON1 concentration and 15.4 units' decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes. PMID:25477710

Macharia, M.; Kengne, A. P.; Blackhurst, D. M.; Erasmus, R. T.; Matsha, T. E.

2014-01-01

107

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers  

Microsoft Academic Search

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a poly- merase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in

G. Yan; J. Romero-Severson; M. Walton; D. D. CHADEEand; D. W. Severson

1999-01-01

108

PEARL HARBOR  

Microsoft Academic Search

For Pearl Harbor, ILM created vistas of period battleships under attack and CG planes in combat at Pearl Harbor and in other battles. Simulation software was written for the huge billowing smoke from destroyed battleship row and new rigid body software was developed for the destruction of planes and ships. Other developments included: new environmental lighting techniques to enhance the

2001-01-01

109

Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species  

PubMed Central

When long-lasting, balancing selection can lead to “trans-species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa. PMID:25403856

Gao, Ziyue; Przeworski, Molly; Sella, Guy

2015-01-01

110

TP53 Polymorphisms allow for genetic sub-grouping of the canine transmissible venereal tumor  

PubMed Central

The canine transmissible venereal tumor (CTVT) is found mainly in dogs' sexual organs. Currently, it is widely accepted that all samples of CTVT show similar histopathological characteristics and share common genetic alterations. Despite the common genetic origin of CTVT, mutations in the P53 gene have been reported. In this study, we proposed that tumor samples can be genetically grouped using this gene. The presence of different subgroups of CTVT was determined in Mexican dogs using the TP53 gene sequence in CTVT samples. Four new polymorphisms were found and therefore, the CTVT samples were classified in five subgroups. PMID:19934603

Sánchez-Servín, Abel; Córdova-Alarcon, Emilio; Fajardo, Raúl

2009-01-01

111

TP53 Polymorphisms allow for genetic sub-grouping of the canine transmissible venereal tumor.  

PubMed

The canine transmissible venereal tumor (CTVT) is found mainly in dogs' sexual organs. Currently, it is widely accepted that all samples of CTVT show similar histopathological characteristics and share common genetic alterations. Despite the common genetic origin of CTVT, mutations in the P53 gene have been reported. In this study, we proposed that tumor samples can be genetically grouped using this gene. The presence of different subgroups of CTVT was determined in Mexican dogs using the TP53 gene sequence in CTVT samples. Four new polymorphisms were found and therefore, the CTVT samples were classified in five subgroups. PMID:19934603

Sánchez-Servín, Abel; Martínez, Simón; Córdova-Alarcon, Emilio; Fajardo, Raúl

2009-12-01

112

Functional genetic polymorphisms and female reproductive disorders: Part II—endometriosis  

PubMed Central

BACKGROUND Endometriosis has a strong genetic component, and numerous genetic studies have been reported. METHODS We have systematically reviewed these studies and included 114 in our final selection. RESULTS We found no consistent evidence linking endometriosis with specific polymorphisms in genes encoding inflammatory mediators, proteins involved in sex steroid metabolism, vascular function and tissue remodelling. Although a number of polymorphisms have been associated with endometriosis in selected populations, the associations have not been independently confirmed, either because only single studies were carried out on these markers/genes or because other studies reported no association. The most solid evidence linking specific polymorphisms to endometriosis came from studies investigating glutathione-S-transferase, a phase II detoxification enzyme. Carriage of the GSTT1 null deletion variant showed consistent association with endometriosis with a 29% increased risk; however, it cannot be excluded that this result was due to publication bias, and this association should be independently confirmed in large-scale, well-designed case–control studies. CONCLUSIONS The evidence of an association between genetic polymorphisms and endometriosis is weak. Carriage of the GSTT1 null deletion may moderately increase the risk of this disease. We suggest that the methodology of association studies should be improved in order to identify and validate associations in endometriosis. PMID:18805939

Tempfer, C.B.; Simoni, M.; Destenaves, B.; Fauser, B.C.J.M.

2009-01-01

113

Worker caste polymorphism has a genetic basis in Acromyrmex leaf-cutting ants  

PubMed Central

Division of labor is fundamental to the success of all societies. The most striking examples are the physically polymorphic worker castes in social insects with clear morphological adaptations to different roles. These polymorphic worker castes have previously been thought to be a classic example of nongentically controlled polymorphism, being mediated entirely by environmental cues. Here we show that worker caste development in the leaf-cutting ant Acromyrmex echinatior has a significant genetic component. Individuals of different patrilines within the same colony differ in their propensities to develop into minor or major workers. The mechanism appears to be plastic, with caste destiny resulting from interplay between nurture and nature. Unlike the few other recently discovered examples of a genetic influence on caste determination, the present result does not relate to any rare or exceptional circumstances, such as interspecific hybridization. The results suggest that a significant role of genetics may have been overlooked in our understanding of other complex polymorphisms of social insects. PMID:12878720

Hughes, William O. H.; Sumner, Seirian; Van Borm, Steven; Boomsma, Jacobus J.

2003-01-01

114

Genetic polymorphism of CYP2C19 and lansoprazole pharmacokinetics in Japanese subjects  

Microsoft Academic Search

Objective: We investigated whether interindividual differences in the pharmacokinetic disposition of lansoprazole are attributed to\\u000a the genetic polymorphism of CYP2C19 which occurred by two mutations, CYP2C19m1 and CYP2C19m2, in 20 Japanese subjects.\\u000a \\u000a \\u000a \\u000a Methods: Polymerase chain reaction (PCR) restriction fragment length polymorphism procedures were used to detect the CYP2C19m1 mutation in exon 5 and the CYP2C19m2 mutation in exon 4 using

H. Katsuki; C. Nakamura; K. Arimori; S. Fujiyama; M. Nakano

1997-01-01

115

Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder  

PubMed Central

Background Temporomandibular disorder (TMD) is a multifactorial syndrome related to a critical period of human life. TMD has been associated with psychological dysfunctions, oxidative state and sexual dimorphism with coincidental occurrence along the pubertal development. In this work we study the association between TMD and genetic polymorphisms of folate metabolism, neurotransmission, oxidative and hormonal metabolism. Folate metabolism, which depends on genes variations and diet, is directly involved in genetic and epigenetic variations that can influence the changes of last growing period of development in human and the appearance of the TMD. Methods A case-control study was designed to evaluate the impact of genetic polymorphisms above described on TMD. A total of 229 individuals (69% women) were included at the study; 86 were patients with TMD and 143 were healthy control subjects. Subjects underwent to a clinical examination following the guidelines by the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD). Genotyping of 20 Single Nucleotide Polymorphisms (SNPs), divided in two groups, was performed by multiplex minisequencing preceded by multiplex PCR. Other seven genetic polymorphisms different from SNPs (deletions, insertions, tandem repeat, null genotype) were achieved by a multiplex-PCR. A chi-square test was performed to determine the differences in genotype and allelic frequencies between TMD patients and healthy subjects. To estimate TMD risk, in those polymorphisms that shown significant differences, odds ratio (OR) with a 95% of confidence interval were calculated. Results Six of the polymorphisms showed statistical associations with TMD. Four of them are related to enzymes of folates metabolism: Allele G of Serine Hydoxymethyltransferase 1 (SHMT1) rs1979277 (OR = 3.99; 95%CI 1.72, 9.25; p = 0.002), allele G of SHMT1 rs638416 (OR = 2.80; 95%CI 1.51, 5.21; p = 0.013), allele T of Methylentetrahydrofolate Dehydrogenase (MTHFD) rs2236225 (OR = 3.09; 95%CI 1.27, 7.50; p = 0.016) and allele A of Methionine Synthase Reductase (MTRR) rs1801394 (OR = 2.35; 95CI 1.10, 5.00; p = 0.037). An inflammatory oxidative stress enzyme, Gluthatione S-Tranferase Mu-1(GSTM1), null allele (OR = 2.21; 95%CI 1.24, 4.36; p = 0.030) and a neurotransmission receptor, Dopamine Receptor D4 (DRD4), long allele of 48 bp-repeat (OR = 3.62; 95%CI 0.76, 17.26; p = 0.161). Conclusions Some genetic polymorphisms related to folates metabolism, inflammatory oxidative stress, and neurotransmission responses to pain, has been significantly associated to TMD syndrome PMID:21615938

2011-01-01

116

Genetic association of apolipoprotein E polymorphisms with inflammatory bowel disease  

PubMed Central

AIM: To study the association of apolipoprotein E (APOE) polymorphisms with the susceptibility of inflammatory bowel disease (IBD) in Saudi patients. METHODS: APOE genotyping was performed to evaluate the allele and genotype frequencies in 378 Saudi subjects including IBD patients with ulcerative colitis (n = 84) or Crohn’s disease (n = 94) and matched controls (n = 200) using polymerase chain reaction and reverse-hybridization techniques. RESULTS: The frequencies of the APOE ?2 allele and ?2/?3 and ?2/?4 genotypes were significantly higher in IBD patients than in controls (P < 0.05), suggesting that the ?2 allele and its heterozygous genotypes may increase the susceptibility to IBD. On the contrary, the frequencies of the ?3 allele and ?3/?3 genotype were lower in IBD patients as compared to controls, suggesting a protective effect of APOE ?3 for IBD. The prevalence of the ?4 allele was also higher in the patient group compared to controls, suggesting that the ?4 allele may also increase the risk of IBD. Our results also indicated that the APOE ?4 allele was associated with an early age of IBD onset. No effect of gender or type of IBD (familial or sporadic) on the frequency distribution of APOE alleles and genotypes was noticed in this study. CONCLUSION: APOE polymorphism is associated with risk of developing IBD and early age of onset in Saudi patients, though further studies with a large-size population are warranted. PMID:25624723

Al-Meghaiseeb, Ebtissam Saleh; Al-Otaibi, Mulfi Mubarak; Al-Robayan, Abdulrahman; Al-Amro, Reem; Al-Malki, Ahmd Saad; Arfin, Misbahul; Al-Asmari, Abdulrahman K

2015-01-01

117

Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map1,2  

Microsoft Academic Search

As genetic markers, SNP are well suited for the development of genetic tests for produc- tion traits in livestock. They are stable through many generations and can provide direct assessment of indi- vidual animal's genetic merit if they are in linkage dis- equilibrium and phase with functional genetic varia- tion. Bovine chromosome 5 has been shown to harbor genetic variation

R. T. Stone; E. Casas; T. P. L. Smith; J. W. Keele; G. Harhay; G. L. Bennett; M. Koohmaraie; T. L. Wheeler; S. D. Shackelford; W. M. Snelling

118

Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The\\u000a AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted.\\u000a Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs)\\u000a for AFLP markers among elite public

Vipa Hongtrakul; Gordon M. Huestis; Steven J. Knapp

1997-01-01

119

Characterization of genetic identities and relationships of Brassica oleracea L. via a random amplified polymorphic DNA assay  

Microsoft Academic Search

Effective conservation and the use of plant genetic resources are essential for future agricultural progress. Critical to this conservation effort is the development of genetic markers which not only distinguish individuals and accessions but also reflect the inherent variation and genetic relationships among collection holdings. We have examined the applicability of the random amplified polymorphic DNA (RAPD) assay for quick,

S. Kresovich; J. G. K. Williams; J. R. McFerson; E. J. Routman; B. A. Schaal

1992-01-01

120

Harboring chaos  

E-print Network

Hurricane shelters have become the unknown point of last resort for many coastal communities. Harboring displaced populations during a hurricane and it's chaotic aftermath are no longer seen as a need in a coastal communities ...

Anderson, Jeffrey A. (Jeffrey Arthur)

2007-01-01

121

Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms  

PubMed Central

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). FST, the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that ?50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher FST values have greater resolving power and produce more consistent genetic distance estimates. PMID:12805277

Watkins, W. Scott; Rogers, Alan R.; Ostler, Christopher T.; Wooding, Steve; Bamshad, Michael J.; Brassington, Anna-Marie E.; Carroll, Marion L.; Nguyen, Son V.; Walker, Jerilyn A.; Prasad, B.V. Ravi; Reddy, P. Govinda; Das, Pradipta K.; Batzer, Mark A.; Jorde, Lynn B.

2003-01-01

122

A High-Resolution Single Nucleotide Polymorphism Genetic Map  

E-print Network

.pbio.0040395 Introduction The current genetic map of the mouse is based on data from crosses between inbred be combined to form a map using this approach [8], recombination rates are not constant across the genome [9 to estimate fine-scale recombination rates from linkage-disequilibrium (LD) data, using a coalescent

Nachman, Michael

123

Genetic Polymorphism in the Rabies Virus Nucleoprotein Gene  

Microsoft Academic Search

In an attempt to compare intrinsic and extrinsic genetic diversity of the lyssavirus genotypes, 69 rabies virus isolates from various part of the world were partially sequenced and compared to 13 representative isolates of the 6 lyssavirus genotypes. The analysis of their phylogenetic relationships, performed on the complete nucleoprotein (N) coding gene (1350 bases), established that the rabies virus isolates

Bachir Kissi; Noël Tordo; Hervé Bourhy

1995-01-01

124

Genetic interactions between polymorphisms that affect gene expression in yeast  

E-print Network

) at the primary locus and tested each subgroup for further `secondary' loci. We computed the joint significance at different quantitative trait loci (QTLs) are thought to contribute to the genetics of many traits, and can set of quantitative phenotypes--the levels of all transcripts in a cross between two strains

Kruglyak, Leonid

125

Genetic polymorphisms associated with thrombotic disorders in the Japanese population  

Microsoft Academic Search

Genetic factors in combination with a number of environmental risk factors are involved in a predisposition to thrombotic disorders. Coronary artery disease (CAD) and ischemic cerebrovascular disease are typical human attributes that have a complex multifactorial etiology. There has been an increased awareness of the contribution of inherited factors for multifactorial disorders like thrombosis since the discovery of two prothrombotic

M Murata

2000-01-01

126

Use of simple sequence length polymorphisms for genetic characterization of rat inbred strains.  

PubMed

Genetic monitoring is an essential component of colony management and for the rat has been accomplished primarily by using immunological and biochemical markers. Here, we report that simple sequence length polymorphisms (SSLPs) are a faster and more economical way of monitoring inbred strains of rats. We characterized 61 inbred strains of rats, using primer pairs for 37 SSLPs. Each of these loci appeared to be highly polymorphic, with the number of alleles per locus ranging between 3 and 14 and, as a result, all the 61 inbred strains tested in this study could be provided with a unique strain profile. These strain profiles are also used for estimating the degree of similarity between strains. This information may provide the rationale in selecting strains for genetic crosses or for other specific purposes. PMID:8535065

Otsen, M; Den Bieman, M; Winer, E S; Jacob, H J; Szpirer, J; Szpirer, C; Bender, K; Van Zutphen, L F

1995-09-01

127

Genetic discovery in Xylella fastidiosa through sequence analysis of selected randomly amplified polymorphic DNAs.  

PubMed

Xylella fastidiosa causes many important plant diseases including Pierce's disease (PD) in grape and almond leaf scorch disease (ALSD). DNA-based methodologies, such as randomly amplified polymorphic DNA (RAPD) analysis, have been playing key roles in genetic information collection of the bacterium. This study further analyzed the nucleotide sequences of selected RAPDs from X. fastidiosa strains in conjunction with the available genome sequence databases and unveiled several previously unknown novel genetic traits. These include a sequence highly similar to those in the phage family of Podoviridae. Genome comparisons among X. fastidiosa strains suggested that the "phage" is currently active. Two other RAPDs were also related to horizontal gene transfer: one was part of a broadly distributed cryptic plasmid and the other was associated with conjugal transfer. One RAPD inferred a genomic rearrangement event among X. fastidiosa PD strains and another identified a single nucleotide polymorphism of evolutionary value. PMID:15723179

Chen, Jianchi; Civerolo, Edwin L; Jarret, Robert L; Van Sluys, Marie-Anne; de Oliveira, Mariana C

2005-02-01

128

Polymorphism, Genetic Effect and Association with Egg Production Traits of Chicken Matrix Metalloproteinases 9 Promoter  

PubMed Central

Matrix metalloproteinases (MMP) are key enzymes involved in cell and tissue remodeling during ovarian follicle development and ovulation. The control of MMP9 transcription in ovarian follicles occurs through a core promoter region (?2,400 to ?1,700 bp). The aim of this study was to screen genetic variations in the core promoter region and examine MMP9 transcription regulation and reproduction performance. A single cytosine deletion/insertion polymorphism was found at ?1954 C+/C?. Genetic association analysis indicated significant correlation between the deletion genotype (C?) with total egg numbers at 28 weeks (p = 0.031). Furthermore, luciferase-reporter assay showed the deletion genotype (C?) had significantly lower promoter activity than the insertion genotype (C+) in primary granulosa cells (p<0.01). Therefore, the identified polymorphism could be used for marker-assisted selection to improve chicken laying performance. PMID:25358310

Zhu, Guiyu; Jiang, Yunliang

2014-01-01

129

Genetic polymorphisms associated with adverse events and elimination of methotrexate in childhood acute lymphoblastic leukemia and malignant lymphoma  

Microsoft Academic Search

Methotrexate is administered in high doses to treat childhood acute lymphoblastic leukemia and malignant lymphoma. Hepatotoxicity\\u000a and bone marrow suppression often limit its use, however. The objective of this study was to determine the genetic polymorphisms\\u000a associated with the hepatotoxicity and elimination of methotrexate. Genetic polymorphisms of glutathione S-transferase (GST)\\u000a genes including GSTT1 positive\\/null, GSTM1 positive\\/null, and GSTP1 A313G, and

Hiroyuki Imanishi; Noboru Okamura; Mariko Yagi; Yukari Noro; Yuka Moriya; Tsutomu Nakamura; Akira Hayakawa; Yasuhiro Takeshima; Toshiyuki Sakaeda; Masafumi Matsuo; Katsuhiko Okumura

2007-01-01

130

Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum field isolates from Myanmar  

Microsoft Academic Search

BACKGROUND: Merozoite surface protein-1 (MSP-1) and MSP-2 of Plasmodium falciparum are potential vaccine candidate antigens for malaria vaccine development. However, extensive genetic polymorphism of the antigens in field isolates of P. falciparum represents a major obstacle for the development of an effective vaccine. In this study, genetic polymorphism of MSP-1 and MSP-2 among P. falciparum field isolates from Myanmar was

Jung-Mi Kang; Sung-Ung Moon; Jung-Yeon Kim; Shin-Hyeong Cho; Khin Lin; Woon-Mok Sohn; Tong-Soo Kim; Byoung-Kuk Na

2010-01-01

131

Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms  

Microsoft Academic Search

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557),

W. Scott Watkins; Alan R. Rogers; Christopher T. Ostler; Steve Wooding; Michael J. Bamshad; Anna-Marie E. Brassington; Marion L. Carroll; Son V. Nguyen; Jerilyn A. Walker; B. V. Ravi Prasad; P. Govinda Reddy; Pradipta K. Das; Mark A. Batzer; Lynn B. Jorde

2003-01-01

132

PERMANENT GENETIC RESOURCES: Ten polymorphic microsatellite markers for the pygmy rabbit (Brachylagus idahoensis).  

PubMed

We developed 10 polymorphic microsatellite loci for the pygmy rabbit (Brachylagus idahoensis). Nine of the 10 loci amplified reliably and had a low frequency of null alleles. Number of alleles per locus ranged from four to 12, and observed and expected heterozygosities ranged from 0.26 to 0.89 and from 0.63 to 0.88, respectively. These loci will be useful in determining population genetic structure and assessing patterns of gene flow in the pygmy rabbit. PMID:21585792

Estes-Zumpf, Wendy A; Rachlow, Janet L; Waits, Lisette P

2008-03-01

133

Frequencies of genetic polymorphisms related to triptans metabolism in chronic migraine  

Microsoft Academic Search

Chronic migraine (CM) prevalence ranges around 1–5%. Most of these patients usually treat their acute attacks with triptans,\\u000a whose efficacy is extremely variable. A genetic basis for migraine is evident and many susceptibility genes have been described,\\u000a as well as gene polymorphisms possibly implied in therapy response. Several factors could be involved in the evolution of\\u000a episodic migraine into a

Giovanna Gentile; Serena Missori; Marina Borro; Alisa Sebastianelli; Maurizio Simmaco; Paolo Martelletti

2010-01-01

134

Genetically Determined Protein Polymorphism in the Rabbit Nervous System  

Microsoft Academic Search

One of the polypeptides (H1) of the rabbit nervous system occurs in an altered form (H2) in some rabbits. The electrophoretic mobility of H2 on sodium dodecyl sulfate-polyacrylamide gels is about 6% greater than that of H1, suggesting that the two polypeptides differ in molecular weight by about 10,000. The alteration is genetically determined since (i) rabbit phenotypes corresponding to

Mark B. Willard

1976-01-01

135

Ethnical disparities of prostate cancer predisposition: genetic polymorphisms in androgen-related genes  

PubMed Central

Prostate cancer (PCa) is the most commonly diagnosed male malignancy and the second biggest cause of cancer death in men of the Western world. Higher incidences of PCa occur in men from North America, Oceania and Western countries, whereas men from Asia and North Africa have a much lower PCa incidence rate. Investigations into this population disparity of PCa incidence, in order to identify potential preventive factors or targets for the therapeutic intervention of PCa, have found differences in both environmental and genetic variations between these populations. Environmental variations include both diet and lifestyle, which vary widely between populations. Evidence that diet comes into play has been shown by men who immigrate from Eastern to Western countries. PCa incidence in these men is higher than men in their native countries. However the number of immigrants developing PCa still doesn’t match native black/white men, therefore genetic factors also contribute to PCa risk, which are supported by familial studies. There are a number of genetic polymorphisms that are differentially presented between Western and Eastern men, which are potentially associated with PCa incidence. Androgen and its receptor (AR) play a major role in PCa development and progression. In this study, we focus on genes involved in androgen biosynthesis and metabolism, as well as those associated with AR pathway, whose polymorphisms affect androgen level and biological or physiological functions of androgen. While many of the genetic polymorphisms in this androgen/AR system showed different frequencies between populations, contradictory evidences exist for most of these genes investigated individually as to the true contribution to PCa risk. More accurate measurements of androgen activity within the prostate are required and further studies need to include more African and Asian subjects. As many of these genetic polymorphisms may contribute to different steps in the same biological/physiological function of androgen and AR pathway, an integrated analysis considering the combined effect of all the genetic polymorphisms may be necessary to assess their contribution to PCa initiation and progression. PMID:23593537

Li, Jie; Mercer, Emma; Gou, Xin; Lu, Yong-Jie

2013-01-01

136

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji  

USGS Publications Warehouse

We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency. ?? 2011 The Authors.

Talbot, S.L.; Palmer, A.G.; Sage, G.K.; Sonsthagen, S.A.; Swem, T.; Brimm, D.J.; White, C.M.

2011-01-01

137

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji  

USGS Publications Warehouse

We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.

Talbot, Sandra; Palmer, A.G.; Sage, G.K.; Sonsthagen, Sarah A.; Swem, T.; Brimm, D.J.

2014-01-01

138

Study of the Association between ITPKC Genetic Polymorphisms and Calcium Nephrolithiasis  

PubMed Central

Nephrolithiasis is a multifactorial disease caused by environmental, hormonal, and genetic factors. Genetic polymorphisms of ORAI1, which codes for the main subunit of the store-operated calcium (SOC) channel, were reported to be associated with the risk and recurrence of calcium nephrolithiasis. Inositol 1,4,5-trisphosphate (IP3) 3-kinase C (ITPKC) is a negative regulator of the SOC channel-mediated signaling pathway. We investigated the association between calcium containing nephrolithiasis and genetic variants of ITPKC gene in Taiwanese patients. 365 patients were recruited in this study. Eight tagging single nucleotide polymorphisms of ITPKC were selected for genotyping. ITPKC genotypes were determined by TaqMan assay. ITPKC plasmids were transfected into cells to evaluate the intracellular calcium mobilization. Our results indicated that rs2607420 CC genotype in the intron region of the ITPKC gene is associated with a lower eGFR by both Modification of Diet in Renal Diseases (P = 0.0405) and Cockcroft-Gault (P = 0.0215) equations in patients with calcium nephrolithiasis. Our results identify a novel polymorphism for renal function and highlight the importance of ITPKC as a key molecule to regulate calcium signaling. PMID:24800221

Chou, Yii-Her; Chiu, Siou-Jin; Hsu, Yu-Wen; Lu, Hsing-Fang; Hsu, Wenli; Chang, Wei-Chiao

2014-01-01

139

4P: fast computing of population genetics statistics from large DNA polymorphism panels  

PubMed Central

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations. PMID:25628874

Benazzo, Andrea; Panziera, Alex; Bertorelle, Giorgio

2015-01-01

140

4P: fast computing of population genetics statistics from large DNA polymorphism panels.  

PubMed

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations. PMID:25628874

Benazzo, Andrea; Panziera, Alex; Bertorelle, Giorgio

2015-01-01

141

The association between serum ApoE genetic polymorphism and serum lipid level in hemodialysis patients.  

PubMed

Growing evidence indicates that apolipoprotein E (ApoE) is one of the most important candidate genes for influencing the development of hemodialysis (HD). This study aims to detect the potential association between serum ApoE genetic polymorphism and serum lipid level in HD. A total of 485 subjects were enrolled in this case-control study. The created restriction site polymerase chain reaction and DNA sequencing methods were used to investigate ApoE c.109G>A genetic polymorphism. Our data suggested that there were significant differences in the distribution of allelic and genotypic frequencies between HD patients and healthy controls. The levels of total cholesterol, triglyceride, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, ApoA-I, ApoB, ApoE, and lipoprotein (a) for genotype AA were different from genotype GG in HD patients and healthy controls. Our findings support that the ApoE c.109G>A genetic polymorphism might influence the development of HD and could be a risk factor for assessing HD. PMID:25565166

Zhang, Yong; Zhang, Linlin; Cao, Bo

2015-02-01

142

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers.  

PubMed

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow. PMID:17568929

González, Ranulfo; Wilkerson, Richard; Suárez, Marco Fidel; García, Felipe; Gallego, Gerardo; Cárdenas, Heiber; Posso, Carmen Elisa; Duque, Myriam Cristina

2007-06-01

143

Genetic diversity and population structure in Harpadon nehereus based on sequence-related amplified polymorphism markers.  

PubMed

In this study, the genetic diversity among ten populations of the Bombay duck was studied on the basis of sequence-related amplified polymorphism (SRAP). The ten populations were collected from the East China Sea and South China Sea areas. A total of 98 loci were obtained from 292 individuals using eight SRAP primers. The average proportion of polymorphic loci, genetic diversity (H), and Shannon's information index were 75.20%, 0.2478, and 0.3735, respectively. Nei's genetic distance and Shannon's information index between the ten populations ranged from 0.0410 to 0.3841 and from 0.2396 to 0.4506, and the averages Nei's gene diversity index (H = 0.2478) and Shannon's information index (I = 0.3735) at the population level were high. AMOVA showed that most of the variation was within populations (71.74%), and only 28.26% of the variation was between populations. The neighbor-joining tree based on genetic distance revealed that significant genealogical structure existed throughout the examined range of the Bombay duck. The results demonstrated that SRAP marker was an effective tool for the assessment of genetic diversity in the Bombay duck. The results could be used for further protection of the germplasm resource of the Bombay duck. PMID:25117356

Zhu, Z H; Li, H Y; Qin, Y; Wang, R X

2014-01-01

144

Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms  

PubMed Central

Background Genetic variation explains a considerable part of observed phenotypic variation in gene expression networks. This variation has been shown to be located both locally (cis) and distally (trans) to the genes being measured. Here we explore to which degree the phenotypic manifestation of local and distant polymorphisms is a dynamic feature of regulatory design. Results By combining mathematical models of gene expression networks with genetic maps and linkage analysis we find that very different network structures and regulatory motifs give similar cis/trans linkage patterns. However, when the shape of the cis-regulatory input functions is more nonlinear or threshold-like, we observe for all networks a dramatic increase in the phenotypic expression of distant compared to local polymorphisms under otherwise equal conditions. Conclusion Our findings indicate that genetic variation affecting the form of cis-regulatory input functions may reshape the genotype-phenotype map by changing the relative importance of cis and trans variation. Our approach combining nonlinear dynamic models with statistical genetics opens up for a systematic investigation of how functional genetic variation is translated into phenotypic variation under various systemic conditions. PMID:17651484

Gjuvsland, Arne B; Hayes, Ben J; Meuwissen, Theo HE; Plahte, Erik; Omholt, Stig W

2007-01-01

145

Genetic Analysis of 430 Chinese Cynodon dactylon Accessions Using Sequence-Related Amplified Polymorphism Markers  

PubMed Central

Although Cynodon dactylon (C. dactylon) is widely distributed in China, information on its genetic diversity within the germplasm pool is limited. The objective of this study was to reveal the genetic variation and relationships of 430 C. dactylon accessions collected from 22 Chinese provinces using sequence-related amplified polymorphism (SRAP) markers. Fifteen primer pairs were used to amplify specific C. dactylon genomic sequences. A total of 481 SRAP fragments were generated, with fragment sizes ranging from 260–1800 base pairs (bp). Genetic similarity coefficients (GSC) among the 430 accessions averaged 0.72 and ranged from 0.53–0.96. Cluster analysis conducted by two methods, namely the unweighted pair-group method with arithmetic averages (UPGMA) and principle coordinate analysis (PCoA), separated the accessions into eight distinct groups. Our findings verify that Chinese C. dactylon germplasms have rich genetic diversity, which is an excellent basis for C. dactylon breeding for new cultivars. PMID:25338051

Huang, Chunqiong; Liu, Guodao; Bai, Changjun; Wang, Wenqiang

2014-01-01

146

Polymorphs  

E-print Network

) ? Thermomechanical analysis (TMA) ? Microthermal analysis ? Isothermal Calorimetry 28 Differential Scanning Calorimetry Measures the heat flux as a function of temperature ? Premafloxacin Forms I and III ? Exothermic transitions suggest monotropic pairs I, II... by change in extinction. After rotation of the stage, extinction of polarized light is restored. From Nichols, Light microscopy, in Hilfiker, Polymorphism, Wiley-VCH (2005) Ch. 7 22 43 Thermomechanical Analysis Two major types ? Compression ? Allows...

Prankerd, Richard

2006-10-26

147

Genetic polymorphisms of drug-metabolising enzymes and drug transporters in the chemotherapeutic treatment of cancer.  

PubMed

There is wide variability in the response of individuals to standard doses of drug therapy. This is an important problem in clinical practice, where it can lead to therapeutic failures or adverse drug reactions. Polymorphisms in genes coding for metabolising enzymes and drug transporters can affect drug efficacy and toxicity. Pharmacogenetics aims to identify individuals predisposed to a high risk of toxicity and low response from standard doses of anti-cancer drugs. This review focuses on the clinical significance of polymorphisms in drug-metabolising enzymes (cytochrome P450 [CYP] 2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, dihydropyrimidine dehydrogenase, uridine diphosphate glucuronosyltransferase [UGT] 1A1, glutathione S-transferase, sulfotransferase [SULT] 1A1, N-acetyltransferase [NAT], thiopurine methyltransferase [TPMT]) and drug transporters (P-glycoprotein [multidrug resistance 1], multidrug resistance protein 2 [MRP2], breast cancer resistance protein [BCRP]) in influencing efficacy and toxicity of chemotherapy. The most important example to demonstrate the influence of pharmacogenetics on anti-cancer therapy is TPMT. A decreased activity of TPMT, caused by genetic polymorphisms in the TPMT gene, causes severe toxicity with mercaptopurine. Dosage reduction is necessary for patients with heterozygous or homozygous mutation in this gene. Other polymorphisms showing the influence of pharmacogenetics in the chemotherapeutic treatment of cancer are discussed, such as UGT1A1*28. This polymorphism is associated with an increase in toxicity with irinotecan. Also, polymorphisms in the DPYD gene show a relation with fluorouracil-related toxicity; however, in most cases no clear association has been found for polymorphisms in drug-metabolising enzymes and drug transporters, and pharmacokinetics or pharmacodynamics of anti-cancer drugs. The studies discussed evaluate different regimens and tumour types and show that polymorphisms can have different, sometimes even contradictory, pharmacokinetic and pharmacodynamic effects in different tumours in response to different drugs. The clinical application of pharmacogenetics in cancer treatment will therefore require more detailed information of the different polymorphisms in drug-metabolising enzymes and drug transporters. Larger studies, in different ethnic populations, and extended with haplotype and linkage disequilibrium analysis, will be necessary for each anti-cancer drug separately. PMID:16509759

Bosch, Tessa M; Meijerman, Irma; Beijnen, Jos H; Schellens, Jan H M

2006-01-01

148

COMT val158met and 5-HTTLPR genetic polymorphisms moderate executive control in cannabis users.  

PubMed

The adverse effects of cannabis use on executive functions are still controversial, fostering the need for novel biomarkers able to unveil individual differences in the cognitive impact of cannabis consumption. Two common genetic polymorphisms have been linked to the neuroadaptive impact of ?9-tetrahydrocannabinol (THC) exposure and to executive functions in animals: the catechol-O-methyltransferase (COMT) gene val158met polymorphism and the SLC6A4 gene 5-HTTLPR polymorphism. We aimed to test if these polymorphisms moderate the harmful effects of cannabis use on executive function in young cannabis users. We recruited 144 participants: 86 cannabis users and 58 non-drug user controls. Both groups were genotyped and matched for genetic makeup, sex, age, education, and IQ. We used a computerized neuropsychological battery to assess different aspects of executive functions: sustained attention (CANTAB Rapid Visual Information Processing Test, RVIP), working memory (N-back), monitoring/shifting (CANTAB ID/ED set shifting), planning (CANTAB Stockings of Cambridge, SOC), and decision-making (Iowa Gambling Task, IGT). We used general linear model-based analyses to test performance differences between cannabis users and controls as a function of genotypes. We found that: (i) daily cannabis use is not associated with executive function deficits; and (ii) COMT val158met and 5-HTTLPR polymorphisms moderate the link between cannabis use and executive performance. Cannabis users carrying the COMT val/val genotype exhibited lower accuracy of sustained attention, associated with a more strict response bias, than val/val non-users. Cannabis users carrying the COMT val allele also committed more monitoring/shifting errors than cannabis users carrying the met/met genotype. Finally, cannabis users carrying the 5-HTTLPR s/s genotype had worse IGT performance than s/s non-users. COMT and SLC6A4 genes moderate the impact of cannabis use on executive functions. PMID:23449176

Verdejo-García, Antonio; Fagundo, Ana Beatriz; Cuenca, Aida; Rodriguez, Joan; Cuyás, Elisabet; Langohr, Klaus; de Sola Llopis, Susana; Civit, Ester; Farré, Magí; Peña-Casanova, Jordi; de la Torre, Rafael

2013-07-01

149

Genetic Polymorphism Characteristics of Brucella canis Isolated in China  

PubMed Central

In China, brucellosis is an endemic disease typically caused by Brucella melitensis infection (biovars 1 and 3). Brucella canis infection in dogs has not traditionally recognized as a major problem. In recent years however, brucellosis resulting from Brucella canis infection has also been reported, suggesting that infections from this species may be increasing. Data concerning the epidemiology of brucellosis resulting from Brucella canis infection is limited. Therefore, the purpose of this study was to assess the diversity among Chinese Brucella canis strains for epidemiological purposes. First, we employed a 16-marker VNTR assay (Brucella MLVA-16) to assess the diversity and epidemiological relationship of 29 Brucella canis isolates from diverse locations throughout China with 38 isolates from other countries. MLVA-16 analysis separated the 67 Brucella canis isolates into 57 genotypes that grouped into five clusters with genetic similarity coefficients ranging from 67.73 to 100%. Moreover, this analysis revealed a new genotype (2-3-9-11-3-1-5-1:118), which was present in two isolates recovered from Guangxi in 1986 and 1987. Second, multiplex PCR and sequencing analysis were used to determine whether the 29 Chinese Brucella canis isolates had the characteristic BMEI1435 gene deletion. Only two isolates had this deletion. Third, amplification of the omp25 gene revealed that 26 isolates from China had a T545C mutation. Collectively, this study reveals that considerable diversity exists among Brucella canis isolates in China and provides resources for studying the genetic variation and microevolution of Brucella. PMID:24465442

Wang, Heng; Zhao, Hongyan; Piao, Dongri; Tian, Lili; Tian, Guozhong; Kang, Jingli; Mao, Xiang; Zhang, Xiaojun; Du, Pengfei; Zhu, Lin; Zhao, Zhuo; Mao, Lingling; Yao, Wenqing; Guan, Pingyuan; Fan, Weixing; Jiang, Hai

2014-01-01

150

Investigating the potential genetic association between RANBP9 polymorphisms and the risk of schizophrenia.  

PubMed

Schizophrenia is a serious mental disorder that is affected by genetic and environmental factors. As the disease has a high heritability rate, genetic studies identifying candidate genes for schizophrenia have been conducted in various populations. The gene for human Ran?binding protein 9 (RANBP9) is a newly discovered candidate gene for schizophrenia. As RANBP9 is a small guanosine?5'?triphosphate?binding protein that interacts with the disrupted in schizophrenia 1 protein, it is considered to be an important molecule in the pathogenesis of schizophrenia. However, to date, no study has examined the possible association between the genetic variations of RANBP9 and the risk of schizophrenia. In the present study, it was hypothesized that RANBP9 variations may influence the risk of schizophrenia. In order to investigate the association between RANBP9 polymorphisms and the risk of schizophrenia and smooth pursuit eye movement (SPEM) abnormalities, a case?control association analysis was performed. Using a TaqMan assay, five single?nucleotide polymorphisms and an insertion/deletion variation within the start codon region of RANBP9 were genotyped. Five major haplotypes were identified in 449 patients with schizophrenia and 393 unrelated healthy individuals as controls (total, n=842). However, the association analyses revealed no associations between all genetic variants and schizophrenia and SPEM abnormality. To the best of our knowledge, this is the first study to investigate an association between RANBP9 polymorphisms and schizophrenia and SPEM abnormality. The findings of allele frequencies and association results in this study may aid in further genetic etiological studies in schizophrenia in various populations. PMID:25482375

Bae, Joon Seol; Kim, Jason Yongha; Park, Byung-Lae; Cheong, Hyun Sub; Kim, Jeong-Hyun; Namgoong, Suhg; Kim, Ji-On; Park, Chul Soo; Kim, Bong-Jo; Lee, Cheol-Soon; Lee, Migyung; Choi, Woo Hyuk; Shin, Tae-Min; Hwang, Jaeuk; Shin, Hyoung Doo; Woo, Sung-Il

2015-04-01

151

A natural genetic polymorphism affects retroactive interference in Drosophila melanogaster.  

PubMed

As environments change, animals update their internal representations of the external world. New information about the environment is learned and retained whereas outdated information is disregarded or forgotten. Retroactive interference (RI) occurs when the retrieval of previously learned information is less available owing to the acquisition of recently acquired information. Even though RI is thought to be a major cause of forgetting, its functional significance is still under debate. We find that natural allelic variants of the Drosophila melanogaster foraging gene known to affect rover and sitter behaviour differ in RI. More specifically, rovers who were previously shown to experience greater environmental heterogeneity while foraging display RI whereas sitters do not. Rover responses are biased towards more recent learning events. These results provide an ecological context to investigate the function of forgetting via RI and a suitable genetic model organism to address the evolutionary relevance of cognitive tasks. PMID:20667877

Reaume, Christopher J; Sokolowski, Marla B; Mery, Frederic

2011-01-01

152

Random amplified polymorphic markers as indicator for genetic conservation program in Iranian pheasant (Phasianus colchicus).  

PubMed

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

153

Random Amplified Polymorphic Markers as Indicator for Genetic Conservation Program in Iranian Pheasant (Phasianus colchicus)  

PubMed Central

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500?bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings. PMID:23002388

Elyasi Zarringhabaie, Ghorban; Javanmard, Arash; Pirahary, Ommolbanin

2012-01-01

154

Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism.  

PubMed

In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation. PMID:24779012

Que, Youxiong; Pan, Yongbao; Lu, Yunhai; Yang, Cui; Yang, Yuting; Huang, Ning; Xu, Liping

2014-01-01

155

Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism  

PubMed Central

In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation. PMID:24779012

Que, Youxiong; Pan, Yongbao; Lu, Yunhai; Yang, Cui; Yang, Yuting; Huang, Ning; Xu, Liping

2014-01-01

156

Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms.  

PubMed Central

A new method for typing single nucleotide polymorphisms in DNA is described. In this method, specific fragments of genomic DNA containing the polymorphic site(s) are first amplified by the polymerase chain reaction (PCR) using one regular and one phosphorothioate-modified primer. The double-stranded PCR product is rendered single-stranded by treatment with the enzyme T7 gene 6 exonuclease, and captured onto individual wells of a 96 well polystyrene plate by hybridization to an immobilized oligonucleotide primer. This primer is designed to hybridize to the single-stranded target DNA immediately adjacent from the polymorphic site of interest. Using the Klenow fragment of E. coli DNA polymerase I or the modified T7 DNA polymerase (Sequenase), the 3' end of the capture oligonucleotide is extended by one base using a mixture of one biotin-labeled, one fluorescein-labeled, and two unlabeled dideoxynucleoside triphosphates. Antibody conjugates of alkaline phosphatase and horseradish peroxidase are then used to determine the nature of the extended base in an ELISA format. This paper describes biochemical features of this method in detail. A semi-automated version of the method, which we call Genetic Bit Analysis (GBA), is being used on a large scale for the parentage verification of thoroughbred horses using a predetermined set of 26 diallelic polymorphisms in the equine genome. Images PMID:7937143

Nikiforov, T T; Rendle, R B; Goelet, P; Rogers, Y H; Kotewicz, M L; Anderson, S; Trainor, G L; Knapp, M R

1994-01-01

157

Genetic Diversity Analysis of Hypsizygus marmoreus with Target Region Amplification Polymorphism  

PubMed Central

Hypsizygus marmoreus is an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis of H. marmoreus sequences from GenBank database. The genomic DNA extracted from H. marmoreus was amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains of H. marmoreus were classified into two main groups. PMID:25013861

Qiu, Chengshu; Yan, Wenjuan; Deng, Wangqiu; Song, Bin; Li, Taihui

2014-01-01

158

The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera  

PubMed Central

Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data. PMID:22303334

Coates, Brad Steven; Bayles, Darrell O.; Wanner, Kevin W.; Robertson, Hugh M.; Hellmich, Richard L.; Sappington, Thomas W.

2011-01-01

159

Hodgkin Lymphoma Risk: Role of Genetic Polymorphisms and Gene-Gene Interactions in DNA repair pathways  

PubMed Central

DNA repair variants may play a potentially important role in an individual’s susceptibility to developing cancer. Numerous studies have reported the association between genetic single nucleotide polymorphisms (SNPs) in DNA repair genes and different types of hematologic cancers. However, to date, the effects of such SNPs on modulating Hodgkin Lymphoma (HL) risk have not yet been investigated. We hypothesized that gene-gene interaction between candidate genes in Direct Reversal, Nucleotide excision repair (NER), Base excision repair (BER) and Double strand break (DSB) pathways may contribute to susceptibility to HL. To test this hypothesis, we conducted a study on 200 HL cases and 220 controls to assess associations between HL risk and 21 functional SNPs in DNA repair genes. We evaluated potential gene-gene interactions and the association of multiple polymorphisms in a chromosome region using a multi-analytic strategy combining logistic regression, multi-factor dimensionality reduction and classification and regression tree approaches. We observed that, in combination, allelic variants in the XPC Ala499Val, NBN Glu185Gln, XRCC3 Thr241Me, XRCC1 Arg194Trp and XRCC1 399Gln polymorphisms modify the risk for developing HL. Moreover, the cumulative genetic risk score revealed a significant trend where the risk for developing HL increases as the number of adverse alleles in BER and DSB genes increase. These findings suggest that DNA repair variants in BER and DSB pathways may play an important role in the development of HL. PMID:21374732

Monroy, Claudia M.; Cortes, Andrea C.; Lopez, Mirtha; Rourke, Elizabeth; Etzel, Carol J.; Younes, Anas; Strom, Sara S.; El-Zein, Randa

2011-01-01

160

A worldwide population study of the Ag-system haplotypes, a genetic polymorphism of human low-density lipoprotein.  

PubMed Central

The aim of this investigation is to examine the distribution of the Ag immunological polymorphism in human populations on a worldwide scale and to look for possible explanations of this distribution in the field of modern human peopling history and Ag-system evolution. Extensive Ag-antigene typings were carried out on 13 human population samples, including sub-Saharan African, European, west and east Asiatic, Melanesian, Australian aborigine, and Amerindian groups. Complete Ag-haplotype frequencies were estimated by maximum-likelihood-score procedures, and the data were analyzed by genetic distance computations and principal coordinate projections. With the exception of the Amerindian sample, the Ag polymorphism is shown to be highly polymorphic in all the populations tested. Their genetic relationships appear to be closely correlated to their geographical distribution. This suggests that the Ag system has evolved as a neutral or nearly neutral polymorphism and that it is highly informative for modern human peopling history studies. From the worldwide Ag haplotypic distributions, a model for the Ag molecular structure is derived. According to this model and to the most recent results obtained from molecular data, the establishment of the Ag polymorphism could be explained by several mutations and recombination events between the haplotypes most frequently found in human populations today. As a conclusion, genetic and paleontological data suggest that the genetic structure of caucasoid populations (located from North Africa to India) may be the least differentiated from an ancestral genetic stock. Worldwide genetic differentiations are properly explained as the results of westward and eastward human migrations from a Near East-centered but undefined geographical area where modern humans may have originated. The importance of Ag polymorphism analyses for the reconstruction of human settlement history and origins is discussed in the light of the main conclusions of the most recent genetic polymorphism studies. PMID:1689953

Breguet, G; Bütler, R; Bütler-Brunner, E; Sanchez-Mazas, A

1990-01-01

161

Genetic polymorphisms of lipoprotein lipase gene and their associations with growth traits in Xiangxi cattle.  

PubMed

Lipoprotein lipase (LPL), involved in the metabolism and transport of lipids, regulate energy balance, fat deposition and growth traits. The objective of this study was to investigate the single nucleotide polymorphisms (SNPs) of LPL gene and to determine their associations between these polymorphisms and growth traits in Xiangxi cattle breed. In this study, six novel SNPs (C355157T, T355169C, T355186G, A355210G, T355348A and T355420C) and one reported SNP (A355427T, has been recorded in dbSNP, ID rs110590698) were detected using polymerase chain reaction and DNA sequencing method. Genotyping and genetic diversity analysis were performed in 240 Xiangxi cattle on the basis of sequence alignment, which indicated that five SNPs (C355157T, 355186G, T355348A, T355420C, A355427T) were in abundant genetic diversity, and the other two SNPs (T355169C and TA355210G) were in low genetic diversity. Linkage disequilibrium analysis showed that 18 different haplotypes were identified in these animals. Moreover, the results of the association between LPL gene polymorphisms and growth traits indicated that the individuals with H1H1 haplotype combination had higher BW and HG than those with other haplotype combinations (P < 0.05). The animals with CC genotype maintain higher mean values for BW than those with the CT and TT genotypes (P < 0.05) at T355420C locus. The animals with the AA genotype have lower mean values for WH, BL, HG and BW than those with the AT and TT genotypes at A355427T locus (P < 0.05). The results suggested that the SNPs of the LPL gene might be useful genetic markers for growth traits in the bovine reproduction and breeding. PMID:23053937

Wang, Xing Ping; Luoreng, Zhuo Ma; Li, Feng; Wang, Jin Ren; Li, Na; Li, Shu Hong

2012-12-01

162

[Pearl Harbor.  

ERIC Educational Resources Information Center

This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor, and with a…

Johnson, Jennifer, Ed.

1992-01-01

163

Sequence-Related Amplified Polymorphism (SRAP) markers for assessing interrelationships and genetic diversity among members of the Saccharum complex  

Technology Transfer Automated Retrieval System (TEKTRAN)

Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic rela...

164

A Genetic Map of Lettuce (Lactuca sativa L.) With Restriction Fragment Length Polymorphism, Isozyme, Disease Resistance and Morphological Markers  

Microsoft Academic Search

A detailed linkage map of lettuce was constructed using 53 genetic markers including 4 1 restriction fragment length polymorphism (RFLP) loci, five downy mildew resistance genes, four isozyme loci and three morphological markers. The genetic markers were distributed into nine linkage groups and cover 404 cM which may be 25-30% of the lettuce genome. The majority (31 of 34) of

Benoit S. Landry; Rick V. Kesseli; Barry Farrara; Richard W. Michelmore

1987-01-01

165

Low genetic polymorphism of merozoite surface proteins 7 and 10 in Colombian Plasmodium vivax isolates.  

PubMed

The merozoite surface protein (MSP) family is involved in the initial interaction between merozoites and erythrocytes in Plasmodium species, its members are therefore becoming major targets for vaccine development. Considering that antigens included in a subunit malaria vaccine should be both accessible to the immune system and lack genetic diversity or have very limited polymorphism, we have analyzed the genetic diversity of three msp genes (msp-7A, msp-7K and msp-10) in different geographical regions of Colombia. The results showed that these genes follow the neutral model of evolution and also display low genetic diversity. The strong conservation found for msp-7 haplotypes in isolates from geographically different regions further suggests that these proteins could be good components of a vaccine against Plasmodium vivax malaria, thereby avoiding strain-specific immune responses. PMID:21182986

Garzón-Ospina, Diego; Romero-Murillo, Liza; Tobón, Luisa F; Patarroyo, Manuel A

2011-03-01

166

Comparison of Randomly Amplified Polymorphic DNA with Amplified Fragment Length Polymorphism To Assess Genetic Diversity and Genetic Relatedness within Genospecies III of Pseudomonas syringae  

PubMed Central

Recently, DNA pairing analyses showed that Pseudomonas syringae pv. tomato and related pathovars, including P. syringae pv. maculicola, form a genomic species (Pseudomonas tomato) (L. Gardan, H. L. Shafik, and P. A. D. Grimont, p. 445–448, in K. Rudolph, T. J. Burr, J. W. Mansfield, D. Stead, A. Vivian, and J. von Kietzell, ed., Pseudomonas syringae Pathovars and Related Pathogens, 1997). The genetic diversity of 23 strains belonging to this genomic species and 4 outgroup strains was analyzed with randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphic (AFLP) techniques. Simple boiling of P. syringae cells was suitable for subsequent DNA amplification to obtain reliable patterns in RAPD and AFLP analyses. In general, the grouping of P. syringae strains by both analysis techniques corresponded well with the classification obtained from an RFLP analysis of ribosomal DNA operons, DNA pairing studies, and an analysis of pathogenicity data. However, two strains of P. syringae pv. maculicola produced distinct DNA patterns compared to the DNA patterns of other P. syringae pv. maculicola strains; these patterns led us to assume that horizontal transfer of DNA could occur between bacterial populations. Both techniques used in this study have high discriminating power because strains of P. syringae pv. tomato and P. syringae pv. maculicola which were indistinguishable by other techniques, including pathogenicity tests on tomato, were separated into two groups by both RAPD and AFLP analyses. In addition, data analysis showed that the AFLP method was more efficient for assessing intrapathovar diversity than RAPD analysis and allowed clear delineation between intraspecific and interspecific genetic distances, suggesting that it could be an alternative to DNA pairing studies. However, it was not possible to distinguish the two races of P. syringae pv. tomato on the basis of an analysis of the data provided by either the AFLP or RAPD technique. PMID:16349533

Clerc, Agathe; Manceau, Charles; Nesme, Xavier

1998-01-01

167

Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker.  

PubMed

Genetic diversity and interrelationships among 31 lentil genotypes were evaluated using 10 Inter-Simple Sequence Repeat (ISSR) and 10 directed amplification of minisatellite DNA region (DAMD) primers. A total of 43 and 48 polymorphic bands were amplified by ISSR and DAMD markers, respectively. Average polymorphism information content (PIC) for ISSR and DAMD markers were 0.37 and 0.41, respectively. All 31 lentil genotypes could be distinguished by ISSR markers into three groups and by DAMD markers into two groups. Various molecular markers show a different efficiency for evaluating DNA polymorphism in lentil and indicate that the patterns of variation are clearly influenced by the genetic marker used. Comparatively, the genetic diversity of examined lentil genotypes by two different marker techniques (ISSR and DAMD) was high and indicated that ISSR and DAMD are effective and promising marker systems for fingerprinting in lentil and give useful information on its genetic relationships. PMID:25320472

Seyedimoradi, Hiva; Talebi, Reza

2014-10-01

168

Amplified fragment length polymorphism for genetic diversity assessment in globe artichoke.  

PubMed

Globe artichoke ( Cynara cardunculus L. var. scolymus L.) is a diploid (2 n=2 x=34), predominantly cross-pollinated plant native to the Mediterranean basin, and Italy contains the richest primary cultivated 'gene pool'. Commercial production is mainly based on perennial cultivation of vegetatively propagated clones that are highly heterozygous and segregate widely when progeny-tested. Analysis of the artichoke genome by means of molecular markers has been limited to a few studies; here we report on the genetic relatedness among 118 artichoke accessions, including clones belonging to the same varietal type, two accessions of cultivated cardoon ( C. cardunculus L. var. altilis DC.) and four accessions of wild cardoon [ C. cardunculus L. var. sylvestris (Lamk) Fiori] as measured by amplified fragment length polymorphism (AFLP). Eight primer combinations yielded a total of 667 bands, of which 519 were polymorphic. Genetic similarities among accessions were calculated according to Jaccard's Similarity Index and used to construct a dendrogram based on the unweighted pair group method using arithmetic averages. Our results demonstrate that AFLP markers can be useful in evaluating Cynara cardunculus genetic diversity and in classifying accessions to phylogenetic groups based on their genetic similarity values. Genetic variation among artichoke clones belonging to the same varietal type was in some cases higher than that found among accessions differently named and coming from different areas. The lowest Jaccard's Similarity Index found within a varietal type can be considered as a threshold for the identification of accessions which share an analogous genetic background. This will enable the selection of representatives in order to develop and manage a germplasm 'core collection' as well as the identification of suitable material for future artichoke breeding efforts. PMID:14968303

Lanteri, S; Saba, E; Cadinu, M; Mallica, G M; Baghino, L; Portis, E

2004-05-01

169

Repeated suicidal behaviour: Stressful life events and 5-HTTLPR genetic polymorphism.  

PubMed

Stressful life events and dysregulated mono-aminergic neurotransmission have been associated with suicidal behaviour. The aim of this investigation was to analyze suicidal behaviour in multiple attempters in relation to the stressful life events, and to the polymorphism of the serotonin transporter (SERT) gene. Multiple suicide attempters, admitted to the University Psychiatric Clinic, were interviewed for the number of previous suicide attempts and for the occurrence of stressful life events, recorded in a Life History Calendar. The patients were further genotyped for 5-HTTLPR polymorphism of SERT. The number of suicide attempts was found to be significantly correlated with the number of negative life events experienced during the 6 months preceding each suicide attempt. The L/L genotype was associated with a reduced number of multiple suicide attempts. These results should prompt future study with a larger number of subjects to further investigate the interaction of genetic and environmental factors in repeated suicidal behaviour. PMID:24916825

Schillani, Giulia; Goljevscek, Serena; Carlino, Davide; De Vanna, Maurizio; Aguglia, Eugenio; Giraldi, Tullio

2009-01-01

170

Muju virus, harbored by Myodes regulus in Korea, might represent a genetic variant of Puumala virus, the prototype arvicolid rodent-borne hantavirus.  

PubMed

The genome of Muju virus (MUJV), identified originally in the royal vole (Myodes regulus) in Korea, was fully sequenced to ascertain its genetic and phylogenetic relationship with Puumala virus (PUUV), harbored by the bank vole (My. glareolus), and a PUUV-like virus, named Hokkaido virus (HOKV), in the grey red-backed vole (My. rufocanus) in Japan. Whole genome sequence analysis of the 6544-nucleotide large (L), 3652-nucleotide medium (M) and 1831-nucleotide small (S) segments of MUJV, as well as the amino acid sequences of their gene products, indicated that MUJV strains from different capture sites might represent genetic variants of PUUV, the prototype arvicolid rodent-borne hantavirus in Europe. Distinct geographic-specific clustering of MUJV was found in different provinces in Korea, and phylogenetic analyses revealed that MUJV and HOKV share a common ancestry with PUUV. A better understanding of the taxonomic classification and pathogenic potential of MUJV must await its isolation in cell culture. PMID:24736214

Lee, Jin Goo; Gu, Se Hun; Baek, Luck Ju; Shin, Ok Sarah; Park, Kwang Sook; Kim, Heung-Chul; Klein, Terry A; Yanagihara, Richard; Song, Jin-Won

2014-04-01

171

Muju Virus, Harbored by Myodes regulus in Korea, Might Represent a Genetic Variant of Puumala Virus, the Prototype Arvicolid Rodent-Borne Hantavirus  

PubMed Central

The genome of Muju virus (MUJV), identified originally in the royal vole (Myodes regulus) in Korea, was fully sequenced to ascertain its genetic and phylogenetic relationship with Puumala virus (PUUV), harbored by the bank vole (My. glareolus), and a PUUV-like virus, named Hokkaido virus (HOKV), in the grey red-backed vole (My. rufocanus) in Japan. Whole genome sequence analysis of the 6544-nucleotide large (L), 3652-nucleotide medium (M) and 1831-nucleotide small (S) segments of MUJV, as well as the amino acid sequences of their gene products, indicated that MUJV strains from different capture sites might represent genetic variants of PUUV, the prototype arvicolid rodent-borne hantavirus in Europe. Distinct geographic-specific clustering of MUJV was found in different provinces in Korea, and phylogenetic analyses revealed that MUJV and HOKV share a common ancestry with PUUV. A better understanding of the taxonomic classification and pathogenic potential of MUJV must await its isolation in cell culture. PMID:24736214

Lee, Jin Goo; Gu, Se Hun; Baek, Luck Ju; Shin, Ok Sarah; Park, Kwang Sook; Kim, Heung-Chul; Klein, Terry A.; Yanagihara, Richard; Song, Jin-Won

2014-01-01

172

The genetic polymorphisms of cathepsin S were associated with metabolic disorders in a Chinese Han population.  

PubMed

Cathepsin S (CTSS) played an important role in the etiology of cardiovascular disease and metabolic syndrome. Few studies had been reported on the association between the polymorphisms of CTSS and metabolic disorders in Asian population. Therefore we explored the association between the polymorphisms of CTSS and metabolic disorders in a Chinese Han population. The subjects were a Chinese Han cohort with 1160 participants, and the genotyping was performed with PCR-RFLP. Polymorphism rs16827671 was associated with BMI and serum total cholesterol (P=0.001; P=0.02, respectively). Subjects with CT genotype of rs16827671 had a higher risk of hypercholesterolemia (OR=1.64, 95% CI: 1.15-2.33, P=0.006) compared with TT genotype. Subjects with AG genotype of rs11576175 had lower risks of hypertriglyceridemia and borderline hypercholesterolemia (OR=0.52, 95% CI: 0.36-0.73, P=0.0001; OR=0.52, 95% CI: 0.35-0.77, P=0.001, respectively) compared with GG genotype. Compared with the haplotype TG, haplotype TA had a lower risk of hypertriglyceridemia and a higher risk of borderline hypercholesterolemia (OR=0.62, 95% CI: 0.44-0.88, P=0.002; OR=1.59, 95% CI: 1.10-2.31, P=0.008, respectively), and haplotype CA had a lower risk of hypercholesterolemia (OR=0.35, 95% CI: 0.18-0.68, P=0.002). In conclusion, we found that the genetic polymorphisms of CTSS were associated with metabolic disorders in a Chinese Han population, which would enrich the knowledge on genetic mechanisms of the pathogenesis of metabolic disorders. PMID:23747398

Ou, Zejin; Wang, Guanghai; Li, Qiang; Ma, Zuliang; Lin, Danmiao; Dai, Meng; Zou, Fei

2013-09-10

173

CCR5 gene polymorphism is a genetic risk factor for radiographic severity of rheumatoid arthritis.  

PubMed

The chemokine receptor [C-C chemokine receptor 5 (CCR5)] is expressed on diverse immune effecter cells and has been implicated in the pathogenesis of rheumatoid arthritis (RA). This study sought to determine whether single-nucleotide polymorphisms (SNPs) in the CCR5 gene and their haplotypes were associated with susceptibility to and severity of RA. Three hundred fifty-seven patients with RA and 383 healthy unrelated controls were recruited. Using a pyrosequencing assay, we examined four polymorphisms -1118 CTAT(ins) (/del) (rs10577983), 303 A>G (rs1799987), 927 C>T (rs1800024), and 4838 G>T (rs1800874) of the CCR5 gene, which were distributed over the promoter region as well as the 5' and 3' untranslated regions. No significant difference in the genotype, allele, and haplotype frequencies of the four selected SNPs was observed between RA patients and controls. CCR5 polymorphisms of -1118 CTAT(del) (P = 0.012; corrected P = 0.048) and 303 A>G (P = 0.012; corrected P = 0.048) showed a significant association with radiographic severity in a recessive model, and, as a result of multivariate logistic regression analysis, were found to be an independent predictor of radiographic severity. When we separated the erosion score from the total Sharp score, the statistical significance of CCR5 polymorphisms showed an increase; -1118 CTAT(ins) (/del) (P = 0.007; corrected P = 0.028) and 303 A>G (P = 0.007; corrected P = 0.028). Neither SNPs nor haplotypes of the CCR5 gene showed a significant association with joint space narrowing score. These results indicate that genetic polymorphisms of CCR5 are an independent risk factor for radiographic severity denoted by modified Sharp score, particularly joint erosion in RA. PMID:22924548

Han, S W; Sa, K H; Kim, S I; Lee, S I; Park, Y W; Lee, S S; Yoo, W H; Soe, J S; Nam, E J; Lee, J; Park, J Y; Kang, Y M

2012-11-01

174

Genetic diversity of gabiroba based on random amplified polymorphic DNA markers and morphological characteristics.  

PubMed

The fragmentation of the original vegetation of the Cerrado biome, caused by the expansion of agricultural areas, mainly in central-west Brazil, calls for an assessment of the native population of this vegetation, especially of the species of interest for domestication and sustainable use. The purpose of this study was to characterize the genetic diversity of 140 gabiroba mother plants (Campomanesia spp) and their progenies from 17 locations in Goiás. The morphological characteristics of the mother plants were evaluated, and the leaflets were collected for molecular analysis using 12 random amplified polymorphic DNA primers. The seed progenies of these matrices were transplanted to the field and morphologically evaluated. Distance matrices of the morphological data of the mother plants and progenies as well as the molecular data of the mother plants were constructed, and groups were formed using the Tocher method and the unweighted pair-group method based on arithmetic averages. The polymorphism level in the matrix was 90.44%. The greatest molecular distance (0.66) was observed between mother plants from Santa Rita do Araguaia and Alexânia. By the Tocher method, 10, 13, and 17 groups were formed. The morphological evaluation of the mother plants and progenies as well as the molecular analysis of the mother plants showed genetic diversity. Significant genetic variability was detected in the progenies of the gabiroba base collection planted in Campus Jataí, Goiás. PMID:23546976

de Assis, E S; Dos Reis, E F; Pinto, J F N; Contim, L A S; Dias, L A S

2013-01-01

175

Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: A meta-analysis  

PubMed Central

Various DNA alterations can be caused by exposure to environmental and endogenous carcinogens. Most of these alterations, if not repaired, can result in genetic instability, mutagenesis and cell death. DNA repair mechanisms are important for maintaining DNA integrity and preventing carcinogenesis. Recent lung cancer studies have focused on identifying the effects of single nucleotide polymorphisms (SNPs) in candidate genes, among which DNA repair genes are increasingly being studied. Genetic variations in DNA repair genes are thought to modulate DNA repair capacity and are suggested to be related to lung cancer risk. We identified a sufficient number of epidemiologic studies on lung cancer to conduct a meta-analysis for genetic polymorphisms in nucleotide excision repair pathway genes, focusing on xeroderma pigmentosum group A (XPA), excision repair cross complementing group 1 (ERCC1), ERCC2/XPD, ERCC4/XPF and ERCC5/XPG. We found an increased risk of lung cancer among subjects carrying the ERCC2 751Gln/Gln genotype (odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.14 - 1.49). We found a protective effect of the XPA 23G/G genotype (OR = 0.75, 95% CI = 0.59 - 0.95). Considering the data available, it can be conjectured that if there is any risk association between a single SNP and lung cancer, the risk fluctuation will probably be minimal. Advances in the identification of new polymorphisms and in high-throughput genotyping techniques will facilitate the analysis of multiple genes in multiple DNA repair pathways. Therefore, it is likely that the defining feature of future epidemiologic studies will be the simultaneous analysis of large samples. PMID:17299578

Kiyohara, Chikako; Yoshimasu, Kouichi

2007-01-01

176

The Significance of Genetic Polymorphisms within and between Founder Populations of Ceratitis capitata (Wied.) from Argentina  

PubMed Central

Background The Mediterranean fruit fly Ceratitis Capitata (DIPTERA: Tephritidae) is a major agricultural pest in Argentina. One main cause for the success of non-contaminant control programs based on genetic strategies is compatibility between natural and laboratory germplasms. A comprehensive characterization of the fruit fly based on genetic studies and compatibility analysis was undertaken on two founder populations from the provinces of Buenos Aires and Mendoza, used in pioneering sterile male technique control programmes in our country. The locations are 1,000 km apart from each other. Methodology/Principal Findings We compared the genetic composition of both populations based on cytological, physiological and morphological characterization. Compatibility studies were performed in order to determine the presence of isolation barriers. Results indicate that the Buenos Aires germplasm described previously is partially different from that of the Mendoza population. Both laboratory colonies are a reservoir of mutational and cytological polymorphisms. Some sexual chromosome variants such as the XL and the YL resulting from attachment of a B-chromosome to the X-chromosome or Y-chromosome behave as a lethal sex-linked factor. Our results also show incompatibility between both germplasms and pre-zygotic isolation barriers between them. Our evidence is consistent with the fact that polymorphisms are responsible for the lack of compatibility. Conclusions The genetic control mechanism should be directly produced in the germplasm of the target population in order to favour mating conditions. This is an additional requirement for the biological as well as economic success of control programs based on genetic strategies such as the sterile insect technique. The analysis of representative samples also revealed natural auto-control mechanisms which could be used in modifying pest population dynamics. PMID:19252742

Basso, Alicia; Martinez, Laura; Manso, Fanny

2009-01-01

177

Construction of a Genetic Linkage Map Based on Amplified Fragment Length Polymorphism Markers and Development of Sequence-Tagged Site Markers for Marker-Assisted Selection of the Sporeless Trait in the Oyster Mushroom (Pleurotus eryngii)  

PubMed Central

A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Quél. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection. PMID:22210222

Ueda, Jun; Obatake, Yasushi; Murakami, Shigeyuki; Fukumasa, Yukitaka; Matsumoto, Teruyuki

2012-01-01

178

Melanic through nature or nurture: genetic polymorphism and phenotypic plasticity in Harmonia axyridis  

E-print Network

Melanic through nature or nurture: genetic polymorphism and phenotypic plasticity in Harmonia56@cam.ac.uk ª 2 0 1 0 T H E A U T H O R S . J . E V O L . B I O L . 2 3 ( 2 0 1 0 ) 1 6 9 9 ­ 1 7 0 7 J O U R N A L C O M P I L A T I O N ª 2 0 1 0 E U R O P E A N S O C I E T Y F O R E V O L U T I O

Jiggins, Francis

179

Genetic and population study of a Y-linked tetranucleotide repeat DNA polymorphism with a simple non-isotopic technique  

Microsoft Academic Search

A polymorphic microsatellite (Y-27H39) based on a (GATA)n repeat was recently discovered on the short arm of the human Y chromosome. We have used a simple technique based on polymerase chain reaction amplification and native polyacrylamide gel electrophoresis followed by highly sensitive silver staining to study the inheritance, the genetic stability and the allele frequency distribution of this polymorphism in

Fabrício R. Santos; Sergio D. J. Pena; Jiirg T. Epplen

1993-01-01

180

Genetic polymorphisms in folate and alcohol metabolism and breast cancer risk: a case–control study in Thai women  

Microsoft Academic Search

Dietary folate as well as polymorphic variants in one-carbon metabolism genes may modulate risk of breast cancer through aberrant\\u000a DNA methylation and altered nucleotide synthesis and repair. Alcohol is well recognized as a risk factor for breast cancer,\\u000a and interactions with one-carbon metabolism has also been suggested. The purpose of this study is to test the hypothesis that\\u000a genetic polymorphisms

Suleeporn SangrajrangYasunori Sato; Yasunori Sato; Hiromi Sakamoto; Sumiko Ohnami; Thiravud Khuhaprema; Teruhiko Yoshida

2010-01-01

181

ENPP1\\/PC1 K121Q polymorphism and genetic susceptibility to type 2 diabetes in North Indians  

Microsoft Academic Search

Genetic susceptibility may be responsible for high prevalence of type 2 diabetes worldwide. A common missense single nucleotide\\u000a polymorphism, K121Q in the ectoenzyme nucleotide pyrophosphate phosphodiesterase (ENPP1) gene, has recently been associated with type 2 diabetes in Italian, South Indian, and American populations. The objective\\u000a of this study was to investigate the possible role of K121Q polymorphism in ENPP1 gene

Jasvinder Singh BhattiG; G. K. Bhatti; S. S. Mastana; S. Ralhan; A. Joshi; R. Tewari

2010-01-01

182

Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers.  

PubMed

Sequence-related amplified polymorphism (SRAP), amplified fragment length polymorphism (AFLP), and inter-simple sequence repeat (ISSR) markers were used to estimate the genetic diversity and relationships among Eucommia ulmoides cultivars in China. A total of 240, 192, and 150 DNA fragments were detected by 10 SRAP primer combinations, 10 AFLP primer combinations, and 10 ISSR primers, among which 89.2, 65.1, and 88.0% of the fragments were polymorphic, respectively. Cluster analysis revealed that Qinzhong No. 3, Xiaoyeci, Qinzhong No. 1, and Qinzhong No. 2 formed independent clusters. The other 15 cultivars exhibited two clusters. The results of this study will help in the selection of parents for both genome mapping and crossbreeding purposes. PMID:25366761

Li, Y; Wang, S H; Li, Z Q; Jin, C F; Liu, M H

2014-01-01

183

Genetic polymorphisms of interleukin-16 are associated with susceptibility to primary knee osteoarthritis  

PubMed Central

Interleukin-16 (IL-16) polymorphisms have been associated with various disease states, and its activity is dysregulated in synovial fibroblasts of individuals with rheumatoid arthritis. Here, the association between genetic polymorphisms in the gene encoding IL-16 and susceptibility to primary knee osteoarthritis was investigated in the Chinese Han population. The study included 228 unrelated patients, half of whom presented with primary knee osteoarthritis (OA); the remainder was healthy individuals. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to examine single nucleotide polymorphisms (SNPs) in IL16 in these patients. Statistical analysis was performed using the chi-square goodness-of-fit test, Hardy-Weinberg (H-W) equilibrium, linkage disequilibrium analysis, and logistic regression analysis. The genotype distributions of three IL16 SNPs, rs11556218, rs4778889, and rs4072111, were found to be in line with Hardy-Weinberg equilibrium criteria (P > 0.05). The single-factor logistic regression analysis showed that, compared with the T/T genotype, the T/G genotype decreased the risk of primary knee OA in rs11556218 (OR = 0.37, 95% CI = 0.18~0.82) and, compared with the C/C genotype, the C/T genotype increased the risk of primary knee OA in rs4072111 (OR = 1.83, 95% CI = 1.07~3.59). There was linkage disequilibrium between rs4778889 and rs11556218 (D= 0.592, r2 = 0.213). Finally, logistic regression analysis showed that compared to haplotype TTC, the TTT haplotype was associated with an increased risk of primary knee OA (OR = 2.10, 95% CI = 1.09-4.98); however, the GCC haplotype was associated with a reduced risk of primary knee OA (OR = 0.36, 95% CI = 0.12-0.93). Thus, the genetic polymorphisms rs11556218, rs4778889, and rs4072111 in the gene encoding IL-16 are associated with primary knee OA in Chinese Han population.

Liu, Zhibao; Ma, Li; Qiu, Shenqiang; Jia, Tanghong

2015-01-01

184

Expression levels and genetic polymorphisms of interleukin-2 and interleukin-10 as biomarkers of Graves’ disease  

PubMed Central

The aim of the present study was to determine whether the expression levels of interleukin (IL)-2 and IL-10 may be used as biological markers in Graves’ disease (GD) patients. A total of 256 individuals, including 118 GD patients and 138 healthy individuals, were enrolled into the study. Blood samples were collected from each patient and healthy individual, which were then subjected to enzyme-linked immunosorbent assay (ELISA). Total RNA and total proteins were determined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis, respectively. In addition, restriction fragment length polymorphism (RFLP) analysis was performed to detect the presence of genetic polymorphisms. The ELISA results indicated that the IL-2 and IL-10 serum levels in the GD patients were increased by ~5.2 and ~7-fold when compared with the levels in the healthy controls. The results of RT-qPCR indicated that the mRNA expression levels of IL-2 and IL-10 were upregulated in the GD patients when compared with the healthy controls. Furthermore, the western blot analysis results revealed that the protein expression levels of IL-2 and IL-10 were significantly increased in the GD patients. RFLP analysis indicated that the increased number of GG single nucleotide polymorphisms (SNPs) in the GD group were detected in the ?330 locus of the IL-2 promoter and the ?1082 locus of the IL-10 promoter. In addition, the results indicated that the relatively high rates of homozygous GG SNPs (IL-2 ?330T/G and IL-10 ?1082A/G polymorphisms) on the alleles may be associated with the incidence of GD. The serum, mRNA and protein expression levels of IL-2 and IL-10 were significantly increased in GD patients when compared with the levels in the healthy controls. In conclusion, the expression levels and genetic polymorphisms of IL-2 and IL-10 may be potential biomarkers for the incidence of Graves’ disease in the population studied. PMID:25667655

LIANG, CUIGE; DU, WENHUA; DONG, QINGYU; LIU, XIAOMENG; LI, WENXIA; WANG, YUELI; GAO, GUANQI

2015-01-01

185

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean  

PubMed Central

Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364?×?G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93?×?JALO EEP558 and DOR364?×?BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041?cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop. PMID:22734675

2012-01-01

186

Genetic polymorphisms of interleukin-16 are associated with susceptibility to primary knee osteoarthritis.  

PubMed

Interleukin-16 (IL-16) polymorphisms have been associated with various disease states, and its activity is dysregulated in synovial fibroblasts of individuals with rheumatoid arthritis. Here, the association between genetic polymorphisms in the gene encoding IL-16 and susceptibility to primary knee osteoarthritis was investigated in the Chinese Han population. The study included 228 unrelated patients, half of whom presented with primary knee osteoarthritis (OA); the remainder was healthy individuals. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to examine single nucleotide polymorphisms (SNPs) in IL16 in these patients. Statistical analysis was performed using the chi-square goodness-of-fit test, Hardy-Weinberg (H-W) equilibrium, linkage disequilibrium analysis, and logistic regression analysis. The genotype distributions of three IL16 SNPs, rs11556218, rs4778889, and rs4072111, were found to be in line with Hardy-Weinberg equilibrium criteria (P > 0.05). The single-factor logistic regression analysis showed that, compared with the T/T genotype, the T/G genotype decreased the risk of primary knee OA in rs11556218 (OR = 0.37, 95% CI = 0.18~0.82) and, compared with the C/C genotype, the C/T genotype increased the risk of primary knee OA in rs4072111 (OR = 1.83, 95% CI = 1.07~3.59). There was linkage disequilibrium between rs4778889 and rs11556218 (D= 0.592, r(2) = 0.213). Finally, logistic regression analysis showed that compared to haplotype TTC, the TTT haplotype was associated with an increased risk of primary knee OA (OR = 2.10, 95% CI = 1.09-4.98); however, the GCC haplotype was associated with a reduced risk of primary knee OA (OR = 0.36, 95% CI = 0.12-0.93). Thus, the genetic polymorphisms rs11556218, rs4778889, and rs4072111 in the gene encoding IL-16 are associated with primary knee OA in Chinese Han population. PMID:25785145

Liu, Zhibao; Ma, Li; Qiu, Shenqiang; Jia, Tanghong

2015-01-01

187

Comparative genetic analysis of tritrichomonadid protozoa by the random amplified polymorphic DNA technique.  

PubMed

The taxonomic classification within the genus Tritrichomonas is a subject of controversy, and, potentially, separation of the tritrichomonads from cattle and swine on the species level is not valid. To tackle this hypothesis we comparatively assessed several isolates of protozoan parasites from the three Tritrichomonas species T. foetus, T. suis, and T. mobilensis by the RAPD (random amplified polymorphic DNA) technique. In this method with 20 different primers, all T. foetus and T. suis isolates resulted in identical genomic fingerprints, thus yielding additional evidence for the genetic identity of T. foetus and T. suis. In contrast, it turned out that the species T. mobilensis isolated from the squirrel monkey is genetically distinct and can clearly be discriminated from the other tritrichomonads. Consequently, the results obtained in this study support a possible future revision of the taxonomic classification of the genus Tritrichomonas. PMID:9493217

Felleisen, R S

1998-01-01

188

Single strand conformation polymorphism of genomic and EST-SSRs marker and its utility in genetic evaluation of sugarcane.  

PubMed

Sugarcane is an important crop producing around 75 % of sugar in world and used as first generation biofuel. In present study, the genomic and gene based microsatellite markers were analyzed by low cost Single Strand Confirmation Polymorphism technique for genetic evaluation of 22 selected sugarcane genotypes. Total 16 genomic and 12 Expression Sequence Tag derived markers were able to amplify the selected sugarcane genotypes. Total 138 alleles were amplified of which 99 alleles (72 %) found polymorphic with an average of 4.9 alleles per locus. Microsatellite marker, VCSSR7 and VCSSR 12 showed monomorphic alleles with frequency 7.1 % over the average of 3.5 obtained for polymorphic locus. The level of Polymorphic Information Content (PIC) varied from 0.09 in VCSSR 6 to 0.88 in VCSSR 11 marker respectively with a mean of 0.49. Genomic SSRs showed more polymorphism than EST-SSRs markers on selected sugarcane genotypes whereas, the genetic similarity indices calculated by Jaccard's similarity coefficient varied from 0.55 to 0.81 indicate a high level of genetic similarity among the genotypes that was mainly attributed to intra specific diversity. Hence, the SSR-SSCP technique helped to identify the genetically diverse clones which could be used in crossing program for introgression of sugar and stress related traits in hybrid sugarcane. PMID:25049458

Kalwade, Sachin B; Devarumath, Rachayya M

2014-07-01

189

Genetic basis for GPI-anchor merozoite surface antigen polymorphism of Babesia and resulting antigenic diversity.  

PubMed

Glycosyl-phosphatidylinositol anchor merozoite surface antigens (GPI-anchor MSA) are proposed to act in the invasion process of infective merozoites of Babesia into host erythrocytes. Because of their essential function in the survival of Babesia parasites, they constitute good candidates for the development of vaccines against babesiosis and they have been extensively analyzed. These include Babesia bovis variable MSA (VMSA) and Babesia bigemina gp45/gp55 proteins of the agents of bovine babesiosis from tropical and subtropical countries, and the Babesia divergens Bd37 and Babesia canis Bc28 proteins of the main agents of bovine and canine babesiosis in Europe, respectively. However, these are very polymorphic antigens and Babesia parasites have evolved molecular mechanisms that enable these antigens to evade the host immune system as a survival strategy. This review focuses on the genetic basis of GPI-anchor MSA polymorphism and the antigenic diversity of B-cell epitopes that might be generated in each of these Babesia species. The picture is incomplete and no Babesia genome sequence is yet available. However, the available sequences suggest that two distinct, non cross-reactive GPI-anchor MSA (i.e., with unique B-cell epitopes) may be required by all Babesia species for invasion, and that these two distinct GPI-anchor MSA would be encoded by a multigene family. Furthermore, the data are consistent with the ability of biological clones from Babesia to use these multigene families for the expression of GPI-anchor MSA, either conserved (B. canis and B. bovis) or polymorphic (B. divergens and B. bigemina) in their amino acid sequence. Moreover, as a consequence for successful parasitism, the data suggest that both conserved and polymorphic GPI-anchor MSA would present unique B-cell epitopes. PMID:16551492

Carcy, Bernard; Précigout, Eric; Schetters, Theo; Gorenflot, André

2006-05-31

190

A Genetic Polymorphism in RBP4 Is Associated with Coronary Artery Disease  

PubMed Central

Insulin resistance and obesity is influenced by the retinol binding protein 4 (RBP4) adipokine. This study aims to determine if genetic polymorphisms in RBP4 are associated with the risk of coronary artery disease (CAD) in Chinese patients. RBP4 polymorphisms were analyzed by high resolution melting (HRM) analysis in a case-control study of 392 unrelated CAD patients and 368 controls from China. The Gensini score was used to determine the severity of CAD. The genotypic and allelic frequencies of RBP4 single-nucleotide polymorphisms were evaluated for associations with CAD and severity of disease. The A allele frequency was significantly higher in CAD case groups compared to control groups (16.7% vs. 8.8%) at the RBP4 rs7094671 locus. Compared to the G allele, this allele was associated with a higher risk of CAD (OR = 2.07 (1.50–2.84)). Polymorphisms at rs7094671 were found to associate with CAD using either a dominant or recessive model (OR, 95% CI: 1.97, 1.38–2.81; 3.81, 1.53–9.51, respectively). Adjusting for sex, history of smoking, serum TC, TG, LDL-c, and HDL-c, the risk of CAD for carriers remained significantly higher in both dominant and recessive models (OR, 95% CI: 1.68, 1.12–2.51; 2.74, 1.00–7.52, respectively). However, this SNP was not significantly associated with severity of CAD using angiographic scores in multivariable linear regression models (p = 0.373). The RBP4 rs7094671 SNP is associated with CAD; however, our results do not indicate that this locus is associated with clinical severity of CAD or the extent of coronary lesions. PMID:25479076

Wan, Ke; Zhao, Jianxun; Deng, Ying; Chen, Xi; Zhang, Qing; Zeng, Zhi; Zhang, Li; Chen, Yucheng

2014-01-01

191

Genetic Polymorphism G894T and the Prognosis of Heart Failure Outpatients  

PubMed Central

Background Previous studies have analyzed the role of the genetic polymorphism of endothelial nitric oxide synthase on heart failure prognosis. However, there are no studies relating the G894T and heart failure in Brazil. Objective To evaluate the association between G894T GP and the prognosis of a sample of Brazilian outpatients with heart failure. Methods Cohort study included 145 patients with systolic heart failure, followed for up to 40 months (mean = 22), at two university hospitals, in the State of Rio de Janeiro. We evaluated the relationship between G894T and the following outcomes: reverse remodeling, improvement in functional class (NYHA), and mortality and hospitalization rates. The diameters of the left atrium and ventricle, as well as the ejection fraction of the left ventricle, were evaluated at baseline and at 6 months to assess reverse remodeling. The improvement in functional class was evaluated after 6 months, and mortality rate and hospitalization were evaluated during follow-up. Race was self-declared. G894T polymorphism was analyzed by polymerase chain reaction and restriction fragment length polymorphism. Results The genotypic frequencies were GG (40%), GT (48.3%) and TT (11.7%). The allele frequency was guanine (64.1%) and thiamine (35.8%). There were no differences between the genotype or allelic frequencies according to self declared race, either as baseline characteristics. There was no relationship between genotype or allele frequency and the outcome measures. Conclusion No association was observed between the G894T polymorphism (Glu298Asp) and prognosis in this sample of Brazilian outpatients with systolic heart failure. PMID:23949326

Tardin, Oziel Marcio Araujo; Pereira, Sabrina Bernardez; Velloso, Monica Wanderley Monçores; Balieiro, Henrique Miller; Costa, Bruno; Alves, Thiago Oliveira e; Giro, Camila; Pessoa, Leandro Pontes; Ribeiro, Georgina Severo; Mesquita, Evandro Tinoco

2013-01-01

192

Mammalian flavin-containing monooxygenases: structure/function, genetic polymorphisms and role in drug metabolism  

PubMed Central

Flavin-containing monooxygenase (FMO) oxygenates drugs and xenobiotics containing a “soft-nucleophile”, usually nitrogen or sulfur. FMO, like cytochrome P450 (CYP), is a monooxygenase, utilizing the reducing equivalents of NADPH to reduce 1 atom of molecular oxygen to water, while the other atom is used to oxidize the substrate. FMO and CYP also exhibit similar tissue and cellular location, molecular weight, substrate specificity, and exist as multiple enzymes under developmental control. The human FMO functional gene family is much smaller (5 families each with a single member) than CYP. FMO does not require a reductase to transfer electrons from NADPH and the catalytic cycle of the 2 monooxygenases is strikingly different. Another distinction is the lack of induction of FMOs by xenobiotics. In general, CYP is the major contributor to oxidative xenobiotic metabolism. However, FMO activity may be of significance in a number of cases and should not be overlooked. FMO and CYP have overlapping substrate specificities, but often yield distinct metabolites with potentially significant toxicological/pharmacological consequences. The physiological function(s) of FMO are poorly understood. Three of the 5 expressed human FMO genes, FMO1, FMO2 and FMO3, exhibit genetic polymorphisms. The most studied of these is FMO3 (adult human liver) in which mutant alleles contribute to the disease known as trimethylaminuria. The consequences of these FMO genetic polymorphisms in drug metabolism and human health are areas of research requiring further exploration. PMID:15922018

Krueger, Sharon K.; Williams, David E.

2005-01-01

193

Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.  

PubMed

Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations. PMID:23872234

Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

2013-11-01

194

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard ( Brassica juncea ) and its relationship to heterosis  

Microsoft Academic Search

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism

A. Jain; S. Bhatia; S. S. Banga; S. Prakash; M. Lakshmikumaran

1994-01-01

195

Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite  

PubMed Central

Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates. PMID:20813140

Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A.; Upcroft, Jacqui; Sullivan, Steven A.; Tachezy, Jan; Carlton, Jane M.

2010-01-01

196

Genetic map of randomly amplified DNA polymorphisms closely linked to the mating type locus of tetrahymenta thermophila  

SciTech Connect

We have used the PCR-based randomly amplified polymorphic DNA (RAPD) method to efficiently identify and map DNA polymorphisms in the ciliated protozoan Tetrahymena thermophila. The polymorphisms segregate as Mendelian genetic markers. A targeted screen, using DNA from pooled meiotic segregants, yielded the polymorphisms most closely linked to the mat locus. A total of 10 polymorphisms linked to the mat-Pmr segment of the left arm of micronuclear chromosome 2 have been identified. This constitutes the largest linkage group described in T. thermophila. We also provide here the first crude estimate of the frequency of meiotic recombination in the mat region, 20 kb/cM. This frequency is much higher than that observed in most other eukaryotes. Special features of Tetrahymena genetics enhanced the power of the RAPD method: the ability to obtain in a single step meiotic segregants that are whole-genome homozygotes and the availability of nullisomic strains permitting quick deletion mapping of polymorphisms to micronuclear chromosomes or chromosomes segments. The RAPD method appears to provide a practical and relatively inexpensive approach to the construction of a high-resolution map of the Tetrahymena genome. 39 refs., 5 figs., 4 tabs.

Lynch, T.J.; Brickner, J.; Orias, E.; Nakano, K.J. [Univ. of California, Santa Barbara, CA (United States)

1995-12-01

197

Genetic polymorphisms of innate and adaptive immunity as predictors of outcome in critically ill patients.  

PubMed

Sepsis and septic shock frequently cause the admission or complicate the clinical course of critically ill patients admitted in the intensive care units (ICU). Genetic variations disrupting the immune sensing of infectious organisms, could affect the ability of the immune system to respond to infection, and may influence both the genetic predisposition to infection and the diversity of the clinical presentation of sepsis. The aim of this study was to uncover possible associations between common functional immune gene polymorphisms (of both innate and adaptive immunity) and ICU-acquired sepsis and mortality. The TLR4-D299G (rs4986790), TLR4-T399I (rs4986791), C2-c.841_849+19del28 (rs9332736), TACI-C104R (rs34557412), BAFFR-P21R (rs77874543), and BAFFR-H159Y (rs61756766) polymorphisms were detected in a cohort of 215 critically ill patients, admitted in an 8-bed medical/surgical ICU. Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated with a lower risk of ICU-acquired sepsis. This association applied particularly in medical patients, while in trauma and surgical patients no significant associations were observed. Moreover, carriers of TACI-C104R displayed an undiagnosed mild to moderate hypogammaglobulinemia along with a significantly lower survival rate in the ICU, although lethal events were not attributed to sepsis. These findings further elucidate the role that host immune genetic variations may play in the susceptibility to ICU-acquired sepsis and ICU mortality. PMID:25454804

Kompoti, Maria; Michopoulos, Alexandros; Michalia, Martha; Clouva-Molyvdas, Phyllis-Maria; Germenis, Anastasios E; Speletas, Matthaios

2015-03-01

198

miR-124 rs531564 polymorphism influences genetic susceptibility to cervical cancer  

PubMed Central

Cervical cancer is the fourth most common cancer among women worldwide. It most frequently results from human papillomavirus (HPV) infection; however, recent evidence suggests that there may be underlying genetic factors, specifically in regions encoding microRNAs, dictating susceptibility to cervical cancer. This study investigated the relationship between the miR-124 rs531564 gene polymorphism and genetic susceptibility to cervical cancer in Chinese Han women. From January 2011 to July 2013, 158 Chinese Han cervical cancer patients and 260 healthy Chinese Han females were recruited to provide blood samples. The miR-124 rs531564 (C > G) polymorphism genotype was determined by polymerase chain reaction-based ligase detection reaction (PCR-LDR), and multivariate logistic regression analysis was used to deduce the relationship between the miR-124 rs531564 variant and cancer diagnosis. As expected, the incidence of HPV infection in cervical cancer patients was significantly higher than controls (P < 0.001). Logistic regression analysis showed that a CG genotype was associated with reduced risk of cervical cancer compared to the wildtype CC genotype (OR = 0.46, 95% CI: 0.19-0.92); the findings were similar when the variant genotypes were combined (CG + GG; OR = 0.42, 95% CI: 0.17-0.86). The G allele was associated with reduced risk of cervical cancer (OR = 0.45, 95% CI: 0.14-0.89) particularly among women over age 40 (OR = 0.31, 95% CI: 0.12-0.84), as well as reduced risk of HPV infection (OR = 0.59, 95% CI: 0.28-0.93). These results further support a role for genetic susceptibility in miR-124 rs531564 in determining the risk of cervical cancer in Chinese Han women. PMID:25664118

Wu, Henghui; Zhang, Juxin

2014-01-01

199

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.  

PubMed

DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences. PMID:24958856

Qi, Ji; Chen, Yamao; Copenhaver, Gregory P; Ma, Hong

2014-07-01

200

GENETIC DIVERSITY AND STRUCTURE OF AN ESTUARINE FISH (FUNDULUS HETEROCLITIS) INDIGENOUS TO SITES ASSOCIATED WITH A HIGHLY CONTAMINATED URBAN HARBOR  

EPA Science Inventory

Intense directional selection on isolated populations can result in loss of genetic diversity, which if persistent, reduces adaptive potential and increases extinction probability. Phenotypic evidence of inherited tolerance suggests that toxic pollutants, specifically, polychlor...

201

GENETIC DIVERSITY AND STRUCTURE OF AN ESTUARINE FISH (FUNDULUS HETEROCLITUS) INDIGENOUS TO A HIGHLY CONTAMINATED URBAN HARBOR  

EPA Science Inventory

Intense directional selection on isolated populations can result in loss of genetic diversity, which if persistent, reduces adaptive potential and increases extinction probability. Phenotypic evidence of inherited tolerance suggests that toxic pollutants, specifically, polychlor...

202

A genetic polymorphism evolving in parallel in two cell compartments and in two clades  

PubMed Central

Background The enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae). PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions. Results PEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5?, exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ? Ser, Asp 503 ? Glu, and Ile 629 ? Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another?s sites which are distant in PEPCK?s structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms? cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001???P???0.006 under differing scenarios. Conclusion Our results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes? effects on function, organismal performance, and fitness. This case emphasizes the importance, for evolutionary insight, of studying gene-specific mechanisms affected by natural genetic variation as an essential complement to surveys of such variation. PMID:23311980

2013-01-01

203

Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples  

PubMed Central

Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP) in the catechol-0-methyltransferase gene (COMT rs4680) and one representative variable number of tandem repeats (VNTR) in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region) were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 ?g DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days), repeated freeze-thaw cycles (up to 6 cycles), and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using 10 ng of DNA per genotyping reaction, the obtained samples can be used for more than one hundred candidate gene assays. When saliva is collected with an absorbent device, most of the nucleic acid content remains in the device, therefore it is advisable to collect the device separately for later genetic analyses. PMID:22182470

2011-01-01

204

Genetic polymorphisms of NQO1, CYP1A1 and TPMT and susceptibility to acute lymphoblastic leukemia  

E-print Network

Genetic polymorphisms of NQO1, CYP1A1 and TPMT and susceptibility to acute lymphoblastic leukemia Acute lymphoblastic leukemia (ALL) is the major pediatric cancer in developed countries. The etiology related to environmental exposures. Keywords Leukemia Á Tunisia Á TPMT Á NQO1 Á CYP1A1 Introduction Acute

Paris-Sud XI, Université de

205

Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns  

Microsoft Academic Search

BACKGROUND: The analysis of Inter-Alu PCR patterns obtained from human genomic DNA samples is a promising technique for a simultaneous analysis of many genomic loci flanked by Alu repetitive sequences in order to detect the presence of genetic polymorphisms. Inter-Alu PCR products may be separated and analyzed by capillary electrophoresis using an automatic sequencer that generates a complex pattern of

Maurizio Cardelli; Matteo Nicoli; Armando Bazzani; Claudio Franceschi

2010-01-01

206

Impact of Erythrocyte Duffy Antigen Genetic Polymorphism on the Distribution of Gro?-T, a Novel Human CXC Chemokine  

Microsoft Academic Search

Purpose. Gro?-T, a human CXC chemokine, has been studied for its potential to mobilize stem cells. Chemokines bind specifically to receptors on target immune cells but also to a homologous erythrocyte blood group antigen, the Duffy Antigen\\/Receptor for Chemokines (DARC) that is subject to genetic polymorphism in humans. A mutation in the DARC gene is common among African Americans and

Timothy W Hepburn; LeeAnn P Tobia; Wei Shi; Timothy A McIntyre; Charles B Davis

2007-01-01

207

Intraspecific genetic structure of white sucker ( Catostomus commersoni ) in northeastern North America as revealed by mitochondrial DNA polymorphism  

Microsoft Academic Search

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to study the influence of Pleistocene glaciations on the intraspecific genetic structure and distribution of the white sucker (Catostomus commersoni )i n northeastern North America. A total of 312 white sucker from 13 populations, including a population of dwarf ecotypes (Catostomus commersoni utawana), were analysed. An average of 93 fragments

Pascale Lafontaine; Julian J. Dodson

1997-01-01

208

Twin pregnancy with complete hydatidiform mole (46,XX) and fetus (46,XY): genetic origin proved by analysis of chromosome polymorphisms  

Microsoft Academic Search

In a case of complete hydatidiform mole with fetus the genetic origins were defined by the use of chromosomal polymorphisms. The fetus had a normal 46,XY karyotype with evidence of the presence of both maternal and paternal chromosomes. The mole was 46,XX and of androgenetic origin. There was no evidence of a maternal contribution, and duplication of paternal chromosomes was

R A Fisher; D M Sheppard; S D Lawler

1982-01-01

209

Genetic diversity of Dioscorea dumetorum (Kunth) Pax using Amplified Fragment Length Polymorphisms (AFLP) and cpDNA  

Microsoft Academic Search

We have utilized Amplified Fragment Length Polymorphisms (AFLP) in conjunction with chloroplast DNA (cpDNA) sequence data to study the genetic diversity in 53 accessions of Dioscorea dumetorum from six countries in West and Central Africa. Our results provide a comparison of the two marker systems with regards to their applicability to differentiate intraspecific genotypes and the grouping of the accessions

Mubo A. Sonibare; Robert Asiedu; Dirk C. Albach

2010-01-01

210

Estimating Genetic Relationships Among Semi-Dormant and Nondormant Alfalfa Cultivars with Sequence Related Amplified Polymorphisms (SRAPs)  

Technology Transfer Automated Retrieval System (TEKTRAN)

The objective of the present study was to assess the utility of molecular marker data generated by Sequence Related Amplified Polymorphisms (SRAPs) to assess genetic relationships among semi-dormant and non-dormant modern alfalfa cultivars using bulked DNAs. Marker data was also used to examine rel...

211

Genetic relatedness among Tunisian plum cultivars by random amplified polymorphic DNA analysis and evaluation of phenotypic characters  

Microsoft Academic Search

Analysis of differentiation among local and introduced plum cultivars using morphological, pomological and RAPD markers revealed considerable genetic diversity. The phenotypic analysis shows that pomological and tree growth traits were permitted to evaluate morphological variability of plum cultivars. Ten arbitrary primers used to assay 27 cultivars revealed 143 RAPD markers. The percentage of polymorphic bands (97.28) and the resolving power

Ben Tamarzizt Hend; Baraket Ghada; Ben Mustapha Sana; Marrakchi Mohamed; Trifi Mokhtar; Salhi-Hannachi Amel

2009-01-01

212

Analysis of Single Nucleotide Polymorphisms in Three Genes Shows Evidence for Genetic Isolation of Certain Aspergillus flavus Vegetative Compatibility Groups  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic exchange among populations of asexual filamentous fungi is presumed to be limited to isolates in the same vegetative compatibility group (VCG). To test this hypothesis, we compared the distribution of single nucleotide polymorphisms (SNP's) in Aspergills flavus isolates from six different V...

213

Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm  

Technology Transfer Automated Retrieval System (TEKTRAN)

Utilization of crop diversity held in genebanks is dependent on knowledge of useful traits including those identified genotypically. Target region amplification polymorphism (TRAP) markers were used to evaluate the genetic diversity and relationship among a sample of 263 chickpea landrace germplasm ...

214

Influence of DPYD Genetic Polymorphisms on 5-Fluorouracil Toxicities in Patients with Colorectal Cancer: A Meta-Analysis  

PubMed Central

Our meta-analysis aggregated existing results from relevant studies to comprehensively investigate the correlations between genetic polymorphisms in dihydropyrimidine dehydrogenase (DPYD) gene and 5-fluorouracil (5-FU) toxicities in patients with colorectal cancer (CRC). The MEDLINE (1966?2013), the Cochrane Library Database (Issue 12, 2013), EMBASE (1980?2013), CINAHL (1982?2013), Web of Science (1945?2013), and the Chinese Biomedical Database (CBM) (1982?2013) were searched without language restrictions. Meta-analyses were conducted with the use of STATA software (Version 12.0, Stata Corporation, College Station, TX, USA). Seven clinical cohort studies with a total of 946 CRC patients met our inclusion criteria, and NOS scores of each of the included studies were ?5. Our findings showed that DPYD genetic polymorphisms were significantly correlated with high incidences of 5-FU-related toxicity in CRC patients. SNP-stratified analysis indicated that there were remarkable connections of IVS14+1G>A, 464T>A, and 2194G>A polymorphisms with the incidence of marrow suppression in CRC patients receiving 5-FU chemotherapy. Furthermore, we found that IVS14+1G>A, 496A>G, and 2194G>A polymorphisms were correlated with the incidence of gastrointestinal reaction. Ethnicity-stratified analysis also revealed that DPYD genetic polymorphisms might contribute to the development of marrow suppression and gastrointestinal reaction among Asians, but not among Caucasians. The present meta-analysis suggests that DPYD genetic polymorphisms may be correlated with the incidence of 5-FU-related toxicity in CRC patients. PMID:25614737

Li, Qiang; Liu, Ying; Zhang, Hong-Mei; Huang, Yin-Peng; Wang, Tian-Yi; Li, Dong-Sheng; Sun, Hong-Zhi

2014-01-01

215

Genetic diversity in populations of Slovak Spotted cattle based on single nucleotide polymorphisms analyses.  

PubMed

The aim of this study was to identify SNPs in leptin (LEP), leptin receptor (LEPR) and growth hormone (GH) genes in order to analyze genetic diversity of Slovak Spotted cattle. The total numbers of blood samples were taken from 353 Slovak Spotted cows originating from four farms. Genomic DNA was isolated by phenol-chloroform extraction method and analyzed by PCR-RFLP method. After digestion with restriction, enzymes were detected in whole population of cow's alleles with frequency: LEP/Sau3AI A 0.84 and B 0.16 (±0.0152); LEPR/BseGI C 0.95 and T 0.05 (±0.0089) and GH/AluI L 0.70 and V 0.30 (±0.0188). Based on the observed vs. expected genotypes frequencies populations across loci were in Hardy-Weinberg equilibrium (P\\>0.05). Predominant for SNP LEP/Sau3AI was AA genotype (0.70), for SNP LEPR/T945M CC genotype (0.91), and LL genotype (0.48) was most frequent for SNP GH/AluI. The observed heterozygosity of SNPs across populations was also transferred to the low or median polymorphic information content 0.24 (He 0.28), 0.08 (He 0.09) and 0.33 (He 0.47) for LEP, LEPR and GH genes, respectively. Within genetic variability estimating negative values of fixation indexes FIS (-0.09-0.05) and FIT (-0.07-0.03) indicating heterozygote excess were observed. The value of FST indexes (0.018-0.023) shows very low levels of genetic differentiation in allele frequencies of loci among evaluated subpopulations. The low values of genetic distances (0.0018-0.0159) indicated high genetic relatedness among animals in subpopulations caused probably by common ancestry used in breeding program at farms. PMID:24432337

Morav?íková, Nina; Trakovická, Anna; Navrátilová, Alica

2013-01-01

216

Molecular epidemiology of genetic susceptibility to gastric cancer: focus on single nucleotide polymorphisms in gastric carcinogenesis  

PubMed Central

Gastric cancer is a disease of gene-environment interactions, as suggested by the varying geographic patterns of its incidence. Even in areas with high rates of Helicobacter pylori infection, only a small proportion of infected individuals develop gastric cancer. Genetic susceptibility to gastric cancer can be investigated by common genetic variants, such as single nucleotide polymorphisms (SNPs), in various genes that regulate multiple biological pathways. The susceptibility to gastric carcinogenesis has a substantial influence on the population attributable risk by modulating the effects of environmental risk factors. Despite recent progress in the field of the molecular epidemiology of cancer, a re-evaluation of gastric cancer susceptibility and potentially functional SNPs in candidate genes is necessary, given the inconsistency of previous reported studies. This review focuses on genetic variants that contribute to the etiology of gastric cancer, particularly those SNPs involved in inflammatory response, metabolism of chemical carcinogens, DNA repair, and tumor suppression. In the future, well-designed large multicenter population-based studies will be needed to validate current findings and provide the rationale for identifying at-risk subpopulations for primary prevention of gastric cancer. PMID:19966937

Yin, Ming; Hu, Zhibin; Tan, Dongfeng; Ajani, Jaffer A.; Wei, Qingyi

2009-01-01

217

Evolution of a genetic polymorphism with climate change in a Mediterranean landscape  

PubMed Central

Many species show changes in distribution and phenotypic trait variation in response to climatic warming. Evidence of genetically based trait responses to climate change is, however, less common. Here, we detected evolutionary variation in the landscape-scale distribution of a genetically based chemical polymorphism in Mediterranean wild thyme (Thymus vulgaris) in association with modified extreme winter freezing events. By comparing current data on morph distribution with that observed in the early 1970s, we detected a significant increase in the proportion of morphs that are sensitive to winter freezing. This increase in frequency was observed in 17 of the 24 populations in which, since the 1970s, annual extreme winter freezing temperatures have risen above the thresholds that cause mortality of freezing-sensitive morphs. Our results provide an original example of rapid ongoing evolutionary change associated with relaxed selection (less extreme freezing events) on a local landscape scale. In species whose distribution and genetic variability are shaped by strong selection gradients, there may be little time lag associated with their ecological and evolutionary response to long-term environmental change. PMID:23382198

Thompson, John; Charpentier, Anne; Bouguet, Guillaume; Charmasson, Faustine; Roset, Stephanie; Buatois, Bruno; Vernet, Philippe; Gouyon, Pierre-Henri

2013-01-01

218

A second genetic polymorphism in methylenetetrahydrofolate reductase (MTHFR) associated with decreased enzyme activity.  

PubMed

A common mutation in methylenetetrahydrofolate reductase (MTHFR), C677T, results in a thermolabile variant with reduced activity. Homozygous mutant individuals (approximately 10% of North Americans) are predisposed to mild hyperhomocysteinemia, when their folate status is low. This genetic-nutrient interactive effect is believed to increase the risk for neural tube defects and vascular disease. In this communication, we characterize a second common variant in MTHFR (A1298C), an E to A substitution. Homozygosity was observed in approximately 10% of Canadian individuals. This polymorphism was associated with decreased enzyme activity; homozygotes had approximately 60% of control activity in lymphocytes. Heterozygotes for both the C677T and the A1298C mutation, approximately 15% of individuals, had 50-60% of control activity, a value that was lower than that seen in single heterozygotes for the C677T variant. No individuals were homozygous for both mutations. Additional studies of the A1298C mutation, in the absence and presence of the C677T mutation, are warranted, to adequately address the role of this new genetic variant in complex traits. A silent genetic variant, T1317C, was identified in the same exon. It was relatively infrequent (allele frequency 5%) in our study group, but was quite common in a small sample of African individuals (allele frequency 39%). PMID:9719624

Weisberg, I; Tran, P; Christensen, B; Sibani, S; Rozen, R

1998-07-01

219

Genetic Polymorphisms at TIMP3 Are Associated with Survival of Adenocarcinoma of the Gastroesophageal Junction  

PubMed Central

The poor survival of adenocarcinomas of the gastroesophageal junction (GEJ) makes them clinically important. Discovery of host genetic factors that affect outcome may guide more individualized treatment. This study tests whether constitutional genetic variants in matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP) genes are associated with outcome of GEJ adenocarcinoma. Single nucleotide polymorphisms (SNPs) at four TIMP (TIMP1-4) and three MMP genes (MMP2, MMP7 and MMP9) were genotyped in DNA samples from a prospective cohort of patients with primary adenocarcinoma of the GEJ admitted to the British Columbia Cancer Agency. Cox proportional hazards regression, with adjustment for patient, disease and treatment variables, was used to estimate the association of SNPs with survival. Genotypes for 85 samples and 48 SNPs were analyzed. Four SNPs across TIMP3, (rs130274, rs715572, rs1962223 and rs5754312) were associated with survival. Interaction analyses revealed that the survival associations with rs715572 and rs5754312 are specific and significant for 5FU+cisplatin treated patients. Sanger sequencing of the TIMP3 coding and promoter regions revealed an additional SNP, rs9862, also associated with survival. TIMP3 genetic variants are associated with survival and may be potentially useful in optimizing treatment strategies for individual patients. PMID:23527119

Bashash, Morteza; Shah, Amil; Hislop, Greg; Treml, Martin; Bretherick, Karla; Janoo-Gilani, Rozmin; Leach, Stephen; Le, Nhu

2013-01-01

220

Original article Transferrin polymorphism  

E-print Network

Original article Transferrin polymorphism of red deer in France: evidence for spatial genetic, France (Received 26 April 1993; accepted 3 January 1994) Summary - Population genetics of the transferrin at Chambord is distinguished by its elevated heterozygosity. transferrin polymorphism / Cervus elaphus

Paris-Sud XI, Université de

221

Investigating the genetic polymorphism of sheep milk proteins: a useful tool for dairy production.  

PubMed

Sheep is the second most important dairy species after cow worldwide, and especially in the Mediterranean and Middle East regions. In some countries, the difficult environmental conditions require a peculiar adaptation and, in these contexts, sheep are able to provide higher quality protein than cattle. In the least-developed countries, the amount of dairy sheep and ovine milk production is progressively increasing. In order to improve dairy productions, in particular those with local connotations, it is necessary to obtain in-depth information regarding milk quality and rheological properties. The genetic polymorphisms of milk proteins are often associated with quantitative and qualitative parameters in milk and are potential candidate markers that should be included in breeding strategies similar to those already available for cattle. Due to the current and growing interest in this topic and considering the large amount of new information, the aim of this study was to review the literature on sheep milk protein polymorphisms with a particular emphasis on recent findings in order to give scientists useful support. Moreover, the effects of different protein variants on milk yield and composition are discussed. PMID:24862201

Selvaggi, Maria; Laudadio, Vito; Dario, Cataldo; Tufarelli, Vincenzo

2014-12-01

222

A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms  

SciTech Connect

We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines--contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

Wong, G K; Hillier, L; Brandstrom, M; Croojmans, R; Ovcharenko, I; Gordon, L; Stubbs, L; Lucas, S; Glavina, T; Kaiser, P; Gunnarsson, U; Webber, C; Overton, I

2005-02-20

223

Population genetics of insertion-deletion polymorphisms in South Koreans using Investigator DIPplex kit.  

PubMed

We assessed the applicability of 30 insertion-deletion polymorphisms (INDELs) in forensic use and the level of genetic diversity in South Korea (n=373) using the Investigator DIPplex kit (Qiagen). Allele frequencies, heterozygocities, and forensic efficacy parameters were determined. No deviation from Hardy-Weinberg equilibrium was observed for any of the INDEL markers. A high level of discrimination power was observed (combined power of discrimination: 0.99999999995). The combined match probability value was 2.84 × 10(-11) and the mean typical paternity indices were 0.878. Furthermore, we found one microvariant allele at HLD93 (rs2307570) that has not been reported. We expect that these 30 loci of INDEL markers will be useful for forensic identification and paternity testing in the South Korean population. PMID:24315593

Seong, Ki Min; Park, Ji Hye; Hyun, Young Se; Kang, Pil Won; Choi, Dong Ho; Han, Myun Soo; Park, Ki Won; Chung, Ki Wha

2014-01-01

224

Genetic polymorphisms in uridine diphospho-glucuronosyltransferase 1A1 and breast cancer risk in Africans  

PubMed Central

The UDP-glucuronosylatransferase 1A1 (UGT1A1) gene is involved in the metabolism of estrogen and detoxification of potential carcinogens. The number of TA repeats in the promoter region of UGT1A1 has been linked to breast cancer risk, but results varied by race. We performed a comprehensive assessment of genetic polymorphisms in the UGT1A1 gene, and examined these polymorphisms and TA repeats in relation to breast cancer risk in a case-control study in Nigeria. 512 breast cancer cases and 226 community controls were genotyped for UGT1A1. Compared with high-activity TA repeat genotypes, the odds ratios (OR) for low-activity and moderate-activity genotypes were 0.47 (95% confidence interval CI, 0.26–0.83) and 0.64 (95% CI, 0.39–1.06), respectively, in premenopausal women (P = 0.009 for trend), but no association was observed in postmenopausal women (P = 0.24). The effect of TA repeats was also differentiated by age: the OR was 0.39 (95% CI 0.21–0.71) for low-activity genotypes and 0.58 (95% CI 0.33–1.00) for moderate-activity genotypes in women <45 years old (P = 0.002 for trend), but no association was observed in women ?45 years old (P = 0.15). Haplotype analysis showed that UGT1A1 haplotypes were highly diverse with blocked structures. We found a specific haplotype in block 2 that was significantly associated with a 2.1-fold elevated risk (95% CI 1.05–4.39; P = 0.04). In contrast with previous studies, we found low-activity TA repeat alleles were protective against breast cancer among premenopausal indigenous Africans, suggesting that the role of UGT1A1 in breast cancer development may vary by population, presumably due to different environmental and genetic modifier effects. PMID:17909964

Huo, Dezheng; Kim, Hee-Jin; Adebamowo, Clement A.; Ogundiran, Temidayo O.; Akang, Effiong E.; Campbell, Oladapo; Adenipekun, Adeniyi; Niu, Qun; Sveen, Lise; Fackenthal, James D.; Fackenthal, Donna Lee; Das, Soma; Cox, Nancy; Di Rienzo, Anna

2015-01-01

225

Association of genetic polymorphisms in the telomerase reverse transcriptase gene with prostate cancer aggressiveness.  

PubMed

Telomerase reverse transcriptase (TERT), encoded by the TERT gene, is an essential component of telomerase, essential for the maintenance of telomere DNA length, chromosomal stability and cellular immortality. The aim of the present study was to evaluate the association between common genetic variations across the TERT gene region and prostate cancer (PCa) aggressiveness in a Chinese population. A total of 12 TERT tagging single?nucleotide polymorphisms (SNPs) were genotyped on the Sequenom Mass?ARRAY iPLEX® platform in a case?case study with 1,210 Chinese patients with PCa. Unconditional logistic regression was used to investigate the association of genotypes with PCa aggressiveness, Gleason grade and risk of developing early?onset PCa. It was observed that the C allele of the TERT intron 2 SNP (rs2736100) was significantly associated with reduced risk of PCa aggressiveness [odds ratio (OR)=0.81; 95% confidence interval (CI): 0.66?0.99; P=0.037]. This allele was also significantly correlated with a reduced risk of developing a tumor with a high Gleason score (>7; OR=0.83; 95% CI: 0.70?0.99; P=0.039). The T allele of the intron 4 SNP (rs10069690) was found to be significantly associated with a decreased risk for an aggressive form of PCa (OR=0.76; 95% CI: 0.59?0.97; P=0.030). In addition, the A allele of rs10078761 located at the 3' end of the TERT gene exhibited a statistically significant association with the reduced risk of developing a higher grade disease (OR=0.48; 95% CI: 0.28?0.81; P=0.006). However, no association between TERT polymorphisms and age at diagnosis was observed in the present study. The present findings demonstrated for the first time, to the best of our knowledge, that genetic variations across the TERT gene are associated with PCa aggressiveness in a Chinese Han population. PMID:25738283

Wu, Dapeng; Yu, Hongjie; Sun, Jielin; Qi, Jun; Liu, Qiang; Li, Ruipeng; Zheng, Siqun Lily; Xu, Jianfeng; Kang, Jian

2015-07-01

226

Genetic polymorphisms in folate and homocysteine metabolism as risk factors for DNA damage.  

PubMed

Epidemiological studies indicated a role for polymorphisms in genes of folate and homocysteine (Hcy) metabolism in the etiology of neurodegenerative disease, congenital defects and coronary artery disease (CAD). This study investigated the effect of several polymorphisms [C677 T, A1298C of methylenetetrahydrofolate reductase (MTHFR) and A66G of methionine synthase reductase (MTRR) genes] on Hcy levels and DNA damage in 68 patients who underwent coronary angiography. Plasma Hcy concentrations were higher in patients with multivessel disease with respect to monovessel disease and no-CAD patients (19.4+/-2.6 vs 11.6+/-1.2 and 13.7+/-1.4 micromol/l, respectively; P=0.03). 677TT patients had higher Hcy levels than those with 677CC or 677CT genotypes (26.2+/-4.3 vs 13.1+/-1.4 and 13.0+/-1.4 micromol/l, respectively; P=0.0006). No significant associations were found between A1298C and A66G polymorphisms and plasma Hcy levels. Among patients with 677CC genotype, 66GG individuals tended to have higher levels of Hcy than 66AA homozygotes (14.5+/-1.9 vs 8.9+/-0.7 micromol/l, P=0.06). Multivessel disease patients showed an increased frequency of DNA damage, measured by the micronucleus (MN) frequency, as compared to monovessel disease and no-CAD subjects (12.5+/-1.1 vs 8.5+/-0.8 and 8.2+/-0.9, respectively; P=0.006). The MN were positively correlated with Hcy levels (r=0.33, P=0.006) and were significantly higher in subjects with the 677TT genotype compared with the 677CC or 677CT genotypes (14.4+/-2.0 vs 8.8+/-1.2 and 9.5+/-0.7, respectively; P=0.006). A1298C and A66G polymorphisms had no effect on MN frequency. However, among 677TT patients, 66GG subjects tended to have higher levels of MN than those 66AG and 66AA (18.2+/-3.6 vs 13.8+/-4.0 and 10.3+/-1.7, respectively; P=NS). Our results indicate that genetic instability may be associated with increased risk for multiple Hcy-related diseases. PMID:12939653

Botto, Nicoletta; Andreassi, Maria Grazia; Manfredi, Samantha; Masetti, Serena; Cocci, Franca; Colombo, Maria Giovanna; Storti, Simona; Rizza, Antonio; Biagini, Andrea

2003-09-01

227

Genetic Association Between PER3 Genetic Polymorphisms and Cancer Susceptibility: A Meta-Analysis.  

PubMed

The genes along the circadian pathways control and modulate circadian rhythms essential for the maintenance of physiological homeostasis through self-sustained transcription-translation feedback loops. PER3 (period 3) is a circadian pathway gene and its variants (rs1012477, 4/5-repeat) have frequently been associated with human cancer. The mixed findings, however, make the role of the 2 variants in cancer susceptibility elusive. We aimed in this article to clarify the association of PER3 variants with cancer.We collected genetic data from 8 studies, providing 6149 individuals for rs1012477 and 5241 individuals for 4/5-repeat. Based on the genotype and allele frequency, we chose the fixed-effects model to estimate risk of cancer.Overall analysis did not suggest a global role of rs1012477 in cancer susceptibility. For PER3 4/5-repeat variant, we found a moderate increase in risk of cancer among individuals with the 5-allele compared to individuals with the 4-allele, although this association was not statistically significant (homozygous model: odds ratio [OR] 1.17, 95% confidence interval [CI] 0.81-1.67; recessive model: OR 1.17, 95% CI 0.82-1.67). No substantial heterogeneity was revealed in this analysis.Our meta-analysis provides no evidence supporting a global association of PER3 genetic variants with the incidence of cancer. PMID:25837749

Geng, Peiliang; Ou, Juanjuan; Li, Jianjun; Wang, Ning; Xie, Ganfeng; Sa, Rina; Liu, Chen; Xiang, Lisha; Liang, Houjie

2015-04-01

228

Study of population genetic polymorphism and gene flow rate in Indian snow trout, Schizothorax richardsonii fish of Himalaya, India.  

PubMed

The genetic polymorphism and gene flow rate among the Indian snow trout fish population S. richadsonii from three different locations viz., Chirapani stream of Champawat district, Kosi and Gola river of Nainital district, Uttarakhand State, India were assessed by employing twenty numbers of Randomly Amplified Polymorphic DNA (RAPD) markers. The overall percent polymorphisms among these three populations were 14.76 with 6.56, 4.92 and 3.28 in Chirapani, Kosi and Gola river population, respectively. Chirapani population had higher proportion of polymorphic loci as compared to the Kosi and Gola. The higher value of genetic distance (0.1565) was obtained between Chirapani and Gola population and the lower value of genetic distance was observed between Chirapani and Kosi (0.1058) river population. The cluster analysis revealed that in the formation of two clusters, one consisted of Chirapani and Kosi and the other was Gola fish population. Gst estimates among these populations showed some extent of homogeneity with lower genetic differentiation rate between populations and further suggested that higher tolerance to mutation, as expected that RAPD bands, arose from both coding and non-coding DNA regions. The findings revealed that the rate of gene flow in three populations seemed very low i.e. highly conserved its genetic diversity in their natural waterbodies and indicative of little migration among populations (geographically isolated and not the possibilities man made interventions/introduction of similar kind of fish species). It is further concluded that the Chirapani, Kosi and Gola river populations of S. richardsonii were being conserved naturally in their habitat and the species actual genetic potential were being maintained (adaptation to local climatic conditions, reproduction, production traits and disease resistance trait etc) in their natural habitat. PMID:25522514

Sivaraman, G K; Barat, A; Ali, S; Mahanta, P C

2014-11-01

229

Genetic Diversity of Thottapalayam Virus, a Hantavirus Harbored by the Asian House Shrew (Suncus murinus) in Nepal  

PubMed Central

Despite the recent discovery of genetically divergent hantaviruses in shrews of multiple species in widely separated geographic regions, data are unavailable about the genetic diversity and phylogeography of Thottapalayam virus (TPMV), a hantavirus originally isolated from an Asian house shrew (Suncus murinus) captured in southern India more than four decades ago. To bridge this knowledge gap, the S, M, and L segments of hantavirus RNA were amplified by reverse transcription polymerase chain reaction from archival lung tissues of Asian house shrews captured in Nepal from January to September 1996. Pair-wise alignment and comparison revealed approximately 80% nucleotide and > 94% amino acid sequence similarity to prototype TPMV. Phylogenetic analyses, generated by maximum likelihood and Bayesian methods, showed geographic-specific clustering of TPMV, similar to that observed for rodent- and soricid-borne hantaviruses. These findings confirm that the Asian house shrew is the natural reservoir of TPMV and suggest a long-standing virus–host relationship. PMID:21896819

Kang, Hae Ji; Kosoy, Michael Y.; Shrestha, Sanjaya K.; Shrestha, Mrigendra P.; Pavlin, Julie A.; Gibbons, Robert V.; Yanagihara, Richard

2011-01-01

230

A genetic map of Lophopyrum ponticum chromosome 7E, harboring resistance genes to Fusarium head blight and leaf rust  

Microsoft Academic Search

The leaf rust resistance gene Lr19 and Fusarium head blight (FHB) resistance quantitative trait loci (QTL) derived from the wild wheatgrass Lophopyrum ponticum have been located on chromosome 7E. The main objectives of the present study were to develop a genetic map of chromosome\\u000a 7E and map the two resistance loci using a population of 237 F7:8 recombinant inbred lines

Xiuli Zhang; Xiaorong Shen; Yuanfeng Hao; Jinjin Cai; Herbert W. Ohm; Lingrang Kong

2011-01-01

231

Babesia canis: evidence for genetic diversity among isolates revealed by restriction fragment length polymorphism analysis.  

PubMed

The genetic diversity of B. canis was investigated by restriction fragment length polymorphism analysis. For this purpose, we identified a Babesia canis specific DNA probe named pS8. This 1.2 kbp probe can detect as low as 20 pg of B. canis DNA. Results suggest that the pS8 probe is distributed in multiple copies throughout the genome though is probably not itself internally repetitious, i.e. not structured into blocks of tandem units. This probe reveals discrete hybridizing fragments in B. canis enzyme-digested genomic DNA. RFLP patterns obtained with the pS8 probe revealed a large genetic diversity between various isolates and led us to distinguish several clones derived from a single isolate. Results suggest that for a single isolate, the fingerprints obtained reflect those of a few quantitatively dominant clones. This technique can now be routinely applied and provides a convenient tool for the characterization and the identification of B. canis isolates, strains and clones. PMID:8533020

Citard, T; Mähl, P; Boulouis, H J; Chavigny, C; Druilhe, P

1995-09-01

232

Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.  

PubMed

The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC) of guppies (Poecilia reticulata) to study the turnover rate of alleles (temporal genetic differentiation, G'(ST)). Temporal fluctuations in MHC allele frequencies can be ??order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1) overdominant selection, (2) fluctuating population size within a metapopulation, and (3) the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST) outlier analysis may obscure the signal of selection. PMID:22900006

McMullan, Mark; van Oosterhout, Cock

2012-01-01

233

Genetic imaging of the association of oxytocin receptor gene (OXTR) polymorphisms with positive maternal parenting  

PubMed Central

Background: Well-validated models of maternal behavior in small-brain mammals posit a central role of oxytocin in parenting, by reducing stress and enhancing the reward value of social interactions with offspring. In contrast, human studies are only beginning to gain insights into how oxytocin modulates maternal behavior and affiliation. Methods: To explore associations between oxytocin receptor genes and maternal parenting behavior in humans, we conducted a genetic imaging study of women selected to exhibit a wide range of observed parenting when their children were 4–6 years old. Results: In response to child stimuli during functional magnetic resonance imaging (fMRI), hemodynamic responses in brain regions that mediate affect, reward, and social behavior were significantly correlated with observed positive parenting. Furthermore, single nucleotide polymorphisms (SNPs) (rs53576 and rs1042778) in the gene encoding the oxytocin receptor were significantly associated with both positive parenting and hemodynamic responses to child stimuli in orbitofrontal cortex (OFC), anterior cingulate cortex (ACC), and hippocampus. Conclusions: These findings contribute to the emerging literature on the role of oxytocin in human social behavior and support the feasibility of tracing biological pathways from genes to neural regions to positive maternal parenting behaviors in humans using genetic imaging methods. PMID:24550797

Michalska, Kalina J.; Decety, Jean; Liu, Chunyu; Chen, Qi; Martz, Meghan E.; Jacob, Suma; Hipwell, Alison E.; Lee, Steve S.; Chronis-Tuscano, Andrea; Waldman, Irwin D.; Lahey, Benjamin B.

2013-01-01

234

Ecogenetics of mercury: from genetic polymorphisms and epigenetics to risk assessment and decision-making.  

PubMed

The risk assessment of mercury (Hg), in both humans and wildlife, is made challenging by great variability in exposure and health effects. Although disease risk arises following complex interactions between genetic ("nature") and environmental ("nurture") factors, most Hg studies thus far have focused solely on environmental factors. In recent years, ecogenetic-based studies have emerged and have started to document genetic and epigenetic factors that may indeed influence the toxicokinetics or toxicodynamics of Hg. The present study reviews these studies and discusses their utility in terms of Hg risk assessment, management, and policy and offers perspectives on fruitful areas for future research. In brief, epidemiological studies on populations exposed to inorganic Hg (e.g., dentists and miners) or methylmercury (e.g., fish consumers) are showing that polymorphisms in a number of environmentally responsive genes can explain variations in Hg biomarker values and health outcomes. Studies on mammals (wildlife, humans, rodents) are showing Hg exposures to be related to epigenetic marks such as DNA methylation. Such findings are beginning to increase understanding of the mechanisms of action of Hg, and in doing so they may help identify candidate biomarkers and pinpoint susceptible groups or life stages. Furthermore, they may help refine uncertainty factors and thus lead to more accurate risk assessments and improved decision-making. PMID:24038486

Basu, Niladri; Goodrich, Jaclyn M; Head, Jessica

2014-06-01

235

Alternative genetic foundations for a key social polymorphism in fire ants.  

PubMed Central

Little is known about the genetic foundations of colony social organization. One rare example in which a single major gene is implicated in the expression of alternative social organizations involves the presumed odorant-binding protein gene Gp-9 in fire ants. Specific amino acid substitutions in this gene invariably are associated with the expression of monogyny (single queen per colony) or polygyny (multiple queens per colony) in fire ant species of the Solenopsis richteri clade. These substitutions are hypothesized to alter the abilities of workers to recognize queens and thereby regulate their numbers in a colony. We examined whether these same substitutions underlie the monogyny/polygyny social polymorphism in the distantly related fire ant S. geminata. We found that Gp-9 coding region sequences are identical in the polygyne and monogyne forms of this species, disproving our hypothesis that one or a few specific amino acid replacements in the protein are necessary to induce transitions in social organization in fire ants. On the other hand, polygyne S. geminata differs genetically from the monogyne form in ways not mirrored in the two forms of S. invicta, a well-studied member of the S. richteri clade, supporting the conclusion that polygyny did not evolve via analogous routes in the two lineages. Specifically, polygyne S. geminata has lower genetic diversity and different gene frequencies than the monogyne form, suggesting that the polygyne form originated via a founder event from a local monogyne population. These comparative data suggest an alternative route to polygyny in S. geminata in which loss of allelic variation at genes encoding recognition cues has led to a breakdown in discrimination abilities and the consequent acceptance of multiple queens in colonies. PMID:14704171

Ross, Kenneth G; Krieger, Michael J B; Shoemaker, D DeWayne

2003-01-01

236

Alternative genetic foundations for a key social polymorphism in fire ants.  

PubMed

Little is known about the genetic foundations of colony social organization. One rare example in which a single major gene is implicated in the expression of alternative social organizations involves the presumed odorant-binding protein gene Gp-9 in fire ants. Specific amino acid substitutions in this gene invariably are associated with the expression of monogyny (single queen per colony) or polygyny (multiple queens per colony) in fire ant species of the Solenopsis richteri clade. These substitutions are hypothesized to alter the abilities of workers to recognize queens and thereby regulate their numbers in a colony. We examined whether these same substitutions underlie the monogyny/polygyny social polymorphism in the distantly related fire ant S. geminata. We found that Gp-9 coding region sequences are identical in the polygyne and monogyne forms of this species, disproving our hypothesis that one or a few specific amino acid replacements in the protein are necessary to induce transitions in social organization in fire ants. On the other hand, polygyne S. geminata differs genetically from the monogyne form in ways not mirrored in the two forms of S. invicta, a well-studied member of the S. richteri clade, supporting the conclusion that polygyny did not evolve via analogous routes in the two lineages. Specifically, polygyne S. geminata has lower genetic diversity and different gene frequencies than the monogyne form, suggesting that the polygyne form originated via a founder event from a local monogyne population. These comparative data suggest an alternative route to polygyny in S. geminata in which loss of allelic variation at genes encoding recognition cues has led to a breakdown in discrimination abilities and the consequent acceptance of multiple queens in colonies. PMID:14704171

Ross, Kenneth G; Krieger, Michael J B; Shoemaker, D DeWayne

2003-12-01

237

Short Communication: Fc Gamma Receptors IIa and IIIa Genetic Polymorphisms Do Not Predict HIV-1 Disease Progression in Kenyan Women.  

PubMed

Genetic polymorphisms of the Fc gamma receptors (Fc?R) IIa and IIIa have been implicated in the rate of HIV-1 disease progression, but results are inconsistent. We aimed to determine the association between these polymorphisms and disease progression in a cohort of HIV-1 seroconverters from Mombasa, Kenya. Neither Fc?RIIa nor Fc?RIIIa genotypes were predictive of set point viral load, viral load increase, CD4 decline, or HIV-1 disease progression (time to CD4 count <200 cells/mm(3), death, or treatment initiation). Our results suggest that Fc?R polymorphisms might not be an important indicator of viral control and disease progression in this population. PMID:25312792

Weis, Julie F; McClelland, R Scott; Jaoko, Walter; Mandaliya, Kishor N; Overbaugh, Julie; Graham, Susan M

2015-03-01

238

The role of genetic polymorphisms of the Renin–Angiotensin System in renal diseases: A meta-analysis  

PubMed Central

Renal failure has a complex phenotype resulting from an underlying kidney disease as well as environmental and genetic factors. In the present study we performed a systematic review and meta-analyses to evaluate the association of the A1166C polymorphism of Angiotensin II type 1 Receptor gene (AGTR1) with Chronic Kidney Disease (CKD), End Stage Renal Disease (ESRD), IgA Nephropathy (IgAN) and Vesicoureteral Reflux (VUR) as well as the association of A1332G polymorphism of Angiotensin II type 2 Receptor (AGTR2) gene with Vesicoureteral Reflux (VUR). We found that neither AGTR1 ?1166C, nor AGTR2 A1332G polymorphisms were significantly associated with any of the aforementioned renal diseases, suggesting that they cannot be used as predictive markers in either general or subgroup ethnic populations. PMID:25210592

Braliou, Georgia G.; Grigoriadou, Athina-Maria G.; Kontou, Panagiota I.; Bagos, Pantelis G.

2014-01-01

239

Lung Adenocarcinoma of Never Smokers and Smokers Harbor Differential Regions of Genetic Alteration and Exhibit Different Levels of Genomic Instability  

PubMed Central

Recent evidence suggests that the observed clinical distinctions between lung tumors in smokers and never smokers (NS) extend beyond specific gene mutations, such as EGFR, EML4-ALK, and KRAS, some of which have been translated into targeted therapies. However, the molecular alterations identified thus far cannot explain all of the clinical and biological disparities observed in lung tumors of NS and smokers. To this end, we performed an unbiased genome-wide, comparative study to identify novel genomic aberrations that differ between smokers and NS. High resolution whole genome DNA copy number profiling of 69 lung adenocarcinomas from smokers (n?=?39) and NS (n?=?30) revealed both global and regional disparities in the tumor genomes of these two groups. We found that NS lung tumors had a greater proportion of their genomes altered than those of smokers. Moreover, copy number gains on chromosomes 5q, 7p, and 16p occurred more frequently in NS. We validated our findings in two independently generated public datasets. Our findings provide a novel line of evidence distinguishing genetic differences between smoker and NS lung tumors, namely, that the extent of segmental genomic alterations is greater in NS tumors. Collectively, our findings provide evidence that these lung tumors are globally and genetically different, which implies they are likely driven by distinct molecular mechanisms. PMID:22412972

Thu, Kelsie L.; Vucic, Emily A.; Chari, Raj; Zhang, Wei; Lockwood, William W.; English, John C.; Fu, Rong; Wang, Pei; Feng, Ziding; MacAulay, Calum E.; Gazdar, Adi F.; Lam, Stephen; Lam, Wan L.

2012-01-01

240

Association of interleukin-4 genetic polymorphisms with sporadic Alzheimer's disease in Chinese Han population.  

PubMed

Cytokine interleukin-4 (IL-4) is thought to play a role in the pathogenesis of Alzheimer's disease (AD). This study aimed to evaluate the potential association between single nucleotide polymorphisms (SNP) of IL-4 gene and AD susceptibility. This case-control study was conducted in Chinese Han populations consisting of 203 AD patients and 205 controls. Three common SNPs of IL-4 gene, including -590C>T (rs2243250), -33C>T (rs2070874), and -1098T>G (rs2243248), were determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and verified using DNA sequencing methods. Our data show that -590C and -1098G alleles of IL-4 were more common in AD patients (30.5% vs 22.2% p=0.007; 14.3% vs 3.4% p<0.0001) and significantly associated with elevated risk for AD (OR=1.51 95% CI 1.05-2.23; OR=4.78 95% CI 2.37-7.67). Haplotype analysis revealed five common haplotypes CCG (OR=4.41), CCT (OR=1.22), TTT (OR=1.02), CTT (OR=0.7), and TCT (OR=0.14), from highest to lowest risk for AD. None of the associations appeared to be modified by APOE ?4 genetic variant. Bioinformatic analysis shows that -590C>T and -1098T>G have a linkage disequilibrium (LD) with multiple potentially functional SNPs inside IL-4 gene. Our findings indicate that the -590C and -1098G alleles located in the promoter of IL-4 may increase the susceptibility to AD among the Han Chinese and might be used as molecular markers for AD risk evaluation. PMID:24463336

Li, Wei; Qian, Xiaohua; Teng, Hong; Ding, Ying; Zhang, Li

2014-03-20

241

Correlation of IL-1F genetic polymorphisms with the risk of colorectal cancer among Chinese populations.  

PubMed

Inflammatory/immune cells have the power of infiltrating almost all human solid tumors and influencing all stages of carcinogenesis because of their stimulation of various cytokine subsets. This study aims to determine the correlation of single nucleotide polymorphisms in the IL-17F gene and the risk of colorectal cancer (CRC). One thousand patients diagnosed with CRC and a control group of 354 healthy controls were involved. Peripheral blood samples were collected. The PCR-RFLP method was used to detect the 7383A>G (rs2397084) and 7488T>C (rs763780) in the IL-17F gene. Statistical analyses were conducted with version 12.0 STATA statistical software. We found that the allele model suggested that patients carrying C allele were 1.67 times more likely to develop CRC than healthy controls (odds ratio (OR)?=?1.67, 95% confidence interval (CI)?=?1.22-2.27, P?=?0.001). Similarly, the homozygous and dominant models also revealed that the minor IL-17F 7488C allele conferred an increased CRC risk compared to the major T allele among our study participants (CC vs. TT: OR?=?4.15, 95% CI?=?1.26-13.36, P?=?0.011; TC+CC vs. TT: OR?=?1.46, 95% CI?=?1.04-2.05, P?=?0.027). However, all genetic models indicated that the IL-17F 7383A>G (rs2397084) polymorphism was not associated with CRC risk (all P?>?0.05). The results of this study indicate that the 7488T>C (rs763780) in the IL-17F gene may be correlated with increased risk of CRC. PMID:25296730

Ma, Ming; Jin, Guo-Jiang; Yun, Ke; Mu, Run-Qing; Zhao, Min; Yu, Xiao-Ou; Wang, Shuo; Shang, Hong

2015-02-01

242

Genetic polymorphisms in metabolic enzymes and susceptibility to anti-tuberculosis drug-induced hepatic injury.  

PubMed

We examined the relationships between N-transacetylase 2 (NAT2), cytochrome P450 (CYP) 2E1 enzyme, glutathione S-transferase M1, T1 (GSTM1/GSTT1) gene polymorphisms, and anti-tuberculosis drug-induced hepatic injury (ADIH). A one-to-one matched case-control study was carried out using clinical data. NAT2, CYP2E1, GSTM1, and GSTT1 polymorphisms were identified in 173 pairs of research subjects. Statistical analysis was performed to determine risk factors of ADIH. The results showed that low body mass index and alcohol consumption were risk factors of ADIH, with odds ratios of 6.852 and 3.203, respectively. The frequencies of NAT2 slow acetylator, CYP2E1 -1259G>C, -1019C>T wild-type, and the GSTM1 null genotype were higher in the case group than in the control group, with odds ratios of 2.260, 2.696, 4.714, and 2.440, respectively. GSTT1 was not found to be related to ADIH. Interactive analysis showed that NAT2 slow acetylator and the GSTM1 null genotype were mutually synergistic, while an antagonistic relationship was observed between the CYP2E1 wild-type genotype and the other 3 genetic types. The risks of hepatic injury were higher after anti-tuberculosis therapy in patients carrying the NAT2 slow acetylator, CYP2E1 -1259G>C, -1019C>T wild-type, and GSTM1 null genotype. PMID:25501156

Feng, F M; Guo, M; Chen, Y; Li, S M; Zhang, P; Sun, S F; Zhang, G S

2014-01-01

243

Genetics of VEGF Serum Variation in Human Isolated Populations of Cilento: Importance of VEGF Polymorphisms  

PubMed Central

Vascular Endothelial Growth Factor (VEGF) is the main player in angiogenesis. Because of its crucial role in this process, the study of the genetic factors controlling VEGF variability may be of particular interest for many angiogenesis-associated diseases. Although some polymorphisms in the VEGF gene have been associated with a susceptibility to several disorders, no genome-wide search on VEGF serum levels has been reported so far. We carried out a genome-wide linkage analysis in three isolated populations and we detected a strong linkage between VEGF serum levels and the 6p21.1 VEGF region in all samples. A new locus on chromosome 3p26.3 significantly linked to VEGF serum levels was also detected in a combined population sample. A sequencing of the gene followed by an association study identified three common single nucleotide polymorphisms (SNPs) influencing VEGF serum levels in one population (Campora), two already reported in the literature (rs3025039, rs25648) and one new signal (rs3025020). A fourth SNP (rs41282644) was found to affect VEGF serum levels in another population (Cardile). All the identified SNPs contribute to the related population linkages (35% of the linkage explained in Campora and 15% in Cardile). Interestingly, none of the SNPs influencing VEGF serum levels in one population was found to be associated in the two other populations. These results allow us to exclude the hypothesis that the common variants located in the exons, intron-exon junctions, promoter and regulative regions of the VEGF gene may have a causal effect on the VEGF variation. The data support the alternative hypothesis of a multiple rare variant model, possibly consisting in distinct variants in different populations, influencing VEGF serum levels. PMID:21347390

Ruggiero, Daniela; Dalmasso, Cyril; Nutile, Teresa; Sorice, Rossella; Dionisi, Laura; Aversano, Mario; Bröet, Philippe; Leutenegger, Anne-Louise; Bourgain, Catherine; Ciullo, Marina

2011-01-01

244

Prediction Formulas for Individual Opioid Analgesic Requirements Based on Genetic Polymorphism Analyses  

PubMed Central

Background The analgesic efficacy of opioids is well known to vary widely among individuals, and various factors related to individual differences in opioid sensitivity have been identified. However, a prediction model to calculate appropriate opioid analgesic requirements has not yet been established. The present study sought to construct prediction formulas for individual opioid analgesic requirements based on genetic polymorphisms and clinical data from patients who underwent cosmetic orthognathic surgery and validate the utility of the prediction formulas in patients who underwent major open abdominal surgery. Methods To construct the prediction formulas, we performed multiple linear regression analyses using data from subjects who underwent cosmetic orthognathic surgery. The dependent variable was 24-h postoperative or perioperative fentanyl use, and the independent variables were age, gender, height, weight, pain perception latencies (PPL), and genotype data of five single-nucleotide polymorphisms (SNPs). To examine the utility of the prediction formulas, we performed simple linear regression analyses using subjects who underwent major open abdominal surgery. Actual 24-h postoperative or perioperative analgesic use and the predicted values that were calculated using the multiple regression equations were incorporated as dependent and independent variables, respectively. Results Multiple linear regression analyses showed that the four SNPs, PPL, and weight were retained as independent predictors of 24-h postoperative fentanyl use (R2 = 0.145, P = 5.66 × 10-10) and the two SNPs and weight were retained as independent predictors of perioperative fentanyl use (R2 = 0.185, P = 1.99 × 10-15). Simple linear regression analyses showed that the predicted values were retained as an independent predictor of actual 24-h postoperative analgesic use (R2 = 0.033, P = 0.030) and perioperative analgesic use (R2 = 0.100, P = 1.09 × 10-4), respectively. Conclusions We constructed prediction formulas, and the possible utility of these prediction formulas was found in another type of surgery. PMID:25615449

Yoshida, Kaori; Nishizawa, Daisuke; Ichinomiya, Takashi; Ichinohe, Tatsuya; Hayashida, Masakazu; Fukuda, Ken-ichi; Ikeda, Kazutaka

2015-01-01

245

Relationships between genetic polymorphisms in inflammation-related factor gene and the pathogenesis of nasopharyngeal cancer.  

PubMed

Our study aims to discuss the association between inflammation-related factors such as single nucleotide polymorphisms (SNPs) with susceptibility and recurrence in nasopharyngeal carcinoma. We used Taqman real-time polymerase chain reaction (PCR) to characterize the genetic variation of five SNPs in 194 nasopharyngeal carcinoma patients and 231 healthy subjects. All statistical analysis is performed with statistical product and service solutions v13.0; odds ratio (OR) value and 95 % confidence interval (CI) were calculated. There is no relationship between TGF?1 -869 T/C, IL-6 -634C/G, TGF?1 -509C/T, IL1 -511C/T and nasopharyngeal carcinoma susceptibility. Both single factor and multiple factors analysis showed that IL1a -889 T/T genotype is significantly associated with nasopharyngeal carcinoma in decreasing the risk of nasopharyngeal carcinoma. A highly significant association was found between IL1a -889 T/T genotype and protective genotype as defined by various pathological types. This is more obvious in the protective genotype of the non-keratin-type squamous carcinoma undifferentiated type. We also discovered that genotype G/G and C/G?+?G/G of IL6 -634 gene are associated with reduced recurrence of nasopharyngeal carcinoma. IL1a -889 gene polymorphism and susceptibility is related to nasopharyngeal carcinoma and can potentially decrease the risk of nasopharyngeal carcinoma in the Han Chinese population in north China. IL1-889 TT genotype is protective genotype for nasopharyngeal carcinoma. We have provided evidence that the GG genotype of the IL6 -634 gene is associated with recurrent risk of nasopharyngeal carcinoma. The G allele is the protective gene of nasopharyngeal carcinoma recurrence. PMID:24952889

Qu, Yan-Li; Yu, Hong; Chen, Yan-Zhi; Zhao, Yu-Xia; Chen, Guang-Jun; Bai, Lu; Liu, Dan; Su, Hong-Xin; Wang, He-Tong

2014-09-01

246

Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms.  

PubMed

Vascular Endothelial Growth Factor (VEGF) is the main player in angiogenesis. Because of its crucial role in this process, the study of the genetic factors controlling VEGF variability may be of particular interest for many angiogenesis-associated diseases. Although some polymorphisms in the VEGF gene have been associated with a susceptibility to several disorders, no genome-wide search on VEGF serum levels has been reported so far. We carried out a genome-wide linkage analysis in three isolated populations and we detected a strong linkage between VEGF serum levels and the 6p21.1 VEGF region in all samples. A new locus on chromosome 3p26.3 significantly linked to VEGF serum levels was also detected in a combined population sample. A sequencing of the gene followed by an association study identified three common single nucleotide polymorphisms (SNPs) influencing VEGF serum levels in one population (Campora), two already reported in the literature (rs3025039, rs25648) and one new signal (rs3025020). A fourth SNP (rs41282644) was found to affect VEGF serum levels in another population (Cardile). All the identified SNPs contribute to the related population linkages (35% of the linkage explained in Campora and 15% in Cardile). Interestingly, none of the SNPs influencing VEGF serum levels in one population was found to be associated in the two other populations. These results allow us to exclude the hypothesis that the common variants located in the exons, intron-exon junctions, promoter and regulative regions of the VEGF gene may have a causal effect on the VEGF variation. The data support the alternative hypothesis of a multiple rare variant model, possibly consisting in distinct variants in different populations, influencing VEGF serum levels. PMID:21347390

Ruggiero, Daniela; Dalmasso, Cyril; Nutile, Teresa; Sorice, Rossella; Dionisi, Laura; Aversano, Mario; Bröet, Philippe; Leutenegger, Anne-Louise; Bourgain, Catherine; Ciullo, Marina

2011-01-01

247

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species.  

PubMed

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. PMID:25750860

Satya, Pratik; Karan, Maya; Jana, Sourav; Mitra, Sabyasachi; Sharma, Amit; Karmakar, P G; Ray, D P

2015-02-01

248

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species  

PubMed Central

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. PMID:25750860

Satya, Pratik; Karan, Maya; Jana, Sourav; Mitra, Sabyasachi; Sharma, Amit; Karmakar, P.G.; Ray, D.P.

2015-01-01

249

Insertion-deletion polymorphisms in 3? regions of maize genes occur frequently and can be used as highly informative genetic markers  

Microsoft Academic Search

Single-nucleotide polymorphisms (SNPs) are the most frequent variations in the genome of any organism. SNP discovery approaches such as resequencing or data mining enable the identification of insertion deletion (indel) polymorphisms. These indels can be treated as biallelic markers and can be utilized for genetic mapping and diagnostics. In this study 655 indels have been identified by resequencing 502 maize

Dinakar Bhattramakki; Maureen Dolan; Mike Hanafey; Robin Wineland; Dave Vaske; James C. Register; Scott V. Tingey; Antoni Rafalski

2002-01-01

250

Effects of genetic polymorphisms of UCP2 and UCP3 on very low calorie diet-induced body fat reduction in Korean female subjects  

Microsoft Academic Search

The uncoupling protein (UCP) family has been suggested as a possible determinant affecting obesity risk given their function in the regulation of energy metabolism. In an effort to elucidate the effects of UCP family polymorphisms on obesity phenotypes, we genotyped 10 polymorphisms in UCP2 and UCP3 among overweight female subjects (n=458), and genetic effects on BMI and changes after a

Yoosik Yoon; Byung Lae Park; Min Ho Cha; Kil Soo Kim; Hyun Sub Cheong; Yoo Hyun Choi; Hyoung Doo Shin

2007-01-01

251

A regimen combining the Wee1 inhibitor AZD1775 with HDAC inhibitors targets human acute myeloid leukemia cells harboring various genetic mutations.  

PubMed

AZD1775 targets the cell cycle checkpoint kinase Wee1 and potentiates genotoxic agent cytotoxicity through p53-dependent or -independent mechanisms. Here, we report that AZD1775 interacted synergistically with histone deacetylase inhibitors (HDACIs, for example, Vorinostat), which interrupt the DNA damage response, to kill p53-wild type (wt) or -deficient as well as FLT3-ITD leukemia cells in association with pronounced Wee1 inhibition and diminished cdc2/Cdk1 Y15 phosphorylation. Similarly, Wee1 shRNA knockdown significantly sensitized cells to HDACIs. Although AZD1775 induced Chk1 activation, reflected by markedly increased Chk1 S296/S317/S345 phosphorylation leading to inhibitory T14 phosphorylation of cdc2/Cdk1, these compensatory responses were sharply abrogated by HDACIs. This was accompanied by premature mitotic entry, multiple mitotic abnormalities and accumulation of early S-phase cells displaying increased newly replicated DNA, culminating in robust DNA damage and apoptosis. The regimen was active against patient-derived acute myelogenous leukemia (AML) cells harboring either wt or mutant p53 and various next-generation sequencing-defined mutations. Primitive CD34(+)/CD123(+)/CD38(-) populations enriched for leukemia-initiating progenitors, but not normal CD34(+) hematopoietic cells, were highly susceptible to this regimen. Finally, combining AZD1775 with Vorinostat in AML murine xenografts significantly reduced tumor burden and prolonged animal survival. A strategy combining Wee1 with HDACI inhibition warrants further investigation in AML with poor prognostic genetic aberrations. PMID:25283841

Zhou, L; Zhang, Y; Chen, S; Kmieciak, M; Leng, Y; Lin, H; Rizzo, K A; Dumur, C I; Ferreira-Gonzalez, A; Dai, Y; Grant, S

2015-04-01

252

Upper petal lip colour polymorphism in Collinsia heterophylla (Plantaginaceae): genetic basis within a population and its use as a genetic marker.  

PubMed

Understanding the genetics of a polymorphic trait is important to predict its likely evolution. In Collinsia heterophylla, the upper petal lip colour can be either be white or white with a purple band, while the lower petal lip colour is invariably purple. Because the corolla is only partly polymorphic, the polymorphism can not have evolved due to a mutation where a pigment was lost in the entire plant, which is common in other polymorphic species. In a previous study, high frequency of the purple band was found in populations with darker flowers, indicating possible selection for this trait. In this study, I determined inheritance of the colour polymorphism using two populations (one with only white morph and other with both morphs). I conducted experimental crosses within and between floral morphs to determine whether patterns of segregation in offspring conform to single-gene predictions. Data from F1, F2, F3 and backcross progeny are consistent with a genetic model of one major locus with presence of the band being completely dominant, as indicated in earlier studies using distantly related populations. A novel finding in this study was that the two morphs did not show a difference in seed germination frequency or seedling survival. This trait can thus be valuable as a genetic marker. Even though more thorough ecological data are needed to understand the potential selection pressures on upper petal lip colour in C. heterophylla, its simple inheritance may indicate the possibility of fast evolutionary response to selective forces acting on this trait. PMID:19700859

Lankinen, Asa

2009-08-01

253

Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species.  

PubMed Central

Direct amplification of length polymorphisms (DALP) uses an arbitrarily primed PCR (AP-PCR) to produce genomic fingerprints and to enable sequencing of DNA polymorphisms in virtually any species. Oligonucleotide pairs were designed to each produce a specific multi-banded pattern and all the fragments thus generated can be directly sequenced with the same two universal M13 sequencing primers. This strategy combines the advantages of a high resolution fingerprint technique and the possibility of characterizing the polymorphisms. The use of family members as templates in the multi-locus detection step allows a direct test of allele transmission, as well as early mapping of the markers or selection of loci associated with some traits or diseases. We used this method to detect micro-deletions/insertions and microsatellite DNA loci useful in population genetics studies, but it could be applied in many other fields of biology, such as genome mapping for definition of polymorphic sequence tagged sites, directly localized on a genetic map. PMID:9490792

Desmarais, E; Lanneluc, I; Lagnel, J

1998-01-01

254

Genetic Polymorphisms of Interleukin-1 Alpha and the Vitamin D Receptor in Mexican Mestizo Patients with Intervertebral Disc Degeneration  

PubMed Central

Intervertebral disc degeneration (IDD) is the most common diagnosis in patients with back pain, a leading cause of musculoskeletal disability worldwide. Several conditions, such as occupational activities, gender, age, and obesity, have been associated with IDD. However, the development of this disease has strong genetic determinants. In this study, we explore the possible association between rs1800587 (c.-949C>T) of interleukin-1 alpha (IL1A) and rs2228570 (c.2T>V) and rs731236 (c.1056T>C) of vitamin D receptor (VDR) gene polymorphisms and the development of IDD in northwestern Mexican Mestizo population. Gene polymorphisms were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism, in two groups matched by age and gender: patients with symptomatic lumbar IDD (n = 100) and subjects with normal lumbar-spine MRI-scans (n = 100). Distribution of the mutated alleles in patients and controls was 27.0% versus 28.0% (P = 0.455) for T of rs1800587 (IL1A); 53.0% versus 58.0% (P = 0.183) for V of rs2228570 (VDR); and 18.0% versus 21.0% (P = 0.262) for C of rs731236 (VDR). Our results showed no association between the studied polymorphisms and IDD in this population. This is the first report on the contribution of gene polymorphisms on IDD in a Mexican population. PMID:25506053

Cervin Serrano, Salvador; González Villareal, Dalia; Aguilar-Medina, Maribel; Romero-Navarro, Jose Guillermo; Romero Quintana, Jose Geovanni; Arámbula Meraz, Eliakym; Osuna Ramírez, Ignacio; Picos-Cárdenas, Veronica; Granados, Julio; Estrada-García, Iris; Sánchez-Schmitz, Guzman; Ramos-Payán, Rosalío

2014-01-01

255

Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle  

Microsoft Academic Search

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing\\u000a methods, a new allelic variant corresponding to the A ? G mutation (aspartic to glycine amino acid replacement) of the bovine\\u000a CACNA2D1 gene was detected. Two alleles and three

Guan-Yu HouZheng-Rong; Zheng-Rong Yuan; Xue Gao; Jun-Ya Li; Hui-Jiang Gao; Jin-Bao Chen; Shang-Zhong Xu

2010-01-01

256

Common genetic polymorphisms in the promoter of resistin gene are major determinants of plasma resistin concentrations in humans  

Microsoft Academic Search

Aims\\/hypothesis  Resistin is thought to be an important link between obesity and insulin resistance. It has been suggested that genetic polymorphism in the promoter of resistin gene is a determinant of resistin mRNA expression and possibly associated with obesity and insulin resistance. In this study, we investigated the association between the genotype of resistin promoter and its plasma concentrations.Methods  We examined g.-537A>C

Y. M. Cho; B.-S. Youn; S. S. Chung; K. W. Kim; H. K. Lee; K.-Y. Yu; H. J. Park; H. D. Shin; K. S. Park

2004-01-01

257

Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits  

Microsoft Academic Search

An analysis of 11 Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans; Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting

David Comas; Francesc Calafell; Noufissa Benchemsi; Ahmed Helal; Gerard Lefranc; Mark Stoneking; Mark A. Batzer; Jaume Bertranpetit; Antti Sajantila

2000-01-01

258

Evaluation of the Association between the AC3 Genetic Polymorphisms and Obesity in a Chinese Han Population  

Microsoft Academic Search

BackgroundAC3 is one of adenylyl cyclase isoforms involved in cAMP and insulin signaling pathway. Recent reports have demonstrated that the AC3 genetic polymorphisms are associated with obesity in a Swedish population. AC3 knock out mice exhibit obese when they age. These findings suggest that AC3 plays an important role in the regulation of body weight.Methodology\\/Principal FindingsIn the present study, we

Hairu Wang; Ming Wu; Weiguang Zhu; Jin Shen; Xiaoming Shi; Jie Yang; Qihui Zhao; Chuan Ni; Yaochu Xu; Hongbing Shen; Chong Shen; Harvest F. Gu; Adrian Vella

2010-01-01

259

Associations between genetic polymorphisms of Phase I and II metabolizing enzymes, p53 and susceptibility to esophageal adenocarcinoma  

Microsoft Academic Search

The objectives of this exploratory case–control study were to evaluate whether genetic polymorphisms of selected Phase I and II metabolizing enzymes are associated with the risk of developing primary esophageal adenocarcinoma, and to investigate potential associations between genotypes and p53 tumor suppressor gene alterations. Cases comprised 45 patients with surgically resected esophageal adenocarcinomas, defined according to strict clinico-pathologic criteria. PCR-based

A. G Casson; Z Zheng; D Chiasson; K MacDonald; D. C Riddell; J. R Guernsey; D. L Guernsey; J McLaughlin

2003-01-01

260

Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.  

PubMed

Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin. PMID:25730081

Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

2015-01-01

261

Alternans in Genetically Modified Langendorff-Perfused Murine Hearts Modeling Catecholaminergic Polymorphic Ventricular Tachycardia  

PubMed Central

The relationship between alternans and arrhythmogenicity was studied in genetically modified murine hearts modeling catecholaminergic polymorphic ventricular tachycardia (CPVT) during Langendorff perfusion, before and after treatment with catecholamines and a ?-adrenergic antagonist. Heterozygous (RyR2p/s) and homozygous (RyR2s/s) RyR2-P2328S hearts, and wild-type (WT) controls, were studied before and after treatment with epinephrine (100?nM and 1 ?M) and propranolol (100?nM). Monophasic action potential recordings demonstrated significantly greater incidences of arrhythmia in RyR2p/s and RyR2s/s hearts as compared to WTs. Arrhythmogenicity in RyR2s/s hearts was associated with alternans, particularly at short baseline cycle lengths. Both phenomena were significantly accentuated by treatment with epinephrine and significantly diminished by treatment with propranolol, in full agreement with clinical expectations. These changes took place, however, despite an absence of changes in mean action potential durations, ventricular effective refractory periods or restitution curve characteristics. Furthermore pooled data from all hearts in which arrhythmia occurred demonstrated significantly greater alternans magnitudes, but similar restitution curve slopes, to hearts that did not demonstrate arrhythmia. These findings thus further validate the RyR2-P2328S murine heart as a model for human CPVT, confirming an alternans phenotype in common with murine genetic models of the Brugada syndrome and the congenital long-QT syndrome type 3. In contrast to these latter similarities, however, this report demonstrates the dissociation of alternans from changes in the properties of restitution curves for the first time in a murine model of a human arrhythmic syndrome. PMID:21423368

Sabir, Ian N.; Ma, Nan; Jones, Victoria J.; Goddard, Catharine A.; Zhang, Yanmin; Kalin, Asli; Grace, Andrew A.; Huang, Christopher L.-H.

2010-01-01

262

Association of Genetic Polymorphisms with Warfarin Dose Requirements in Chinese Patients  

PubMed Central

Objective: Warfarin is a commonly used anticoagulant with a narrow therapeutic range and large interindividual differences in dosing requirements. Previously, studies have identified that the interindividual variability was influenced by varieties of factors, including age, body size, vitamin K intake, interacting medications, as well as genetic variants. We aimed to investigate the effect of single-nucleotide polymorphisms (SNPs) on the interindividual variability of warfarin dose requirements in Chinese patients. Methods: The study population consisted of 300 patients with a stable maintenance dose of warfarin. We examined SNPs in eight genes involving in the biotransformation and mode of action of warfarin (i.e., CYP4F2, CYP2C19, APOE, CALU, EPHX1, PROC, CYP2C9, and GGCX) using the SNaPshot assay. Results: The mean daily warfarin dose in patients carrying CYP2C19 rs3814637CC, CYP2C9 rs1057910AA, and GGCX rs699664AA genotype was 3.39, 3.34, and 3.51?mg/day, respectively, which was higher than those carrying CYP2C19 rs3814637TT, CYP2C9 rs1057910CC, and rs699664GG genotype (2.00, 0.81, and 3.09?mg/day, respectively). Conclusion: These findings indicate that individuals carrying the CYP2C19 rs3814637CC or CYP2C9 rs1057910AA or GGCX rs699664AA genotype needed higher warfarin doses in the Chinese population. PMID:23941071

Liang, Yundan; Chen, Zhiyu; Guo, Gang; Dong, Xuemei; Wu, Chunting; Li, He; Wang, Tong

2013-01-01

263

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis  

PubMed Central

Newcastle disease and Avian Influenza are considered to be the most dangerous fowl diseases which may cause huge economic losses. Newcastle disease is caused by the enveloped, and single-stranded RNA virus (NDV, APMV-1; belonging to Paramyxoviridae family), which can be further divided into sixteen different genotypes grouped into five pathotypes according to their pathogenicity. It has been reported that low pathogenic virus can greatly increase its pathogenicity even during a single passage. Additionally, due to the widespread use of live vaccines, a mixture of two or more different viruses in one sample can be detected. Hence, there is a great need for establishment of fast, inexpensive, sensitive, and relatively simple diagnostic method for multistrain and quasispecies detection of NDV infection. In this paper we describe a diagnostic method based on RT-PCR followed by a modified version of single-stranded conformational polymorphism analysis using short DNA fragments of gene encoding viral F protein. The method allows for rapid diagnosis of genetic variant emerging from previously stable population which may prevent the spread of the pathogenic viral variant. PMID:24812625

Rabalski, Lukasz; Smietanka, Krzysztof

2014-01-01

264

Genetic polymorphisms associated with rubella virus-specific cellular immunity following MMR vaccination.  

PubMed

Rubella virus causes a relatively benign disease in most cases, although infection during pregnancy can result in serious birth defects. An effective vaccine has been available since the early 1970s and outbreaks typically do not occur among highly vaccinated (?2 doses) populations. Nevertheless, considerable inter-individual variation in immune response to rubella immunization does exist, with single-dose seroconversion rates ~95 %. Understanding the mechanisms behind this variability may provide important insights into rubella immunity. In the current study, we examined associations between single nucleotide polymorphisms (SNPs) in selected cytokine, cytokine receptor, and innate/antiviral genes and immune responses following rubella vaccination in order to understand genetic influences on vaccine response. Our approach consisted of a discovery cohort of 887 subjects aged 11-22 at the time of enrollment and a replication cohort of 542 older adolescents and young adults (age 18-40). Our data indicate that SNPs near the butyrophilin genes (BTN3A3/BTN2A1) and cytokine receptors (IL10RB/IFNAR1) are associated with variations in IFN? secretion and that multiple SNPs in the PVR gene, as well as SNPs located in the ADAR gene, exhibit significant associations with rubella virus-specific IL-6 secretion. This information may be useful, not only in furthering our understanding immune responses to rubella vaccine, but also in identifying key pathways for targeted adjuvant use to boost immunity in those with weak or absent immunity following vaccination. PMID:25098560

Kennedy, Richard B; Ovsyannikova, Inna G; Haralambieva, Iana H; Lambert, Nathaniel D; Pankratz, V Shane; Poland, Gregory A

2014-11-01

265

Frequency of thrombophilic genetic polymorphisms among Saudi subjects compared with other populations.  

PubMed

Thrombophilic mutations increase the tendency toward thromboembolic disease. The aim of this study was to estimate the prevalence of the genetic variants related to thrombophilia among Saudis compared with other populations. Real-time polymerase chain reaction (PCR) genotyping was carried out to determine the polymorphic variants of factor V Leiden 1695G/A, prothrombin 20210G/A, plasmin activator inhibitor 1 4G/5G, methylene tetrahydrofolate reductase (MTHFR) 677C/T, MTHFR 1298A/C, and angiotensin-converting enzyme (ACE) insertion/deletion (I/D) among a representative sample of healthy Saudi subjects. Carraige rate for each of the mutant variants of factor V Leiden (FVL) and FII genes constituted 2% of the surveyed subjects giving an allele frequency of 0.01, homozygous forms of plasminogen activator inhibitor-1 (PAI-1) gene 4G/4G, MTHFR 677TT, 1298CC, and ACE DD were present among 7.7, 2.55, 7, and 51.8% of subjects with a mutant allele frequency of 0.4, 0.19, 0.29, and 0.73, respectively. This study showed that the Saudi population has a peculiar pattern regarding thrombophilic mutations that might warrant additional considerations for prophylaxis. PMID:22664118

Settin, Ahmad A; Alghasham, Abdullah; Ali, Ahmad; Dowaidar, Moataz; Ismail, Hisham

2012-05-01

266

Associations between Salivary Testosterone Levels, Androgen-Related Genetic Polymorphisms, and Self-Estimated Ejaculation Latency Time  

PubMed Central

Introduction Recently, testosterone (T) has been shown to be associated with premature ejaculation (PE) symptoms in the literature. Furthermore, studies suggest that the etiology of PE is partly under genetic control. Aim The aim of this study was to reassess findings suggesting an association between testosterone (T) and a key symptom of PE, ejaculation latency time (ELT), as well as exploratively investigating associations between six androgen-related genetic polymorphisms and ELT. Materials and Methods Statistical analyses were performed on a population-based sample of 1,429 Finnish men aged 18–45 years (M = 26.9, SD = 4.7). Genotype information was available for 1,345–1,429 of these (depending on the polymorphism), and salivary T samples were available from 384 men. Two androgen receptor gene-linked, two 5-alpha-reductase type 2-gene-linked, and two sex hormone-binding globuline gene-linked polymorphisms were genotyped. Main Outcome Measures Ejaculatory function was assessed using self-reported ELT. Results We found no association between salivary T levels and ELT. We found a nominally significant association between a 5-alpha-reductase type 2-gene-linked polymorphism (rs2208532) and ELT, but this association did not remain significant after correction for multiple testing. One single nucleotide polymorphism in the sex hormone-binding globulin gene (rs1799941) moderated (significantly after correction for multiple testing) the association between salivary T and ELT, so that A:A genotype carriers had significantly lower salivary T levels as a function of increasing ELT compared with other genotype groups. Conclusions We were unable to find support for the hypothesis suggesting an association between T levels and ELT, possibly because of the low number of phenotypically extreme cases (the sample used in the present study was population based). Our results concerning genetic associations should be interpreted with caution until replication studies have been conducted. Jern P, Westberg L, Ankarberg-Lindgren C, Johansson A, Gunst A, Sandnabba NK, and Santtila P. Associations between salivary testosterone levels, androgen-related genetic polymorphisms, and self-estimated ejaculation latency time. Sex Med 2014;2:107–114. PMID:25356307

Jern, Patrick; Westberg, Lars; Ankarberg-Lindgren, Carina; Johansson, Ada; Gunst, Annika; Sandnabba, N Kenneth; Santtila, Pekka

2014-01-01

267

Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project  

PubMed Central

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use. [The sequence data described in this paper have been submitted to the db SNP data library under accession nos. SS8196–SS18418.] PMID:10958644

Clifford, Robert; Edmonson, Michael; Hu, Ying; Nguyen, Cu; Scherpbier, Titia; Buetow, Kenneth H.

2000-01-01

268

Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers.  

PubMed

Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects (MAD), and 4) a full model including all three genetic components (MAED). Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions. PMID:23028912

Su, Guosheng; Christensen, Ole F; Ostersen, Tage; Henryon, Mark; Lund, Mogens S

2012-01-01

269

The impact of genetics profile (gene polymorphisms) in obese non-PCOS women entering an IVF/ICSI program.  

PubMed

Data concerning the effects of increased body mass index (BMI) on ovarian and pregnancy outcome are rich, but the results are rather controversial. Regarding pharmacogenetics, gene polymorphisms of hormonal receptor genes, such as Estrogen Receptor alpha (ESR1), Estrogen Receptor beta (ESR2) and FSH receptor (FSHR) genes, are associated with ovarian stimulation and pregnancy outcome and may constitute a useful tool for ART experts for the prediction of this outcome. The aim of this study is to track differences in the distribution of gene polymorphisms among obese non-PCOS and non-obese patients concerning three distinct genes which are involved in the ovarian stimulation mechanism: PvuII polymorphism of ESR1 gene, RsaI polymorphism of ESR2 gene and Ser680Asn variation of FSHR gene, using restriction fragment length polymorphism analysis and real-time polymerase chain reaction. A total of 151 normally ovulating female patients underwent IVF or ICSI. Interestingly, the pregnancy rate in the BMI?30 kg/m² group was higher in a statistically significant way (40.9% versus 17.8%, p=0.023). The obese patients of this study were in need of increased total FSH dose in order to achieve a satisfactory oocyte number (p<0.001) and needed more days of stimulation (p=0.002), but also presented lower basal FSH levels (p=0.032), which may explain, to an extend, the better pregnancy outcome. Concerning the polymorphisms of ESR1, ESR2 and FSHR genes, we did not observe differences in the genotype distribution when we compared the obese non-PCOS population with the non-obese population. Thus, obesity does not constitute an additional indication to perform a genetic analysis before entering an IVF/ICSI program. PMID:23614677

Anagnostou, Elli; Drakakis, Petros; Marinopoulos, Spyridon; Mavrogianni, Despina; Loutradis, Dimitrios

2013-07-01

270

Overlap Between Common Genetic Polymorphisms Underpinning Kidney Traits and Cardiovascular Disease Phenotypes: The CKDGen Consortium  

PubMed Central

Background Chronic kidney disease is associated with cardiovascular disease. We tested for evidence of a shared genetic basis to these traits. Study Design We conducted two targeted analyses. First, we examined whether known single nucleotide polymorphisms (SNPs) underpinning kidney traits were associated with a series of vascular phenotypes. Additionally, we tested whether vascular SNPs were associated with markers of kidney damage. Significance was set to 1.5 × 10-4 (0.05/325 tests). Setting & Participants Vascular outcomes were analyzed in participants from the AortaGen (20,634), CARDIoGRAM (86,995), CHARGE Eye (15,358), CHARGE IMT (31,181), ICBP (69,395) and NeuroCHARGE (12,385) consortia. Tests for kidney outcomes were conducted in up to 67,093 participants from the CKDGen consortium. Predictor We used 19 kidney SNPs and 64 vascular SNPs. Outcomes & Measurements Vascular outcomes tested were blood pressure, coronary artery disease, carotid intima-media thickness, pulse wave velocity, retinal venular caliber and brain white matter lesions. Kidney outcomes were estimated glomerular filtration rate and albuminuria. Results In general, we found that kidney disease variants were not associated with vascular phenotypes (127 of 133 tests were non-significant). The one exception was rs653178 near SH2B3 (SH2B adaptor protein 3), which showed direction-consistent association with systolic (p=9.3E-10) and diastolic (p=1.6E-14) blood pressure and coronary artery disease (p=2.2E-6), all previously reported. Similarly, the 64 SNPs associated with vascular phenotypes were not associated with kidney phenotypes (187 of 192 tests were non-significant), with the exception of 2 high-correlated SNPs at the SH2B3 locus (p=1.06E-07 and p=7.05E-08). Limitations Combined effect size of the SNPs for kidney and vascular outcomes may be too low to detect shared genetic associations. Conclusions Overall, although we confirmed one locus (SH2B3) as associated with both kidney and cardiovascular disease, our primary findings suggest that there is little overlap between kidney and cardiovascular disease risk variants in the overall population. The reciprocal risks of kidney and cardiovascular disease may not be genetically mediated, but rather a function of the disease milieu itself. PMID:23474010

Olden, Matthias; Teumer, Alexander; Bochud, Murielle; Pattaro, Cristian; Köttgen, Anna; Turner, Stephen T.; Rettig, Rainer; Chen, Ming-Huei; Dehghan, Abbas; Bastardot, Francois; Schmidt, Reinhold; Vollenweider, Peter; Schunkert, Heribert; Reilly, Muredach P.; Fornage, Myriam; Launer, Lenore J.; Verwoert, Germaine C.; Mitchell, Gary F.; Bis, Joshua C.; O'Donnell, Christopher J.; Cheng, Ching-Yu; Sim, Xueling; Siscovick, David S.; Coresh, Josef; Kao, W.H. Linda; Fox, Caroline S.; O'Seaghdha, Conall M.

2013-01-01

271

MicroRNAs related polymorphisms and genetic susceptibility to esophageal squamous cell carcinoma.  

PubMed

Esophageal cancer (EC) is the sixth leading cause of cancer-associated death worldwide and the incidence and mortality in China are the highest. The single nucleotide polymorphisms (SNPs) related to microRNAs could lead to alteration in microRNA expression and contribute to the susceptibility of cancer. To evaluate the association between microRNA-related SNPs and EC, a case-control study including 381 patients with esophageal squamous cell carcinoma (ESCC) and 426 gender, age-matched controls was carried out to investigate the genetic susceptibility of five microRNA-related SNPs (rs2910164 in microRNA-146a, rs11614913 in microRNA-196a-2, rs7813 in GEMIN4, rs1595066 and rs16845990 in ErbB4) as well as the interactions of gene-gene and gene-environment in the development of ESCC. Variant homozygote genotype of rs11614913 in microRNA-196a-2 and rs1595066 in ErbB4 were significantly associated with reduced ESCC risk (OR(adjusted): 0.62, 95 % CI: 0.39-0.99 and OR(adjusted): 0.38, 95 % CI: 0.24-0.61). The analysis of haplotypes in ErbB4 gene showed significant increased ESCC risk in G(rs1595066)C(rs16845990) and G(rs1595066)T(rs16845990) haplotypes (OR(adjusted): 1.46, 95 % CI: 1.08-1.99 and OR(adjusted): 1.33, 95 % CI: 1.10-1.62), and inversely reduced ESCC risk in A(rs1595066)C(rs16845990) and A(rs1595066)T(rs16845990) haplotypes with OR (95 % CI) of 0.75 (0.60-0.94) and 0.65 (0.49-0.86), respectively. These findings suggest that the polymorphisms in the microRNA-related genes may affect susceptibility of ESCC in Chinese Han population and the gene-gene interactions play vital roles in the progression on esophageal cancer. Future studies with larger sample and different ethnic populations are required to support and validate our findings. PMID:24916311

Qu, Yanhong; Qu, Honghong; Luo, Manli; Wang, Peng; Song, Chunhua; Wang, Kaijuan; Zhang, Jianying; Dai, Liping

2014-12-01

272

Trophic polymorphism in a riverine fish: morphological, dietary, and genetic analysis of mountain whitefish  

E-print Network

(Salmonidae: Prosopium williamsoni), which has been hypothesized to exhibit a rare example of reproductively KEYWORDS: Coregonus ­ Gasterosteus ­ microsatellite ­ morphology ­ Prosopium ­ resource polymorphism

Whiteley, Andrew

273

XRCC1 and XPD genetic polymorphisms and susceptibility to age-related cataract: A meta-analysis  

PubMed Central

Objective This meta-analysis aimed to determine the relationships between XRCC1 Arg399Gln (rs25487 G>A) and XPD Lys751Gln (rs1052559 A>C) polymorphisms and susceptibility to age-related cataract. Methods Medline (1966–2013), the Cochrane Library Database (Issue 12, 2013), EMBASE (1980–2013), CINAHL (1982–2013), Web of Science (1945–2013) and the Chinese Biomedical Database (CBM; 1982–2013) were searched without language restrictions. Various combinations of the keywords and MeSH terms were used to screen for potentially relevant studies, specifically “genetic polymorphisms” or “SNPs” or “variation” or “single nucleotide polymorphism” or “polymorphism” or “mutation” or “variant”; “X-ray repair cross complementing protein 1” or “Xeroderma Pigmentosum Group D Protein” or “X-ray repair cross complementing protein 1” or “Xeroderma Pigmentosum Group D Protein” or “XPD” or “Xeroderma Pigmentosum Complementation Group D Protein” or “ERCC2” or “XRCC1” or “XRCC1 DNA repair protein”; and “Cataract” or “ Membranous Cataract” or “ Pseudoaphakia.” Meta-analyses were conducted using Stata 12.0 software. Crude odds ratios (ORs) and their corresponding 95% confidence intervals (95% CI) were calculated. Results Six independent case-control studies were included in the meta-analysis. Our results indicated that the association between the genetic polymorphisms of XRCC1 Arg399Gln G>A and XPD Lys751Gln A>C and increased susceptibility to age-related cataracts was statistically significant (XRCC1 Arg399Gln: OR=1.30, 95% CI=1.17–1.44, p<0.001; XPD Lys751Gln: OR=1.25, 95% CI=1.12–1.40, p<0.001, respectively). Ethnicity-stratified analysis indicated that the XRCC1 Arg399Gln G>A polymorphism was correlated with the development and progression of age-related cataract in China, India, and Turkey in the allele model and the dominant model. For the XPD Lys751Gln A>C variant, the association with the pathogenesis of age-related cataract in China and Turkey in the allele model and the dominant model was investigated. Conclusions The association of XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms with age-related cataract susceptibility observed in our meta-analyses supports the view that XRCC1 and XPD may play important roles in susceptibility to age-related cataract.

Chi, Xin-Xin; Liu, You-Yu; Shi, Su-Ning; Cong, Zhuang; Liang, Yu-Qing

2015-01-01

274

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers  

PubMed Central

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3? untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3? UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3? UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

275

Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)  

PubMed Central

Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

2014-01-01

276

CHARLOTTE HARBOR IR, 2002  

EPA Science Inventory

The 2002 Charlotte Harbor Implementation Review (IR) summarizes the progress and challenges ahead for the Charlotte Harbor National Estuary Program (CHNEP). The implementation review report requires seven components: Status of CCMP implementation (programmatic progress); Environm...

277

The effect of genetic polymorphisms of TLR2 and TLR4 in Turkish patients with coronary artery disease.  

PubMed

Coronary artery disease (CAD), being a multifactorial disease process, has been suggested to be associated by the interaction of both environmental and genetic risk factors. Toll-like receptors (TLRs) are related to the receptors of the innate immune system which serves as the recognition of the conserved pathogen motifs and the activation of the signals that stimulate inflammatory genes. In this study, we investigated the relationship between the polymorphisms in the TLR2-Arg753Gly, TLR4-Asp299Gly and Thr399Ile gene and CAD. The study population consisted of 300 patients (149 men, 151 women) with angiographically documented CAD. The polymorphisms were genotyped by real time PCR. No association between TLR2-Arg677Trp or TLR4-Asp299Gly and -Thr399Ile gene polymorphisms and the presence or the severity of CAD was observed. On the other hand, the TLR2-Arg753Arg genotype seemed to have a protective effect against development of CAD (OR=0.17; 95% CI=0.04-0.83). Our findings suggest that TLR2-Arg753Gly polymorphism is associated with CAD susceptibility in Turkish patients. PMID:25542811

Guven, Mehmet; Ismailoglu, Ziya; Batar, Bahadir; Unal, Selin; Onaran, Ilhan; Karadag, Bilgehan; Ongen, Zeki

2015-03-01

278

Population genetics of four PKLR intragenic polymorphisms in Portugal and São Tomé e Príncipe (Gulf of Guinea).  

PubMed

Four intragenic PKLR polymorphisms [1705A/C, 1738C/T. T10/19, and (ATT)n microsatellite] were studied in normal population samples of Central Portugal and São Tomé e Príncipe, a small archipelago located in the Gulf of Guinea, West Africa. For all loci, the observed genotype distributions do not deviate from Hardy-Weinberg equilibrium. The allele frequencies found in the Portuguese population are similar to those previously described in Caucasian populations. Mother-child pair analysis for the (ATT)n microsatellite does not show deviations to the Mendelian rules. In São Tomé e Príncipe the biallelic polymorphisms 1705A/C, 1738C/T, and T10/19 presented inverse allelic frequencies when compared with the Portuguese population. Two new alleles were found at the (ATT)n microsatellite. Significant statistical differences were found between both populations. The results showed that São Tomeans had higher haplotype diversity and lower linkage disequilibrium among the polymorphic sites. The PKLR intragenic polymorphisms, commonly used in haplotype analysis with the gene mutations in PK-deficient patients, can thus be successfully employed in anthropological genetics. PMID:11459427

Manco, L; Oliveira, A L; Gomes, C; Granjo, A; de Jesus Trovoada, M; Ribeiro, M L; Abade, A; Amorim, A

2001-06-01

279

Myeloperoxidase G-463A polymorphism and lung cancer: a HuGE genetic susceptibility to environmental carcinogens pooled analysis.  

PubMed

Myeloperoxidase is a phase I metabolic enzyme that converts the metabolites of benzo[a]pyrene from tobacco smoke into highly reactive epoxides. A polymorphism in the promoter region of myeloperoxidase (463G-->A) has been found to be inversely associated with lung cancer; differences in the association with age and gender have been suggested. We conducted a pooled analysis of individual data from 10 studies (3688 cases and 3874 controls) from the Genetic Susceptibility to Environmental Carcinogens database. The odds ratio for lung cancer was 0.88 (95% confidence interval: 0.80-0.97) for the AG variant of myeloperoxidase G-463A polymorphism, and 0.71 (95% confidence interval: 0.57-0.88) for the AA variant after adjusting for smoking, age, gender, and ethnicity. The inverse association between lung cancer and myeloperoxidase G-463A polymorphism was equally found in males and females (odds ratio for the AA genotype 0.73 [95% confidence interval: 0.56-0.96] and 0.67 [95% confidence interval: 0.46-0.98], respectively), without differences in the association according to age in the two genders. The myeloperoxidase G-463A polymorphism was significantly protective in "ever" smokers but not in "never" smokers. Myeloperoxidase is a key enzyme in tobacco-induced carcinogenesis. PMID:17304047

Taioli, Emanuela; Benhamou, Simone; Bouchardy, Christine; Cascorbi, Ingolf; Cajas-Salazar, Nohelia; Dally, Heike; Fong, Kwun M; Larsen, Jill E; Le Marchand, Loic; London, Stephanie J; Risch, Angela; Spitz, Margaret R; Stucker, Isabelle; Weinshenker, Brian; Wu, Xifeng; Yang, Ping

2007-02-01

280

MTLRP genetic polymorphism (214C>A) was associated with Type 2 diabetes in Caucasian population: a meta-analysis  

PubMed Central

Background Previous studies reported the relation between MTLRP genetic polymorphism and type 2 diabetes, however, the conclusion were conflicting. In the present study, we performed a meta-analysis to reveal this association. Methods Literature retrieval, selection and assessment, data extraction, and meta-analyses were performed according to the RevMan 5.0 guidelines. In the meta-analysis, we utilized random-effect model or fixed-effect model to pool the Odds ratio (OR) according to the test of heterogeneity. Results A total of nine case–control studies included 4460 type 2 diabetes patients and 4114 healthy control subjects were analyzed. We did not found association between the MTLRP polymorphism and type 2 diabetes risk in the overall population (CC vs CA?+?AA: OR?=?1.02; 95% CI: 0.89-1.17, P?=?0.77; A vs C: OR?=?1.02; 95% CI: 0.84-0.96, P?=?0.62). However, in subgroup analyses stratified by ethnicity, we found significant association of MTLRP polymorphism with type 2 diabetes in Caucasians (CC vs CA?+?AA: OR?=?1.27; 95% CI: 1.02-1.57, P?=?0.03; A vs C: OR?=?0.74, 95% CI: 0.60–0.91, P?=?0.005). Conclusion The MTLRP polymorphism was associated with type 2 diabetes in Caucasians. PMID:25095788

2014-01-01

281

Genetic Dissection of New Genotypes of Drumstick Tree (Moringa oleifera Lam.) Using Random Amplified Polymorphic DNA Marker  

PubMed Central

The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20 Moringa oleifera were carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twenty M. oleifera genotypes from various origins were collected and germinated and raised in nursery before transplanting to the field at University Agricultural Park (TPU). Genetic diversity parameter, such as Shannon's information index and expected heterozygosity, revealed the presence of high genetic divergence with value of 1.80 and 0.13 for Malaysian population and 0.30 and 0.19 for the international population, respectively. Mean of Nei's gene diversity index for the two populations was estimated to be 0.20. In addition, a dendrogram constructed, using UPGMA cluster analysis based on Nei's genetic distance, grouped the twenty M. oleifera into five distinct clusters. The study revealed a great extent of variation which is essential for successful breeding and improvement program. From this study, M. oleifera genotypes of wide genetic origin, such as T-01, T-06, M-01, and M-02, are recommended to be used as parent in future breeding program. PMID:23862149

Rufai, Shamsuddeen; Hanafi, M. M.; Rafii, M. Y.; Ahmad, S.; Arolu, I. W.; Ferdous, Jannatul

2013-01-01

282

Genetic dissection of new genotypes of drumstick tree (Moringa oleifera Lam.) using random amplified polymorphic DNA marker.  

PubMed

The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20 Moringa oleifera were carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twenty M. oleifera genotypes from various origins were collected and germinated and raised in nursery before transplanting to the field at University Agricultural Park (TPU). Genetic diversity parameter, such as Shannon's information index and expected heterozygosity, revealed the presence of high genetic divergence with value of 1.80 and 0.13 for Malaysian population and 0.30 and 0.19 for the international population, respectively. Mean of Nei's gene diversity index for the two populations was estimated to be 0.20. In addition, a dendrogram constructed, using UPGMA cluster analysis based on Nei's genetic distance, grouped the twenty M. oleifera into five distinct clusters. The study revealed a great extent of variation which is essential for successful breeding and improvement program. From this study, M. oleifera genotypes of wide genetic origin, such as T-01, T-06, M-01, and M-02, are recommended to be used as parent in future breeding program. PMID:23862149

Rufai, Shamsuddeen; Hanafi, M M; Rafii, M Y; Ahmad, S; Arolu, I W; Ferdous, Jannatul

2013-01-01

283

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids.  

PubMed

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality. PMID:24155917

Montanari, Sara; Saeed, Munazza; Knäbel, Mareike; Kim, YoonKyeong; Troggio, Michela; Malnoy, Mickael; Velasco, Riccardo; Fontana, Paolo; Won, KyungHo; Durel, Charles-Eric; Perchepied, Laure; Schaffer, Robert; Wiedow, Claudia; Bus, Vincent; Brewer, Lester; Gardiner, Susan E; Crowhurst, Ross N; Chagné, David

2013-01-01

284

Clinical hallmarks and genetic polymorphisms in the CFTR gene contribute to the disclosure of the A1006E mutation.  

PubMed

Since the identification of the Cystic Fibrosis transmembrane conductance regulator (CFTR) gene in 1989, many genetic mutations have been found in cystic fibrosis (CF) patients. Dysfunctions of the CFTR gene are responsible for the highly variable clinical presentation ranging from severe CF, disseminated bronchiectasis, idiopathic chronic pancreatitis and congenital bilateral absence of vas deferens (CBAVD). Linkage disequilibrium studies have shown that some mutations are stringently coupled with polymorphisms in a genetic complex called haplotype. From a familial study of a patient with CBAVD, carrier of the A1006E mutation, we have observed its strict association with the polymorphism 5T-TG11. In order to speed up the genetic diagnosis and to correlate the clinical setting to this genetic feature, we have directly investigated the exon 17a, where the A1006E mutation is located, of five cystic fibrosis patients belonging to two unrelated families. All patients had the 5T-TG11 tract, F508del and one unknown mutation. One more family with two affected individuals carrying the Q220X/A1006E mutations was investigated for the poly-T polymorphism. All the members were found to have the A1006E mutation and the 5T-TG11 in the same DNA strand, demonstrating that this strategy is a reliable and inexpensive method for genotyping the CFTR gene. A detailed description of the clinical presentation and follow-up are provided in order to highlight common phenotypic features useful to improve the management of cystic fibrosis patients. PMID:20691141

Tomaiuolo, Anna Cristina; Alghisi, Federico; Petrocchi, Stefano; Surace, Cecilia; Roberti, Maria Cristina; Bella, Sergio; Lucidi, Vincenzina; Angioni, Adriano

2010-01-01

285

Comparative Analysis of Genetic Diversity in Two Tunisian Collections of Fig Cultivars Based on Random Amplified Polymorphic DNA and Inter Simple Sequence Repeats Fingerprints  

Microsoft Academic Search

This study characterized the genetic diversity of 18 Tunisian fig cultivars using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR). Both random and ISSR primers tested generated a total of 116 RAPD and 47 ISSR markers. Considerable genetic variation was observed among fig cultivars sampled from two regional Tunisian collections with an average diversity of 4.57. RAPD

Salhi-Hannachi Amel; Chatti Khaled; Mars Messaoud; Marrakchi Mohamed; Trifi Mokhtar

2005-01-01

286

Amplified Fragment Length Polymorphism (AFLP) reveals no genetic divergence of the Eastern Alpine endemic Oxytropis campestris subsp. tiroliensis (Fabaceae) from widespread subsp. campestris  

Microsoft Academic Search

Applying Amplified Fragment Length Polymorphism, we explored genetic differences between widespread Oxytropis campestris subsp. campestris and O. campestris subsp. tiroliensis, a presumed glacial relict restricted to a small area along the main chain of the Eastern Alps. We could not find genetic differences between the two “taxa”. Neither do the morphological characters given in the literature discriminate between them. Therefore

Peter Schönswetter; Andreas Tribsch; Harald Niklfeld

2004-01-01

287

Physical and Genetic Mapping of Novel Microsatellite Polymorphisms on Human Chromosome 19  

Microsoft Academic Search

We describe here the identification of 11 novel microsatellite polymorphisms on human chromosome 19. These dinucleotide repeat polymorphisms were detected in chromosome 19-specific cosmids that were physically mapped by fluorescencein situhybridization. For each repeat, flanking oligonucleotide primers were synthesized and the polymerase chain reaction assay was performed on a panel of 100 unrelated individuals to determine the heterozygosity and allele

Gayle B. Collin; Andreas Münch; Jian-Long Mu; Jürgen K. Naggert; Anne S. Olsen; Patsy M. Nishina

1996-01-01

288

Paraoxonase activity and genetic polymorphisms in northern Han Chinese workers exposed to organophosphate pesticides.  

PubMed

Paraoxonase (PON1) is one of the major players in the detoxification of organophosphates (OPs). This study presents our investigation into the effect of OPs on serum PON1 activity and the distribution of common PON1 polymorphisms in Han Chinese workers with repeated high exposure to OP pesticides, and the factors modulating PON1 activity. In all, 400 participants, including 180 workers exposed to OP pesticides occupationally, and 220 controls were investigated. Serum PON1 and cholinesterase (ChE) activity were measured, and genotyping was done using polymerase chain reaction-restriction fragment length polymorphism. The association between PON1 activity and PON1 polymorphisms, and the influencing factors of PON1 activity, were analyzed. The results revealed that repeated OP exposures significantly decreased serum PON1 and ChE activity (P< 0.05), although the exposed workers did not complain of health problems. Higher L and R allele frequencies for the L55M and Q192R polymorphisms of PON1 were observed. PON1 polymorphisms (especially the Q192R polymorphism) and pesticide exposures significantly affected serum PON1 activity in the study population. Therefore, the results of this investigation indicate PON1 polymorphisms and pesticide exposures may be important risk predictors for OP poisoning in the Han Chinese population, who display very high frequencies of the M allele and R allele for PON1 polymorphisms at the positions 55 and 192, respectively. PMID:24326413

Zhang, Xiaofeng; Sui, Hong; Li, Haibo; Zheng, Jing; Wang, Fengqian; Li, Baixiang; Zhang, Yang

2014-02-01

289

Genetic Polymorphisms in Monoamine Systems and Outcome of Cognitive Behavior Therapy for Social Anxiety Disorder  

PubMed Central

Objective The role of genetics for predicting the response to cognitive behavior therapy (CBT) for social anxiety disorder (SAD) has only been studied in one previous investigation. The serotonin transporter (5-HTTLPR), the catechol-o-methyltransferase (COMT) val158met, and the tryptophan hydroxylase-2 (TPH2) G-703Tpolymorphisms are implicated in the regulation of amygdala reactivity and fear extinction and therefore might be of relevance for CBT outcome. The aim of the present study was to investigate if these three gene variants predicted response to CBT in a large sample of SAD patients. Method Participants were recruited from two separate randomized controlled CBT trials (trial 1: n?=?112, trial 2: n?=?202). Genotyping were performed on DNA extracted from blood or saliva samples. Effects were analyzed at follow-up (6 or 12 months after treatment) for both groups and for each group separately at post-treatment. The main outcome measure was the Liebowitz Social Anxiety Scale Self-Report. Results At long-term follow-up, there was no effect of any genotype, or gene × gene interactions, on treatment response. In the subsamples, there was time by genotype interaction effects indicating an influence of the TPH2 G-703T-polymorphism on CBT short-term response, however the direction of the effect was not consistent across trials. Conclusions None of the three gene variants, 5-HTTLPR, COMTval158met and TPH2 G-703T, was associated with long-term response to CBT for SAD. Trial Registration ClinicalTrials.gov (ID-NCT0056496) PMID:24260145

Andersson, Evelyn; Rück, Christian; Lavebratt, Catharina; Hedman, Erik; Schalling, Martin; Lindefors, Nils; Eriksson, Elias; Carlbring, Per; Andersson, Gerhard; Furmark, Tomas

2013-01-01

290

Genetic polymorphisms in arginase I and II and childhood asthma and atopy  

PubMed Central

Background A recent microarray study implicated arginase I (ARG1) and arginase II (ARG2) in mouse allergic asthma models and human asthma. Objectives To examine the association between genetic variation in ARG1 and ARG2 and childhood asthma and atopy risk. Methods We enrolled 433 case-parent triads, consisting of asthmatics 4 to 17 years and their biologic parents, from the allergy clinic of a public hospital in Mexico City between 1998 and 2003. Atopy to 24 aeroallergens was determined by skin prick tests. We genotyped 4 single nucleotide polymorphisms (SNPs) of ARG1 and 4 SNPs of ARG2 with minor allele frequencies over 10% using the TaqMan assay. Results ARG1 SNPs and haplotypes were not associated with asthma but all four ARG1 SNPs were associated with the number of positive skin tests (P = 0.007 to 0.018). Carrying two copies of minor alleles for either of two highly associated ARG2 SNPs was associated with a statistically significant increased relative risk (RR) of asthma [1.5, 95% confidence interval (CI) 1.1–2.1 for arg2s1; RR = 1.6, 95% CI = 1.1–2.3 for arg2s2]. The association was slightly stronger among children with a smoking parent (arg2s1 RR = 2.1, 95% CI = 1.2 – 3.9 with a smoking parent; RR =1.2, 95% CI = 0.8–1.9 without, interaction P = 0.025). Haplotype analyses reduced the sample size but supported the single SNP results. One ARG2 SNP was related to the number of positive skin tests (P = 0.027). Conclusions Variation in arginase genes may contribute to asthma and atopy in children. PMID:16387594

Li, Huiling; Romieu, Isabelle; Sienra-Monge, Juan-Jose; Ramirez-Aguilar, Matiana; Rio-Navarro, Blanca Estela del; Kistner, Emily O.; Gjessing, Håkon K.; Lara-Sanchez, Irma del Carmen; Chiu, Grace Y.; London MD, Stephanie J.

2006-01-01

291

Genetic polymorphisms in transforming growth factor beta-1 (TGFB1) and childhood asthma and atopy  

PubMed Central

Transforming growth factor beta-1 (TGFB1) may influence asthma by modulating allergic airway inflammation and airway remodeling. The role of single nucleotide polymorphisms (SNPs) of TGFB1 in asthma remains inconclusive. We examined TGFB1 SNPs in relation to asthma risk and degree of atopy among 546 case-parent triads, consisting of asthmatics aged 4 to 17 years and their parents in Mexico City. Atopy to 24 aeroallergens was determined by skin prick tests. We genotyped five TGFB1 SNPs, including two known functional SNPs [C-509T (rs1800469), T869C (rs1982073)] and three others (rs7258445, rs1800472, rs8179181), using TaqMan and Masscode assays. We analyzed the data using log-linear and polytomous logistic methods. Three associated SNPs, including the two known functional SNPs, were statistically significantly related to asthma risk. Individuals carrying the T allele of C-509T had an increased risk of asthma [relative risk (RR) = 1.42, 95% confidence interval (CI) = 1.08–1.87 for one copy; RR (95%CI) = 1.95 (1.36–2.78) for two copies]. For T869C, the RRs (95%CI) were 1.47 (1.09–1.98) for one and 2.00 (1.38–2.90) for two copies of the C allele. Similar results were found for rs7258445. The haplotype containing all three risk alleles conferred an increased risk of asthma (RR = 1.48, 95% CI = 1.11–1.95 for one copy; RR = 1.77, 95% CI = 1.22–2.57 for two copies). These three SNPs were also related to the degree of atopy. This largest study to date of genetic variation in TGFB1 and asthma and atopy adds to increasing evidence for a role in these disorders. PMID:17333284

Li, Huiling; Romieu, Isabelle; Wu, Hao; Sienra-Monge, Juan-Jose; Ramírez-Aguilar, Matiana; del Río-Navarro, Blanca Estela; Lara-Sánchez, Irma del Carmen; Kistner, Emily O.; Gjessing, Håkon K.; London, Stephanie J.

2007-01-01

292

Single Nucleotide Polymorphism (SNP)-Strings: An Alternative Method for Assessing Genetic Associations  

PubMed Central

Background Genome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association. Methodology/Principal Findings Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person’s SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS)-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex) and MMEL1 (an endopeptidase that degrades both neuropeptides and ?-amyloid). For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ?200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors) based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1), representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself, suggesting that the SNP-string method is more accurate across the entire region. Conclusions/Significance Accurate haplotype identification will enhance the detection of genetic-associations. The SNP-string method provides a simple means to accomplish this and can be extended to cover larger genomic regions, thereby improving a GWAS’s power, even for those published previously. PMID:24727690

Goodin, Douglas S.; Khankhanian, Pouya

2014-01-01

293

Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity  

PubMed Central

Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature. PMID:24558460

Ophir, Ron; Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Sharabi Schwager, Michal; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Holland, Doron

2014-01-01

294

Plasmodium falciparum Na+/H+ Exchanger (pfnhe-1) Genetic Polymorphism in Indian Ocean Malaria-Endemic Areas  

PubMed Central

To date, 11 studies conducted in different countries to test the association between Plasmodium falciparum Na+/H+ exchanger gene (pfnhe-1; PF13_0019) polymorphisms and in vitro susceptibility to quinine have generated conflicting data. In this context and to extend our knowledge of the genetic polymorphism of Pfnhe gene, we have sequenced the ms4760 locus from 595 isolates collected in the Comoros (N = 250; an area with a high prevalence of chloroquine and sulfadoxine-pyrimethamine resistance) and Madagascar (N = 345; a low drug-resistance area). Among them, 29 different alleles were observed, including 8 (27%) alleles not previously described. Isolates from the Comoros showed more repeats in block II (DNNND), which some studies have found to be positively associated with in vitro resistance to quinine, compared with isolates from Madagascar. Additional studies are required to better define the mechanisms underlying quinine resistance, which involve multiple gene interactions. PMID:23208889

Andriantsoanirina, Valérie; Khim, Nimol; Ratsimbasoa, Arsene; Witkowski, Benoit; Benedet, Christophe; Canier, Lydie; Bouchier, Christiane; Tichit, Magali; Durand, Rémy; Ménard, Didier

2013-01-01

295

Genetic Susceptibility to Cancer: the Role of Polymorphisms in Candidate Genes  

PubMed Central

Context Continuing advances in genotyping technologies and the inclusion of DNA collection in observational studies have resulted in an increasing number of genetic association studies. Objective To evaluate the overall progress and contribution of candidate gene association studies to current understanding of the genetic susceptibility to cancer. Data Sources We systematically examined the results of meta- and pooled analyses for genetic polymorphisms and cancer risk published through March 2008. Study Selection We identified 161 meta- and pooled analyses, encompassing 18 cancer sites and 99 genes. Analyses had to meet the following criteria: 1) at least 500 cases, 2) cancer risk as outcome, 3) not focused on HLA genetic markers, and 4) published in English. Data Extraction Information on cancer site, gene name, variant, point estimate and 95% confidence interval, allelic frequency, number of studies and cases, tests of study heterogeneity and publication bias were extracted by one investigator and reviewed by other investigators. Results These 161 analyses evaluated 344 gene-variant/cancer associations and included on average 7.3 studies and 3,551 cases (range: 508–19,729 cases) per investigated association. The summary OR for 98 (28%) statistically significant associations (p-value <0.05) were further evaluated by estimating the false-positive report probability (FPRP) at a given prior probability and statistical power. At a prior probability level of 0.001 and statistical power to detect an OR of 1.5, thirteen gene-variant/cancer associations remained noteworthy (FPRP<0.2). Assuming a very low prior probability of 0.000001, similar to a probability assumed for a randomly selected SNP in a genome-wide association study, and statistical power to detect an OR of 1.5, four associations were considered noteworthy as denoted by a FPRP value < 0.2: 1) GSTM1 null and bladder cancer (OR:1.5, 95% CI: 1.3–1.6, p-value=1.9×10?14), 2) NAT2 slow acetylator and bladder cancer (OR: 1.46, 95% CI:1.26–1.68, p-value=2.5×10?7), 3) MTHFR C677T and gastric cancer (OR: 1.52, 95% CI: 1.31–1.77, p-value=4.9×10?8), and 4) GSTM1 null and acute leukemia (OR: 1.20, 95% CI: 1.14–1.25, p-value=8.6×10?15). When the OR used to determine statistical power was lowered to 1.2, two of the four noteworthy associations remained so: GSTM1 null with bladder cancer and acute leukemia. Conclusions Phase II enzymes, which are key enzymes involved in the detoxification and excretion of carcinogens (and particularly deletion of GSTM1), were among the most consistent and highly significant associations. PMID:18505952

Dong, Linda M; Potter, John D; White, Emily; Ulrich, Cornelia M; Cardon, Lon R; Peters, Ulrike

2009-01-01

296

Genetic polymorphisms of inflammatory response gene TNF-? and its influence on sporadic pancreatic neuroendocrine tumors predisposition risk.  

PubMed

The diagnosed incidence of pancreatic neuroendocrine tumors (pNETs) is increasing; however, their etiology remains poorly understood. PNETs are a rare, heterogeneous group of tumors arising from the endocrine cells of the pancreas, and genetic risk factors for sporadic pNETs are inadequately understood. It is known that pNETs secrete biogenic amines, hormones and growth factors, tumor necrosis factor-a (TNF-?) being one of them. Furthermore, cytokines and other proinflammatory mediators have been implicated in inflammatory pancreatic diseases including pancreatitis and cancer. The aim of our study was to analyze TNF-? promoter gene polymorphisms as risk factors for pNETs using germline DNA collected in a population-based case-control study of pancreatic cancer [42 pNET cases, 78 pancreatic ductal adenocarcinoma (PDAC) cases, 17 intraductal papillary mucinous neoplasm (IPMN) and 98 healthy controls] conducted in the Athens, Greece and Izmir, Turkey areas. For subsequent analysis, we excluded cases and controls with known genetic syndromes. The CC genotype at the -1031 position was more frequent in pNET and IPMN patients (p=0.0002 and p=0.009, respectively), suggesting its possible role in pNET development. Furthermore, the AA genotype at the -308 position was overrepresented in IPMN cases (p=0.03), and AA genotype at the -238 position was more frequent in PDAC cases (p=0.03) compared to healthy individuals. With regard to tumor characteristics, no statistically significant association was detected. Our findings suggest the putative role of TNF-? -1031 polymorphism in the development of pNET and IPMN, whereas the -308 polymorphism seems to be overrepresented among IPMN cases and -238 polymorphism among PDAC cases. PMID:25213764

Karakaxas, Dimitrios; Gazouli, Maria; Coker, Ahmet; Agalianos, Christos; Papanikolaou, Ioannis S; Patapis, Pavlos; Liakakos, Theodoros; Dervenis, Christos

2014-10-01

297

The role of CYBA (p22phox) and catalase genetic polymorphisms and their possible epistatic interaction in cervical cancer.  

PubMed

Human papillomavirus (HPV) infection is necessary but not a sufficient cause for the development of invasive cervical cancer (ICC). Epithelial tissues, target for HPV, are exposed to reactive oxygen species (ROS) associated with tumor initiation and progression. The NADPH oxidase (NOX) and catalase (CAT) are involved in hydrogen peroxide (H2O2) production and inactivation, respectively. P22phox is the NOX subunit encoded by the CYBA gene that has a functional polymorphism (C-242T). This protein is involved in the regulation of electron transfer to oxygen. CAT is a hemic enzyme that plays a role in regulating H2O2 concentration, with a functional polymorphism (C-262T) in its gene. We evaluated CYBA C-242T and CAT C262T genetic polymorphisms and their interaction in 132 women with ICC. We found that CYBA C-242T and CAT C262T genotype frequencies were significantly different between ICC and controls (? (2) test, p?=?0.017 and p?=?0.009, respectively). Women with the C/T CYBA-242 genotype had a lower risk for ICC development (odds ratio (OR)?=?0.515, 95 % confidence interval (CI) 0.291-0.914, p?=?0.023) whereas T/T CAT-262 genotype carriers present an increased risk for ICC (OR?=?3.034, 95 % CI 1.462-6.298, p?=?0.003). Women with C/C genotype for CYBA and T/T genotype for CAT had an increased risk to develop ICC comparing with the interaction of the other possible genotypes of both genes (OR?=?3.952, 95 % CI 1.075-14.521, p?=?0.032). The CYBA C-242T and CAT C-262T genetic polymorphisms and their epistatic interactions can be associated with ICC through mechanisms related with the role of ROS in cell proliferation and apoptosis. PMID:25307973

Castaldo, Stephanie Anais; da Silva, Alda Pereira; Matos, Andreia; Inácio, Ângela; Bicho, Manuel; Medeiros, Rui; Alho, Irina; Bicho, Maria Clara

2015-02-01

298

Effect of genetic polymorphisms in CA6 gene on the expression and catalytic activity of human salivary carbonic anhydrase VI.  

PubMed

Carbonic anhydrase isoenzyme VI (CA VI) plays an important role in the homeostasis of oral tissues participating in the processes of taste, protection of dental tissues against the loss of minerals, caries, and possibly in the formation of dental calculus in periodontal disease. This study aimed to verify the correlation between changes in the expression and activity of human salivary carbonic anhydrase VI and genetic polymorphisms in its gene (CA6). The study population consisted of 182 healthy volunteers (female and male, aged 18-22). Samples of total saliva were assayed for CA VI concentrations using a specific time-resolved immunofluorometric assay. CA VI catalytic activity was detected by a modified protocol of Kotwica et al. [J Physiol Pharmacol 2006;57(suppl 8):107-123], adapted to CA VI in saliva. Samples of genomic DNA were genotyped for polymorphisms rs2274327 (C/T), rs2274328 (A/C) and rs2274333 (A/G) by TaqMan® SNP Genotyping Assays. The concentration and catalytic activity of the salivary CA VI obtained for the different genotypes were analyzed using the Kruskal-Wallis nonparametric test and the Dunn test. The results showed that individuals with TT genotype (rs2274327) had significantly lower CA VI concentrations than the individuals with genotypes CT or CC (p < 0.05). There was also an association between polymorphism rs2274333 and salivary CA VI concentrations. There were no associations between the three polymorphisms analyzed and variations in CA VI activity. Our results suggest that polymorphisms in the CA6 gene are associated with the concentrations of secreted CA VI. PMID:23652931

Aidar, M; Marques, Rocha; Valjakka, J; Mononen, N; Lehtimäki, T; Parkkila, S; de Souza, A P; Line, S R Peres

2013-01-01

299

Interaction between use of non-steroidal anti-inflammatory drugs and selected genetic polymorphisms in ovarian cancer risk  

PubMed Central

Inflammation and non-steroidal anti-inflammatory agents (NSAIDs) may play important role in ovarian cancer. However, epidemiologic data are inconsistent, possibly reflecting inter-individual genetic differences affecting the metabolism of NSAIDs. We examined whether common polymorphisms affecting the metabolism of NSAIDs modify the association between NSAIDs and ovarian cancer risk. We genotyped 1,353 DNA samples from women who developed ovarian cancer and 1,823 samples from matched controls participating in the New England Case-Control study and the Nurses' Health Studies. Conditional logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CIs) associated with regular use of NSAIDs and with relevant polymorphisms on ovarian cancer risk. Multivariable unconditional logistic regression estimated the association of NSAID use across stratum of each genotype. Regular use of NSAIDs was not associated with ovarian cancer risk. Multivariable OR (95% CI) associated with use NSAIDs was 0.85 (95% CI: 0.71-1.02). Associations between NSAID use and ovarian cancer risk did not differ significantly across strata of genotypes. None of the studied polymorphisms was associated with ovarian cancer risk. The multivariable ORs (95% CI) associated with CYP2C9 and UGT1A6 variant genotypes were 0.99 (0.90-1.08) and 0.93 (0.82-1.05), respectively. The multivariable ORs (95% CI) associated with PPAR-?, COX-2 -765G>C, and COX-2 Ex10+837T>C polymorphisms were 1.02 (0.87-1.20), 0.87 (0.75-1.00), and 0.97 (0.87-1.09), respectively. In this relatively large study, we found no convincing evidence supporting an association between NSAIDs use and ovarian cancer risk. Furthermore, data did not suggest interaction between selected polymorphisms and use of NSAIDs in relation to ovarian cancer risk. PMID:21532843

Pinheiro, Simone P; Gates, Margaret A; DeVivo, Immaculata; Rosner, Bernard A; Tworoger, Shelley S; Titus-Ernstoff, Linda; Hankinson, Susan E; Cramer, Daniel W

2010-01-01

300

Association of Symptoms and Severity of Rift Valley Fever with Genetic Polymorphisms in Human Innate Immune Pathways  

PubMed Central

Background Multiple recent outbreaks of Rift Valley Fever (RVF) in Africa, Madagascar, and the Arabian Peninsula have resulted in significant morbidity, mortality, and financial loss due to related livestock epizootics. Presentation of human RVF varies from mild febrile illness to meningoencephalitis, hemorrhagic diathesis, and/or ophthalmitis with residual retinal scarring, but the determinants for severe disease are not understood. The aim of the present study was to identify human genes associated with RVF clinical disease in a high-risk population in Northeastern Province, Kenya. Methodology/Principal Findings We conducted a cross-sectional survey among residents (N = 1,080; 1–85 yrs) in 6 villages in the Sangailu Division of Ijara District. Participants completed questionnaires on past symptoms and exposures, physical exam, vision testing, and blood collection. Single nucleotide polymorphism (SNP) genotyping was performed on a subset of individuals who reported past clinical symptoms consistent with RVF and unrelated subjects. Four symptom clusters were defined: meningoencephalitis, hemorrhagic fever, eye disease, and RVF-not otherwise specified. SNPs in 46 viral sensing and response genes were investigated. Association was analyzed between SNP genotype, serology and RVF symptom clusters. The meningoencephalitis symptom phenotype cluster among seropositive patients was associated with polymorphisms in DDX58/RIG-I and TLR8. Having three or more RVF-related symptoms was significantly associated with polymorphisms in TICAM1/TRIF, MAVS, IFNAR1 and DDX58/RIG-I. SNPs significantly associated with eye disease included three different polymorphisms TLR8 and hemorrhagic fever symptoms associated with TLR3, TLR7, TLR8 and MyD88. Conclusions/Significance Of the 46 SNPs tested, TLR3, TLR7, TLR8, MyD88, TRIF, MAVS, and RIG-I were repeatedly associated with severe symptomatology, suggesting that these genes may have a robust association with RVFV-associated clinical outcomes. Studies of these and related genetic polymorphisms are warranted to advance understanding of RVF pathogenesis. PMID:25756647

Hise, Amy G.; Traylor, Zachary; Hall, Noémi B.; Sutherland, Laura J.; Dahir, Saidi; Ermler, Megan E.; Muiruri, Samuel; Muchiri, Eric M.; Kazura, James W.; LaBeaud, A. Desirée; King, Charles H.; Stein, Catherine M.

2015-01-01

301

First insights into the genetic diversity of the pinewood nematode in its native area using new polymorphic microsatellite loci.  

PubMed

The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed. PMID:23554990

Mallez, Sophie; Castagnone, Chantal; Espada, Margarida; Vieira, Paulo; Eisenback, Jonathan D; Mota, Manuel; Guillemaud, Thomas; Castagnone-Sereno, Philippe

2013-01-01

302

Genetic polymorphism at an odorant receptor gene (Or39) among mosquitoes of the Anopheles gambiae complex in Senegal (West Africa)  

PubMed Central

Background Olfaction plays a significant role in insect behavior during critical steps of their life-cycle, such as host-seeking during foraging or the search for a mate. Here, we explored genetic polymorphism within and divergence between sibling species of the African malaria mosquito, Anopheles gambiae sensu lato in the gene sequence and encoded peptides of an odorant receptor, Or39. This study included sympatric specimens of An. gambiae sensu stricto, An. coluzzii and An. arabiensis sampled together in the village of Dielmo, Senegal. Results A 1,601 bp genomic sequence composed of 6 exons and 5 introns was obtained for Or39 from 6–8 mosquitoes in each of the 3 species. DNA sequence analysis revealed a high level of molecular polymorphism (??=?0.0154; Haplotype diversity?=?0.867) and high overall genetic differentiation between taxa (Fst?>?0.92, P?polymorphisms in An. gambiae and An. arabiensis as well as species-specific mutations also occurred in the first extracellular domain. Conclusions Although obtained from a limited number of specimens, our results point towards genetic differences between cryptic species within the An. gambiae complex in a gene of biological relevance that might be of evolutionary significance when exposed to disruptive selective forces. PMID:24886539

2014-01-01

303

Genetic polymorphisms in CYP1A1, CYP1B1 and COMT genes in Greenlandic Inuit and Europeans  

PubMed Central

Background The Indigenous Arctic population is of Asian descent, and their genetic background is different from the Caucasian populations. Relatively little is known about the specific genetic polymorphisms in genes involved in the activation and detoxification mechanisms of environmental contaminants in Inuit and its relation to health risk. The Greenlandic Inuit are highly exposed to legacy persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs), and an elucidation of gene–environment interactions in relation to health risks is needed. Objectives The aim of this study was to determine and compare the genotype and allele frequencies of the cytochrome P450 CYP1A1 Ile462Val (rs1048943), CYP1B1 Leu432Val (rs1056836) and catechol-O-methyltransferase COMT Val158Met (rs4680) in Greenlandic Inuit (n=254) and Europeans (n=262) and explore the possible relation between the genotypes and serum levels of POPs. Results The genotype and allele frequency distributions of the three genetic polymorphisms differed significantly between the Inuit and Europeans. For Inuit, the genotype distribution was more similar to those reported for Asian populations. We observed a significant difference in serum polychlorinated biphenyl (CB-153) and the pesticide 1,1-dichloro-2,2-bis(p-chlorophenyl)-ethylene (p,p?-DDE) levels between Inuit and Europeans, and for Inuit also associations between the POP levels and genotypes for CYP1A1, CYP1B1 and COMT. Conclusion Our data provide new information on gene polymorphisms in Greenlandic Inuit that might support evaluation of susceptibility to environmental contaminants and warrant further studies. PMID:23785672

Ghisari, Mandana; Long, Manhai; Bonefeld-Jørgensen, Eva C.

2013-01-01

304

Chapter 7: Molecular Epidemiology of Genetic Polymorphisms in Estrogen Metabolizing Enzymes in Human Breast Cancer  

Microsoft Academic Search

Epidemiologic studies indicate that most risk factors for breast cancer are related to reproductive and hormonal fac- tors. For a number of years, the mechanism for estrogens in carcinogenesis was thought to be that of mitotic stimulation, with the growth promotion of ductal epithelial cells harbor- ing precursor mutations in the breast. However, evidence is now available that estrogens may

Patricia A. Thompson; Christine Ambrosone

2000-01-01

305

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms  

PubMed Central

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6–12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

Mahoney, J. Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A.; Greene, Casey S.; Pioli, Patricia A.; Hinchcliff, Monique E.; Whitfield, Michael L.

2015-01-01

306

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh  

PubMed Central

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies. PMID:25178287

Uzzaman, Md. Rasel; Edea, Zewdu; Bhuiyan, Md. Shamsul Alam; Walker, Jeremy; Bhuiyan, A. K. F. H.; Kim, Kwan-Suk

2014-01-01

307

Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.  

PubMed

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6-12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

Mahoney, J Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A; Greene, Casey S; Pioli, Patricia A; Hinchcliff, Monique E; Whitfield, Michael L

2015-01-01

308

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh.  

PubMed

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F IS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies. PMID:25178287

Uzzaman, Md Rasel; Edea, Zewdu; Bhuiyan, Md Shamsul Alam; Walker, Jeremy; Bhuiyan, A K F H; Kim, Kwan-Suk

2014-10-01

309

Uncoupling protein 3 genetic variants in human obesity: the c-55t promoter polymorphism is negatively correlated with body mass index in a UK Caucasian population  

Microsoft Academic Search

OBJECTIVE: To investigate whether genetic variation at the UCP3 locus contributes to human obesity.SUBJECTS: Ninety-one obese children (BMI>4 standard deviations from age related mean) and 419 Caucasian adults from the Isle of Ely Study.DESIGN: Single strand conformation polymorphism (SSCP) analysis was used to scan the coding region of the UCP3 gene in 91 severely obese children. A common polymorphism identified

DJ Halsall; J Luan; P Saker; S Huxtable; J Keogh; NJ Wareham; S O'Rahilly

2001-01-01

310

Genetic polymorphisms in inflammatory response genes and their associations with breast cancer risk  

PubMed Central

Aim To explore the association of NFKB1 c.-798_-795delATTG (rs28362491), NFKBIA c.-949C>T (rs2233406), IL-8 c.-352A>T (rs4073), IL-10 c.-854T>C (rs1800871), TNF c.-418G>A (rs361525), and TNF c.-488G>A (rs1800629) polymorphisms with breast cancer risk in an East Chinese population. Methods We conducted a case-control study including 975 study participants (474 breast cancer patients and 501 female controls without cancer) and genotyped the polymorphisms employing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Logistic regression was used to assess the association of the polymorphisms with breast cancer risk. Results We found that the ins/del and del/del genotypes of NFKB1 polymorphism and TT genotype of IL-10 polymorphism significantly increased breast cancer risk (NFKB1 ins/del odds ratio [OR] 1.69, 95% [CI] 1.23-2.33, P?=?0.001; NFKB1 del/del OR 2.42, 95% CI 1.72-3.42, P?polymorphism, GA and AA genotypes of TNF c.-418G>A polymorphism, and GA genotype of TNF c.-488G>A polymorphism significantly reduced breast cancer risk (IL-8 TT OR 0.48, 95% CI 0.33-0.72, P?polymorphism significantly reduced the risk among pre-menopausal women (OR 0.63, 95% CI 0.40-0.99, P?=?,043), but not among post-menopausal women. Conclusions NFKB1, NFKBIA, IL-8, IL-10, and TNF polymorphisms could serve as useful predictive biomarkers for breast cancer risk among women in East China. PMID:25559835

Wang, Zhi; Liu, Qiu-Lian; Sun, Wu; Yang, Chun-Jing; Tang, Lei; Zhang, Xian; Zhong, Xiao-Ming

2014-01-01

311

The genetic polymorphisms of HER-2 and the risk of lung cancer in a Korean population  

PubMed Central

Background Human Epidermal Growth Factor Receptor 2 (HER-2; also known as erbB-2 or neu), a proto-oncogene of the receptor tyrosine kinase superfamily, has been associated with carcinogenesis and prognosis of human cancers, acting as a binding partner of other epidermal growth factor receptor (EGFR) family in the activation of EGFR signaling. Amplification of the HER-2 gene has been reported in lung cancer, where it has been associated with poor prognosis. In this study, we investigated whether the four polymorphisms (-3444C>T, -1985 G>T, I655A A>G and P1170A C>G) of the HER-2 gene are associated with the risk of lung cancer in Korean populations. Methods The frequencies of 4 polymorphisms of the HER-2 gene were examined by the polymerase chain reaction-restriction fragment length polymorphism or the single-nucleotide polymorphism-identification technology assay in the 407 lung cancer patients and 407 healthy controls. Results The frequencies of the 4 polymorphisms were not significantly different between patient and control groups in overall subjects. However, in the subgroup analysis, the 3 single nucleotide polymorphisms (-3444C>T, -1985G>T and P1170A C>G) showed statistically significant differences in the subgroups of females, non-smokers, and non-drinkers (p < 0.05). Additionally, we found the association between the risk of lung cancer and the polymorphisms of HER-2 gene in non-smoker subgroups with adenocarcinoma (p < 0.05). Conclusion Our results suggest that the polymorphisms of the HER-2 gene are associated with an increased susceptibility to lung cancer in females, non-smokers and non-drinkers subgroups in the Korean population. PMID:19055823

Jo, Uk Hyun; Han, Sle Gi Lo; Seo, Jae Hong; Park, Kyong Hwa; Lee, Jae Won; Lee, Hyo Jung; Ryu, Jeong Seon; Kim, Yeul Hong

2008-01-01

312

A Genetic linkage map of Pinyon pine (Pinus edulis) based on amplified fragment length polymorphisms  

Microsoft Academic Search

Amplified fragment length polymorphisms (AFLP) were used to rapidly generate a dense linkage map for pinyon pine (Pinus edulis). The map population consisted of 40 megagametophytes derived from one tree at Sunset Crater, Arizona. A total of 78 primer\\u000a combinations, each with three to five selective nucleotides, amplified 542 polymorphic markers. Of these, 33 markers showed\\u000a significant deviation from the

S. E. Travis; K. Ritland; T. G. Whitham; P. Keim

1998-01-01

313

A prospective study of genetic polymorphism in MPO, antioxidant status, and breast cancer risk  

Microsoft Academic Search

Oxidative stress may be involved in breast carcinogenesis. Myeloperoxidase (MPO) is an endogenous oxidant enzyme that generates\\u000a reactive oxygen species (ROS). A single nucleotide polymorphism (SNP) G-463A in the promoter region has been associated with\\u000a a decrease in risk of breast cancer. We assessed the association between this polymorphism and breast cancer risk in a nested\\u000a case-control study within the

Chunyan He; Rulla M. Tamimi; Susan E. Hankinson; David J. Hunter; Jiali Han

2009-01-01

314

Unique Genetic Variation Revealed by a Microsatellite Polymorphism Survey in Ten Wild-Derived Inbred Strains  

Microsoft Academic Search

Here we report on a genome polymorphism survey using 254 microsatellite markers in ten recently wild-derived inbred strains. Allele size analysis showed that the rate of polymorphism of these wild-derived mouse strains when compared with any of the common laboratory strains is on average 79.8%. We found 632 wild-derived alleles that were not present in the common laboratory strains, representing

Susana Campino; Catja Behrschmidt; Sébastien Bagot; Jean-Louis Guénet; Pierre-André Cazenave; Dan Holmberg; Carlos Penha-Gonçalves

2002-01-01

315

Genetic polymorphisms of Interleukin-18 are not associated with allograft function in kidney transplant recipients  

PubMed Central

Interleukin 18 (IL-18) is a proinflammatory cytokine that plays a role in host defense by upregulating both innate and acquired immune responses. Analysis of IL18 polymorphisms may be clinically important since their roles have been recognized in a variety of inflammatory and autoimmune disorders. However, the role of this cytokine polymorphisms in kidney transplant still remains unclear. In this study, we evaluated the associations between IL18 polymorphisms and graft function assessed by creatinine clearance in kidney transplant recipients. A total of 82 kidney transplant recipients and 183 healthy controls were enrolled, and frequencies of alleles, genotypes and haplotypes for IL18 polymorphisms were determined and compared with creatinine clearance. The -607C/A (rs1946518) and -137C/G (rs187238) variant alleles in the IL18 gene were determined by polymerase chain reaction. In our study, no significant association was found between the IL18 variants and creatinine clearance (p > 0.05). Nonetheless, polymorphism analysis revealed an increase in the frequency of the IL18 major haplotype -607C/-137G in kidney transplant patients (odds ratio 2.57, 95% confidence interval 1.45–4.55, p = 0.0014). Finally, we found that IL18 polymorphisms did not influence the renal function and that IL18 haplotype -607C/-137G seems to be associated with kidney transplant recipients. PMID:25071398

do Nascimento, Wenna Gleyce Araújo; Cilião, Daiani Alves; Genre, Julieta; Gondim, Dikson Dibe; Alves, Renata Gomes; Hassan, Neife Deghaide; Lima, Francisco Pignataro; Pereira, Maurício Galvão; Donadi, Eduardo Antônio; de Oliveira Crispim, Janaina Cristiana

2014-01-01

316

The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the repeatability of evolution.  

PubMed

A long-standing question in evolutionary biology asks whether the genetic changes contributing to phenotypic evolution are predictable. Here, we identify a genetic change associated with segregating variation in flower color within a population of Mimulus lewisii. To determine whether these types of changes are predictable, we combined this information with data from other species to investigate whether the spectrum of mutations affecting flower color transitions differs based on the evolutionary time-scale since divergence. We used classic genetic techniques, along with gene expression and population genetic approaches, to identify the putative, loss-of-function mutation that generates rare, white flowers instead of the common, pink color in M. lewisii. We found that a frameshift mutation in an anthocyanin pathway gene is responsible for the white-flowered polymorphism found in this population of M. lewisii. Comparison of our results with data from other species reveals a broader spectrum of flower color mutations segregating within populations relative to those that fix between populations. These results suggest that the genetic basis of fixed differences in flower color may be predictable, but that for segregating variation is not. PMID:24312531

Wu, Carrie A; Streisfeld, Matthew A; Nutter, Laura I; Cross, Kaitlyn A

2013-01-01

317

Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog.  

PubMed

Phenotypic and genetic divergence can be influenced by a variety of factors, including sexual and natural selection, genetic drift and geographic isolation. Investigating the roles of these factors in natural systems can provide insight into the relative influences of allopatric and ecological modes of biological diversification in nature. The strawberry poison frog, Dendrobates pumilio, presents an excellent opportunity for this kind of research, displaying a diverse array of colour morphs and inhabiting a heterogeneous landscape that includes oceanic islands, fragmented rainforest patches and wide expanses of suitable habitat. In this study, we use 15 highly polymorphic microsatellite loci to estimate population structure and gene flow among populations from across the range of D. pumilio and a causal modelling framework to statistically test 12 hypotheses regarding the geographic and phenotypic variables that explain genetic differentiation within this system. Our results demonstrate that the genetic distance between populations is most strongly associated with differences in dorsal coloration. Previous experimental studies have shown that phenotypic differences can result in sexual and natural selection against non-native phenotypes, and our results now show that these forces lead to genetic isolation between different colour morphs in the wild, presenting a potential case of incipient speciation through selection. PMID:20025652

Wang, Ian J; Summers, Kyle

2010-02-01

318

Association of arylhydroxamic acid N,O-acyltransferase and genetically polymorphic N-acetyltransferase in established inbred rabbit strains.  

PubMed

Partially purified liver preparations from 17 inbred and partially inbred rabbit strains were assayed for polymorphic N-acetyltransferase (NAT) and arylhydroxamic acid N,O-acyltransferase (AHAT) activities. The AC/J, AX/J, B/J, WH/J, X/J, Y-l/J, III/J, IIIC/J, III/DwJ, IIIEP/J and IIIVO/J inbred strains were identified as rapid acetylators and had high AHAT activity. The ACEP/J, AXBU/J, OS/J, III/cdJ, IIIVO/ahJ and IIIVO/vptJ strains were identified as slow acetylators and had low AHAT activity. These findings provide added evidence for the hypothesis that polymorphic NAT and AHAT activities are properties of the same enzyme. Additional studies in five of the rapid acetylator strains showed that they had significantly higher levels of liver NAT activity towards other arylamine acetylator predictor drugs and carcinogens than did obligate heterozygous (Rr) rapid acetylators from our rabbit colony. This indicates that the inbred animals are homozygous (RR) rapid acetylators and that there is a gene-dose response difference between the two rapid acetylator genotypes. Availability of established inbred and partially inbred strains shown to possess both acetylator phenotypes enhances the opportunity for using the rabbit as a genetic model for evaluating the role of the isoniazid acetylator polymorphism as a host factor in arylamine-related carcinogenesis. PMID:7152617

Weber, W W; Hein, D W; Glowinski, I B; King, C M; Fox, R R

1982-01-01

319

Effects of endotoxin exposure on childhood asthma risk are modified by a genetic polymorphism in ACAA1  

PubMed Central

Background Polymorphisms in the endotoxin-mediated TLR4 pathway genes have been associated with asthma and atopy. We aimed to examine how genetic polymorphisms in innate immunity pathways interact with endotoxin to influence asthma risk in children. Methods In a previous analysis of 372 children from the Boston Home Allergens and the Connecticut Childhood Asthma studies, 7 SNPs in 6 genes (CARD15, TGFB1, LY96, ACAA1, DEFB1 and IFNG) involved in innate immune pathways were associated with asthma, and 5 SNPs in 3 genes (CD80, STAT4, IRAK2) were associated with eczema. We tested these SNPs for interaction with early life endotoxin exposure (n = 291), in models for asthma and eczema by age 6. Results We found a significant interaction between endotoxin and a SNP (rs156265) in ACAA1 (p = 0.0013 for interaction). Increased endotoxin exposure (by quartile) showed protective effects for asthma in individuals with at least one copy of the minor allele (OR = 0.39 per quartile increase in endotoxin, 95% CI 0.15 to 1.01). Endotoxin exposure did not reduce the risk of asthma in children homozygous for the major allele. Conclusion Our findings suggest that protective effects of endotoxin exposure on asthma may vary depending upon the presence or absence of a polymorphism in ACAA1. PMID:22151743

2011-01-01

320

Genetic diversity in potato field populations of Thanatephorus cucumeris AG-3, revealed by ITS polymorphism and RAPD markers.  

PubMed

DNA sequence analysis of the internal transcribed spacer region 1 (ITS1) and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability in relation to agronomic and regional factors among 60 isolates of Thanatephorus cucumeris (anamorph Rhizoctonia solani) collected from lesions on potato stems or sclerotia of potato tubers. Based on comparative sequence analysis it was shown that all isolates belonged to anastomosis group 3 subgroup Potato Type (AG-3 PT). ITS1 sequence polymorphisms were found within 45 of the 60 isolates showing that different types of the ITS-region are present in individual isolates. Cloning and sequence analysis of the ITS1 region from three selected isolates with sequence polymorphism showed that two different ITS1-types were present in each isolate. RAPD analysis identified 51 RAPD-phenotypes among the 60 investigated isolates indicating a high level of diversity within the subgroup AG-3 PT. Putative clonal isolates with identical RAPD- and ITS1-types were identified within fields, and in one case the same phenotype was found in two different fields separated by several hundred kilometers. Population subdivision analysis based on phenotypic as well as genotypic diversities showed differentiation among populations from different fields when isolates were sampled from tubers, indicating restricted gene flow among soil populations. Low differentiation was seen among field populations sampled from stems, indicating that gene flow is taking place. The population structure was not influenced by the previous crop in the rotation nor by the two cultivars 'Sava' and 'Bintje'. PMID:15000234

Justesen, Annemarie Fejer; Yohalem, David; Bay, Anne; Nicolaisen, Mogens

2003-11-01

321

Genetic polymorphism of glutathione S-transferase P1 (GSTP1) in Delhi population and comparison with other global populations?  

PubMed Central

Glutathione S-transferases (GSTs) belong to a super family of phase II detoxification enzymes, which play an important role in protecting cells from damage caused by endogenous and exogenous compounds by conjugating reactive intermediates with glutathione to produce less reactive water-soluble compounds. In the present study, we determined the frequencies of two polymorphisms in exon 5 and exon 6 of GSTP1 gene in 500 normal individuals from Delhi. GSTP1 polymorphism was analysed by PCR-RFLP using amplification refractory mutation system (ARMS) assay. Two polymorphic sites in GSTP1 (Ile105 ? Val105; Ala114 ? Val114) have been analysed simultaneously, which results in four alleles: GSTP1*A (wild-type Ile105; Ala114), GSTP1*B (Val105; Ala114), GSTP1*C (Val105; Val114) and GSTP1*D (Ile105; Val114). The GSTP1 allele frequency in Delhi population was 0.663, 0.248, 0.069, and 0.020 for GSTP1*A, GSTP1*B, GSTP1*C, and GSTP1*D respectively. The frequency of Ile105 and Val105 allele was 0.683 and 0.317 respectively and it was calculated for the purpose of comparison with published data where all the four alleles were not analysed. GSTP1 alleles from Delhi population were compared with reported frequencies from all over India, and from other ethnic groups worldwide. This study would provide a basic database for future genetic studies. PMID:25606397

Sharma, Anita; Pandey, Arvind; Sharma, Shashi; Chatterjee, Indranil; Mehrotra, Ravi; Sehgal, Ashok; Sharma, Joginder K.

2014-01-01

322

[Molecular-genetic polymorphism of wheat cell lines resistant to metabolites of G. graminis var. tritici and osmotic stress].  

PubMed

It was analyzed polymorphism of DNA loci, flanked by inverted repeats of LTR retrotransposon Cassandra, in cell lines of bread wheat, resistant to the metabolites of ophiobolus root rot (G. graminis var. tritici), under osmotic stress and induced from them plant-regenerants. The differences in the polynucleotide sequences of DNA at the direct and step cell selection it was identified. Assessment of the level of genetic divergence showed that calluses obtained at the direct selection and calluses in the later stages of step selection were the most genetically distant from the original forms (D(NL) = 0.4855), this means that at the sublethal doses of selective factors occur the most significant changes at the genome of the investigated objects. In contrast to the original form at the spectra of products DNA amplification of calluses and regenerated plants showed the emergence of bands approximately 638 bp length, which may indicate the activation of retrotransposon Cassandra. PMID:24791474

Bavol, A V; Zinchenko, M O; Dubrovna, O V

2014-01-01

323

Genetic susceptibility to rheumatoid arthritis and human leukocyte antigen class II polymorphism. The role of shared conformational determinants.  

PubMed

Genetic susceptibility for rheumatoid arthritis has been associated with both human leukocyte antigen (HLA)-DR4 and HLA-DR1, depending on the ethnic origin of the population under study. Furthermore, various subtypes of DR4 exist, only some of which appear to be associated with rheumatoid arthritis. DNA sequence analysis of the DR-beta chain genes encoding the DR4 subtypes as well as DR1 has led to the observation that similar third hypervariable region sequences are found on rheumatoid arthritis-associated DR-beta chain alleles. The data indicate that third hypervariable region sequence polymorphisms strongly influence T cell recognition as well as risk for rheumatoid arthritis. This has led to the hypothesis that genetic susceptibility for rheumatoid arthritis is due to a group of similar third hypervariable region sequences that may share conformational determinants important in antigen presentation and/or immune regulation. PMID:3059797

Gregersen, P K; Silver, J; Winchester, R J

1988-12-23

324

Genetic Polymorphisms in CYP2E1: Association with Schizophrenia Susceptibility and Risperidone Response in the Chinese Han Population  

PubMed Central

Background CYP2E1 is a member of the cytochrome P450 superfamily, which is involved in the metabolism and activation of both endobiotics and xenobiotics. The genetic polymorphisms of CYP2E1 gene (Chromosome 10q26.3, Accession Number NC_000010.10) are reported to be related to the development of several mental diseases and to be involved in the clinical efficacy of some psychiatric medications. We investigated the possible association of CYP2E1 polymorphisms with susceptibility to schizophrenia in the Chinese Han Population as well as the relationship with response to risperidone in schizophrenia patients. Methods In a case-control study, we identified 11 polymorphisms in the 5' flanking region of CYP2E1 in 228 schizophrenia patients and 384 healthy controls of Chinese Han origin. From among the cases, we chose 130 patients who had undergone 8 weeks of risperidone monotherapy to examine the relationship between their response to risperidone and CYP2E1 polymorphisms. Clinical efficacy was assessed using the Brief Psychiatric Rating Scale (BPRS). Results Statistically significant differences in allele or genotype frequencies were found between cases and controls at rs8192766 (genotype p?=?0.0048, permutation p?=?0.0483) and rs2070673 (allele: p?=?0.0018, permutation p?=?0.0199, OR?=?1.4528 95%CI?=?1.1487–1.8374; genotype: p?=?0.0020, permutation p?=?0.0225). In addition, a GTCAC haplotype containing 5 SNPs (rs3813867, rs2031920, rs2031921, rs3813870 and rs2031922) was observed to be significantly associated with schizophrenia (p?=?7.47E-12, permutation p<0.0001). However, no association was found between CYP2E1 polymorphisms/haplotypes and risperidone response. Conclusions Our results suggest that CYP2E1 may be a potential risk gene for schizophrenia in the Chinese Han population. However, polymorphisms of the CYP2E1 gene may not contribute significantly to individual differences in the therapeutic efficacy of risperidone. Further studies in larger groups are warranted to confirm our results. PMID:22606226

Wei, Zhiyun; Shen, Lu; Xiong, Yuyu; Wu, Xi; Niu, Jiamin; Han, Xia; Tian, Zhengan; Yang, Lun; Feng, Guoyin; He, Lin; Qin, Shengying

2012-01-01

325

Relationships of glycoproteins IIb-IIIa and Ib content with mean platelet volume and their genetic polymorphisms.  

PubMed

Quantity of platelet adhesion molecules significantly varies in normal donors and cardiovascular patients and might be affected by platelet size and genetic variations. In this study, we assessed relationships of the content of glycoprotein (GP) IIb-IIIa and GPIb with mean platelet volume (MPV) and their genetic polymorphisms. MPV and GPIIb-IIIa and GPIb numbers were measured in 116 patients with acute coronary syndrome (ACS) at days 1, 3-5 and 8-12 after disease onset and in 32 healthy volunteers. GPIIb-IIIa and GPIb allelic variants were determined in ACS patients. Strong interactions of GPIIb-IIIa and GPIb numbers and MPV were observed in ACS patients and healthy volunteers. In patients, coefficients of correlation (r) were 0.642 and 0.510 (analysis of individual mean values) and in volunteers - 0.594 and 0.508 for GPIIb-IIIa and GPIb, respectively (everywhere P?genetic polymorphisms [GPIIIa Leu33Pro, GPIb? Thr145Met and GPIb? (-5)T/C (Kozak)] determined in ACS patients had no significant impact on their expression. Modest correlation was revealed between MPV and plasma thrombopoietin (TPO) measured at the first day of ACS (r?=?0.279, P?=?0.005). The data obtained indicated that GPIIb-IIIa and GPIb levels are mainly affected by platelet size (MPV) but not by their genetic variations. In some ACS patients, production of large platelets with high GPIIb-IIIa and GPIb contents might be stimulated by elevated TPO. PMID:23941967

Khaspekova, Svetlana G; Zyuryaev, Ilia T; Yakushkin, Vladimir V; Sirotkina, Olga V; Zaytseva, Natalia O; Ruda, Mikhail Y; Panteleev, Mikhail A; Mazurov, Alexey V

2014-03-01

326

HarborTides.com  

NSDL National Science Digital Library

HarborTides.com is a neat, user-friendly facility for tide information for over 2,500 harbors in the US (and Bermuda). Users may browse by state or search by zip code for information on high and low tides, sunrise and sunset, and longitude and latitude for every harbor. After filling out a form for free membership, users can also print out monthly tide tables.

327

FOLFIRI® and Bevacizumab in first-line treatment for colorectal cancer patients: safety, efficacy and genetic polymorphisms  

PubMed Central

Background Over 50% of colorectal cancer (CRC) patients develop metastases. The aim of this study was to evaluate efficacy and tolerance of first-line FOLFIRI®?+?bevacizumab (B) treatment for metastatic CRC, and to assess genetic polymorphisms as potential markers. Methods Adult patients with histologically-proven, non-resectable metastatic CRC and ECOG???2 were included. 14-day cycles consisted of bevacizumab (5 mg/kg), irinotecan (180 mg/m2), bolus FU (400 mg/m2) and leucovorin (400 mg/m2), followed by 46-hour FU infusions (2400 mg/m2). Primary endpoint was response rate according to RECIST criteria. Secondary endpoints were overall (OS) and progression-free (PFS) survivals, response duration, and toxicity. Associations between clinical data, UGT1A1, thymidylate synthase, VEGFA polymorphisms and PFS, OS and toxicity were analyzed. Results Sixty-two patients were enrolled (median age 68y). 59/62 patients were eligible and evaluable for response at 6 months: 28 showed partial response (47.5%; 95% CI; 34.3-60.9), 20 stable disease (33.9%) and 11 progression (18.6%). Grade 3/4 toxicities were as follows: neutropenia 16.1%; diarrhea 11.3%; nausea-vomiting 1.6%. Median response duration was 9.5 months (range 2.7-20); median PFS 10.3 months (range 8.8-11.7); and median OS 25.7 months (range 20.2-29.7). 11/59 initially unresectable patients were resectable after treatment. VEGFA polymorphism (rs25648) was associated with better OS (HR: 3.61; 95% CI: 1.57-8.30). Conclusions FOLFIRI®?+?bevacizumab is active with good response rate, long median OS, and a good safety profile. A VEGFA polymorphism might have a prognostic value in this malignancy. Trial registration Clinicaltrials.gov: NCT00467142 (registration date: April 25, 2007) PMID:24758527

2014-01-01

328

Genetic polymorphism at the glutathione S-transferase (GST) P1 locus is a breast cancer risk modifier.  

PubMed

The isolation of full-length cDNAs of naturally occurring GSTP1 gene variants, and the demonstration that these alleles are distributed in the normal population, have provided conclusive evidence that the human GSTP1 gene locus is polymorphic and that specific GSTP1 alleles may be associated with different risk for cancers or other diseases. Recent data have indicated that the different GSTP1 alleles encode proteins with different enzymatic activities against carcinogens. In this case-control study, we examined the effect of the GSTP1 genetic polymorphism and its interaction with other factors to determine breast cancer risk. GSTP1 and GSTM1 genotypes of 220 breast cancer patients and 196 controls, all residents of western France, were examined. Data on menopausal status and family cancer history were obtained from 195 patients and 147 controls. Exons 5 and 6 of the GSTP1 gene, which contain the polymorphic nucleotide transitions, were analyzed by DNA polymerase chain reaction-restriction fragment length polymorphism to distinguish between the GSTP1 alleles. In the control population, GSTP1 allelic frequencies were 64.3%, 26.0% and 9.7%, respectively, for GSTP1*A, GSTP1*B and GSTP1*C. In the breast cancer patients, the frequencies were 67.9% for GSTP1*A, 26.8% for GSTP1*B and 5.3% for GSTP1*C. In multivariate analysis, breast cancer risk increased by 7.7-fold (p < 0.001) in women with a family history of cancers and 2.18-fold (p = 0.026) in non-GSTP1*C individuals. GSTM1 genotypes did not emerge as risk factor. Our results show that in addition to well-known risk factors, in particular, a family history of cancer, GSTP1 allelopolymorphism is a significant modifier of breast cancer risk. The results also suggest a protective role against breast cancer for the GSTP1*C allele. PMID:11169956

Maugard, C M; Charrier, J; Pitard, A; Campion, L; Akande, O; Pleasants, L; Ali-Osman, F

2001-02-01

329

BAT2 and BAT3 polymorphisms as novel genetic risk factors for rejection after HLA-related SCT.  

PubMed

The genetic background of donor and recipient is an important factor determining the outcome of allogeneic hematopoietic SCT (allo-HSCT). We applied whole-genome analysis to investigate genetic variants-other than HLA class I and II-associated with negative outcome after HLA-identical sibling allo-HSCT in a cohort of 110 ?-Thalassemic patients. We identified two single-nucleotide polymorphisms (SNPs) in BAT2 (A/G) and BAT3 (T/C) genes, SNP rs11538264 and SNP rs10484558, both located in the HLA class III region, in strong linkage disequilibrium between each other (R(2)=0.92). When considered as single SNP, none of them reached a significant association with graft rejection (nominal P<0.00001 for BAT2 SNP rs11538264, and P<0.0001 for BAT3 SNP rs10484558), whereas the BAT2/BAT3 A/C haplotype was present at significantly higher frequency in patients who rejected as compared to those with functional graft (30.0% vs 2.6%, nominal P=1.15 × 10(-8); and adjusted P=0.0071). The BAT2/BAT3 polymorphisms and specifically the A/C haplotype may represent a novel immunogenetic factor associated with graft rejection in patients undergoing allo-HSCT. PMID:25111513

Piras, I S; Angius, A; Andreani, M; Testi, M; Lucarelli, G; Floris, M; Marktel, S; Ciceri, F; Nasa, G La; Fleischhauer, K; Roncarolo, M G; Bulfone, A; Gregori, S; Bacchetta, R

2014-11-01

330

Hyperhomocysteinemia and related genetic polymorphisms correlate with ulcerative colitis in Chinese Han population in Central China [corrected].  

PubMed

Increased levels of homocysteine are found systemically and in intestinal mucosa of patients with inflammatory bowel disease, and, specifically, in ulcerative colitis (UC). However, there are controversial reports regarding the factors contributing to increased levels of homocysteine in UC. Furthermore, little information is available regarding the relationship between hyperhomocysteinemia (HHcy), vitamin status, and genetic polymorphisms of homocysteine-related enzymes in these patients. This study examined four functional polymorphisms linked to homocysteine metabolism (MTHFR C677T and A1298C, MTR A2756G and MTRR A66G), and evaluated plasma levels of homocysteine, folate, and vitamin B(12) in 310 consecutive patients with UC and 936 age- and sex-matched healthy controls from southeast China. The variant allele and genotypic frequencies in MTHFR A1298C, MTR A2756G and MTRR A66G genes were significantly higher in patients with UC compared to healthy controls. Further, HHcy and low levels of folate and vitamin B(12) were more frequent in patients with UC. The MTR 2756G allele, extent of the disease, and gender were the independent determinants of HHcy in these patients. These findings suggest that genetic and nutritional factors have a synergetic effect on HHcy in patients with UC. In conclusion, our data highlight a prevention strategy for moderation of HHcy and supplementation with folate and vitamine B(12) in patients with UC from Southeast China. PMID:21947961

Jiang, Yi; Xia, Xuanping; Wang, Wenxing; Lin, Limiao; Xu, Changlong; Cai, Zhenzai; Zheng, Bo; Pei, Jihua; Shen, Sujian; Xia, Bing

2012-01-01

331

Distribution of genetic polymorphisms associated with hepatitis C virus (HCV) antiviral response in a multiethnic and admixed population.  

PubMed

The prevalence of genetic polymorphisms identified as predictors of therapeutic-induced hepatitis C virus (HCV) clearance differs among ethnic groups. However, there is a paucity of information about their prevalence in South American populations, whose genetic background is highly admixed. Hence, single-nucleotide polymorphisms rs12979860, rs1127354 and rs7270101 were characterized in 1350 healthy individuals, and ethnicity was assessed in 259 randomly selected samples. The frequency of rs12979860CC, associated to HCV treatment response, and rs1127354nonCC, related to protection against hemolytic anemia, were significantly higher among individuals with maternal and paternal Non-native American haplogroups (64.5% and 24.2%), intermediate among admixed samples (44.1% and 20.4%) and the lowest for individuals with Native American ancestry (30.4% and 6.5%). This is the first systematic study focused on analyzing HCV predictors of antiviral response and ethnicity in South American populations. The characterization of these variants is critical to evaluate the risk-benefit of antiviral treatment according to the patient ancestry in admixed populations. PMID:24841973

Trinks, J; Hulaniuk, M L; Caputo, M; Pratx, L Burgos; Ré, V; Fortuny, L; Pontoriero, A; Frías, A; Torres, O; Nuñez, F; Gadano, A; Corach, D; Flichman, D

2014-12-01

332

Population genetics of 30 insertion-deletion polymorphisms in two Chinese populations using Qiagen Investigator® DIPplex kit.  

PubMed

Insertion-deletion polymorphisms (INDELs) are short length diallelic polymorphisms caused by the insertion or deletion of several bases. INDEL markers can serve as useful supplementary or stand-alone assays for human identification. The Qiagen Investigator(®) DIPplex kit multiplexes 30 autosomal INDELs plus amelogenin for forensic use. The objective of this study was to estimate genetic diversity of 30 INDEL markers in the Han (the largest ethnic group of China, n=565) and She population (almost the smallest ethnic group of China, n=119), and to evaluate their usefulness in forensic genetics. In the Han and She, the mean observed heterozygosity values were 0.4133 and 0.3896, and the combined matching probability values were 1.80×10(-11) and 3.17×10(-11), respectively. Furthermore, the allele frequencies for each locus were compared with those in other reported Chinese subpopulations, and the forensic efficacy was compared between this kit and in-house developed INDEL assay. This study demonstrates that the Investigator(®) DIPplex kit can be used as a supplementary tool for human identity testing in China. PMID:24780854

Wang, Zheng; Zhang, Suhua; Zhao, Shumin; Hu, Zhen; Sun, Kuan; Li, Chengtao

2014-07-01

333

Genetic variation in agronomically important species of Stylosanthes determined using random amplified polymorphic DNA markers.  

PubMed

Random amplified polymorphic DNA (RAPD) markers were generated from 20 cultivars and accessions representing four agronomically important species of Stylosanthes, S. scabra, S. hamata, S. guianensis, and S. humilis. Approximately 200 fragments generated by 22 primers of arbitrary sequence were used to assess the level of DNA variation. Relatively low levels of polymorphism (0-16% of total bands in pairwise comparisons) were found within each species, while polymorphisms between the species were much higher (up to 46%). Very few polymorphisms (0-2%) were detected between the individuals of the same cultivar or accession. A phenogram of relationships among the species was constructed based on band sharing. Four main clusters corresponding to each species were readily distinguished on this phenogram. The allotetraploid species S. hamata and its putative diploid progenitor, S. humilis, were more similar to each other than to S. scabra and S. guianensis. No variation in RAPD markers was found between the two commercial S. hamata cvs 'Verano' and 'Amiga'. Cultivar 'Oxley' in S. guianensis was considerably different from the other cultivars and accessions of this species. The phylogenetic distinctions obtained with RAPDs were in agreement with other studies from morphology, cytology, and enzyme electrophoresis. The low level of polymorphisms observed within each species suggested that interspecific crosses may be a better vehicle for the construction of RAPD linkage maps in Stylosanthes. PMID:24196064

Kazan, K; Manners, J M; Cameron, D F

1993-02-01

334

ACE Insertion/Deletion Polymorphism and Diabetic Nephropathy: Clinical Implications of Genetic Information  

PubMed Central

Approximately 20–40% of diabetic patients develop nephropathy which is the leading cause of ESRD in developed countries. The ACE I/D polymorphism is thought to be a marker for functional polymorphism which regulates circulating and tissue ACE activity. While the initial study found a protective effect of the II genotype on the development of nephropathy in IDDM patients, subsequent studies have addressed the role of ACE I/D polymorphism in the development and progression of diabetic nephropathy. RAAS blockers are the first line drugs for the treatment hypertension associated with diabetes and have been widely used in everyday clinical practice for the purpose of reducing proteinuria in patients with various renal diseases. However, the antiproteinuric effect of RAAS blockers is variable and the percentage of reducing proteinuria is in the range of 20–80%. The antiproteinuric effect of RAAS blockers may be related to a number of factors: the type or the dose of RAAS blockers, the duration of therapy, the level of sodium intake, and the type of patient's ACE I/D genotype. Besides the nongenetic factors, drug responses, can be influenced by ACE gene polymorphism. In this review, we discuss the relationship between ACE I/D polymorphism and diabetic nephropathy and therapeutic response of RAAS blockers. PMID:25587546

Ha, Sung-Kyu

2014-01-01

335

Association of genetic polymorphisms with chronic obstructive pulmonary disease in the Hainan population: a case-control study  

PubMed Central

Purpose Chronic obstructive pulmonary disease (COPD) is predicted to become the third most common cause of death and the fifth most common cause of disability in the world by 2020. Recently, variants in the hypoxia-inducible factor 1? (HIF1A), cholinergic receptor, neuronal nicotinic, alpha polypeptide-5, and iron-responsive element-binding protein 2 gene (IREB2) genes were found to be associated with COPD. This study aims to identify whether the variations in these genes are related to COPD in the Hainan population of the People’s Republic of China. Patients and methods We genotyped 12 single nucleotide polymorphisms in a case-control study with 200 COPD cases and 401 controls from Hainan, People’s Republic of China. Odds ratios and 95% confidence intervals were estimated using the chi-squared (?2) test, genetic model analysis, haplotype analysis, and stratification analysis. Results In the genetic model analysis, we found that the genotype T/T of rs13180 of IREB2 decreased the COPD risk by 0.52-fold (P=0.025). But in the further stratification analysis, we failed to find the association between the selected single nucleotide polymorphisms with COPD risk in Han population. In addition, the haplotype analysis of HIF1A gene also was not found to be the possible haplotype associated with COPD risk. Conclusion Our results support that IREB2 rs13180 is associated with COPD in Hainan population. And this is the first time the HIF1A polymorphisms in COPD in a Chinese population has been reported, although we failed to find any significant result. PMID:25565795

Ding, Yipeng; Yang, Danlei; Xun, Xiaojie; Wang, Zhifeng; Sun, Pei; Xu, Dongchuan; He, Ping; Niu, Huan; Jin, Tianbo

2015-01-01

336

Lack of genetic associations between PPAR-? gene rs1801282 polymorphism and Alzheimer's disease in general population: A meta-analysis.  

PubMed

Published studies have evaluated the association between PPAR-? rs1801282 polymorphism and Alzheimer's disease (AD) susceptibility. However, a definitive conclusion remains elusive. The aim of this study was to derive a more precise estimation of this association. We searched PubMed, Embase, Alzgene database, Chinese National Knowledge Infrastructure (CNKI), China Biological Medicine Database and Wanfang Databases for related studies. Twelve case-control studies with a total of 4874 cases and 5439 controls were finally identified to be eligible studies in this meta-analysis. The association was assessed by summarizing the odds ratios (ORs) with the corresponding 95% confidence intervals (CIs). Overall, there was no significant association between PPAR-? rs1801282 polymorphism and Alzheimer's disease risk in all genetic models (the allele model G vs. C: OR=1.09, 95% CI 0.99-1.19, p=0.07; the homozygous model GG vs. CC: OR=1.04, 95% CI 0.75-1.44, p=0.80; heterozygote model GC vs. CC: OR=1.11, 95% CI 1,00-1.22, p=0.05; the dominant model GG+GC vs. CC: OR=1.10, 95% CI 1.00-1.22, p=0.05; the recessive model GG vs. GC+CC: OR=1.02, 95% CI 0.74-1.41, p=0.90). In subgroup analysis by ethnicity, no significant difference was found in both Asians and Caucasians. In summary, the present meta-analysis suggests that the PPAR-? rs1801282 polymorphism may not be associated with genetic susceptibility of AD in general population. PMID:25770052

Wu, Yongfu; Wu, Qingyun; Zhang, Hanbin; Chen, Chuyan; Chen, Guangzhao; Yang, Huiling; Qin, Dongyun; Fu, Hui

2015-06-01

337

CYP1A1 genetic polymorphism and polycyclic aromatic hydrocarbons on pulmonary function in the elderly: haplotype-based approach for gene-environment interaction.  

PubMed

Lung function may be impaired by environmental pollutants not only acting alone, but working with genetic factors as well. Few epidemiologic studies have been conducted to explore the interplay of polycyclic aromatic hydrocarbons (PAHs) exposure and genetic polymorphism on lung function in the elderly. For genetic polymorphism, haplotype is considered a more informative unit than single nucleotide polymorphism markers. Therefore, we examined the role of haplotype based-CYP1A1 polymorphism in the effect of PAHs exposure on lung function in 422 participants from a community-based panel of elderly adults in Seoul, Korea. Linear mixed effect models were fit to evaluate the association of PAH exposure markers (urinary 1-hydroxypyrene and 2-naphthol) with FVC, FEV?, FEV?/FVC, and FEF?????, and then the interaction with CYP1A1 haplotype constructed from three single nucleotide polymorphisms of the gene (rs4646421/rs4646422/rs1048943). Urinary 1-hydroxypyrene levels were inversely associated with FEV?/FVC (p<0.05), whereas urinary 2-naphthol levels failed to show associations with lung function. Urinary 1-hydroxypyrene was significantly associated with decrease in FEV?/FVC among participants with rs4646421 variants (CT+TT), rs4646422 wild-type (GG), and rs1048943 wild-type (AA). At least one TGA haplotype predicted a 0.88% (95% confidence interval, 0.31-1.45%) reduction in FEV?/FVC with an interquartile range increase in 1-hydroxypyrene, whereas no relationship was observed in participants without TGA haplotype (p for interaction=0.045). Similar patterns were also observed in FEF?????. We did not find any main effects of CYP1A1 genetic polymorphisms on lung functions. Our findings suggest that PAH exposure producing 1-hydroxypyrene as a metabolite compromises lung function in the elderly, and that haplotype-based CYP1A1 polymorphism modifies the risk. PMID:23816456

Choi, Yoon-Hyeong; Kim, Jin Hee; Hong, Yun-Chul

2013-08-29

338

Cold Spring Harbor Laboratory  

NSDL National Science Digital Library

Established in 1890, the Cold Spring Harbor Laboratory (CSHL) is one of the best-known and most respected private research institutions in the United States. Over the past century, the Laboratory has supported the careers of seven Nobel Prize recipients and it is particularly well-regarded for its work in the field of genetics research. Today, there are over 400 scientists who work at the facility in Long Island, and their work ranges across the areas of cancer, neuroscience, genomics, and bioinformatics. Their website is a cornucopia of information on their activities, and first-time visitors should start by reading over the "CSHL Headlines" scrolling updates on the homepage. After that, they can look at the "Research" section. Here they will find overviews of their primary research groups and links to some of their specialized facilities, like the Dolan DNA Learning Center. Most visitors will want to visit the "Library and Archives" section. Here they can learn about CSHL authors' publications and look through the digital collections. The digital collections include tributes to Barbara McClintock, who was awarded the Nobel Prize in 1983, and who worked at the Laboratory for four decades.

339

Genetic polymorphisms and activity of PON1 in a Mexican population  

SciTech Connect

Human paraoxonase (PON1) plays a role in detoxification of organophosphorus (OP) compounds by hydrolyzing the bioactive oxons, and in reducing oxidative low-density lipoproteins, which may protect against atherosclerosis. Some PON1 polymorphisms have been found to be responsible for variations in catalytic activity and expression and have been associated with susceptibility to OP poisoning and vascular diseases. Both situations are of public health relevance in Mexico. Therefore, the aim of this study was to evaluate PON1 phenotype and the frequencies of polymorphisms PON1 -162, -108, 55, and 192 in a Mexican population. The studied population consisted of unrelated individuals (n = 214) of either gender, 18-52 years old. Serum PON1 activity was assayed using phenylacetate and paraoxon as substrates. PON1 variants, -162, 55, and 192, were determined by real-time PCR using the TaqMan System, and PON1 -108 genotype by PCR-RFLP. We found a wide interindividual variability of PON1 activity with a unimodal distribution; the range of enzymatic activity toward phenylacetate was 84.72 to 422.0 U/mL, and 88.37 to 1645.6 U/L toward paraoxon. All four PON1 polymorphisms showed strong linkage disequilibrium (D% >90). PON1 polymorphisms -108, 55, and 192 were independently associated with arylesterase activity; whereas the activity toward paraoxon was related only with PON1 192 polymorphism, suggesting that this polymorphism is determinant to infer PON1 activity. A better understanding of the phenotype and genotypes of PON1 in Mexican populations will facilitate further epidemiological studies involving PON1 variability in OP poisoning and in the development of atherosclerosis.

Rojas-Garcia, A.E. [Seccion Externa de Toxicologia, CINVESTAV-IPN, PO Box 14-740, Mexico City, 07300 (Mexico); Solis-Heredia, M.J. [Seccion Externa de Toxicologia, CINVESTAV-IPN, PO Box 14-740, Mexico City, 07300 (Mexico); Pina-Guzman, B. [Seccion Externa de Toxicologia, CINVESTAV-IPN, PO Box 14-740, Mexico City, 07300 (Mexico); Vega, L. [Seccion Externa de Toxicologia, CINVESTAV-IPN, PO Box 14-740, Mexico City, 07300 (Mexico); Lopez-Carrillo, L. [Instituto Nacional de Salud Publica, Ave. Universidad No. 655, Col. Santa Ma. Ahuacatitlan, Cuernavaca, Mor., 62508 (Mexico); Quintanilla-Vega, B. [Seccion Externa de Toxicologia, CINVESTAV-IPN, PO Box 14-740, Mexico City, 07300 (Mexico)]. E-mail: mquintan@cinvestav.mx

2005-06-15

340

A genetic effect of IL-5 receptor ? polymorphism in patients with aspirin-exacerbated respiratory disease.  

PubMed

Persistent eosinophil activation in both the upper and lower airway mucosa is a central feature of aspirin-exacerbated respiratory disease (AERD). Eosinophil activation and survival are profoundly influenced by interleukin 5 (IL-5) and its receptor, IL-5R. In patients susceptible to allergic disorders, IL-5 receptor ? (IL5RA) polymorphisms have been reported; however, an association with AERD remains unclear. We hypothesize that IL5RA polymorphisms may contribute to eosinophil activation in AERD patients. We recruited 139 AERD patients, 171 aspirin-tolerant asthma patients and 160 normal controls. IL5RA polymorphisms (-5993G>A, -5567C>G and -5091G>A) were genotyped and functional activity of polymorphism was assessed by luciferase reporter assay and electrophoretic mobility shift assay (EMSA). There was no significant difference in the genotype frequency of the three polymorphisms among the three groups. AERD patients carrying the AA genotype at -5993G>A had a significantly higher presence of serum-specific immunoglobulin E (IgE) to staphylococcal enterotoxin A (P=0.008) than those with the GG/GA genotype. In vitro, the -5993A allele had a higher promoter activity compared with the -5993G allele in human mast cell (HMC-1; P=0.030) and human promyelocytic leukemia (HL-60; P=0.013) cells. In EMSA, a -5993A probe produced a specific shifted band than the -5993G had. These findings suggest that a functional polymorphism in IL5RA may contribute to eosinophil and mast cell activation along with specific IgE responses to staphylococcal enterotoxin A in AERD patients. PMID:23470716

Losol, Purevsuren; Kim, Seung-Hyun; Shin, Yoo Seob; Ye, Young Min; Park, Hae-Sim

2013-01-01

341

Genetic polymorphism in three glutathione s-transferase genes and breast cancer risk  

SciTech Connect

The role of the glutathione S-transferase (GST) enzyme family is to detoxify environmental toxins and carcinogens and to protect organisms from their adverse effects, including cancer. The genes GSTM1, GSTP1, and GSTT1 code for three GSTs involved in the detoxification of carcinogens, such as polycyclic aromatic hydrocarbons (PAHs) and benzene. In humans, GSTM1 is deleted in about 50% of the population, GSTT1 is absent in about 20%, whereas the GSTP1 gene has a single base polymorphism resulting in an enzyme with reduced activity. Epidemiological studies indicate that GST polymorphisms increase the level of carcinogen-induced DNA damage and several studies have found a correlation of polymorphisms in one of the GST genes and an increased risk for certain cancers. We examined the role of polymorphisms in genes coding for these three GST enzymes in breast cancer. A breast tissue collection consisting of specimens of breast cancer patients and non-cancer controls was analyzed by polymerase chain reaction (PCR) for the presence or absence of the GSTM1 and GSTT1 genes and for GSTP1 single base polymorphism by PCR/RFLP. We found that GSTM1 and GSTT1 deletions occurred more frequently in cases than in controls, and GSTP1 polymorphism was more frequent in controls. The effective detoxifier (putative low-risk) genotype (defined as presence of both GSTM1 and GSTT1 genes and GSTP1 wild type) was less frequent in cases than controls (16% vs. 23%, respectively). The poor detoxifier (putative high-risk) genotype was more frequent in cases than controls. However, the sample size of this study was too small to provide conclusive results.

Woldegiorgis, S.; Ahmed, R.C.; Zhen, Y.; Erdmann, C.A.; Russell, M.L.; Goth-Goldstein, R.

2002-04-01

342

COMT and ANKK1-Taq-Ia genetic polymorphisms influence visual working memory.  

PubMed

Complex cognitive tasks such as visual working memory (WM) involve networks of interacting brain regions. Several neurotransmitters, including an appropriate dopamine concentration, are important for WM performance. A number of gene polymorphisms are associated with individual differences in cognitive task performance. COMT, for example, encodes catechol-o-methyl transferase the enzyme primarily responsible for catabolizing dopamine in the prefrontal cortex. Striatal dopamine function, linked with cognitive tasks as well as habit learning, is influenced by the Taq-Ia polymorphism of the DRD2/ANKK1 gene complex; this gene influences the density of dopamine receptors in the striatum. Here, we investigated the effects of these polymorphisms on a WM task requiring the maintenance of 4 or 6 items over delay durations of 1 or 5 seconds. We explored main effects and interactions between the COMT and DRD2/ANKK1-Taq-Ia polymorphisms on WM performance. Participants were genotyped for COMT (Val(158)Met) and DRD2/ANKK1-Taq-Ia (A1+, A1-) polymorphisms. There was a significant main effect of both polymorphisms. Participants' WM reaction times slowed with increased Val loading such that the Val/Val homozygotes made the slowest responses and the Met/Met homozygotes were the fastest. Similarly, WM reaction times were slower and more variable for the DRD2/ANKK1-Taq-Ia A1+ group than the A1- group. The main effect of COMT was only apparent in the DRD2/ANKK1-Taq-Ia A1- group. These findings link WM performance with slower dopaminergic metabolism in the prefrontal cortex as well as a greater density of dopamine receptors in the striatum. PMID:23383291

Berryhill, Marian E; Wiener, Martin; Stephens, Jaclyn A; Lohoff, Falk W; Coslett, H Branch

2013-01-01

343

COMT and ANKK1-Taq-Ia Genetic Polymorphisms Influence Visual Working Memory  

PubMed Central

Complex cognitive tasks such as visual working memory (WM) involve networks of interacting brain regions. Several neurotransmitters, including an appropriate dopamine concentration, are important for WM performance. A number of gene polymorphisms are associated with individual differences in cognitive task performance. COMT, for example, encodes catechol-o-methyl transferase the enzyme primarily responsible for catabolizing dopamine in the prefrontal cortex. Striatal dopamine function, linked with cognitive tasks as well as habit learning, is influenced by the Taq-Ia polymorphism of the DRD2/ANKK1 gene complex; this gene influences the density of dopamine receptors in the striatum. Here, we investigated the effects of these polymorphisms on a WM task requiring the maintenance of 4 or 6 items over delay durations of 1 or 5 seconds. We explored main effects and interactions between the COMT and DRD2/ANKK1-Taq-Ia polymorphisms on WM performance. Participants were genotyped for COMT (Val158Met) and DRD2/ANKK1-Taq-Ia (A1+, A1?) polymorphisms. There was a significant main effect of both polymorphisms. Participants' WM reaction times slowed with increased Val loading such that the Val/Val homozygotes made the slowest responses and the Met/Met homozygotes were the fastest. Similarly, WM reaction times were slower and more variable for the DRD2/ANKK1-Taq-Ia A1+ group than the A1? group. The main effect of COMT was only apparent in the DRD2/ANKK1-Taq-Ia A1? group. These findings link WM performance with slower dopaminergic metabolism in the prefrontal cortex as well as a greater density of dopamine receptors in the striatum. PMID:23383291

Berryhill, Marian E.; Wiener, Martin; Stephens, Jaclyn A.; Lohoff, Falk W.; Coslett, H. Branch

2013-01-01

344

Genetic differentiation among 6 populations of red deer (Cervus elaphus L.) in Poland based on microsatellite DNA polymorphism.  

PubMed

Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is DNA analysis, which allows for direct determination of the differences and changes within a group of animals. Because the analysis of microsatellite polymorphism in different Cervidae populations revealed considerable genetic variability in individual populations, it was important to test a set of markers in animals from these populations.The study was performed with muscle tissue and blood samples collected from a total of 793 red deer. Six groups (subpopulations) of red deer were defined according to region: Masurian (330 animals), Bieszczady (194 animals), Ma?opolska (80 animals), Sudety (76 animals), Lower Silesian (62 animals) and Lubusz (51 animals). The analysis involved 12 STR markers (BM1818, OarAE129, OarFCB5, OarFCB304, RM188, RT 1, RT 13, T26, T156, T193, T501, TGLA53), for which conditions for simultaneous amplification were established.Based on this study, it is concluded that the chosen set of 12 microsatellite markers could be used to evaluate the genetic structure and to monitor changes in Poland's red deer population. PMID:25475981

Radko, Anna; Zalewski, D; Rubi?, Dominika; Szumiec, Agnieszka

2014-12-01

345

Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae)  

PubMed Central

We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (2–10 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and FST value showed weak genetic structuring (FST = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species. PMID:22481877

de Castro e Souza, Andiara Silos Moraes; Miño, Carolina Isabel; Del Lama, Silvia Nassif

2012-01-01

346

Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae).  

PubMed

We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (2-10 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and F(ST) value showed weak genetic structuring (F(ST) = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species. PMID:22481877

de Castro E Souza, Andiara Silos Moraes; Miño, Carolina Isabel; Del Lama, Silvia Nassif

2012-01-01

347

Scanning of genetic effects of alcohol metabolism gene (ADH1B and ADH1C) polymorphisms on the risk of alcoholism.  

PubMed

Alcoholism is a multifactorial and polygenic disorder involving complex gene-to-gene and gene-to-environment interactions. Alcohol metabolism is one of the biological determinants that could significantly be influenced by genetic polymorphisms in alcohol-metabolism genes. These genetic polymorphisms are believed to influence drinking behavior and development of alcoholism. Direct DNA sequencing of whole ADH1B and ADH1C genes revealed 36 sequence variants, including six nonsynonymous and 14 novel polymorphisms. Seventeen polymorphisms among them were selected for genotyping in a larger study (n = 352) based on linkage disequilibria (LDs) among SNPs, locations, and frequencies. Hardy-Weinberg equilibrium (HWE) analyses of polymorphisms revealed severe deviations only in alcoholics, which strongly suggest that a selection bias (or pressure) may be involved. The analyses of genotype distribution in alcoholics (n = 106) and normal controls (n = 246) showed dramatic associations with the risk of alcoholism. Fourteen polymorphisms in ADH1C and ADH1B showed a series of different strengths of association and magnitudes of risk. Based on referent and subgroup analysis, it was strongly suggested that the genetic effects come from the ADH1B*47Arg/*47Arg genotype, and that the positive signals from other sites are just tracking the genetic effect of ADH1B His47Arg. In this article we present summaries of previous studies and of the present study, to give an overview of the worldwide effects of ADH1B His47Arg on the risk of alcoholism. The information derived from this study could be valuable for understanding the genetic factors involved in the risk of alcoholism and facilitate further investigation in other ethnic groups. PMID:16086315

Choi, Ihn-Geun; Son, Hyun-Gyun; Yang, Byung-Hwan; Kim, Seok Hyeon; Lee, Jun-Suk; Chai, Young-Gyu; Son, Bong Ki; Kee, Baik Seok; Park, Byung Lae; Kim, Lyoung Hyo; Choi, Yoo Hyun; Shin, Hyoung Doo

2005-09-01

348

A LCP 85-384 genetic linkage map enriched with polymorphic SSR markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sugarcane (Saccharum spp. hybrids) cultivars, such as Q165, R570 and LCP 85-384, have been used to construct genetic segregation populations for the development of genetic linkage maps. Based on the genetic linkage map for a selfed-progeny population of R570, the French research group at CIRAD tagge...

349

Adaptive Color Polymorphism and Unusually High Local Genetic Diversity in the Side-Blotched Lizard, Uta stansburiana  

PubMed Central

Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation. PMID:23133520

Micheletti, Steven; Parra, Eliseo; Routman, Eric J.

2012-01-01

350

Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.  

PubMed

Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation. PMID:23133520

Micheletti, Steven; Parra, Eliseo; Routman, Eric J

2012-01-01

351

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers  

USGS Publications Warehouse

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, B.L.; Reed, K.D.

2011-01-01

352

Boston Harbor Ecosystems  

NSDL National Science Digital Library

This United States Geological Survey (USGS) site is designed to summarize and make available results of scientific research conducted in Boston Harbor, Massachusetts since 1985. A computer image of the harbor indicates ecosystem zones with descriptions (watershed, estuary, inner shelf, and basin), sewage outfall sites, and rock types. Links are provided for more information on this region.

353

Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population.  

PubMed

Single nucleotide polymorphisms (SNPs) are an interesting option to facilitate the analysis of highly degraded DNA by allowing the reduction of the size of the DNA amplicons. The SNPforID 52-plex panel is a clear example of the use of non-coding SNPs in forensic genetics. However, nonstop advances in studies of genetic polymorphisms are leading to the discovery of new associations between SNPs and diseases. The aim of this study was to perform a comprehensive review of the state of association between the 52 SNPs in the 52-plex panel and diseases or other traits related to their treatment, such as drug response characters. In order to achieve this goal, we have conducted a bioinformatic search for each SNP included in the panel and the SNPs in linkage disequilibrium (LD) with them in the European population (r (2) ?>?0.8). A total of 424 SNPs (52 in the panel and 372 in LD) were investigated in PubMed, Scopus, and dbSNP databases. Our results show that three SNPs in the SNPforID 52-plex panel (rs2107612, rs1979255, rs1463729) have been associated with diseases such as hypertension or macular degeneration, as well as drug response. Similarly, three out of the 372 SNPs in LD (rs2107614, r (2) ?=?0.859; rs765250, r (2) ?=?0.858; rs11064560, r (2) ?=?0,887) are also associated with various pathologies. In view of these results, we propose the need for a periodic review of the SNPs used in forensic genetics in order to keep their associations with diseases or related phenotypes updated and to evaluate their continuity in forensic panels for avoiding legal and ethical conflicts. PMID:25763762

Pombar-Gomez, Maria; Lopez-Lopez, Elixabet; Martin-Guerrero, Idoia; Carles, Africa Garcia-Orad; de Pancorbo, Marian M

2015-05-01

354

Manganese Superoxide Dismutase (MnSOD) Genetic Polymorphisms, Dietary Antioxidants, and Risk of Breast Cancer 1  

Microsoft Academic Search

Oxidative stress, resulting from the imbalance between prooxidant and antioxidant states, damages DNA, proteins, cell membranes, and mito- chondria and seems to play a role in human breast carcinogenesis. Dietary sources of antioxidants (chemical) and endogenous antioxidants (enzymat- ic), including the polymorphic manganese superoxide dismutase (Mn- SOD), can act to reduce the load of oxidative stress. We hypothesized that the

Christine B. Ambrosone; Jo L. Freudenheim; Patricia A. Thompson; Elise Bowman; John E. Vena; James R. Marshall; Saxon Graham; Rosemary Laughlin; Takuma Nemoto; Peter G. Shields

1999-01-01

355

Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Accurate identification of individual genotypes is important for cacao (Theobroma cacao L.) breeding, germplasm conservation and seed propagation. The development of single nucleotide polymorphism (SNP) markers in cacao offers an effective way to use a high-throughput genotyping system for cacao gen...

356

An insight into the genetic polymorphism among European populations of Lactuca serriola assessed by AFLP  

Microsoft Academic Search

Prickly lettuce (Lactuca serriola) is world-wide distributed and very variable species generally considered as a progenitor of the cultivated lettuce (Lactuca sativa). Altogether, 50 populations of L. serriola were characterized by means of amplified fragment length polymorphism (AFLP) and by isozyme analysis. Relationships among individuals and populations were examined by applying the unweighted pair-group method with the arithmetic averages (UPGMA)

Aleš Lebeda; Miloslav Kitner; Marta Dziechciarková; Ivana Doležalová; Eva K?ístková; Pim Lindhout

2009-01-01

357

Genetic variation and cultivar identification of Jamaican yam germplasm by random amplified polymorphic DNA analysis  

Microsoft Academic Search

We have used random amplified polymorphic DNA (RAPD) analysis to characterize eleven cultivars of the five economically most important yam species grown in Jamaica (Dioscorea alata, D. cayenensis, D. rotundata, D. trifida and D. esculenta). Amplification of genomic DNA samples with nine different arbitrary 10mer primers revealed a total of 338 different band positions, ranging in size from 0.3 to

H. N. Asemota; J. Ramser; C. Lopéz-Peralta; K. Weising; G. Kahl

1995-01-01

358

The Genetic Basis of a Flower Color Polymorphism in the Common Morning Glory (Ipomoea purpurea)  

Microsoft Academic Search

The common morning glory (Ipomoea purpurea) is highly polymorphic for flower color. Part of this phenotypic variation is due to allelic variation at the P locus. This locus determines whether flowers will be purple or pink, where purple is dominant to pink. We have determined that the anthocyanin biosynthetic gene flavonoid 39-hydroxylase (f39h) corresponds to the P locus. In the

R. A. Zufall; M. D. RAUSHER

2003-01-01

359

A genetic polymorphism in the sex-linked ATP5A1 gene is associated with individual fitness in Ovenbirds (Seiurus aurocapilla)  

PubMed Central

While testing genetic sexing techniques in Ovenbirds (Seiurus aurocapilla), we found a genetic polymorphism in the ATP5A1 gene in 38% of individuals. The Z? allele included changes in both intronic and exonic portions of the sequenced region, but there was no evidence that this changed the resulting ATP synthase product. Males that had one or more copies of this allele had higher relative body mass (mass corrected for size) than other genotypes. This allele was unrelated to stable isotope signatures, and so was not a useful predictor of latitude within the eastern portion of the Ovenbird breeding range. Future studies are needed to determine whether this polymorphism may be a useful geographic marker. This study is the first to link polymorphisms in the sex-linked ATP5A1 gene with fitness effects. PMID:22833803

Toms, Judith D; Eggert, Lori S; Arendt, Wayne J; Faaborg, John

2012-01-01

360

Genetic polymorphisms of IL-6 and IL-10 genes correlate with lung cancer in never-smoking Han population in China  

PubMed Central

Lung cancer is one of the most common cancers in the world, especially in China. It is believed that genetic polymorphisms played a role in cancer susceptibility. Here we investigated the association of interleukin-6 (IL-6) and interleukin-10 (IL-10) gene polymorphisms with the susceptibility of lung cancer in never-smoking Chinese Han population. In this study, we performed a case-control study including 330 cases of never-smoking lung cancer patients and 336 cancer-free never-smoking controls in Chinese Han population. We used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to identify gene polymorphisms, and then verified by sequencing method. The results indicated that the four single nucleotide polymorphisms (IL-6 -1363T/G and -572G/C, IL-10 -819T/C and -592A/C) were genotyped by PCR-RFLP and confirmed by sequencing, and we found that the allelic frequencies of G in IL-6 -1363T/G, C in IL-10 -819T/C and C in IL-10 -592A/C were significantly increased in lung cancer patients, by comparing with the control group. However, there was no significant difference in the distribution of the IL-6 572G/C polymorphisms between patients and controls. In conclusion, the IL-6 -1363T/G, IL-10 -819T/C and IL-10 -592A/C polymorphisms are closely related to genetic susceptibility to lung cancer in never-smoking Chinese Han population, and these genetic variants might be used as molecular markers for detecting lung cancer susceptibility.

Zhang, Ying-Min; Mao, Yi-Min; Sun, Yu-Xia

2015-01-01

361

The Associations between Two Vital GSTs Genetic Polymorphisms and Lung Cancer Risk in the Chinese Population: Evidence from 71 Studies  

PubMed Central

Background The genetic polymorphisms of glutathione S-transferase (GSTs) have been suspected to be related to the development of lung cancer while the current results are conflicting, especially in the Chinese population. Methods Data on genetic polymorphisms of glutathione S-transferase Mu 1 (GSTM1) from 68 studies, glutathione S-transferase theta 1 (GSTT1) from 17 studies and GSTM1-GSTT1 from 8 studies in the Chinese population were reanalyzed on their association with lung cancer risk. Odds ratios (OR) were pooled using forest plots. 9 subgroups were all or partly performed in the subgroup analyses. The Galbraith plot was used to identify the heterogeneous records. Potential publication biases were detected by Begg's and Egger's tests. Results 71 eligible studies were identified after screening of 1608 articles. The increased association between two vital GSTs genetic polymorphisms and lung cancer risk was detected by random-effects model based on a comparable heterogeneity. Subgroup analysis showed a significant relationship between squamous carcinoma (SC), adenocarcinoma (AC) or small cell lung carcinoma (SCLC) and GSTM1 null genotype, as well as SC or AC and GSTT1 null genotype. Additionally, smokers with GSTM1 null genotype had a higher lung cancer risk than non-smokers. Our cumulative meta-analysis demonstrated a stable and reliable result of the relationship between GSTM1 null genotype and lung cancer risk. After the possible heterogeneous articles were omitted, the adjusted risk of GSTs and lung cancer susceptibility increased (fixed-effects model: ORGSTM1?=?1.23, 95% CI: 1.19 to 1.27, P<0.001; ORGSTT1?=?1.18, 95% CI: 1.10 to 1.26, P<0.001; ORGSTM1-GSTT1?=?1.33, 95% CI: 1.10 to 1.61, P?=?0.004). Conclusions An increased risk of lung cancer with GSTM1 and GSTT1 null genotype, especially with dual null genotype, was found in the Chinese population. In addition, special histopathological classification of lung cancers and a wide range of gene-environment and gene-gene interaction analysis should be taken into consideration in future studies. PMID:25036724

Ma, Ting; Han, Liyuan; Mao, Guochuan; Chen, Jian; Yue, Xia; Wang, Huiqin; Zhang, Lu; Jin, Guixiu; Jiang, Jianmin; Zhao, Jinshun; Zou, Baobo

2014-01-01

362

Power and Sample Size Calculations for Case-Control Genetic Association Tests when Errors Are Present: Application to Single Nucleotide Polymorphisms  

Microsoft Academic Search

The purpose of this work is to quantify the effects that errors in genotyping have on power and the sample size necessary to maintain constant asymptotic Type I and Type II error rates (SSN) for case-control genetic association studies between a disease phenotype and a di-allelic marker locus, for example a single nucleotide polymorphism (SNP) locus. We consider the effects

Derek Gordon; Stephen J. Finch; Michael Nothnagel; Jürg Ott

2002-01-01

363

Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Single-nucleotide polymorphisms (SNPs) are the most common genetic markers in Theobroma cacao, occurring approximately once in every 200 nucleotides. SNPs, like microsatellites, are co-dominant and PCR-based, but they have several advantages over microsatellites. They are unambiguous, so that a SN...

364

Genetic relationships of tetraploid Elymus species and their genomic donor species inferred from polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions  

Microsoft Academic Search

The genetic relationships of 38 individuals from 13 Elymus tetraploid species, two Pseudoroegneria species and one Hordeum species were examined using polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions. The 13 Elymus species contain SH and SY genomes with either a single spikelet or multiple spikelets per rachis node. The Pseudoroegneria and Hordeum species contain an S genome

Erin McMillan; Genlou Sun

2004-01-01

365

A DNA Science research and training programme for Secondary School and Junior College teachers and students on genetic polymorphisms in human, animals and plants in Singapore  

Microsoft Academic Search

The objective of this project is to train teachers and students to be competent in the principles and practice of DNA science by working on genetic polymorphisms of humans, animals and plants in Singapore. MOE has provided JC and Secondary Schools in Singapore the life sciences research facilities and equipment which cost millions of dollar s. This project is therefore

Koh CL; Chin HLC; Lum SKY; Tan J; Ang DTJ

366

GENETIC DIVERSITY OF FLAVOBACTERIUM COLUMNARE EXAMINED BY RESTRICTION FRAGMENT LENGTH POLYMORPHISM AND SEQUENCING OF THE 16S RIBOSOMAL RNA GENE AND THE 16S-23S RDNA SPACER  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic variability among strains of Flavobacterium columnare, isolated in the United States, was characterized by restriction fragment length polymorphism (RFLP) and phylogenetic analysis based on the sequence of the 16S rRNA gene. Twenty-seven isolates of F. columnare were differentiated into thr...

367

Genetic Relatedness among Environmental, Clinical, and Diseased-Eel Vibrio vulnificus Isolates from Different Geographic Regions by Ribotyping and Randomly Amplified Polymorphic DNA PCR  

Microsoft Academic Search

Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel iso- lates from different geographic origins, as well as seawater and shellfish isolates from the western Mediter- ranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with KpnI and hybridized with an oli-

COVADONGA R. ARIAS; MARIA JESUS PUJALTE; ESPERANZA GARAY; ROSA AZNAR

1998-01-01

368

Genetic polymorphism of PIF (parotid isoelectric focusing variant) proteins with linkage to the PPP (parotid proline-rich protein) gene complex  

Microsoft Academic Search

Genetic polymorphism is found among the PIF (parotid isoelectric focusing variant) salivary proteins after separation by prolonged isoelectric focusing in pH 3.5–5.2 urea polyacrylamide slab gels subsequently stained for protein. Two PIF proteins are either present (PIF +) or absent (PIF -) from all salivas. The phenotypes are determined by autosomal inheritance of two alleles, PIF+ and PIF-. Gene frequencies

Edwin A. Azen; Carter Denniston

1981-01-01

369

Low level maternal smoking and infant birthweight reduction: genetic contributions of GSTT1 and GSTM1 polymorphisms  

PubMed Central

Background Genetic susceptibility to tobacco smoke might modify the effect of smoking on pregnancy outcomes. Methods We conducted a case–control study of 543 women who delivered singleton live births in Kaunas (Lithuania), examining the association between low-level tobacco smoke exposure (mean: 4.8 cigarettes/day) during pregnancy, GSTT1 and GSTM1 polymorphisms and birthweight of the infant. Multiple linear-regression analysis was performed adjusting for gestational age, maternal education, family status, body mass index, blood pressure, and parity. Subsequently, we tested for the interaction effect of maternal smoking, GSTT1 and GSTM1 genes polymorphisms with birthweight by adding all the product terms in the regression models. Results The findings suggested a birthweight reduction among light-smoking with the GSTT1–null genotype (?162.9 g, P = 0.041) and those with the GSTM1–null genotype (?118.7 g, P = 0.069). When a combination of these genotypes was considered, birthweight was significantly lower for infants of smoking women the carriers of the double-null genotypes (?311.2 g, P = 0.008). The interaction effect of maternal smoking, GSTM1 and GSTT1 genotypes was marginally significant on birthweight (?234.5 g, P = 0.078). Among non-smokers, genotype did not independently confer an adverse effect on infant birthweight. Conclusions The study shows the GSTT1–null genotype, either presents only one or both with GSTM1–null genotype in a single subject, have a modifying effect on birthweight among smoking women even though their smoking is low level. Our data also indicate that identification of the group of susceptible subjects should be based on both environmental exposure and gene polymorphism. Findings of this study add additional evidence on the interplay among two key GST genes and maternal smoking on birth weight of newborns. PMID:23268570

2012-01-01

370

Distribution of genetic polymorphisms of genes encoding drug metabolizing enzymes & drug transporters - a review with Indian perspective  

PubMed Central

Phase I and II drug metabolizing enzymes (DME) and drug transporters are involved in the absorption, distribution, metabolism as well as elimination of many therapeutic agents, toxins and various pollutants. Presence of genetic polymorphisms in genes encoding these proteins has been associated with marked inter-individual variability in their activity that could result in variation in drug response, toxicity as well as in disease predisposition. The emergent field pharmacogenetics and pharmacogenomics (PGx) is a promising discipline, as it predicts disease risk, selection of proper medication with regard to response and toxicity, and appropriate drug dosage guidance based on an individual's genetic make-up. Consequently, genetic variations are essential to understand the ethnic differences in disease occurrence, development, prognosis, therapeutic response and toxicity. For that reason, it is necessary to establish the normative frequency of these genes in a particular population before unraveling the genotype-phenotype associations. Although a fair amount of allele frequency data are available in Indian populations, the existing pharmacogenetic data have not been compiled into a database. This review was intended to compile the normative frequency distribution of the variants of genes encoding DMEs (CYP450s, TPMT, GSTs, COMT, SULT1A1, NAT2 and UGTs) and transporter proteins (MDR1, OCT1 and SLCO1B1) with Indian perspective. PMID:24604039

Umamaheswaran, Gurusamy; Kumar, Dhakchinamoorthi Krishna; Adithan, Chandrasekaran

2014-01-01

371

[Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism].  

PubMed

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups. PMID:15174289

Khusainova, R I; Akhmetova, V L; Kutuev, I A; Salimova, A Z; Korshunova, T Iu; Lebedev, Iu B; Khusnutdinova, E K

2004-04-01

372

Functional IL-23R rs10889677 Genetic Polymorphism and Risk of Multiple Solid Tumors: a Meta-Analysis  

PubMed Central

Interleukin-23 receptor (IL23R) can interact with IL-23 and, thus, is involved in the T-helper 17 (Th17) cell-mediated inflammatory process as well as tumorigenesis. Recently, a functional single nucleotide polymorphism (SNP) rs10889677 has been identified in the 3’-untranslated region of IL-23R. It has been showed that the rs10889677AC SNP could increase the binding affinity of microRNA let-7f and downregulate IL-23R expression. Several case-control studies have examined the association between this SNP and genetic susceptibility of multiple solid tumors. However, the conclusions are conflicting. Therefore, we conducted this meta-analysis to systematically study the role of this functional IL-23R SNP in development of multiple solid tumors. There are a total of 5 studies are eligible (6731 cases and 7296 healthy controls). Either fixed-effect model or random-effect model was used to calculate pooled odds ratios (ORs) and the 95% confidence interval (95% CI). Significant association between this functional rs10889677 genetic variant and risk of multiple solid tumors were observed (CC genotype vs. AA genotype: OR = 0.59, 95% CI = 0.53-0.66, P < 0.001). These findings demonstrated that the IL-23R rs10889677 genetic variant might play an important part during malignant transformation of multiple solid tumors. PMID:24278297

Chen, Yunzhi; Yao, Yongjun; Ma, Yanhui; Gao, Yan

2013-01-01

373

Abstract Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of  

E-print Network

and/or hyperaccumulation. Keywords CAPS Ã? Gene marker Ã? Microsatellite Ã? Phytoremediation Ã? Population genetics Introduction The development of studies on phytoremediation greatly increased the interest

Alvarez, Nadir

374

Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancer  

PubMed Central

Abstract MicroRNAs (miRNAs) are small non-coding RNAs, which regulate gene expression. Single nucleotide polymorphisms (SNPs) may occur in miRNA biogenesis pathway genes, primary miRNA, pre-miRNA or a mature miRNA sequence. Such polymorphisms may be functional with respect to biogenesis and actions of mature miRNA. Specific SNPs were identified in predicted miRNA target sites within 3? untranslated regions of mRNAs. These SNPs have a potential to affect the efficiency of miRNA binding to the target sites or can create or disrupt binding sites. Resulting gene dysregulation may involve changes in phenotype and may eventually prove critical for the susceptibility to cancer and its onset as well as for estimates of prognosis and therapy response. In this review, we provide a comprehensive list of potentially functional miRNA-related SNPs and summarize their importance as candidate cancer biomarkers. PMID:21692980

Slaby, Ondrej; Bienertova-Vasku, Julie; Svoboda, Marek; Vyzula, Rostislav

2012-01-01

375

Genetic polymorphisms of glutathione S -transferase T1 and bladder cancer risk: a meta-analysis  

Microsoft Academic Search

In recent years, there have been numerous papers emphasizing the relationship between Glutathione S-transferases polymorphisms and bladder cancer risk, but the findings have not reached a consensus. The relationship between\\u000a glutathione S-transferase T 1 null genotype and bladder cancer susceptibility is now even more disputable. Therefore, we present a meta-analysis\\u000a of (nested) case–controlled, genotype-based studies (including 37 studies, 6,986 cases

Fang-fang Zeng; Sheng-yuan Liu; Wen Wei; Song-po Yao; Shui Zhu; Ke-shen Li; Gang Wan; Hai-tao Zhang; Min Zhong; Bin-you Wang

2010-01-01

376

Genetic Variant BDNF (Val66Met) Polymorphism Alters Anxiety-Related Behavior  

Microsoft Academic Search

A common single-nucleotide polymorphism in the brain-derived neurotrophic factor (BDNF) gene, a methionine (Met) substitution for valine (Val) at codon 66 (Val66Met), is associated with alterations in brain anatomy and memory, but its relevance to clinical disorders is unclear. We generated a variant BDNF mouse (BDNFMet\\/Met) that reproduces the phenotypic hallmarks in humans with the variant allele. BDNFMet was expressed

Zhe-Yu Chen; Deqiang Jing; Kevin G. Bath; Alessandro Ieraci; Tanvir Khan; Chia-Jen Siao; Daniel G. Herrera; Miklos Toth; Chingwen Yang; Bruce S. McEwen; Barbara L. Hempstead; Francis S. Lee

2006-01-01

377

Genetic Polymorphism of Human CYP2E1: Characterization of Two Variant Alleles  

Microsoft Academic Search

SUMMARY Ethanol-inducible CYP2E1 is an enzyme of major toxicological interest because it metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. CYP2E1 has also been implicated in alcohol liver disease because of its contribution to oxidative stress. Previously, polymorphic alleles with mutations in introns and in the 59-flanking regulatory region have been described, and their presence has been related to

YIN HU; MIKAEL OSCARSON; INGER JOHANSSON; MARJA-LIISA DAHL; MARCO TABONE; EMANUELE ALBANO; MAGNUS INGELMAN-SUNDBERG

378

Association of FGFR4 genetic polymorphisms with prostate cancer risk and prognosis  

Microsoft Academic Search

The fibroblast growth factor receptor 4 (FGFR4) is thought to be involved in many critical cellular processes and has been associated with prostate cancer risk. Four single nucleotide polymorphisms (SNPs) within or near FGFR4 were analyzed in a population-based study of 1458 prostate cancer patients and 1352 age-matched controls. We found no evidence to suggest that any of the FGFR4

L M FitzGerald; E Karlins; D M Karyadi; E M Kwon; J S Koopmeiners; J L Stanford; E A Ostrander; EA Ostrander

2009-01-01

379

Combined glutathione-S-transferase M1 and T1 genetic polymorphism and tacrine hepatotoxicity  

Microsoft Academic Search

Background: Glutathione conjugation of tacrine reactive metabolites depends in part on the activity of glutathione-S -transferases (GST), of which two isozymes (GST M1 and GST T1) are polymorphically expressed.Objective and Methods: To determine whether GST M1, GST T1, and the combined GST M1 and GST T1 null genotypes predict individual susceptibility to tacrine hepatotoxicity, 141 patients with mild to moderate

Tabassome Simon; Laurent Becquemont; Murielle Mary-Krause; Isabelle de Waziers; Philippe Beaune; Christian Funck-Brentano; Patrice Jaillon

2000-01-01

380

Genetic polymorphisms of the RGS4 and dorsolateral prefrontal cortex morphometry among first episode schizophrenia patients  

Microsoft Academic Search

Polymorphisms of the gene encoding the regulator of G-protein signaling subtype 4 (RGS4) may confer risk for schizophrenia.1 DNA microarray studies of postmortem brain samples have shown RGS4 underexpression in the dorsolateral prefrontal cortex (DLPFC, area 9), motor and visual cortices in schizophrenia patients relative to control subjects.2 Underexpression of RGS4 in DLPFC is pathophysiologically significant because DLPFC pathology in

K M R Prasad; K V Chowdari; V L Nimgaonkar; M E Talkowski; D A Lewis; M S Keshavan

2005-01-01

381

CYP1A1 and GSTM1 genetic polymorphisms in lung cancer populations exposed to arsenic in drinking water.  

PubMed

Region II of Chile is the most important copper mining area in the world and it shows the highest lung cancer mortality rate in the country (35/100,000). The population in Antofagasta, the main city of Region II, was exposed from 1958 to 1970 to 860 microg m(-3) arsenic (As) in drinking water and has currently been declining to 40 microg m(-3). Glutathione serves as a reducing agent and glutathione S-transferase (GST) may have an important role in As methylation capacity and body retention. In the current study, the null genotype of GSTM1 and the MspI polymorphism of CYP450 1A1 were investigated in lung cancer patients and in healthy volunteers of Region II. In males, the 2A genotype of MspI represented a highly significant estimated relative lung cancer risk (OR=2.60). Relative lung cancer risk for the combined 2A/null GSTM1 genotypes was 2.51, which increased with the smoking habit (OR=2.98). In Region II, the cancer mortality rate for As-associated cancers at least partly might be related to differences in As biotransformation. Genetic biomarkers such as 2A and GSTM1 polymorphisms in addition to DR70 as screening biomarkers might provide relevant information to identify individuals with a high risk for lung cancer as prevention and protection actions to protect public health. PMID:16012082

Adonis, M; Martínez, V; Marín, P; Gil, L

2005-05-01

382

Genetic polymorphisms in miRNAs targeting the estrogen receptor and their effect on breast cancer risk.  

PubMed

Breast cancer is the cancer that most commonly affects women worldwide. This type of cancer is genetically complex, but is strongly linked to steroid hormone signaling systems. Because microRNAs act as translational regulators of multiple genes, including the steroid nuclear receptors, single nucleotide polymorphisms (SNPs) in microRNA genes can have potentially wide-ranging influences on breast cancer development. Thus, this study was conducted to investigate the relationships between six SNPs (rs6977848, rs199981120, rs185641358, rs113054794, rs66461782, and rs12940701) located in four miRNA genes predicted to target the estrogen receptor (miR-148a, miR-221, miR-186, and miR-152) and breast cancer risk in Caucasian Australian women. By using high resolution melt analysis (HRM) and polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), 487 samples including 225 controls and 262 cases were genotyped. Analysis of their genotype and allele frequencies indicated that the differences between case and control populations were not significant for rs6977848, rs66461782, and rs12940701 because their p-values are 0.81, 0.93, and 0.1, respectively, which are all above the threshold value (p = 0.05). Our data thus suggests that these SNPs do not affect breast cancer risk in the tested population. In addition, rs199981120, rs185641358, and rs113054794 could not be found in this population, suggesting that these SNPs do not occur in Caucasian Australians. PMID:25606406

Nguyen-Dien, Giang T; Smith, Robert A; Haupt, Larisa M; Griffiths, Lyn R; Nguyen, Hue T

2014-12-01

383

Genetic polymorphism of the CAPN1 gene is associated with meat quality traits in Japanese quail.  

PubMed

1. The objective of the study was to investigate the polymorphisms in two regions of the calpain 1 (CAPN1) gene and their association with breast and thigh meat quality in Japanese quail (ultimate pH (pHu), lightness, redness, yellowness, drip loss, thawing-cooking loss, water holding capacity and shear force, SF). 2. Blood samples were collected randomly from 100 birds and DNA was extracted using a commercial kit. Genotypes were determined by PCR amplification followed by single-strand conformation polymorphism (SSCP) analysis. The effect of CAPN1 genotypes on meat quality traits were analysed using a general linear model (GLM) procedure. 3. Genotypes of the CAPN1 gene in the first region (217-bp) analysed were significantly associated with yellowness and SF. The TT genotype showed significantly higher yellowness and lower shear force (more tenderness) than CT and CC genotypes. Genotypes of the second region of the gene (intron 4, 800-bp) were significantly associated with pHu, redness and SF of the breast meat. The BB genotype showed significantly lower pHu and redness and higher SF (lower tenderness) than other genotypes. 4. Information on polymorphisms of the CAPN1 gene will eventually provide useful information for improving meat quality of Japanese quail through marker-assisted selection. PMID:23647179

Rasouli, Z; Zerehdaran, S; Azari, M A; Shargh, M S

2013-01-01

384

A Genetic Polymorphism of the Endogenous Opioid Dynorphin Modulates Monetary Reward Anticipation in the Corticostriatal Loop  

PubMed Central

The dynorphin/?-opioid receptor (KOP-R) system has been shown to play a role in different types of behavior regulation, including reward-related behavior and drug craving. It has been shown that alleles with 3 or 4 repeats (HH genotype) of the variable nucleotide tandem repeat (68-bp VNTR) functional polymorphism of the prodynorphin (PDYN) gene are associated with higher levels of dynorphin peptides than alleles with 1 or 2 repeats (LL genotype). We used fMRI on N?=?71 prescreened healthy participants to investigate the effect of this polymorphism on cerebral activation in the limbic-corticostriatal loop during reward anticipation. Individuals with the HH genotype showed higher activation than those with the LL genotype in the medial orbitofrontal cortex (mOFC) when anticipating a possible monetary reward. In addition, the HH genotype showed stronger functional coupling (as assessed by effective connectivity analyses) of mOFC with VMPFC, subgenual anterior cingulate cortex, and ventral striatum during reward anticipation. This hints at a larger sensitivity for upcoming rewards in individuals with the HH genotype, resulting in a higher motivation to attain these rewards. These findings provide first evidence in humans that the PDYN polymorphism modulates neural processes associated with the anticipation of rewards, which ultimately may help to explain differences between genotypes with respect to addiction and drug abuse. PMID:24587148

Votinov, Mikhail; Pripfl, Juergen; Windischberger, Christian; Kalcher, Klaudius; Zimprich, Alexander; Zimprich, Fritz; Moser, Ewald

2014-01-01

385

Polymorphism and genetic mapping of the human oxytocin receptor gene on chromosome 3  

SciTech Connect

Centrally administered oxytocin has been reported to facilitate affiliative and social behaviors, in functional harmony with its well-known peripheral effects on uterine contraction and milk ejection. The biological effects of oxytocin could be perturbed by mutations occurring in the sequence of the oxytocin receptor gene, and it would be of interest to establish the position of this gene on the human linkage map. Therefore we identified a polymorphism at the human oxytocin receptor gene. A portion of the 3{prime} untranslated region containing a 30 bp CA repeat was amplified by polymerase chain reaction (PCR), revealing a polymorphism with two alleles occurring with frequencies of 0.77 and 0.23 in a sample of Caucasian CEPH parents (n = 70). The CA repeat polymorphism we detected was used to map the human oxytocin receptor to chromosome 3p25-3p26, in a region which contains several important genes, including loci for Von Hippel-Lindau disease (VHL) and renal cell carcinoma. 53 refs., 2 figs., 1 tab.

Michelini, S.; Urbanek, M.; Goldman, D. [National Institute of Health-National Institute of Alcohol Abuse and Alcoholism, Rockville, MD (United States)] [and others

1995-06-19

386

APBB2 genetic polymorphisms are associated with severe cognitive impairment in centenarians.  

PubMed

APBB2 gene encodes for ?-amyloid precursor protein-binding family B member 2, (APBB2, FE65-like, FE65L1), an adaptor protein binding to the cytoplasmatic domain of ?-amyloid precursor protein (?APP). Over-expression of APBB2 promotes formation of ?-amyloid (A?), the main constituent of senile plaques. Polymorphisms within APBB2 gene have been proposed as candidate risk factors for Alzheimer's disease. However, their association with longevity has never been investigated. Here we present the first attempt to analyze APBB2 polymorphisms in centenarians. We used a PCR-RFLP method to analyze two intronic nucleotide substitutions: hCV1558625 (rs17443013) and rs13133980. We found no differences in genotype or allele distribution between centenarians and young controls. After stratification of centenarians upon their cognitive performance, the APBB2 rs13133980 G allele was over-represented in centenarians with severe cognitive impairment compared to individuals without this disability. Also the hCV1558625-rs13133980 AG haplotype increased relative risk for severe cognitive impairment in centenarians. Our results support the concept of APBB2 polymorphism association with cognitive performance in the oldest age. PMID:23384821

Golanska, Ewa; Sieruta, Monika; Gresner, Sylwia M; Pfeffer, Anna; Chodakowska-Zebrowska, Malgorzata; Sobow, Tomasz M; Klich, Izabela; Mossakowska, Malgorzata; Szybinska, Aleksandra; Barcikowska, Maria; Liberski, Pawel P

2013-04-01

387

Metallothionein 2A genetic polymorphisms and risk of prostate cancer in a Polish population.  

PubMed

Metallothionein 2A (MT2A) is the most expressed metallothionein (MT) isoform in prostate cells. A number of studies have demonstrated altered MT2A expression in various human tumors, including prostate cancer. We conducted an association study to examine whether MT2A gene polymorphisms are associated with a risk of prostate cancer. Genotyping was conducted using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Three single nucleotide polymorphisms (SNPs), rs28366003, rs1610216, and rs10636, were genotyped in 358 prostate cancer cases and 406 population controls. One SNP in MT2A (rs28366003) showed a positive association with prostate cancer. Compared to homozygous common allele carriers, heterozygosity for the G variant (odds ratio (OR)=2.30, 95% confidence interval (CI): 1.50-3.47, P-trend<0.0001; the OR assuming a dominant model 2.43 (95% CI: 1.62-3.61, P(dominant)=0.001) after adjustment for age) had a significantly increased risk of prostate cancer in a Polish population. Our data suggest that the rs28366003 SNP in MT2A is associated with the risk of prostate cancer in a Polish population. PMID:22824183

Forma, Ewa; Krzeslak, Anna; Wilkosz, Jacek; Jozwiak, Pawel; Szymczyk, Agnieszka; Rozanski, Waldemar; Brys, Magdalena

2012-09-01

388

Polymorphic populations of Dactylorhiza incarnata s.l. (Orchidaceae) on the Baltic island of Gotland: morphology, habitat preference and genetic differentiation  

PubMed Central

Background and Aims Organisms may be polymorphic within natural populations, but often the significance and genetic background to such polymorphism is not known. To understand the colour polymorphism expressed in the diploid marsh-orchids Dactylorhiza incarnata, morphological, habitat and genetic differentiation was studied in mixed populations on the island of Gotland, supplemented with genetic marker data from adjacent areas. Methods A total of 398 accessions was investigated for plastid haplotype and three nuclear microsatellites. Morphometric data and vegetation data were obtained from a subset of 104 plants. Key Results No clear pattern of habitat differentiation was found among the colour morphs. Within sites, the yellow-flowered morph (ochroleuca) was slightly larger than the others in some flower characters, whereas the purple-flowered morph with spotted leaves (cruenta) was on average smaller. However, populations of the same colour morph differed considerably between sites, and there was also considerable overlap between morphs. Morphs were often genetically differentiated but imperfectly separated within sites. Most populations were characterized by significant levels of inbreeding. The ochroleuca morph constitutes a coherent, highly homozygous sublineage, although introgression from purple-flowered morphs occurs at some sites. The cruenta morph was genetically variable, although Gotland populations formed a coherent group. Purple-flowered plants with unspotted leaves (incarnata in the strict sense) were even more variable and spanned the entire genetic diversity seen in the other morphs. Conclusions Colour polymorphism in D. incarnata is maintained by inbreeding, but possibly also by other ecological factors. The yellow-flowered morph may best be recognized as a variety of D. incarnata, var. ochroleuca, and the lack of anthocyanins is probably due to a particular recessive allele in homozygous form. Presence of spotted leaves is an uncertain taxonomic character, and genetic differentiation within D. incarnata would be better described by other morphological characters such as leaf shape and stature and size and shape of lip and spur. PMID:19458026

Hedrén, Mikael; Nordström, Sofie

2009-01-01

389

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)  

Microsoft Academic Search

BACKGROUND: Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in

Jeffrey T Foster; Gerard J Allan; Agnes P Chan; Pablo D Rabinowicz; Jacques Ravel; Paul J Jackson; Paul Keim

2010-01-01

390

A Genetic Linkage Map of the Baboon ( Papio hamadryas) Genome Based on Human Microsatellite Polymorphisms  

Microsoft Academic Search

A first-generation genetic linkage map of the baboon (Papio hamadryas) genome was developed for use in biomedical and evolutionary genetics. Pedigreed baboons (n = 694) were selected from the breeding colony maintained by the Southwest Foundation for Biomedical Research. To facilitate comparison with the human genome, the baboon linkage map consists primarily of human microsatellite loci amplified using published human

Jeffrey Rogers; Michael C. Mahaney; Shelly M. Witte; Shalini Nair; Deborah Newman; Steven Wedel; Lawrence A. Rodriguez; Karen S. Rice; Susan H. Slifer; Andrey Perelygin; Michael Slifer; Paula Palladino-Negro; Timothy Newman; Karen Chambers; Geoff Joslyn; Pauline Parry; Phillip A. Morin

2000-01-01

391

Genetic association of the Phosphoinositide-3 kinase in schizophrenia and bipolar disorder and interaction with a BDNF gene polymorphism.  

PubMed

Phosphoinositide-3-kinase, class III (PIK3C3) is a member of the phosphoinosite-3-kinases family, involved in cell signaling, membrane trafficking, and neurodevelopment. Previous studies have indeed shown an association between PIK3C3 gene variants and both bipolar disorder (BD) and schizophrenia (SZ). Brain-derived neurotrophic factor (BDNF) is a neurodevelopmental factor, which can regulate the PI3K signaling pathway. Associations have been reported between BDNF gene polymorphisms and affective and psychotic disorders. The aim of the present study was to replicate an association between PIK3C3 and BDNF gene variants in SZ and BD and a putative epistasis between the two genes. Patients meeting the DSM-IV criteria of BD and SZ were included in this study (98 BD and 79 SZ) as well as 158 healthy controls. Blood DNA was extracted and genotyping was performed either by the polymerase chain reaction (PCR) technique followed by enzymatic digestion or by the high-resolution melt (HRM) method. Genotype and haplotype association was assessed with the UNPHASED statistical program.The results showed one nominal association with BD (P < 0.02) and two risk haplotypes in both SZ (P < 0.001) and BP (P < 0.0005), which survived multiple testing correction. A modest interaction between a BDNF variant and PI3KC3 polymorphism was observed (P < 0.04).These preliminary results confirm the genetic association of PI3K gene variants with both SZ and BD, and support the hypothesis that SZ and BD share a genetic background. PMID:22399091

Carrard, Anthony; Salzmann, Annick; Perroud, Nader; Gafner, Jérémie; Malafosse, Alain; Karege, Félicien

2011-11-01

392

Genetic polymorphisms of DNA double strand break gene Ku70 and gastric cancer in Taiwan  

PubMed Central

Background and aim The DNA repair gene Ku70, an important member of non-homologous end-joining repair system, is thought to play an important role in the repairing of DNA double strand breaks. It is known that defects in double strand break repair capacity can lead to irreversible genomic instability. However, the polymorphic variants of Ku70, have never been reported about their association with gastric cancer susceptibility. Methods In this hospital-based case-control study, the associations of Ku70 promoter T-991C (rs5751129), promoter G-57C (rs2267437), promoter A-31G (rs132770), and intron 3 (rs132774) polymorphisms with gastric cancer risk in a Taiwanese population were investigated. In total, 136 patients with gastric cancer and 560 age- and gender-matched healthy controls recruited from the China Medical Hospital in Taiwan were genotyped. Results As for Ku70 promoter T-991C, the ORs after adjusted by age and gender of the people carrying TC and CC genotypes were 2.41 (95% CI = 1.53-3.88) and 3.21 (95% CI = 0.96-9.41) respectively, compared to those carrying TT wild-type genotype. The P for trend was significant (P < 0.0001). In the dominant model (TC plus CC versus TT), the association between Ku70 promoter T-991C polymorphism and the risk for gastric cancer was also significant (adjusted OR = 2.48, 95% CI = 1.74-3.92). When stratified by age and gender, the association was restricted to those at the age of 55 or elder of age (TC vs TT: adjusted OR = 2.52, 95% CI = 1.37-4.68, P = 0.0139) and male (TC vs TT: adjusted OR = 2.58, 95% CI = 1.33-4.47, P = 0.0085). As for the other three polymorphisms, there was no difference between both groups in the distributions of their genotype frequencies. Conclusion In conclusion, the Ku70 promoter T-991C (rs5751129), but not the Ku70 promoter C-57G (rs2267437), promoter A-31G (rs132770) or intron 3 (rs132774), is associated with gastric cancer susceptibility. This polymorphism may be a novel useful marker for gastric carcinogenesis. PMID:21575261

2011-01-01

393

RET and PHOX2B Genetic Polymorphisms and Hirschsprung's Disease Susceptibility: A Meta-Analysis  

PubMed Central

Background Many publications have evaluated the correlation between RET, PHOX2B polymorphisms and Hirschsprung's disease with conflicting results. We performed this meta-analysis to clarify the association of RET, PHOX2B polymorphisms with HSCR. Methods We searched Pubmed, Elsevier Science Direct, China National Knowledge Infrastructure database, Chinese Biomedical database, Google scholar. The combined odds ratio (OR) with 95% CI was calculated to estimate the strength of the association. Heterogeneity and publication bias were also assessed. Results In total, 16 studies concerning RET and 4 studies concerning PHOX2B were included in the meta-analysis. The effects of five polymorphisms of RET (rs1800858, rs1800860, rs1800861, rs10900297, rs2435357) and one polymorphism (rs28647582) of PHOX2B were evaluated. We found a significant correlation between RET polymorphisms and HSCR. For rs1800858, the overall ORs (95% CI) of the A versus G, AA versus GG, AA/AG versus GG and AA versus GG/AG were 3.81 (2.28–6.35); 8.36 (3.45–20.25); 3.59 (1.83–7.02); and 6.60 (3.66–11.89). For rs1800861, the comparison of subjects in the G versus T, GG versus TT, GG/TG versus TT and GG versus TT/TG were 2.85(1.81–4.47); 5.38(2.68–10.80); 3.07(2.17–4.34) and 4.14(1.84–9.30) respectively. For rs10900297, the comparison results showed statistically significant. (ORC versus A?=?5.05,95%CI?=?4.16–6.13; ORCC versus AA?=?9.73, 95%CI?=?5.94–15.94; ORCC/AC versus AA?=?5.31, 95%CI?=?3.27–6.82; ORCC versus AC/AA?=?7.06,95%CI?=?5.60–8.91.) But, for rs1800860, the GG/GA versus AA did not reach statistical association (OR?=?3.77, 95% CI?=?0.94–15.07) and the G versus A, GG versus AA, GG versus GA/AA were 2.23 (1.60–3.11);4.56 (1.14–18.27); 2.38 (1.66–3.43) respectively. For rs2435357, the T versus C, TT versus CC, TT/TC versus CC and TT versus CC/TC were 4.53 (3.27–6.27); 11.44 (5.67–23.10); 4.04 (2.92–5.57), and 9.01(5.25–15.46).The single polymorphism of PHOX2B gene wasn't related to the risk for HSCR. Conclusions This meta-analysis shows a significant association between RET polymorphisms and HSCR. PMID:24651702

Yuan, Xu; Ren, Ling-ling; Shen, Juan; Zhang, Hai-yan

2014-01-01

394

Association of the Genetic Polymorphisms in Pre-MicroRNAs with Risk of Ischemic Stroke in a Chinese Population  

PubMed Central

microRNA (miRNA) plays a role in the pathogenesis of ischemic stroke, and single nucleotide polymorphisms in miRNA genes may contribute to disease susceptibility. However, the effect of miR-146a, miR-196a2, and miR-499 polymorphisms on ischemic stroke susceptibility has been rarely reported. Using the TaqMan assay, we evaluated the association of hsa-miR-146a/rs2910164, hsa-miR-196a2/rs11614913, and hsa-miR-499/rs3746444 polymorphisms with the risk of ischemic stroke in a Chinese population with 531 ischemic stroke patients and 531 control subjects. Rs2910164 C/G genotypes were significantly associated with increased risk of ischemic stroke in different genetic model (homozygote comparison: OR = 2.00, 95% CI, 1.29–3.12, P = 0.002; additive model: OR = 1.35, 95% CI, 1.10–1.65, P = 0.004;dominant model: OR = 1.33, 95% CI, 1.00–1.75, P = 0.049; recessive model: OR = 1.82, 95% CI, 1.20–2.74, P = 0.004). Subjects with allele G of hsa-miR-146a/ rs2910164 also showed increased risk of ischemic stroke (OR = 1.33, 95% CI, 1.09–1.62, P = 0.005). Stratification analysis showed that the association between rs2910164 and the risk of ischemic stroke was more pronounced in subjects over 60 years old, females, non-drinkers, subjects without hypertension or diabetes mellitus. There were significant combined effects between miR-146a/rs2910164 and fasting glucose/low-density lipoprotein cholesterol levels on ischemic stroke susceptibility. However, we failed to find any association between the alleles/genotypes of rs11614913 T/C and ischemic stroke, respectively (P> 0.05). In summary, this study provides evidence that miR-146a/rs2910164 might be associated with a significantly increased risk of ischemic stroke in a Chinese population, and the combined effects between miRNA polymorphism and fasting glucose /blood lipid levels may contribute to stroke pathogenesis. PMID:25658319

Huang, Suli; Zhou, Shiquan; Zhang, Yanwei; Lv, Ziquan; Li, Shanshan; Xie, Changhui; Ke, Yuebin; Deng, Pingjian; Geng, Yijie; Zhang, Qian; Chu, Xiaofan; Yi, Zhaohui; Zhang, Ying; Wu, Tangchun; Cheng, Jinquan

2015-01-01

395

Associations between genetic polymorphisms of Phase I and II metabolizing enzymes, p53 and susceptibility to esophageal adenocarcinoma.  

PubMed

The objectives of this exploratory case-control study were to evaluate whether genetic polymorphisms of selected Phase I and II metabolizing enzymes are associated with the risk of developing primary esophageal adenocarcinoma, and to investigate potential associations between genotypes and p53 tumor suppressor gene alterations. Cases comprised 45 patients with surgically resected esophageal adenocarcinomas, defined according to strict clinico-pathologic criteria. PCR-based assays (RFLP/SSCP) were used to genotype cytochrome P450 (CYP) 1A1 [MspI; Ile:Val], microsomal epoxide hydroxylase (mEH) (fast and slow alleles), and glutathione S-transferase (GST) T1, M1 and P1. Healthy controls (n=45) from the same geographic region were matched for age, gender and smoking history. For GSTP1, the Ile/Val (a/b) and Val/Val (b/b) variants were seen at increased frequency in cases compared to controls (49% versus 27% and 15% versus 9%, respectively), although these differences achieved only borderline statistical significance (P=0.09). For mEH (exon 3), the presence of the Tyr polymorphism (slow allele) was reduced in cases (42%) compared to controls (53%; P=0.05). Predicted high mEH activity was seen more frequently in cases than controls (OR, 2.2; 95% CI, 0.7-7.3). Polymorphism frequencies for GSTT1, GSTM1, and CYP1A1 were not statistically different between cases and controls. Cases with the GSTT1 null genotype had tumors with altered p53 more frequently than did cases with the common form of GSTT1 (25 versus 6%, respectively; P=0.08). We conclude that polymorphisms of GSTP1 and mEH may be implicated in individual susceptibility to esophageal adenocarcinoma, possibly as a result of increased Phase I activation (mEH) and impaired Phase II detoxification (GSTP1). GSTT1 may also play a role in esophageal tumorigenesis through a pathway that involves abnormalities in the p53 tumor suppressor gene. PMID:12670526

Casson, A G; Zheng, Z; Chiasson, D; MacDonald, K; Riddell, D C; Guernsey, J R; Guernsey, D L; McLaughlin, J

2003-01-01

396

Platelet CD36 surface expression levels affect functional responses to oxidized LDL and are associated with inheritance of specific genetic polymorphisms  

PubMed Central

CD36 modulates platelet function via binding to oxidized LDL (oxLDL), cell-derived microparticles, and thrombospondin-1. We hypothesized that the level of platelet CD36 expression may be associated with inheritance of specific genetic polymorphisms and that this would determine platelet reactivity to oxLDL. Analysis of more than 500 subjects revealed that CD36 expression levels were consistent in individual donors over time but varied widely among donors (200-14 000 molecules per platelet). Platelet aggregometry and flow cytometry in a subset of subjects with various CD36 expression levels revealed a high level of correlation (r2 = 0.87) between platelet activation responses to oxLDL and level of CD36 expression. A genome-wide association study of 374 white subjects from the Cleveland Clinic ASCLOGEN study showed strong associations of single nucleotide polymorphisms in CD36 with platelet surface CD36 expression. Most of these findings were replicated in a smaller subset of 25 black subjects. An innovative gene-based genome-wide scan provided further evidence that single nucleotide polymorphisms in CD36 were strongly associated with CD36 expression. These studies show that CD36 expression on platelets varies widely, correlates with functional responses to oxLDL, and is associated with inheritance of specific CD36 genetic polymorphisms, and suggest that inheritance of specific CD36 polymorphisms could affect thrombotic risk. PMID:21478428

Ghosh, Arunima; Murugesan, Gurunathan; Chen, Kan; Zhang, Li; Wang, Qing; Febbraio, Maria; Anselmo, Rita Marie; Marchant, Kandice; Barnard, John

2011-01-01

397

Toward autonomous harbor surveillance  

E-print Network

In this thesis we address the problem of drift-free navigation for underwater vehicles performing harbor surveillance and ship hull inspection. Maintaining accurate localization for the duration of a mission is important ...

Johannsson, Hordur

2010-01-01

398

The KCNH2 Genetic Polymorphism (1956, C>T) Is a Novel Biomarker That Is Associated with CCB and ?,?-ADR Blocker Response in EH Patients in China  

PubMed Central

Background KCNH2 (hERG) potassium channels have an integral role in regulating the excitability of smooth muscle cells. Some pathways driven by angiotensin II, nitric oxide and adrenergic receptors blocker are involved in modulating the properties of KCNH2 potassium channels. And these pathways are closely related to blood pressure regulation. Therefore, we hypothesized that KCNH2 genetic polymorphisms may affect blood pressure response to the antihypertensive drug therapies. Materials and Methods To evaluate the interactions between KCNH2 genetic polymorphisms and individual blood pressure response to antihypertensive drugs, 370 subjects with essential hypertension (EH) were studied. In evaluating the interactions between KCNH2 genetic polymorphisms and drug response to blood pressure, multivariable ANOVA analysis followed by Bonferroni correction were carried out. Results There were statistically significant interactions between KCNH2 (1956, C>T) polymorphism and DBP change (P?=?0.010), MAP change (P?=?0.014) on azelnidipine or nitrendipine therapy patients at the end of 6 weeks. We found that the KCNH2 (1956,C>T) polymorphism was associated with the hypotensive effects of ?,?-ADR blockers of DBP change at the end of 4 and 6 weeks' treatment in an age- and gender-dependent manner (P?=?0.007 and 0.019, respectively). Similar results were also observed for changes in MAP at the end of 4 and 6 weeks (P-values were 0.035 and 0.078, respectively). While patients who received imidapril, candesartan and irbesartan therapy, no significant difference in drug response among KCNH2(1956,C>T) genotype was observed. Conclusion We have reported for the first time that KCNH2 (1956, C>T) polymorphism is associated with efficacy of antihypertensive drugs CCBs and ADR blockers, and may serve as a novel biomarker for individualized therapy for certain antihypertensive drugs. PMID:23613831

He, Fazhong; Luo, Jianquan; Luo, Zhiying; Fan, Lan; He, Yijing; Zhu, Dingliang; Gao, Jinping; Deng, Sheng; Wang, Yan; Qian, Yuesheng; Zhou, Honghao; Chen, Xiaoping; Zhang, Wei

2013-01-01

399

Apolipoprotein E genetic polymorphism, serum lipoprotein levels and breast cancer risk: A case-control study.  

PubMed

The purpose of this study was to evaluate the association between apolipoprotein E (APOE) allelic frequency, serum lipoproteins and breast cancer (BC). We conducted a nested case-control study within a cohort including 47 cases and 165 controls. Polymerase chain reaction-restriction fragment length polymorphism analyses of the APOE polymorphism were performed. In general, participants with the genotype including alleles e2 and e3 tended to have lower serum triglycerides, total cholesterol and low-density lipoprotein cholesterol levels and higher high-density lipoprotein (HDL) cholesterol levels compared to participants homozygous for the e3 allele and participants heterozygous for the e3 and e4 alleles, respectively. BC patients exhibited higher mean levels of total serum cholesterol (P=0.070), dietary fat intake (P=0.020) and dietary cholesterol intake (P=0.017) compared to control subjects. The allelic distribution between the two groups revealed that the presence of the e2 allele was positively associated with the absence of BC, whereas the e4 allele was positively associated with the BC case group (P=0.019). The distribution of the APOE genotypes was not significantly different between cases and controls (P=0.172). The concomitant presence of the e2 and e4 alleles was positively associated with the absence of BC and e4/e4 homozygosity was positively associated with BC (P=0.021). Our findings suggested that APOE polymorphism plays an important role in the development of BC, particularly when associated with higher serum triglyceride levels. PMID:25279190

Cibeira, Gabriela Herrmann; Giacomazzi, Juliana; Aguiar, Ernestina; Schneider, Silvana; Ettrich, Betina; DE Souza, Caroline Isoppo; Camey, Suzi; Caleffi, Maira; Weber, Bernardete; Ashton-Prolla, Patricia; Moriguchi, Emilio Hideyuki

2014-11-01

400

Amplification-based nucleic acid scanning techniques to assess genetic polymorphism in Candida.  

PubMed

Opportunistic pathogen Candida causes common fungal infections that manifest both superficially and systemically, especially in compromised patients. Although C. albicans is by far the main etiological agent of candidosis, the frequency of isolation of other non-albicans species such as C. glabrata and C. krusei is increasing at an alarming rate. Therefore, the epidemiology, pathogenicity, and diagnosis of infections due to these organisms are of great importance. Of a variety of genotyping methods utilized for strain delineation of these Candida species, amplification-based techniques such as randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), restriction digestion-mediated PCR (RFLP-PCR), and single-stranded conformational polymorphism (SSCP) and microsatellite PCR (interrepeat PCR, IR-PCR) are the most popular and widely used. In the last decade or so these techniques have helped unravel the clinical epidemiological features of pathogenicity, diversity, microevolution, and natural heterozygosity in Candida species. Here we review in detail the basic principles of RAPD, the nature of the primer and factors influencing its selection, and the limitations of RAPD assays as well as analysis and interpretation of banding profiles generated using the software programs. In addition, the principles of other RAPD-based amplification techniques (AFLP, RFLP-PCR, SSCP, and IR-PCR) and their application in molecular epidemiologic studies of Candida species in particular and other fungi in general are also reviewed. It is concluded that these methods have wide applicability in genotyping fungi, although they differ greatly in their resolution and have advantages and drawbacks depending on the task in question. PMID:12638716

Dassanayake, R S; Samaranayake, L P

2003-01-01

401

Apolipoprotein E genetic polymorphism, serum lipoprotein levels and breast cancer risk: A case-control study  

PubMed Central

The purpose of this study was to evaluate the association between apolipoprotein E (APOE) allelic frequency, serum lipoproteins and breast cancer (BC). We conducted a nested case-control study within a cohort including 47 cases and 165 controls. Polymerase chain reaction-restriction fragment length polymorphism analyses of the APOE polymorphism were performed. In general, participants with the genotype including alleles e2 and e3 tended to have lower serum triglycerides, total cholesterol and low-density lipoprotein cholesterol levels and higher high-density lipoprotein (HDL) cholesterol levels compared to participants homozygous for the e3 allele and participants heterozygous for the e3 and e4 alleles, respectively. BC patients exhibited higher mean levels of total serum cholesterol (P=0.070), dietary fat intake (P=0.020) and dietary cholesterol intake (P=0.017) compared to control subjects. The allelic distribution between the two groups revealed that the presence of the e2 allele was positively associated with the absence of BC, whereas the e4 allele was positively associated with the BC case group (P=0.019). The distribution of the APOE genotypes was not significantly different between cases and controls (P=0.172). The concomitant presence of the e2 and e4 alleles was positively associated with the absence of BC and e4/e4 homozygosity was positively associated with BC (P=0.021). Our findings suggested that APOE polymorphism plays an important role in the development of BC, particularly when associated with higher serum triglyceride levels. PMID:25279190

CIBEIRA, GABRIELA HERRMANN; GIACOMAZZI, JULIANA; AGUIAR, ERNESTINA; SCHNEIDER, SILVANA; ETTRICH, BETINA; DE SOUZA, CAROLINE ISOPPO; CAMEY, SUZI; CALEFFI, MAIRA; WEBER, BERNARDETE; ASHTON-PROLLA, PATRICIA; MORIGUCHI, EMILIO HIDEYUKI

2014-01-01