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Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies?  

PubMed Central

Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-?32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-?32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of zoonoses in the actual CCR5-?32 distribution. PMID:18925940

Faure, Eric



High prevalence of the CCR5Delta32 HIV-resistance mutation among Estonian HIV type 1-infected individuals.  


The aim of this survey was to investigate human immunodeficiency virus type 1 (HIV-1) coreceptor, chemokine receptor 5 (CCR5), polymorphism among Estonian HIV-1-infected individuals. Homozygous CCR5Delta32 genotypes have been associated with resistance to HIV-1 infection; however, inconsistent evidence exists as to whether a single copy of a mutant allele among heterozygotes confers protection from HIV-1 infection. In an Estonian population the frequency of the CCR5Delta32 allele has been found to be among the greatest observed to date. Ironically, Estonia is concomitantly characterized by a very high HIV-1 prevalence. We compared the allele frequencies in a healthy control population to the HIV-positive group. The frequency of heterozygous individuals did not differ significantly between the HIV-positive group and the control population. Allele frequencies were analyzed among different risk groups as well as groups with different HIV genetic backgrounds. We did not find a difference between CCR5Delta32 allele frequencies among intravenous drug users (IDUs) and sexually infected persons. Likewise, the distribution of CCR5Delta32 allele frequencies among patients infected with different subtypes did not differ while data from "pure" subtypes A, B, and CRF06_cpx were pooled and evaluated against unique recombinant forms. PMID:17331026

Adojaan, Maarja; Mölder, Tarmo; Männik, Andres; Kivisild, Toomas; Villems, Richard; Krispin, Tõnu; Ustav, Mart



Effects of CCR5Delta32, CCR2-64I, and SDF-1 3'A alleles on HIV1 disease progression: An international meta-analysis of individual-patient data  

Microsoft Academic Search

BACKGROUND: Studies relating certain chemokine and chemokine receptor gene alleles with the outcome of HIV-1 infection have yielded inconsistent results. OBJECTIVE: To examine postulated associations of genetic alleles with HIV-1 disease progression. DESIGN: Meta-analysis of individual-patient data. SETTING: 19 prospective cohort studies and case-control studies from the United States, Europe, and Australia. PATIENTS: Patients with HIV-1 infection who were of

John P. A. Ioannidis; Philip S. Rosenberg; James J. Goedert; Lesley J. Ashton; Thomas L. Benfield; Susan P. Buchbinder; Roel A. Coutinho; Jesper Eugen-Olsen; Teresa Gallart; Terese L. Katzenstein; Leondios G. Kostrikis; Harmjan Kuipers; Leslie G. Louie; Simon A. Mallal; Joseph B. Margolick; Olga P. Martinez; Laurence Meyer; Nelson L. Michael; Eva Operskalski; Giusseppe Pantaleo; G. Paolo Rizzardi; Hanneke Schuitemaker; Haynes W. Sheppard; Graeme J. Stewart; Ioannis D. Theodorou; Henrik Ullum; Elisa Vicenzi; David Vlahov; David Wilkinson; Cassy Workman; Jean-Francois Zagury; Thomas R. O'Brien



Coregulation of HIV-1 dependency factors in individuals heterozygous to the CCR5-delta32 deletion  

PubMed Central

Background CCR5-delta32 heterozygous individuals are susceptible to HIV-1. However, it is not clear if there is a relevant protective effect against transmission and a beneficial effect in terms of HIV progression which cannot be attributed to CCR5 surface density alone. Therefore we investigated HIV-1 dependency factors (HDF) which might be differently regulated in CCR5 wild type (WT) and CCR5-delta32 heterozygous individuals. Methods We examined CD34+ hematopoietic progenitor cells derived from bone marrow samples from 19 healthy volunteers, 12 individuals with CCR5 WT and 7 with heterozygous CCR5-delta32 deletion. Samples were analyzed using a global gene expression oligonucleotide microarray (HG-U133plus 2.0, Affymetrix Inc.). Results A total of 205 genes were found with altered expression (3fold difference, present call rate of 75%, p?CCR5-delta32 heterozygotes. Conclusion The CCR5-delta32 deletion is associated with other HDFs in HIV-1 pathogenesis as a possible explanation for beneficial effects regarding the deletion leading to a variant expression profile in heterozygous carriers of this mutation. PMID:24245779



Effects of the Chemokine Receptor 5 (CCR5)-Delta32 Mutation on Hepatitis C Virus-Specific Immune Responses and Liver Tissue Pathology in HCV Infected Patients  

PubMed Central

Background: The specific antiviral T cells provide CC chemokine receptor 5 (CCR5) for the immune response during the hepatitis C virus (HCV) infection. Heterogenous and/or homozygous 32 base pair deletion in CCR5 gene (CCR5?32 bpdel) leads to reduced protein expression. Objectives: In the current case control study, we aimed to compare the histopathological findings of liver to the CCR5?32 bpdel mutation profiles, expression and some other clinical findings in patients with chronic HCV infection. Materials and Methods: Multiple Strip Assay reverse hybridisation and Real Time PCR techniques were used to determine the germline CCR5 mutations and immunohistochemical technique was used to evaluate the gene expression in targer tissue biopsies. Results: Target CCR5 WT/WT, WT/?32, and ?32/?32 genotypes were observed in 91.4%, 8.6% and 0.0% for HCV positive patients and 98.3%, 1.7% and 0.0% for control group respectively. The histologic activity index (HAI) was significantly lower (4.0 ± 1.0) in the mutated group than the non-mutated group (5.7 ± 1.0). Decreased fibrosis levels were detected in HCV positive mutated group. Conclusions: Results showed that CCR5 polymorphism was more frequent in HCV positive patients than in healthy population in Turkish population. Current results also showed that mutated CCR5 signalling pathway due to CCR5-Delta32 may potentially result in subtle reduction of HCV specifity to the drug responses due to the positive impact on liver inflammation, fibrosis levels and liver destruction in HCV infection. PMID:25067937

Yilmaz, Abdulkerim; Alagozlu, Hakan; Ozdemir, Ozturk; Arici, Sema



A comparison of type 2 diabetes risk allele load between African Americans and European Americans.  


The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38-67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38-65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10(-89)) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that there are ethnic-specific differences in genetic architecture underlying T2D, and that these differences complicate our understanding of how risk allele load impacts disease susceptibility. PMID:25273842

Keaton, Jacob M; Cooke Bailey, Jessica N; Palmer, Nicholette D; Freedman, Barry I; Langefeld, Carl D; Ng, Maggie C Y; Bowden, Donald W



Host inflammatory response and development of complications of Chlamydia trachomatis genital infection in CCR5-deficient mice and subfertile women with the CCR5delta32 gene deletion  

Microsoft Academic Search

T cell immunity protects against diseases caused by the obligate intracellular bacterium Chlamydia trachomatis. Incidentally, host inflammatory response that includes T cells appears to also contribute to the pathogenesis of chlamydial diseases such as trachoma and tubal factor infertility (TFI). Therefore, designing effective prevention strategies requires a delineation of immune processes responsible for pathology and those mediating immunity, and identification

Erika L. Barr; Sander Ouburg; Joseph U. Igietseme; Servaas A. Morré; Edith Okwandu; Francis O. Eko; Godwin Ifere; Tesfaye Belay; Qing He; Deborah Lyn; Gift Nwankwo; James Lillard; Carolyn M. Black; Godwin A. Ananaba


Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models.  


The interplay between C-C chemokine receptor type 5 (CCR5) host genetic background, disease progression, and intrahost HIV-1 evolutionary dynamics remains unclear because differences in viral evolution between hosts limit the ability to draw conclusions across hosts stratified into clinically relevant populations. Similar inference problems are proliferating across many measurably evolving pathogens for which intrahost sequence samples are readily available. To this end, we propose novel hierarchical phylogenetic models (HPMs) that incorporate fixed effects to test for differences in dynamics across host populations in a formal statistical framework employing stochastic search variable selection and model averaging. To clarify the role of CCR5 host genetic background and disease progression on viral evolutionary patterns, we obtain gp120 envelope sequences from clonal HIV-1 variants isolated at multiple time points in the course of infection from populations of HIV-1-infected individuals who only harbored CCR5-using HIV-1 variants at all time points. Presence or absence of a CCR5 wt/?32 genotype and progressive or long-term nonprogressive course of infection stratify the clinical populations in a two-way design. As compared with the standard approach of analyzing sequences from each patient independently, the HPM provides more efficient estimation of evolutionary parameters such as nucleotide substitution rates and d(N)/d(S) rate ratios, as shown by significant shrinkage of the estimator variance. The fixed effects also correct for nonindependence of data between populations and results in even further shrinkage of individual patient estimates. Model selection suggests an association between nucleotide substitution rate and disease progression, but a role for CCR5 genotype remains elusive. Given the absence of clear d(N)/d(S) differences between patient groups, delayed onset of AIDS symptoms appears to be solely associated with lower viral replication rates rather than with differences in selection on amino acid fixation. PMID:21135151

Edo-Matas, Diana; Lemey, Philippe; Tom, Jennifer A; Serna-Bolea, Cèlia; van den Blink, Agnes E; van 't Wout, Angélique B; Schuitemaker, Hanneke; Suchard, Marc A



CC chemokine receptor 5 delta32 polymorphism in two independent cohorts of hepatitis C virus infected patients without hemophilia.  


Recently CC chemokine receptor 5 (CCR5) related immune mechanisms and a functional mutation of the CCR5 gene have been implicated in hepatitis C virus (HCV) infection in a cohort of predominantly hemophiliac patients. The present study investigated the frequency and clinical consequences of the CCR5 Delta32 mutation in two genetically homogeneous populations of HCV infected patients with a different risk profile for infection. Genomic DNA samples from 333 German patients with chronic HCV infection were screened by PCR for the presence of the CCR5 Delta32 polymorphism. In-hospital patients admitted for other diseases than viral hepatitis but with a comparable risk for HCV exposure were used as control population ( n=125). Allele frequencies of CCR5 Delta32 polymorphism did not differ significantly between the two groups (7.6% and 9.5%, respectively) and control subjects (10.4%), and did not deviate from Hardy-Weinberg equilibrium in any group. Furthermore, there were no major differences between patients with respect to HCV genotypes, viral loads, liver enzymes, or fibrosis scores in relation to the presence or absence of the heterozygous CCR5 Delta32 mutation. Differences in inflammatory scores in liver biopsy samples and response to antiviral therapy in CCR5 Delta32 heterozygotes in one cohort could neither be reproduced in the other group of patients nor when both cohorts were pooled. These results argue against a strong effect of the CCR5 Delta32 deletion regarding these phenotypes. In conclusion, we found no increased frequency of the CCR5 Delta32 polymorphism in two independent cohorts of patients with HCV infection but without hemophilia as the main risk factor for infection. As the major difference to investigations demonstrating an association between CCR5 Delta32 and HCV infection is the selection of cases and controls, our study emphasizes the importance of epidemiological criteria for association studies of HCV infection. PMID:14673528

Wasmuth, Hermann E; Werth, Alexa; Mueller, Tobias; Berg, Thomas; Dietrich, Christoph G; Geier, Andreas; Schirin-Sokhan, Ramin; Gartung, Carsten; Lorenzen, Johann; Matern, Siegfried; Lammert, Frank



Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech.  

PubMed Central

Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity parameters, such as bottlenecks due to long-distance founding events, selection during population establishment, and increased gene flow at low population densities. PMID:11139519

Comps, B; Gomory, D; Letouzey, J; Thiebaut, B; Petit, R J



A Human Immunodeficiency Virus Type 1 Isolate from an Infected Person Homozygous for CCR5Delta32 Exhibits Dual Tropism by Infecting Macrophages and MT2 Cells via CXCR4  

Microsoft Academic Search

The mechanisms of human immunodeficiency virus (HIV) infection of a man (VH) homozygous for the CCR532 mutation were investigated, and coreceptors other than CCR5 used by HIV type 1 (HIV-1) isolated from this individual were identified. In contrast to previous reports, this individual's rate of disease progres- sion was not accelerated. Homozygosity for CCR532 mutation was demonstrated by PCR and

Hassan M. Naif; Anthony L. Cunningham; Mohammed Alali; Shan Li; Najla Nasr; Marc M. Buhler; Dominique Schols; Erik de Clercq; Graeme Stewart



The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.  


Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. PMID:24244186

Basu Mallick, Chandana; Iliescu, Florin Mircea; Möls, Märt; Hill, Sarah; Tamang, Rakesh; Chaubey, Gyaneshwer; Goto, Rie; Ho, Simon Y W; Gallego Romero, Irene; Crivellaro, Federica; Hudjashov, Georgi; Rai, Niraj; Metspalu, Mait; Mascie-Taylor, C G Nicholas; Pitchappan, Ramasamy; Singh, Lalji; Mirazon-Lahr, Marta; Thangaraj, Kumarasamy; Villems, Richard; Kivisild, Toomas



[Geographical variation of allele frequencies at the LDH-A* locus in the arctic grayling Thymallus arcticus Pall. and in the European grayling Thymallus arcticus L].  


The allele frequencies of LDH-A* locus were studied in the population of Siberian grayling from the Kozhym River (Pechora basin) and in the population of European grayling from Pechora, Mezen', and Vym' rivers (Northern Dvina basin). In samples of both species (n = 134), three LDH-A phenotypes have been identified in total, which proved to be under the control of two alleles: LDH-A*100 and LDH-A*50. The alternative alleles of LDH-A* locus were identified in the populations of Siberian grayling from Kozhym River and in the population of European grayling from the same river and other Pechora tributaries, namely, LDH-A*100 and LDH-A*50 in the Siberian and the European grayling, respectively. However, in the European grayling populations from the Mezen' and Vym' rivers, both alleles occur at the frequencies of the rare LDH-A*100 allele of 0.143 and 0.222, respectively. According to the published data, the frequency of LDH-A*100 allele increases in the European grayling populations of northwestern (Finland) and southern (France) rivers, reaching 0.872 and 1.000 in Rhone and Loire, respectively, i.e., the values characteristic of the Siberian grayling populations. PMID:15575515

Shubin, P N; Efimtseva, é A; shubin, Iu P; Chelpanova, T I



Allele frequencies of the new European Standard Set (ESS) loci in a population of Apulia (Southern Italy).  


Allele frequencies of five miniSTRs loci (D1S1656, D2S441, D12S391, D10S1248 and D22S1045) included in the new European Standard Set (ESS) were calculated from a sample of 150 unrelated individuals from Apulia, a Region of Southern Italy. Two different PCR Amplification Kits were used, in order to evaluate the concordance of the genotypes. The results obtained with the two kits showed no differences in all genotype profiles. No deviation from Hardy-Weinberg expectations was detected at either locus. Moreover genetic analysis using Fst estimation showed no evidence for differentiation at the five new loci between Apulia and Italian populations. The high levels of polymorphisms of the analyzed markers in the Apulian population allow to confirm that these markers are useful tools in paternity and forensic analysis from degraded DNA samples. PMID:23127759

Piglionica, M; Baldassarra, S Lonero; Giardina, E; Tonino Marsella, L; Resta, N; Dell'Erba, A



Identification of functionally variant MDR1 alleles among European Americans and African Americans  

Microsoft Academic Search

MDR1 (P-glycoprotein) is an important factor in the disposition of many drugs, and the involved processes often exhibit considerable interindividual variability that may be genetically determined. Single-strand conformational polymorphism analysis and direct sequencing of exonic MDR1 deoxyribonucleic acid from 37 healthy European American and 23 healthy African American subjects identified 10 single nucleotide polymorphisms (SNPs), including 6 nonsynonymous variants, occurring

Richard B. Kim; Brenda F. Leake; Edna F. Choo; George K. Dresser; Samir V. Kubba; Ute I. Schwarz; Amanda Taylor; Hong-Guang Xie; Joel McKinsey; Sheng Zhou; Lu-Bin Lan; John D. Schuetz; Erin G. Schuetz; Grant R. Wilkinson



Geographical Variation of Allele Frequencies at the LDH-A* Locus in the Arctic Grayling Thymallus arcticus Pall. and in the European Grayling Thymallus thymallus L  

Microsoft Academic Search

The allele frequencies of LDH-A* locus were studied in the populations of Siberian grayling from the Kozhym River (Pechora basin) and in the population of European grayling from Pechora, Mezen', and Vym' rivers (Northern Dvina basin). In samples of both species (n = 134), three LDH-A phenotypes have been identified in total, which proved to be under the control of

P. N. Shubin; E. A. Efimtzeva; Yu. P. Shubin; T. I. Chelpanova



Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility  

PubMed Central

Bipolar disorder (BD) is a polygenic disorder that shares substantial genetic risk factors with major depressive disorder (MDD). Genetic analyses have reported numerous BD susceptibility genes, while some variants, such as single-nucleotide polymorphisms (SNPs) in CACNA1C have been successfully replicated, many others have not and subsequently their effects on the intermediate phenotypes cannot be verified. Here, we studied the MDD-related gene CREB1 in a set of independent BD sample groups of European ancestry (a total of 64 888 subjects) and identified multiple SNPs significantly associated with BD (the most significant being SNP rs6785[A], P = 6.32 × 10?5, odds ratio (OR) = 1.090). Risk SNPs were then subjected to further analyses in healthy Europeans for intermediate phenotypes of BD, including hippocampal volume, hippocampal function and cognitive performance. Our results showed that the risk SNPs were significantly associated with hippocampal volume and hippocampal function, with the risk alleles showing a decreased hippocampal volume and diminished activation of the left hippocampus, adding further evidence for their involvement in BD susceptibility. We also found the risk SNPs were strongly associated with CREB1 expression in lymphoblastoid cells (P<0.005) and the prefrontal cortex (P<1.0 × 10?6). Remarkably, population genetic analysis indicated that CREB1 displayed striking differences in allele frequencies between continental populations, and the risk alleles were completely absent in East Asian populations. We demonstrated that the regional prevalence of the CREB1 risk alleles in Europeans is likely caused by genetic hitchhiking due to natural selection acting on a nearby gene. Our results suggest that differential population histories due to natural selection on regional populations may lead to genetic heterogeneity of susceptibility to complex diseases, such as BD, and explain inconsistencies in detecting the genetic markers of these diseases among different ethnic populations. PMID:23568192

Li, M; Luo, X-j; Rietschel, M; Lewis, CM; Mattheisen, M; Muller-Myhsok, B; Jamain, S; Leboyer, M; Landen, M; Thompson, PM; Cichon, S; Nothen, MM; Schulze, TG; Sullivan, PF; Bergen, SE; Donohoe, G; Morris, DW; Hargreaves, A; Gill, M; Corvin, A; Hultman, C; Toga, AW; Shi, L; Lin, Q; Shi, H; Gan, L; Meyer-Lindenberg, A; Czamara, D; Henry, C; Etain, B; Bis, JC; Ikram, MA; Fornage, M; Debette, S; Launer, LJ; Seshadri, S; Erk, S; Walter, H; Heinz, A; Bellivier, F; Stein, JL; Medland, SE; Vasquez, A Arias; Hibar, DP; Franke, B; Martin, NG; Wright, MJ; Su, B



Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility.  


Bipolar disorder (BD) is a polygenic disorder that shares substantial genetic risk factors with major depressive disorder (MDD). Genetic analyses have reported numerous BD susceptibility genes, while some variants, such as single-nucleotide polymorphisms (SNPs) in CACNA1C have been successfully replicated, many others have not and subsequently their effects on the intermediate phenotypes cannot be verified. Here, we studied the MDD-related gene CREB1 in a set of independent BD sample groups of European ancestry (a total of 64,888 subjects) and identified multiple SNPs significantly associated with BD (the most significant being SNP rs6785[A], P=6.32 × 10(-5), odds ratio (OR)=1.090). Risk SNPs were then subjected to further analyses in healthy Europeans for intermediate phenotypes of BD, including hippocampal volume, hippocampal function and cognitive performance. Our results showed that the risk SNPs were significantly associated with hippocampal volume and hippocampal function, with the risk alleles showing a decreased hippocampal volume and diminished activation of the left hippocampus, adding further evidence for their involvement in BD susceptibility. We also found the risk SNPs were strongly associated with CREB1 expression in lymphoblastoid cells (P<0.005) and the prefrontal cortex (P<1.0 × 10(-6)). Remarkably, population genetic analysis indicated that CREB1 displayed striking differences in allele frequencies between continental populations, and the risk alleles were completely absent in East Asian populations. We demonstrated that the regional prevalence of the CREB1 risk alleles in Europeans is likely caused by genetic hitchhiking due to natural selection acting on a nearby gene. Our results suggest that differential population histories due to natural selection on regional populations may lead to genetic heterogeneity of susceptibility to complex diseases, such as BD, and explain inconsistencies in detecting the genetic markers of these diseases among different ethnic populations. PMID:23568192

Li, M; Luo, X-J; Rietschel, M; Lewis, C M; Mattheisen, M; Müller-Myhsok, B; Jamain, S; Leboyer, M; Landén, M; Thompson, P M; Cichon, S; Nöthen, M M; Schulze, T G; Sullivan, P F; Bergen, S E; Donohoe, G; Morris, D W; Hargreaves, A; Gill, M; Corvin, A; Hultman, C; Toga, A W; Shi, L; Lin, Q; Shi, H; Gan, L; Meyer-Lindenberg, A; Czamara, D; Henry, C; Etain, B; Bis, J C; Ikram, M A; Fornage, M; Debette, S; Launer, L J; Seshadri, S; Erk, S; Walter, H; Heinz, A; Bellivier, F; Stein, J L; Medland, S E; Arias Vasquez, A; Hibar, D P; Franke, B; Martin, N G; Wright, M J; Su, B



RHD allele distribution in Africans of Mali  

Microsoft Academic Search

BACKGROUND: Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. RESULTS: We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa)

Franz F Wagner; Joann M Moulds; Anatole Tounkara; Bourema Kouriba; Willy A Flegel



Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture.  


It is valuable to extend genotyping studies of Helicobacter pylori to strains from indigenous communities across the world to better define adaption, evolution, and associated diseases. We aimed to genetically characterize both human individuals and their infecting H. pylori from indigenous communities of Mexico, and to compare them with those from other human groups. We studied individuals from three indigenous groups, Tarahumaras from the North, Huichols from the West and Nahuas from the center of Mexico. Volunteers were sampled at their community site, DNA was isolated from white blood cells and mtDNA, Y-chromosome, and STR alleles were studied. H. pylori was cultured from gastric juice, and DNA extracted for genotyping of virulence and housekeeping genes. We found Amerindian mtDNA haplogroups (A, B, C, and D), Y-chromosome DYS19T, and Amerindian STRs alleles frequent in the three groups, confirming Amerindian ancestry in these Mexican groups. Concerning H.pylori cagA phylogenetic analyses, although most isolates were of the Western type, a new Amerindian cluster neither Western nor Asian, was formed by some indigenous Mexican, Colombian, Peruvian and Venezuelan isolates. Similarly, vacA phylogenetic analyses showed the existence of a novel Amerindian type in isolates from Alaska, Mexico and Colombia. With hspA strains from Mexico and other American groups clustered within the three major groups, Asian, African or European. Genotyping of housekeeping genes confirmed that Mexican strains formed a novel Asian-related Amerindian group together with strains from remote Amazon Aborigines. This study shows that Mexican indigenous people with Amerindian markers are colonized with H. pylori showing admixture of Asian, European and African strains in genes known to interact with the gastric mucosa. We present evidence of novel Amerindian cagA and vacA alleles in indigenous groups of North and South America. PMID:22073291

Camorlinga-Ponce, Margarita; Perez-Perez, Guillermo; Gonzalez-Valencia, Gerardo; Mendoza, Irma; Peñaloza-Espinosa, Rosenda; Ramos, Irma; Kersulyte, Dangeruta; Reyes-Leon, Adriana; Romo, Carolina; Granados, Julio; Muñoz, Leopoldo; Berg, Douglas E; Torres, Javier



Influence of the CXCL1 rs4074 A Allele on Alcohol Induced Cirrhosis and HCC in Patients of European Descent  

PubMed Central

Background and Aims CXCL1 (CXC chemokine-ligand-1) is a ligand for CXC chemokine receptor 2 expressed on hepatic stellate cells (HSC). Thus, CXCL1 might contribute to HSC activation and fibrogenesis. In the present study, we investigated the influence of the CXCL1 rs4074 polymorphism on the occurrence of alcohol induced liver cirrhosis and hepatocellular carcinoma (HCC). Methods The study involved 458 patients with alcoholic cirrhosis (170 with HCC), 115 alcoholics without liver disease and 342 healthy controls. All subjects were genotyped for the CXCL1 rs4074 polymorphism and CXCL1 serum levels of 132 patients were measured. In vitro CXCL1 secretion in TLR-transfected cell lines were studied by ELISA. Results Distribution of the CXCL1 genotypes (GG/GA/AA) was 159/219/80 in patients with alcoholic cirrhosis, 52/44/19 in alcoholic controls and 158/140/44 in healthy controls. Patients with alcohol-induced cirrhosis were significantly more often carriers of the CXCL1 rs4074 A allele (65.3%) than alcoholics without liver disease (54.8%, OR=1.55; 95%CI=1.025-2.350; p=0.04) and healthy controls (53.8%, OR=1.62; 95%CI=1.212-2.151; p=0.001). Accordingly, the frequency of the CXCL1 rs4074 A allele was significantly higher in the cirrhotic patients than in the subjects without cirrhosis (41.4% vs. 33.9%, OR=1.38, 95% CI:1.14–1.66, p=0.001). Furthermore cirrhotic carriers of the CXCL1 rs4074 A allele had significantly higher CXCL1 serum levels than carriers of the GG genotype. In contrast to sera from healthy controls, sera from patients with alcoholic cirrhosis induced CXCL1 secretion in TLR2- (p=0.016) and TLR4- (p=0.008) transfected HEK293 cells. This finding indicates that sera from patients with alcoholic cirrhosis contain soluble ligands that can induce CXCL1 production via stimulation of TLRs. Conclusion The enhanced CXCL1 serum levels in carriers of the rs4074 A allele together with their increased frequency in patients with alcohol induced cirrhosis suggest the CXCL1 rs4074 A allele as a genetic risk factor for alcoholic cirrhosis. PMID:24260493

Lutz, Philipp; Langhans, Bettina; Wolter, Franziska; Eisenhardt, Marianne; Kramer, Benjamin; Kokordelis, Pavlos; Glassner, Andreas; Muller, Tobias; Rosendahl, Jonas; Fischer, Janett; Berg, Thomas; Grunhage, Frank; Leifeld, Ludger; Soyka, Michael; Nattermann, Jacob; Sauerbruch, Tilman; Stickel, Felix; Spengler, Ulrich



The interplay between natural selection and susceptibility to melanoma on allele 374F of SLC45A2 gene in a South European population.  


We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans. PMID:25093503

López, Saioa; García, Oscar; Yurrebaso, Iñaki; Flores, Carlos; Acosta-Herrera, Marialbert; Chen, Hua; Gardeazabal, Jesús; Careaga, Jesús María; Boyano, María Dolores; Sánchez, Ana; Ratón-Nieto, Juan Antonio; Sevilla, Arrate; Smith-Zubiaga, Isabel; de Galdeano, Alicia García; Martinez-Cadenas, Conrado; Izagirre, Neskuts; de la Rúa, Concepción; Alonso, Santos



Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.  


Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications. PMID:24465990

Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina



Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe  

PubMed Central

Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications. PMID:24465990

Akgul, Gulfirde; Della Casa, Philippe; Ruhli, Frank; Warinner, Christina



One mutation in the galactocerebrosidase gene is responsible for a majority of mutant alleles in Northern European patients with infantile Krabbe disease  

SciTech Connect

Globoid cell leukodystrophy (GCL) or Krabbe disease is an autosomal recessive disorder resulting from a deficiency of galactocerebrosidase (GALC) activity. The typical human patient presents with symptoms of spasticity, developmental delay and irritability by 6 months of age. Older patients, including adults, are also diagnosed with this disorder. While patients from all ethnic groups are included within the more than 230 patients diagnosed in this laboratory, many trace their ancestry to Northern Europe. Patients are easy to diagnose by their low GALC activity. However, carriers are difficult to identify due to a large overlap in the {open_quotes}control{close_quotes} and carrier ranges. With our cloning of the GALC gene we have undertaken a study to identify mutations causing GCL in some of our families. We have identified a C to T transition at position {open_quotes}502{close_quotes} (counting form the A of the initiation codon) in about 65% of the mutant alleles in patients with Northern European ancestry. Identification of an intron 32 nucleotides downstream from the site of the mutation permits amplification of genomic DNA samples and rapid cycle sequencing. This mutation was found primarily in classic infantile patients, however it was found in the heterozygous state in a juvenile patient and in an African-American patient. This mutation changes the codon for arginine to one for cysteine, and computer analysis predicts a significant change in the secondary structure of this multi-subunit enzyme. A G to A transition at position {open_quotes}694{close_quotes} was found in the homozygous state in another infantile patient from a consanguineous mating. We are in the process of looking for this mutation in other patients. It is hoped that a few mutations will be found to be responsible for infantile Krabbe disease so that carrier identification can be improved for some families.

Rafi, M.A.; Luzi, P.; Hershberger, M. [Jefferson Medical College, Philadelphia, PA (United States)] [and others



Role of Homozygous DC-SIGNR 5\\/5 Tandem Repeat Polymorphism in HIV1 Exposed Seronegative North Indian Individuals  

Microsoft Academic Search

Despite multiple sexual exposures to HIV-1 virus, some individuals remain HIV-1 seronegative. Although several genetic factors\\u000a have been related to HIV-1 resistance, the homozygosity for a mutation in CCR5 gene (the 32-bp deletion, i.e., CCR5-Delta32\\u000a allele) is presently considered the most relevant one. The C-type lectins, DC-SIGN (present on dendritic cells and macrophages)\\u000a and DC-SIGNR (present on endothelial cells in

Anurag Rathore; Animesh Chatterjee; P. Sivarama; Naohiko Yamamoto; Tapan N. Dhole




Microsoft Academic Search

Abstract As a strategy of self-representation and a device of power, Europeanization is fundamentally reorganizing territoriality and peoplehood, the two principles of group identification that have shaped modern European order. It is the result of a new level and intensity of integration that has been a reaction to the destruction of this century's first and second world wars and the

John Borneman; Nick Fowler



RHD allele distribution in Africans of Mali  

PubMed Central

Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHD? for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHD? . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHD? and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A



Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania  

PubMed Central

Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

Stanciu, Florin; Vladu, Simona; Cutar, Veronica; Cocioaba, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius



Improved metastasis-free survival in nonadjuvantly treated postmenopausal breast cancer patients with chemokine receptor 5 del32 frameshift mutations.  


The CC-chemokine receptor CCR5 has been associated with cancer progression and metastasis. CCR5 blockers such as Maraviroc are tested in metastatic cancer patients. A mutant allele of CCR5, CCR5-delta32 (CCR5del32), which encodes for a protein with a trans-dominant negative effect on the wildtype protein, is frequently found in populations of northern European origin. We set out to determine if the CCR5del32 genotype is associated with progression of breast cancer. Here, we genotyped 414 breast cancer patients and investigated whether the CCR5 genotype had an association with the likelihood to metastasize within specific subgroups of this cohort. The findings were subsequently confirmed in an independent cohort of 1,017 breast cancer patients. Specifically within the postmenopausal subgroup of the initial cohort (n?=?325) individuals carrying the CCR5del32 genotype exhibited a significantly longer metastasis-free survival (MFS, p?=?0.038). In an independent cohort, CCR5del32 genotype was confirmed to be associated with prolonged MFS only in postmenopausal patients (n?=?579, hazard ratio [HR]?=?0.61, 95% confidence interval [95% CI]?=?0.38-0.99, p?=?0.044), and not in premenopausal patients (n?=?438, HR?=?1.01, 95% CI?=?0.70-1.48, p?=?0.94). Our results indicate that CCR5del32 genotype is associated with good prognosis in postmenopausal breast cancer patients. Considering this result, postmenopausal breast cancer patients who are wildtype for CCR5 genotype might benefit from CCR5 blockers, such as Maraviroc. PMID:24807072

Span, P N; Pollakis, G; Paxton, W A; Sweep, F C G J; Foekens, J A; Martens, J W M; Sieuwerts, A M; van Laarhoven, H W M



Resolution of HLA-B*44:02:01G, -DRB1*14:01:01G and -DQB1*03:01:01G reveals a high allelic variability among 12 European populations.  


Within the framework of the EU-funded HLA-NET action, an analysis of three G-group alleles, HLA-B*44:02:01G, DRB1*14:01:01G and DQB1*03:01:01G, was undertaken in 12 European populations. Ambiguities were resolved by polymerase chain reaction-sequence-specific amplification (PCR-SSP) or PCR-sequence-based typing (PCR-SBT) in a total of 5095 individuals. The results of the DRB1*14:01/14:54 ambiguity showed high relative ratios (24-53%) of DRB1*14:01 in Bulgarians, Croatians, Greeks, Italians and Slovenians, contrasting with low ratios (6-13%) in Austrians, Finnish, French, Hungarians, Norwegians and Swiss. Resolution of the B*44:02/44:27 ambiguity showed that B*44:27 had a high relative ratio in Slovenians (25.5%) and Bulgarians (37%) and low in French and Swiss (0.02-1%), and was not observed in Greeks and Italians. The highest relative ratio of DQB1*03:19 was found in Portuguese (11%), by contrast with low ratios (0-3%) in the other five populations. Analysis of the A, B, DRB1 phenotypes and family-derived haplotypes in 1719 and 403 individuals positive for either HLA-B*44:02G or DRB1*14:01G ambiguities, respectively, showed some preferential associations, such as A*26?DRB1*14:01, B*35?DRB1*14:01, B*38?DRB1*14:01 and B*44:27?DRB1*16. Because these ambiguities are located outside the peptide-binding site, they may not be recognized by alloreactive T-cells. However, because of strong linkage disequilibrium (LD), the DRB1*14:01 vs DRB1*14:54 and the B*44:02 vs B*44:27 mismatches are associated to DRB3-, and C-mismatches, respectively. These results are informative for algorithms searching unrelated hematopoietic stem cell donors. For B*44:27-positive patients, searches are expected to be more successful when requesting donors from Southeastern-European ancestry. Furthermore, the introduction of human leukocyte antigen (HLA)-typing strategies that allow resolving exon 4 (for class I) and exon 3 (for class II) polymorphisms can be expected to contribute significantly to population genetics studies. PMID:25209151

Vidan-Jeras, B; Buhler, S; Dubois, V; Grubic, Z; Ivanova, M; Jaatinen, T; Ligeiro, D; Lokki, M-L; Papasteriades, C; Poli, F; Spyropoulou-Vlachou, M; Tordai, A; Viken, M K; Wenda, S; Nunes, J M; Sanchez-Mazas, A; Tiercy, J-M



Allelic structures at hypervariable minisatellite B6.7 in Japanese show population specificity.  


Human minisatellite B6.7 shows extensive allele length and structural variability in north Europeans. We analysed this locus in the Japanese population. Allele size distributions showed that Japanese retain extensive allele length variability but have significantly smaller alleles compared with north Europeans. In contrast, there is very little variation in flanking DNA, with only one single-nucleotide polymorphism (SNP) near the minisatellite. Ninety-two Japanese alleles were further characterised by minisatellite variant repeat mapping by polymerase chain reaction (MVR-PCR). These alleles showed a wide variety of internal MVR structures, despite their relative shortness, with most alleles observed only once in the sample. The true heterozygosity is estimated at 99.95%, with well in excess of 2000 different alleles existing in the Japanese population. Dot matrix analysis showed that groups of related alleles sharing structural motifs could be identified within Japanese and in north Europeans, and that these groups are population specific with no examples of significant similarity between any Japanese and north European alleles. Minisatellite B6.7 therefore shows huge allele variability and fast repeat turnover in Japanese as well as north European populations, and provides novel lineage markers for exploring very recent events in human population history. PMID:12032590

Mizukoshi, Tsunenori; Tamaki, Keiji; Azumi, Jun-ichi; Matsumoto, Hiroshi; Imai, Kohzoh; Jeffreys, Alec J



Microsatellite Variation in Honey Bee (Apis MeZZfera L.) Populations: Hierarchical Genetic Structure and Test of the Infinite Allele and Stepwise Mutation Models  

Microsoft Academic Search

Samples from nine populations belonging to three African (intmissa, scutellata and capensis) and four European (mellijima, liptica, carnica and cecropia) Apis mellifea subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies,

Lionel Garnery; Michel Solignac; Jean-Marie Cornuett


Allelic association between marker loci  

PubMed Central

Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker × oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage. PMID:9990074

Lonjou, C.; Collins, A.; Morton, N. E.



Georg-August-Universitt Gttingen, Bereich Humanmedizin Publikationen und Hochschulschriften 2005  

E-print Network

in a multiple sclerosis model. BLOOD, 106(5): 1875-83. 16. Hohlfeld R, Kerschensteiner M, Stadelmann C, Lassmann, Ransohoff RM, Lassmann H, Bruck W, Weinshenker BG, Lucchinetti CF (2005) CCR5Delta32 polym

Gollisch, Tim


Stromal cell-derived factor-1 genotype, coreceptor tropism, and HIV type 1 disease progression.  


This study used a well characterized cohort of human immunodeficiency virus type 1 (HIV-1)-infected hemophiliacs to define the relationship between the SDF1-3'A allele, the plasma HIV-1 coreceptor tropism, and the natural history of HIV-1 disease. Subjects heterozygous or homozygous for the SDF1-3'A allele experienced higher rates of decline in CD4+ T cell counts over time than did those without the allele (P=.009). Moreover, they had an increased risk of progression to acquired immunodeficiency syndrome and death, a relationship that persisted even when baseline plasma HIV-1 RNA levels and CD4+ T cell counts or CCR5 Delta 32 and CCR2-64I genotype were controlled for. This relationship was even stronger in a subgroup of subjects for whom tropism data were available. Subjects with the SDF1-3'A allele were also more likely to have detectable X4-tropic viruses (P=.012), and, when tropism was included in the survival analyses, the effect of the SDF1-3'A allele on disease progression was no longer significant. Therefore, the increased frequency of X4-tropic viruses in subjects carrying the SDF1-3'A allele may explain the observed adverse effect that this allele has on the natural history of HIV-1 disease. PMID:16206074

Daar, Eric S; Lynn, Henry S; Donfield, Sharyne M; Lail, Alice; O'Brien, Stephen J; Huang, Wei; Winkler, Cheryl A



Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing® technology  

PubMed Central

Background Identification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology. Methods A single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow. Results Pyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics. Conclusion This Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies. PMID:19703308

Koontz, Deborah A; Huckins, Jacqueline J; Spencer, Antonina; Gallagher, Margaret L



On the allelic spectrum of human disease.  


Human disease genes show enormous variation in their allelic spectra; that is, in the number and population frequency of the disease-predisposing alleles at the loci. For some genes, there are a few predominant disease alleles. For others, there is a wide range of disease alleles, each relatively rare. The allelic spectrum is important: disease genes with only a few deleterious alleles can be more readily identified and are more amenable to clinical testing. Here, we weave together strands from the human mutation and population genetics literature to provide a framework for understanding and predicting the allelic spectra of disease genes. The theory does a reasonable job for diseases where the genetic etiology is well understood. It also has bearing on the Common Disease/Common Variants (CD/CV) hypothesis, predicting that at loci where the total frequency of disease alleles is not too small, disease loci will have relatively simple spectra. PMID:11525833

Reich, D E; Lander, E S



Chemokine coreceptor usage by diverse primary isolates of human immunodeficiency virus type 1.  


We tested chemokine receptor subset usage by diverse, well-characterized primary viruses isolated from peripheral blood by monitoring viral replication with CCR1, CCR2b, CCR3, CCR5, and CXCR4 U87MG.CD4 transformed cell lines and STRL33/BONZO/TYMSTR and GPR15/BOB HOS.CD4 transformed cell lines. Primary viruses were isolated from 79 men with confirmed human immunodeficiency virus type 1 (HIV-1) infection from the Chicago component of the Multicenter AIDS Cohort Study at interval time points. Thirty-five additional well-characterized primary viruses representing HIV-1 group M subtypes A, B, C, D, and E and group O and three primary simian immunodeficiency virus (SIV) isolates were also used for these studies. The restricted use of the CCR5 chemokine receptor for viral entry was associated with infection by a virus having a non-syncytium-inducing phenotype and correlated with a reduced rate of disease progression and a prolonged disease-free interval. Conversely, broadening chemokine receptor usage from CCR5 to both CCR5 and CXCR4 was associated with infection by a virus having a syncytium-inducing phenotype and correlated with a faster rate of CD4 T-cell decline and progression of disease. We also observed a greater tendency for infection with a virus having a syncytium-inducing phenotype in men heterozygous for the defective CCR5 Delta32 allele (25%) than in those men homozygous for the wild-type CCR5 allele (6%) (P = 0.03). The propensity for infection with a virus having a syncytium-inducing phenotype provides a partial explanation for the rapid disease progression among some men heterozygous for the defective CCR5 Delta32 allele. Furthermore, we did not identify any primary viruses that used CCR3 as an entry cofactor, despite this CC chemokine receptor being expressed on the cell surface at a level commensurate with or higher than that observed for primary peripheral blood mononuclear cells. Whereas isolates of primary viruses of SIV also used STRL33/BONZO/TYMSTR and GPR15/BOB, no primary isolates of HIV-1 used these particular chemokine receptor-like orphan molecules as entry cofactors, suggesting a limited contribution of these other chemokine receptors to viral evolution. Thus, despite the number of chemokine receptors implicated in viral entry, CCR5 and CXCR4 are likely to be the physiologically relevant chemokine receptors used as entry cofactors in vivo by diverse strains of primary viruses isolated from blood. PMID:9765480

Zhang, L; He, T; Huang, Y; Chen, Z; Guo, Y; Wu, S; Kunstman, K J; Brown, R C; Phair, J P; Neumann, A U; Ho, D D; Wolinsky, S M



A novel measurement of allele discrimination for assessment of allele-specific silencing by RNA interference.  


Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs. PMID:25037272

Takahashi, Masaki; Hohjoh, Hirohiko



An historical perspective on "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus".  


Human population genetics is a completely different science today compared to two decades ago, at least at the empiric level. Our paper [Chang (Hum Genet 98:91-101, 1996a)] demonstrated that three different alleles were common when one considered many populations although other low frequency alleles occurred. Because previous work had been largely done on European subjects, our findings involved 36 distinct populations and showed that East Asian populations had nearly lost the 7-repeat allele, and that Native American populations had the highest frequencies of that allele globally, was a significant early empiric demonstration of the potential magnitude of population variation at important genes. There are thousands of loci tested on many of the same populations and the gene frequency pattern seen for the DRD4 7-repeat allele is seen at other loci, arguing that this pattern commonly reflects the pattern of divergence of populations and accumulated random genetic drift. PMID:24162668

Kidd, Kenneth K; Pakstis, Andrew J; Yun, Libing



Estimating the probability of allelic drop-out of STR alleles in forensic genetics  

Microsoft Academic Search

In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop-out using the results of all STR loci

Torben Tvedebrink; Poul Svante Eriksen; Helle Smidt Mogensen; Niels Morling



Alleles for Longevity Kenneth W. Wachter  

E-print Network

Alleles for Longevity Kenneth W. Wachter Departments of Demography and Statistics University of California at Berkeley Demography Brown-Bag Luncheon Talk 1 September 2010 Kenneth W. Wachter Alleles Signalling Pathways Human Forkhead Box 03A Gene: FOX03A Bradley J. Willcox et al. (2008) FOXO3A genotype

Wachter, Kenneth W.


Prevalence of HLA-DQA1 alleles and haplotypes in blood donors resident in Wales.  


Two hundred and fifty-four normal blood donors, from a largely UK European population, were sequence-based typed for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1 and HLA-DQB1. The fit to Hardy-Weinberg expectations was good for all loci (all P values >0.5). Fifteen DQA1 alleles were identified to the second field. DQA1 carriage, allele and DQA1-DQB1 and DRB1-DQA1-DQB1 haplotype frequencies, linkage disequilibria and related values are presented. PMID:25345618

Lemin, A J; Darke, C



Characterization of the treefrog null allele, 1991  

SciTech Connect

Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

Guttman, S.I. (Miami Univ., Oxford, OH (United States). Dept. of Zoology)



Characterization of the treefrog null allele  

SciTech Connect

As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

Guttman, S.I. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)



Bovine Polledness - An Autosomal Dominant Trait with Allelic Heterogeneity  

PubMed Central

The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a ?381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations. PMID:22737241

Medugorac, Ivica; Seichter, Doris; Graf, Alexander; Russ, Ingolf; Blum, Helmut; Gopel, Karl Heinrich; Rothammer, Sophie; Forster, Martin; Krebs, Stefan



Bovine polledness--an autosomal dominant trait with allelic heterogeneity.  


The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a ?381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations. PMID:22737241

Medugorac, Ivica; Seichter, Doris; Graf, Alexander; Russ, Ingolf; Blum, Helmut; Göpel, Karl Heinrich; Rothammer, Sophie; Förster, Martin; Krebs, Stefan



Most parsimonious haplotype allele sharing determination  

PubMed Central

Background The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on quantitative traits, and the description of the full allelic spectrum is deemed still far from reach. Given increasing density of single nucleotide polymorphisms available and suggested by the block-like structure of the human genome, a popular and prosperous strategy is to use haplotypes to try to capture the correlation structure of SNPs in regions of little recombination. The key to the success of this strategy is thus the ability to unambiguously determine the haplotype allele sharing status among the members. The association studies based on haplotype sharing status would have significantly reduced degrees of freedom and be able to capture the combined effects of tightly linked causal variants. Results For pedigree genotype datasets of medium density of SNPs, we present two methods for haplotype allele sharing status determination among the pedigree members. Extensive simulation study showed that both methods performed nearly perfectly on breakpoint discovery, mutation haplotype allele discovery, and shared chromosomal region discovery. Conclusion For pedigree genotype datasets, the haplotype allele sharing status among the members can be deterministically, efficiently, and accurately determined, even for very small pedigrees. Given their excellent performance, the presented haplotype allele sharing status determination programs can be useful in many downstream applications including haplotype based association studies. PMID:19379528

Cai, Zhipeng; Sabaa, Hadi; Wang, Yining; Goebel, Randy; Wang, Zhiquan; Xu, Jiaofen; Stothard, Paul; Lin, Guohui



Functional analysis of 11 novel GBA alleles.  


Gaucher disease is the most frequent lysosomal storage disorder due to the deficiency of the acid ?-glucosidase, encoded by the GBA gene. In this study, we report the structural and functional characterization of 11 novel GBA alleles. Seven single missense alleles, P159S, N188I, E235K, P245T, W312S, S366R and W381C, and two alleles carrying in cis mutations, (N188S; G265R) and (E326K; D380N), were studied for enzyme activity in transiently transfected cells. All mutants were inactive except the P159S, which retained 15% of wild-type activity. To further characterize the alleles carrying two in cis mutations, we expressed constructs bearing singly each mutation. The presence of G265R or D380N mutations completely abolished enzyme activity, while N188S and E326K mutants retained 25 and 54% of wild-type activity, respectively. Two mutations, affecting the acceptor splice site of introns 5 (c.589-1G>A) and 9 (c.1389-1G>A), led to the synthesis of aberrant mRNA. Unpredictably, family studies showed that two alleles resulted from germline or 'de novo' mutations. These results strengthen the importance of performing a complete and accurate molecular analysis of the GBA gene in order to avoid misleading conclusions and provide a comprehensive functional analysis of new GBA mutations. PMID:24022302

Malini, Erika; Grossi, Serena; Deganuto, Marta; Rosano, Camillo; Parini, Rossella; Dominisini, Silvia; Cariati, Roberta; Zampieri, Stefania; Bembi, Bruno; Filocamo, Mirella; Dardis, Andrea



ALFREDthe ALlele FREquency Database ALFRED is a free, web-accessible, curated compilation of allele frequency  

E-print Network

ALFREDthe ALlele FREquency Database ALFRED is a free, web-accessible, curated compilation of allele publication or source as well as to molecular and ethnographic databases. ALFRED is supported by a grant from position Populations by geographic region Versatile Keyword search Published SNP and STRP sets of forensic

Lee, Daeyeol


Frequency of CCR5?32 allele in healthy Bosniak population.  


Recent evidence has demonstrated the role of CCR5?32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5?32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and lower in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5?32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Hercegovina population. Therefore, the aim of our study was to assess the frequency of CCR5?32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5?32 was detected by sequence-specific PCR in a sample of 100 healthy subjects from Bosnia and Herzegovina (DNA collected 2011-2013). Mean age of the cohort being 58.8 (± 10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ?32 allele frequency of 9.5%. CCR5?32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. PMID:25172974

Adler, Gra?yna; Valjevac, Amina; Skonieczna-?ydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Mi?osz; Urba?ska, Anna; Salkic, Nermin Nusret



Demographic history and rare allele sharing among human populations.  


High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ?1,000 sequenced chromosomes per population, whereas ?2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D



Demographic history and rare allele sharing among human populations  

PubMed Central

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ?1,000 sequenced chromosomes per population, whereas ?2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Goncalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stutz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.



Overcoming Allelic Specificity by Immunization with Five Allelic Forms of Plasmodium falciparum Apical Membrane Antigen 1  

PubMed Central

Apical membrane antigen 1 (AMA1) is a leading vaccine candidate, but the allelic polymorphism is a stumbling block for vaccine development. We previously showed that a global set of AMA1 haplotypes could be grouped into six genetic populations. Using this information, six recombinant AMA1 proteins representing each population were produced. Rabbits were immunized with either a single recombinant AMA1 protein or mixtures of recombinant AMA1 proteins (mixtures of 4, 5, or 6 AMA1 proteins). Antibody levels were measured by enzyme-linked immunosorbent assay (ELISA), and purified IgG from each rabbit was used for growth inhibition assay (GIA) with 12 different clones of parasites (a total of 108 immunogen-parasite combinations). Levels of antibodies to all six AMA1 proteins were similar when the antibodies were tested against homologous antigens. When the percent inhibitions in GIA were plotted against the number of ELISA units measured with homologous AMA1, all data points followed a sigmoid curve, regardless of the immunogen. In homologous combinations, there were no differences in the percent inhibition between the single-allele and allele mixture groups. However, all allele mixture groups showed significantly higher percent inhibition than the single-allele groups in heterologous combinations. The 5-allele-mixture group showed significantly higher inhibition to heterologous parasites than the 4-allele-mixture group. On the other hand, there was no difference between the 5- and 6-allele-mixture groups. These data indicate that mixtures with a limited number of alleles may cover a majority of the parasite population. In addition, using the data from 72 immunogen-parasite combinations, we mathematically identified 13 amino acid polymorphic sites which significantly impact GIA activities. These results could be a foundation for the rational design of a future AMA1 vaccine. PMID:23429537

Herrera, Raul; Diouf, Ababacar; Zhou, Hong; Mu, Jianbing; Hu, Zonghui; MacDonald, Nicholas J.; Reiter, Karine; Nguyen, Vu; Shimp, Richard L.; Singh, Kavita; Narum, David L.; Long, Carole A.; Miller, Louis H.



RHD alleles in the Tunisian population  

PubMed Central

Background: A comprehensive survey of RHD alleles in Tunisia population was lacking. The aim of this study was to use a multiplex RHD typing assay for simultaneous detection of partial D especially with RHD/RHCE deoxyribonucleic acid (DNA) sequence exchange mechanism and some weak D alleles. Materials and Methods: Six RHD specific primer sets were designed to amplify RHD exons 3, 4, 5, 6, 7 and 9. DNA from 2000 blood donors (1777 D+ and 223 D-) from several regions was selected for RHD genotyping using a PCR multiplex assay. Further molecular investigations were done to characterize the RHD variants that were identified by the PCR multiplex assay. Results: In the 1777 D+ samples, only 10 individuals showed the absence of amplification of exons 4 and 5 that were subsequently identified by PCR-SSP as weak D type 4 variants. No hybrid allele was detected. In the 223 D-, RHD amplification of some exons was observed only in 5 samples: 4 individuals expressed only RHD exon 9, and one subject lacking exons 4 and 5. These samples were then screened by PCR-SSPs on d(C) ces and weak D type 4, respectively. Conclusion: The weak D type 4 appears to be the most common D variant allele. We have not found any partial D variant. Findings also indicated that RHD gene deletion is the most prevalent cause of the D- phenotype in the Tunisian population. PMID:24014941

Ouchari, Mouna; Jemni-Yaacoub, Saloua; Chakroun, Taher; Abdelkefi, Saida; Houissa, Batoul; Hmida, Slama



HLA genes in the Chuvashian population from European Russia: admixture of Central European and Mediterranean populations.  


HLA alleles have been determined for the first time in individuals from the Chuvashian population by DNA typing and sequencing. HLA-A, -B, -DR, and -DQ allele frequencies and extended haplotypes have also been determined, and the results compared to those for Central Europeans, Siberians and other Asians, Caucasians, Middle Easterners, and Mediterranean peoples. Genetic distances, neighbor-joining dendrograms, and correspondence analysis have been performed. Present-day Chuvash speak an Altaic-Turkic language and are genetically related to Caucasians (Georgians), Mediterraneans, and Middle Easterners, and not only to Central or Northern Europeans; Chuvash contain little indications of Central Asian-Altaic gene flow. Thus, present-day Chuvash who speak an Altaic-Turkic language are probably more closely related to ancient Mesopotamian-Hittites and northern European populations than to central Asia-Altaic people. PMID:14527201

Arnaiz-Villena, Antonio; Martinez-Laso, Jorge; Moscoso, Juan; Livshits, Gregory; Zamora, Jorge; Gomez-Casado, Eduardo; Silvera-Redondo, Carlos; Melvin, Kristin; Crawford, Michael H



Estimating the probability of allelic drop-out of STR alleles in forensic genetics.  


In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework. PMID:19647706

Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels



Allelic variation of gene expression in maize hybrids.  


Allelic expression variation of nonimprinted autosomal genes has recently been uncovered in mouse hybrids and humans. The allelic expression variation is attributed to differences in noncoding DNA sequences and does not involve epigenetic regulation or gene imprinting. This expression variation is suggested to play important roles in determining phenotypic diversity. Virtually nothing is known about such allele-specific expression variation in a hybrid plant where two alleles are compared in the same genetic context. We examined parental transcript accumulation in maize (Zea mays) hybrids using allele-specific RT-PCR analysis. Among 15 genes analyzed, 11 showed differences at the RNA level, ranging from unequal expression of the two alleles (biallelic) to expression of a single allele (monoallelic). Maternal or paternal transmission had little effect on the allele-specific transcript ratio of nearly all genes analyzed, suggesting that parent-of-origin effect was minimal. We analyzed the allelic difference in genetically contrasting hybrids and hybrids under high planting density and drought stress. Whereas a genetically improved modern hybrid expressed both alleles, a less improved old hybrid frequently showed mono-allelic expression. Furthermore, the two alleles in the hybrid responded differentially to abiotic stresses. The results of allele-specific regulation in different tissues in responding to environment and stress suggest an unequivalent function of the parental alleles in the hybrid, which may have an impact on heterosis. PMID:15194819

Guo, Mei; Rupe, Mary A; Zinselmeier, Christopher; Habben, Jeffrey; Bowen, Benjamin A; Smith, Oscar S



Determination of the HUMTH01 alleles by the APLP method.  


We present a simple and rapid technique for determination of alleles at the HUMTH01 locus. The amplified product length polymorphism (APLP) method using two primers different in length, permits the differentiation between allele 9.3 and other alleles. The primers were designed to have an allele-specific nucleotide at the 3' terminal and 11 non-complementary nucleotides were added to the 5' terminal of one of the primers for the allele 9.3. The amplified fragment sizes for the alleles 9.3 and 10 were 80 bp and 70 bp, respectively. This method has proved to be very useful for forensic applications. PMID:10048673

Watanabe, G; Umetsu, K; Suzuki, T



The allelic spectra of common diseases may resemble the allelic spectrum of the full genome.  


Identification of the genes responsible for common human diseases promises to be one of the most significant advances in medical knowledge and treatment. To date, the numerous attempts to identify the genes responsible for complex and multi-factorial common diseases have met with only a handful of successes. The key to calculating the optimal effort and ideal approach to successful identifications lies with understanding the likely allelic spectrum of the target disease. The allelic spectrum describes the number of disease loci and the frequency of each disease allele. It has been implicitly assumed that disease spectra are biased towards either commonness or rareness relative to the allelic spectrum of the overall human genome. We present a hypothesis that the allelic spectra of common diseases are generally similar to the spectrum that characterizes the entire genome. This hypothesis is supported by the fact that only a few loci have major significance to familial disease risks and that there may be many disease loci which each make a minor contribution to a disease. Additionally, although relatively few alleles of the human genome have been examined for disease involvement, current estimates of the number of disease genes are very high. Because selection will have been operating only weakly and for a relatively short time on most of the alleles associated with complex diseases, spectra that are characteristic of near-neutral selection may well apply. We thus propose that the hitherto neglected hypothesis that puts the likely allelic spectra of common diseases in the middle ground between the prevailing hypotheses of spectral skew towards rareness or commonness is the most likely. By using this hypothesis as the null, research resources may be optimally allocated and greater success in identifying disease genes may be achieved. PMID:15325027

Wang, William Y S; Pike, Nathan



European Mistletoe  


... campaign . Top Sources American mistletoe. Natural Medicines Comprehensive Database Web site. Accessed at on July 7, 2009. European mistletoe. Natural Medicines Comprehensive Database Web site. Accessed at on ...


European Community.  


The European Community was established in 1951 to reconcile France and Germany after World War II and to make possible the eventual federation of Europe. By 1986, there were 12 member countries: France, Italy, Belgium, the Federal Republic of Germany, Luxembourg, the Netherlands, Denmark, Ireland, the United Kingdom, Greece, Spain, and Portugal. Principal areas of concern are internal and external trade, agriculture, monetary coordination, fisheries, common industrial and commercial policies, assistance, science and research, and common social and regional policies. The European Community has a budget of US$34.035 billion/year, funded by customs duties and 1.4% of each member's value-added tax. The treaties establishing the European Community call for members to form a common market, a common customs tariff, and common agricultural, transport, economic, and nuclear policies. Major European Community institutions include the Commission, Council of Ministers, European Parliament, Court of Justice, and Economic and Social Committee. The Community is the world's largest trading unit, accounting for 15% of world trade. The 2 main goals of the Community's industrial policy are to create an open internal market and to promote technological innovation in order to improve international competitiveness. The European Community aims to contribute to the economic and social development of Third World countries as well. PMID:12177941



Evaluation of Allele-Specific Somatic Changes of Genome-Wide Association Study Susceptibility Alleles in Human Colorectal Cancers  

PubMed Central

Background Tumors frequently exhibit loss of tumor suppressor genes or allelic gains of activated oncogenes. A significant proportion of cancer susceptibility loci in the mouse show somatic losses or gains consistent with the presence of a tumor susceptibility or resistance allele. Thus, allele-specific somatic gains or losses at loci may demarcate the presence of resistance or susceptibility alleles. The goal of this study was to determine if previously mapped susceptibility loci for colorectal cancer show evidence of allele-specific somatic events in colon tumors. Methods We performed quantitative genotyping of 16 single nucleotide polymorphisms (SNPs) showing statistically significant association with colorectal cancer in published genome-wide association studies (GWAS). We genotyped 194 paired normal and colorectal tumor DNA samples and 296 paired validation samples to investigate these SNPs for allele-specific somatic gains and losses. We combined analysis of our data with published data for seven of these SNPs. Results No statistically significant evidence for allele-specific somatic selection was observed for the tested polymorphisms in the discovery set. The rs6983267 variant, which has shown preferential loss of the non-risk T allele and relative gain of the risk G allele in previous studies, favored relative gain of the G allele in the combined discovery and validation samples (corrected p-value?=?0.03). When we combined our data with published allele-specific imbalance data for this SNP, the G allele of rs6983267 showed statistically significant evidence of relative retention (p-value?=?2.06×10?4). Conclusions Our results suggest that the majority of variants identified as colon cancer susceptibility alleles through GWAS do not exhibit somatic allele-specific imbalance in colon tumors. Our data confirm previously published results showing allele-specific imbalance for rs6983267. These results indicate that allele-specific imbalance of cancer susceptibility alleles may not be a common phenomenon in colon cancer. PMID:22629442

Gerber, Madelyn M.; Hampel, Heather; Schulz, Nathan P.; Fernandez, Soledad; Wei, Lai; Zhou, Xiao-Ping; de la Chapelle, Albert; Toland, Amanda Ewart



Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level.  

PubMed Central

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow. PMID:9611207

Veuille, M; Bénassi, V; Aulard, S; Depaulis, F



Generation of conditional Cited2 null alleles.  


Cited2 is a transcriptional co-factor that is widely expressed in both embryonic and extraembryonic cells during early development. It is essential for embryonic development with Cited2 null embryos showing abnormal development of organs including heart, neural tube, adrenal glands, and placenta (both in trophoblast derivatives and invading fetal vasculature), as well as having defects in the establishment of the left-right body axis. We report the generation of two conditional null alleles allowing Cre-recombinase-mediated somatic cell gene inactivation. Mice heterozygous or homozygous for these alleles are viable and fertile. Crossing conditional mutants with CMV-Cre transgenic mice produces an embryonic-lethal phenotype in the offspring indistinguishable from germline null mutants. We also demonstrate that conditional deletion results in lacZ expression under the control of the Cited2 promoter. These alleles are therefore useful genetic tools for dissecting the functions of Cited2 in the formation of different organs and patterning of the developing embryo. genesis PMID:17133411

Preis, Jost I; Wise, Natalie; Solloway, Mark J; Harvey, Richard P; Sparrow, Duncan B; Dunwoodie, Sally L



Mutant maize variety containing the glt1-1 allele  


A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating. 2 figs.

Nelson, O.E.; Pan, D.



Development of microsatellite loci in the European Dipper, Cinclus cinclus  

Microsoft Academic Search

Eighteen polymorphic microsatellite DNA loci were isolated in the Central European subspecies of the European Dipper (Cinclus cinclus aquaticus). The loci were tested for polymorphism using a test panel of 24 breeding birds. Numbers of alleles ranged from 2 to 21 per\\u000a locus and expected heterozygosities varied between 0.47 and 0.83. Two loci (Cici10 and Cici12) proved to be Z-linked.

T. B. Bucher; P. Wandeler; J. Hegelbach; L. F. Keller



The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective  

Microsoft Academic Search

A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant

Ornella Semino; Giuseppe Passarino; Peter J. Oefner; Alice A. Lin; Svetlana Arbuzova; Lars E. Beckman; Giovanna De Benedictis; Paolo Francalacci; Anastasia Kouvatsi; Svetlana Limborska; Mladen Marcikiæ; Anna Mika; Barbara Mika; Dragan Primorac; A. Silvana Santachiara-Benerecetti; L. Luca Cavalli-Sforza; Peter A. Underhill



HLA-DRB1 Alleles Are Associated with the Susceptibility to Sporadic Parkinson's Disease in Chinese Han Population  

PubMed Central

Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The ?2 test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate. PMID:23139797

Sun, Congcong; Wei, Lei; Luo, Feifei; Li, Yi; Li, Jiaobiao; Zhu, Feiqi; Kang, Ping; Xu, Rensi; Xiao, LuLu; Liu, Zhuolin; Xu, Pingyi



Distribution of CYP2D6 Alleles and Phenotypes in the Brazilian Population  

PubMed Central

Abstract The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

Sortica, Vinicius A.; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D. J.; dos Santos, Andrea K. Ribeiro; Romano-Silva, Marco A.; Hutz, Mara H.



SIBLING family genes and bone mineral density: association and allele-specific expression in humans.  


Osteoporosis is a common complex disorder with reduced bone mineral density (BMD) and increased susceptibility to fracture. Peak BMD is one of the primary determinants of osteoporotic fracture risk, and is under substantial genetic control. Extracellular matrix, a major component of the bone, influences BMD by regulating mineral deposition and maintaining cellular activity. It contains several SIBLING family proteins, null mutations of which cause mineralization defects in humans. In this study, we tested 59 single-nucleotide polymorphisms (SNPs) located in the 5 SIBLING family genes (DSPP, DMP1, IBSP, MEPE and SPP1) for association with normal variation in peak BMD in healthy men and women. We measured femoral neck (FN) and lumbar spine (LS) areal BMD by dual energy x-ray absorptiometry (DXA) in 1692 premenopausal European-American women, 512 premenopausal African-American women and 715 European-American men. SNPs were tested for association with FN and LS-BMD in the 3 subsamples. In the European-American women, we observed association (p?0.005) with LS-BMD for SNPs in DSPP, IBSP and MEPE, and for FN-BMD with SNPs in DMP1 and IBSP. Allele-specific regulation of gene expression (ASE) is an important mechanism in which an allele giving rise to modest influence in transcript abundance might result in a predisposition to disease. To identify whether there was ASE of SIBLING family genes at these SNPs, we examined 52 human bone samples obtained from the femoral neck during surgical hip replacement (27 female, 25 male; 44 European-American and 8 African-American). We observed unidirectional ASE for the IBSP gene, with lower expression of the G allele compared to the A allele for SNP rs17013181. Our data suggest that SNPs within the SIBLING genes may contribute to normal variation of peak BMD. Further studies are necessary to identify the functional variants and to determine the mechanisms underlying the differences in ASE and how these differences relate to the pathophysiology of osteoporosis. PMID:24747200

Alam, Imranul; Padgett, Leah R; Ichikawa, Shoji; Alkhouli, Mohammed; Koller, Daniel L; Lai, Dongbing; Peacock, Munro; Xuei, Xiaoling; Foroud, Tatiana; Edenberg, Howard J; Econs, Michael J



Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.  


Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ? 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications. PMID:25279983

Lachance, Joseph; Tishkoff, Sarah A



Allele frequencies of a SNP and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene  

Microsoft Academic Search

Allele frequencies for a SNP (rs17822931) and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene were investigated in seven Japanese, one Korean, and one German populations. The SNP will be useful as one of ancestry information markers, because it showed marked difference in frequencies between Asian and European populations.

Takashi Kitano; Isao Yuasa; Kentaro Yamazaki; Nori Nakayashiki; Aya Miyoshi; Kyung Sook Park; Kazuo Umetsu



Exquisite allele discrimination by toehold hairpin primers  

PubMed Central

The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer. PMID:24990378

Byrom, Michelle; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.



Demography can favour female-advantageous alleles.  


When female fecundity is relatively independent of male abundance, while male reproduction is proportional to female abundance, females have a larger effect on population dynamics than males (i.e. female demographic dominance). This population dynamic phenomenon might not appear to influence evolution, because male and female genomes still contribute equally much to the next generation. However, here we examine two evolutionary scenarios to provide a proof of principle that spatial structure can make female demographic dominance matter. Our two simulation models combine dispersal evolution with local adaptation subjected to intralocus sexual conflict and environmentally driven sex ratio biases, respectively. Both models have equilibria where one environment (without being intrinsically poorer) has so few reproductive females that trait evolution becomes disproportionately determined by those environments where females survive better (intralocus sexual conflict model), or where daughters are overproduced (environmental sex determination model). Surprisingly, however, the two facts that selection favours alleles that benefit females, and population growth is improved when female fitness is high, together do not imply that all measures of population performance are improved. The sex-specificity of the source-sink dynamics predicts that populations can evolve to fail to persist in habitats where alleles do poorly when expressed in females. PMID:25056617

Harts, Anna M F; Schwanz, Lisa E; Kokko, Hanna



Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.  

PubMed Central

Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

Thompson, E A; Neel, J V



Construction of Bald Eagle (Haliaeetus leucocephalus) Hal01 Locus Allelic Ladder  

Microsoft Academic Search

Allelic ladders contain all the alleles at a given locus and since the components of the allelic ladder and the sample fragments have the same length and sequence, sizing is very accurate when conducted with an allelic ladder. Allelic ladders are therefore very useful in population genetics studies. For this study, an allelic ladder for the Bald Eagle, Haliaeetus leucocephalus,

Manali Patel



Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis.  


Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ? 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems. PMID:25223217

Pajkovic, Mila; Lappe, Sylvain; Barman, Rachel; Parisod, Christian; Neuenschwander, Samuel; Goudet, Jerome; Alvarez, Nadir; Guadagnuolo, Roberto; Felber, François; Arrigo, Nils



Can one learn history from the allelic spectrum?  


It is well known that the neutral allelic frequency spectrum of a population is affected by the history of population size. A number of authors have used this fact to infer history given observed allele frequency data. We ask whether perfect information concerning the spectrum allows precise recovery of the history, and with an explicit example show that the answer is in the negative. This implies some limitations on how informative allelic spectra can be. PMID:18321552

Myers, Simon; Fefferman, Charles; Patterson, Nick



Characterisation of novel S- alleles from cherry ( Prunus avium L.)  

Microsoft Academic Search

In plant populations exhibiting gametophytic self-incompatibility, individuals harbouring rare S alleles are likely to have a reproductive advantage over individuals having more common alleles. Consequently, determination\\u000a of the self-incompatibility haplotype of individuals is essential for genetic studies and the development of informed management\\u000a strategies. This study characterises six new S alleles identified in wild cherry (Prunus avium L.). Investigations to

S. P. Vaughan; R. I. Boškovi?; A. Gisbert-Climent; K. Russell; K. R. Tobutt



Four novel PEPD alleles causing prolidase deficiency  

SciTech Connect

Mutations at the PEPD locus cause prolidase (an enzyme specific for proline- and hydroxyproline-terminated dipeptides) deficiency (McKusick 170100), a rare autosomal recessive disorder characterized by iminodipeptiduria, skin ulcers, mental retardation, and recurrent infections. Four PEPD mutations from five severely affected individuals were characterized by analysis of reverse-transcribed, PCR-amplified (RT-PCR) cDNA. The authors used SSCP analysis on four overlapping cDNA fragments covering the entire coding region of the PEPD gene and detected abnormal SSCP bands for the fragments spanning all or part of exons 13-15 in three of the probands. Direct sequencing of the mutant cDNAs showed a G[yields]A, 1342 substitution (G448R) in two patients and a 3-bp deletion ([Delta]E452 or [Delta]E453) in another. In the other two probands the amplified products were of reduced size. Direct sequencing of these mutant cDNAs revealed a deletion of exon 5 in one patient and of exon 7 in the other. Intronic sequences flanking exons 5 and 7 were identified using inverse PCR followed by direct sequencing. Conventional PCR and direct sequencing then established the intron-exon borders of the mutant genomic DNA revealing two splice acceptor mutations: a G[yields]C substitution at position -1 of intron 4 and an A[yields]G substitution at position -2 of intron 6. The results indicate that the severe form of prolidase deficiency is caused by multiple PEPD alleles. In this report the authors attempt to begin the process of describing these alleles and cataloging their phenotype expression. 31 refs., 8 figs., 2 tabs.

Ledoux, P.; Scriver, C.; Hechtman, P. (McGill Univ., Montreal (Canada))



Mutated tumor alleles are expressed according to their DNA frequency  

PubMed Central

The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency. PMID:24752137

Castle, John C.; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D.; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Tureci, Ozlem; Sahin, Ugur



Association of prostate cancer risk alleles with unfavourable pathological characteristics in potential candidates for active surveillance  

PubMed Central

OBJECTIVE To assess whether the carrier status of 35 risk alleles for prostate cancer (CaP) is associated with having unfavourable pathological features in the radical prostatectomy specimen in men with clinically low risk CaP who fulfil commonly accepted criteria as candidates for active surveillance. PATIENTS AND METHODS We studied men of European ancestry with CaP who fulfilled the commonly accepted clinical criteria for active surveillance (T1c, prostate-specific antigen < 10 ng/mL, biopsy Gleason ? 6, three or fewer positive cores, ? 50% tumour involvement/core) but instead underwent early radical prostatectomy. We genotyped these men for 35 CaP risk alleles. We defined ‘ unfavourable ’ pathological characteristics to be Gleason ? 7 and/or ? pT2b in their radical prostatectomy specimen. RESULTS In all, 263 men (median age 60 [46 – 72] years) fulfilled our selection criteria for active surveillance, and 58 of 263 (22.1%) were found to have ‘ unfavourable ’ pathological characteristics. The frequencies of three CaP risk alleles (rs1447295 [8q24], P = 0.004; rs1571801 [9q33.2], P = 0.03; rs11228565 [11q13], P = 0.02) were significantly higher in men with ‘ unfavourable ’ pathological characteristics. Two other risk alleles were proportionately more frequent (rs10934853 [3q21], P = 0.06; rs1859962 [17q24], P = 0.07) but did not achieve nominal statistical significance. Carriers of any one of the significantly over-represented risk alleles had twice the likelihood of unfavourable tumour features (P = 0.03), and carriers of any two had a sevenfold increased likelihood (P = 0.001). Receiver – operator curve analysis demonstrated an area under the curve of 0.66, suggesting that the number of single nucleotide polymorphisms carried provided discrimination between men with ‘ favourable ’ and ‘ unfavourable ’ tumour features in their prostatectomy specimen. CONCLUSION In potential candidates for active surveillance, certain CaP risk alleles are more prevalent in patients with ‘ unfavourable ’ pathological characteristics in their radical prostatectomy specimen. PMID:22077888

Kundu, Shilajit; Hu, Qiaoyan; Banks, Jessica A.; Cooper, Phillip; Catalona, William J.




Microsoft Academic Search

Mathematical theories of the population dynamics of sex-determining alleles in honey bees are developed. It is shown that in an infinitely large population the equilibrium frequency of a sex allele is l\\/n, where n is the number of alleles in the population, and the asymptotic rate of approach to this equilibrium is 2\\/(3n) per generation. Formulae for the distribution of



and Evolution. All rights reserved. For permissions, please e-mail: The Author 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology  

E-print Network

inference36 37 Running head: HIV-1 Hierarchical Phylogenetic Hypothesis Testing38 39 40 #12;3 ABSTRACT40 of CCR5delta32 host genetic background and disease progression on1 HIV-1 intra-host evolutionary processes: efficient hypothesis testing through2 hierarchical phylogenetic models3 4 Research article5 6

Suchard, Marc A.


Detection of Borrelia burgdorferi Sensu Stricto ospC Alleles Associated with Human Lyme Borreliosis Worldwide in Non-Human-Biting Tick Ixodes affinis and Rodent Hosts in Southeastern United States  

PubMed Central

Comparative analysis of ospC genes from 127 Borrelia burgdorferi sensu stricto strains collected in European and North American regions where Lyme disease is endemic and where it is not endemic revealed a close relatedness of geographically distinct populations. ospC alleles A, B, and L were detected on both continents in vectors and hosts, including humans. Six ospC alleles, A, B, L, Q, R, and V, were prevalent in Europe; 4 of them were detected in samples of human origin. Ten ospC alleles, A, B, D, E3, F, G, H, H3, I3, and M, were identified in the far-western United States. Four ospC alleles, B, G, H, and L, were abundant in the southeastern United States. Here we present the first expanded analysis of ospC alleles of B. burgdorferi strains from the southeastern United States with respect to their relatedness to strains from other North American and European localities. We demonstrate that ospC genotypes commonly associated with human Lyme disease in European and North American regions where the disease is endemic were detected in B. burgdorferi strains isolated from the non-human-biting tick Ixodes affinis and rodent hosts in the southeastern United States. We discovered that some ospC alleles previously known only from Europe are widely distributed in the southeastern United States, a finding that confirms the hypothesis of transoceanic migration of Borrelia species. PMID:23263953

Golovchenko, Maryna; Hönig, Václav; Mallátová, Nadja; Krbková, Lenka; Mikulášek, Peter; Fedorova, Natalia; Belfiore, Natalia M.; Grubhoffer, Libor; Lane, Robert S.; Oliver, James H.



RESEARCH ARTICLE Open Access MHC allele frequency distributions under  

E-print Network

immune response [5]. Para- sites are under evolutionary pressure to evade detection by the host immune in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because, having hundreds of alleles in human populations and, generally, dozens of alleles in other vertebrate

Richner, Heinz


Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus  

PubMed Central

With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ? 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ? 0.95) and monomorphic (0.95 ? 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi



Black Europeans  

NSDL National Science Digital Library

The British Library has been producing quality online features for close to a decade now, and this latest offering is worth a close look. This particular feature offers some insights and commentary on five prominent black Europeans. It may even come as a surprise to some visitors that several of the individuals profiled were black, such as Alexandre Dumas, the celebrated author of The Three Musketeers. These profiles are supplemented with essays by Dr. Mike Phillips, a writer, scholar, and journalist. The essays are accompanied by a series of images, including engravings, portraits, and illustrations. Visitors may also want to view and print out extended versions of Phillipsâ essays, which are available here in the pdf format.


Allele-Specific H3K79 Di- versus Trimethylation Distinguishes Opposite Parental Alleles at Imprinted Regions? †  

PubMed Central

Imprinted gene expression corresponds to parental allele-specific DNA CpG methylation and chromatin composition. Histone tail covalent modifications have been extensively studied, but it is not known whether modifications in the histone globular domains can also discriminate between the parental alleles. Using multiplex chromatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the allele-specific enrichment of H3K79 methylation and H4K91 acetylation along the H19/Igf2 imprinted domain. Whereas H3K79me1, H3K79me2, and H4K91ac displayed a paternal-specific enrichment at the paternally expressed Igf2 locus, H3K79me3 was paternally biased at the maternally expressed H19 locus, including the paternally methylated imprinting control region (ICR). We found that these allele-specific differences depended on CTCF binding in the maternal ICR allele. We analyzed an additional 11 differentially methylated regions (DMRs) and found that, in general, H3K79me3 was associated with the CpG-methylated alleles, whereas H3K79me1, H3K79me2, and H4K91ac enrichment was specific to the unmethylated alleles. Our data suggest that allele-specific differences in the globular histone domains may constitute a layer of the “histone code” at imprinted genes. PMID:20351169

Singh, Purnima; Han, Li; Rivas, Guillermo E.; Lee, Dong-Hoon; Nicholson, Thomas B.; Larson, Garrett P.; Chen, Taiping; Szabo, Piroska E.



Polymorphic microsatellites identified by cross-species amplifications in the European Coot Fulica atra  

Microsoft Academic Search

We tested the cross-amplification of 26 microsatellites developed for passerines and an additional three developed for Gallinula species in eight European Coots from two populations. Sixteen microsatellite markers successfully amplified, of which nine\\u000a were polymorphic with 2–6 alleles (mean 3.7 alleles) and an expected heterozygosity (H\\u000a e) ranging from 0.375 to 0.805 (mean H\\u000a e = 0.589). On average, we found 2.22 alleles\\/locus

Adeline Loyau; Dirk S. Schmeller



Characterization of phenylalanine hydroxylase alleles in untreated phenylketonuria patients from Victoria, Australia: origin of alleles and haplotypes.  


Mutations in the phenylalanine hydroxylase (PAH) gene were identified in a group of untreated phenylketonuria patients from Victoria, Australia. Ninety-eight percent of the alleles were identified, and a total of 26 different mutations were detected on 83 independent chromosomes. The three most prevalent mutations--R408W, I65T, and IVS12nt1--together accounted for 54% of the alleles. A number of alleles were demonstrated, by genealogical studies, to be of Irish or Scottish origin, including a newly described mutation 1197/1198 del A. The distribution and relative frequencies of the more common alleles in this population parallel observed frequencies in the British Isles and are consistent with the known history of Caucasian settlement of this region of Australia. We have analyzed the haplotype and polymorphic short tandem-repeat allele of the mutant chromosomes and describe a number of new associations. PMID:7726156

Ramus, S J; Treacy, E P; Cotton, R G



Characterization of phenylalanine hydroxylase alleles in untreated phenylketonuria patients from Victoria, Australia: origin of alleles and haplotypes.  

PubMed Central

Mutations in the phenylalanine hydroxylase (PAH) gene were identified in a group of untreated phenylketonuria patients from Victoria, Australia. Ninety-eight percent of the alleles were identified, and a total of 26 different mutations were detected on 83 independent chromosomes. The three most prevalent mutations--R408W, I65T, and IVS12nt1--together accounted for 54% of the alleles. A number of alleles were demonstrated, by genealogical studies, to be of Irish or Scottish origin, including a newly described mutation 1197/1198 del A. The distribution and relative frequencies of the more common alleles in this population parallel observed frequencies in the British Isles and are consistent with the known history of Caucasian settlement of this region of Australia. We have analyzed the haplotype and polymorphic short tandem-repeat allele of the mutant chromosomes and describe a number of new associations. Images Figure 2 PMID:7726156

Ramus, S J; Treacy, E P; Cotton, R G



Recurrence of the R408W mutation in the phenylalanine hydroxylase locus in Europeans.  


The relative frequency of the common phenylalanine hydroxylase (PAH) mutation R408W and its associations with polymorphic RFLP, VNTR, and short-tandem-repeat (STR) sites in the PAH gene were examined in many European populations and one representative North American population of defined European descent. This mutation was found to cluster in two regions: in northwest Europe among Irish and Scottish peoples, and in eastern Europe, including the Commonwealth of Independent States. This allele was significantly less frequent in intervening populations. In eastern European populations, the R408W mutation is strongly associated with RFLP haplotype 2, the three-copy VNTR allele (VNTR 3), and the 240-bp STR allele. In northwestern European populations, it is strongly associated with RFLP haplotype 1, the VNTR allele containing eight repeats (VNTR 8), and the 244-bp STR allele. An examination of the linkage between the R408W mutation and highly polymorphic RFLP, VNTR, and STR haplotypes suggests that recurrence is the most likely mechanism to account for the two different major haplotype associations of R408W in Europe. PMID:7825588

Eisensmith, R C; Goltsov, A A; O'Neill, C; Tyfield, L A; Schwartz, E I; Kuzmin, A I; Baranovskaya, S S; Tsukerman, G L; Treacy, E; Scriver, C R



Recurrence of the R408W Mutation in the Phenylalanine Hydroxylase Locus in Europeans  

PubMed Central

The relative frequency of the common phenylalanine hydroxylase (PAH) mutation R408W and its associations with polymorphic RFLP, VNTR, and short-tandem-repeat (STR) sites in the PAH gene were examined in many European populations and one representative North American population of defined European descent. This mutation was found to cluster in two regions: in northwest Europe among Irish and Scottish peoples, and in eastern Europe, including the Commonwealth of Independent States. This allele was significantly less frequent in intervening populations. In eastern European populations, the R408W mutation is strongly associated with RFLP haplotype 2, the three-copy VNTR allele (VNTR 3), and the 240-bp STR allele. In northwestern European populations, it is strongly associated with RFLP haplotype 1, the VNTR allele containing eight repeats (VNTR 8), and the 244-bp STR allele. An examination of the linkage between the R408W mutation and highly polymorphic RFLP, VNTR, and STR haplotypes suggests that recurrence is the most likely mechanism to account for the two different major haplotype associations of R408W in Europe. ImagesFigure 1Figure 2 PMID:7825588

Eisensmith, Randy C.; Goltsov, Alexei A.; O'Neill, Charles; Tyfield, Linda A.; Schwartz, Eugene I.; Kuzmin, Alexei I.; Baranovskaya, Svetlana S.; Tsukerman, Gennady L.; Treacy, Eileen; Scriver, Charles R.; Guttler, Flemming; Guldberg, Per; Eiken, Hans G.; Apold, Jaran; Svensson, Elisabeth; Naughten, Eileen; Cahalane, Seamus F.; Croke, David T.; Cockburn, Forrester; Woo, Savio L. C.



CGG allele size somatic mosaicism and methylation in FMR1 premutation alleles  

PubMed Central

Background Greater than 200 CGG repeats in the 5?UTR of the FMR1 gene leads to epigenetic silencing and lack of the FMR1 protein, causing Fragile X Syndrome. Individuals carriers of a premutation (PM) allele with 55–200 CGG repeats are typically unmethylated and can present with clinical features defined as FMR1 associated conditions. Methods Blood samples from 17 male PM carriers were assessed clinically and molecularly by Southern Blot, Western Blot, PCR and QRT-PCR. Blood and brain tissue from additional 18 PM males were also similarly examined. Continuous outcomes were modeled using linear regression and binary outcomes were modeled using logistic regression. Results Methylated alleles were detected in different fractions of blood cells in all PM cases (n= 17). CGG repeat numbers correlated with percent of methylation and mRNA levels and, especially in the upper PM range, with greater number of clinical involvements. Inter/intra- tissue somatic instability and differences in percent methylation were observed between blood and fibroblasts (n=4) and also observed between blood and different brain regions in three of the 18 premutation cases examined. CGG repeat lengths in lymphocytes remained unchanged over a period of time ranging from 2–6 years, three cases for whom multiple samples were available. Conclusion In addition to CGG size instability, individuals with a PM expanded alleles can exhibit methylation and display more clinical features likely due to RNA toxicity and/or FMR1 silencing. The observed association between CGG repeat length and percent of methylation with the severity of the clinical phenotypes underscores the potential value of methylation in affected PM to further understand penetrance, inform diagnosis and to expand treatment options. PMID:24591415

Pretto, Dalyir I.; Mendoza-Morales, Guadalupe; Lo, Joyce; Cao, Ru; Hadd, Andrew; Latham, Gary J.; Durbin-Johnson, Blythe; Hagerman, Randi; Tassone, Flora



European Dialogue: The Magazine for European Integration  

NSDL National Science Digital Library

This new bimonthly magazine published by the European Commission is targeted at "decision-makers/opinion formers having an impact on European Integration" in the ten Central European and Baltic countries that have applied to join the EU. The electronic version of the first issue contains articles on humanitarian aid, membership negotiations, pensions, and economic forecasts.



Allelic sequence heterozygosity in single Giardia parasites  

PubMed Central

Background Genetic heterogeneity has become a major inconvenience in the genotyping and molecular epidemiology of the intestinal protozoan parasite Giardia intestinalis, in particular for the major human infecting genotype, assemblage B. Sequence-based genotyping of assemblage B Giardia from patient fecal samples, where one or several of the commonly used genotyping loci (beta-giardin, triosephosphate isomerase and glutamate dehydrogenase) are implemented, is often hampered due to the presence of sequence heterogeneity in the sequencing chromatograms. This can be due to allelic sequence heterozygosity (ASH) and /or co-infections with parasites of different assemblage B sub-genotypes. Thus, two important questions have arisen; i) does ASH occur at the single cell level, and/or ii) do multiple sub-genotype infections commonly occur in patients infected with assemblage B, G. intestinalis isolates? Results We used micromanipulation in order to isolate single Giardia intestinalis, assemblage B trophozoites (GS isolate) and cysts from human patients. Molecular analysis at the tpi loci of trophozoites from the GS lineage indicated that ASH is present at the single cell level. Analyses of assemblage B Giardia cysts from clinical samples at the bg and tpi loci also indicated ASH at the single cell level. Additionally, alignment of sequence data from several different cysts that originated from the same patient yielded different sequence patterns, thus suggesting the presence of multiple sub-assemblage infections in congruence with ASH within the same patient. Conclusions Our results conclusively show that ASH does occur at the single cell level in assemblage B Giardia. Furthermore, sequence heterogeneity generated during sequence-based genotyping of assemblage B isolates may possess the complexity of single cell ASH in concurrence with co-infections of different assemblage B sub-genotypes. These findings explain the high abundance of sequence heterogeneity commonly found when performing sequence based genotyping of assemblage B Giardia, and illuminates the necessity of developing new G. intestinalis genotyping tools. PMID:22554281



Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.  


In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (<150 bp), whereas American isolates had telomeres approximately three times as long (>400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres. PMID:19763176

Liti, Gianni; Haricharan, Svasti; Cubillos, Francisco A; Tierney, Anna L; Sharp, Sarah; Bertuch, Alison A; Parts, Leopold; Bailes, Elizabeth; Louis, Edward J



Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast  

PubMed Central

In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (<150 bp), whereas American isolates had telomeres approximately three times as long (>400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres. PMID:19763176

Liti, Gianni; Haricharan, Svasti; Cubillos, Francisco A.; Tierney, Anna L.; Sharp, Sarah; Bertuch, Alison A.; Parts, Leopold; Bailes, Elizabeth; Louis, Edward J.



Analysis of maize brittle-1 alleles and a defective Suppressor-mutator-induced mutable allele.  

PubMed Central

A mutant allele of the maize brittle-1 (bt1) locus, brittle-1-mutable (bt1-m), was shown genetically and molecularly to result from the insertion of a defective Suppressor-mutator (dSpm) transposable element. An Spm-hybridizing restriction enzyme fragment, which cosegregates with the bt1-m allele and is absent from wild-type revertants of bt1-m, was identified and cloned. Non-Spm portions of it were used as probes to identify wild-type (Bt1) cDNAs in an endosperm library. The 4.3-kb bt1-m genomic clone contains a 3.3-kb dSpm, which is inserted in an exon and is composed of Spm termini flanking non-Spm sequences. RNA gel blot analyses, using a cloned Bt1 cDNA probe, indicated that Bt1 mRNA is present in the endosperm of developing kernels and is absent from embryo or leaf tissues. Several transcripts are produced by bt1-m. The deduced translation product from a 1.7-kb Bt1 cDNA clone has an apparent plastid transit peptide at its amino terminus and sequence similarity to several mitochondrial inner-envelope translocator proteins, suggesting a possible role in amyloplast membrane transport. PMID:1668652

Sullivan, T D; Strelow, L I; Illingworth, C A; Phillips, R L; Nelson, O E



A new classification of HLA-DRB1 alleles differentiates predisposing and protective alleles for autoantibody production in rheumatoid arthritis  

PubMed Central

The HLA-DRB1 gene was reported to be associated with anticitrullinated protein/peptide autoantibody (ACPA) production in rheumatoid arthritis (RA) patients. A new classification of HLA-DRB1 alleles, reshaping the shared epitope (SE) hypothesis, was recently found relevant in terms of RA susceptibility and structural severity. We investigated the relevance of this new classification of HLA-DRB1 SE+ alleles in terms of rheumatoid factor (RF) and ACPA production in a sample of French RA patients. We studied 160 early RA patients included in a prospective longitudinal cohort of French Caucasian patients with recent-onset arthritis. RF, anticyclic citrullinated peptide 2 (anti-CCP2) and antideiminated human fibrinogen autoantibodies (AhFibA) were assessed in all patients at inclusion. The HLA-DRB1 gene was typed by PCR-sequence specific oligonucleotides probes (PCR-SSOP), and SE+ alleles were classified into four groups (S1, S2, S3P, S3D) according to the new classification. The new classification of HLA-DRB1 SE+ alleles distinguishes predisposing and protective alleles for RF, anti-CCP2 or AhFibA production. The presence of S2 or S3P alleles is associated with both RF, anti-CCP2 or AhFibA positivity, whereas the presence of S3D or S1 alleles appears to be protective for RF, anti-CCP2 or AhFibA positivity. The new classification of HLA-DRB1 SE+ alleles is relevant in terms of autoantibody production in early RA patients by differentiating predisposing and protective alleles for RF or ACPA production. PMID:17328818

Gourraud, Pierre-Antoine; Dieude, Philippe; Boyer, Jean-Frederic; Nogueira, Leonor; Cambon-Thomsen, Anne; Mazieres, Bernard; Cornelis, Francois; Serre, Guy; Cantagrel, Alain; Constantin, Arnaud



Allelic exclusion of immunoglobulin genes: models and mechanisms  

PubMed Central

Summary The allelic exclusion of immunoglobulin (Ig) genes is one of the most evolutionarily conserved features of the adaptive immune system and underlies the monospecificity of B cells. While much has been learned about how Ig allelic exclusion is established during B-cell development, the relevance of monospecificity to B-cell function remains enigmatic. Here, we review the theoretical models that have been proposed to explain the establishment of Ig allelic exclusion and focus on the molecular mechanisms utilized by developing B cells to ensure the monoallelic expression of Ig? and Ig? light chain genes. We also discuss the physiological consequences of Ig allelic exclusion and speculate on the importance of monospecificity of B cells for immune recognition. PMID:20727027

Vettermann, Christian; Schlissel, Mark S.



Differential and limited expression of mutant alleles in multiple myeloma.  


Recent work has delineated mutational profiles in multiple myeloma and reported a median of 52 mutations per patient, as well as a set of commonly mutated genes across multiple patients. In this study, we have used deep sequencing of RNA from a subset of these patients to evaluate the proportion of expressed mutations. We find that the majority of previously identified mutations occur within genes with very low or no detectable expression. On average, 27% (range, 11% to 47%) of mutated alleles are found to be expressed, and among mutated genes that are expressed, there often is allele-specific expression where either the mutant or wild-type allele is suppressed. Even in the absence of an overall change in gene expression, the presence of differential allelic expression within malignant cells highlights the important contribution of RNA-sequencing in identifying clinically significant mutational changes relevant to our understanding of myeloma biology and also for therapeutic applications. PMID:25237203

Rashid, Naim U; Sperling, Adam S; Bolli, Niccolo; Wedge, David C; Van Loo, Peter; Tai, Yu-Tzu; Shammas, Masood A; Fulciniti, Mariateresa; Samur, Mehmet K; Richardson, Paul G; Magrangeas, Florence; Minvielle, Stephane; Futreal, P Andrew; Anderson, Kenneth C; Avet-Loiseau, Herve; Campbell, Peter J; Parmigiani, Giovanni; Munshi, Nikhil C



DRD4 dopamine receptor allelic diversity in various primate species  

SciTech Connect

The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

Adamson, M.; Higley, D. [NIAAA, Rockville, MD (United States); O`Brien, S. [NCI, Frederick, MD (United States)] [and others



Identification of incompatibility alleles in the tetraploid species sour cherry.  


The incompatibility genetics of sour cherry ( Prunus cerasus), an allotetraploid species thought to be derived from sweet cherry (diploid) and ground cherry (tetraploid), were investigated by test crossing and by analysis of stylar ribonucleases which are known to be the products of incompatibility alleles in sweet cherry. Stylar extracts of 36 accessions of sour cherry were separated electrophoretically and stained for ribonuclease activity. The zymograms of most accessions showed three bands, some two or four. Of the ten bands seen, six co-migrated with bands that in sweet cherry are attributed to the incompatibility alleles S(1), S(3), S(4), S(6, ) S(9) and S(13). 'Cacanski Rubin', 'Erdi Botermo B', 'Koros' and 'Ujfehertoi Furtos', which showed bands apparently corresponding to S(1) and S(4), were test pollinated with the sweet cherry 'Merton Late' ( S(1) S(4)). Monitoring pollen tube growth, and, in one case, fruit set, showed that these crosses were incompatible and that the four sour cherries indeed have the alleles S(1) and S(4). Likewise, test pollination of 'Marasca Piemonte', 'Marasca Savena' and 'Morello, Dutch' with 'Noble' ( S(6) S(13)) showed that these three sour cherries have the alleles S(6) and S(13). S(13) was very frequent in sour cherry cultivars, but is rare in sweet cherry cultivars, whereas with S(3) the situation is reversed. It was suggested that the other four bands are derived from ground cherry and one of these, provisionally attributed to S(B), occurred frequently in a small set of ground cherry accessions surveyed. Analysing some progenies from sour by sweet crosses by S allele-specific PCR and monitoring the success of some sweet by sour crosses were informative. They indicated mostly disomic inheritance, with sweet cherry S alleles belonging to one locus and, presumably, the ground cherry alleles to the other, and helped clarify the genomic arrangement of the alleles and the interactions in heteroallelic pollen. PMID:14689184

Tobutt, K R; Boskovi?, R; Cerovi?, R; Sonneveld, T; Ruzi?, D



Robust Identification of Local Adaptation from Allele Frequencies  

PubMed Central

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from PMID:23821598

Gunther, Torsten; Coop, Graham



Are ‘Endurance’ Alleles ‘Survival’ Alleles? Insights from the ACTN3 R577X Polymorphism  

PubMed Central

Exercise phenotypes have played a key role for ensuring survival over human evolution. We speculated that some genetic variants that influence exercise phenotypes could be associated with exceptional survival (i.e. reaching ?100years of age). Owing to its effects on muscle structure/function, a potential candidate is the Arg(R)577Ter(X) polymorphism (rs1815739) in ACTN3, the structural gene encoding the skeletal muscle protein ?-actinin-3. We compared the ACTN3 R577X genotype/allele frequencies between the following groups of ethnically-matched (Spanish) individuals: centenarians (cases, n?=?64; 57 female; age range: 100–108 years), young healthy controls (n?=?283, 67 females, 216 males; 21±2 years), and humans who are at the two end-points of exercise capacity phenotypes, i.e. muscle endurance (50 male professional road cyclists) and muscle power (63 male jumpers/sprinters). Although there were no differences in genotype/allele frequencies between centenarians (RR:28.8%; RX:47.5%; XX:23.7%), and controls (RR:31.8%; RX:49.8%; XX:18.4%) or endurance athletes (RR:28.0%; RX:46%; XX:26.0%), we observed a significantly higher frequency of the X allele (P?=?0.019) and XX genotype (P?=?0.011) in centenarians compared with power athletes (RR:47.6%; RX:36.5%;XX:15.9%). Notably, the frequency of the null XX (?-actinin-3 deficient) genotype in centenarians was the highest ever reported in non-athletic Caucasian populations. In conclusion, despite there were no significant differences with the younger, control population, overall the ACTN3 genotype of centenarians resembles that of world-class elite endurance athletes and differs from that of elite power athletes. Our preliminary data would suggest a certain ‘survival’ advantage brought about by ?-actinin-3 deficiency and the ‘endurance’/oxidative muscle phenotype that is commonly associated with this condition. PMID:21407828

Fiuza-Luces, Carmen; Ruiz, Jonatan R.; Rodríguez-Romo, Gabriel; Santiago, Catalina; Gómez-Gallego, Félix; Yvert, Thomas; Cano-Nieto, Amalia; Garatachea, Nuria



Patterns of allelic loss at the BRCA1 locus in Arabic women with breast cancer.  


Loss of heterozygosity (LOH) of BRCA1, a tumor suppressor gene, is one mechanism of genetic inactivation in both sporadic and familial forms of breast cancer. Studies reported in breast cancers from women of Northern European descent have shown LOH in 30-50% of sporadic tumors. Microsatellite instability (MSI) has served as evidence for involvement of DNA repair genes. This study investigates the extent of allelic imbalance at the BRCA1 region in Arabic women with breast cancer. Paired normal and tumor tissue were available for DNA analysis in 13 cases. Results using fluorescent tagged primers to microsatellite markers D17S1323, D17S1325 and D17S855 intragenic to BRCA1 were analyzed using an ABI 310 DNA sequencer. As compared to normal DNA, MSI and LOH were recognized as a gain and a loss, respectively, of one signal in one allele in the tumor DNA. Microsatellite analyses showed 12 of 13 (92%) cases with LOH or MSI or both. Three cases demonstrated LOH alone, 3 cases with MSI alone. Six cases indicated both LOH and MSI; 2 cases with either LOH or MSI in separate markers. The combined finding of LOH and MSI in the same marker was detected only with D17S1325 in 4/6 cases. The proportion of aberrant findings of the BRCA1 locus in breast cancer appears to be higher in Arabic women than in other populations studied to date. PMID:11029525

Rouba, A; Kaisi, N; Al-Chaty, E; Badin, R; Pals, G; Young, C; Worsham, M J



Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and –DPB1  

PubMed Central

Background The expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype structure, but the performance of these methods in admixed populations (such as African Americans) has not been adequately evaluated. We compared genotype-based—derived from both genome-wide genotyping and targeted sequencing—imputation results to existing allele data for HLA–DRB1, ?DQB1, and –DPB1. Results In European Americans, the newly-developed HLA Genotype Imputation with Attribute Bagging (HIBAG) method outperformed HLA*IMP:02. In African Americans, HLA*IMP:02 performed marginally better than HIBAG pre-built models, but HIBAG models constructed using a portion of our African American sample with both SNP genotyping and four-digit HLA class II allele typing had consistently higher accuracy than HLA*IMP:02. However, HIBAG was significantly less accurate in individuals heterozygous for local ancestry (p??0.04). Accuracy improved in models with equal numbers of African and European chromosomes. Variants added by targeted sequencing and SNP imputation further improved both imputation accuracy and the proportion of high quality calls. Conclusion Combining the HIBAG approach with local ancestry and dense variant data can produce highly-accurate HLA class II allele imputation in African Americans. PMID:24935557



The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.  


We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data. PMID:15020430

Marth, Gabor T; Czabarka, Eva; Murvai, Janos; Sherry, Stephen T



Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases.  


The rs2476601-T allele at the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene has been consistently associated with several autoimmune diseases in European-derived populations. However, little is known about the allele and haplotype frequency distributions in PTPN22 among populations derived from other ethnic groups. In the present study, the allele and haplotype frequency distributions of six single nucleotide polymorphisms (SNPs) in the PTPN22 gene were compared among Brazilian populations and HapMap phase 3 dataset. A total of 10 different population samples were evaluated. Additionally, in admixed populations, individual genetic ancestries were estimated for Native American, African, and European contributions. Estimated individual ancestries were used as quantitative traits in a conditional approach for single-marker and haplotype-specific regression analyses. It was shown that several SNPs and haplotypes have different frequencies among different ethnic populations. Individual genetic ancestries were not associated with the rs2476601-T allele, but were associated with PTPN22 haplotypes in Brazilian, Mexican, and African-American admixed populations. Our results suggest caution in the interpretation of results found in association studies involving PTPN22 polymorphisms in admixed populations. Correction for stratification generated by admixture should be mandatory to minimize or avoid chances of spurious association. PMID:20166877

Lins, Tulio C; Vieira, Rodrigo G; Grattapaglia, Dario; Pereira, Rinaldo W



Allele-specific Silencing of Mutant Myh6 Allele in Mice Suppresses Hypertrophic Cardiomyopathy  

PubMed Central

Dominant mutations in sarcomere proteins such as the myosin heavy chains (MHC) are the leading genetic causes of human hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). Here we demonstrate that expression of the HCM cardiac MHC gene (Myh6) R403Q mutation in mice can be selectively silenced by an RNAi cassette delivered by an adeno-associated virus vector. RNAi-transduced MHC403/+ mice had neither hypertrophy or myocardial fibrosis, the pathologic manifestations of HCM for at least 6 months. As inhibition of HCM was achieved by only a 25% reduction in the levels of the mutant transcripts, we suggest that the variable clinical phenotype in HCM patients reflects allelic-specific expression and that partial silencing of mutant transcripts may have therapeutic benefit. PMID:24092743

Jiang, Jianming; Wakimoto, Hiroko; Seidman, J. G.; Seidman, Christine E.



Failure to confirm allelic and haplotypic association between markers at the chromosome 6p22.3 dystrobrevin-binding protein 1 (DTNBP1) locus and schizophrenia  

PubMed Central

Background Previous linkage and association studies may have implicated the Dystrobrevin-binding protein 1 (DTNBP1) gene locus or a gene in linkage disequilibrium with DTNBP1 on chromosome 6p22.3 in genetic susceptibility to schizophrenia. Methods We used the case control design to test for of allelic and haplotypic association with schizophrenia in a sample of four hundred and fifty research subjects with schizophrenia and four hundred and fifty ancestrally matched supernormal controls. We genotyped the SNP markers previously found to be significantly associated with schizophrenia in the original study and also other markers found to be positive in subsequent studies. Results We could find no evidence of allelic, genotypic or haplotypic association with schizophrenia in our UK sample. Conclusion The results suggest that the DTNBP1 gene contribution to schizophrenia must be rare or absent in our sample. The discrepant allelic association results in previous studies of association between DTNBP1 and schizophrenia could be due population admixture. However, even positive studies of European populations do not show any consistent DTNBP1 alleles or haplotypes associated with schizophrenia. Further research is needed to resolve these issues. The possible confounding of linkage with association in family samples already showing linkage at 6p22.3 might be revealed by testing genes closely linked to DTNBP1 for allelic association and by restricting family based tests of association to only one case per family. PMID:17888175

Datta, Susmita R; McQuillin, Andrew; Puri, Vinay; Choudhury, Khalid; Thirumalai, Srinivasa; Lawrence, Jacob; Pimm, Jonathan; Bass, Nicholas; Lamb, Graham; Moorey, Helen; Morgan, Jenny; Punukollu, Bhaskar; Kandasami, Gomathinayagam; Kirwin, Simon; Sule, Akeem; Quested, Digby; Curtis, David; Gurling, Hugh MD



Allelic and genotypic associations of DRD2 TaqI A polymorphism with heroin dependence in Spanish subjects: a case control study  

PubMed Central

Background Conflicting associations with heroin dependence have been found involving the A1 allele of dopamine D2 receptor gene (DRD2) TaqI A polymorphism. Methods We compared two samples of unrelated Spanish individuals, all of European origin: 281 methadone-maintained heroin-dependent patients (207 males and 74 females) who frequently used non-opioid substances, and 145 control subjects (98 males and 47 females). Results The A1-A1 genotype was detected in 7.1% of patients and 1.4% of controls (P = 0.011, odds ratio = 5.48, 95% CI 1.26–23.78). Although the A1 allele was not associated with heroin dependence in the entire sample, the frequency of A1 allele was higher in male patients than in male controls (24.4% vs. 16.3%, P = 0.024, odds ratio = 1.65, 95% CI 1.07–2.57). A logistic regression analysis showed an interaction between DRD2 alleles and gender (odds ratio = 1.77, 95% CI 1.15–2.70). Conclusion Our results indicate that, in Spanish individuals, genotypes of the DRD2 TaqI A polymorphism contribute to variations in the risk of heroin dependence, while single alleles contribute only in males. PMID:17543096

Perez de los Cobos, Jose; Baiget, Montserrat; Trujols, Joan; Sinol, Nuria; Volpini, Victor; Banuls, Enrique; Calafell, Francesc; Luquero, Elena; del Rio, Elisabeth; Alvarez, Enric



Indo-European origins: a computer-simulation test of five hypotheses.  


Allele frequency distributions were generated by computer simulation of five models of microevolution in European populations. Genetic distances calculated from these distributions were compared with observed genetic distances among Indo-European speakers. The simulated models differ in complexity, but all incorporate random genetic drift and short-range gene flow (isolation by distance). The best correlations between observed and simulated data were obtained for two models where dispersal of Neolithic farmers from the Near East depends only on population growth. More complex models, where the timing of the farmers' expansion is constrained by archaeological time data, fail to account for a larger fraction of the observed genetic variation; this is also the case for a model including late Neolithic migrations from the Pontic steppes. The genetic structure of current populations speaking Indo-European languages seems therefore to largely reflect a Neolithic expansion. This is consistent with the hypothesis of a parallel spread of farming technologies and a proto-Indo-European language in the Neolithic. Allele-frequency gradients among Indo-European speakers may be due either to incomplete admixture between dispersing farmers, who presumably spoke proto-Indo-European, and pre-existing hunters and gatherers (as in the traditional demic diffusion hypothesis), or to founder effects during the farmers' dispersal. By contrast, successive migrational waves from the East, if any, do not seem to have had genetic consequences detectable by the present comparison of observed and simulated allele frequencies. PMID:7755103

Barbujani, G; Sokal, R R; Oden, N L



Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans.  


Adult body height is a quantitative trait for which genome-wide association studies (GWAS) have identified numerous loci, primarily in European populations. These loci, comprising common variants, explain <10% of the phenotypic variance in height. We searched for novel associations between height and common (minor allele frequency, MAF ?5%) or infrequent (0.5% < MAF < 5%) variants across the exome in African Americans. Using a reference panel of 1692 African Americans and 471 Europeans from the National Heart, Lung, and Blood Institute's (NHLBI) Exome Sequencing Project (ESP), we imputed whole-exome sequence data into 13 719 African Americans with existing array-based GWAS data (discovery). Variants achieving a height-association threshold of P < 5E-06 in the imputed dataset were followed up in an independent sample of 1989 African Americans with whole-exome sequence data (replication). We used P < 2.5E-07 (=0.05/196 779 variants) to define statistically significant associations in meta-analyses combining the discovery and replication sets (N = 15 708). We discovered and replicated three independent loci for association: 5p13.3/C5orf22/rs17410035 (MAF = 0.10, ? = 0.64 cm, P = 8.3E-08), 13q14.2/SPRYD7/rs114089985 (MAF = 0.03, ? = 1.46 cm, P = 4.8E-10) and 17q23.3/GH2/rs2006123 (MAF = 0.30; ? = 0.47 cm; P = 4.7E-09). Conditional analyses suggested 5p13.3 (C5orf22/rs17410035) and 13q14.2 (SPRYD7/rs114089985) may harbor novel height alleles independent of previous GWAS-identified variants (r(2) with GWAS loci <0.01); whereas 17q23.3/GH2/rs2006123 was correlated with GWAS-identified variants in European and African populations. Notably, 13q14.2/rs114089985 is infrequent in African Americans (MAF = 3%), extremely rare in European Americans (MAF = 0.03%), and monomorphic in Asian populations, suggesting it may be an African-American-specific height allele. Our findings demonstrate that whole-exome imputation of sequence variants can identify low-frequency variants and discover novel variants in non-European populations. PMID:25027330

Du, Mengmeng; Auer, Paul L; Jiao, Shuo; Haessler, Jeffrey; Altshuler, David; Boerwinkle, Eric; Carlson, Christopher S; Carty, Cara L; Chen, Yii-Der Ida; Curtis, Keith; Franceschini, Nora; Hsu, Li; Jackson, Rebecca; Lange, Leslie A; Lettre, Guillaume; Monda, Keri L; Nickerson, Deborah A; Reiner, Alex P; Rich, Stephen S; Rosse, Stephanie A; Rotter, Jerome I; Willer, Cristen J; Wilson, James G; North, Kari; Kooperberg, Charles; Heard-Costa, Nancy; Peters, Ulrike



Allele-Dependent Barley Grain ?-Amylase Activity1  

PubMed Central

The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high ?-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and ?-amy1 gene characterization to demonstrate that the high ?-amylase trait in the backcross line is co-inherited with the ?-amy1 gene from the H. spontaneum parent. We have analyzed the ?-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct ?-amy1 alleles. Two of these ?-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain ?-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated ?-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of ?-amylase activity in barley grain is proposed. PMID:9625721

Erkkila, Maria J.; Leah, Robert; Ahokas, Hannu; Cameron-Mills, Verena



Twenty-nine new HLA-B alleles associated with antigens in the 5C CREG.  


This paper describes 29 novel HLA-B locus alleles identified during low-resolution typing. The majority of the novel alleles carry new patterns of previously known polymorphic motifs or codons. Three alleles carry alterations in the Bw4/Bw6 epitope. Five alleles carry novel substitutions. PMID:11556976

Steiner, N K; Kosman, C; Jones, P F; Gans, C P; Rodriguez-Marino, S G; Rizzuto, G; Baldassarre, L A; Edson, S; Koester, R; Sese, D; Mitton, W; Ng, J; Hartzman, R J; Hurley, C K



Distribution of the FYBES and RHCE*ce(733C>G) alleles in an Argentinean population: Implications for transfusion medicine  

PubMed Central

Background The understanding of the molecular bases of blood groups makes possible the identification of red cell antigens and antibodies using molecular approaches, especially when haemagglutination is of limited value. The practical application of DNA typing requires the analysis of the polymorphism and allele distribution of the blood group genes under study since genetic variability was observed among different ethnic groups. Urban populations of Argentina are assumed to have a white Caucasian European genetic component. However, historical and biological data account for the influence of other ethnic groups. In this work we analyse FY and RH blood group alleles attributed to Africans and that could have clinical implications in the immune destruction of erythrocytes. Methods We studied 103 white trios (father, mother and child, 309 samples) from the city of Rosario by allele specific PCRs and serological methods. The data obtained were analysed with the appropriate statistical test considering only fathers and mothers (n = 206). Results We found the presence of the FY*BES and RHCE*ce(733C>G) alleles and an elevated frequency (0.0583) for the Dce haplotype. The number of individuals with a concomitant occurrence of both alleles was significantly higher than that expected by chance. We found that 4.68% of the present gene pool is composed by alleles primarily associated with African ancestry and about 10% of the individuals carried at least one RH or FY allele that is predominantly observed among African populations. Thirteen percent of Fy(b-) subjects were FY*A/FY*BES. Conclusion Taken together, the results suggest that admixture events between African slaves and European immigrants at the beginning of the 20th century made the physical characteristics of black Africans to be invisible nowadays. Considering that it was a recent historical event, the FY*BES and RHCE*ce(733C>G) alleles did not have time to become widespread but remain concentrated within families. These findings have considerable impact for typing and transfusion strategy in our population, increasing the pool of compatible units for Fy(b-) individuals requiring chronic transfusion. Possible difficulties in transfusion therapy and in genotyping could be anticipated and appropriately improved strategies devised, allowing a better management of the alloimmunization in the blood bank. PMID:18460195

Cotorruelo, Carlos M; Fiori, Silvana V; Borrás, Silvia E García; Racca, Liliana L; Biondi, Claudia S; Racca, Amelia L



Human allelic variation: perspective from protein function, structure, and evolution.  


It is widely anticipated that the coming year will be marked by the complete characterization of DNA sequence of protein-coding regions of thousands of human individuals. A number of existing computational methods use comparative protein sequence analysis and analysis of protein structure to predict the functional effect of coding human alleles. Functional and structural analysis of coding allelic variants can inform various aspects of research on human genetic variation. In population and evolutionary genetics it helps estimate the strength of purifying selection against deleterious missense mutations and study the imprint of demographic history on deleterious genetic variation. In medical genetics it may assist in the interpretation of uncharacterized mutations in genes involved in monogenic and oligogenic diseases. It has a potential to facilitate medical sequencing studies searching for genes underlying Mendelian diseases or harboring rare alleles involved in complex traits. PMID:20399638

Jordan, Daniel M; Ramensky, Vasily E; Sunyaev, Shamil R



Generation and characterization of an analog-sensitive PERK allele.  


Restriction of nutrients and oxygen in the tumor microenvironment disrupts ER homeostasis and adaptation to such stress is mediated by the key UPR effector PERK. Given its pro-tumorigenic activity, significant efforts have been made to elucidate the molecular mechanisms that underlie PERK function. Chemical-genetic approaches have recently proven instrumental in pathway mapping and interrogating kinase function. To enable a detailed study of PERK signaling we have generated an analog-sensitive PERK allele that accepts N(6)-alkylated ATP analogs. We find that this allele can be regulated by bulky ATP-competitive inhibitors, confirming the identity of the PERK gatekeeper residue as methionine 886. Furthermore, this analog-sensitive allele can be used to specifically label substrates with thiophosphate both in vitro and in cells. These data highlight the potential for using chemical-genetic techniques to identify novel PERK substrates, thereby providing an expanded view of PERK function and further definition of its signaling networks. PMID:24846185

Maas, Nancy L; Singh, Nickpreet; Diehl, J Alan



Enhancement of Allele Discrimination by Introduction of Nucleotide Mismatches into siRNA in Allele-Specific Gene Silencing by RNAi  

Microsoft Academic Search

Allele-specific gene silencing by RNA interference (RNAi) is therapeutically useful for specifically inhibiting the expression of disease-associated alleles without suppressing the expression of corresponding wild-type alleles. To realize such allele-specific RNAi (ASP-RNAi), the design and assessment of small interfering RNA (siRNA) duplexes conferring ASP-RNAi is vital; however, it is also difficult. In a previous study, we developed an assay system

Yusuke Ohnishi; Yoshiko Tamura; Mariko Yoshida; Katsushi Tokunaga; Hirohiko Hohjoh; Luis M. Corrochano



MHC class II DR allelic diversity in bighorn sheep.  


We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA and DRB transcripts from 24 captive BHS (Ovca-DRA and Ovca-DRB) were sequenced. Based on exon 2 (?1 domain) sequences, eight different Ovca-DRB cDNA sequences were identified in BHS. Six of them were 100% identical to previously reported Ovca-DRB genomic DNA sequences. The new alleles DRB*23 and DRB*24, were closely related to two other Ovca-DRB exon 2 genomic DNA sequences. Nineteen out of 24 BHS (79%) Ovca-DRB exon 3 (?2 domain) sequences were 100% identical to exon 3 sequence of DRB1 of DS (Ovar-DRB1). Ovca-DRA full length cDNA sequences exhibited >99% identity. Based upon exon 2 sequences, this BHS herd yielded higher Ovca-DRB allelic diversity than that reported in the previous study. Positively selected amino acid positions were identified in the peptide-binding groove of BHS and DS, but BHS showed more such sites. This highlights differing population histories, and may suggest differing needs for DR peptide-binding specificities. Presence of glutamine at position 52 (52Q) in some of the desert and captive BHS is predicted to alter the efficiency of DR dimerization, which may influence antigen presentation and T(h) cell activation. Functional assays with unique alleles should reveal whether the presentation of M. haemolytica leukotoxin peptides to T(h) cells by Ovca-DRB alleles is equivalent to that of Ovar-DRB1 alleles. PMID:22750296

Subramaniam, Renuka; White, Stephen N; Herrmann-Hoesing, Lynn M; Srikumaran, Subramaniam



A common allele on chromosome 9 associated with coronary heartdisease  

SciTech Connect

Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.

McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R.; Hinds, David; Pennachio, Len; Tybjaerg-Hansen, Anne; Folsom, Aaron R.; Boerwinkle,Eric; Hobbs, Helen H.; Cohen, Jonathan C.



Twenty-five novel HLA-B alleles.  


Twenty-five novel HLA-B alleles are described in this paper: B*0729, B*1309, B*1814, B*1815, B*2724, B*2725, B*3539, B*3926, B*4037, B*4040, B*4042, B*4043, B*4044, B*4204, B*440203, B*4428, B*4429, B*4430, B*4505, B*5308, B*5309, B*5510, B*5511, B*570102, and B*5709. Most of the variants are single nucleotide substitutions. Two involve variants at the Bw4/Bw6 epitope. Two alleles carry substitutions of conserved amino acids. PMID:12956882

Steiner, N K; Gans, C; Baldassarre, L; Bradshaw, D; Rizzo, M; Divekar, S; Koester, R; Ng, J; Hartzman, R J; Hurley, C K



Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers  

Microsoft Academic Search

PCR-based identification of all 13 known self-incompatibility ( S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S 1 to S 6 S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S

T. Sonneveld; K. R. Tobutt; T. P. Robbins



Parental Analysis of Introgressive Hybridization between African and European Honeybees Using Nuclear DNA Rflps  

PubMed Central

African honeybees, introduced into Brazil 33 years ago, have spread through most of South and Central America and have largely replaced the extant European bees. Due to a paucity of genetic markers, genetic interactions between European and African bees are not well understood. Three restriction fragment length polymorphisms (RFLPs), detected with random, nuclear DNA probes, are described. The polymorphisms are specific to bees of European descent, possibly specific to certain European races. Each European marker was found present at a high frequency in U.S. colonies but absent in South African bees. Previous mitochondrial DNA studies of neotropical bees have revealed negligible maternal gene flow from managed European apiaries into feral African populations. The findings reported here with nuclear DNA show paternal gene flow between the two but suggest asymmetries in levels of introgressive hybridization. Managed colonies in southern Mexico, derived from European maternal lines, showed diminished levels of the European nuclear markers, reflecting significant hybridization with African drones. The European alleles were present only at low frequencies in feral swarms from the same area. The swarms were of African maternal descent. In Venezuelan colonies, also derived from African maternal lines, the European markers were almost totally absent. The results point to limited paternal introgression from European colonies into the African honeybee populations. These findings dispute other views regarding modes of Africanization. PMID:1974226

Hall, H. G.



Allelic Imbalance on 16q in Small, Unifocal Hepatocellular Carcinoma  

Microsoft Academic Search

In advanced hepatocellular carcinoma (HCC), allelic loss on chromosome 16q may occur. To better define the frequency of this alteration in small HCC and to more closely identify the affected region for further positional cloning of the putative tumor suppressor gene contained in this region, microsatellite polymorphism analysis was conducted on small, unifocal HCC, without signs of intrahepatic or systemic

Laura Gramantieri; Davide Trerè; Annalisa Pession; Fabio Piscaglia; Livia Masi; Stefano Gaiani; Alighieri Mazziotti; Luigi Bolondi



Rescue of Progeria in Trichothiodystrophy by Homozygous Lethal Xpd Alleles  

Microsoft Academic Search

Although compound heterozygosity, or the presence of two different mutant alleles of the same gene, is common in human recessive disease, its potential to impact disease outcome has not been well documented. This is most likely because of the inherent difficulty in distinguishing specific biallelic effects from differences in environment or genetic background. We addressed the potential of different recessive

Jaan-Olle Andressoo; Judith Jans; Jan de Wit; Frederic Coin; Deborah Hoogstraten; Marieke van de Ven; Wendy Toussaint; Jan Huijmans; H. Bing Thio; Wibeke J. van Leeuwen; Jan de Boer; Jean-Marc Egly; Jan H. J. Hoeijmakers; James R. Mitchell



Rescue of Progeria in Trichothiodystrophy by Homozygous Lethal Xpd Alleles  

E-print Network

Rescue of Progeria in Trichothiodystrophy by Homozygous Lethal Xpd Alleles Jaan-Olle Andressoo1¤a sensitivity and cancer predisposition to accelerated segmental progeria. We report a variety of biallelic, Jans J, de Wit J, Coin F, Hoogstraten D, et al. (2006) Rescue of progeria in trichothiodystrophy

Boyer, Edmond


Efficient nonmeiotic allele introgression in livestock using custom endonucleases.  


We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10-50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications. PMID:24014591

Tan, Wenfang; Carlson, Daniel F; Lancto, Cheryl A; Garbe, John R; Webster, Dennis A; Hackett, Perry B; Fahrenkrug, Scott C



Selection against Adh null alleles in Drosophila melanogaster  

Microsoft Academic Search

Populations of Drosophila melanogaster polymorphic for an Adh null and an Adh positive allele (either Adhs or AdhF), were founded on regular food, on food supplemented with ethanol and on food suplemented with methanol. On ethanol-supplemented food Adh null was rapidly eliminated, but on regular food and on food supplemented with methanol a consistent decline in the frequency of the

W van Delden; A Kamping



ALFRED: an allele frequency resource for research and teaching  

E-print Network

ALFRED: an allele frequency resource for research and teaching Haseena Rajeevan1,2, *, Usha Soundararajan1 , Judith R. Kidd1 , Andrew J. Pakstis1 and Kenneth K. Kidd1 1 Department of Genetics and 2 Center the literature; (ii) data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics

Kidd, Kenneth


Number of incompatibility alleles in clover and other species  

Microsoft Academic Search

Atwood’s (1942, 1944) data on Trifolium repens, those of Williams & Williams (1947) on T. pratense and those of Williams (1951) on T. hybridum have been re-analysed to provide maximum likelihood estimates of the number of incompatibility alleles in the populations or breeders' stocks from which the samples investigated were obtained. These new estimates suggest that populations of T. repens

M J Lawrence



Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis  

USGS Publications Warehouse

Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

Brock, M.K.; White, B.N.



Estimating the age of alleles by use of intraallelic variability  

SciTech Connect

A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

Slatkin, M.; Rannala, B. [Univ of California, Berkeley, CA (United States)



Allelic imbalance of 14q32 in esophageal carcinoma  

Microsoft Academic Search

It has been demonstrated that the accumulation of alterations in several oncogenes and tumor suppressor genes plays a role in the initiation and progression of esophageal carcinoma. However, to our knowledge, very few studies have described the molecular genetic changes of chromosome arm 14q in esophageal carcinoma. In this study, we examined 35 primary esophageal carcinomas for allelic imbalance on

Yuji Ihara; Yuji Kato; Tadashi Bando; Fuminori Yamagishi; Tetsuji Minamimura; Takashi Sakamoto; Kazuhiro Tsukada; Masaharu Isobe



The Allele Metamodel - Developing a Common Language for Genetic Algorithms  

Microsoft Academic Search

Due to the lot of difierent Genetic Algorithm variants, en- codings, and attacked problems, very little general theory is available to explain the internal functioning of Genetic Algorithms. Consequently it is very di-cult for researchers to flnd a common language to document quality improvements of newly developed algorithms. In this paper the authors present a new Allele Meta-Model enabling a

Stefan Wagner; Michael Affenzeller



Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study  

Microsoft Academic Search

Background Multiple sclerosis has a clinically significant heritable component. We conducted a ge- nomewide association study to identify alleles associated with the risk of multiple sclerosis. Methods We used DNA microarray technology to identify common DNA sequence variants in 931 family trios (consisting of an affected child and both parents) and tested them for association. For replication, we genotyped another

David A. Hafler; Alastair Compston; Stephen Sawcer; Eric S. Lander; Mark J. Daly; Philip L. De Jager; Paul I. W. de Bakker; Stacey B. Gabriel; Daniel B. Mirel; Adrian J. Ivinson; Margaret A. Pericak-Vance; Simon G. Gregory; John D. Rioux; Jacob L. McCauley; Jonathan L. Haines; Lisa F. Barcellos; Bruce Cree; Jorge R. Oksen-berg; Stephen L. Hauser



Nonfrequent but well-documented, rare and very rare HLA alleles observed in the Croatian population.  


The aim of the study was to evaluate the presence of nonfrequent, rare and very rare alleles among Croats and to estimate whether they are associated with specific alleles at other human leukocyte antigen (HLA) loci. This retrospective study included the typing results from the last 10?years; total number of individuals included was approximately 45,000. Among 17 alleles so far observed only once in our population, 6 (A*24:41, B*07:02:28, B*35:03:03, B*39:40N, DRB1*13:23 and DRB1*14:111) belong to very rare alleles, 2 (B*44:16 and DRB1*01:31) belong to rare alleles according to the 'Rare Alleles Detector' tool (, while for the B*35:101:01 allele published data exist only in the IMGT/HLA database. The remaining eight HLA alleles observed only once among Croats are considered as frequent according to the 'Rare Alleles Detector'. Those 17 HLA alleles are not declared as common well defined (CWD) alleles in the CWD allele catalogue 2.0.0. Haplotype analysis of nonfrequent alleles detected in our sample supports the idea that different populations, although similar in some aspects regarding HLA allele and haplotype distribution, still have some unique characteristics. This is the case for A*01:02, B*39:10 and DRB1*13:32 which form haplotypes unreported to date among our subjects. PMID:25413106

Grubic, Z; Burek Kamenaric, M; Maskalan, M; Stingl Jankovic, K; Zunec, R



Tri-allelic pattern at the TPOX locus: a familial study.  


Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern. PMID:24144843

Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Paskulin, Giorgio Adriano; Alvarez, Luís; Amorim, António; Batista Dos Santos, Sidney Emanuel; Alho, Clarice Sampaio



Characterization a novel HLA-B40 allele with serological Bw4 motif, HLA-B*4047, in the Finnish population and confirmation of B*270503 allele.  


We describe a novel HLA-B*40 allele assigned as B*4047*. The B*4047 allele was detected in a Finnish patient awaiting kidney transplantation. The patient had a "short" B60-like serological specificity with Bw4 association. After sequencing, the B*4047 allele was found to be identical to B*4001, except having five amino acid changes in exon 2, including the entire motif corresponding to Bw4 and w6 specificity. As a result of recombination or gene conversion, B*4047 has the Bw4 motif instead of expected Bw6. Screening of B40 alleles in the Finnish population revealed no other cases with this pattern, suggesting that this allele is rare. The sequence of B*270503 presented here provides the complete sequence for exons 2 and 3 for this allele. B*270503 allele differs from B*270502 by a single synonymous nucleotide substitution at non-variable position 489 in exon 3. PMID:15140040

Peräsaari, J P; Koskela, S; Partanen, J



A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly  

PubMed Central

A recently identified variant within the fat mass and obesity-associated (FTO) gene is carried by 46% of Western Europeans and is associated with an ~1.2 kg higher weight, on average, in adults and an ~1 cm greater waist circumference. With >1 billion overweight and 300 million obese persons worldwide, it is crucial to understand the implications of carrying this very common allele for the health of our aging population. FTO is highly expressed in the brain and elevated body mass index (BMI) is associated with brain atrophy, but it is unknown how the obesity-associated risk allele affects human brain structure. We therefore generated 3D maps of regional brain volume differences in 206 healthy elderly subjects scanned with MRI and genotyped as part of the Alzheimer's Disease Neuroimaging Initiative. We found a pattern of systematic brain volume deficits in carriers of the obesity-associated risk allele versus noncarriers. Relative to structure volumes in the mean template, FTO risk allele carriers versus noncarriers had an average brain volume difference of ~8% in the frontal lobes and 12% in the occipital lobes—these regions also showed significant volume deficits in subjects with higher BMI. These brain differences were not attributable to differences in cholesterol levels, hypertension, or the volume of white matter hyperintensities; which were not detectably higher in FTO risk allele carriers versus noncarriers. These brain maps reveal that a commonly carried susceptibility allele for obesity is associated with structural brain atrophy, with implications for the health of the elderly. PMID:20404173

Stein, Jason L.; Hua, Xue; Lee, Suh; Hibar, Derrek P.; Leow, Alex D.; Dinov, Ivo D.; Toga, Arthur W.; Saykin, Andrew J.; Shen, Li; Foroud, Tatiana; Pankratz, Nathan; Huentelman, Matthew J.; Craig, David W.; Gerber, Jill D.; Allen, April N.; Corneveaux, Jason J.; Stephan, Dietrich A.; DeCarli, Charles S.; DeChairo, Bryan M.; Potkin, Steven G.; Jack, Clifford R.; Weiner, Michael W.; Raji, Cyrus A.; Lopez, Oscar L.; Becker, James T.; Carmichael, Owen T.; Thompson, Paul M.; Weiner, Michael; Thal, Leon; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowki, John; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Gamst, Anthony; Potter, William Z.; Montine, Tom; Anders, Dale; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Trojanowki, John; Shaw, Les; Lee, Virginia M.-Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Harvey, Danielle; Gamst, Anthony; Kornak, John; Kachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Vorobik, Remi; Quinn, Joseph; Schneider, Lon; Pawluczyk, Sonia; Spann, Bryan; Fleisher, Adam S.; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Badger, Beverly; Grossman, Hillel; Tang, Cheuk; Stern, Jessica; deToledo-Morrell, Leyla; Shah, Raj C.; Bach, Julie; Duara, Ranjan; Isaacson, Richard; Strauman, Silvia; Albert, Marilyn S.; Pedroso, Julia; Toroney, Jaimie; Rusinek, Henry; de Leon, Mony J; De Santi, Susan M; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Aiello, Marilyn; Clark, Christopher M.; Pham, Cassie; Nunez, Jessica; Smith, Charles D.; Given II, Curtis A.; Hardy, Peter; DeKosky, Steven T.; Oakley, MaryAnn; Simpson, Donna M.; Ismail, M. Saleem; Porsteinsson, Anton; McCallum, Colleen; Cramer, Steven C.; Mulnard, Ruth A.; McAdams-Ortiz, Catherine; Diaz-Arrastia, Ramon; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Laubinger, Mary M.; Bartzokis, George; Silverman, Daniel H.S.; Lu, Po H.; Fletcher, Rita; Parfitt, Francine; Johnson, Heather; Farlow, Martin; Herring, Scott; Hake, Ann M.; van Dyck, Christopher H.; MacAvoy, Martha G.; Bifano, Laurel A.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Graham, Simon; Caldwell, Curtis; Feldman, Howard; Assaly, Michele; Hsiung, Ging-Yuek R.; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Gitelman, Darren; Johnson, Nancy; Mesulam, Marsel; Sadowsky, Carl; Villena, Teresa; Mesner, Scott; Aisen, Paul S.; Johnson, Kathleen B.; Behan, Kelly E.; Sperling, Reisa A.; Rentz, Dorene M.; Johnson, Keith A.; Rosen, Allyson; Tinklenberg, Jared; Ashford, Wes; Sabbagh, Marwan; Connor, Donald; Obradov, Sanja; Killiany, Ron; Norbash, Alex; Obisesan, Thomas O.; Jayam-Trouth, Annapurni; Wang, Paul; Auchus, Alexander P.; Huang, Juebin; Friedland, Robert P.; DeCarli, Charles; Fletcher, Evan; Carmichael, Owen; Kittur, Smita; Mirje, Seema; Johnson, Sterling C.; Borrie, Michael; Lee, T-Y; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Highum, Diane; Preda, Adrian; Nguyen, Dana; Tariot, Pierre N.; Hendin, Barry A.; Scharre, Douglas W.; Kataki, Maria; Beversdorf, David Q.; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Gandy, Sam; Marenberg, Marjorie E.; Rovner, Barry W.; Pearlson, Godfrey; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Pare, Nadia; Williamson, Jeff D.; Sink, Kaycee M.; Potter, Huntington; Ashok Raj, B.; Giordano, Amy; Ott, Brian R.; Wu, Chuang-Kuo; Cohen, Ronald; Wilks, Kerri L.



Testing allele homogeneity: the problem of nested hypotheses  

PubMed Central

Background The evaluation of associations between genotypes and diseases in a case-control framework plays an important role in genetic epidemiology. This paper focuses on the evaluation of the homogeneity of both genotypic and allelic frequencies. The traditional test that is used to check allelic homogeneity is known to be valid only under Hardy-Weinberg equilibrium, a property that may not hold in practice. Results We first describe the flaws of the traditional (chi-squared) tests for both allelic and genotypic homogeneity. Besides the known problem of the allelic procedure, we show that whenever these tests are used, an incoherence may arise: sometimes the genotypic homogeneity hypothesis is not rejected, but the allelic hypothesis is. As we argue, this is logically impossible. Some methods that were recently proposed implicitly rely on the idea that this does not happen. In an attempt to correct this incoherence, we describe an alternative frequentist approach that is appropriate even when Hardy-Weinberg equilibrium does not hold. It is then shown that the problem remains and is intrinsic of frequentist procedures. Finally, we introduce the Full Bayesian Significance Test to test both hypotheses and prove that the incoherence cannot happen with these new tests. To illustrate this, all five tests are applied to real and simulated datasets. Using the celebrated power analysis, we show that the Bayesian method is comparable to the frequentist one and has the advantage of being coherent. Conclusions Contrary to more traditional approaches, the Full Bayesian Significance Test for association studies provides a simple, coherent and powerful tool for detecting associations. PMID:23176636



Nomenclature for alleles of the thiopurine methyltransferase gene  

PubMed Central

The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors’ articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website ( serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G > A) from TPMT*24 to TPMT*30 and position 611 (T > C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged. PMID:23407052

Appell, Malin L.; Berg, Jonathan; Duley, John; Evans, William E.; Kennedy, Martin A.; Lennard, Lynne; Marinaki, Tony; McLeod, Howard L.; Relling, Mary V.; Schaeffeler, Elke; Schwab, Matthias; Weinshilboum, Richard; Yeoh, Allen E.J.; McDonagh, Ellen M.; Hebert, Joan M.; Klein, Teri E.; Coulthard, Sally A.



Bipolar disorder risk alleles in children with ADHD.  


Bipolar disorder (BD) and attention deficit/hyperactivity disorder (ADHD) may share common genetic risk factors as indicated by the high co-morbidity of BD and ADHD, their phenotypic overlap especially in pediatric populations, the high heritability of both disorders, and the co-occurrence in families. We therefore examined whether known polygenic BD risk alleles are associated with ADHD. We chose the eight best SNPs of the recent genome-wide association study (GWAS) of BD patients of German ancestry and the nine SNPs from international GWAS meeting a 'genome-wide significance' level of ? = 5 × 10(-8). A GWAS was performed in 495 ADHD children and 1,300 population-based controls using HumanHap550v3 and Human660 W-Quadv1 BeadArrays. We found no significant association of childhood ADHD with single BD risk alleles surviving adjustment for multiple testing. Yet, risk alleles for BD and ADHD were directionally consistent at eight of nine loci with the strongest support for three SNPs in or near NCAN, BRE, and LMAN2L. The polygene analysis for the BP risk alleles at all 14 loci indicated a higher probability of being a BD risk allele carrier in the ADHD cases as compared to the controls. At a moderate power to detect association with ADHD, if true effects were close to estimates from GWAS for BD, our results suggest that the possible contribution of BD risk variants to childhood ADHD risk is considerably lower than for BD. Yet, our findings should encourage researchers to search for common genetic risk factors in BD and childhood ADHD in future studies. PMID:23712748

Schimmelmann, B G; Hinney, A; Scherag, A; Pütter, C; Pechlivanis, S; Cichon, S; Jöckel, K-H; Schreiber, S; Wichmann, H E; Albayrak, Ö; Dauvermann, M; Konrad, K; Wilhelm, C; Herpertz-Dahlmann, B; Lehmkuhl, G; Sinzig, J; Renner, T J; Romanos, M; Warnke, A; Lesch, K P; Reif, A; Hebebrand, J



Clinical and immunogenetic characteristics of European multicase rheumatoid arthritis families  

PubMed Central

OBJECTIVE—To describe the characteristics of a new set of European families with affected sib pairs (ASP) collected by the European Consortium on Rheumatoid Arthritis Families (ECRAF) to replicate the results of our first genome scan. Potential gradients for disease severity in Europe and concordance within families were studied.?PATIENTS AND METHODS—From 1996 to 1998 European white families with at least two affected siblings were enrolled in the study. Demographic (sex, age at onset), clinical data (rheumatoid factor (RF), disease duration, erosive disease, extra-articular features (EF)), and HLA-DRB1 oligotyping were analysed.?RESULTS—565 patients with rheumatoid arthritis (RA), belonging to 271 families including 319 affected sib pairs (ASP) were collected. Belgium, France, Italy, the Netherlands, Portugal, and Spain contributed 20, 96, 52, 24, 9, and 70 families, respectively. Sex (78% women), age at onset (mean 44 years), and RF positivity (79%) were similar among the countries. Differences were found in disease duration (11-18 years) and in the prevalence of erosive disease (70-93%), nodules (15-44%), subjective Sjögren's syndrome (5-38%), and EF (3-16%) (p<0.05 in all cases). A total of 22% RA sibs were shared epitope (SE) negative, whereas 47% and 30% carried one and two SE alleles respectively. Carriage of SE differed widely among countries (p<0.0001): no SE alleles (6-36%), one allele (43-60%), and two alleles (20-39%). SE encoding alleles were mainly DRB1*04 in the Netherlands and Belgium, whereas SE carriage was less common and evenly distributed between DRB1*01, *04, and *10 in Mediterranean countries. No concordance within families was found either in age/calendar year of onset (intraclass correlation coefficient <0.50) or in clinical and radiological features (?<0.22).?CONCLUSIONS—The differences in RA characteristics between European countries and within families underline the heterogeneity of the disease. No clear cut gradient of disease severity was seen in Europe.?? PMID:11350845

Balsa, A; Barrera, P; Westhovens, R; Alves, H; Maenaut, K; Pascual-Salcedo, D; Cornelis, F; Bardin, T; Riente, L; Radstake, T; de Almeida, G; Lepage, V; Stravopoulos, C; Spaepen, M; Lopes-Vaz, A; Charron, D; Martinez, M; Prudhomme, J; Migliorini, P; Fritz, P



ATM allelic variants associated to hereditary breast cancer in 94 Chilean women: susceptibility or ethnic influences?  


Besides BRCA1 and BRCA2, two genes accounting for a small proportion of breast cancer cases, ATM has been widely proposed as a low-penetrance susceptibility gene. Several nucleotide changes have been proposed to be associated with breast cancer, still remaining a high controversy in this sense. We screened the ATM gene in 94 breast cancer patients selected from 78 high-risk families, not presenting a mutation in BRCA1 or BRCA2. We found three novel allelic variants: IVS64 + 51delT and p.L752L, not showing association with hereditary breast cancer, and p.L694L found in one family in two breast cancer patients. Two amino acid substitutions p.S707P and p.F858L, previously reported to be associated with breast cancer, were present in our study in cases and controls, lacking of association with breast cancer. A positive association of c.5557G>A (p.D1853N) was found (OR 2.52, P = 0.008), when analyzed alone and in combination with an intronic variant IVS24-9delT (OR 3.97; P = 0.0003). We postulate that our discrepancies with other reports related to the associated ATM alleles to hereditary breast cancer, as well as discrepancies in the literature between other groups, could be explained by the diversity in the ethnic origins of families gathered in a sole study, and the selection of the control group. In relation to this issue, and based on genetic markers, we found that the Chilean group of breast cancer families in this study has a stronger European genetic component than our control sample selected randomly from the Chilean population. PMID:17351744

Tapia, Teresa; Sanchez, Alejandro; Vallejos, Maricarmen; Alvarez, Carolina; Moraga, Mauricio; Smalley, Susan; Camus, Mauricio; Alvarez, Manuel; Carvallo, Pilar



Allelic variation in a fatty-acyl reductase gene causes divergence in moth sex pheromones.  


Pheromone-based behaviours are crucial in animals from insects to mammals, and reproductive isolation is often based on pheromone differences. However, the genetic mechanisms by which pheromone signals change during the evolution of new species are largely unknown. In the sexual communication system of moths (Insecta: Lepidoptera), females emit a species-specific pheromone blend that attracts males over long distances. The European corn borer, Ostrinia nubilalis, consists of two sex pheromone races, Z and E, that use different ratios of the cis and trans isomers of acetate pheromone components. This subtle difference leads to strong reproductive isolation in the field between the two races, which could represent a first step in speciation. Female sex pheromone production and male behavioural response are under the control of different major genes, but the identity of these genes is unknown. Here we show that allelic variation in a fatty-acyl reductase gene essential for pheromone biosynthesis accounts for the phenotypic variation in female pheromone production, leading to race-specific signals. Both the cis and trans isomers of the pheromone precursors are produced by both races, but the precursors are differentially reduced to yield opposite ratios in the final pheromone blend as a result of the substrate specificity of the enzymes encoded by the Z and E alleles. This is the first functional characterization of a gene contributing to intraspecific behavioural reproductive isolation in moths, highlighting the importance of evolutionary diversification in a lepidopteran-specific family of reductases. Accumulation of substitutions in the coding region of a single biosynthetic enzyme can produce pheromone differences resulting in reproductive isolation, with speciation as a potential end result. PMID:20592730

Lassance, Jean-Marc; Groot, Astrid T; Liénard, Marjorie A; Antony, Binu; Borgwardt, Christin; Andersson, Fredrik; Hedenström, Erik; Heckel, David G; Löfstedt, Christer



A cis-eQTL of HLA-DRB1 and a frameshift mutation of MICA contribute to the pattern of association of HLA alleles with cervical cancer  

PubMed Central

The association of classic human leukocyte antigen (HLA) alleles with risk of cervical cancer has been extensively studied, and a protective effect has consistently been found for DRB1*1301, DQA1*0103, and/or DQB1*0603 (these three alleles are in perfect linkage disequilibrium [LD] and often occur on the same haplotype in Europeans), while reports have differed widely with respect to the effect of HLA-B*07, DRB1*1501, and/or DQB1*0602 (the last two alleles are also in perfect LD in Europeans). It is not clear whether the reported HLA alleles are responsible for the differences in cervical cancer susceptibility, or if functional variants at other locations within the major histocompatibility complex (MHC) region may explain the effect. In order to assess the relative contribution of both classic HLA alleles and single-nucleotide polymorphisms (SNPs) within the MHC region to cervical cancer susceptibility, we have imputed classic HLA alleles in 1034 cervical cancer patients and 3948 controls in a Swedish population for an integrated analysis. We found that the protective haplotype DRB1*1301-DQA1*0103-DQB1*0603 has a direct effect on cervical cancer and always occurs together with the C allele of a HLA-DRB1 cis-eQTL (rs9272143), which increases the expression of HLA-DRB1. The haplotype rs9272143C-DRB1*1301-DQA1*0103-DQB1*0603 conferred the strongest protection against cervical cancer (odds ratio [OR] = 0.41, 95% confidence interval [CI] = 0.32–0.52, P = 6.2 × 10?13). On the other hand, the associations with HLA-B*0702 and DRB1*1501-DQB1*0602 are attributable to the joint effects of both the HLA-DRB1 cis-eQTL (rs9272143) and a frameshift mutation (G inserion of rs67841474, also known as A5.1) of the MHC class I polypeptide-related sequence A gene (MICA). Variation in LD between the classic HLA loci, rs9272143 and rs67841474 between populations may explain the different associations of HLA-B*07 and DRB1*1501-DQB1*0602 with cervical cancer between studies. The mechanism suggested may also explain similar inconsistent results for other HLA-associated diseases. PMID:24520070

Chen, Dan; Gyllensten, Ulf



Microsatellite Variation in Honey Bee (Apis Mellifera L.) Populations: Hierarchical Genetic Structure and Test of the Infinite Allele and Stepwise Mutation Models  

PubMed Central

Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population X loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites). PMID:7498746

Estoup, A.; Garnery, L.; Solignac, M.; Cornuet, J. M.



Polymorphism of trinucleotide repeats in loci DM, DRPLA and SCA1 in East European populations.  


A normal polymorphism at three triplet repeat loci (myotonic dystrophy (DM), dentatorubral-pallidoluysian atrophy (DRPLA) and spinocerebellar ataxia type 1 (SCA1)) were examined in healthy unrelated individuals from the Siberian Yakut (Mongoloid) population, the Adygei (Caucasian) population and nine East European populations: populations from Russia (Holmogory, Oshevensk, Kursk, Novgorod, Udmurts, Bashkir), two Ukrainian populations (Lviv and Alchevsk) and one Belarussian. The distribution of alleles for DRPLA and SCA1 were similar for all East-European populations. For the DM locus, East European populations had typical allele distribution profiles with two modes, (CTG)5 and (CTG)11-14, but some differences were found for the Bashkir population where alleles containing 11-14 CTG repeats had relatively higher frequency. The Yakut population had different allele spectra for all types of repeats studied. Higher heterozygosity levels and insignificant differences between expected and observed heterozygosity were found for all tested loci. The latter led us to suggest that the trinucleotide repeat loci analysed are not influenced by selection factors and could be useful for genetic relationship investigations in different populations. PMID:11781699

Popova, S N; Slominsky, P A; Pocheshnova, E A; Balanovskaya, E V; Tarskaya, L A; Bebyakova, N A; Bets, L V; Ivanov, V P; Livshits, L A; Khusnutdinova, E K; Spitcyn, V A; Limborska, S A



Turkey and European Security  

Microsoft Academic Search

Turkish membership in the European Union has been and, it is safe to assume, will continue to be an issue hotly debated by\\u000a experts, policymakers and public opinion alike. As argued by EU Commissioner for Internal Market and Services, Frits Bolkenstein\\u000a , in a view shared by many European officials and a majority of European public opinion, because of Turkey's

Thanos Dokos


Novel complex disease allele mutations in cleidocranial dysplasia patients.  


This study reports a novel identical complex disease allele harboring two non-synonymous mutations that were identified in two southern Chinese individuals of the same family with cleidocranial dysplasia (CCD). Blood samples were obtained from the proband, his parents, plus 100 matched control subjects. Exons 0 to 7 of the RUNX2 gene were amplified using specific primers and sequenced. Multiple sequence alignment and protein structure modeling was performed using ClustalW2 and MODBASE software while PolyPhen-2 and MutationTaster applications were employed to predict the disease-causing potential of the identified mutations. A complex disease allele in two affected individuals harboring two non-synonymous mutations in a cis-position on exons 4 (D273N) and 5 (P299L) were identified. The identified mutations were in the conserved region and changed the protein structure. PMID:24935264

Anthonappa, Robert P; Yan-Hui, Fan; King, Nigel M; Rabie, Abu Bakr M; You-Qiang, Song



Allelic loss at TP53 in metastatic human endometrial carcinomas  

Microsoft Academic Search

Loss of heterozygosity (LOH) is implicated in the initiation and progression of various human neoplasia, and is observed in\\u000a both early or in advanced-stage human cancers. The current study was aimed at investigating the frequency of LOH TP53 in human endometrial carcinoma (EC) metastases. LOH was analyzed using 3 intragenic polymorphisms in 38 primary ECs and corresponding\\u000a metastatic lesions. Allelic

Wiktor Szewczuk; Danuta Skomra; Marek Cybulski; Dorota Prz?dka-Rabaniuk; Agata Filip; Maciej Jó?wik; Piotr Olcha; Albert Roessner; Andrzej Semczuk



Allelic Sequence Divergence in the Apomictic Boechera holboellii Complex  

Microsoft Academic Search

\\u000a It has been suggested that the absence of meiosis in asexual lineages should lead to higher interallelic divergence at any\\u000a given locus within an individual (i.e., allelic sequence divergence – ASD) compared to sexual populations (i.e., Meselson effect; Mark Welch\\u000a and Meselson 2000). In the present study, ASD was investigated in 2 diploid sexual, 3 diploid apomictic and 3 triploid

Jose M. Corral; Marcin Piwczynski; Tim F. Sharbel


Prediction of bone density from vitamin D receptor alleles  

Microsoft Academic Search

BONE density achieved in early adulthood is the major determinant of risk of osteoporotic fracture. Up to 60% of women1,2 suffer osteoporotic fractures as a result of low bone density2, which is under strong genetic control3-6 acting through effects on bone turnover7,8. Here we show that common allelic variants in the gene encoding the vitamin D receptor9 can be used

Nigel A. Morrison; Jian Cheng Qi; Akifumi Tokita; Paul J. Kelly; Linda Crofts; Tuan V. Nguyen; Philip N. Sambrook; John A. Eisman



Inferring selection intensity and allele age from multilocus haplotype structure.  


It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144-0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

Chen, Hua; Slatkin, Montgomery



Human leptin locus (LEP) alleles and BMI in Samoans  

Microsoft Academic Search

Objectives: Because of their location in known candidate gene regions for obesity the associations between six microsatellite markers (D2S2170, D2S144, D2S1268, D2S1788, D2S1348 and a tetranucleotide repeat in the 3? UTR of the LEP locus) and body mass index (BMI) were studied in adult Samoans.Design: The study was designed to detect differences in the proportion of alleles at the six

ST McGarvey; W Forrest; G Sun; D Smelser; J Tufa; S Viali; R Deka



Human APC2 Localization and Allelic Imbalance1  

Microsoft Academic Search

A second adenomatous polyposis coli (APC)-like gene, APC2\\/APCL, was recently described and localized to chromosome 19. We have fine mapped APC2 to a small region of chromosome 19p13.3 containing mark- ers D19S883 and WI-19632, a region commonly lost in a variety of cancers, particularly ovarian cancer. Interphase fluorescence in situ hy- bridization analysis revealed an APC2 allelic imbalance in 19

Christy Rothwell Jarrett; Jan Blancato; Tin Cao; D. S. Bressette; M. Cepeda; Paul E. Young; C. Richter King; Stephen W. Byers



Molecular typing of HLA-B27 alleles  

Microsoft Academic Search

HLA-B27 represents a family of closely related antigens. Six alleles which differ in a limited number of nucleotide substitutions have been described (B*2701—B*2706). These changes are clustered in a1 and a2 domains. Polymerase chain reaction strategies were designed to amplify specific regions of class I exons 2 and 3. Amplified sequences were tested with eight sequence-specific oligonucleotides to distinguish all

O. Dominguez; E. Coto; E. Martinez-Naves; S. Y. Choo; C. López-Larrea



Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates.  

PubMed Central

Genetic studies of Mycobacterium tuberculosis have been greatly hampered by the inability to introduce specific chromosomal mutations. Whereas the ability to perform allelic exchanges has provided a useful method of gene disruption in other organisms, in the clinically important species of mycobacteria, such as M. tuberculosis and Mycobacterium bovis, similar approaches have thus far been unsuccessful. In this communication, we report the development of a shuttle mutagenesis strategy that involves the use of long linear recombination substrates to reproducibly obtain recombinants by allelic exchange in M. tuberculosis. Long linear recombination substrates, approximately 40 to 50 kb in length, were generated by constructing libraries in the excisable cosmid vector pYUB328. The cosmid vector could be readily excised from the recombinant cosmids by digestion with PacI, a restriction endonuclease for which there exist few, if any, sites in mycobacterial genomes. A cosmid containing the mycobacterial leuD gene was isolated, and a selectable marker conferring resistance to kanamycin was inserted into the leuD gene in the recombinant cosmid by interplasmid recombination in Escherichia coli. A long linear recombination substrate containing the insertionally mutated leuD gene was generated by PacI digestion. Electroporation of this recombination substrate containing the insertionally mutated leuD allele resulted in the generation of leucine auxotrophic mutants by homologous recombination in 6% of the kanamycin-resistant transformants for both the Erdman and H37Rv strains of M. tuberculosis. The ability to perform allelic exchanges provides an important approach for investigating the biology of this pathogen as well as developing new live-cell M. tuberculosis-based vaccines. PMID:8550428

Balasubramanian, V; Pavelka, M S; Bardarov, S S; Martin, J; Weisbrod, T R; McAdam, R A; Bloom, B R; Jacobs, W R



Genetic Comparison of a Croatian Isolate and CEPH European Founders  

PubMed Central

Human isolates have been postulated as a good resource for the identification of QTL due to reduced genetic diversity and a more homogeneous environment. Isolates may also have increased linkage disequilibrium (LD) due to small effective population size and, either loss or increase in frequency of alleles that are rare in the general population from which they originate. Here we investigate the difference in allele and genotype frequencies, LD and homozygous tracts between an isolate—several villages from the island of Vis in Croatia—and an outbred population of European origin: the Hapmap CEPH founders. Using the HumanHap300 v1 Genotyping BeadChip, we show that our population does not differ greatly from the reference CEU outbred population despite having a slightly higher proportion of monomorphic loci, a slightly higher long-range LD, and a greater proportion of individuals with long homozygous tracts. We conclude that genotyping arrays should perform equally well in our isolate as in outbred European populations for disease mapping studies and that SNP–trait associations discovered in our well-characterized Croatian isolate should be valid in the general European population from which they descend. Genet. Epidemiol. 34: 140–145, 2010. © 2009 Wiley-Liss, Inc. PMID:19697321

Navarro, Pau; Vitart, Véronique; Hayward, Caroline; Tenesa, Albert; Zgaga, Lina; Juricic, Danica; Polasek, Ozren; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Wright, Alan F; Haley, Chris S; Knott, Sara A



Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.  


To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported. PMID:20703243

Sato, Takehiro; Kazuta, Hisako; Amano, Tetsuya; Ono, Hiroko; Ishida, Hajime; Kodera, Haruto; Matsumura, Hirofumi; Yoneda, Minoru; Dodo, Yukio; Masuda, Ryuichi



Allele frequencies and population data for 17 Y-STR loci (The AmpFlSTR® Y-filer™) in Casablanca resident population.  


Allele frequencies and population data for 17 Y-STR loci included in the AmpFlSTR® Y-filer™ PCR amplification kit (Applied Biosystems, Foster City, USA), that permit the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 166 healthy unrelated males resident in Casablanca (from Morocco). A total of 166 haplotypes were identified, of which 142 were unique. The overall haplotype diversity for the 17 Y-STR loci reached 0.9974, and a discrimination capacity was 0.855. We report some non-standard situations, including duplications and microvariant alleles. PMID:21126935

Laouina, Adil; El Houate, Brahim; Yahia, Hakima; Azeddoug, Houssine; Boulouiz, Redouane; Chbel, Faiza



Progression of uremic hyperparathyroidism involves allelic loss on chromosome 11  

SciTech Connect

In occasional cases of secondary hyperparathyroidism, long term stimulation of the parathyroid glands leads from compensatory to autonomous hyperfunction, and thus, hypercalcemia develops. This clinical entity, named tertiary hyperparathyroidism, is possibly due to the formation of an adenoma in one of the hyperplastic glands. Previous studies have shown that parathyroid adenomas may arise with allelic loss on chromosome 11. The authors tested for allelic loss at several loci on chromosome 11 in 12 enlarged parathyroid glands from 6 uremic patients and found loss of heterozygosity in 2 of the glands from 2 different patients with higher serum calcium levels (11.3 [+-] 0.29 vs. 9.8 [+-] 0.28 mg/dL; P < 0.004) and, therefore, ascribable to the so-called tertiary hyperparathyroidism. The 2 glands with allelic loss were significantly greater in mass than those without loss (3.42 [+-] 0.37 vs. 1.60 [+-] 0.54 g; P < 0.001). These data offer new evidence that autonomous parathyroid proliferation in uremic patients can develop through over-growth by a monoclonal tumor, presumably with inactivation of a tumor suppressor gene(s) on chromosome 11. 33 refs., 4 figs., 2 tabs.

Falchetti, A.; Brandi, M.L. (Univ. of Florence (Italy) Yale Univ. School of Medicine, New Haven, CT (United States)); Amorosi, A.; Cicchi, P.; Bandini, S. (Univ. of Florence (Italy)); Bordi, C. (Univ. of Parma (Italy)); Marx, S.J. (National Institute of Health, Bethesda, MD (United States))



S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae)  

Microsoft Academic Search

RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only

O Raspé; J R Kohn



Allele-specific detection of single mRNA molecules in situ  

PubMed Central

We describe a method for fluorescent in situ identification of individual mRNA molecules, allowing quantitative and accurate measurements of allele-specific transcripts that differ by only a few nucleotides, in single cells. By using a combination of allele-specific and non-allele-specific probe libraries, we achieve over 95% detection accuracy. We investigate the allele-specific stochastic expression of the pluripotency factor Nanog in murine embryonic stem cells. PMID:23934076

Hansen, Clinton H.; van Oudenaarden, Alexander



Allele-specific detection of single mRNA molecules in situ.  


We describe a method for fluorescence in situ identification of individual mRNA molecules, allowing quantitative and accurate measurement, in single cells, of allele-specific transcripts that differ by only a few nucleotides. By using a combination of allele-specific and non-allele-specific probe libraries, we achieve >95% detection accuracy. We investigate the allele-specific stochastic expression of Nanog, which encodes a pluripotency factor, in murine embryonic stem cells. PMID:23934076

Hansen, Clinton H; van Oudenaarden, Alexander



European Biodiesel Board  

NSDL National Science Digital Library

The European Biodiesel Board (EBB), a nonprofit organization, works to promote biodiesel use in the European Union (EU). The EBB website offers downloadable articles regarding biodiesel in the EU, downloadable reports from EU member states, a list of upcoming events, an EBB email information service, and basic statistical tables representing biodiesel production by country.



Being ‘European’ in Gibraltar  

Microsoft Academic Search

This paper explores the question of how Gibraltar’s contemporary identity is evolving as its inhabitants manipulate their status as citizens of a contested territory of the European Union. The people of Gibraltar exploit the connotations of ‘being European’ as part of their ongoing battle to resist Spanish and British efforts to negotiate a bilateral solution to the question of Gibraltar’s





E-print Network

NUMBER OF SEX ALLELES IN A SAMPLE OF HONEYBEE COLONIES Jean-Marie CORNUET Franck ARIES Station of bree- ding work, this paper gives the theoretical distribution of the number of sex alleles in a sample the factors interfering with this trait, there is the possible identity of sex alleles of the workers' parents

Paris-Sud XI, Université de


Evidence for a genetic association between alleles of monoamine oxidase A gene and bipolar affective disorder  

Microsoft Academic Search

We present evidence of a genetic association between bipolar disorder and alleles at 3 monoamine oxidase A (MAOA) markers, but not with alleles of a monoamine oxidase B (MAOB) polymorphism. The 3 MAOA markers, including one associated with low MAOA activity, show strong allelic association with each other but surprisingly not with MAOB. Our results are significantly only for females,

Lionel C. C. Lim; P. Sham; D. Castle; Neil Hunt; Robin Murray; Michael Gill



Survival and Growth of Subyearling Steelhead Homozygous for Alternative Alleles at the Dipeptidase Locus  

Microsoft Academic Search

Juvenile steelhead Oncorhynchus mykiss (formerly Salmo gairdneri) that were homozygous for two alternative alleles at the dipeptidase locus were released into stream sections of the Palouse River drainage, Idaho, to test the neutrality of the alleles with respect to survival or growth. After 4 months in the stream sections, juveniles homozygous for either of the two major alleles did not

G. L. Chandler; T. C. Bjornn



Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human  

E-print Network

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human Kun method for quantitatively interrogating allele-specific gene expression. This method involves ultra 11­22% of the heterozygous mRNA-associated SNPs showed allele- specific expression in each cell line

Church, George M.


Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y  

PubMed Central

Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways—HERC2, SLC45A2, and TYR—using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2–10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y. PMID:24616518

Wilde, Sandra; Timpson, Adrian; Kirsanow, Karola; Kaiser, Elke; Kayser, Manfred; Unterlander, Martina; Hollfelder, Nina; Potekhina, Inna D.; Schier, Wolfram; Thomas, Mark G.; Burger, Joachim



Shades of gray: A comparison of linkage disequilibrium between Hutterites and Europeans  

PubMed Central

Founder or isolated populations have advantages for genetic studies due to decreased genetic and environmental heterogeneity. However, whereas longer range linkage disequilibrium (LD) in these populations is expected to facilitate gene localization, extensive LD may actually limit the ability for gene discovery. The North American Hutterite population is one of the best characterized young founder populations and members of this isolate have been the subjects of our studies of complex traits, including fertility, asthma and cardiovascular disease, for >20 years. Here, we directly assess the patterns and extent of global LD using single nucleotide polymorphism (SNP) genotypes with minor allele frequencies (MAFs) ?5% from the Affymetrix GeneChip® Mapping 500K array in 60 relatively unrelated Hutterites and 60 unrelated Europeans (HapMap CEU). Although LD among some marker pairs extends further in the Hutterites than in Europeans, the pattern of LD and minor allele frequencies are surprisingly similar. These results indicate that 1) identifying disease genes should be no more difficult in the Hutterites than in outbred European populations, 2) the same common susceptibility alleles for complex diseases should be present in the Hutterites and outbred European populations, and 3) imputation algorithms based on HapMap CEU should be applicable to the Hutterites. PMID:19697328

Thompson, Emma E; Sun, Ying; Nicolae, Dan; Ober, Carole



European Commission: Public Opinion  

NSDL National Science Digital Library

Some Scout Report readers might be wondering "How do Europeans feel about the euro?" or even "What do Europeans think about the effectiveness of different energy policies?" All of the answers to these questions (and many more) can be found on the European Commission's Public Opinion site. The site contains the results from surveys conducted with Europeans on their attitudes towards alcohol, the role of the European Union in formulating security policy, and a number of other topics. Visitors will definitely want to make their way to the Eurobarometer Interactive Search System, which allows them to choose a subject or country which is of interest to them. Visitors should also take a look at their very fine "Qualitative Studies" section, which includes reports such as "The Future of Europe" and "Integrating Gender Mainstreaming into Employment Policies". Needless to say, summaries of the reports are available in a wide range of languages, including Dutch, German, Italian, and French.


Slovenian population data for five new European Standard Set Short tandem repeat loci and SE33 locus  

PubMed Central

Aim To establish the allele distribution and statistical parameters of forensic interest for the D10S1248, D22S1045, D2S441, D1S1656, D12S391, and SE33 loci in Slovenian population and to compare allele frequencies with those from other populations. Methods We analyzed blood and buccal swab samples from 333 unrelated, healthy Slovenian individuals. All samples were genotyped using the AmpFlSTR NGM Kit to obtain the allele frequency data for the loci D10S1248, D22S1045, D2S441, D1S1656, and D12S391. Samples from 113 individuals were also analyzed using the PowerPlex ESX 17 system to obtain the allele frequency data for the SE33 locus. Allele frequencies and statistical parameters of forensic interest were determined and frequency profiles compared between Slovenian and other European Caucasian populations using the Arlequin software, version Results The investigated short tandem repeat (STR) loci in Slovenian population had a great discriminating potential with a combined discrimination power of 0.99999998. The highest discrimination power and polymorphism information content were observed for the SE33 locus, followed by loci D1S1656, D12S391, D10S1248, D2S441, and D22S1045. When Slovenian allele frequency distribution was compared with other European populations, deviations were found only for Spanish and Italian population for D2S441 and D12S391. Conclusion Slovenian population does not differ significantly from other European populations in terms of allele frequency distributions for the six analyzed STR loci. Based on forensic efficiency values, SE33 may be considered the most informative locus, which makes it especially useful in forensic investigations. PMID:24577822

Zupanic Pajnic, Irena; Podovsovnik Axelsson, Eva; Balazic, Joze



Allelic Frequencies of 20 Visible Phenotype Variants in the Korean Population  

PubMed Central

The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population. PMID:23843775

Lim, Ji Eun



Expression and loss of alleles in cultured mouse embryonic fibroblasts and stem cells carrying allelic fluorescent protein genes  

PubMed Central

Background Loss of heterozygosity (LOH) contributes to many cancers, but the rate at which these events occur in normal cells of the body is not clear. LOH would be detectable in diverse cell types in the body if this event were to confer an obvious cellular phenotype. Mice that carry two different fluorescent protein genes as alleles of a locus would seem to be a useful tool for addressing this issue because LOH would change a cell's phenotype from dichromatic to monochromatic. In addition, LOH caused by mitotic crossing over might be discernable in tissues because this event produces a pair of neighboring monochromatic cells that are different colors. Results As a step in assessing the utility of this approach, we derived primary embryonic fibroblast populations and embryonic stem cell lines from mice that carried two different fluorescent protein genes as alleles at the chromosome 6 locus, ROSA26. Fluorescence activated cell sorting (FACS) showed that the vast majority of cells in each line expressed the two marker proteins at similar levels, and that populations exhibited expression noise similar to that seen in bacteria and yeast. Cells with a monochromatic phenotype were present at frequencies on the order of 10-4 and appeared to be produced at a rate of approximately 10-5 variant cells per mitosis. 45 of 45 stably monochromatic ES cell clones exhibited loss of the expected allele at the ROSA26 locus. More than half of these clones retained heterozygosity at a locus between ROSA26 and the centromere. Other clones exhibited LOH near the centromere, but were disomic for chromosome 6. Conclusion Allelic fluorescent markers allowed LOH at the ROSA26 locus to be detected by FACS. LOH at this locus was usually not accompanied by LOH near the centromere, suggesting that mitotic recombination was the major cause of ROSA26 LOH. Dichromatic mouse embryonic cells provide a novel system for studying genetic/karyotypic stability and factors influencing expression from allelic genes. Similar approaches will allow these phenomena to be studied in tissues. PMID:17042952

Larson, Jon S; Yin, Moying; Fischer, Jared M; Stringer, Saundra L; Stringer, James R



HLA-B*40 Allele Plays a Role in the Development of Acute Leukemia in Mexican Population: A Case-Control Study  

PubMed Central

Among oncohematological diseases, acute lymphoid leukemia (ALL) and acute myeloid leukemia (AML) are characterized by the uncontrolled production and accumulation of blasts that can lead to death. Although the physiopathology of these diseases is multifactorial, a genetic factor seems to be at play. Several studies worldwide have shown association of ALL and AML with several alleles of the major histocompatibility complex (MHC). Objective. To determine gene frequencies of HLA-B alleles in Mexicans (individuals with Native American genetic background admixed with European descent) with ALL and AML. Methods. We compared the HLA-B alleles in 213 patients with ALL and 85 patients with AML to those present in 731 umbilical cord blood (UCB) samples as a control group; this was done by means of the PCR-SSP technique. Results. We found an increased frequency of the HLA-B*40 allele in ALL patients as compared to the control group (14.5% versus 9.84%, P = 0.003, OR = 1.67); this was particularly evident in a subgroup of young (less than 18?years old) ALL patients (P = 0.002, OR = 1.76); likewise, a decreased frequency of HLA-B*40 allele in AML patients was observed as compared to the control group (4.70% versus 9.84%, P = 0.02, OR = 0.42). Conclusions. These results might suggest opposing effects of the HLA-B*40 in the genetic susceptibility to develop ALL or AML and offer the possibility to study further the molecular mechanisms of cell differentiation within the bone marrow lineage. PMID:24364037

Fernandez-Torres, Javier; Flores-Jimenez, Denhi; Arroyo-Perez, Antonio; Granados, Julio; Lopez-Reyes, Alberto



Autoantibodies, autoimmune risk alleles and clinical associations in rheumatoid arthritis cases and non-RA controls in the electronic medical records  

PubMed Central

Objectives The significance of non-RA autoantibodies in patients with rheumatoid arthritis (RA) is unclear. We studied associations between autoimmune risk alleles and autoantibodies in RA cases and non-RA controls, and autoantibodies and clinical diagnoses from the electronic medical records (EMR). Methods We studied 1,290 RA cases and 1,236 non-RA controls of European genetic ancestry from the EMR from two large academic centers. We measured antibodies to citrullinated peptides (ACPA), anti-nuclear antibodies (ANA), antibodies to tissue transglutaminase (anti-tTG), antibodies to thyroid peroxidase (anti-TPO). We genotyped subjects for autoimmune risk alleles, and studied the association between number of autoimmune risk alleles and number of types of autoantibodies present. We conducted a phenome-wide association study (PheWAS) to study potential associations between autoantibodies and clinical diagnoses among RA cases and controls. Results Mean age was 60.7 in RA and 64.6 years in controls, and both were 79% female. The prevalence of ACPA and ANA was higher in RA cases compared to controls (p<0.0001, both); we observed no difference in anti-TPO and anti-tTG. Carriage of higher numbers of autoimmune risk alleles was associated with increasing types of autoantibodies in RA cases (p=4.4x10?6) and controls (p=0.002). From the PheWAS, ANA was significantly associated with Sjogren’s/siccain RA cases. Conclusion The increased frequency of autoantibodies in RA cases and controls was associated with the number of autoimmune risk alleles carried by an individual. PheWAS analyses within the EMR linked to blood samples provide a novel method to test for the clinical significance of biomarkers in disease. PMID:23233247

Liao, Katherine P.; Kurreeman, Fina; Li, Gang; Duclos, Grant; Murphy, Shawn; Raul Guzman, P; Cai, Tianxi; Gupta, Namrata; Gainer, Vivian; Schur, Peter; Cui, Jing; Denny, Joshua C.; Szolovits, Peter; Churchill, Susanne; Kohane, Isaac; Karlson, Elizabeth W.; Plenge, Robert M.



The genealogy, site frequency spectrum and ages of two nested mutant alleles.  


In this paper we consider the genealogy of two nested mutant alleles, assuming the constant-size neutral coalescent model with infinite sites mutation. We study the conditional genealogy and derive explicit formulas for the joint and marginal site frequency spectra for the double, single and zero mutant allele. In addition, we find the mean ages of the two mutations. We show that the age of the youngest mutation does not depend on the frequency of the single mutant allele and that the frequency spectra for the single mutant allele and the zero mutant allele are the same. PMID:19249321

Hobolth, Asger; Wiuf, Carsten



A family with two female compound heterozygous for the FMR1 premutation alleles  

PubMed Central

Premutation alleles (55-200 CGG repeats) of the fragile X mental retardation (FMR1) gene have been linked to various types of clinical involvement ranging from mood and anxiety disorders to immunological disorders and executive function deficits. Carrier females typically have a premutation allele and a normal allele (<55 CGG repeats). Although rare, 7 cases of females that carry two expanded alleles (compound heterozygous premutation) have been reported. Here we report on four members of a family including two compound heterozygous premutation sisters with similar CGG allele sizes, affected with different levels of clinical severity. PMID:23786467

Basuta, Kirin; Lozano, Reymundo; Schneider, Andrea; Yrigollen, Carolyn M.; Hessl, David; Hagerman, Randi J.; Tassone, Flora



CCR5 as a Natural and Modulated Target for Inhibition of HIV  

PubMed Central

Human immunodeficiency virus type 1 (HIV-1) infection of target cells requires CD4 and a co-receptor, predominantly the chemokine receptor CCR5. CCR5-delta32 homozygosity results in a truncated protein providing natural protection against HIV infection—this without detrimental effects to the host—and transplantation of CCR5-delta32 stem cells in a patient with HIV (“Berlin patient”) achieved viral eradication. As a more feasible approach gene-modification strategies are being developed to engineer cellular resistance to HIV using autologous cells. We have developed a dual therapeutic anti-HIV lentiviral vector (LVsh5/C46) that down-regulates CCR5 and inhibits HIV-1 fusion via cell surface expression of the gp41-derived peptide, C46. This construct, effective against multiple strains of both R5- and X4-tropic HIV-1, is being tested in Phase I/II trials by engineering HIV-resistant hematopoietic cells. PMID:24381033

Burke, Bryan P.; Boyd, Maureen P.; Impey, Helen; Breton, Louis R.; Bartlett, Jeffrey S.; Symonds, Geoff P.; Hutter, Gero



Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project  

PubMed Central

Background In the last hundred years, the development of improved wheat cultivars has led to the replacement of landraces and traditional varieties by modern cultivars. This has resulted in a decline in the genetic diversity of agriculturally used wheat. However, the diversity lost in the elite material is somewhat preserved in crop gene banks. Therefore, the gene bank accessions provide the basis for genetic improvement of crops for specific traits and and represent rich sources of novel allelic variation. Results We have undertaken large scale molecular allele mining to isolate new alleles of the powdery mildew resistance gene Pm3 from wheat gene bank accessions. The search for new Pm3 alleles was carried out on a geographically diverse set of 733 wheat accessions originating from 20 countries. Pm3 specific molecular tools as well as classical pathogenicity tests were used to characterize the accessions. Two new functional Pm3 alleles were identified out of the eight newly cloned Pm3 sequences. These new resistance alleles were isolated from accessions from China and Nepal. Thus, the repertoire of functional Pm3 alleles now includes 17 genes, making it one of the largest allelic series of plant resistance genes. The combined information on resistant and susceptible Pm3 sequences will allow to study molecular function and specificity of functional Pm3 alleles. Conclusions This study demonstrates that molecular allele mining on geographically defined accessions is a useful strategy to rapidly characterize the diversity of gene bank accessions at a specific genetic locus of agronomical importance. The identified wheat accessions with new resistance specificities can be used for marker-assisted transfer of the Pm3 alleles to modern wheat lines. PMID:20470444



The European Values Study  

NSDL National Science Digital Library

Curious minds want to know: "What exactly do Europeans believe?" It's an important and interesting question, and the directors and researchers in charge of the European Values Study (EVS) have been looking into this subject since the early 1980s. Based in the Netherlands the EVS concerns itself with asking Europeans about religion and morality, politics, work and leisure, and relationships. On their homepage, visitors can learn about their work and view previous and current surveys. While visitors do not have access to the raw data on the site, they can look at the questionnaires and read publications based on this research.


The European Spallation Source  

SciTech Connect

In 2003 the joint European effort to design a European Spallation Source (ESS) resulted in a set of reports, and in May 2009 Lund was agreed to be the ESS site. The ESS Scandinavia office has since then worked on setting all the necessary legal and organizational matters in place so that the Design Update and construction can be started in January 2011, in collaboration with European partners. The Design Update phase is expected to end in 2012, to be followed by a construction phase, with first neutrons expected in 2018-2019.

Lindroos M.; Calaga R.; Bousson S.; Danared H.; Devanz G. et al



Bi-allelic gene targeting in mouse embryonic stem cells.  


The EUCOMM and KOMP programs have generated targeted conditional alleles in mouse embryonic stem cells for nearly 10,000 genes. The availability of these stem cell resources will greatly accelerate the functional analysis of genes in mice and in cultured cells. We present a method for conditional ablation of genes in ES cells using vectors and targeted clones from the EUCOMM and KOMP conditional resources. Inducible homozygous cells described here provide a precisely controlled experimental system to study gene function in a model cell. PMID:21288739

Tate, Peri H; Skarnes, William C



AB0 blood subgroup allele frequencies in the Turkish population.  


We determined the AB0 blood group system with a PCR based technique termed APLP (Amplified Product Length Polymorphism) in the Turkish population. The method includes ten different allele specific primers and permits identification of the major AB0 genotypes and its suballeles (A1-A2-B-0A-02-0G-AG). The suballeles were amplified in a single tube reaction. We have determined AB0 phenotypes in 129 Turkish individuals. No significant deviation from the Hardy-Weinberg equilibrium was observed. PMID:14523998

Akbas, Fahri; Aydin, Müge; Cenani, Asim



European Scientific Notes.  

National Technical Information Service (NTIS)

The monthly publication presents brief articles concerning recent developments in European Scientific Research. It is hoped that these articles which do not constitute part of the scientific literature may prove of value to American scientists by disclosi...

R. F. Potter, V. S. Hewitson



European Judicial Network  

NSDL National Science Digital Library

As a part of the European Commission, the European Judicial Network is primarily concerned with providing information about community law, European law, and various aspects of civil and commercial law. The homepage is well-organized, and visitors can start by clicking on the topic page sections, which cover everything from bringing a case to court to alternative dispute resolutions. On the right-side of the homepage, visitors can click on the flags of member states to learn more about each nation's legal system. The site will certainly be of interest to those with a legal background, but the main stated objective of the site is "to make life easier for people facing litigation of whatever kind where there is a transnational element." Not surprisingly, all of this information is available in the twenty official languages of the European Union.



European psychotraumatology - alongside the recent European history  

PubMed Central

This article outlines a personal reflection of experiences within the field of traumatic stress, especially in relation to specific events, which affected the author's professional life. Conclusions for further challenges for European Society for Traumatic Stress Studies (ESTSS) are delineated. ESTSS's role in the global network of traumatic stress societies is discussed. This is a personal view of Brigitte Lueger-Schuster, president of ESTSS on behalf of the 20th birthday of ESTSS. PMID:23755321

Lueger-Schuster, Brigitte



The other allele: Exploring the long allele of the serotonin transporter gene as a potential risk factor for psychopathy: A review of the parallels in findings  

PubMed Central

Converging evidence suggests that the short allele of the serotonin transporter gene polymorphism increases risk for a variety of psychological disorders, including depression, anxiety, and alcoholism. Thus, the short allele is typically considered the “risk” allele, and findings related to the long allele are rarely discussed. However, upon closer examination, findings associated with the long allele of the serotonin transporter gene share striking similarities with findings from studies of psychopathy. Here, the parallels between findings associated with the long/long genotype and findings associated with psychopathic traits in the areas of neuropsychology, psychophysiology, hormones, and brain imaging are reviewed. It is suggested that the long/long genotype may be a potential risk factor for the development of psychopathic traits. PMID:20674598

Glenn, Andrea L.



Archive of European Integration  

NSDL National Science Digital Library

The creation of a so-called âÂÂcommon marketâ and throughout the European countries has taken decades, and this valuable scholarly resource created by a team of academics will be of great interest to anyone with a penchant for this subject. The idea for this archive of European Integration was devised by Phil Wilkin (who now serves as its editor), and over the years, his efforts have been aided by a team of other dedicated individuals. Simply put, the Archive of European Integration (AEI) is âÂÂan electronic repository and archive for research materials on the topic of European integration and unification.â As such, it is primarily concerned with collecting official European Community/European Union documents and certain independently-produced research materials. First-time visitors to the site can search the archive by six different methods, view a list of the latest additions, and also register at no charge for an account that will let them submit items to the archive. All told, the archive currently contains over 4800 documents ranging from working papers on topics such as the common agricultural policy as well as cultural policy.


Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes  

PubMed Central

Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%). PMID:25027508



An allele of the crm gene blocks cyanobacterial circadian rhythms.  


The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (rpaA) is the only gene other than kaiA, kaiB, and kaiC, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of rpaA in Synechococcus elongatus PCC 7942 termed crm (for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The crm ORF complements the defect when expressed in trans, but only if it can be translated, suggesting that crm encodes a small protein. The crm1 insertion allele phenotypes are distinct from those of an rpaA null; crm1 mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the crm1 mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA. PMID:23918383

Boyd, Joseph S; Bordowitz, Juliana R; Bree, Anna C; Golden, Susan S



An allele of the crm gene blocks cyanobacterial circadian rhythms  

PubMed Central

The SasA-RpaA two-component system constitutes a key output pathway of the cyanobacterial Kai circadian oscillator. To date, rhythm of phycobilisome associated (rpaA) is the only gene other than kaiA, kaiB, and kaiC, which encode the oscillator itself, whose mutation causes completely arrhythmic gene expression. Here we report a unique transposon insertion allele in a small ORF located immediately upstream of rpaA in Synechococcus elongatus PCC 7942 termed crm (for circadian rhythmicity modulator), which results in arrhythmic promoter activity but does not affect steady-state levels of RpaA. The crm ORF complements the defect when expressed in trans, but only if it can be translated, suggesting that crm encodes a small protein. The crm1 insertion allele phenotypes are distinct from those of an rpaA null; crm1 mutants are able to grow in a light:dark cycle and have no detectable oscillations of KaiC phosphorylation, whereas low-amplitude KaiC phosphorylation rhythms persist in the absence of RpaA. Levels of phosphorylated RpaA in vivo measured over time are significantly altered compared with WT in the crm1 mutant as well as in the absence of KaiC. Taken together, these results are consistent with the hypothesis that the Crm polypeptide modulates a circadian-specific activity of RpaA. PMID:23918383

Boyd, Joseph S.; Bordowitz, Juliana R.; Bree, Anna C.; Golden, Susan S.



Allelic variations of glut-1 deficiency syndrome: the chinese experience.  


Glucose transporter type 1 deficiency syndrome is characterized by infantile onset seizures, development delay, movement disorders, and acquired microcephaly. The phenotype includes allelic variants such as intermittent ataxia, choreoathetosis, dystonia, and alternating hemiplegia of childhood with or without epilepsy. Dystonias involve allelic variants of glucose transporter type 1 deficiency syndrome. Three Chinese patients presented with paroxysmal behavioral disturbance, weakness, ataxia (especially after fasting), and exercise intolerance. Electroencephalogram findings did not correlate with clinical manifestations. Cranial magnetic resonance imaging produced normal results or mild hypomyelination. Hypoglycorrhachia was evident in all cases. Cerebrospinal fluid glucose ranged from 1.63-2.45 mmol/L. Erythrocyte 3-O-methyl-d-glucose uptake was decreased to 58% in patient 1. Three SLC2A1 disease-causing mutations (761delA, P383H, and R400C) were observed. No patient tolerated ketogenic diets. Two patients responded to frequent meals with snacks. Cerebrospinal fluid evaluation constitutes the diagnostic testing permitting early treatment of glucose transporter type 1 deficiency syndrome. Early diagnosis and treatment improve prognoses. PMID:22704013

Liu, Yanyan; Bao, Xinhua; Wang, Dong; Fu, Na; Zhang, Xiaoying; Cao, Guangna; Song, Fuying; Wang, Shuang; Zhang, Yuehua; Qin, Jiong; Yang, Hong; Engelstad, Kristin; De Vivo, Darryl C; Wu, Xiru



Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution  

PubMed Central

Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster–Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes. PMID:22319150

Graze, R. M.; Novelo, L. L.; Amin, V.; Fear, J. M.; Casella, G.; Nuzhdin, S. V.; McIntyre, L. M.



Genomic landscape of human allele-specific DNA methylation  

PubMed Central

DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for full-genome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species. PMID:22523239

Fang, Fang; Hodges, Emily; Molaro, Antoine; Dean, Matthew; Hannon, Gregory J.; Smith, Andrew D.



Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers  

NASA Astrophysics Data System (ADS)

The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.

Kijewski, T.; ?mietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.



Epigenetic allelic states of a maize transcriptional regulatory locus exhibit overdominant gene action.  

PubMed Central

Using alleles of the maize purple plant locus (pl), which encodes a transcriptional regulator of anthocyanin pigment synthesis, we describe a case of single-locus heterosis, or overdominance, where the heterozygote displays a phenotype that is greater than either homozygote. The Pl-Rhoades (Pl-Rh) allele is subject to epigenetic changes in gene expression, resulting in quantitatively distinct expression states. Allelic states with low-expression levels, designated Pl'-mahogany (Pl'-mah), are dominant to the high-expression state of Pl-Rh. Pl'-mah states retain low-expression levels in subsequent generations when homozygous or heterozygous with Pl-Rh. However, Pl'-mah alleles frequently exhibit higher expression levels when heterozygous with other pl alleles; illustrating an overdominant allelic relationship. Higher expression levels are also observed when Pl'-mah is hemizygous. These results suggest that persistent allelic interactions between Pl'-mah and Pl-Rh are required to maintain the low-expression state and that other pl alleles are missing sequences required for this interaction. The Pl-Rh state can be sexually transmitted from Pl'-mah/pl heterozygotes, but not from Pl'-mah hemizygotes, suggesting that fixation of the high-expression state may involve synapsis. The existence of such allele-dependent regulatory mechanisms implicates a novel importance of allele polymorphisms in the genesis and maintenance of genetic variation. PMID:9755217

Hollick, J B; Chandler, V L



An association between the risk of ovarian cancer and rare HRAS1 alleles  

SciTech Connect

The highly polymorphic HRAS1 minisatellite locus just downstream from the proto-oncogene H-ras-1 on chromosome 11p consists of four common progenitor alleles and several dozen rare alleles, which apparently derive from mutations of the progenitors. Mutant alleles of this locus represent a major risk factor for common types of cancer. Rare-sized HRAS1 alleles have been found more frequently in patients with carcinoma of the breast, colorectum, and urinary bladder and acute leukemia, compared to cancer-free controls. This highly significant association (p<1.001) results in a modest relative risk for patients with one rare allele, but the prevalence of this class of mutant alleles implies an important attributable risk: 1 in 11 cancers of the breast, colorectum, and bladder. Therefore, we performed a case-control study using conventional (Southern blot) and PCR-based methods to score HRAS1 alleles in the leukocyte DNA from 59 patients with ovarian cancer, and 51 cancer-free controls. Our preliminary data suggest an increased incidence of rare and intermediate HRAS1 alleles in caucasian ovarian cancer patients (13%) compared to cancer-free controls (4%). These results parallel the allele distribution seen in the large published series, and lend support for a significant association between rare HRAS1 alleles and ovarian cancer predisposition.

Weitzel, J.N.; Patel, J.; Smith, D.M. [Tufts Univ. Medical School, Boston, MA (United States)] [and others



Extra Alleles in FMR1 Triple-Primed PCR: Artifact, Aneuploidy, or Somatic Mosaicism?  


Triple-primed PCR assays have become the preferred fragile X syndrome testing method. Using a commercially available assay, we detected a reproducible extra peak(s) in 0.5% of 13,161 clinical samples. The objectives of this study were to determine the cause of these extra peaks; to identify whether these peaks represent an assay specific artifact, an underlying chromosome aneuploidy, or somatic mosaicism; and to ascertain their clinical relevance. The presence of an extra allele(s) was confirmed by a laboratory-developed PCR, with sequencing of the FMR1 5' UTR or Southern blot for some samples. The laboratory-developed procedure detected the extra allele(s) in 57 of 64 samples. Thus, we confirmed an extra peak, typically of lower abundance, in approximately 0.4% of all samples. Of these samples, 5 were from males and 52 were from heterozygous or homozygous females. Six patients likely had X chromosome aneuploidies. In 82.3% of samples, the extra allele had fewer repeats than the predominant allele(s). Additional alleles detected by FMR1 triple-primed PCR are not an assay-specific artifact and are likely due to X chromosome aneuploidies or somatic repeat instability. Additional normal alleles likely have no clinical significance for fragile X syndrome carrier or affected status. Extra alleles in individuals with normal karyotypes probably represent FMR1 somatic variation. PMID:25307758

Wakeling, Erin N; Nahhas, Fatimah A; Feldman, Gerald L



Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield.  


Crop improvement for yield and drought tolerance is challenging due to the complex genetic nature of these traits and environmental dependencies. This study reports that transgenic over-expression of Zea mays AR GOS1 (ZAR1) enhanced maize organ growth, grain yield, and drought-stress tolerance. The ZAR1 transgene exhibited environmental interactions, with yield increase under Temperate Dry and yield reduction under Temperate Humid or High Latitude environments. Native ZAR1 allele variation associated with drought-stress tolerance. Two founder alleles identified in the mid-maturity germplasm of North America now predominate in Pioneer's modern breeding programme, and have distinct proteins, promoters and expression patterns. These two major alleles show heterotic group partitioning, with one predominant in Pioneer's female and the other in the male heterotic groups, respectively. These two alleles also associate with favourable crop performance when heterozygous. Allele-specific transgene testing showed that, of the two alleles discussed here, each allele differed in their impact on yield and environmental interactions. Moreover, when transgenically stacked together the allelic pair showed yield and environmental performance advantages over either single allele, resembling heterosis effects. This work demonstrates differences in transgenic efficacy of native alleles and the differences reflect their association with hybrid breeding performance. PMID:24218327

Guo, Mei; Rupe, Mary A; Wei, Jun; Winkler, Chris; Goncalves-Butruille, Marymar; Weers, Ben P; Cerwick, Sharon F; Dieter, Jo Ann; Duncan, Keith E; Howard, Richard J; Hou, Zhenglin; Löffler, Carlos M; Cooper, Mark; Simmons, Carl R



Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus).  


In this study, the cross-amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross-amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2-4, 0.086-0.629 and 0.288-0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison. PMID:17177698

Roth, T; Pfeiffer, I; Weising, K; Brenig, B



Waxy genes from spelt wheat: new alleles for modern wheat breeding and new phylogenetic inferences about the origin of this species  

PubMed Central

Background and Aims Waxy proteins are responsible for amylose synthesis in wheat seeds, being encoded by three waxy genes (Wx-A1, Wx-B1 and Wx-D1) in hexaploid wheat. In addition to their role in starch quality, waxy loci have been used to study the phylogeny of wheat. The origin of European spelt (Triticum aestivum ssp. spelta) is not clear. This study compared waxy gene sequences of a Spanish spelt collection with their homologous genes in emmer (T. turgidum ssp. dicoccum), durum (T. turgidum ssp. durum) and common wheat (T. aestivum ssp. aestivum), together with other Asian and European spelt that could be used to determine the origin of European spelt. Methods waxy genes were amplified and sequenced. Geneious Pro software, DNAsp and MEGA5 were used for sequence, nucleotide diversity and phylogenetic analysis, respectively. Key Results Three, four and three new alleles were described for the Wx-A1, Wx-B1 and Wx-D1 loci, respectively. Spelt accessions were classified into two groups based on the variation in Wx-B1, which suggests that there were two different origins for the emmer wheat that has been found to be part of the spelt genetic make-up. One of these groups was only detected in Iberian material. No differences were found between the rest of the European spelt and the Asiatic spelt, which suggested that the Iberian material had a different origin from the other spelt sources. Conclusions The results suggested that the waxy gene variability present in wheat is undervalued. The evaluation of this variability has permitted the detection of ten new waxy alleles that could affect starch quality and thus could be used in modern wheat breeding. In addition, two different classes of Wx-B1 were detected that could be used for evaluating the phylogenetic relationships and the origins of different types of wheat. PMID:22984164

Guzman, Carlos; Caballero, Leonor; Martin, Luis M.; Alvarez, Juan B.



European Union Scandal  

NSDL National Science Digital Library

This week's In the News examines the recent high-level corruption scandal in the European Union. Last Tuesday, the European Commission -- the executive body that initiates and implements EU legislation -- resigned en masse, plunging the supranational organization into unprecedented political chaos. All 20 commissioners, led by commission President Jacques Santer of Luxembourg, abdicated their positions the day after the release of a scathing report by the Committee of Independent Experts. The independent panel of experts, who were appointed by the European Parliament, had investigated allegations of bureaucratic malfeasance perpetrated by the European Commission. The committee's report collectively accused the commission of financial "fraud, mismanagement, and nepotism." In the wake of the incriminating report and subsequent resignations, EU foreign ministers are scrambling to find successors for the commissioners to placate the bewildered European citizenry and return to business as usual. This political upheaval happened at a crucial transitional time in the EU's 42-year history, undermining its credibility at a time when it plans to expand into eastern Europe. The current tumult occurred just three months after launching a new unified currency, seven weeks before the new Treaty of Amsterdam commences, and three months before the next European Parliamentary elections, which will determine the future composition of the EU's 626-member assembly. During the next two days, distracted leaders from all fifteen EU member states will meet in Berlin to discuss the reconstruction of the European Commission and formulate a seven-year budget for the entire EU, an organization with about 18,000 officials who administer nearly $100 billion annually. The eight resources discussed provide news, commentary, and analysis.

Osmond, Andrew.


Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas.  


The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC. PMID:24743946

Koutsogiannouli, Evagelia A; Moutou, Katerina A; Stamatis, Costas; Walter, Lutz; Mamuris, Zissis



Report of the European DNA profiling group (EDNAP): an investigation of the complex STR loci D21S11 and HUMFIBRA (FGA)  

Microsoft Academic Search

This paper describes a collaborative exercise which was intended to demonstrate whether uniformity of DNA profiling results could be achieved between European laboratories using two complex short tandem repeat (STR) loci. The loci D21S11 and HUMFIBRA (FGA) were chosen because they are commonly used by different European laboratories. D21S11 has approximately 14 common alleles (f>0.001), whereas HUMFIBRA has 19 common

Peter Gill; E d'Aloja; J Andersen; B Dupuy; M Jangblad; V Johnsson; A. D Kloosterman; A Kratzer; M. V Lareu; M Meldegaard; C Phillips; H Pfitzinger; S Rand; M Sabatier; R Scheithauer; H Schmitter; P Schneider; M. C Vide



Identification of the putative ancestral allele of bovine single-nucleotide polymorphisms.  


Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single-nucleotide polymorphism (SNP) data sets for many species and of high-throughput SNP genotyping methods, whole-genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19 551 488 SNPs and identified the putative ancestral allele for 14 339 107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic-based approach to identify putative ancestral alleles is reliable. PMID:24862839

Rocha, D; Billerey, C; Samson, F; Boichard, D; Boussaha, M



Identification of a novel allele HLA-A*1113 in a Japanese donor.  


Anew HLA-A*11 allele, A*1113, was identified in a healthy Japanese female. She was typed as HLA-A11?, A2, B46, B67, Cw1, Cw7 (Bw6) with unusual serological reactivity of A11, suggesting possible presence of a new A*11 allele. The novel A*1113 allele was identified by haplotypic group-specific allele amplification using A*11 allele-specific primer pairs and sequence-based typing. The A*1113 allele differs from A*11011 by one nucleotide substitution in exon 3 at position 503 (A --> G) which causes an amino acid change in the alfa2 domain at residue 144 (lysine : K --> arginine : R), thus resulting in the unusual serological reactivity. PMID:15191528

Takahashi, D; Miyazaki, T; Araseki, M; Sekimoto, T; Sato, S; Kato, T; Ikeda, H



Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio.  

PubMed Central

Natural populations carry deleterious recessive alleles which cause inbreeding depression. We compared mortality and growth of inbred and outbred zebrafish, Danio rerio, between 6 and 48 days of age. Grandparents of the studied fish were caught in the wild. Inbred fish were generated by brother-sister mating. Mortality was 9% in outbred fish, and 42% in inbred fish, which implies at least 3.6 lethal equivalents of deleterious recessive alleles per zygote. There was no significant inbreeding depression in the growth, perhaps because the surviving inbred fish lived under less crowded conditions. In contrast to alleles that cause embryonic and early larval mortality in the same population, alleles responsible for late larval and early juvenile mortality did not result in any gross morphological abnormalities. Thus, deleterious recessive alleles that segregate in a wild zebrafish population belong to two sharply distinct classes: early-acting, morphologically overt, unconditional lethals; and later-acting, morphologically cryptic, and presumably milder alleles. PMID:15451692

McCune, Amy R.; Houle, David; McMillan, Kyle; Annable, Rebecca; Kondrashov, Alexey S.



European Monetary Institute (EMI)  

NSDL National Science Digital Library

The European Monetary Institute was established in 1994 to oversee the implementation of a single currency for Europe. The EMI site contains information on its staff, organization, structure, and financial resources, and outlines the process of entering the third and final phase of the European Monetary Union. After months of doubt and political difficulties in France, Germany, and most recently, Italy, it now appears that the unified European currency, the Euro, will indeed begin on January 1, 1999 to replace the national currencies of as many as 10 or 11 countries. The path to a unified currency is by no means smooth, however. Many European Union member states are finding it politically difficult to reduce their budget deficit to 3 percent of gross domestic product and other states, such as Britain and Denmark, are choosing to remain out for now regardless. On the other hand, European economic growth will apparently exceed earlier expectations, allowing leaders to use increased tax revenues instead of cutting social services to qualify.


Generation of Humoral Immune Responses to Multi-Allele PfAMA1 Vaccines; Effect of Adjuvant and Number of Component Alleles on the Breadth of Response  

PubMed Central

There is increasing interest in multi-allele vaccines to overcome strain-specificity against polymorphic vaccine targets such as Apical Membrane Antigen 1 (AMA1). These have been shown to induce broad inhibitory antibodies in vitro and formed the basis for the design of three Diversity-Covering (DiCo) proteins with similar immunological effects. The antibodies produced are to epitopes that are shared between vaccine alleles and theoretically, increasing the number of component AMA1 alleles is expected to broaden the antibody response. A plateau effect could however impose a limit on the number of alleles needed to achieve the broadest specificity. Moreover, production cost and the vaccine formulation process would limit the number of component alleles. In this paper, we compare rabbit antibody responses elicited with multi-allele vaccines incorporating seven (three DiCos and four natural AMA1 alleles) and three (DiCo mix) antigens for gains in broadened specificity. We also investigate the effect of three adjuvant platforms on antigen specificity and antibody functionality. Our data confirms a broadened response after immunisation with DiCo mix in all three adjuvants. Higher antibody titres were elicited with either CoVaccine HT™ or Montanide ISA 51, resulting in similar in vitro inhibition (65–82%) of five out of six culture-adapted P. falciparum strains. The antigen binding specificities of elicited antibodies were also similar and independent of the adjuvant used or the number of vaccine component alleles. Thus neither the four extra antigens nor adjuvant had any observable benefits with respect to specificity broadening, although adjuvant choice influenced the absolute antibody levels and thus the extent of parasite inhibition. Our data confirms the feasibility and potential of multi-allele PfAMA1 formulations, and highlights the need for adjuvants with improved antibody potentiation properties for AMA1-based vaccines. PMID:21082025

Kusi, Kwadwo A.; Faber, Bart W.; Riasat, Vanessa; Thomas, Alan W.; Kocken, Clemens H. M.; Remarque, Edmond J.



Low frequency of the scrapie resistance-associated allele and presence of lysine-171 allele of the prion protein gene in Italian Biellese ovine breed.  


Frequencies of polymorphisms at codons 136, 154 and 171 of the prion protein (PrP) gene were studied in 1207 pure-bred and cross-bred Italian Biellese rams, a small ovine breed of about 65 000 head in Italy. Aside from the five most common alleles (VRQ, ARQ, ARR, AHQ and ARH), the rare ARK allele was also found, with the highest frequency reported so far in an ovine breed (2.5 %). ARK/--- genotypes had a total frequency of 4.9 %. The resistance-associated ARR allele was seen at a low frequency (8.3 %). Only 1.4 % of animals examined had a resistant ARR/ARR PrP genotype. Semi-resistant (ARR/ARQ, ARR/ARH and ARR/AHQ) PrP genotypes had a total frequency of 12.6 % and PrP genotypes that are associated with high scrapie susceptibility (e.g. VRQ/VRQ and ARQ/ARQ) had a total frequency of 81.1 %. Statistical analysis comparing PrP allele frequencies between pure-bred and cross-bred animals showed that the ARR allele occurred at a significantly lower frequency in pure-bred rams. Furthermore, comparison of PrP allele frequencies between pure-bred rams over 18 months of age and those below 18 months of age showed a significant decrease in the ARR allele in breeding rams over 18 months of age. Based on these results, breeding for scrapie resistance in the Biellese breed will have to take into account the low frequency of the ARR allele, which also seems to be subject to negative selection by farmers. Further investigation is required to understand whether the ARK allele is also associated with resistance to transmissible spongiform encephalopathies. PMID:15448380

Acutis, P L; Sbaiz, L; Verburg, F; Riina, M V; Ru, G; Moda, G; Caramelli, M; Bossers, A



Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances.  


Y chromosome short tandem repeats (Y-STRs) are valuable genetic markers in certain areas of forensic case-work. However, when the Y-STR DNA profile is weak, the observed Y-STR profile may not be complete--i.e. locus drop-out may have occurred. Another explanation could be that the stain DNA did not have a Y-STR allele that was detectable with the method used (the allele is a 'null allele'). If the Y-STR profile of a stain is strong, one would be reluctant to consider drop-out as a reasonable explanation of lack of a Y-STR allele and would maybe consider 'null allele' as an explanation. On the other hand, if the signal strengths are weak, one would most likely accept drop-out as a possible explanation. We created a logistic regression model to estimate the probability of allele drop-out with the Life Technologies/Applied Biosystems AmpFlSTR(®) Yfiler(®) kit such that the trade-off between drop-outs and null alleles could be quantified using a statistical model. The model to estimate the probability of drop-out uses information about locus imbalances, signal strength, the number of PCR cycles, and the fragment size of Yfiler. We made two temporarily separated experiments and found no evidence of temporal variation in the probability of drop-out. Using our model, we found that for 30 PCR cycles with a 150 bp allele, the probability of drop-out was 1:5000 corresponding to the average estimate of the probability of Y-STR null alleles at a signal strength of 1249 RFU. This means that the probability of a null allele is higher than that of an allele drop-out at e.g. 4000 RFU and the probability of drop-out is higher than that of a null allele at e.g. 75 RFU. PMID:23453365

Andersen, Mikkel Meyer; Mogensen, Helle Smidt; Eriksen, Poul Svante; Olofsson, Jill Katharina; Asplund, Maria; Morling, Niels



Association between clozapine response and allelic variation in 5HT 2A receptor gene  

Microsoft Academic Search

We report allelic association between a polymorphism (T102C) within the coding region of the 5-HT2A gene (HTR2A, 13q14-21) and response to clozapine in schizophrenic patients. Homozygosity for the C102 allele was more frequent (30\\/57, 53%) among patients who did not respond to clozapine than in those who responded (23\\/92, 25%). This finding is evidence that allelic variation of genes which

M. J. Arranz; D. A. Collier; M. Sodhi; D. Ball; G. W. Roberts; P. Sham; R. Kerwin; J. Price



Fine-mapping natural alleles: quantitative complementation to the rescue  

PubMed Central

Mapping the genes responsible for natural variation and divergence is a challenging task. Many studies have mapped genes to genomic regions, or generated lists of candidates, but few studies have implicated specific genes with a high standard of evidence. I propose that combining recent advances in genomic engineering with a modified version of the quantitative complementation test will help turn candidate genes into causal genes. By creating loss-of-function mutations in natural strains, and using these mutations to quantitatively fail-to-complement natural alleles, fine mapping should be greatly facilitated. As an example, I propose that the CRISPR/Cas9 system could be combined with the FLP/FRT system to fine-map genes in the numerous systems where inversions have frustrated these efforts. PMID:24628660

Turner, Thomas L.



A Likelihood Approach to Populations Samples of Microsatellite Alleles  

PubMed Central

This paper presents a likelihood approach to population samples of microsatellite alleles. A Markov chain recursion method previously published by GRIFFITHS and TAVARE is applied to estimate the likelihood function under different models of microsatellite evolution. The method presented can be applied to estimate a fundamental population genetics parameter ? as well as parameters of the mutational model. The new likelihood estimator provides a better estimator of ? in terms of the mean square error than previous approaches. Furthermore, it is demonstrated how the method may easily be applied to test models of microsatellite evolution. In particular it is shown how to compare a one-step model of microsatellite evolution to a multi-step model by a likelihood ratio test. PMID:9178018

Nielsen, R.



Non-equilibrium allele frequency spectra via spectral methods.  


A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright-Fisher process with migration of K populations, influx of mutations, and multiple population splitting events. PMID:21376069

Luki?, Sergio; Hey, Jody; Chen, Kevin



New York State TrueAllele ® casework validation study.  


DNA evidence can pose interpretation challenges, particularly with low-level or mixed samples. It would be desirable to make full use of the quantitative data, consider every genotype possibility, and objectively produce accurate and reproducible DNA match results. Probabilistic genotype computing is designed to achieve these goals. This validation study assessed TrueAllele(®) probabilistic computer interpretation on 368 evidence items in 41 test cases and compared the results with human review of the same data. Whenever there was a human result, the computer's genotype was concordant. Further, the computer produced a match statistic on 81 mixture items (for 87 inferred matching genotypes) in the test cases, while human review reported a statistic on 25 of these items (30.9%). Using match statistics to quantify information, probabilistic genotyping was shown to be sensitive, specific, and reproducible. These results demonstrate that objective probabilistic genotyping of biological evidence can reliably preserve DNA identification information. PMID:23865896

Perlin, Mark W; Belrose, Jamie L; Duceman, Barry W



Leukemogenic Ptpn11 Allele Causes Defective Erythropoiesis in Mice  

PubMed Central

Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2), encoded by PTPN11, regulates signaling networks and cell fate in many tissues. Expression of oncogenic PTPN11 in the hematopoietic compartment causes myeloproliferative neoplasm (MPN) in humans and mice. However, the stage-specific effect(s) of mutant Ptpn11 on erythroid development have remained unknown. We found that expression of an activated, leukemogenic Ptpn11 allele, Ptpn11D61Y, specifically in the erythroid lineage causes dyserythropoiesis in mice. Ptpn11D61Y progenitors produce excess cKIT+CD71+Ter119? cells and aberrant numbers of cKITl°CD71+ erythroblasts. Mutant erythroblasts show elevated activation of ERK, AKT and STAT3 in response to EPO stimulation, and MEK inhibitor treatment blocks Ptpn11D61Y-evoked erythroid hyperproliferation in vitro. Thus, the expression of oncogenic Ptpn11 causes dyserythropoiesis in a cell-autonomous manner in vivo. PMID:25289670

Usenko, Tatiana; Chan, Gordon; Torlakovic, Emina; Klingmuller, Ursula; Neel, Benjamin G.



Pollinator-mediated selection on flower color allele drives reinforcement.  


Reinforcement is the process by which reduced hybrid fitness generates selection favoring the evolution of stronger prezygotic reproductive barriers between emerging species. Using common-garden field experiments, we quantified the strength of reinforcing selection in nature by demonstrating strong selection favoring an allele conferring increased pigment intensity in the plant Phlox drummondii in areas of sympatry with the closely related species Phlox cuspidata. Incomplete hybrid sterility between the two species generates selection for traits that decrease interspecies hybridization. In contrast, selection on this locus is undetectable in the absence of P. cuspidata. We demonstrate that reinforcing selection is generated by nonrandom pollinator movement, in which pollinators move less frequently between intensely pigmented P. drummondii and P. cuspidata than between lightly pigmented P. drummondii and P. cuspidata. PMID:22300852

Hopkins, Robin; Rausher, Mark D



A sequencing-based survey of functional APAF1 alleles in a large sample of individuals with affective illness and population controls.  


Rare apoptosis-promoting functional variants in the apoptosis protease activating factor 1 (APAF1) gene were recently reported to co-segregate with major depression in male members of families from Utah. In order to estimate the impact of these variants on risk for major depressive disorder (MDD) in the general population, we surveyed the frequency of the APAF1 putative MDD risk alleles using re-sequencing in a large sample of northern European and European-American subjects, including a large number of males with MDD. The E777K and N782T APAF1 variants previously described by Harlan et al. [Harlan et al. (2006) Mol Psychiatry 11(1):76-85] were found at low frequencies in affected individuals and population controls. The C450W and Q465R variants were not detected in any of the 632 subjects sequenced. These results show that the APAF1 variants associated with risk for MDD in the Utah pedigrees are very rare in Northern European and European-American populations. In addition, the E777K and N782T variants were found at low frequencies both in patients and population controls, suggesting that these variants have limited impact on risk for MDD. PMID:19455599

Amin, Zenab; Kanarek, Katarzyna; Krupitsky, Evgeny; Walderhaug, Espen; Ilomäki, Risto; Blumberg, Hilary; Price, Lawrence H; Bhagwagar, Zubin; Carpenter, Linda L; Tyrka, Audrey R; Magnusson, Andres; Landrø, Nils Inge; Zvartau, Edwin; Gelernter, Joel; Epperson, C Neill; Räsänen, Pirkko; Siironen, Jari; Lappalainen, Jaakko



A Sequencing-Based Survey of Functional APAF1 Alleles in a Large Sample of Individuals with Affective Illness and Population Controls  

PubMed Central

Rare apoptosis-promoting functional variants in the apoptosis protease activating factor 1 (APAF1) gene were recently reported to co-segregate with major depression in male members of families from Utah. In order to estimate the impact of these variants on risk for major depressive disorder (MDD) in the general population, we surveyed the frequency of the APAF1 putative MDD risk alleles using re-sequencing in a large sample of northern European and European-American subjects, including a large number of males with MDD. The E777K and N782T APAF1 variants previously described by Harlan et al. [Harlan et al. (2006) Mol Psychiatry 11(1):76–85] were found at low frequencies in affected individuals and population controls. The C450W and Q465R variants were not detected in any of the 632 subjects sequenced. These results show that the APAF1 variants associated with risk for MDD in the Utah pedigrees are very rare in Northern European and European-American populations. In addition, the E777K and N782T variants were found at low frequencies both in patients and population controls, suggesting that these variants have limited impact on risk for MDD. PMID:19455599

Amin, Zenab; Kanarek, Katarzyna; Krupitsky, Evgeny; Walderhaug, Espen; Ilomaki, Risto; Blumberg, Hilary; Price, Lawrence H.; Bhagwagar, Zubin; Carpenter, Linda L.; Tyrka, Audrey R.; Magnusson, Andres; Landr?, Nils Inge; Zvartau, Edwin; Gelernter, Joel; Epperson, C. Neill; Rasanen, Pirkko; Siironen, Jari; Lappalainen, Jaakko



European Universe Awareness  

NASA Astrophysics Data System (ADS)

The European Universe Awareness (EU-UNAWE) programme uses the beauty and grandeur of the cosmos to encourage young children, particularly those from underprivileged backgrounds, to develop an interest in science and technology and to foster a sense of global citizenship. EU-UNAWE is already active in 40 countries and comprises a global network of almost 500 astronomers, teachers and other educators. The programme was recently awarded a grant of 1.9 million euros by the European Union so that it can be further developed in five European countries and South Africa. The grant will be used to organise teacher training workshops and to develop educational materials, such as an astronomy news service for children and games. During this presentation we will outline some of the biggest achievements of EU-UNAWE to date and discuss future plans for the programme.

Russo, P.; Miley, G.; Westra van Holthe, F.; Schrier, W.; Reed, S.



Identification of Allelic Heterogeneity at Type-2 Diabetes Loci and Impact on Prediction  

PubMed Central

Although over 60 single nucleotide polymorphisms (SNPs) have been identified by meta-analysis of genome-wide association studies for type-2 diabetes (T2D) among individuals of European descent, much of the genetic variation remains unexplained. There are likely many more SNPs that contribute to variation in T2D risk, some of which may lie in the regions surrounding established SNPs - a phenomenon often referred to as allelic heterogeneity. Here, we use the summary statistics from the DIAGRAM consortium meta-analysis of T2D genome-wide association studies along with linkage disequilibrium patterns inferred from a large reference sample to identify novel SNPs associated with T2D surrounding each of the previously established risk loci. We then examine the extent to which the use of these additional SNPs improves prediction of T2D risk in an independent validation dataset. Our results suggest that multiple SNPs at each of 3 loci contribute to T2D susceptibility (TCF7L2, CDKN2A/B, and KCNQ1; p<5×10?8). Using a less stringent threshold (p<5×10?4), we identify 34 additional loci with multiple associated SNPs. The addition of these SNPs slightly improves T2D prediction compared to the use of only the respective lead SNPs, when assessed using an independent validation cohort. Our findings suggest that some currently established T2D risk loci likely harbor multiple polymorphisms which contribute independently and collectively to T2D risk. This opens a promising avenue for improving prediction of T2D, and for a better understanding of the genetic architecture of T2D. PMID:25393876

Klimentidis, Yann C.; Zhou, Jin; Wineinger, Nathan E.



A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation  

PubMed Central

We conducted a multi-stage genome-wide association study of natural hair color in more than 10,000 men and women of European ancestry from the United States and Australia. An initial analysis of 528,173 single nucleotide polymorphisms (SNPs) genotyped on 2,287 women identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. We confirmed these associations in 7,028 individuals from three additional studies. Across these four studies, SLC24A4 rs12896399 and IRF4 rs12203592 showed strong associations with hair color, with p?=?6.0×10?62 and p?=?7.46×10?127, respectively. The IRF4 SNP was also associated with skin color (p?=?6.2×10?14), eye color (p?=?6.1×10?13), and skin tanning response to sunlight (p?=?3.9×10?89). A multivariable analysis pooling data from the initial GWAS and an additional 1,440 individuals suggested that the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. After adjustment for rs12203592, the association between rs1540771 and hair color was not significant (p?=?0.52). One variant in the MATP gene was associated with hair color. A variant in the HERC2 gene upstream of the OCA2 gene showed the strongest and independent association with hair color compared with other SNPs in this region, including three previously reported SNPs. The signals detected in a region around the MC1R gene were explained by MC1R red hair color alleles. Our results suggest that the IRF4 and SLC24A4 loci are associated with human hair color and skin pigmentation. PMID:18483556

Han, Jiali; Kraft, Peter; Nan, Hongmei; Guo, Qun; Chen, Constance; Qureshi, Abrar; Hankinson, Susan E.; Hu, Frank B.; Duffy, David L.; Zhao, Zhen Zhen; Martin, Nicholas G.; Montgomery, Grant W.; Hayward, Nicholas K.; Thomas, Gilles; Hoover, Robert N.; Chanock, Stephen; Hunter, David J.



Haplotype Variation of Glu-D1 Locus and the Origin of Glu-D1d Allele Conferring Superior End-Use Qualities in Common Wheat  

PubMed Central

In higher plants, seed storage proteins (SSPs) are frequently expressed from complex gene families, and allelic variation of SSP genes often affects the quality traits of crops. In common wheat, the Glu-D1 locus, encoding 1Dx and 1Dy SSPs, has multiple alleles. The Glu-D1d allele frequently confers superior end-use qualities to commercial wheat varieties. Here, we studied the haplotype structure of Glu-D1 genomic region and the origin of Glu-D1d. Using seven diagnostic DNA markers, 12 Glu-D1 haplotypes were detected among common wheat, European spelt wheat (T. spelta, a primitive hexaploid relative of common wheat), and Aegilops tauschii (the D genome donor of hexaploid wheat). By comparatively analyzing Glu-D1 haplotypes and their associated 1Dx and 1Dy genes, we deduce that the haplotype carrying Glu-D1d was likely differentiated in the ancestral hexaploid wheat around 10,000 years ago, and was subsequently transmitted to domesticated common wheat and T. spelta. A group of relatively ancient Glu-D1 haplotypes was discovered in Ae. tauschii, which may serve for the evolution of other haplotypes. Moreover, a number of new Glu-D1d variants were found in T. spelta. The main steps in Glu-D1d differentiation are proposed. The implications of our work for enhancing the utility of Glu-D1d in wheat quality improvement and studying the SSP alleles in other crop species are discussed. PMID:24098671

Li, Yiwen; Zhang, Kunpu; Lou, Haijuan; An, Xueli; Dong, Lingli; Gu, Yong Qiang; Anderson, Olin D.; Liu, Xin; Qin, Huanju; Wang, Daowen



European Regional Science Association 51s t European Congress  

E-print Network

European Regional Science Association ­ 51s t European Congress Barcelona, Spain, 30t h August ­ 3r.253.7694, Abstract Investments decisions for airport capacity expansion are usually taken, either Association ­ 51s t European Congress Barcelona, Spain, 30t h August ­ 3r d September 2011 2 Introduction


Research Design in European Studies: The Case of Europeanization &ast  

Microsoft Academic Search

AbstractIn this article, we contribute to the debate on research design and causal analysis in European integration studies by considering the sub-field of Europeanization. First, we examine the awareness of research design issues in the literature on Europeanization through a review of the debate on causality, concept formation and methods. Second, we analyse how much of the discussion of the




Novel single nucleotide polymorphism associations with colorectal cancer on chromosome 8q24 in African and European Americans.  


Regions on chromosome 8q24 harbor susceptibility alleles for multiple cancers including colorectal (region 3) and prostate cancer (regions 1-4). The objectives of the present study were (i) to test whether single-nucleotide polymorphisms (SNPs) in region 4 are associated with colorectal cancer (CRC) in European or African Americans; (ii) to test whether 8q24 SNPs previously shown to be associated with colorectal and prostate cancer also show association in our multiethnic series and (iii) to test for association between 100 ancestry informative markers (AIMs) and CRC in both the African American and European American cohorts. In total, we genotyped nine markers on 8q24 and 100 unlinked AIMs in 569 CRC cases and 439 controls (490 European Americans and 518 African Americans) obtained retrospectively from a hospital-based sample. We found rs7008482 in 8q24 region 4 to be significantly associated with CRC in European Americans (P = 0.03). Also in region 4, we found that a second SNP, rs16900305, trended toward association with CRC in African Americans. The rs6983267 in region 3, previously implicated in CRC risk, trended toward association with disease in European Americans but not in African Americans. Finally, none of the 100 AIMs tested for association reached statistical significance after correction for multiple hypothesis testing. In summary, these results are evidence that 8q24 region 4 contains novel CRC-associated alleles in European and African Americans. PMID:19520795

Kupfer, Sonia S; Torres, Jada Benn; Hooker, Stanley; Anderson, Jeffrey R; Skol, Andrew D; Ellis, Nathan A; Kittles, Rick A



Novel single nucleotide polymorphism associations with colorectal cancer on chromosome 8q24 in African and European Americans  

PubMed Central

Regions on chromosome 8q24 harbor susceptibility alleles for multiple cancers including colorectal (region 3) and prostate cancer (regions 1–4). The objectives of the present study were (i) to test whether single-nucleotide polymorphisms (SNPs) in region 4 are associated with colorectal cancer (CRC) in European or African Americans; (ii) to test whether 8q24 SNPs previously shown to be associated with colorectal and prostate cancer also show association in our multiethnic series and (iii) to test for association between 100 ancestry informative markers (AIMs) and CRC in both the African American and European American cohorts. In total, we genotyped nine markers on 8q24 and 100 unlinked AIMs in 569 CRC cases and 439 controls (490 European Americans and 518 African Americans) obtained retrospectively from a hospital-based sample. We found rs7008482 in 8q24 region 4 to be significantly associated with CRC in European Americans (P = 0.03). Also in region 4, we found that a second SNP, rs16900305, trended toward association with CRC in African Americans. The rs6983267 in region 3, previously implicated in CRC risk, trended toward association with disease in European Americans but not in African Americans. Finally, none of the 100 AIMs tested for association reached statistical significance after correction for multiple hypothesis testing. In summary, these results are evidence that 8q24 region 4 contains novel CRC-associated alleles in European and African Americans. PMID:19520795

Kupfer, Sonia S.; Torres, Jada Benn; Hooker, Stanley; Anderson, Jeffrey R.; Skol, Andrew D.; Ellis, Nathan A.; Kittles, Rick A.



Presence of allele alphaLELY in an Amazonian Indian population.  


Allele alphaLELY is a low-expression allele of the erythroid spectrin alpha-chain that is characterized by a C --> G mutation at position alpha1857 in exon 40 and a C --> T (nt -12) mutation in intron 45. This second mutation is probably responsible for the partial skipping of exon 46. This exon is essential for the nucleation of the alpha-chains by the beta-chains during erythropoeisis. Although allele alphaLELY remains asymptomatic in both heterozygotes and homozygotes, it enhances the expression of deleterious alpha-alleles that occur and, as such, has clinical importance. In this study, the frequency of allele alphaLELY was estimated in two ethnically different Brazilian populations: a random sample of blood donors from Campinas, a city located in São Paulo State, in the southeastern region of Brazil, and a sample of Parakanã Indians (Tupi tribe), a very isolated population with a high degree of inbreeding. The frequency of allele alphaLELY in the blood donor's sample (n = 54) was 24.1% whereas in the indigenous sample (n = 41), it was 15.9%. These frequencies were not significantly different at the 5% level (chi2 = 1.931). Similarly, when the frequencies of our samples were compared with those of the four ethnic groups studied by Maréchal et al. [Br J Haematol 90:553-556, 1995], no significant differences were found at the 5% level (chi2 = 6.686). These results suggest that allele alphaLELY is a very ancient allele since it occurs with a relatively uniform and high frequency in all human ethnic groups studied so far. These findings confirm the importance of allele alphaLELY in influencing the expression of deleterious alpha-spectrin alleles. To our knowledge, these are the first data concerning allele alphaLELY in native Americans. PMID:9495371

Bassères, D S; Salles, T S; Costa, F F; Saad, S T



Apolipoprotein E alleles in Alzheimer`s and Parkinson`s patients  

SciTech Connect

A number of investigators have found an association between the apolipoprotein E4 allele and Alzheimer`s disease. The E4 allele appears at a higher frequency in late onset familial Alzheimer`s patients. In our studies we obtained blood samples from early and late onset familial and sporadic Alzheimer`s patients and spouses, as well as from Parkinson`s patients. The patients were diagnosed as probable Alzheimer`s patients after a neurological examination, extensive blood work, and a CAT scan. The diagnosis was made according to the NINCDS-ADRDA criteria. The apolipoprotein E4 polymorphism was detected after PCR amplification of genomic DNA, restriction enzyme digestion with Hhal, and polyacrylamide gel electrophoresis. Ethidium bromide-stained bands at 91 bp were designated as allele 3, at 83 bp as allele 2, and at 72 bp as allele 4. Of the 84 probable Alzheimer`s patients (all of whom were Caucasian), 47 were heterozygous and 13 were homozygous for the E4 allele. There were 26 early onset patients; 13 were heterozygous and 7 homozygous for the E4 allele. The frequencies for the E4 allele for late onset familial patients was 0.45 and for sporadic patients was 0.37. We analyzed 77 spouses with an average age of 71.9 {plus_minus} 7.4 years as controls, and 15 were heterozygous for the E4 allele for an E4 frequency of 0.097. Of the 53 Parkinson`s patients, 11 had the E4 allele for a frequency of 0.113. Thus our findings support the association of the ApoE4 allele with Alzheimer`s disease.

Poduslo, S.E. [Texas Tech Univ., Lubbock, TX (United States); Schwankhaus, J.D. [Department of Veterans Affairs, Lubbock, TX (United States)



Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project  

PubMed Central

Background There is a lack of knowledge regarding the frequency of disease associated polymorphisms in populations and population attributable risk for many populations remains unknown. Factors that could affect the association of the allele with disease, either positively or negatively, such as race, ethnicity, and gender, may not be possible to determine without population based allele frequencies. Here we used a panel of 51 polymorphisms previously associated with at least one disease and determined the allele frequencies within the entire Personalized Medicine Research Project population based cohort. We compared these allele frequencies to those in dbSNP and other data sources stratified by race. Differences in allele frequencies between self reported race, region of origin, and sex were determined. Results There were 19544 individuals who self reported a single racial category, 19027 or (97.4%) self reported white Caucasian, and 11205 (57.3%) individuals were female. Of the 11,208 (57%) individuals with an identifiable region of origin 8337 or (74.4%) were German. 41 polymorphisms were significantly different between self reported race at the 0.05 level. Stratification of our Caucasian population by self reported region of origin revealed 19 polymorphisms that were significantly different (p = 0.05) between individuals of different origins. Further stratification of the population by gender revealed few significant differences in allele frequencies between the genders. Conclusions This represents one of the largest population based allele frequency studies to date. Stratification by self reported race and region of origin revealed wide differences in allele frequencies not only by race but also by region of origin within a single racial group. We report allele frequencies for our Asian/Hmong and American Indian populations; these two minority groups are not typically selected for population allele frequency detection. Population wide allele frequencies are important for the design and implementation of studies and for determining the relevance of a disease associated polymorphism for a given population. PMID:20565774



European Southern Observatory  

E-print Network

Observatory Multi-Conjugate AO concept 1-2' FoV, Near IR, medium Strehl ratio AO using NGSs 6 Visible Shack Deformable Mirror at M6 Computing power: 2000 x NAOS Or 10 x VLT AO Facility On-axis, NIR, medium Strehl ratio AO using NGSs #12;5 European Southern Observatory SCAO Wavefront sensor pick-up arm Patrolling

Liske, Jochen


European tax law  

Microsoft Academic Search

This book is intended as a textbook for students reading tax law or EC law. It offers a systematic survey of the tax implications of the EC Treaty and of European integration and of the EC tax harmonization policy, a discussion of the Community tax rules in force, and a discussion of the EC Court's case law in tax matters.

B. J. M. Terra; P. J. Wattel



European Polistes venom allergy.  


The American Polistes species venom mixture--that of P. annularis, P. fuscatus, P. metricus and P. exclamans--was the only commercially available mixture for diagnosis and therapy until 1996. However, these species of Polistes are not present in Europe, where P. dominulus and P. gallicus and to a lesser extent P. nimphus are widespread. The aim of this study was to assess the allergenic differences among the commercial American mix, P. dominulus and P. gallicus venom in European patients and therefore to verify if this mixture is suitable for diagnosis in these patients. We carried out skin tests, radioallergosorbent tests (RAST) and RAST inhibition in Italian patients with adverse reactions to Polistes stings. RAST inhibition results demonstrated that cross-reactivity between the American and European species is only partial and that P. dominulus and P. gallicus venoms have exclusive allergens. Skin tests and direct RAST confirmed these results and also showed that European Polistes venom is more suitable than the American mix in Italian patients. Moreover, we found a high rate of cross-reactivity between P. dominulus and P. gallicus. To conclude, P. dominulus and/or P. gallicus venoms are necessary for diagnosis and therefore in the therapy of European patients. PMID:16792585

Severino, M G; Campi, P; Macchia, D; Manfredi, M; Turillazzi, S; Spadolini, I; Bilò, M B; Bonifazi, F



Trends in European English.  

ERIC Educational Resources Information Center

It is proposed that a European variety of English without native speakers is emerging as a language of international communication in Europe. This is a consequence of many factors, including the strength of the American economy, the breadth and depth of American research in science and technology, the pervasive influence of American-style popular…

Wilkinson, Robert


European Space Agency (ESA)  

NSDL National Science Digital Library

The European Space Agency's homepage provides information on the ESA's telecommunications, navigations, Earth observations, human spaceflight missions, launches, space science, technology, industry, space operations, technical and quality management and television broadcasting. The site also contains a multimedia gallery, press releases, and an educational page for kids.



European Commission Agriculture and  

E-print Network

European Commission Agriculture and Rural Development Good practice guidance on the sustainable Commission (EC) DG Agriculture and Rural Development 130, Rue de la Loi B ­ 1049 Brussels, Belgium Phone: +32 (0) 2-2969909 Fax: +32 (0) 2-29211 33 E-mail: Web:


Multilingualism in European Workplaces  

ERIC Educational Resources Information Center

This state-of-the-art article includes a review of past and recent studies on multilingualism at work in European environments. One aim is to provide the reader with a cross-cultural picture of workplace studies on various languages in Europe, another to discuss both positive and problem-based accounts of multilingualism at work. The overview…

Gunnarsson, Britt-Louise



European Telecommunications Environmental Charter  

Microsoft Academic Search

The European Telecommunications Environmental Charter is a common environmental policy of the signatories who commit themselves to improve their environmental performance. To achieve this, an ETNO working group Environment has been established. Based on common requests, this group works out joint activities, e.g. common environmental indicators: environmental benchmarking; common ecological requests for products: guideline for environmentally responsible procurement; common environmental

A. Kuhn




E-print Network

and the Neumarkt--the German small cap attempt at venture capital. And big companies, too, are in the game. EuropeSept. 1999 EUROPEAN RESTRUCTURING Rudi Dornbusch Massachusetts Institute of Technology Europe recognizing the dramatic importance of modern information technology and are finding their way to the Internet

Bilbao Arrese, Jesús Mario


European inflation dynamics  

Microsoft Academic Search

We provide evidence on the fit of the New Phillips Curve (NPC) for the Euro area over the period 1970–1998, and use it as a tool to compare the characteristics of European inflation dynamics with those observed in the U.S. We also analyze the factors underlying inflation inertia by examining the cyclical behavior of marginal costs, as well as that

Jordi Gal??; Mark Gertler; J. David López-Salido




E-print Network

: Larger longitudinal studies supported by the Wellcome Trust in the UK and in developing countries 46 #12EUROPEAN COMMISSION FROM BIOBANKS TO BIOMARKERS Translating the potential of human population genetics research to improve the quality of health of the EU citizen #12;FROM BIOBANKS TO BIOMARKERS

Rambaut, Andrew


European Southern Observatory  

E-print Network

performance Maximum deflection under gravity load 150 mm Maximum deflection under operational wind load 200 mm Maximum deflection under OBE 300 mm Maximum deflection under survival wind load 450 mm Maximum deflection. Required power to move against maximum operational wind (27 m/s or 100 km/h) is 5.3 MW. #12;8 European

Liske, Jochen


Russian and East European Studies  

E-print Network

complementary for Russian, political science, economics, history, geography, journalism, global studiesRussian and East European Studies Certificate About Us The Russian and East European Studies (REES a Russian and East European Certificate would be valu- able include print and broadcast journalism, civil

Saldin, Dilano


The European Mobile System (EMS)  

NASA Technical Reports Server (NTRS)

The European Space Agency is presently procuring an L band payload in order to promote a regional European L band system coping with the specific needs of the European market. The payload, and the two communications systems to be supported, are described below. The potential market for EMS in Europe is discussed.

Jongejans, A.; Rogard, R.; Mistretta, I.; Ananasso, F.



European Active Citizenship Introductory Guidelines for Practitioners  

E-print Network

Grundtvig G2 Learning Partnership EUROPEAN PUZZLE European Active Citizenship: Introductory Guidelines for Adult Educators 1 #12;European Active Citizenship Introductory Section B: Theory The European Union 8 Debates on Citizenship 10


Allelic expression of deleterious protein-coding variants across human tissues.  


Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. However, for each allele, accurate interpretation of its effect will depend on both its penetrance and the trait's expressivity. In this regard, an important factor that can modify the effect of a pathogenic coding allele is its level of expression; a factor which itself characteristically changes across tissues. To better inform the degree to which pathogenic alleles can be modified by expression level across multiple tissues, we have conducted exome, RNA and deep, targeted allele-specific expression (ASE) sequencing in ten tissues obtained from a single individual. By combining such data, we report the impact of rare and common loss-of-function variants on allelic expression exposing stronger allelic bias for rare stop-gain variants and informing the extent to which rare deleterious coding alleles are consistently expressed across tissues. This study demonstrates the potential importance of transcriptome data to the interpretation of pathogenic protein-coding variants. PMID:24786518

Kukurba, Kimberly R; Zhang, Rui; Li, Xin; Smith, Kevin S; Knowles, David A; How Tan, Meng; Piskol, Robert; Lek, Monkol; Snyder, Michael; Macarthur, Daniel G; Li, Jin Billy; Montgomery, Stephen B



Biased Tests of Association: Comparisons of Allele Frequencies when Departing from Hardy-Weinberg Proportions  

Microsoft Academic Search

Association studies of genetic markers or candidate genes with disease are often conducted using the traditional case-control design. Cases and controls are sampled from genetically unrelated subjects, and allele frequencies compared between cases and controls using Pearson's chi-square statistic. An assumption of this analysis method is that the two alleles within each subject are statistically independent, at least when no

Daniel J. Schaid; Steven J. Jacobsen


Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci  

Microsoft Academic Search

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for

B. Budowle; K. L. Monson; R. Chakraborty



Testing for association based on excess allele sharing in a sample of related cases and controls.  


Samples consisting of a mix of unrelated cases and controls, small pedigrees, and much larger pedigrees present a unique challenge for association studies. Few methods are available for efficient analysis of such a broad spectrum of data structures. In this paper we introduce a new matching statistic that is well suited to complex data structures and compare it with frequency-based methods available in the literature. To investigate and compare the power of these methods we simulate datasets based on complex pedigrees. We examine the influence of various levels of linkage disequilibrium (LD) of the disease allele with a marker allele (or equivalently a haplotype). For low frequency marker alleles/haplotypes, frequency-based statistics are more powerful in detecting association. In contrast, for high frequency marker alleles, the matching statistic has greater power. The highest power for frequency-based statistics occurs when the disease allele frequency closely matches the frequency of the linked marker allele. In contrast maximum power of the matching statistic always occurs for intermediate marker allele frequency regardless of the disease allele frequency. Moreover, the matching and frequency-based statistics exhibit little correlation. We conclude that these two approaches can be viewed as complementary in finding possible association between a disease and a marker for many different situations. PMID:17342507

Klei, Lambertus; Roeder, Kathyrn



Object-Oriented Bayesian Networks for Paternity Cases with Allelic Dependencies  

E-print Network

examples: the most common scenario where DNA evidence is available from the alleged father, the mother incorporate the effects of allelic dependence caused by evolutionary relatedness. Key words: DNA Evidence evaluating DNA evidence. 1.1 Allelic Dependencies and Paternity Calculations A body of evidence can

Guillas, Serge


Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays  

Microsoft Academic Search

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use

Rui Mei; Patricia C. Galipeau; Cynthia Prass; Anthony Berno; Ghassan Ghandour; Nila Patil; Roger K. Wolff; Mark S. Chee; Brian J. Reid; David J. Lockhart



Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools  

Microsoft Academic Search

Detecting alleles that confer small increments in susceptibility to disease will require large-scale allelic association studies of single-nucleotide polymorphisms (SNPs) in candidate, or positional candidate, genes. However, current genotyping technologies are one to two orders of magnitude too expensive to permit the analysis of thousands of SNPs in large samples. We have developed and thoroughly validated a highly accurate protocol

Nadine Norton; Nigel M. Williams; Hywel J. Williams; Gillian Spurlock; George Kirov; Derek W. Morris; Bastiaan Hoogendoorn; Michael J. Owen; Michael C. O'Donovan



Allelic Loss on Chromosome 8pl2-21 in Microdissected Prostatic Intraepithelial Neoplasia  

Microsoft Academic Search

The development and progression of human prostate cancer is associ ated with genetic abnormalities in tumor cells. Inactivation of tumor suppressor genes due to allelic loss is thought to be an important mech anism of gene alteration in prostatic neoplasms. In this study we examined allelic loss on chromosome Sp 12-21 in microdissected samples of normal prostatic epithelium, high grade

Michael R. Emmert-Buck; Cathy D. Vocke; Rudy O. Pozzatti; Paul H. Duray; Scott B. Jennings; Charles D. Florence; David G. Bostwick; Lance A. Liotta; W. Marston Linchan




E-print Network

PREDICTION OF PEPTIDES BINDING TO MHC CLASS I ALLELES BY PARTIAL PERIODIC PATTERN MINING Cem Meydan peptides will bind to a spe- cific MHC allele and which will not, creating possibilities for controlling in the computational binding prediction methods for MHC class I is the presence of bulges and loops in the peptides

Yanikoglu, Berrin


Autosomal microsatellite allele frequencies for a nationwide dataset from the Australian Caucasian sub-population  

Microsoft Academic Search

DNA profiling results presented in court must be accompanied by a statistical estimate of its evidential weight. In calculating such statistics, allele frequencies from the tested loci are required. This paper reports allele frequencies and the results of population genetic testing of datasets of autosomal microsatellite profiles from Australian Caucasian donors. In contrast to previous practice in Australia these data

Simon J. Walsh; John S. Buckleton



Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues  

PubMed Central

Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. However, for each allele, accurate interpretation of its effect will depend on both its penetrance and the trait's expressivity. In this regard, an important factor that can modify the effect of a pathogenic coding allele is its level of expression; a factor which itself characteristically changes across tissues. To better inform the degree to which pathogenic alleles can be modified by expression level across multiple tissues, we have conducted exome, RNA and deep, targeted allele-specific expression (ASE) sequencing in ten tissues obtained from a single individual. By combining such data, we report the impact of rare and common loss-of-function variants on allelic expression exposing stronger allelic bias for rare stop-gain variants and informing the extent to which rare deleterious coding alleles are consistently expressed across tissues. This study demonstrates the potential importance of transcriptome data to the interpretation of pathogenic protein-coding variants. PMID:24786518

Kukurba, Kimberly R.; Zhang, Rui; Li, Xin; Smith, Kevin S.; Knowles, David A.; How Tan, Meng; Piskol, Robert; Lek, Monkol; Snyder, Michael; MacArthur, Daniel G.; Li, Jin Billy; Montgomery, Stephen B.



RESEARCH ARTICLE Open Access Sequence analysis of two alleles reveals that  

E-print Network

recombination played a role in the evolution of the radish fertility restorer (Rfo) José R Hernandez Mora1 sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence

Boyer, Edmond


Gene and Allelic Genealogies at a Gametophytic Self-Incompatibility Locus  

Microsoft Academic Search

The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is found that, as with overdominant loci, there are two genealogical processes with markedly different time scales. First, func- tionally distinct allelic lines diverge on an extremely long time scale which is inversely related to

Xavier Vekemans; Montgomery Slatkin



Comparing Computational Methods for Identification of Allele-Specific Expression based on Next Generation Sequencing Data.  


Allele-specific expression (ASE) studies have wide-ranging implications for genome biology and medicine. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying ASE, but suffers from mapping bias favoring reference alleles. Two categories of methods are adopted nowadays, to reduce the effect of mapping bias on ASE identification-normalizing RNA allelic ratio with the parallel genomic allelic ratio (pDNAar) and modifying reference genome to make reads carrying both alleles with the same chance to be mapped (mREF). We compared the sensitivity and specificity of both methods with simulated data, and demonstrated that the pDNAar, though ideally practical, was lower in sensitivity, because of its lower mapping rate of reads carrying nonreference (alternative) alleles, although mREF achieved higher sensitivity and specificity for its efficiency in mapping reads carrying both alleles. Application of these two methods in real sequencing data showed that mREF were able to identify more ASE loci because of its higher mapping efficiency, and able to correcting some seemly incorrect ASE loci identified by pDNAar due to the inefficiency in mapping reads carrying alternative alleles of pDNAar. Our study provides useful information for RNA sequencing data processing in the identification of ASE. PMID:25183311

Liu, Zhi; Yang, Jing; Xu, Huayong; Li, Chao; Wang, Zhen; Li, Yuanyuan; Dong, Xiao; Li, Yixue



Surrogate Genetics and Metabolic Profiling for Characterization of Human Disease Alleles  

PubMed Central

Cystathionine-?-synthase (CBS) deficiency is a human genetic disease causing homocystinuria, thrombosis, mental retardation, and a suite of other devastating manifestations. Early detection coupled with dietary modification greatly reduces pathology, but the response to treatment differs with the allele of CBS. A better understanding of the relationship between allelic variants and protein function will improve both diagnosis and treatment. To this end, we tested the function of 84 CBS alleles previously sequenced from patients with homocystinuria by ortholog replacement in Saccharomyces cerevisiae. Within this clinically associated set, 15% of variant alleles were indistinguishable from the predominant CBS allele in function, suggesting enzymatic activity was retained. An additional 37% of the alleles were partially functional or could be rescued by cofactor supplementation in the growth medium. This large class included alleles rescued by elevated levels of the cofactor vitamin B6, but also alleles rescued by elevated heme, a second CBS cofactor. Measurement of the metabolite levels in CBS-substituted yeast grown with different B6 levels using LC–MS revealed changes in metabolism that propagated beyond the substrate and product of CBS. Production of the critical antioxidant glutathione through the CBS pathway was greatly decreased when CBS function was restricted through genetic, cofactor, or substrate restriction, a metabolic consequence with implications for treatment. PMID:22267502

Mayfield, Jacob A.; Davies, Meara W.; Dimster-Denk, Dago; Pleskac, Nick; McCarthy, Sean; Boydston, Elizabeth A.; Fink, Logan; Lin, Xin Xin; Narain, Ankur S.; Meighan, Michael; Rine, Jasper




E-print Network

THE EFFECT OF COMBINING ALLELES INTO ELECTROPHORETIC CLASSES ON DETECTING LINKAGE DISEQUILIBRIUM E ABSTRACT When alleles are combined into few detectable classes, linkage correlations are underestimated most of the time. The probability that the linkage correla- tion will be underestimated is a function

Mackay, Trudy F.C.


Global distribution of allele frequencies at the human dopamine D4 receptor locus  

SciTech Connect

The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

Chang, F.M.; Kidd, J.R. [Yale Univ. School of Medicine, New Haven, CT (United States); Livak, K.J. [DuPont-Merch Pharmaceutical Company, Wilmington, DE (United States)] [and others



Evolutionary fate of an unstable human minisatellite deduced from sperm-mutation spectra of individual alleles.  


Although mutation processes at some human minisatellites have been extensively characterized, the evolutionary fate of these unstable loci is unknown. Minisatellite instability is largely germline specific, with mutation rates up to several percent and with expansion events predominating over contractions. Using allele-specific small-pool polymerase chain reaction, we have determined sperm-mutation spectra of individual alleles of the highly unstable human minisatellite CEB1 (i.e., D2S90). We show that, as allele size increases, the proportion of contractions rises from <5% to 50%, with the average size of deletion increasing and eventually exceeding the average size of expansion. The expected net effect of these trends after many generations is an equilibrium distribution of allele sizes, and allele-frequency data suggest that this equilibrium state has been reached in some contemporary human populations. PMID:11859482

Buard, Jérôme; Brenner, Charles; Jeffreys, Alec J



Identification of a novel human leukocyte antigen allele B?46:34.  


A new human leukocyte antigen (HLA) B allele was found in a healthy male Chinese Kazak individual. Sequencing-based typing (SBT) was used to identify and analyze the difference between the new allele and the closest matching HLA-B allele. HLA-B(?)46 new allele has 1nt change from B(?)46:01:01 at nt 853 where G->C (condon 260 GTA->CTA), resulting in a coding change: 260 Val is changed to Leu. The new HLA-B(?)46:34 allele was identified, and was named officially by the World Health Organization (WHO) Nomenclature Committee in June 2012. The GenBank sequence accession number is JX035785. PMID:23137878

Shen, Chun-mei; Wang, Hong-dan; Deng, Ya-jun; Wang, Shi-ying; Zhang, Li-ping; Zhang, Bo; Pu, Hong-wei; Wu, Qiang-ju; Liu, Wen-juan; Zhu, Bo-feng



Identification of 32 major histocompatibility complex class I alleles in African green monkeys.  


The African green monkey may be an ideal replacement for the rhesus monkey in biomedical research, but relatively little is known about the genetic background of major histocompatibility complex (MHC) class I molecules. In analysis of 12 African green monkeys, 13 Chae-A and 19 Chae-B alleles were identified. Among these alleles, 12 Chae-A and 9 Chae-B were new lineages. The full amino acid length deduced for Chae-A genes is 365 amino acids, but for Chae-B genes, the lengths are 365, 362, 361, and 359 amino acids, respectively. There were 1-3 Chae-A alleles and 2-5 Chae-B alleles in each animal. In African green monkeys, rhesus monkeys, and cynomolgus monkeys, the MHC-A and MHC-B alleles display trans-species polymorphism, rather than being clustered in a species-specific fashion. PMID:24899078

Cao, Y; Li, A; Li, L; Yan, X; Fa, Y; Zeng, L; Fan, J; Liu, B; Sun, Z



Chromosome-Wide Analysis of Parental Allele-Specific Chromatin and DNA Methylation ? §  

PubMed Central

To reveal the extent of domain-wide epigenetic features at imprinted gene clusters, we performed a high-resolution allele-specific chromatin analysis of over 100 megabases along the maternally or paternally duplicated distal chromosome 7 (Chr7) and Chr15 in mouse embryo fibroblasts (MEFs). We found that reciprocal allele-specific features are limited to imprinted genes and their differentially methylated regions (DMRs), whereas broad local enrichment of H3K27me3 (BLOC) is a domain-wide feature at imprinted clusters. We uncovered novel allele-specific features of BLOCs. A maternally biased BLOC was found along the H19-Igf2 domain. A paternal allele-specific gap was found along Kcnq1ot1, interrupting a biallelic BLOC in the Kcnq1-Cdkn1c domain. We report novel allele-specific chromatin marks at the Peg13 and Slc38a4 DMRs, Cdkn1c upstream region, and Inpp5f_v2 DMR and paternal allele-specific CTCF binding at the Peg13 DMR. Additionally, we derived an imprinted gene predictor algorithm based on our allele-specific chromatin mapping data. The binary predictor H3K9ac and CTCF or H3K4me3 in one allele and H3K9me3 in the reciprocal allele, using a sliding-window approach, recognized with precision the parental allele specificity of known imprinted genes, H19, Igf2, Igf2as, Cdkn1c, Kcnq1ot1, and Inpp5f_v2 on Chr7 and Peg13 and Slc38a4 on Chr15. Chromatin features, therefore, can unequivocally identify genes with imprinted expression. PMID:21321082

Singh, Purnima; Wu, Xiwei; Lee, Dong-Hoon; Li, Arthur X.; Rauch, Tibor A.; Pfeifer, Gerd P.; Mann, Jeffrey R.; Szabo, Piroska E.



Unexpected Bw4 and Bw6 reactivity patterns in new alleles.  


The Bw4 and Bw6 epitopes were the first HLA-B differences to be recognized by serological methods. Since then 44 serological groups have been identified and more than 250 alleles assigned by molecular typing methods. In general each serological HLA-B group is associated with the presence of either the Bw4 or the Bw6 epitope. There are several exceptions to this rule. Four alleles, B*4601, *7301, *5503 and *1806, show no serological reactivity with either Bw4 or Bw6. Although the Bw6 motif at residues 77-83 is present in these alleles the Bw6 epitope is modified by a valine at residue 76. One or more alleles from the B8, B40 and B62 groups are identified as Bw4 positive, whereas all others are Bw6 positive. In the groups B27, B44 and B47 several alleles are found to be Bw6 positive, while the majority is Bw4 positive. Histocompatibility testing of dialysis patients and their families revealed the serological presence of an unexpected Bw4 epitope associated with B18 in one patient and B56 in another. Allele-specific amplification and sequencing of exons 2 and 3 of these HLA-B alleles revealed the presence of the Bw4 sequence motif for both. The new alleles were assigned B*1809 and B*5607, respectively. In 2 other patients the presence of a new B*07 allele was determined by sequence based typing. Although the new allele, B*0715, showed the Bw6 sequence motif at positions 77 to 83, a substitution of amino acid 76 from glutamic acid to valine was identified. This change resulted in an aberrant Bw6 serological reaction pattern. PMID:11098937

Voorter, C E; van der Vlies, S; Kik, M; van den Berg-Loonen, E M



Allelic Prevalence of ABO Blood Group Genes in Iranian Azari Population  

PubMed Central

Introduction ABO blood group system is the most important blood group in transfusion and has been widely used in population studies. Several molecular techniques for ABO allele’s detection are widely used for distinguishing various alleles of glycosyl transferase locus on chromosome 9. Methods 744 randomly selected samples from Azari donors of East Azerbaijan province (Iran) were examined using well-adjusted multiplex allele- specific PCR ABO genotyping technique. Results The results were consistent for all individuals. The ABO blood group genotype of 744 healthy Azari blood donors was: 25.8% AA/AO (2), 7.6% AO (1), 1.6% BB, 11.3% B0 (1), 10% AB, 9.3% 0(1)0(1) and 15.3%0(1)0(2). The highest genotype frequency belonged to O01/O02 genotype (15.3%) and the lowest frequency belonged to A101/A102 genotype (0.4%). Conclusions: The frequencies of ABO alleles didn’t show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05). Conclusions The frequencies of ABO alleles didn’t show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05). PMID:23678461

Nojavan, Mohammad; Shamsasenjan, Karrim; Movassaghpour, Ali Akbar; Akbarzadehlaleh, Parvin; Torabi, Seyd Esmail; Ghojazadeh, Morteza




E-print Network

and normative reflection on the potentialities of European citizenship, and a growing body of quantitative be considered prototypical European citizens. They are the very image of the European Commission's highest ideals 188 1 I would like to thank the editors of the journal and this special edition, as well

Boyer, Edmond


Pharmacogenomic diversity in Singaporean populations and Europeans.  


Differences in the frequency of pharmacogenomic variants may influence inter-population variability in drug efficacy and risk of adverse drug reactions (ADRs). We investigated the diversity of ?4500 genetic variants in key drug-biotransformation and -response genes among three South East Asian populations compared with individuals of European ancestry. We compared rates of reported ADRs in these Asian populations to determine if the allelic differentiation corresponded to an excess of the associated ADR. We identified an excess of ADRs related to clopidogrel in Singaporean Chinese, consistent with a higher frequency of a known risk variant in CYP2C19 in that population. We also observed an excess of ADRs related to platinum compounds in Singaporean CHS, despite a very low frequency of known ADR risk variants, suggesting the presence of additional genetic and non-genetic risk factors. Our results point to substantial diversity at specific pharmacogenomic loci that may contribute to inter-population variability in drug response phenotypes. PMID:24861855

Brunham, L R; Chan, S L; Li, R; Aminkeng, F; Liu, X; Saw, W Y; Ong, R T H; Pillai, E N; Carleton, B C; Toh, D; Tan, S H; Koo, S H; Lee, E J D; Chia, K S; Ross, C J D; Hayden, M R; Sung, C; Teo, Y Y



European Space Agency  

NSDL National Science Digital Library

This is the home page of the European Space Agency (ESA), the European equivalent to NASA, formed of 16 member countries. Users can access information on ESA's activities, including such topics as Earth observation, human spaceflight, and various aspects of space science. The educational section includes exercises for high school and college students and a teachers' section with projects, classroom tools, and training information. The kids' section includes lab activities, games, and news articles written for younger students. A multimedia gallery is provided that contains imagery of Mars, Earth, and other objects in the solar system, artists' conceptions of spacecraft, and others. There is also a media center which provides press releases, information notes, and information on ESA television broadcasts. Miscellaneous services include an events calendar, list of publications, and a "frequently asked questions" section. The site can be translated into a variety of languages.


European Environment Agency (EEA)  

NSDL National Science Digital Library

The European Environment Agency (EEA) Website contains a huge selection of online environmental information, data, and reports pertaining to all fifteen EU states, as well as Iceland, Lichtenstein, and Norway. Information is organized by themes, and the site employs a powerful multilingual search feature. Themes include environmental issues, sectors and activities, information related to specific media, regions, and actions for environmental improvement. The site also contains EEA publications and reports, as well as a data service providing access to data sets covering at least all EU member states. Finally, the European Environment Information and Observation Network (EIONET) provides a network which "facilitates co-operation and flow of data and information between EIONET partners and with the EEA." The EEA Website is a large, research-oriented repository of information.


Nice European Council  

NSDL National Science Digital Library

EU members met last week in Nice, France to revise the manner in which the European Union reaches decisions in preparation for the entry of new member countries. Among the key provisions of the Treaty of Nice are a new formula for qualified majority voting (QMV), majority voting in some areas will now override individual country vetoes, and a reduction in the size of the European Commission. Background information on the meeting, progress reports, photos, speeches, and other materials are available at the official site of the Nice Council. Most of these resources are available in multiple languages. The full text of the Treaty itself is available in .pdf format from the main page.


Do Basque- and Caucasian-speaking populations share non-Indo-European ancestors?  


Genetic evidence is consistent with the view that the Indo-European languages were propagated in Europe by the diffusion of early farmers. The existence of phylogenetic relationships between European populations speaking other languages has been proposed on linguistic and archaeological grounds, and is here tested by analyzing allele frequencies at ten polymorphic protein and blood group loci. Genetic distances between speakers of Basque and Caucasian languages are compared with those between controls, i.e. contiguous populations speaking Indo-European and Altaic. Although some statistical tests show an excess of genetic similarity between Basque and South Caucasian speakers, most results do not support their common origin. If the Basques and the Caucasian-speaking populations share common ancestors, recent evolutionary phenomena must have caused divergence between them, so that their gene frequencies do not appear more similar now than those of random pairs of populations separated by the same geographic distance. PMID:8528674

Bertorelle, G; Bertranpetit, J; Calafell, F; Nasidze, I S; Barbujani, G




Microsoft Academic Search

The European X-ray Free Electron Laser XFEL is a 4th generation synchrotron radiation facility based on the SASE FEL concept and the superconducting TESLA technology for the linear accelerator. This multi-user facility will provide photon beams in a wavelength regime from 0.1nm to 5nm in three FEL beam lines and hard X-rays in two spontaneous radiation beam lines, serving in

R. Brinkmann


European Monetary Union  

NSDL National Science Digital Library

The EMU site was created by a group of students at the King's Hospital Secondary School in Palmerston, Dublin, Ireland. Their site discusses the potential positive and negative effects of the EMU, popular opinion on the Euro, and the possible side effects for Ireland, which will join, when its neighbor Britain does not join. After months of doubt and political difficulties in France, Germany, and most recently, Italy, it now appears that the unified European currency, the Euro, will indeed begin on January 1, 1999 to replace the national currencies of as many as 10 or 11 countries. The path to a unified currency is by no means smooth, however. Many European Union member states are finding it politically difficult to reduce their budget deficit to 3 percent of gross domestic product and other states, such as Britain and Denmark, are choosing to remain out for now regardless. On the other hand, European economic growth will apparently exceed earlier expectations, allowing leaders to use increased tax revenues instead of cutting social services to qualify.


Upper bounds on FST in terms of the frequency of the most frequent allele and total homozygosity: The case of a specified number of alleles.  


FST is one of the most frequently-used indices of genetic differentiation among groups. Though FST takes values between 0 and 1, authors going back to Wright have noted that under many circumstances, FST is constrained to be less than 1. Recently, we showed that at a genetic locus with an unspecified number of alleles, FST for two subpopulations is strictly bounded from above by functions of both the frequency of the most frequent allele (M) and the homozygosity of the total population (HT). In the two-subpopulation case, FST can equal one only when the frequency of the most frequent allele and the total homozygosity are 1/2. Here, we extend this work by deriving strict bounds on FST for two subpopulations when the number of alleles at the locus is specified to be I. We show that restricting to I alleles produces the same upper bound on FST over much of the allowable domain for M and HT, and we derive more restrictive bounds in the windows M?[1/I,1/(I-1)) and HT?[1/I,I/(I(2)-1)). These results extend our understanding of the behavior of FST in relation to other population-genetic statistics. PMID:25132646

Edge, Michael D; Rosenberg, Noah A



Polymorphic haplotypes on R408BW PKU and normal PAH chromosomes in Quebec and European populations  

SciTech Connect

The R408W mutation in the phenylalanine hydroxylase gene (PAH) is associated with haplotype 2.3 (RFLP haplotype 2, VNTR 3 of the HindIII system) in most European populations. Another chromosome, first observed in Quebec and then in northwest Europe, carries R408W on haplotype 1.8. The occurrence of the R408W mutation on two different PKU chromosomes could be the result of intragenic recombination, recurrent mutation or gene conversion. In this study, we analyzed both normal and R408W chromosomes carrying 1.8 and 2.3 haplotypes in Quebec and European populations; we used the TCTA{sub (n)} short tandem repeat sequence (STR) at the 5{prime} end of the PAH gene and the HindIII VNTR system at the 3{prime} end of the PAH gene to characterize chromosomes. Fourteen of sixteen R408W chromosomes from {open_quotes}Celtic{close_quotes} families in Quebec and the United Kingdom (UK) harbor a 244 bp STR allele; the remaining two chromosomes, carry a 240 bp or 248bp STR allele. Normal chromosomes (n=18) carry the 240 bp STR allele. R408W chromosomes are different from mutant H1.8 chromosomes; mutant H2.3 carries the 240 bp STR allele (14 of 16 chromosomes) or the 236 allele (2 of 16 chromosomes). The HindIII VNTR comprises variable numbers of 30 bp repeats (cassettes); the repeats also vary in nucleotide sequence. Variation clusters toward the 3{prime} end of cassettes and VNTRs. VNTR 3 alleles on normal H2 (n=9) and mutant R408W H2 (n=19) chromosomes were identical. VNTR 8 alleles on normal H1 chromosomes (n=9) and on R408W H1 chromosomes (n=15) differ by 1 bp substitution near the 3{prime} end of the 6th cassette. In summary, the mutant H1.8 chromosome harboring the R408W mutation has unique features at both the 5{prime} and 3{prime} end of the gene that distinguish it from the mutant H2.3 and normal H1.8 and H2.3 counterparts. The explanation for the occurrence of R408W on two different PAH haplotypes is recurrent mutation affecting the CpG dinucleotide in PAH codon 408.

Byck, S.; Morgan, K.; Scriver, C.R. [McGill Univ., Montreal (Canada)] [and others



S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae).  


RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only other family with RNase-based incompatibility for which estimates are available. The nucleotide diversity of S-allele sequences was found to be much lower in the two Rosaceae species as compared with the Solanaceae. This was not due to a lower sequence divergence among most closely related alleles. Rather, it is the depth of the entire genealogy that differs markedly in the two families, with Rosaceae S-alleles exhibiting more recent apparent coalescence. We also investigated patterns of selection at the molecular level by comparing nucleotide diversity at synonymous and nonsynonymous sites. Stabilizing selection was inferred for the 5' region of the molecule, while evidence of diversifying selection was present elsewhere. PMID:12180088

Raspé, O; Kohn, J R



Genetic Dissection of the Drosophila melanogaster Female Head Transcriptome Reveals Widespread Allelic Heterogeneity  

PubMed Central

Modern genetic mapping is plagued by the “missing heritability” problem, which refers to the discordance between the estimated heritabilities of quantitative traits and the variance accounted for by mapped causative variants. One major potential explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS) implicitly assume that a single SNP can explain all the variance for a causative locus. However, if allelic heterogeneity is prevalent, a substantial amount of genetic variance will remain unexplained. In this paper, we take a haplotype-based mapping approach and quantify the number of alleles segregating at each locus using a large set of 7922 eQTL contributing to regulatory variation in the Drosophila melanogaster female head. Not only does this study provide a comprehensive eQTL map for a major community genetic resource, the Drosophila Synthetic Population Resource, but it also provides a direct test of the allelic heterogeneity hypothesis. We find that 95% of cis-eQTLs and 78% of trans-eQTLs are due to multiple alleles, demonstrating that allelic heterogeneity is widespread in Drosophila eQTL. Allelic heterogeneity likely contributes significantly to the missing heritability problem common in GWAS studies. PMID:24810915

King, Elizabeth G.; Sanderson, Brian J.; McNeil, Casey L.; Long, Anthony D.; Macdonald, Stuart J.



Thr54 allele of the FABP2 gene affects resting metabolic rate and visceral obesity.  


We investigated the relationship between Ala54Thr variant allele of the fatty acid-binding protein 2 (FABP2) gene (Ala54Thr) and development of obesity in Japanese obese women. FABP2 genotypes were determined with a fluorescent allele-specific DNA primer assay system. Body weight, waist and hip circumference, amounts of visceral and subcutaneous white adipose tissue measured by computed tomography (CT) were compared between subjects with Thr allele and without Thr allele before and after the diet and exercise therapy in 80 Japanese obese women. The frequency of the Thr54 allele did not differ between obese and control subjects (0.388 versus 0.329, respectively). In subjects with Ala/Thr and Thr/Thr genotype, adjusted resting metabolic rate (RMR) was significantly lower than the subjects with Ala/Ala genotype. Subjects with the Thr54 allele showed significantly greater waist circumference after diet and exercise therapy than subjects with Ala/Ala genotype. They also demonstrated greater body weight at 20 years of age compared to subjects with Ala/Ala genotype. In conclusion, Thr54 allele of FABP2 has associations with lower adjusted resting metabolic rate, resistance in reducing visceral white adipose tissue (WAT) and early onset of obesity in Japanese obese women. PMID:15620432

Takakura, Yasuto; Yoshioka, Keiji; Umekawa, Tsunekazu; Kogure, Akinori; Toda, Hitoshi; Yoshikawa, Toshikazu; Yoshida, Toshihide



The frequency of HLA alleles in a population of Inuit women of northern Quebec  

PubMed Central

Background Human leukocyte antigen (HLA) alleles code for proteins that are involved in the recognition of foreign antigens and activation of the immune system. The frequency of HLA alleles varies across different populations. Objective To describe the frequency of HLA alleles in a population of Inuit women of Nunavik, Quebec, Canada. Design A cohort of women was recruited from 4 different communities between January 2002 and December 2007. HLA-B*07, HLA-DQB1*03, DQB1*06:02, DRB1*13 and DRB1*15:01 alleles were typed by PCR sequence-specific primers (PCR-SSP) and HLA-E and G alleles were type by DNA-sequencing procedures. Results We obtained data on 524 participants. The most frequent HLA alleles in this population were HLA-E*01:03, HLA-G*01:04:01 and HLA-DQB1*03, and they were found in 89, 75 and 94% of the population, respectively. Conclusions The distribution of HLA alleles in Nunavik, Quebec is unique when compared to other populations in Canada or around the world. PMID:23986892

Metcalfe, Stephanie; Roger, Michel; Faucher, Marie-Claude; Coutlee, Francois; Franco, Eduardo L.; Brassard, Paul



A comprehensive analysis reveals mutational spectra and common alleles in Chinese patients with oculocutaneous albinism.  


Oculocutaneous albinism (OCA) is a heterogeneous recessive disorder with hypopigmentation in the skin, hair, and eyes. At least 16 genes have been identified as causative genes for human OCA. No comprehensive analysis has been conducted to study the spectral distribution of OCA in Chinese patients. We screened 127 unrelated and unselected Chinese OCA patients for mutations in the TYR, OCA2, TYRP1, SLC45A2, and HPS1 genes. We found that the spectrum of mutational genes and alleles of OCA is population specific. OCA1 is the most common (70.1% of cases) form of Chinese OCA, whereas OCA2, OCA4, and HPS1 account for 10.2%, 12.6%, and 1.6%, respectively. No apparent pathological mutation of TYRP1 has been found. Thirty-eight previously unreported mutational alleles were identified from these OCA patients and were not found in 100 nonalbinism subjects. Of the TYR mutational alleles, 81.1% were clustered on exons 1 and 2. Ten common alleles account for 74.6% of the mutational TYR alleles in Chinese OCA1 patients. The p.D160H allele accounts for 55.6% of the mutational SLC45A2 alleles in Chinese OCA4 patients. These results provide useful information for the establishment of an optimized strategy of gene diagnosis and genetic counseling of Chinese OCA patients. PMID:19865097

Wei, Aihua; Wang, Yu; Long, Yan; Wang, Yi; Guo, Xiaoli; Zhou, Zhiyong; Zhu, Wei; Liu, Juntao; Bian, Xuming; Lian, Shi; Li, Wei



Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates.  


Most Neotropical primate species possess a polymorphic X-linked and a monomorphic autosomal color vision gene. Consequently, populations are composed of both dichromatics and trichromatics. Most theories on the maintenance of this genetic system revolve around possible advantages for foraging ecology. To examine the issue from a different angle, we compared the numbers and relative frequencies of alleles at the X-linked locus among three species of Saimiri representing a wide range of geographical and behavioral variation in the genus. Exons 3, 4, and 5 of the X-linked opsin gene were sequenced for a large number of X chromosomes for all three species. Several synonymous mutations were detected in exons 4 and 5 for the originally reported alleles but only a single nonsynonymous change was detected. Two alleles were found that appeared to be the result of recombination events. The low occurrence of recombinant alleles and absence of mutations in the amino acids critical for spectral tuning indicates that stabilizing selection acts to maintain the combinations of critical sites specific to each allele. Allele frequencies were approximately the same for all Saimiri species, with a slight but significant difference between S. boliviensis and S. oerstedii. No apparent correlation exists between allele frequencies and behavioral or biogeographical differences between species, casting doubt on the speculation that the spectral sensitivities of the alleles have been maintained because they are specifically well-tuned to Saimiri visual ecology. Rather, the spectral tuning peaks might have been maintained because they are as widely spaced as possible within the limited range of middlewave to longwave spectra useful to all primates. This arrangement creates a balance between maximizing the distance between spectral tuning peaks (allowing the color opponency of the visual system to distinguish between peaks) and maximizing the number of alleles within a limited range (yielding the greatest possible frequency of heterozygotes). PMID:12029355

Cropp, Susan; Boinski, Sue; Li, Wen-Hsiung



HLA class-II allele frequencies in Turkish breast cancer patients.  


Class-II human leukocyte antigens (HLA) present tumor antigenic peptides on the cell surface in order to be recognized by T lymphocytes. Thereby, these molecules can play an important role in the immune response to breast cancer tumor antigens. The aim of this study was to determine the relation between breast cancer and HLA class-II alleles in Turkey. The study groups consisted of 69 breast cancer patients and 45 healthy controls. Typing of HLA-DRB1 and HLA-DQB1 from DNA samples was performed by Sequence Specific Oligonucletide Hybridisation. Significant negative correlations were observed between HLA-DRB1 03 and HLA-DQB1 02 alleles and breast cancer (p1 = 0.019; p2 = 0.019) and also between HLA-DQB1 02 allele and postmenopausal breast cancer (P = 0.022) and c-erb-B2 positivity (P = 0.038). Furthermore, there was a significant positive correlation between HLA-DRB1 13 and HLA-DQB1 06 alleles and progesteron receptor positivity (p1 = 0.012; p2 = 0.001); and a significant negative correlation between HLA-DQB1 03 allele and progesteron receptor positivity (P = 0.009) in breast cancer. Additionally, another significant positive correlation was seen between HLA-DRB1 04 allele and c-erb-B2 positivity (P = 0.036). As a result, while HLA-DRB1 03, HLA-DQB1 02, HLA-DRB1 13, and HLA-DQB1 06 alleles were found to be involved in protectiveness against breast cancer and good prognosis; HLA-DQB1 03 and HLA-DRB1 04 alleles were found to be involved in poor prognosis. In conclusion, by determining allele types showing predisposition to breast cancer, a systematical screening and follow up systems can be developed for patients who are at high risk. PMID:21373933

Gun, Faik Deniz; Ozturk, Ozlem Goruroglu; Polat, Ayse; Polat, Gurbuz



Reliability assessment of null allele detection: inconsistencies between and within different methods.  


Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations. PMID:24119056

D?browski, M J; Pilot, M; Kruczyk, M; ?mihorski, M; Umer, H M; Gliwicz, J



Global diversity and genetic contributions of chicken populations from African, Asian and European regions.  


Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds. PMID:25315897

Lyimo, C M; Weigend, A; Msoffe, P L; Eding, H; Simianer, H; Weigend, S



Distribution of self-incompatibility alleles and breeding structure of open-pollinated cultivars of Brussels sprouts  

Microsoft Academic Search

Nineteen different S alleles were found in 488 plants representing 16 cultivars of Brussels sprouts. Twelve of these S alleles have previously been found in kale, and 7 are known only from Brussels sprouts. The number of S alleles per cultivar varied from 4 to 13, but for most cultivars the number fell in the range 7–10. Relatively unselected cultivars

D J Ockendon



No association between an allele at the D sub 2 dopamine receptor gene (DRD2) and alcoholism  

SciTech Connect

The author attempted to replicate a positive allelic association between the A1 allele of DRD2 (the D{sub 2} dopamine receptor locus) and alcoholism that has been reported. They compared allele frequencies at the previously described Taq I restriction fragment length polymorphism system of DRD2 in alcoholics and random population controls.

Gelernter, J.; Krystal, J.; Kennedy, J.L. (Yale Univ., New Haven, CT (United States) West Haven Dept. of Veterans Affairs Medical Center, CT (United States)); O'Malley, S.; Risch, N.; Merikangas, K.; Kidd, K.K. (Yale Univ., New Haven, CT (United States)); Kranzler, H.R. (Univ. of Connecticut, Farmington (United States))



EAC: The European Astronauts Centre  

NASA Astrophysics Data System (ADS)

The newly established European Astronauts Centre (EAC) in Cologne represents the European Astronauts Home Base and will become a centre of expertise on European astronauts activities. The paper gives an overview of the European approach to man-in-space, describes the European Astronauts Policy and presents the major EAC roles and responsibilities including the management of selection, recruitment and flight assignment of astronauts; the astronauts support and medical surveillance; the supervision of the astronauts' non-flight assignments; crew safety; the definition of the overall astronauts training programme; the scheduling and supervision of the training facilities; the implementation of Basic Training; the recruitment, training and certification of instructors, and the interface to NASA in the framework of the Space Station Freedom programme. An overview is given on the organisation of EAC, and on the European candidate astronauts selection performed in 1991.

Ripoll, Andres


Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection  

PubMed Central

Background The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. Methods We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3?dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. Results We showed that the addition of the 3?dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. Conclusions QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer. PMID:23617802



ADH1B is associated with alcohol dependence and alcohol consumption in populations of European and African ancestry.  


A coding variant in alcohol dehydrogenase 1B (ADH1B) (rs1229984) that leads to the replacement of Arg48 with His48 is common in Asian populations and reduces their risk for alcoholism, but because of very low allele frequencies the effects in European or African populations have been difficult to detect. We genotyped and analyzed this variant in three large European and African-American case-control studies in which alcohol dependence was defined by the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria, and demonstrated a strong protective effect of the His48 variant (odds ratio (OR) 0.34, 95% confidence interval (CI) 0.24, 0.48) on alcohol dependence, with genome-wide significance (6.6 × 10(-10)). The hypothesized mechanism of action involves an increased aversive reaction to alcohol; in keeping with this hypothesis, the same allele is strongly associated with a lower maximum number of drinks in a 24-hour period (lifetime), with P=3 × 10(-13). We also tested the effects of this allele on the development of alcoholism in adolescents and young adults, and demonstrated a significantly protective effect. This variant has the strongest effect on risk for alcohol dependence compared with any other tested variant in European populations. PMID:21968928

Bierut, L J; Goate, A M; Breslau, N; Johnson, E O; Bertelsen, S; Fox, L; Agrawal, A; Bucholz, K K; Grucza, R; Hesselbrock, V; Kramer, J; Kuperman, S; Nurnberger, J; Porjesz, B; Saccone, N L; Schuckit, M; Tischfield, J; Wang, J C; Foroud, T; Rice, J P; Edenberg, H J



European space developments  

NASA Astrophysics Data System (ADS)

Unable to keep up with the level of spending which the US and former USSR deemed necessary during the 1960s and 1970s as the frontiers of space science were rolled back and the 'space race' gained momentum, Europe progresses at a steadier pace, moving into niche sectors, notably scientific and communication satellites. Momentum has been steadily built up, with the Ariane launchers proving that an ambitious program could be both attained and maintained. This year, the European Space Agency (ESA) is scheduled to place six more spacecraft in orbit - four of them via Ariane-5.

Birch, Stuart



European Museum Guide  

NSDL National Science Digital Library

Museum Media Publishers publishes this guide to the major museums in twelve European countries. The current edition describes some 1500 exhibitions planned between May 1997 and May 1998. Museums and exhibitions are listed alphabetically by country and city. Each entry describes the museum's collection, visiting information, and a description of their exhibitions through May 1998. When possible, a hyperlink to the museum's web site is also provided. Users can also view a chronological index of all the exhibitions in each country or search the site by museum or exhibition.


European Anti Poverty Network (EAPN)  

NSDL National Science Digital Library

European Anti Poverty Network was created in 1989 "to put the fight against poverty and social exclusion on the political agenda of the European Union." The Network consists of 25 European organizations that work to alleviate poverty and 15 national networks that fight poverty specifically inside the EU. EAPN offers a nice collection of position papers and reports analyzing the ongoings of the European Union, its member countries and their policies, as well as news releases and news flashes. The site gives general information about the EAPN including its mission, members, and activities, as well as providing a tightly organized set of links.


European Conference on Computational Mechanics  

E-print Network

ECCM-2001 European Conference on Computational Mechanics June 26-29, 2001 Cracow, Poland NEW: { }/,,+, - , (2) ( ) ]}[,...,][:,...,{)][],...,[( n11n121 nxxxxxxfxxf = . (3) #12;ECCM-2001, Cracow, Poland 3

Pownuk, Andrzej


European Industrial Relations Observatory Online  

NSDL National Science Digital Library

The European Industrial Relations Observatory Online (EIROnline) was developed by the European Foundation for the Improvement of Living and Working Conditions, an autonomous body created by the European Community. The aim of the site is to "initiate, collect, store, disseminate and provide access to information and analysis on developments in industrial relations" in the 15 European Union member states and Norway. Visitors will find the latest industrial relations news and feature articles arranged by country. There is also a bimonthly publication called the EIRObserver summarizing the news and items over the past two months.


Null alleles of ABCG2 encoding the breast cancer resistance protein define the new blood group system Junior  

PubMed Central

The breast cancer resistance protein, also known as ABCG2, is one of the most studied ATP-binding cassette (ABC) transporters, due to its ability to confer multidrug resistance1,2. The lack of information on the physiological roles of ABCG2 in humans severely limits cancer chemotherapeutic approaches targeting this transporter. We report here that ABCG2 comprises the molecular basis of a new blood group system (Junior, Jr), and that individuals of the Jr(a?) blood type have inherited two null alleles of ABCG2. We thus identified 5 frameshift and 3 nonsense mutations in ABCG2. Furthermore, we show that the prevalence of the Jr(a?) blood type in the Japanese and European Gypsy populations is related to the mutations p.Q126X and p.R236X, respectively. The identification of ABCG2?/? (Jr(a?)) individuals, who appear phenotypically normal, is an essential step towards targeting ABCG2 in cancer, but also understanding the physiological and pharmacological roles of this promiscuous transporter in humans. PMID:22246505

Saison, Carole; Helias, Virginie; Ballif, Bryan A.; Peyrard, Thierry; Puy, Herve; Miyazaki, Toru; Perrot, Sebastien; Vayssier-Taussat, Muriel; Waldner, Mauro; Pennec, Pierre-Yves Le; Cartron, Jean-Pierre; Arnaud, Lionel



Null alleles of ABCG2 encoding the breast cancer resistance protein define the new blood group system Junior.  


The breast cancer resistance protein, also known as ABCG2, is one of the most highly studied ATP-binding cassette (ABC) transporters because of its ability to confer multidrug resistance. The lack of information on the physiological role of ABCG2 in humans severely limits cancer chemotherapeutic approaches targeting this transporter. We report here that ABCG2 comprises the molecular basis of a new blood group system (Junior, Jr) and that individuals of the Jr(a-) blood type have inherited two null alleles of ABCG2. We identified five frameshift and three nonsense mutations in ABCG2. We also show that the prevalence of the Jr(a-) blood type in the Japanese and European Gypsy populations is related to the p.Gln126* and p.Arg236* protein alterations, respectively. The identification of ABCG2(-/-) (Jr(a-)) individuals who appear phenotypically normal is an essential step toward targeting ABCG2 in cancer and also in understanding the physiological and pharmacological roles of this promiscuous transporter in humans. PMID:22246505

Saison, Carole; Helias, Virginie; Ballif, Bryan A; Peyrard, Thierry; Puy, Hervé; Miyazaki, Toru; Perrot, Sébastien; Vayssier-Taussat, Muriel; Waldner, Mauro; Le Pennec, Pierre-Yves; Cartron, Jean-Pierre; Arnaud, Lionel



Generation and properties of a human immunodeficiency virus type 1 isolate resistant to the small molecule CCR5 inhibitor, SCH-417690 (SCH-D).  


We describe the generation of two genetically related human immunodeficiency virus type 1 (HIV-1) isolates highly (>20,000-fold) resistant to the small molecule CCR5 inhibitor, SCH-417690 (formerly SCH-D). Both viruses were cross-resistant to other small molecules targeting entry via CCR5, but they were inhibited by some MAbs against the same coreceptor on primary CD4+ T-cells. The resistant isolates remained sensitive to inhibitors of other stages of virus entry, and to replication inhibitors acting post-entry. Neither escape mutant could replicate detectably in peripheral blood mononuclear cells (PBMC) from two donors homozygous for the CCR5-Delta32 allele and both were insensitive to the CXCR4-specific inhibitor, AMD3100. Hence, the SCH-D escape mutants retained the R5 phenotype. One of the resistant isolates was, however, capable of replication in U87.CD4.CXCR4 cells and, after expansion in those cells, was sensitive to AMD3100 in primary CD4+ T-cells. Hence, some X4 variants may be present in this escape mutant swarm. A notable observation was that the SCH-D escape mutants were also cross-resistant to PSC-RANTES and AOP-RANTES, chemokine derivatives that are reported to down-regulate cell surface CCR5 almost completely. However, the extent to which CCR5 is down-regulated was dependent upon the detection MAb. Hence, the escape mutants may be using a CCR5 configuration that is only detected by some anti-CCR5 MAbs. Finally, two SCH-D-resistant clonal viruses revealed no amino acid changes in the gp120 V3 region relative to the parental viruses, in marked contrast to clones resistant to the AD101 small molecule CCR5 inhibitor that possess 4 such sequence changes. Several sequence changes elsewhere in gp120 (V2, C3 and V4) were present in the SCH-D-resistant clones. Their influence on the resistant phenotype remains to be determined. PMID:15935415

Marozsan, Andre J; Kuhmann, Shawn E; Morgan, Thomas; Herrera, Carolina; Rivera-Troche, Enid; Xu, Serena; Baroudy, Bahige M; Strizki, Julie; Moore, John P



Known unknowns for allele-specific expression and genomic imprinting effects  

PubMed Central

Recent studies have provided evidence for non-canonical imprinting effects that are associated with allele-specific expression biases at the tissue level in mice. These imprinting effects have features that are distinct from canonical imprinting effects that involve allele silencing. Here, I discuss some of the evidence for non-canonical imprinting effects in the context of random X-inactivation and epigenetic allele-specific expression effects on the autosomes. I propose several mechanisms that may underlie non-canonical imprinting effects and outline future directions and approaches to study these effects at the cellular level in vivo. The growing evidence for complex allele-specific expression effects that are cell- and developmental stage-specific has opened a new frontier for study. Currently, the function of these effects and the underlying regulatory mechanisms are largely unknown. PMID:25343032



Stacking Pima S-6 fiber length alleles in a Tamcot 2111 background  

E-print Network

Molecular markers can be used to stack fiber quality alleles among recombinant inbred lines and thus, aid in the development of unique genotypes. The objective of this study was to determine the potential for stacking Gossypium barbadense (Pima S-6...

Souder, Christopher Lee



Characterization of major histocompatibility complex class I allele polymorphisms in common marmosets.  


Currently, little information is available for major histocompatibility complex (MHC)-I that conditions the T-cell response of marmosets. In this study, 471 clones of MHC-I cDNA sequences were isolated from 12 marmosets. Twenty full-length sequences of class I G (Caja-G) alleles were obtained from these marmosets, 15 of them were novel. Among these 20 Caja-G alleles, 10 were found in individual animals while the rests were in two to four marmosets, but none was common to all animals. Ten marmosets possessed one to three Caja-G alleles, and two marmosets carried five or six alleles, which suggested that the Caja-G locus was duplicated in marmoset's genome. The high polymorphisms of Caja-G sequences provided important information helpful for understanding the cellular immune response in virus-infected marmosets. PMID:25355647

Li, T; Xu, Y; Yin, S; Liu, B; Zhu, S; Wang, W; Wang, Y; Liu, F; Allain, J-P; Li, C



Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana  

E-print Network

(Fig. 1a, b). Using a recombinant inbred line (RIL) population14 , we identified single major), with the Est-1 alleles acting in a semi-dominant manner. We fine-mapped both QTL to the same 12-kilobase (kb

Robinson, Michael


Identification of low penetrance alleles for lung cancer: The GEnetic Lung CAncer Predisposition Study (GELCAPS)  

E-print Network

Abstract Background Part of the inherited risk to lung cancer is likely to include common, low risk alleles. The identification of this class of susceptibility is contingent on association-based analyses. We established GEnetic Lung CAncer...

Eisen, Tim; Matakidou, Athena; Consortium, Gelcaps; Houlston, Richard



Genetic Dissection of the Drosophila melanogaster Female Head Transcriptome Reveals Widespread Allelic Heterogeneity  

E-print Network

explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS) implicitly assume...

King, Elizabeth G.; Sanderson, Brian J.; McNeil, Casey Lee; Long, Anthony D.; Macdonald, Stuart J.



SNP-specific array-based allele-specific expression analysis  

PubMed Central

We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39–49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples. PMID:18369178

Bjornsson, Hans T.; Albert, Thomas J.; Ladd-Acosta, Christine M.; Green, Roland D.; Rongione, Michael A.; Middle, Christina M.; Irizarry, Rafael A.; Broman, Karl W.; Feinberg, Andrew P.



Selection on Alleles Affecting Human Longevity and Late-Life Disease: The Example of Apolipoprotein E  

PubMed Central

It is often claimed that genes affecting health in old age, such as cardiovascular and Alzheimer diseases, are beyond the reach of natural selection. We show in a simulation study based on known genetic (apolipoprotein E) and non-genetic risk factors (gender, diet, smoking, alcohol, exercise) that, because there is a statistical distribution of ages at which these genes exert their influence on morbidity and mortality, the effects of selection are in fact non-negligible. A gradual increase with each generation of the ?2 and ?3 alleles of the gene at the expense of the ?4 allele was predicted from the model. The ?2 allele frequency was found to increase slightly more rapidly than that for ?3, although there was no statistically significant difference between the two. Our result may explain the recent evolutionary history of the epsilon 2, 3 and 4 alleles of the apolipoprotein E gene and has wider relevance for genes affecting human longevity. PMID:20368805

Drenos, Fotios; Kirkwood, Thomas B. L.



Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars  

PubMed Central

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.



A human-specific allelic group of the MHC DRB1 gene in primates  

PubMed Central

Background Diversity among human leukocyte antigen (HLA) molecules has been maintained by host-pathogen coevolution over a long period of time. Reflecting this diversity, the HLA loci are the most polymorphic in the human genome. One characteristic of HLA diversity is long-term persistence of allelic lineages, which causes trans-species polymorphisms to be shared among closely related species. Modern humans have disseminated across the world after their exodus from Africa, while chimpanzees have remained in Africa since the speciation event between humans and chimpanzees. It is thought that modern humans have recently acquired resistance to novel pathogens outside Africa. In the present study, we investigated HLA alleles that could contribute to this local adaptation in humans and also studied the contribution of natural selection to human evolution by using molecular data. Results Phylogenetic analysis of HLA-DRB1 genes identified two major groups, HLA Groups A and B. Group A formed a monophyletic clade distinct from DRB1 alleles in other Catarrhini, suggesting that Group A is a human-specific allelic group. Our estimates of divergence time suggested that seven HLA-DRB1 Group A allelic lineages in humans have been maintained since before the speciation event between humans and chimpanzees, while chimpanzees possess only one DRB1 allelic lineage (Patr-DRB1*03), which is a sister group to Group A. Experimental data showed that some Group A alleles bound to peptides derived from human-specific pathogens. Of the Group A alleles, three exist at high frequencies in several local populations outside Africa. Conclusions HLA Group A alleles are likely to have been retained in human lineages for a long period of time and have not expanded since the divergence of humans and chimpanzees. On the other hand, most orthologs of HLA Group A alleles may have been lost in the chimpanzee due to differences in selective pressures. The presence of alleles with high frequency outside of Africa suggests these HLA molecules result from the local adaptations of humans. Our study helps elucidate the mechanism by which the human adaptive immune system has coevolved with pathogens over a long period of time. PMID:24928070



The first modern Europeans.  


The discovery of new human fossil remains is one of the most obvious ways to improve our understanding of the dynamics of human evolution. The reanalysis of existing fossils using newer methods is also crucial, and may lead to a reconsideration of the biological and taxonomical status of some specimens, and improve our understanding of highly debated periods in human prehistory. This is particularly true for those remains that have previously been studied using traditional approaches, with only morphological descriptions and standard calliper measurements available. My own interest in the Uluzzian, and its associated human remains grew from my interest in applying recently developed analytical techniques to quantify morphological variation. Discovered more than 40 years ago, the two deciduous molars from Grotta del Cavallo (Apulia, Italy) are the only human remains associated with the Uluzzian culture (one of the main three European "transitional" cultures). These teeth were previously attributed to Neanderthals. This attribution contributed to a consensus view that the Uluzzian, with its associated ornament and tool complexes, was produced by Neanderthals. A reassessment of these deciduous teeth by means of digital morphometric analysis revealed that these remains belong to anatomically modern humans (AMHs). This finding contradicts previous assumptions and suggests that modern humans, and not Neanderthals, created the Uluzzian culture. Of equal importance, new chronometric analyses date these dental remains to 43,000-45,000 cal BP. Thus, the teeth from Grotta del Cavallo represent the oldest European AMH currently known. PMID:22781582

Benazzi, Stefano



A new DRB1 allele ( DRB1 * 0811 ) identified in Native Americans  

Microsoft Academic Search

A novel DRB1 allele was identified in a potential bone marrow transplantation recipient and her father. Both are Native Americans of Navajo descent. Class II serologic typing of the patient demonstrated the presence of DR8, DR14, DR52, and DQ3. Sequence specific polymerase chain reaction (PCR) amplification of genomic DNA was consistent with the DRB1 alleles *08 and *14. Direct DNA

Thomas M. Williams; Jin Wu; Terry Foutz; Joan D. McAuley; Gary M. Troup



Adenosine deaminase deficiency: genotype-phenotype correlations based on expressed activity of 29 mutant alleles.  

PubMed Central

Adenosine deaminase (ADA) deficiency causes lymphopenia and immunodeficiency due to toxic effects of its substrates. Most patients are infants with severe combined immunodeficiency disease (SCID), but others are diagnosed later in childhood (delayed onset) or as adults (late onset); healthy individuals with "partial" ADA deficiency have been identified. More than 50 ADA mutations are known; most patients are heteroallelic, and most alleles are rare. To analyze the relationship of genotype to phenotype, we quantitated the expression of 29 amino acid sequence-altering alleles in the ADA-deleted Escherichia coli strain SO3834. Expressed ADA activity of wild-type and mutant alleles ranged over five orders of magnitude. The 26 disease-associated alleles expressed 0.001%-0.6% of wild-type activity, versus 5%-28% for 3 alleles from "partials." We related these data to the clinical phenotypes and erythrocyte deoxyadenosine nucleotide (dAXP) levels of 52 patients (49 immunodeficient and 3 with partial deficiency) who had 43 genotypes derived from 42 different mutations, including 28 of the expressed alleles. We reduced this complexity to 13 "genotype categories," ranked according to the potential of their constituent alleles to provide ADA activity. Of 31 SCID patients, 28 fell into 3 genotype categories that could express <=0.05% of wild-type ADA activity. Only 2 of 21 patients with delayed, late-onset, or partial phenotypes had one of these "severe" genotypes. Among 37 patients for whom pretreatment metabolic data were available, we found a strong inverse correlation between red-cell dAXP level and total ADA activity expressed by each patient's alleles in SO3834. Our system provides a quantitative framework and ranking system for relating genotype to phenotype. PMID:9758612

Arredondo-Vega, F X; Santisteban, I; Daniels, S; Toutain, S; Hershfield, M S



Dual-allele dipstick assay for genotyping single nucleotide polymorphisms by primer extension reaction  

Microsoft Academic Search

We have developed a dry-reagent dipstick test for simultaneous visual detection of two alleles in single nucleotide polymorphisms (SNPs). The strip comprises two test zones and a control zone. Oligonucleotide-functionalized gold nanoparticles are used as reporters. PCR-amplified DNA that spans the interrogated sequence is subjected to primer extension (PEXT) reactions using allele-specific primers. Digoxigenin-dUTP and biotin-dUTP are incorporated in the

Jessica K Konstantou; Penelope C Ioannou; Theodore K Christopoulos



Intermediate FMR1 alleles and cognitive and\\/or behavioural phenotypes  

Microsoft Academic Search

During the last few years, several studies have reported an excess of intermediate FMR1 alleles in patients with cognitive and\\/or behavioural phenotypes. Here, we report the frequency of intermediate alleles (IAs) in three pathologies, intellectual disabilities (IDs), attention-deficit\\/hyperactivity disorder and autism, from different Spanish regions. We found 142 IAs among 9015 patients with ID (1.6%), 4 among the 415 ADHD

Irene Madrigal; Mar Xunclà; Maria Isabel Tejada; Francisco Martínez; Isabel Fernández-Carvajal; Luís Alberto Pérez-Jurado; Laia Rodriguez-Revenga; Montserrat Milà



Multiple crm- mutations in familial hypercholesterolemia. Evidence for 13 alleles, including four deletions.  

PubMed Central

The low density lipoprotein (LDL) receptors in fibroblasts from 132 subjects with the clinical syndrome of homozygous familial hypercholesterolemia were analyzed by immunoprecipitation with an anti-LDL receptor monoclonal antibody. 16 of the 132 cell strains (12%) synthesized no immunodetectable LDL receptor protein, indicating the presence of two mutant genes that failed to produce cross-reacting material (crm- mutations). DNA and mRNA from 15 of the 16 crm- patients, representing 30 crm- genes, were available for further study. Haplotype analysis based on 10 restriction fragment length polymorphisms (RFLPs) suggested that the 30 crm- genes represent 13 mutant alleles. Four of the alleles produced no mRNA. Three of these four mRNA- alleles had large deletions ranging from 6 to 20 kb that eliminated the promoter region of the gene. The fourth mRNA- allele did not contain any deletion or alteration in the promoter sequence; the reason for the mRNA- phenotype was not apparent. Nine alleles were positive for mRNAs, of which three encoded mRNAs of abnormal size. One of the abnormal mRNAs was produced by a gene harboring a deletion, and another was produced by a gene with a complex rearrangement. The third abnormal-sized mRNA (3.1 kb larger than normal) was produced by an allele that had no detectable alterations as judged by Southern blotting. The other six mRNA+ alleles appeared normal by Southern blotting and produced normal-sized mRNA but no receptor protein. The current studies demonstrate that mRNA analysis coupled with haplotype determination by Southern blot analysis can be used to classify crm- mutations at a genetic locus where multiple alleles exist. Images PMID:3343347

Hobbs, H H; Leitersdorf, E; Goldstein, J L; Brown, M S; Russell, D W



Common and Well-Documented HLA Alleles: 2012 Update to the CWD Catalogue  

PubMed Central

We have updated the catalogue of common and well-documented (CWD) HLA alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and –DPB1 loci in IMGT/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and –DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being “common” (having known frequencies) and 707 as being “well-documented” on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program’s bioinformatics web pages. PMID:23510415

Mack, Steven J.; Cano, Pedro; Hollenbach, Jill A.; He, Jun; Hurley, Carolyn Katovich; Middleton, Derek; Moraes, Maria Elisa; Pereira, Shalini E.; Kempenich, Jane H.; Reed, Elaine F.; Setterholm, Michelle; Smith, AnaJane G.; Tilanus, Marcel G.; Torres, Margareth; Varney, Michael D.; Voorter, Christien E. M.; Fischer, Gottfried F.; Fleischhauer, Katharina; Goodridge, Damian; Klitz, William; Little, Ann-Margaret; Maiers, Martin; Marsh, Steven G. E.; Muller, Carlheinz R.; Noreen, Harriet; Rozemuller, Erik H.; Sanchez-Mazas, Alicia; Senitzer, David; Trachtenberg, Elizabeth; Fernandez-Vina, Marcelo



A new ENU-induced allele of mouse quaking causes severe CNS dysmyelination.  


The mutant allelic series of the mouse quaking gene consists of the spontaneous quaking(viable) (qk(v)) allele, which is homozygous viable with a dysmyelination phenotype, and four ENU-induced alleles (qk(kt 1), qk(k2), qk(kt3/4), and qk(l-1)), which are homozygous embryonic lethal. Here we report the isolation of qk(e5), the first ENU-induced viable allele of quaking. Unlike qk(v)/qk(v), qk(e5)/qk(e5) animals have early-onset seizures, severe ataxia, and a dramatically reduced lifespan. Ultrastructural analysis of qk(e5)/qk(e5) brains reveals severe dysmyelination when compared with both wild-type and qk(v)/qk(v) brains. In addition, Calbindin detection in young adult qk(e5)/qk(e5) mice reveals Purkinje cell axonal swellings indicative of neurodegeneration , which is not seen in young adult qk(v)/qk(v) mice. Although the molecular defect in the qk(e5) allele is not evident by sequencing, protein expression studies show that qk(e5)/qk(e5) postnatal oligodendrocytes lack the QKI-6 and QKI-7 isoforms and have reduced QKI-5 levels. The oligodendrocyte developmental markers PDGF alpha R, NG 2, O4, CNP, and MBP are also present in the qk(e5)/qk(e5) postnatal brain although CNP and MBP levels are considerably reduced. Because the qk(v) allele is a large deletion that affects the expression of three genes, the new neurologic qk(e5) allele is an important addition to this allelic series. PMID:16245024

Noveroske, Janice K; Hardy, Rebecca; Dapper, Jason D; Vogel, Hannes; Justice, Monica J



Receptor function, dominant negative activity and phenotype correlations for MC1R variant alleles  

Microsoft Academic Search

The human melanocortin-1 receptor (MC1R) is a G-protein coupled receptor involved in the regulation of pigmentation. Several MC1R variant alleles are associated with red hair, fair skin and increased skin cancer risk. We have performed a systematic functional analysis of nine common MC1R variants and corre- lated these results with the strength of the genetic association of each variant allele

Kimberley A. Beaumont; Sri L. Shekar; Richard A. Newton; Michael R. James; Jennifer L. Stow; David L. Duffy; Richard A. Sturm



SPECT and MRI analysis in Alzheimer's disease: relation to apolipoprotein E epsilon 4 allele.  

PubMed Central

OBJECTIVES--The epsilon 4 allele of apolipoprotein E (ApoE) is a risk factor for late onset Alzheimer's disease. ApoE is present in senile plaques, neurofibrillary tangles, and cerebrovascular amyloid, and it is implicated in synaptogenesis. The effect of ApoE polymorphism on the volumes of hippocampus, amygdala, and frontal lobe was studied. The hypothesis was that the patients with Alzheimer's disease carrying the epsilon 4 allele have more pronounced atrophy. The relation of ApoE and cerebral blood flow on cortical areas was also assessed. METHODS--Fifty eight patients with Alzheimer's disease at the early stage of the disease and 34 control subjects were studied. Patients with Alzheimer's disease were divided into subgroups according to the number of the epsilon 4 alleles. Volumes were measured by MRI and regional cerebral blood flow ratios referred to the cerebellum were examined by 99mTc-HMPAO SPECT. ApoE genotypes were determined by digestion of ApoE polymerase chain reaction products with the restriction enzyme Hha1. RESULTS--patients with Alzheimer's disease had smaller volumes of hippocampi and amygdala compared with control subjects, and the patients with Alzheimer's disease homozygous for the epsilon 4 allele had the most prominent volume loss in the medial temporal lobe structures. The frontal lobe volumes did not differ significantly. All patients with Alzheimer's disease had bilateral temporoparietal hypoperfusion and the subgroups with one or no epsilon 4 alleles also had frontal hypoperfusion compared with control subjects. The occipital perfusion ratios tended to decrease with increasing number of epsilon 4 alleles. CONCLUSIONS--Patients with Alzheimer's disease homozygous for the epsilon 4 allele seem to have severe damage in the medial temporal lobe structures early in the disease process and differ from the patients with Alzheimer's disease with one or no epsilon 4 alleles. PMID:8648331

Lehtovirta, M; Soininen, H; Laakso, M P; Partanen, K; Helisalmi, S; Mannermaa, A; Ryynanen, M; Kuikka, J; Hartikainen, P; Riekkinen, P J



Global patterns of cis variation in human cells revealed by high-density allelic expression analysis  

Microsoft Academic Search

Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid

Bing Ge; Dmitry K Pokholok; Tony Kwan; Elin Grundberg; Lisanne Morcos; Dominique J Verlaan; Jennie Le; Vonda Koka; Kevin C L Lam; Vincent Gagné; Joana Dias; Rose Hoberman; Alexandre Montpetit; Marie-Michele Joly; Edward J Harvey; Daniel Sinnett; Patrick Beaulieu; Robert Hamon; Alexandru Graziani; Ken Dewar; Eef Harmsen; Jacek Majewski; Harald H H Göring; Anna K Naumova; Mathieu Blanchette; Kevin L Gunderson; Tomi Pastinen



Identification of new Mamu-DRB alleles using DGGE and direct sequencing  

Microsoft Academic Search

Rhesus macaques represent important animal models for biomedical research. The ability to identify macaque major histocompatibility\\u000a complex (Mhc) alleles is crucial for fully understanding these models of autoimmune and infectious disease. Here we describe a rapid and\\u000a unambiguous way to distinguish DRB alleles in the rhesus macaque using the polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE), and direct\\u000a sequencing.

L. A. Knapp; Luis F. Cadavid; Mary E. Eberle; Stuart J. Knechtle; Ronald E. Bontrop; David I. Watkins



Power for Genetic Association Studies with Random Allele Frequencies and Genotype Distributions  

PubMed Central

One of the first and most important steps in planning a genetic association study is the accurate estimation of the statistical power under a proposed study design and sample size. In association studies for candidate genes or in fine-mapping applications, allele and genotype frequencies are often assumed to be known when, in fact, they are unknown (i.e., random variables from some distribution). For example, if we consider a diallelic marker with allele frequencies of 0.5 and 0.5 and Hardy-Weinberg proportions, the three genotype frequencies are often assumed to be 0.25, 0.50, and 0.25, and the statistical power is calculated. Unfortunately, ignoring this source of variation can inflate the estimated power of the study. In the present article, we propose averaging the estimates of power over the distribution of the genotype frequencies to calculate the true estimate of power for a fixed allele frequency. For the usual situation, in which allele frequencies in a population are not known, we propose placing a prior distribution on the allele frequency, taking advantage of any available genotype information. This Bayesian approach provides a more accurate estimate of power. We present examples for quantitative and qualitative traits in cohort studies of unrelated individuals and results from an extensive series of examples that show that ignoring the uncertainty in allele frequencies can inflate the estimated power of the study. We also present the results from case-control studies and show that standard methods may also overestimate power. As discussed in this article, the approach of fixing allele frequencies even if they are not known is the common approach to power calculations. We show that ignoring the sources of variation in allele frequencies tends to result in overestimates of power and, consequently, in studies that are underpowered. Software in C is available at PMID:15024689

Ambrosius, Walter T.; Lange, Ethan M.; Langefeld, Carl D.



Gene-Based Rare Allele Analysis Identified a Risk Gene of Alzheimer's Disease  

PubMed Central

Alzheimer’s disease (AD) has a strong propensity to run in families. However, the known risk genes excluding APOE are not clinically useful. In various complex diseases, gene studies have targeted rare alleles for unsolved heritability. Our study aims to elucidate previously unknown risk genes for AD by targeting rare alleles. We used data from five publicly available genetic studies from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the database of Genotypes and Phenotypes (dbGaP). A total of 4,171 cases and 9,358 controls were included. The genotype information of rare alleles was imputed using 1,000 genomes. We performed gene-based analysis of rare alleles (minor allele frequency?3%). The genome-wide significance level was defined as meta P<1.8×10–6 (0.05/number of genes in human genome?=?0.05/28,517). ZNF628, which is located at chromosome 19q13.42, showed a genome-wide significant association with AD. The association of ZNF628 with AD was not dependent on APOE ?4. APOE and TREM2 were also significantly associated with AD, although not at genome-wide significance levels. Other genes identified by targeting common alleles could not be replicated in our gene-based rare allele analysis. We identified that rare variants in ZNF628 are associated with AD. The protein encoded by ZNF628 is known as a transcription factor. Furthermore, the associations of APOE and TREM2 with AD were highly significant, even in gene-based rare allele analysis, which implies that further deep sequencing of these genes is required in AD heritability studies. PMID:25329708

Kim, Jong Hun; Song, Pamela; Lim, Hyunsun; Lee, Jae-Hyung; Lee, Jun Hong; Park, Sun Ah



The inheritance, linkage, and fiber development of a new mutant allele in cotton, Gossypium hirsutum L.  

E-print Network

THE INHERITANCE, LINKAGE, AND FIBER DEVELOPMENT OF A NEW MUTANT ALLELE IN COTTON, GOSSYPIUM HIRSUTUM L. A Thesis by EDWARD VERNON NARBUTH Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE May 1989 Major Subject: Plant Breeding THE INHERITANCE, LINKAGE, AND FIBER DEVELOPMENT OF A NEW MUTANT ALLELE IN COTTON, GOSSYPIUM HIRSUTUM L. A Thesis by EDWARD VERNON NARBUTH Ap d as to st...

Narbuth, Edward Vernon



How European is the European Journal of Developmental Psychology?  

Microsoft Academic Search

This paper tries to make clear why a European journal of developmental psychology makes sense. First it is explained that so-called European culture is a complicated matter: historically and culturally many fault lines are to be detected, from the borders of the Roman empire to the iron curtain. These fault lines separate different cultural areas within Europe.?Developmental thinking came into

Willem Koops



G-allele of Intronic rs10830963 in MTNR1B Confers Increased Risk of Impaired Fasting Glycemia and Type 2 Diabetes Through an Impaired Glucose-Stimulated Insulin Release  

PubMed Central

OBJECTIVE Genome-wide association studies have identified several variants within the MTNR1B locus that are associated with fasting plasma glucose (FPG) and type 2 diabetes. We refined the association signal by direct genotyping and examined for associations of the variant displaying the most independent effect on FPG with isolated impaired fasting glycemia (i-IFG), isolated impaired glucose tolerance (i-IGT), type 2 diabetes, and measures of insulin release and peripheral and hepatic insulin sensitivity. RESEARCH DESIGN AND METHODS We examined European-descent participants in the Inter99 study (n = 5,553), in a sample of young healthy Danes (n = 372), in Danish twins (n = 77 elderly and n = 97 young), in additional Danish type 2 diabetic patients (n = 1,626) and control subjects (n = 505), in the Data from the Epidemiological Study on the Insulin Resistance Syndrome (DESIR) study (n = 4,656), in the North Finland Birth Cohort 86 (n = 5,258), and in the Haguenau study (n = 1,461). RESULTS The MTNR1B intronic variant, rs10830963, carried most of the effect on FPG and showed the strongest association with FPG (combined P = 5.3 × 10?31) and type 2 diabetes. The rs10830963 G-allele increased the risk of i-IFG (odds ratio [OR] 1.64, P = 5.5 × 10?11) but not i-IGT. The G-allele was associated with a decreased insulin release after oral and intravenous glucose challenges (P < 0.01) but not after injection of tolbutamide. In elderly twins, the G-allele associated with hepatic insulin resistance (P = 0.017). CONCLUSIONS The G-allele of MTNR1B rs10830963 increases risk of type 2 diabetes through a state of i-IFG and not through i-IGT. The same allele associates with estimates of ?-cell dysfunction and hepatic insulin resistance. PMID:19324940

Spars?, Thomas; Bonnefond, Amelie; Andersson, Ehm; Bouatia-Naji, Nabila; Holmkvist, Johan; Wegner, Lise; Grarup, Niels; Gjesing, Anette P.; Banasik, Karina; Cavalcanti-Proenca, Christine; Marchand, Marion; Vaxillaire, Martine; Charpentier, Guillaume; Jarvelin, Marjo-Riitta; Tichet, Jean; Balkau, Beverley; Marre, Michel; Levy-Marchal, Claire; Faerch, Kristine; Borch-Johnsen, Knut; J?rgensen, Torben; Madsbad, Sten; Poulsen, Pernille; Vaag, Allan; Dina, Christian; Hansen, Torben; Pedersen, Oluf; Froguel, Philippe



Common HLA Alleles Associated with Health, but Not with Facial Attractiveness  

PubMed Central

Three adaptive hypotheses have been proposed to explain the link between the human leucocyte antigen (HLA) genes, health measures and facial attractiveness: inbreeding avoidance, heterozygote advantage and frequency-dependent selection. This paper reports findings that support a new hypothesis relating HLA to health. We suggest a new method to quantify the level of heterozygosity. HLA heterozygosity did not significantly predict health measures in women, but allele frequency did. Women with more common HLA alleles reported fewer cold and flu bouts per year, fewer illnesses in the previous year and rated themselves healthier than women with rare alleles. To our knowledge, this is the first study to show a positive correlation between HLA allele frequency and general health measures. We propose that certain common HLA alleles confer resistance to prevalent pathogens. Nevertheless, neither HLA heterozygosity nor allele frequency significantly predicted how healthy or attractive men rated the female volunteers. Three non-mutually exclusive explanations are put forward to explain this finding. PMID:17653267

Coetzee, Vinet; Barrett, Louise; Greeff, Jaco M.; Henzi, S. Peter; Perrett, David I.; Wadee, Ahmed A.



Activation of the Arabidopsis thaliana Immune System by Combinations of Common ACD6 Alleles  

PubMed Central

A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to pathogens. Known causes for such autonomous activation of the immune system are hyperactive alleles of immune regulators, or epistatic interactions between immune regulators and unlinked genes. We have discovered a third class, in which the Arabidopsis thaliana immune system is activated by interactions between natural alleles at a single locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these interacting alleles, one of which has evolved recently by partial resurrection of a pseudogene, and each type includes multiple functional variants. Most previously studies hybrid necrosis cases involve rare alleles found in geographically unrelated populations. These two types of ACD6 alleles instead occur at low frequency throughout the range of the species, and have risen to high frequency in the Northeast of Spain, suggesting a role in local adaptation. In addition, such hybrids occur in these populations in the wild. The extensive functional variation among ACD6 alleles points to a central role of this locus in fine-tuning pathogen defenses in natural populations. PMID:25010663

Todesco, Marco; Kim, Sang-Tae; Chae, Eunyoung; Bomblies, Kirsten; Zaidem, Maricris; Smith, Lisa M.; Weigel, Detlef; Laitinen, Roosa A. E.



Small CGG repeat expansion alleles of FMR1 gene are associated with parkinsonism  

PubMed Central

Fragile X associated tremor/ataxia (FXTAS) affects older males carrying premutation, that is, expansions of the CGG repeat (in the 55-200 range), in the FMR1 gene. The neurological changes are linked to the excessive FMR1 mRNA, becoming toxic through a ‘gain-of-function’. Since elevated levels of this mRNA are also found in carriers of the smaller expansion (grey zone) alleles, ranging from 40 to 54 CGGs, we tested for a possible role of these alleles in the origin of movement disorders associated with tremor. We screened 228 Australian males affected with idiopathic Parkinson’s disease and other causes of parkinsonism recruited from Victoria and Tasmania, for premutation and grey zone alleles. The frequencies of either of these alleles were compared with the frequencies in a population-based sample of 578 Guthrie spots from consecutive Tasmanian male newborns (controls). There was a significant excess of premutation carriers (Fisher’s exact test P =.006). There was also a more than 2-fold increase in grey zone carriers in the combined sample of the Victorian and Tasmanian cases, with odds ratio (OR)=2.36, and 95% confidence intervals (CI):1.20-4.63, as well as in Tasmanian cases only (OR=2.33, 95% CI:1.06-5.13), compared with controls. The results suggest that the FMR1 grey zone alleles, as well as premutation alleles, might contribute to the aetiology of disorders associated with parkinsonism. PMID:19796183

Loesch, Danuta Z; Khaniani, Mahmoud S; Slater, Howard R; Rubio, Justin P.; Bui, Quang M; Kotschet, Kate; D'Souza, Wendy; Venn, Alison; Kalitsis, Paul; Choo, Andy KH; Burgess, Trent; Johnson, Laura; Evans, Andrew; Horne, Malcolm



Multiple and independent origins of short seeded alleles of GS3 in rice  

PubMed Central

GRAIN SIZE 3 (GS3) is a cloned gene that is related to seed length. Here we report the discovery of new deletion alleles at the GS3 locus, each of which confer short seed. We selected ten short seeded cultivars from a collection of 282 diverse cultivars. Sequence analysis across the GS3 gene in these ten cultivars identified three novel alleles and a known allele that contain several independent deletion(s) in the fifth exon of GS. These independent deletion variants each resulted in a frameshift mutation that caused a premature stop codon, and they were functionally similar to one another. Each coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. Haplotype analysis of these sequence variants indicated that two of the variants were of japonica origin, and two were from indica. Transformation experiments demonstrated that one of the deletion alleles of GS3 decrease the cell number in the upper epidermis of the glume, resulting in a significant reduction in seed length. The multiple and independent origins of these short seeded alleles indicate that farmers and early breeders imposed artificial selection favoring short seeds. PMID:23641184

Takano-Kai, Noriko; Jiang, Hui; Powell, Adrian; McCouch, Susan; Takamure, Itsuro; Furuya, Naruto; Doi, Kazuyuki; Yoshimura, Atsushi



Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles?  

PubMed Central

Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host–pathogen coevolution and the ability of species to resist disease epidemics. PMID:18799711

Blouin, Michael S.



Genome-wide detection of allelic gene expression in hepatocellular carcinoma cells using a human exome SNP chip.  


Allelic variations in gene expression influence many biological responses and cause phenotypic variations in humans. In this study, Illumina Human Exome BeadChips containing more than 240,000 single nucleotide polymorphisms (SNPs) were used to identify changes in allelic gene expression in hepatocellular carcinoma cells following lipopolysaccharide (LPS) stimulation. We found 17 monoallelically expressed genes, 58 allelic imbalanced genes, and 7 genes showing allele substitution. In addition, we also detected 33 differentially expressed genes following LPS treatment in vitro using these human exome SNP chips. However, alterations in allelic gene expression following LPS treatment were detected in only three genes (MLXIPL, TNC, and MX2), which were observed in one cell line sample only, indicating that changes in allelic gene expression following LPS stimulation of liver cells are rare events. Among a total of 75 genes showing allelic expression in hepatocellular carcinoma cells, either monoallelic or imbalanced, 43 genes (57.33%) had expression quantitative trait loci (eQTL) data, indicating that high-density exome SNP chips are useful and reliable for studying allelic gene expression. Furthermore, most genes showing allelic expression were regulated by cis-acting mechanisms and were also significantly associated with several human diseases. Overall, our study provides a better understanding of allele-specific gene expression in hepatocellular carcinoma cells with and without LPS stimulation and potential clues for the cause of human disease due to alterations in allelic gene expression. PMID:25192659

Park, Yon Mi; Cheong, Hyun Sub; Lee, Jong-Keuk



Self-incompatibility of Prunus tenella and evidence that reproductively isolated species of Prunus have different SFB alleles coupled with an identical S-RNase allele.  


Many species of Prunus display an S-RNase-based gametophytic self-incompatibility (SI), controlled by a single highly polymorphic multigene complex termed the S-locus. This comprises tightly linked stylar- and pollen-expressed genes that determine the specificity of the SI response. We investigated SI of Prunus tenella, a wild species found in small, isolated populations on the Balkan peninsula, initially by pollination experiments and identifying stylar-expressed RNase alleles. Nine P. tenella S-RNase alleles (S(1)-S(9)) were cloned; their sequence analysis showed a very high ratio of non-synonymous to synonymous nucleotide substitutions (K(a)/K(s)) and revealed that S-RNase alleles of P. tenella, unlike those of Prunus dulcis, show positive selection in all regions except the conserved regions and that between C2 and RHV. Remarkably, S(8)-RNase, was found to be identical to S(1)-RNase from Prunus avium, a species that does not interbreed with P. tenella and, except for just one amino acid, to S(11) of P. dulcis. However, the corresponding introns and S-RNase-SFB intergenic regions showed considerable differences. Moreover, protein sequences of the pollen-expressed SFB alleles were not identical, harbouring 12 amino-acid replacements between those of P. tenella SFB(8) and P. avium SFB(1). Implications of this finding for hypotheses about the evolution of new S-specificities are discussed. PMID:17461794

Surbanovski, Nada; Tobutt, Kenneth R; Konstantinovi?, Miroslav; Maksimovi?, Vesna; Sargent, Daniel J; Stevanovi?, Vladimir; Boskovi?, Radovan I



Olivier Arino European Space Agency  

E-print Network

Olivier Arino European Space Agency Presented by Hugh Eva European Commission Joint Research Centre GlobCover ­ a land cover map for the year 2005 #12;GlobCover Land Cover Version 2 #12;Heritage: IGBP and `change assessment' Objectives: A Global Land Cover Map 2005/2006 by using MERIS data at 300m #12


Biotechnology products and European consumers  

Microsoft Academic Search

More than 100 interviews conducted during 1997 with European food manufacturers and retailers, trade associations, government departments, consumer groups, environmental organizations and some individual academic scientists revealed how differences in the perceived attitudes of consumers gave rise to varying approaches by suppliers to the possible introduction of transgenic foods. European consumers generally are not against the pharmaceutical products of biotechnology

Vivian Moses



Cybergeo : European Journal of Geography  

E-print Network

Cybergeo : European Journal of Geography Systèmes, Modélisation, Géostatistiques context », Cybergeo : European Journal of Geography [En ligne], Systèmes, Modélisation, Géostatistiques of Geography Mehdi Saqalli, Charles L. Bielders, Pierre Defourny et Bruno Gérard Reconstituting family

Paris-Sud XI, Université de


Cybergeo : European Journal of Geography  

E-print Network

Cybergeo : European Journal of Geography Systèmes, Modélisation, Géostatistiques of Geography [En ligne], Systèmes, Modélisation, Géostatistiques, document 413, mis en ligne le 25 février 2008 environment at a regional level 2 Cybergeo : European Journal of Geography Isabelle Thomas, Cécile Tannier et

Paris-Sud XI, Université de



E-print Network

Conference, adopted a Declaration on combating terrorism and addressed a number of issues arising out European Council. II. TERRORISM 5. The European Council expresses its sympathy and solidarity the Declaration on Combating Terrorism. #12;Presidency Conclusions ­ Brussels, 25/26 March 2004 2 EN III



E-print Network

Constitutional Treaty is a good basis for starting in the Intergovernmental Conference. It requests the future. IMMIGRATION, FRONTIERS AND ASYLUM 8. The European Council of Seville emphasised the need to speed up to the development of a common European policy on asylum and migration. #12;Presidency Conclusions ­ Thessaloniki, 19

Sussex, University of



Microsoft Academic Search

Automatic spoken language identification is the problem of identifying the language being spoken from a sample of speech by an unknown speaker. In this paper we studied the problem of language identification in the context of the European languages, which allowed us to study the effect of language proximity in Indo-European languages. The results reveal a significant impact on the

Diamantino Caseiro; Isabel Trancoso



European Identity: Diversity in Union  

Microsoft Academic Search

This paper discusses the dynamics of identity within the European Union. The authors describe the necessary preconditions for the development of European Identity; including the value of freedom, equal rights and a re-conceptualization of the concept of solidarity in the context of citizenship. Highlighted are how debates about immigrant rights, the rise of neo-racist movements, and the role of political

Rik Pinxten; Marijke Cornelis; Robert A. Rubinstein



International alliances in European retailing  

Microsoft Academic Search

Alliances within European retailing can be seen as either compact and tight alliances, with highly developed interactions amongst alliance partners, or as a much looser concept of collaborative activity amongst retailers. This paper accepts the broad definition of retail alliances that Dawson and Shaw (1992b) propose, and investigates whether this definition is helpful to the study of European retail alliance

Terry Robinson; Colin M. Clarke-Hill



Participation in European water policy  

Microsoft Academic Search

This paper considers the possibilities for interactive policy-making in European water management. In the new European Water Framework Directive, public information and consultation are major elements in the procedure (process) that leads to River Basin Management Plans. In general, decision making in integrated water management should not be limited to the application of models and desk studies. Important decisions need

J. A. van Ast; S. P. Boot



Recent European Manpower Policy Initiatives.  

National Technical Information Service (NTIS)

The report describes the ways that European nations were dealing with complex manpower problems similar to the ones faced by the United States during the recession of 1974-75. It reviews the methods used by the Western European countries during the recess...

C. D. Stewart



FRIGIDA LIKE 2 Is a Functional Allele in Landsberg erecta and Compensates for a Nonsense Allele of FRIGIDA LIKE 11[W][OA  

PubMed Central

The Landsberg erecta (Ler) accession of Arabidopsis (Arabidopsis thaliana) has a weak allele of the floral inhibitor FLOWERING LOCUS C (FLC). FLC-Ler is weakly up-regulated by the active San Feliu-2 (Sf2) allele of FRIGIDA (FRI-Sf2), resulting in a moderately late-flowering phenotype. By contrast, the Columbia (Col) allele of FLC is strongly up-regulated by FRI-Sf2, resulting in a very late-flowering phenotype. In Col, the FRI-related gene FRI LIKE 1 (FRL1) is required for FRI-mediated up-regulation of FLC. It is shown here that in Ler, the FRL1-related gene FRI LIKE 2 (FRL2), but not FRL1, is required for FRI-mediated up-regulation of FLC. FRL1-Ler is shown to be a nonsense allele of FRL1 due to a naturally occurring premature stop codon in the middle of the conceptual protein sequence, suggesting that FRL1-Ler is nonfunctional. Compared to FRL2-Col, FRL2-Ler has two amino acid changes in the conceptual protein sequence. Plants homozygous for FRI-Sf2, FLC-Ler, FRL1-Ler, and FRL2-Col have no detectable FLC expression, resulting in an extremely early flowering phenotype. Transformation of a genomic fragment of FRL2-Ler, but not of FRL2-Col, into a recombinant inbred line derived from these plants restores both FRI-mediated up-regulation of FLC expression and a late-flowering phenotype, indicating that FRL2-Ler is the functional allele of FRL2. Taken together, these results suggest that in the two different Arabidopsis accessions Col and Ler, either FRL1 or FRL2, but not both, is functional and required for FRI-mediated up-regulation of FLC. PMID:17056759

Schlappi, Michael R.



DIIIa and DIII Type 5 are encoded by the same allele and are associated with altered RHCE*ce alleles: clinical implications  

PubMed Central

BACKGROUND The partial D phenotype DIIIa was originally reported to be associated with 455A>C in Exon 3, 602C>G in Exon 4, and 667T>G in Exon 5. Other alleles with these changes were subsequently identified and designated DIII Types 5, 6, and 7, as they had additional alterations. The observation that DNA samples associated with the DIIIa phenotype had more changes than those originally reported motivated us to reanalyze the DIIIa probands (BP and DJ) from the original study. We also studied additional DIIIa samples to clarify the RHD background and establish the associated RHCE. STUDY DESIGN AND METHODS Hemagglutination testing was performed by standard methods. RHD and RHCE were analyzed by combinations of polymerase chain reaction–restriction fragment length polymorphism, exon-specific sequencing, cloning, or direct sequencing of Rh-cDNAs. RESULTS The RHD alleles from BP, DJ, and 58 additional DIIIa samples had the three reported nucleotide changes as well as 186G>T, 410C>T, and 819G>A. The DIIIa allele was associated with several altered RHCE*ce-alleles, the prominent one being ceS (48C, 733G, 1006T). CONCLUSION The DIIIa phenotype is associated with six RHD changes, five of which encode amino acid changes, and partial DIIIa and DIII Type 5 are encoded by the same RHD allele. In all samples, RHD*DIIIa was inherited with altered RHCE*ce. Patients with partial DIIIa are at risk for production of alloanti-D, but they are also at risk for alloanti-e, -c, or antibodies to high-prevalence Rh antigens if there is no conventional RHCE*ce in trans. Among 39 patients studied, 16 had alloanti-D and 27 had alloanti-e or anti-hrB. PMID:20088832

Westhoff, Connie M.; Vege, Sunitha; Halter-Hipsky, Christine; Whorley, Trina; Hue-Roye, Kim; Lomas-Francis, Christine; Reid, Marion E.



Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns.  


Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those labelled with JOE (green) and fluorescein (blue). Overall, the marker D10S1248 has the lowest allele dropout probability and D8S1179 the highest. The marker effect is mainly pronounced for 30-32 PCR cycles. Such effects would not be expected if the amplification efficiencies were identical for all markers. Understanding allele dropout risks and the variability in peak heights and balances is important for correct interpretation of forensic DNA profiles. PMID:25282604

Hedell, Ronny; Dufva, Charlotte; Ansell, Ricky; Mostad, Petter; Hedman, Johannes



Haplotypic Background of a Private Allele at High Frequency in the Americas  

PubMed Central

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ?500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas. PMID:19221006

Schroeder, Kari B.; Jakobsson, Mattias; Crawford, Michael H.; Schurr, Theodore G.; Boca, Simina M.; Conrad, Donald F.; Tito, Raul Y.; Osipova, Ludmilla P.; Tarskaia, Larissa A.; Zhadanov, Sergey I.; Wall, Jeffrey D.; Pritchard, Jonathan K.; Malhi, Ripan S.; Smith, David G.; Rosenberg, Noah A.



Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus  

PubMed Central

A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (Ho?=?0.1180) was lower than expected (He?=?0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P?=?0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P?=?0.000006 and P?=?0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark. PMID:24069299

Iacovakis, Christos; Mamuris, Zissis; Moutou, Katerina A.; Touloudi, Antonia; Hammer, Anne Sofie; Valiakos, George; Giannoulis, Themis; Stamatis, Costas; Spyrou, Vassiliki; Athanasiou, Labrini V.; Kantere, Maria; Asferg, Tommy; Giannakopoulos, Alexios; Salomonsen, Charlotte M.; Bogdanos, Dimitrios; Birtsas, Periklis; Petrovska, Liljana; Hannant, Duncan; Billinis, Charalambos



European Citizenship and European Union Expansion: Perspectives on Europeanness and Citizenship Education from Britain and Turkey  

ERIC Educational Resources Information Center

This article discusses some perspectives on citizenship education in Turkey and Britain in the context of current contested discourses on the nature of European identity and of the European Union (EU). It is based on data collected during an EU-funded student teacher exchange programme between three universities in Turkey and Leicester University…

Wilkins, Chris; Busher, Hugh; Lawson, Tony; Acun, Ismail; Goz, Nur Leman



Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene  

SciTech Connect

At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

Pena, S.D.J.; De Souza, K.T. (Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte (Brazil)); De Andrade, M.; Chakraborty, R. (Univ. of Texas Graduate School of Biomedical Sciences, Houston, TX (United States))



Allelic analysis of sheath blight resistance with association mapping in rice.  


Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r?=?-0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice. PMID:22427867

Jia, Limeng; Yan, Wengui; Zhu, Chengsong; Agrama, Hesham A; Jackson, Aaron; Yeater, Kathleen; Li, Xiaobai; Huang, Bihu; Hu, Biaolin; McClung, Anna; Wu, Dianxing



Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism.  

PubMed Central

We analyzed the origin of allelic diversity at the class II HLA-DRB1 locus, using a complex microsatellite located in intron 2, close to the polymorphic second exon. A phylogenetic analysis of human, gorilla, and chimpanzee DRB1 sequences indicated that the structure of the microsatellite has evolved, primarily by point mutations, from a putative ancestral (GT)x(GA)y-complex-dinucleotide repeat. In all contemporary DRB1 allelic lineages, with the exception of the human *04 and the gorilla *08 lineages, the (GA)y repeat is interrupted, often by a G-->C substitution. In general, the length of the 3' (GA)y repeat correlates with the allelic lineage and thus evolves more slowly than a middle (GA)z repeat, whose length correlates with specific alleles within the lineage. Comparison of the microsatellite sequence from 30 human DRB1 alleles showed the longer 5' (GT)x to be more variable than the shorter middle (GA)z and 3' (GA)y repeats. Analysis of multiple samples with the same exon sequence, derived from different continents, showed that the 5' (GT)x repeat evolves more rapidly than the middle (GA)z and the 3' (GA)y repeats, which is consistent with findings of a higher mutation rate for longer tracts. The microsatellite-repeat-length variation was used to trace the origin of new DRB1 alleles, such as the new *08 alleles found in the Cayapa people of Ecuador and the Ticuna people of Brazil. PMID:10330359

Bergstrom, T F; Engkvist, H; Erlandsson, R; Josefsson, A; Mack, S J; Erlich, H A; Gyllensten, U



Prediction of HLA Class II Alleles Using SNPs in an African Population  

PubMed Central

Background Despite the importance of the human leukocyte antigen (HLA) gene locus in research and clinical practice, direct HLA typing is laborious and expensive. Furthermore, the analysis requires specialized software and expertise which are unavailable in most developing country settings. Recently, in silico methods have been developed for predicting HLA alleles using single nucleotide polymorphisms (SNPs). However, the utility of these methods in African populations has not been systematically evaluated. Methodology/Principal Findings In the present study, we investigate prediction of HLA class II (HLA-DRB1 and HLA-DQB1) alleles using SNPs in the Wolaita population, southern Ethiopia. The subjects comprised 297 Ethiopians with genome-wide SNP data, of whom 188 had also been HLA typed and were used for training and testing the model. The 109 subjects with SNP data alone were used for empirical prediction using the multi-allelic gene prediction method. We evaluated accuracy of the prediction, agreement between predicted and HLA typed alleles, and discriminative ability of the prediction probability supplied by the model. We found that the model predicted intermediate (two-digit) resolution for HLA-DRB1 and HLA-DQB1 alleles at accuracy levels of 96% and 87%, respectively. All measures of performance showed high accuracy and reliability for prediction. The distribution of the majority of HLA alleles in the study was similar to that previously reported for the Oromo and Amhara ethnic groups from Ethiopia. Conclusions/Significance We demonstrate that HLA class II alleles can be predicted from SNP genotype data with a high level of accuracy at intermediate (two-digit) resolution in an African population. This finding offers new opportunities for HLA studies of disease epidemiology and population genetics in developing countries. PMID:22761960

Ayele, Fasil Tekola; Hailu, Elena; Finan, Chris; Aseffa, Abraham; Davey, Gail; Newport, Melanie J.; Rotimi, Charles N.; Adeyemo, Adebowale



Quantification of BRAF V600E alleles predicts papillary thyroid cancer progression.  


The BRAF V600E mutation is the most common genetic alteration in thyroid cancer. However, its clinicopathological significance and clonal mutation frequency remain unclear. To clarify the inconsistent results, we investigated the association between the allelic frequency of BRAF V600E and the clinicopathological features of classic papillary thyroid carcinoma (PTC). Tumour tissues from two independent sets of patients with classic PTC were manually microdissected and analysed for the presence or absence of the BRAF mutation and the mutant allelic frequency using quantitative pyrosequencing. For external validation, the Cancer Genome Atlas (TCGA) data were analysed. The BRAF V600E mutation was found in 264 (82.2%) out of 321 classic PTCs in the training set. The presence of BRAF V600E was only associated with extrathyroidal extension and the absence of thyroiditis. In BRAF V600E-positive tumours, the mutant allelic frequency varied from 8 to 41% of the total BRAF alleles (median, 20%) and directly correlated with tumour size and the number of metastatic lymph nodes. Lymph node metastases were more frequent in PTCs with a high (?20%) abundance of mutant alleles than in those with a low abundance of mutant alleles (P=0.010). These results were reinforced by validation dataset (n=348) analysis but were not reproduced in the TCGA dataset. In a population with prevalent BRAF mutations, quantitative analysis of the BRAF mutation could provide additional information regarding tumour behaviour, which is not reflected by qualitative analysis. Nonetheless, prospective studies are needed before the mutated allele percentage can be considered as a prognostic factor. PMID:25266729

Kim, Min-Hee; Bae, Ja Seong; Lim, Dong-Jun; Lee, Hyoungnam; Jeon, So Ra; Park, Gyeong Sin; Jung, Chan Kwon



HLA alleles associated with the adaptive immune response to smallpox vaccine: a replication study.  


We previously reported HLA allelic associations with vaccinia virus (VACV)-induced adaptive immune responses in a cohort of healthy individuals (n = 1,071 subjects) after a single dose of the licensed smallpox (Dryvax) vaccine. This study demonstrated that specific HLA alleles were significantly associated with VACV-induced neutralizing antibody (NA) titers (HLA-B*13:02, *38:02, *44:03, *48:01, and HLA-DQB1*03:02, *06:04) and cytokine (HLA-DRB1*01:03, *03:01, *10:01, *13:01, *15:01) immune responses. We undertook an independent study of 1,053 healthy individuals and examined associations between HLA alleles and measures of adaptive immunity after a single dose of Dryvax-derived ACAM2000 vaccine to evaluate previously discovered HLA allelic associations from the Dryvax study and determine if these associations are replicated with ACAM2000. Females had significantly higher NA titers than male subjects in both study cohorts [median ID50 discovery cohort 159 (93, 256) vs. 125 (75, 186), p < 0.001; replication cohort 144 (82, 204) vs. 110 (61, 189), p = 0.024]. The association between the DQB1*03:02 allele (median ID50 discovery cohort 152, p = 0.015; replication cohort 134, p = 0.010) and higher NA titers was replicated. Two HLA associations of comparable magnitudes were consistently found between DRB1*04:03 and DRB1*08:01 alleles and IFN-? ELISPOT responses. The association between the DRB1*15:01 allele with IFN-? secretion was also replicated (median pg/mL discovery cohort 182, p = 0.052; replication cohort 203, p = 0.014). Our results suggest that smallpox vaccine-induced adaptive immune responses are significantly influenced by HLA gene polymorphisms. These data provide information for functional studies and design of novel candidate smallpox vaccines. PMID:24880604

Ovsyannikova, Inna G; Pankratz, V Shane; Salk, Hannah M; Kennedy, Richard B; Poland, Gregory A



Cis-Regulatory Variants Affect CHRNA5 mRNA Expression in Populations of African and European Ancestry  

PubMed Central

Variants within the gene cluster encoding ?3, ?5, and ?4 nicotinic receptor subunits are major risk factors for substance dependence. The strongest impact on risk is associated with variation in the CHRNA5 gene, where at least two mechanisms are at work: amino acid variation and altered mRNA expression levels. The risk allele of the non-synonymous variant (rs16969968; D398N) primarily occurs on the haplotype containing the low mRNA expression allele. In populations of European ancestry, there are approximately 50 highly correlated variants in the CHRNA5-CHRNA3-CHRNB4 gene cluster and the adjacent PSMA4 gene region that are associated with CHRNA5 mRNA levels. It is not clear which of these variants contribute to the changes in CHRNA5 transcript level. Because populations of African ancestry have reduced linkage disequilibrium among variants spanning this gene cluster, eQTL mapping in subjects of African ancestry could potentially aid in defining the functional variants that affect CHRNA5 mRNA levels. We performed quantitative allele specific gene expression using frontal cortices derived from 49 subjects of African ancestry and 111 subjects of European ancestry. This method measures allele-specific transcript levels in the same individual, which eliminates other biological variation that occurs when comparing expression levels between different samples. This analysis confirmed that substance dependence associated variants have a direct cis-regulatory effect on CHRNA5 transcript levels in human frontal cortices of African and European ancestry and identified 10 highly correlated variants, located in a 9 kb region, that are potential functional variants modifying CHRNA5 mRNA expression levels. PMID:24303001

Wang, Jen-Chyong; Spiegel, Noah; Bertelsen, Sarah; Le, Nhung; McKenna, Nicholas; Budde, John P.; Harari, Oscar; Kapoor, Manav; Brooks, Andrew; Hancock, Dana; Tischfield, Jay; Foroud, Tatiana; Bierut, Laura J.; Steinbach, Joe Henry; Edenberg, Howard J.; Traynor, Bryan J.; Goate, Alison M.



Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations.  


Previous studies have emphasized ethnically heterogeneous human leukocyte antigen (HLA) classical allele associations to rheumatoid arthritis (RA) risk. We fine-mapped RA risk alleles within the major histocompatibility complex (MHC) in 2782 seropositive RA cases and 4315 controls of Asian descent. We applied imputation to determine genotypes for eight class I and II HLA genes to Asian populations for the first time using a newly constructed pan-Asian reference panel. First, we empirically measured high imputation accuracy in Asian samples. Then we observed the most significant association in HLA-DR?1 at amino acid position 13, located outside the classical shared epitope (Pomnibus = 6.9 × 10(-135)). The individual residues at position 13 have relative effects that are consistent with published effects in European populations (His > Phe > Arg > Tyr ? Gly > Ser)-but the observed effects in Asians are generally smaller. Applying stepwise conditional analysis, we identified additional independent associations at positions 57 (conditional Pomnibus = 2.2 × 10(-33)) and 74 (conditional Pomnibus = 1.1 × 10(-8)). Outside of HLA-DR?1, we observed independent effects for amino acid polymorphisms within HLA-B (Asp9, conditional P = 3.8 × 10(-6)) and HLA-DP?1 (Phe9, conditional P = 3.0 × 10(-5)) concordant with European populations. Our trans-ethnic HLA fine-mapping study reveals that (i) a common set of amino acid residues confer shared effects in European and Asian populations and (ii) these same effects can explain ethnically heterogeneous classical allelic associations (e.g. HLA-DRB1*09:01) due to allele frequency differences between populations. Our study illustrates the value of high-resolution imputation for fine-mapping causal variants in the MHC. PMID:25070946

Okada, Yukinori; Kim, Kwangwoo; Han, Buhm; Pillai, Nisha E; Ong, Rick T-H; Saw, Woei-Yuh; Luo, Ma; Jiang, Lei; Yin, Jian; Bang, So-Young; Lee, Hye-Soon; Brown, Matthew A; Bae, Sang-Cheol; Xu, Huji; Teo, Yik-Ying; de Bakker, Paul I W; Raychaudhuri, Soumya



Human Leukocyte Antigen Class I and II Alleles and Cervical Adenocarcinoma  

PubMed Central

Background: Associations between human leukocyte antigens (HLA) alleles and cervical cancer are largely representative of squamous cell carcinoma (SCC), the major histologic subtype. We evaluated the association between HLA class I (A, B, and C) and class II (DRB1 and DQB1) loci and risk of cervical adenocarcinoma (ADC), a less common but aggressive histologic subtype. Methods: We pooled data from the Eastern and Western US Cervical Cancer studies, and evaluated the association between individual alleles and allele combinations and ADC (n?=?630 ADC; n?=?775 controls). Risk estimates were calculated for 11 a priori (based on known associations with cervical cancer regardless of histologic type) and 38 non a priori common alleles, as odds ratios (OR) and 95% confidence intervals (CI), adjusted for age and study. In exploratory analysis, we compared the risk associations between subgroups with HPV16 or HPV18 DNA in ADC tumor tissues in the Western US study cases and controls. Results: Three of the a priori alleles were significantly associated with decreased risk of ADC [DRB1*13:01 (OR?=?0.61; 95% CI: 0.41–0.93), DRB1*13:02 (OR?=?0.49; 95% CI: 0.31–0.77), and DQB1*06:03 (OR?=?0.64; 95% CI: 0.42–0.95)]; one was associated with increased risk [B*07:02 (OR?=?1.39; 95% CI: 1.07–1.79)]. Among alleles not previously reported, DQB1*06:04 (OR?=?0.46; 95% CI: 0.27–0.78) was associated with decreased risk of ADC and remained significant after correction for multiple comparisons, and C*07:02 (OR?=?1.41; 95% CI: 1.09–1.81) was associated with increased risk. We did not observe a difference by histologic subtype. ADC was most strongly associated with increased risk with B*07:02/C*07:02 alleles (OR?=?1.33; 95% CI: 1.01–1.76) and decreased risk with DRB1*13:02/DQB1*06:04 (OR?=?0.41; 95% CI: 0.21–0.80). Conclusion: Results suggest that HLA allele associations with cervical ADC are similar to those for cervical SCC. An intriguing finding was the difference in risk associated with several alleles restricted to HPV16 or HPV18-related tumors, consistent with the hypothesis that HLA recognition is HPV type-specific. PMID:24995157

Safaeian, Mahboobeh; Johnson, Lisa G.; Yu, Kai; Wang, Sophia S.; Gravitt, Patti E.; Hansen, John A.; Carrington, Mary; Schwartz, Stephen M.; Gao, Xiaojiang; Hildesheim, Allan; Madeleine, Margaret M.



Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences  

SciTech Connect

Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I. [Humboldt Univ., Berlin (Germany)



A pseudodeficiency allele common in non-Jewish Tay-Sachs carriers: Implications for carrier screening  

SciTech Connect

Deficiency of [beta]-hexosaminidase A (Hex A) activity typically results in Tay-Sachs disease. However, healthy subjects found to be deficient in Hex A activity (i.e., pseudodeficient) by means of in vitro biochemical tests have been described. The authors analyzed the HEXA gene of one pseudodeficient subject and identified both a C[sub 739]-to-T substitution that changes Arg[sub 247][yields]Trp on one allele and a previously identified Tay-Sachs disease mutation of the second allele. Six additional pseudodeficient subjects were found to have the C[sub 739]-to-T but for none of 36 Jewish enzyme-defined carries who did not have one of three known mutations common to this group. The C[sub 739]-to-T allele, together with a [open quotes]true[close quotes] Tay-Sachs disease allele, causes Hex A pseudodeficiency. Given both the large proportion of non-Jewish carriers with this allele and that standard biochemical screening cannot differentiate between heterozygotes for the C[sub 739]-to-T mutations and Tay-Sachs disease carriers, DNA testing for this mutation in at-risk couples is essential. This could prevent unnecessary or incorrect prenatal diagnoses. 40 refs., 3 figs., 4 tabs.

Triggs-Raine, B.L.; Akerman, B.R.; Gravel, R.A. (McGill Univ.-Montreal Children's Hospital Research Institute, Montreal, Quebec (Canada)); Mules, E.H.; Thomas, G.H.; Dowling, C.E. (Johns Hopkins School of Medicine, Baltimore, MD (United States)); Kaback, M.M.; Lim-Steele, J.S.T. (Univ. of California, San Diego, CA (United States)); Natowicz, M.R. (Eunice Kennedy Shriver Center for Mental Retardation, Waltham, MA (United States)); Grebner, E.E. (Thomas Jefferson Univ., Philadelphia, PA (United States)); Navon, R.R. (Tel-Aviv Univ., Kfar-Sava (Israel)); Welch, J.P. (Dalhousie Univ., Halifax, Nova, Scotia (Canada)); Greenberg, C.R. (Univ. of Manitoba, Winnipeg (Canada))



HLA-B*4012: a new allele with unique serological features.  


We have defined the new allele HLA-B*4012, which had been isolated from a black individual. It was initially recognized as a serologically unique allele when typing her father for renal transplantation. The HLA class I phenotype was A*0201,*6602; B*4001,*4012; Bw6; Cw*0304,*1505. Sequencing from exon 1 through intron 3 of B*4012 was performed. B*4012 is identical to B*4001 and B*4010 in exon 3, and in the 3' part of exon 2, but it is unique in that exon 1 and the 5' part of exon 2 are identical to B*1503, B*1509, B*1510, B*1518, B*1523, and B*1529. The generation of this allele is best explained by a recombination event in exon 2 (break point between nucleotides 205 and 222 from the beginning of the coding region) of B*4001 or B*4010 with one of these B*15 variants as a donor allele. Its unique serological feature (B48, B60, B70, and B72 reactivity) is consistent with the sequence data of its donor alleles. PMID:11019923

Elsner, H A; O'Brien, B J; Bryan, C F; Meyer, J A; Diederich, D A; Pierce, G E; Lau, M; Terasaki, P I; Blasczyk, R



Osteogensis imperfecta type I is commonly due to a COLIAI null allel of type I collagen  

SciTech Connect

Dermal fibroblasts from most individuals with osteogenesis imperfecta (OI) type I produce about half the normal amount of type I procollagen, as a result of decreased synthesis of one of its constituent chains, pro[alpha](I). To test the hypothesis that decreased synthesis of pro[alpha](I) chains results from mutations in the COL1A1 gene, the authors used primer extension with nucleotide-specific chain termination to measure the contribution of individual COL1A1 alleles to the mRNA pool in fibroblasts from affected individuals. A polymorphic Mn/I restriction endonuclease site in the 3'-untranslated region of COL1A1 was used to distinguish the transcripts of the two alleles in heterozygous individuals. Twenty-three individuals from 21 unrelated families were studied. In each case there was marked diminution in steady-state mRNA levels from one COL1A2 allele. Loss of an allele through deletion or rearrangement was not the cause of the diminished COL1A1 mRNA levels. Primer extension with nucleotide-specific chain termination allows identification of the mutant COL1A1 allele in cell strains that are heterozygous for an expressed polymorphism. It is applicable to sporadic cases, to small families, and to large families in whom key individuals are uninformative at the polymorphic sites used in linkage analysis, making it a useful adjunct to the biochemical screening of collagenous proteins for OI. 40 refs., 3 figs., 1 tab.

Willing, M.C.; Pruchno, C.J. (Univ. of Iowa, Iowa City, IA (United States)); Atkinson, M.; Byers, P.H. (Univ. of Washington, Seattle, WA (United States))



Microsatellite allele sizing: difference between automated capillary electrophoresis and manual technique.  


By comparing data collected with different automated sequencers and a manual technique (fragment separation in a silver-stained polyacrylamide gel), we found strong discrepancies in allele size of microsatellite loci. To quantify the sizing bias generated by automated capillary electrophoresis, we typed 51 alleles at seven loci andfound that differences between actual (manual) and called (automated) sizing were inversely related to locus size. This result seems independent of the fluorescent dye but might be due to different migration patterns of the size standard and the microsatellite loci. Thus, it is essential to distinguish between actual (that can only be confirmed by sequencing) and called (obtained with automated sequencer) allele sizes. To enable the comparison of data collected by different laboratories on different instruments, the greatest attention should be paid to material and protocol descriptions used for allele sizing, and reference standard DNA genotypes should be shared between collaborating laboratories. Without these precautions, scoring errors in allele size might result in important misleading conclusions. PMID:11680712

Delmotte, F; Leterme, N; Simon, J C



[Frequencies of high-resolution HLA-Cw* alleles in China Northern Han population].  


This study was purposed to investigate the frequencies of HLA-Cw* loci in China Northern Han population at gene level and to analyze the population genetic characteristics of HLA-Cw* alleles and distribution difference of gene frequency in regions. The high resolution genotyping for HLA-Cw* loci of 420 cases in China Northern Han population was performed by using PCR-SSP typing technique and their distribution regularity was analyzed statistically. The results showed that 30 HLA-Cw* alleles were detected, among which the frequency of Cw* 0102 (0.1776), 0702 (0.1217), 0602 (0.1150) were highest; other alleles with higher frequency were as follow in proper order: Cw* 0304, 0801, 0303, 0302, 0401, 1402. The rare observed HLA-Cw* 0506, 0810, 1510, 1601 and 1701 were detected firstly in this population. The statistical analysis indicated that the genotype distribution of HLA-Cw* loci coincides with the Hardy-Weinberg test. In conclusion, application of high resolution allele typing can accurately understand the distribution regularity and characteristics of HLA-Cw* alleles in China Northern Han population which provides the basis for research related with HLA-Cw* loci. PMID:20416195

Liang, Xiao-Lan; Han, Jun-Ling; Li, Qian; Sun, Le-Jing; Du, Ying; Liu, Lan-Ting; Qiu, Lu-Gui



Allele-specific binding of airway nuclear extracts to polymorphic beta2-adrenergic receptor 5' sequence.  


Like other intronless G protein-coupled receptor genes, the beta(2)-adrenergic receptor (beta(2)AR) has minimal genetic space for population variability, and has attained such via multiple coding and noncoding polymorphisms. Yet most clinical studies use the two nonsynonymous polymorphisms of the coding region for association analysis despite low levels of linkage disequilibrium with some promoter and 5'UTR polymorphisms. To assess the potential for allele-specific transcription factor binding to beta(2)AR 5'-flanking sequence, 3'-biotin-labeled oligonucleotide duplexes were synthesized. Each was centered on variable sites representing major or minor alleles found in the human population with frequencies of 5% or greater (20 polymorphic sites). Electrophoretic mobility shift assays were performed using human airway smooth muscle or airway epithelial cell nuclear extracts. Many of these polymorphisms resulted in an alteration in binding, and both major allele and minor allele dominance were observed. For example, in airway smooth muscle nuclear extracts, 10 polymorphisms decreased and 2 increased binding, whereas 5 showed no differences. Concordance between airway smooth muscle and epithelial cell nuclear extract binding to polymorphic alleles was found in only approximately 50% of cases. There was no tendency for the rare variants to be more likely to have altered nuclear extract binding compared to the more common variants. Taken together, these results provide potential mechanisms by which beta(2)AR 5'-flanking polymorphisms affect obstructive lung phenotypes. PMID:17255556

Panebra, Alfredo; Schwarb, Mary Rose; Glinka, Clare B; Liggett, Stephen B



Specificity and promiscuity among naturally processed peptides bound to HLA-DR alleles  

PubMed Central

Naturally processed peptides were acid extracted from immunoaffinity- purified HLA-DR2, DR3, DR4, DR7, and DR8. Using the complementary techniques of mass spectrometry and Edman microsequencing, > 200 unique peptide masses were identified from each allele, ranging from 1,200 to 4,000 daltons (10-34 residues in length), and a total of 201 peptide sequences were obtained. These peptides were derived from 66 different source proteins and represented sets nested at both the amino- and carboxy-terminal ends with an average length of 15-18 amino acids. Strikingly, most of the peptides (> 85%) were derived from endogenous proteins that intersect the endocytic/class II pathway, even though class II molecules are thought to function mainly in the presentation of exogenous foreign peptide antigens. The predominant endogenous peptides were derived from major histocompatibility complex-related molecules. A few peptides derived from exogenous bovine serum proteins were also bound to every allele. Four prominent promiscuous self- peptide sets (capable of binding to multiple HLA-DR alleles) as well as 84 allele-specific peptide sets were identified. Binding experiments confirmed that the promiscuous peptides have high affinity for the binding groove of all HLA-DR alleles examined. A potential physiologic role for these endogenous self-peptides as immunomodulators of the cellular immune response is discussed. PMID:8315383



Allelic distribution of human leucocyte antigen in historical and recently diagnosed tuberculosis patients in Southern Italy  

PubMed Central

This study addresses the analysis of the human leucocyte antigen (HLA) allele distribution in 54 historical and in 68 recently diagnosed tuberculosis (TB) patients. The historical cohort was characterized by the presence of large fibrocavernous lesions effectively treated with therapeutic pneumothorax during the period 1950–55. Patients and healthy controls enrolled in the study were from the Campania region of southern Italy. No significant association between HLA alleles and TB in the population of recently diagnosed TB patients was observed. On the contrary, among the historical TB patients there was a strong association with an increased frequency of the HLA-DR4 allele alone and/or in the presence of the HLA-B14 allele (P = 0·000004; Pc = 0·0008), as well as with a decreased frequency of the HLA-A2+,-B14?,DR4? allele association (P = 0·00005; Pc = 0·01). In order to exclude any interference from age-related factors, these results were confirmed by comparing the historical cohort of TB patients with an age-matched healthy control population of the same ethnic origin (P = 0·00004; Pc = 0·008; and P = 0·0001; and Pc = 0·02, respectively). PMID:15009432

Ruggiero, Giuseppina; Cosentini, Elena; Zanzi, Delia; Sanna, Veronica; Terrazzano, Giuseppe; Matarese, Giuseppe; Sanduzzi, Alessandro; Perna, Francesco; Zappacosta, Serafino



Resistance allele frequency to bt cotton in field populations of helicoverpa armigera (Lepidoptera: Noctuidae) in China.  


Resistance evolution in target insects to Bacillus thurningiensis (Bt) cotton, Gossypium hirsutum L., is a main threat to Bt cotton technology. An increasing trend of population density of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) has been observed since 2001 in Qiuxian County (Hebei, China), where Bt cotton has been planted dominantly since 1998. This region was selected in 2006 and 2007 for estimating frequency of gene alleles conferring resistance to Bt cotton by screening the F1 progeny from single-pair cross between field-collected male and laboratory female of the Bt-resistant strain of H. armigera (F1 screen). F1 offspring from each single-pair line were screened for resistance alleles based on larval growth, development, and survival on Bt cotton leaves for 5 d. Two-year results indicated that approximately equal to 20% of field-collected males carried resistance alleles. The conservative estimate of the resistance allele frequency was 0.094 (95% CI, 0.044-0.145) for 2006 and 0.107 (95% CI, 0.055-0.159) for 2007. This is the first report of resistance allele frequency increase to such a high level in the field in China. Long-term adoption of Bt sprays, dominant planting of single-toxin-producing Bt cotton, and lack of conventional cotton refuge system might accelerate the resistance evolution in the region. PMID:18613597

Liu, Fengyi; Xu, Zhiping; Chang, Juhua; Chen, Jin; Meng, Fengxia; Zhu, Yu Cheng; Shen, Jinliang



Spatial heterogeneity in the strength of selection against deleterious alleles and the mutation load.  


According to current estimates of genomic deleterious mutation rates (which are often of the order 0.1-1) the mutation load (defined as a reduction in the average fitness of a population due to the presence of deleterious alleles) may be important in many populations. In this paper, I use multilocus simulations to explore the effect of spatial heterogeneity in the strength of selection against deleterious alleles on the mutation load (for example, it has been suggested that stressful environments may increase the strength of selection). These simulations show contrasted results: in some situations, spatial heterogeneity may greatly reduce the mutation load, due to the fact that migrants coming from demes under stronger selection carry relatively few deleterious alleles, and benefit from a strong advantage within demes under weaker selection (where individuals carry many more deleterious alleles); in other situations, however, deleterious alleles accumulate within demes under stronger selection, due to migration pressure from demes under weaker selection, leading to fitness erosion within those demes. This second situation is more frequent when the productivity of the different demes is proportional to their mean fitness. The effect of spatial heterogeneity is greatly reduced, however, when the response to environmental differences is inconsistent across loci. PMID:22588129

Roze, D



Genome Destabilizing Mutator Alleles Drive Specific Mutational Trajectories in Saccharomyces cerevisiae  

PubMed Central

In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POL? and the Cdc13–Stn1–Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes. PMID:24336748

Stirling, Peter C.; Shen, Yaoqing; Corbett, Richard; Jones, Steven J. M.; Hieter, Philip



The Sampling Distribution of Linkage Disequilibrium under an Infinite Allele Model without Selection  

PubMed Central

The sampling distributions of several statistics that measure the association of alleles on gametes (linkage disequilibrium) are estimated under a two-locus neutral infinite allele model using an efficient Monte Carlo method. An often used approximation for the mean squared linkage disequilibrium is shown to be inaccurate unless the proper statistical conditioning is used. The joint distribution of linkage disequilibrium and the allele frequencies in the sample is studied. This estimated joint distribution is sufficient for obtaining an approximate maximum likelihood estimate of C = 4 Nc, where N is the population size and c is the recombination rate. It has been suggested that observations of high linkage disequilibrium might be a good basis for rejecting a neutral model in favor of a model in which natural selection maintains genetic variation. It is found that a single sample of chromosomes, examined at two loci cannot provide sufficient information for such a test if C < 10, because with C this small, very high levels of linkage disequilibrium are not unexpected under the neutral model. In samples of size 50, it is found that, even when C is as large as 50, the distribution of linkage disequilibrium conditional on the allele frequencies is substantially different from the distribution when there is no linkage between the loci. When conditioned on the number of alleles at each locus in the sample, all of the sample statistics examined are nearly independent of ? = 4Nµ, where µ is the neutral mutation rate. PMID:3979817

Hudson, Richard R.



Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating  

PubMed Central

It is still debated whether main individual fitness differences in natural populations can be attributed to genome-wide effects or to particular loci of outstanding functional importance such as the major histocompatibility complex (MHC). In a long-term monitoring project on Galápagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating data for a total of 506 individuals. Controlling for genome-wide inbreeding, we find strong associations between the MHC locus and nearly all fitness traits. The effect was mainly attributable to MHC sequence divergence and could be decomposed into contributions of own and maternal genotypes. In consequence, the population seems to have evolved a pool of highly divergent alleles conveying near-optimal MHC divergence even by random mating. Our results demonstrate that a single locus can significantly contribute to fitness in the wild and provide conclusive evidence for the ‘divergent allele advantage’ hypothesis, a special form of balancing selection with interesting evolutionary implications. PMID:23677346

Lenz, Tobias L.; Mueller, Birte; Trillmich, Fritz; Wolf, Jochen B. W.



European Southern Observatory  

NSDL National Science Digital Library

The European Southern Observatory (ESO) is an intergovernmental organization comprised of 14 member countries. Its headquarters are in Germany, but they have three observatories in Chile as well. Their website is loaded with information and visitors shouldn't miss going on the "Virtual Tours", on the far right side of the homepage. The tours are of the three observatories in Chile, and offer almost 360 degree views of beautiful, yet sparse landscapes. The tour of La Silla has two particularly beautiful views, "La Silla Moonlight" and "La Silla Sunset". Visitors interested in seeing a panning of an artist's 3D rendering of the Orion Nebula must go to the "Video" link on the left hand menu on the homepage. There are over 1400 videos to choose from, so for those not into the Orion Nebula, never fear, there are plenty of other video choices. Finally, visitors must go to the "Top 100 Images" link on the right side of the homepage to see amazing and gorgeous images taken from the ESO's various observatories.


European Union: Constraints vs. Opportunities  

E-print Network

During the early 1980s, Europe suffered from slow economic growth. As a result of this stagnant growth pattern, the European Union created new economic policies and reforms, which eliminated tariffs and barriers among ...

Kahiha, Nguvitjita



Encon Motivation in European Refineries  

E-print Network

One essential element in a successful energy conservation or Encon program is effective motivation of employees and organizations to conserve energy. Encon motivation in our European refineries is a continuing effort that requires utilization...

Gambera, S.; Lockett, W., Jr.



European pain management discussion forum.  


Queries from European physicians about analgesic pharmacotherapy and responses from the author are presented. Topics addressed in this issue pertain to epidural injection for painful central lumbar stenosis and epicondolysis. PMID:23216190

Breivik, Harald



Natural Selection VS. Random Drift: Evidence from Temporal Variation in Allele Frequencies in Nature  

PubMed Central

We have obtained monthly samples of two species, Drosophila pseudoobscura and Drosophila persimilis, in a natural population from Napa County, California. In each species, about 300 genes have been assayed by electrophoresis for each of seven enzyme loci in each monthly sample from March 1972 to June 1975. Using statistical methods developed for the purpose, we have examined whether the allele frequencies at different loci vary in a correlated fashion. The methods used do not detect natural selection when it is deterministic (e.g., overdominance or directional selection), but only when alleles at different loci vary simultaneously in response to the same environmental variations. Moreover, only relatively large fitness differences (of the order of 15%) are detectable. We have found strong evidence of correlated allele frequency variation in 13–20% of the cases examined. We interpret this as evidence that natural selection plays a major role in the evolution of protein polymorphisms in nature. PMID:4054608

Mueller, Laurence D.; Barr, Lorraine G.; Ayala, Francisco J.



Allelic database and accession divergence of a Brazilian mango collection based on microsatellite markers.  


Allelic patterns and genetic distances were examined in a collection of 103 foreign and Brazilian mango (Mangifera indica) accessions in order to develop a reference database to support cultivar protection and breeding programs. An UPGMA dendrogram was generated using Jaccard's coefficients from a distance matrix based on 50 alleles of 12 microsatellite loci. The base pair number was estimated by the method of inverse mobility. The cophenetic correlation was 0.8. The accessions had a coefficient of similarity from 30 to 100%, which reflects high genetic variability. Three groups were observed in the UPGMA dendrogram; the first group was formed predominantly by foreign accessions, the second group was formed by Brazilian accessions, and the Dashehari accession was isolated from the others. The 50 microsatellite alleles did not separate all 103 accessions, indicating that there are duplicates in this mango collection. These 12 microsatellites need to be validated in order to establish a reliable set to identify mango cultivars. PMID:23096906

Dos Santos Ribeiro, I C N; Lima Neto, F P; Santos, C A F



Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations.  


When positioned into the integrin ?-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting. PMID:23818637

Lonfat, Nicolas; Montavon, Thomas; Jebb, David; Tschopp, Patrick; Nguyen Huynh, Thi Hanh; Zakany, Jozsef; Duboule, Denis



SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data.  


We present a statistical framework for estimation and application of sample allele frequency spectra from New-Generation Sequencing (NGS) data. In this method, we first estimate the allele frequency spectrum using maximum likelihood. In contrast to previous methods, the likelihood function is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives. We then use a bayesian method for estimating the sample allele frequency in a single site, and show how the method can be used for genotype calling and SNP calling. We also show how the method can be extended to various other cases including cases with deviations from Hardy-Weinberg equilibrium. We evaluate the statistical properties of the methods using simulations and by application to a real data set. PMID:22911679

Nielsen, Rasmus; Korneliussen, Thorfinn; Albrechtsen, Anders; Li, Yingrui; Wang, Jun



Extreme Clonality in Lymphoblastoid Cell Lines with Implications for Allele Specific Expression Analyses  

PubMed Central

Lymphoblastoid cell lines (LCL) are being actively and extensively used to examine the expression of specific genes and genome-wide expression profiles, including allele specific expression assays. However, it has recently been shown that approximately 10% of human genes exhibit random patterns of monoallelic expression within single clones of LCLs. Consequently allelic imbalance studies could be significantly compromised if bulk populations of donor cells are clonal, or near clonal. Here, using X chromosome inactivation as a readout, we confirm and quantify widespread near monoclonality in two independent sets of cell lines. Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays. PMID:18698422

Plagnol, Vincent; Uz, Elif; Wallace, Chris; Stevens, Helen; Clayton, David; Ozcelik, Tayfun; Todd, John A.



Modification of primers for GRHPR genotyping: avoiding allele dropout by single nucleotide polymorphisms and homology sequence.  


Mutation of primer site for genotyping by polymerase chain reaction (PCR) may cause allele dropout and other genotyping failures. Primary hyperoxaluria type 2 (PH2) is a rare inherited disease caused by overproduction of endogenous oxalate due to mutations in the glyoxylate/hydroxypyruvate reductase (GRHPR) gene. Here, to avoid allele dropout and primer annealing to multiple sites, and given the discrepancy in intron length between GRHPR gene data, we updated the primers used in the sequence assay of the GRHPR gene. These redesigned primers show potential in reducing detection failure of GRHPR mutations. In addition, we performed a single nucleotide polymorphism (SNP) linkage analysis of the GRHPR gene using direct sequencing with PCR amplification of specific alleles (DS-PASA). Using this technique, we sequenced four common SNPs between intron E and exon 6, which show linkage disequilibrium (LD) consisting of three types of haplotypes, similar to data from the HapMap SNP database. PMID:18982322

Takaoka, Naohisa; Takayama, Tatsuya; Miyazaki, Miki; Nagata, Masao; Ozono, Seiichiro



Allelic association at the D14S43 locus in early onset Alzheimer`s disease  

SciTech Connect

The D14S43 marker is closely linked to the major gene for early onset autosomal dominant Alzheimer`s disease on chromosome 14. Allelic frequencies at the D14S43 locus were compared in 113 familial and isolated cases of early onset Alzheimer`s disease (<60 years of age at onset) (EOAD) and 109 unaffected individuals of the same geographic origin. Allele 7 was significantly (P = 0.033) more frequent in type 1 EOAD patients (13.2%), defined by the presence of at least another first degree relative with EOAD, than in controls (4.1%). Since an autosomal dominant gene is probably responsible for type 1 patients, allelic association may reflect linkage disequilibrium at the D14S43 locus. This would mean that some patients share a common ancestral mutation. However, since multiple tests were carried out, this result must be interpreted with caution, and needs confirmation in an independent sample. 16 refs., 2 tabs.

Brice, A.; Tardieu, S.; Campion, D.; Martinez, M. [and others



TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum  

PubMed Central

Ciliary dysfunction leads to a broad range of overlapping phenotypes, termed collectively as ciliopathies. This grouping is underscored by genetic overlap, where causal genes can also contribute modifying alleles to clinically distinct disorders. Here we show that mutations in TTC21B/IFT139, encoding a retrograde intraflagellar transport (IFT) protein, cause both isolated nephronophthisis (NPHP) and syndromic Jeune Asphyxiating Thoracic Dystrophy (JATD). Moreover, although systematic medical resequencing of a large, clinically diverse ciliopathy cohort and matched controls showed a similar frequency of rare changes, in vivo and in vitro evaluations unmasked a significant enrichment of pathogenic alleles in cases, suggesting that TTC21B contributes pathogenic alleles to ?5% of ciliopathy patients. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies, as well as interact in trans with other disease-causing genes, and highlight how saturated resequencing followed by functional analysis of all variants informs the genetic architecture of disorders. PMID:21258341

Davis, Erica E.; Zhang, Qi; Liu, Qin; Diplas, Bill H.; Davey, Lisa M.; Hartley, Jane; Stoetzel, Corinne; Szymanska, Katarzyna; Ramaswami, Gokul; Logan, Clare V.; Muzny, Donna M.; Young, Alice C.; Wheeler, David A.; Cruz, Pedro; Morgan, Margaret; Lewis, Lora R.; Cherukuri, Praveen; Maskeri, Baishali; Hansen, Nancy F.; Mullikin, James C.; Blakesley, Robert W.; Bouffard, Gerard G.; Gyapay, Gabor; Reiger, Susanne; Tonshoff, Burkhard; Kern, Ilse; Soliman, Neveen A.; Neuhaus, Thomas J.; Swoboda, Kathryn J.; Kayserili, Hulya; Gallagher, Tomas E.; Lewis, Richard A.; Bergmann, Carsten; Otto, Edgar A.; Saunier, Sophie; Scambler, Peter J.; Beales, Philip L.; Gleeson, Joseph G.; Maher, Eamonn R.; Attie-Bitach, Tania; Dollfus, Helene; Johnson, Colin A.; Green, Eric D.; Gibbs, Richard A.; Hildebrandt, Friedhelm; Pierce, Eric A.; Katsanis, Nicholas



Mechanisms for dominance: Adh heterodimer formation in heterozygotes between ENU or x-ray induced null alleles and normal alleles in drosophila melanogaster  

SciTech Connect

To study mechanisms for dominance of phenotype, eight ENU- and four x-ray-induced mutations at the alcohol dehydrogenase (Adh) locus were analyzed for partial dominance in their interaction with normal alleles. All ENU and one of the x-ray mutations were single base substitutions; the other three x-ray mutations were 9-21 base deletions. All but one of the 12 mutant alleles were selected for this study because they produced detectable mutant polypeptides, but seven of the 11 producing a peptide could not form dimers with the normal peptide and the enzyme activity of heterozygotes was about half that of normal homozygotes. Four mutations formed dimers with a decreased catalytic efficiency and two of these were near the limit of detectability; these two also inhibited the formation of normal homodimers. The mutant alleles therefore show multiple mechanisms leading to partial enzyme expression in heterozygotes and a wide range of dominance ranging from almost complete recessive to nearly dominant. All amino acid changes in mutant peptides that form dimers are located between amino acids 182 and 194, so this region is not critical for dimerization. It may, however, be an important surface domain for catalyzation. 34 refs., 8 figs., 2 tabs.

Jiang, J.C.; Lee, W.R.; Chang, S.H.; Silverman, H. (Louisiana State Univ., Baton Rouge (United States))



European Citizenship and the Regions  

Microsoft Academic Search

This article reconsiders the relationship between European citizenship and the regions in the light of theoretical developments in citizenship studies and empirical research in four sub-nation-state territories in Europe (Scotland in the UK, Catalonia in Spain, the Veneto in Italy and Upper Silesia in Poland).The article begins with an outline of the development of the idea of European citizenship and

Joe Painter



Collyriclosis in Central European hirundines  

Microsoft Academic Search

Cutaneous monostome trematode Collyriclum faba (Bremser in Schmalz 1831) is a digenetic flatworm with unknown life cycle. Here, we provide the first compelling evidence\\u000a that despite low prevalence of the parasite, European hirundines are parasitized by this species. First host record for sand\\u000a martin (Riparia riparia) and first European host record for barn swallow (Hirundo rustica) is provided. The birds

Petr Heneberg; Tibor Szép; Tomasz Iciek; Ivan Literák


[European general practice research agenda].  


The EGPRN (European General Practice Research Network) research agenda is a review compiling the strengths and areas of development of European general practice, based on a systematic literature survey and its versatile analysis. The research agenda is a framework paper sharpening the definition and functions of general practice as well as its significance for researchers and decisionmakers. The agenda is useful in structuring the research, evaluation of research needs, strengthening of infrastructure and strategic planning of new research. PMID:24961062

Mäntyselkä, Pekka; Koskela, Tuomas



European Strategy for Tobacco Control  

Microsoft Academic Search

The European Strategy for Tobacco Control (ESTC) reflects the increased political commitment to, and public health expectations of, tobacco control in WHO’s European Region. It was adopted by the WHO Regional Committee for Europe at its fifty-second session in September 2002 and provides an evidence-based framework and guidance for effective national action and international cooperation. The ESTC builds on the



Yahoo! Groups: EuropeanArchaeology  

NSDL National Science Digital Library

This moderated mailing list is intended for a discussion of European prehistoric and historic archaeology, from the Early Paleolithic period through the 1800s. EuropeanArchaeology is a general purpose academic list that is designed to include book and article announcements, field school announcements, discuss new discoveries, theories and interpretations, and related topics. At the site, users can subscribe to the list and read the discussion logs.


High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta  

Microsoft Academic Search

BACKGROUND: Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common

Caroline Daelemans; Matthew E Ritchie; Guillaume Smits; Sayeda Abu-Amero; Ian M Sudbery; Matthew S Forrest; Susana Campino; Taane G Clark; Philip Stanier; Dominic Kwiatkowski; Panos Deloukas; Emmanouil T Dermitzakis; Simon Tavaré; Gudrun E Moore; Ian Dunham



Cloning and characterization of genomic DNA sequences of four self-incompatibility alleles in sweet cherry ( Prunus avium L.)  

Microsoft Academic Search

Gametophytic self-incompatibility (GSI) in sweet cherry is determined by a locus S with multiple alleles. In the style, the S-locus codifies for an allele-specific ribonuclease ( S-RNase) that is involved in the rejection of pollen that carries the same S allele. In this work we report the cloning and genomic DNA sequence analysis including the 5' flanking regions of four

A. Wünsch; J. I. Hormaza



GATA C4 allele 17 as a marker for sub-Saharan origin of Y-chromosome lineages  

Microsoft Academic Search

In 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain, GATA allele 17 was found exclusively in Mozambique [Forensic Sci. Int. 135 (2003) 158]. In the present work, allele 17 was further observed in samples from Angola (9.33%), Mozambique (10.79%) and S. Tomé e Pr??ncipe (3.53%). This allele differs by at least

Leonor Gusmão; Paula Sánchez-Diz; C??ntia Alves; Maria Brión; Sandra Beleza; Lu??sa Pereira; Alejandro Blanco; Maria João Prata; Angel Carracedo; António Amorim



Genetic Exchange of Fimbrial Alleles Exemplifies the Adaptive Virulence Strategy of Porphyromonas gingivalis  

PubMed Central

Porphyromonas gingivalis is a gram–negative anaerobic bacterium, a member of the human oral microbiome, and a proposed “keystone” pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions. PMID:24626479

Kerr, Jennifer E.; Abramian, Jared R.; Dao, Doan-Hieu V.; Rigney, Todd W.; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D.



Monooxygenase Levels and Knockdown Resistance (kdr) Allele Frequencies in Anopheles gambiae and Anopheles arabiensis in Kenya  

PubMed Central

Pyrethroid-treated bed nets and indoor spray are important components of malaria control strategies in Kenya. Information on resistance to pyrethroid insecticides in Anopheles gambiae and An. arabiensis populations is essential to the selection of appropriate insecticides and the management of insecticide resistance. Monooxygenase activity and knockdown resistance (kdr) allele frequency are biochemical and molecular indicators of mosquito resistance to pyrethroids. This study determined baseline information on monooxygenase activity and kdr allele frequency in anopheline mosquitoes in the western region, the Great Rift Valley-central province region, and the coastal region of Kenya. A total of 1990 field-collected individuals, representing 12 An. gambiae and 22 An. arabiensis populations was analyzed. We found significant among-population variation in monooxygenase activity in An. gambiae and An. arabiensis and substantial variability among individuals within populations. Nine out of 12 An. gambiae populations exhibited significantly higher average monooxygenase activity than the susceptible Kisumu reference strain. The kdr alleles (L1014S) were detected in three An. gambiae populations, and one An. arabiensis population in western Kenya, but not in the Rift Valley-central region and the coastal Kenya region. All genotypes with the kdr alleles were heterozygous, and the conservative estimation of kdr allele frequency was below 1% in these four populations. Information on monooxygenase activity and kdr allele frequency reported in this study provided baseline data for monitoring insecticide resistance changes in Kenya during the era when large-scale insecticide-treated bednet and indoor residual spray campaigns were being implemented. PMID:18402140

Chen, Hong; Githeko, Andrew K; Githure, John I; Mutunga, James; Zhou, Guofa; Yan, Guiyun



Allelic Variation in a Willow Warbler Genomic Region Is Associated with Climate Clines  

PubMed Central

Local adaptation is an important process contributing to population differentiation which can occur in continuous or isolated populations connected by various amounts of gene flow. The willow warbler (Phylloscopus trochilus) is one of the most common songbirds in Fennoscandia. It has a continuous breeding distribution where it is found in all forested habitats from sea level to the tree line and therefore constitutes an ideal species for the study of locally adapted genes associated with environmental gradients. Previous studies in this species identified a genetic marker (AFLP-WW1) that showed a steep north-south cline in central Sweden with one allele associated with coastal lowland habitats and the other with mountainous habitats. It was further demonstrated that this marker is embedded in a highly differentiated chromosome region that spans several megabases. In the present study, we sampled 2,355 individuals at 128 sites across all of Fennoscandia to study the geographic and climatic variables associated with the allele frequency distributions of WW1. Our results demonstrate that 1) allele frequency patterns significantly differ between mountain and lowland populations, 2) these allele differences coincide with extreme temperature conditions and the short growing season in the mountains, and milder conditions in coastal areas, and 3) the northern-allele or “altitude variant” of WW1 occurs in willow warblers that occupy mountainous habitat regardless of subspecies. Finally these results suggest that climate may exert selection on the genomic region associated with these alleles and would allow us to develop testable predictions for the distribution of the genetic marker based on climate change scenarios. PMID:24788148

Larson, Keith W.; Liedvogel, Miriam; Addison, BriAnne; Kleven, Oddmund; Laskemoen, Terje; Lifjeld, Jan T.; Lundberg, Max; Akesson, Susanne; Bensch, Staffan



Mining the human phenome using allelic scores that index biological intermediates.  


It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Long