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Minor Allele Frequency (minor + allele_frequency)
Selected AbstractsA Mediterranean diet rich in virgin olive oil may reverse the effects of the -174G/C IL6 gene variant on 3-year body weight changeMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue S1 2010Cristina Razquin Abstract Only a few studies have analyzed the effects of the potential interaction between the -174G/C polymorphism of IL6 gene and the adherence to the Mediterranean diet (MD) on adiposity indexes. Our aim was to investigate the interplay between the -174G/C polymorphism of the IL6 gene and a Mediterranean-style diet on body weight changes after 3 years of nutritional intervention in a high cardiovascular risk population. A total of 737 participants, aged 55,80 years were assigned to a low-fat diet or to a Mediterranean-style diet group with high intake of virgin olive oil (VOO) or nuts. Anthropometric measurements were taken at baseline and after 3-year follow-up. The -174G/C polymorphism of the IL6 gene was genotyped. Minor allele frequency (C) was 0.39. At baseline, the CC genotype was associated with higher measures of adiposity. After 3 years, a significant interaction (p=0.028) was found between the polymorphism (GG+GC versus CC) and the nutritional intervention: CC subjects following the MD+VOO had the lowest body weight gain. In conclusion, at baseline, CC subjects for the -174G/C polymorphism of IL6 had the highest body weight and BMI. However, after 3 years of nutritional intervention with MD+VOO, these subjects were predicted to have the greatest reduction in body weight. [source] Effect of RBP4 gene variants on circulating RBP4 concentration and Type 2 diabetes in a Chinese populationDIABETIC MEDICINE, Issue 1 2008C. Hu Abstract Aims Retinol binding protein 4 (RBP4) is a newly discovered adipokine, which plays a role in insulin resistance and obesity. The aim of this study was to determine the relationship between genetic variants of the RBP4 gene, circulating RBP4 concentrations and phenotypes related to glucose and lipid metabolism in the Chinese population. Methods We sequenced exons and the putative promoter region to identify single nucleotide polymorphisms (SNPs) in the RBP4 gene in 32 Chinese subjects. Additional SNPs were selected from a public database to increase marker density. Taking account of the pairwise linkage disequilibrium and minor allele frequencies, a subset of SNPs was further genotyped in 255 Type 2 diabetic patients and 372 normal control subjects. Circulating RBP4 concentrations and phenotypes related to glucose and lipid metabolism were measured. Results Ten SNPs were identified and five were further genotyped in the full sample. No individual SNP was significantly associated with Type 2 diabetes, but a rare haplotype CAA formed by +5388 C>T, +8201 T>A and +8204 T>A was more frequent in diabetic patients (P = 0.0343, empirical P = 0.0659 on 10 000 permutations). In both groups, non-coding SNPs were associated with circulating RBP4 concentrations (P < 0.05). In the normal control subjects, the SNP +5388 C>T was associated with serum C-peptide levels both fasting and 2 h after an oral glucose tolerance test (P = 0.0162 and P = 0.0075, respectively). Conclusion Our findings suggest that genetic variants in the RBP4 gene may be associated with circulating RBP4 concentration and phenotypes related to glucose metabolism. [source] Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and qualityANIMAL GENETICS, Issue 4 2009J. L. Williams Summary A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 individuals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed. [source] Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markersANIMAL SCIENCE JOURNAL, Issue 3 2010Bang Zhong LIN ABSTRACT The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE. [source] Linkage Disequilibrium Pattern in Asthma Candidate Genes from 5q31-q33 in the Singapore Chinese PopulationANNALS OF HUMAN GENETICS, Issue 2 2010Pallavi N. Parate Summary Studies have shown linkage between microsatellite markers from the chromosome 5q31-q33 region with asthma, atopy and total IgE levels in the Singapore Chinese population. However, subsequent case-control studies failed to show association between the polymorphisms in the candidate genes from this region and asthma or related phenotypes. In this study, we investigated 20 asthma candidate genes from this region for all possible informative polymorphisms within our population, linkage disequilibrium (LD) structure and tagging SNP transferability from HapMap populations. We re-sequenced these genes and identified 267 polymorphisms including 26 insertion-deletions, four microsatellite markers and 237 single nucleotide polymorphisms. The region contained 17 distinct LD blocks with the largest within the serine peptidase inhibitor kazal type 5 (SPINK5) gene spanning 23 kb. Of the 267 polymorphisms identified, 40% are represented in HapMap Han Chinese from Beijing and 29% in Han Chinese from Denver. 72% of the polymorphisms can be represented by tagged SNPs from the HapMap Beijing Han Chinese population and are highly correlated in terms of minor allele frequencies and LD structure. Our data suggest that although the HapMap Han Chinese population from Beijing is very similar to the Singapore Chinese population, this similarity is insufficient to account for up to 28% of the polymorphisms in the local population. [source] Evaluating the Ability of Tree-Based Methods and Logistic Regression for the Detection of SNP-SNP InteractionANNALS OF HUMAN GENETICS, Issue 3 2009M. García-Magariños Summary Most common human diseases are likely to have complex etiologies. Methods of analysis that allow for the phenomenon of epistasis are of growing interest in the genetic dissection of complex diseases. By allowing for epistatic interactions between potential disease loci, we may succeed in identifying genetic variants that might otherwise have remained undetected. Here we aimed to analyze the ability of logistic regression (LR) and two tree-based supervised learning methods, classification and regression trees (CART) and random forest (RF), to detect epistasis. Multifactor-dimensionality reduction (MDR) was also used for comparison. Our approach involves first the simulation of datasets of autosomal biallelic unphased and unlinked single nucleotide polymorphisms (SNPs), each containing a two-loci interaction (causal SNPs) and 98 ,noise' SNPs. We modelled interactions under different scenarios of sample size, missing data, minor allele frequencies (MAF) and several penetrance models: three involving both (indistinguishable) marginal effects and interaction, and two simulating pure interaction effects. In total, we have simulated 99 different scenarios. Although CART, RF, and LR yield similar results in terms of detection of true association, CART and RF perform better than LR with respect to classification error. MAF, penetrance model, and sample size are greater determining factors than percentage of missing data in the ability of the different techniques to detect true association. In pure interaction models, only RF detects association. In conclusion, tree-based methods and LR are important statistical tools for the detection of unknown interactions among true risk-associated SNPs with marginal effects and in the presence of a significant number of noise SNPs. In pure interaction models, RF performs reasonably well in the presence of large sample sizes and low percentages of missing data. However, when the study design is suboptimal (unfavourable to detect interaction in terms of e.g. sample size and MAF) there is a high chance of detecting false, spurious associations. [source] The influence of common gene variants of the xenobiotic receptor (PXR) in genetic susceptibility to intrahepatic cholestasis of pregnancyALIMENTARY PHARMACOLOGY & THERAPEUTICS, Issue 5 2010G. CASTAÑO Aliment Pharmacol Ther,31, 583,592 Summary Background, The xenobiotic nuclear pregnane X receptor is implicated in many physiological pathways and diseases, including bile acid detoxification and cholestasis. Aim, To estimate the contribution of common gene variants of the xenobiotic receptor (pregnane X receptor, PXR) to genetic susceptibility to intrahepatic cholestasis of pregnancy. Methods, A total of 101 intrahepatic cholestasis of pregnancy patients and 171 healthy pregnant women in the third trimester of their pregnancies were included. Four tag single nucleotide polymorphisms (SNPs) (rs12488820 C/T, rs2472671 C/T, rs2461823 A/G, and rs1054191 A/G) encompassing 36 kb in chromosome 3, with a minor allele frequency ,0.10 and representing 33 polymorphic sites were genotyped. Besides these, three additional SNPs (rs3814057, rs6785049, and rs7643645) were included because they showed previous evidence of functionality. Results, Genotypic test for single SNPs showed that rs2461823 genotypes were significantly associated with intrahepatic cholestasis of pregnancy (P < 0.0069), OR per G allele: 1.44, 95% CI: 1.01,2.05, P < 0.042. The Cochran-Armitage test for trend and the allelic test showed a significant association with disease status (P < 0.04 and 0.03 respectively), G being the risk allele. A positive association between rs2461823 and ALT, AST, and bilirubin concentrations was observed. Neonate birth weight adjusted by the Capurro index was significantly associated with rs2461823 (P < 0.05); the proportion of the total variation attributed to rs2461823 genotypes was 7.8%. Conclusion, Common PXR polymorphisms may contribute to the genetic susceptibility to intrahepatic cholestasis of pregnancy. [source] The effect of BDNF gene variants on asthma in German childrenALLERGY, Issue 12 2009S. Zeilinger Background:, Allergic inflammation can trigger neuronal dysfunction and structural changes in the airways and the skin. Levels of brain-derived neurotrophic factor (BDNF) are strongly up regulated at the location of allergic inflammation. Aim:, We systematically investigated whether polymorphisms in the BDNF gene influence the development or severity of asthma and atopic diseases. Methods:, The BDNF gene was screened for mutations in 80 chromosomes. Genotyping of six BDNF tagging polymorphisms was performed in a cross-sectional study population of 3099 children from Dresden and Munich (age 9,11 years, ISAAC II). Furthermore, polymorphisms were also investigated in an additional 655 asthma cases analysed with a random sample of 767 children selected from ISAAC II. Associations were calculated via chi-square test and anova using SAS Genetics and spss. Results:, We identified nine polymorphisms with minor allele frequency ,0.03, one of them leading to an amino acid change from Valine to Methionine. In the cross-sectional study population, no significant association was found with asthma or any atopic disease. However, when more severe asthma cases from the MAGIC study were analysed, significant asthma effects were observed with rs6265 (odds ratio 1.37, 95% confidence interval 1.14,1.64, P = 0.001), rs11030101 (OR 0.82, 95%CI 0.70,0.95, P = 0.009) and rs11030100 (OR 1.19, 95%CI 1.00,1.42, P = 0.05). Conclusions:, As in previous studies, effects of BDNF polymorphisms on asthma remain controversial. The data may suggest that BDNF polymorphisms contribute to severe forms of asthma. [source] Distinct association of genetic variations of vascular endothelial growth factor, transforming growth factor-,, and fibroblast growth factor receptors with atopy and airway hyperresponsivenessALLERGY, Issue 4 2008H.-K. Park Background:, Recent studies showed that high levels of transforming growth factor (TGF)-,1 in the airways reduced airway responsiveness, which was reversed in conditions of basic fibroblast growth factor (FGF2) deficiency, whereas high levels of vascular endothelial growth factor (VEGF) enhanced airway sensitization to allergens and airway hyperresponsiveness (AHR). Objective:, We investigated the effect of single-nucleotide polymorphisms (SNPs) in the VEGF, TGF-,1, and FGF2 receptors on the expression of atopy and AHR in the general population. Methods:, Atopy and AHR were evaluated in a cohort of 2055 children and adolescents. Direct sequencing was used to identify informative SNPs (minor allele frequency >5%) in the receptors of candidate genes. Tagging SNPs were scored using the high-throughput single-base pair extension method, and the statistical significance of these scores was assessed via haplotype analysis. Results:, Informative SNPs were identified for VEGF receptors 1 (Flt-1); TGF-, receptor 3 (TGFBR3); and FGR receptors 1, 2, and 4 (FGFR1, FGFR2, and FGFR4), and 13 tagging SNPs were scored in the cohort. Atopy was significantly associated with haplotypes of TGFBR3, FGFR1, and FGFR2. Meanwhile, AHR was significantly associated with haplotypes of Flt-1, FGFR1, and FGFR4. However, atopy was not associated with genetic variations of Flt-1 and FGFR4, whereas AHR not associated with TGFBR3 and FGFR2. Conclusion:, The expression of atopy and AHR is distinctly associated with genetic variations in VEGF, TGF-,1, and FGFR in the Korean population. [source] Prospects for inferring pairwise relationships with single nucleotide polymorphismsMOLECULAR ECOLOGY, Issue 4 2003Jeffrey C. Glaubitz Abstract An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full-sibs from half-sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al. (1996). We have explored a ,best case scenario' in which 100 independently segregating SNPs are available. For discrimination among single-generation relationships or for the identification of parent,offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16,20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future. [source] Discovery, validation and characterization of 1039 cattle single nucleotide polymorphismsANIMAL GENETICS, Issue 4 2010R. Donthu Summary We identified ,13 000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat-masked BAC-end sequences from the cattle RPCI-42 BAC library with whole-genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency ,0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every ,3 Mbp on average. Twenty-four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi-breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome-wide association studies and applications in animal breeding. [source] The combined effect of SNP-marker and phenotype attributes in genome-wide association studiesANIMAL GENETICS, Issue 2 2009E. K. F. Chan Summary The last decade has seen rapid improvements in high-throughput single nucleotide polymorphism (SNP) genotyping technologies that have consequently made genome-wide association studies (GWAS) possible. With tens to hundreds of thousands of SNP markers being tested simultaneously in GWAS, it is imperative to appropriately pre-process, or filter out, those SNPs that may lead to false associations. This paper explores the relationships between various SNP genotype and phenotype attributes and their effects on false associations. We show that (i) uniformly distributed ordinal data as well as binary data are more easily influenced, though not necessarily negatively, by differences in various SNP attributes compared with normally distributed data; (ii) filtering SNPs on minor allele frequency (MAF) and extent of Hardy,Weinberg equilibrium (HWE) deviation has little effect on the overall false positive rate; (iii) in some cases, filtering on MAF only serves to exclude SNPs from the analysis without reduction of the overall proportion of false associations; and (iv) HWE, MAF and heterozygosity are all dependent on minor genotype frequency, a newly proposed measure for genotype integrity. [source] The Cost Effectiveness of Duplicate Genotyping for Testing Genetic AssociationANNALS OF HUMAN GENETICS, Issue 3 2009Nathan Tintle Summary We consider a modification to the traditional genome wide association (GWA) study design: duplicate genotyping. Duplicate genotyping (re-genotyping some of the samples) has long been suggested for quality control reasons; however, it has not been evaluated for its statistical cost-effectiveness. We demonstrate that when genotyping error rates are at least m%, duplicate genotyping provides a cost-effective (more statistical power for the same price) design alternative when relative genotype to phenotype/sample acquisition costs are no more than m%. In addition to cost and error rate, duplicate genotyping is most cost-effective for SNPs with low minor allele frequency. In general, relative genotype to phenotype/sample acquisition costs will be low when following up a limited number of SNPs in the second stage of a two-stage GWA study design, and, thus, duplicate genotyping may be useful in these situations. In cases where many SNPs are being followed up at the second stage, duplicate genotyping only low-quality SNPs with low minor allele frequency may be cost-effective. We also find that in almost all cases where duplicate genotyping is cost-effective, the most cost-effective design strategy involves duplicate genotyping all samples. Free software is provided which evaluates the cost-effectiveness of duplicate genotyping based on user inputs. [source] Polymorphism of matrix metalloproteinase genes (MMP1 and MMP3) in patients with varicose veinsCLINICAL & EXPERIMENTAL DERMATOLOGY, Issue 5 2009M. Kurzawski Summary Background., Several risk factors for varicose veins have been identified: female gender, combined with obesity and pregnancy, occupations requiring standing for long periods, sedentary lifestyle, history of deep-vein thrombosis and family history. However, no specific gene variants related to a wide prevalence of varicosities in general population have been identified. Extracellular matrix composition, predominantly maintained by matrix metalloproteinases (MMPs), may affect the vein-wall structure, which may lead to dilation of vessels and cause varicosities. Aims., MMP-1 (tissue collagenase I) and MMP-3 (stromelysin I) expression was found to be raised in varicose veins compared with normal vessels. Therefore, a study was conducted to evaluate a potential association between MMP1 and MMP3 promoter polymorphisms and a risk of varicose veins. Methods., Genotyping for the presence of the polymorphisms ,1607dupG (rs1799750) in MMP1 and ,1171dupA (rs3025058) in the MMP3 promoter region was performed using PCR and restriction-fragment length polymorphism assays in a group of 109 patients diagnosed with varicose veins and 112 healthy controls. Results., The frequencies of the MMP1 and MMP3 alleles (minor allele frequency 0.440 in patients vs. 0.451 in the controls for MMP1,1607*G and 0.514 vs. 0.469 for MMP3,1171*dupA, respectively) and of genotypes did not differ significantly between patients and controls. Conclusions., The MMP1,1607dupG and MMP3,1171dupA promoter polymorphisms are not valuable markers of susceptibility for varicose veins. [source] CYR61 polymorphisms are associated with plasma HDL-cholesterol levels in obese individualsCLINICAL GENETICS, Issue 3 2007L Bouchard We have recently characterized the transcriptome of the omental adipose tissue of non-diabetic, obese men with and without the metabolic syndrome (MS). The cysteine-rich protein 61 (CYR61) is one of the most differentially expressed genes between the groups and has been selected for a detailed molecular investigation. Direct sequencing of complete CYR61 gene revealed five polymorphisms with minor allele frequency >5% in the promoter region (rs3753794, rs3753793 and rs2297140), intron 1 (rs2297141) and intron 2 (IVS2+50). Chi-square test and logistic regression were applied to test for association between CYR61 polymorphisms and the individual MS components in a cohort of 697 obese individuals. In men and women, rs3753794 and rs3753793 (r2 = 0.77) were associated plasma HDL-cholesterol levels (p = 0.016 and p = 0.008). Carriers of the A allele for rs3753794 were more likely to have high plasma HDL-cholesterol levels (1.50-fold; p = 0.016), as compared with G/G homozygotes and the A/A homozygotes for rs3753793 were more likely to exhibit low plasma HDL-cholesterol levels (1.56-fold; p = 0.008), as compared with C/C homozygotes. Furthermore, an association between IVS2+50 polymorphism and HDL-cholesterol was found in women and in men analyzed separately (p = 0.002 and p = 0.038, respectively). These results suggest that CYR61 is a promising candidate gene for lipoprotein/lipid perturbations. [source] | |||||||||||||