Dataset Information

FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.

ABSTRACT: UNLABELLED:The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a genomewide test on allele frequency variation among 11 HapMap3 samples. Common SNPs with minor allele frequency greater than 5 cent from each of 11 HapMap3 samples were included in the present analysis. The population differentiation is measured in terms of fixation index (Fst), and the SNPs with Fst values over 0.5 were defined as highly differentiated SNPs. Our tests were carried out between all pairs of the 11 HapMap3 samples or among subgroups with the same continental ancestries. Altogether we carried out 64 genomewide Fst tests and identified 28,215 highly differentiated SNPs for 49 different combinations of HapMap3 samples in the current database. AVAILABILITY:http://FstSNP-hapmap3.googlecode.com/

SUBMITTER: Duan S

PROVIDER: S-EPMC2639690 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.

Duan Shiwei S Zhang Wei W Cox Nancy Jean NJ Dolan Mary Eileen ME

Bioinformation 20081109 3

<h4>Unlabelled</h4>The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differenti ...[more]

PMID: 19238253

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Project description:BACKGROUND:Recent genome-wide association (GWA) studies have provided compelling evidence of association between genetic variants and common complex diseases. These studies have made use of cases and controls almost exclusively from populations of European ancestry and little is known about the frequency of risk alleles in other populations. The present study addresses the transferability of disease associations across human populations by examining levels of population differentiation at disease-associated single nucleotide polymorphisms (SNPs). METHODS:We genotyped ~1000 individuals from 53 populations worldwide at 25 SNPs which show robust association with 6 complex human diseases (Crohn's disease, type 1 diabetes, type 2 diabetes, rheumatoid arthritis, coronary artery disease and obesity). Allele frequency differences between populations for these SNPs were measured using Fst. The Fst values for the disease-associated SNPs were compared to Fst values from 2750 random SNPs typed in the same set of individuals. RESULTS:On average, disease SNPs are not significantly more differentiated between populations than random SNPs in the genome. Risk allele frequencies, however, do show substantial variation across human populations and may contribute to differences in disease prevalence between populations. We demonstrate that, in some cases, risk allele frequency differences are unusually high compared to random SNPs and may be due to the action of local (i.e. geographically-restricted) positive natural selection. Moreover, some risk alleles were absent or fixed in a population, which implies that risk alleles identified in one population do not necessarily account for disease prevalence in all human populations. CONCLUSION:Although differences in risk allele frequencies between human populations are not unusually large and are thus likely not due to positive local selection, there is substantial variation in risk allele frequencies between populations which may account for differences in disease prevalence between human populations.

Project description:BackgroundObesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms).ResultsWe collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R2 = 0.35, P = 0.0060) with obesity prevalence.ConclusionsWe have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population disparities in obesity prevalence.

Project description:Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.

Dataset Information

FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.

Publications

FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.

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