Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia

Harvard University, Cambridge, Massachusetts, United States
Nature Genetics (Impact Factor: 29.35). 03/2006; 38(2):214-7. DOI: 10.1038/ng1712
Source: PubMed


Whole-genome association studies are predicted to be especially powerful in isolated populations owing to increased linkage disequilibrium (LD) and decreased allelic diversity, but this possibility has not been empirically tested. We compared genome-wide data on 113,240 SNPs typed on 30 trios from the Pacific island of Kosrae to the same markers typed in the 270 samples from the International HapMap Project. The extent of LD is longer and haplotype diversity is lower in Kosrae than in the HapMap populations. More than 98% of Kosraen haplotypes are present in HapMap populations, indicating that HapMap will be useful for genetic studies on Kosrae. The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'.

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Available from: Itsik Pe'er, Aug 28, 2014
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    • "In addition to variation introduced by major continental ancestry, substantial intra-continental clines have been reliably demonstrated, typically mapping onto geographic patterns of historic migration [3-5]. By contrast, population isolates and relatively small founder populations demonstrate less background diversity, which may provide increased power to detect disease-related alleles [6,7]. Nevertheless, even these populations tend to reveal very subtle patterns of genetic structure that reflect demographic history and may affect interpretation of disease association studies [8-10]. "
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    ABSTRACT: Relatively small, reproductively isolated populations with reduced genetic diversity may have advantages for genomewide association mapping in disease genetics. The Ashkenazi Jewish population represents a unique population for study based on its recent (< 1,000 year) history of a limited number of founders, population bottlenecks and tradition of marriage within the community. We genotyped more than 1,300 Ashkenazi Jewish healthy volunteers from the Hebrew University Genetic Resource with the Illumina HumanOmni1-Quad platform. Comparison of the genotyping data with that of neighboring European and Asian populations enabled the Ashkenazi Jewish-specific component of the variance to be characterized with respect to disease-relevant alleles and pathways. Using clustering, principal components, and pairwise genetic distance as converging approaches, we identified an Ashkenazi Jewish-specific genetic signature that differentiated these subjects from both European and Middle Eastern samples. Most notably, gene ontology analysis of the Ashkenazi Jewish genetic signature revealed an enrichment of genes functioning in transepithelial chloride transport, such as CFTR, and in equilibrioception, potentially shedding light on cystic fibrosis, Usher syndrome and other diseases over-represented in the Ashkenazi Jewish population. Results also impact risk profiles for autoimmune and metabolic disorders in this population. Finally, residual intra-Ashkenazi population structure was minimal, primarily determined by class 1 MHC alleles, and not related to host country of origin. The Ashkenazi Jewish population is of potential utility in disease-mapping studies due to its relative homogeneity and distinct genomic signature. Results suggest that Ashkenazi-associated disease genes may be components of population-specific genomic differences in key functional pathways.
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    • "Based on common SNPs, which comprised 74 and 66% of autosomal SNPs in the OOA and CEU, respectively, the distribution and extent of LD were remarkably similar between these two samples. These data are consistent with previous theoretical predictions [Kruglyak, 1999; Pritchard and Przeworski, 2001] and recent empirical data [Bonnen et al., 2006; Service et al., 2006; Navarro et al., 2009; Thompson et al., 2009], all of which point to modest differences in LD between isolated and cosmopolitan populations for common alleles. The situation for rare alleles, however, is likely to be different as has been demonstrated in applications of LD mapping for monogenic diseases and traits. "
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    ABSTRACT: Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02-0.09, and for autosomal SNPs 10-20 kb apart with common alleles (minor allele frequency > or =0.05), the LD measure r(2) was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA ( approximately 88%) at r(2) > or =0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations.
    Full-text · Article · Feb 2010 · Genetic Epidemiology
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    • "These data are widely used in the genetic research communities to assess the LD for these four populations and for other purposes. For example, Bonnen et al. [3] used these four HapMap populations and a sample of 30 trios from Kosrae to compare the LD patterns of these populations and to assess the feasibility of whole-genome association study using the Kosrae population. This year, HapMap Project released its HapMap 3 SNP data, which includes 90 to 180 persons in each of 11 populations. "
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    ABSTRACT: Linkage disequilibrium (LD) is an important measure used in the analysis of single-nucleotide polymorphism (SNP) data. We used the Genetic Analysis Workshop 16 (GAW16) Framingham Heart Study 500 k SNP data to explore the effect of sampling methods on estimating of LD for SNP data. Method and data We found 332 trios in the GAW16 Framingham SNP data. Repeated random samples without replacement, of different sizes of trios and independent individuals, are drawn from these 332 trios. For each sample, the LD is calculated using the Haploview program for the chromosome 1 SNP data. Percents of D' > 0.8 and r2 > 0.8 are calculated for different distance bins based on the Haploview output. The results are summarized by sample size and sampling methods to give us an overall view of the effect of sample size and sampling methods on the LD estimation. Results Trios design gave stable estimates. A sample of 30 to 40 trios gave estimates of percent of LD > 0.8 very close to those from 332 trios. When independent individuals are used, the estimates are less stable and are different from those obtained from the 332 trios for both D' and r2, with larger differences for D'. Conclusion Our results suggest that trio design gives a stable estimate of LD. Therefore it may be more suitable for LD analysis than using independent individuals. We must be cautious when comparing the LD estimates from trios, and those from independent individuals.
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