Allele frequency determination of publicly available cSNPs in the Korean population

Abstract

Purpose: As a first step toward the construction of a single-nucleotide polymorphism (SNP) database of the Korean population, the authors determined the allele frequencies of 406 cSNPs selected from the public database.Methods: A pooled DNA sequencing approach was used to determine the allele frequencies of 406 cSNPs selected from 120 genes in 24 individuals. Results: Of 406 cSNPs, 53% were monomorphic in the Korean samples. Among tested SNPs, 292 SNPs (72%) were uncommon (minor allele Ͻ20%) and 114 SNPs (28%) were common (minor allele Ն20%) in our population. Conclusion: An extensive SNP characterization would be necessary, and the ethnic and population-based differences should be considered in the selection of SNPs for the study of complex diseases with association mapping methods. Genet Med 2002:4(6, Supplement):49S-51S. The central aim of genetics is to correlate specific molecular variation with particular phenotype changes. Since the human genome draft sequence was announced in June 2000, it has become possible to understand the spectrum of genetic variation in the human gene pool and its relation to diseases, individual responses to environmental factors, and biological processes such as development and aging. Geneticists have so far used familial linkage methods for studying simple single-gene diseases. 1 However, complex, high-incidence, multigene diseases are thought to require a different approach, that is, an association study, for which single-nucleotide polymorphisms (SNPs) can play a key role. [1][2][3] SNPs consist of the most abundant form of genetic variation and have great potential for mapping complex genetic traits. 4 -7 Because of their potential as genetic markers, scientists in the public and private sectors have begun to focus their attention on searching for SNPs throughout the human genome. 3,8 -12 For whole-genome association studies, it is estimated that approximately 100,000 to 500,000 SNPs would be required. 5,6 Currently, a great deal of effort is being invested in the identification of SNPs. As of June 14, 2002, 4,275,093 SNPs had been deposited into public databases (http://www.ncbi.nlm.nih. gov/SNP) compared with 7,000 SNPs in April 1999. As the SNP identification process accelerates, it becomes necessary to characterize a large number of publicly available SNPs in a population. For an association mapping study, SNP allele frequencies in the population would be critical.We decided to characterize publicly available cSNPs in the Korean population because (1) many SNPs are publicly available already, (2) those SNPs were discovered using rather limited samples, (3) some SNPs may not be common in a given population, and (4) SNP allele frequencies in the population would be critical for an association mapping study. Here, we present the allele frequencies of 406 publicly available cSNPs in 24 Koreans. MATERIALS AND METHODS Collection of candidate cSNPsCandidate cSNPs were identified in the Whitehead Institute for Genome Research (http://www.genome.wi.mit.edu) databases. We picke...