Genome-wide analysis of CNV and SNP in Koreans

초록

To date, single-marker association analysis in genome-wide association studies (GWAS) has identified a large number of single nucleotide polymorphisms (SNPs) that are highly associated with complex diseases, but only a small portion of genetic heritability is explained by these variants. A copy number variation (CNV) is a physical change of genomic segment ranging from a kilobase to several megabases. CNV may alter disease susceptibility and gene dosage for genetic risk, so is a useful source for finding missing heritability. Recent studies have reported that 60% of the detected CNVs were called with a single copy-number class, which cannot be tested for association and that well-defined polymorphic CNVs tagged by SNPs are more likely to affect multiple expression traits than frequency-matched variants. CNVs encompassing single genes or a set of genes can be more causative variants of genetic disease than SNPs alone. Therefore, SNPs correlated with CNVs are a valuable resource for GWAS. Most CNV databases (except SCAN) do not consider polymorphic CNV (multi copy-number class). SCAN database also contains CNV data of Caucasian and Yoruba populations, and does not provide Asian CNV data. Due to the difference in CNVs between distinct ethnic groups, providing polymorphic CNVs and allele frequency of each genotype in Asian populations will help investigate CNV-association with diseases and ethnic differences. In this study we developed a database called Korean Genomic Variant Database (KGVDB), which provides polymorphic CNV regions and well-tagged SNP information. The data were obtained from 4,700 individuals using two different genotyping platforms and publicly available CNV data. The large data set of KGVDB will provide a rich public resource for the study of CNV and SNP.