title: Identification of Korean-specific SNP markers from whole-exome sequencing data.
abstract: Analysis of large numbers of single-nucleotide polymorphisms (SNPs) can increase individual discrimination power, and, particularly, it can supply important evidence for kinship or ethnic identification. We identified 300 Korean-specific SNPs from 306 Korean whole-exome sequencing (WES) data. Functionally significant SNPs (variants in splicing site, missense, nonsense, and exonic indels) were filtered out from the variant pool, and SNPs with minor allele frequencies (MAFs) of <0.3 in the 1000 Genomes (1000G) database but >0.3 in the Korean population were selected. Genotypes obtained from WES were confirmed by the Sanger sequencing method. The identified markers were evenly distributed throughout the autosomal chromosomes. All the SNPs were in the Hardy-Weinberg equilibrium with a mean MAF of 0.415 (0.161 in 1000G). The mean heterozygosities were 0.476 (observed) and 0.470 (experimental). The combined power of discrimination was very high. Korean MAFs in most SNPs were similar to those for the Chinese and Japanese populations, but were significantly higher than those for several other ethnic populations. These selected SNPs will be used to develop forensic markers and are expected to be widely used for additional individual identification, ethnic discrimination, and linkage analysis for kinship tests.
authors: Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea.
authors: Sung Min
authors: SM
authors: Kim
authors: Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea.|Department of DNA Analysis, Seoul Institute, National Forensic Service, 139 Jiyang-ro, Seoul, 158-707, Republic of Korea.
authors: Seong Yeon
authors: SY
authors: Yoo
authors: Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea.
authors: Soo Hyun
authors: SH
authors: Nam
authors: Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea.
authors: Jae Moon
authors: JM
authors: Lee
authors: Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea. kwchung@kongju.ac.kr.
authors: Ki Wha
authors: KW
authors: Chung
mesh_terms: D044466:Asian People / Q000235:genetics*; D059472:Exome; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D005819:Genetic Markers
keywords: Korean; Minor allele frequency (MAF); Next-generation sequencing (NGS); Single-nucleotide polymorphisms (SNPs); Whole-exome sequencing (WES)