Identification of Korean-specific SNP markers from whole-exome sequencing data

详细信息    查看全文

• 作者：Sung Min Kim ; Seong Yeon Yoo ; Soo Hyun Nam…
• 刊名：International Journal of Legal Medicine
• 出版年：2016
• 出版时间：May 2016
• 年：2016
• 卷：130
• 期：3
• 页码：669-677
• 全文大小：574 KB
• 刊物类别：Medicine
• 刊物主题：Medicine & Public Health
  Forensic Medicine
  Medical Law
  Medicine/Public Health, general
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1437-1596
• 卷排序：130

文摘

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.KeywordsSingle-nucleotide polymorphisms (SNPs)KoreanMinor allele frequency (MAF)Next-generation sequencing (NGS)Whole-exome sequencing (WES)