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

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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.

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Acknowledgments

This study was supported by a grant from the National Forensic Service (NFS), Republic of Korea.

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    Authors and Affiliations

    1. Department of Biological Sciences, Kongju National University, 56 Gongjudaehak-ro, Gongju, 32588, Republic of Korea

      Sung Min Kim, Seong Yeon Yoo, Soo Hyun Nam, Jae Moon Lee & Ki Wha Chung

    2. Department of DNA Analysis, Seoul Institute, National Forensic Service, 139 Jiyang-ro, Seoul, 158-707, Republic of Korea

      Seong Yeon Yoo

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    1. Sung Min Kim
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    Correspondence to Ki Wha Chung.

    Ethics declarations

    The experiments comply with the current laws of our country.

    All samples were collected with informed consent according to the protocol approved by the Institutional Review Board for Kongju National University.

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    The authors declare that they have no competing interests.

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    Sung Min Kim and Seong Yeon Yoo contributed equally to this work.

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    Kim, S.M., Yoo, S.Y., Nam, S.H. et al. Identification of Korean-specific SNP markers from whole-exome sequencing data. Int J Legal Med 130, 669–677 (2016). https://doi.org/10.1007/s00414-015-1313-0

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    • DOI: https://doi.org/10.1007/s00414-015-1313-0

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