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

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. Functi...

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Bibliographic Details
Published in:International journal of legal medicine 2016-05, Vol.130 (3), p.669-677
Main Authors: Kim, Sung Min, Yoo, Seong Yeon, Nam, Soo Hyun, Lee, Jae Moon, Chung, Ki Wha
Format: Article
Language:English
Subjects:
Asian Continental Ancestry Group - genetics
Exome
Forensic Medicine
Gene Frequency
Genetic Markers
Genetic testing
Genomes
Genotype
Heterozygote
Humans
Identification
Medical Law
Medicine & Public Health
Mutation
Paternity
Polymorphism, Single Nucleotide
Power
Republic of Korea
Sequence Analysis, DNA - methods
Short Communication
Software
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Summary: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 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.
ISSN:0937-9827
1437-1596
DOI:10.1007/s00414-015-1313-0