The number of SNPs required for distinguishing Japanese from other East Asians

• Published in: Legal medicine (Tokyo, Japan) Vol. 49; p. 101849
• Main Authors: Mizuno, Fuzuki, Naka, Izumi, Ueda, Shintaroh, Ohashi, Jun, Kurosaki, Kunihiko
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.03.2021
• Subjects: 1000 Genomes Project data; East Asians; Hierarchical cluster analysis; Japanese; Principal component analysis; SNPs; SNPs; 1000 Genomes Project data; East Asians; Japanese; Hierarchical cluster analysis; Principal component analysis
• ISSN: 1344-6223; 1873-4162; 1873-4162
• DOI: 10.1016/j.legalmed.2021.101849

•Using SNP genotype data, we developed an objective approach to estimate the population to which an unknown subject belongs.•Japanese can be distinguished from other East Asians by using 3000 randomly selected SNPs in principal component analysis.•The statistical approach used in this study will allow us to determine the number of SNPs required to identify groups of individuals other than Japanese. In some cases, it is necessary to estimate the national origin of an unknown subject in forensic medicine. The use of single nucleotide polymorphism (SNP) markers appears to be very effective for this purpose, since genome-wide SNP genotype data of many human populations are publicly available. In this study, we examined the number of SNPs that could objectively and accurately distinguish Japanese subjects (1KG-JPT) from the other East Asians (1KG-CDX, -CHB, -CHS, and -KHV) using the combination of principal component analysis and hierarchical cluster analysis. A computer simulation showed that approximately 3000 randomly selected SNPs were enough for the discrimination. Our results suggest that at least a 0.024% coverage is needed in the next generation sequencing experiment to objectively determine whether an unknown person is Japanese or not if the amount of DNA sample from him/her is insufficient or the quality is low.