Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles

• Published in: Legal medicine (Tokyo, Japan) Vol. 33; pp. 17 - 22
• Main Authors: Yuasa, Isao, Akane, Atsushi, Yamamoto, Toshimichi, Matsusue, Aya, Endoh, Minoru, Nakagawa, Mayumi, Umetsu, Kazuo, Ishikawa, Takaki, Iino, Morio
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.07.2018
• Subjects: Biogeographical ancestry; Japanese-specific; Japaneseplex; Single nucleotide polymorphism; SNaPshot; Japaneseplex; Japanese-specific; Single nucleotide polymorphism; SNaPshot; Biogeographical ancestry
• ISSN: 1344-6223; 1873-4162
• DOI: 10.1016/j.legalmed.2018.04.008

[Display omitted] •A new assay was developed to differentiate Japanese people from others.•Japanese-specific SNPs were used as ancestry-informative markers.•Single base extension reaction was used for genotyping.•This assay was successfully applied to forensic casework.•This Japanese-specific SNP assay was named Japaneseplex. It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0–4 Japanese-specific alleles per individual, whereas the Japanese had 4–26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.