Y-SNP miniplexes for East Asian Y-chromosomal haplogroup determination in degraded DNA

Abstract

Four multiplex PCR systems followed by single base extension reactions were developed to score 22 single nucleotide polymorphisms (SNPs) and identify the most frequent East Asian Y chromosome haplogroups. Select Y chromosome SNPs allowed hierarchical testing for almost all of the major East Asian haplogroups along the revised Y chromosome tree. The first multiplex consists of six SNPs defining world-wide major haplogroups (M145, RPS4Y711, M89, M9, M214, and M175). The second multiplex includes six SNPs of subhaplogroup O (M119, P31, M95, SRY465, 47z, and M122). The third multiplex contains six SNPs that subdivide the subhaplogroup O3 (M324, P201, M159, M7, M134, and M133). The fourth multiplex comprises four SNPs of subhaplogroup C (M217, M48, M407, and P53.1). The sizes of the PCR amplicons ranged from 70 to 100 bp to facilitate their application to degraded forensic and ancient samples. Validation experiments demonstrated that the multiplexes were optimized for analysis of low template DNA and highly degraded DNA. In a test using DNA samples from 300 Korean males, 16 different Y chromosome haplogroups were identified; haplogroup O2b* was the most frequently observed (29.3%), followed by haplogroups C3 (xC3c, C3d, C3e) (16.0%) and O3a3c1 (11.0%). These multiplex sets will be useful tools for Y-chromosomal haplogroup determination in anthropological and forensic studies of East Asian populations.