Validation of 58 autosomal individual identification SNPs in three Chinese populations

Abstract

Aim: To genotype and evaluate a panel of single-nucleotide polymorphisms for individual identification (IISNPs) in three Chinese populations: Chinese Han, Uyghur, and Tibetan.

Methods: Two previously identified panels of IISNPs, 86 unlinked IISNPs and SNPforID 52-plex markers, were pooled and analyzed. Four SNPs were included in both panels. In total, 132 SNPs were typed on Sequenom MassARRAY® platform in 330 individuals from Han Chinese, Uyghur, and Tibetan populations. Population genetic indices and forensic parameters were determined for all studied markers.

Results: No significant deviation from Hardy-Weinberg equilibrium was observed for any of the SNPs in 3 populations. Expected heterozygosity (He) ranged from 0.144 to 0.500 in Han Chinese, from 0.197 to 0.500 in Uyghur, and from 0.018 to 0.500 in Tibetan population. Wright's Fst values ranged from 0.0001 to 0.1613. Pairwise linkage disequilibrium (LD) calculations for all 132 SNPs showed no significant LD across the populations (r(2)<0.147). A subset of 58 unlinked IISNPs (r(2)<0.094) with He>0.450 and Fst values from 0.0002 to 0.0536 gave match probabilities of 10-25 and a cumulative probability of exclusion of 0.999992.

Conclusion: The 58 unlinked IISNPs with high heterozygosity have low allele frequency variation among 3 Chinese populations, which makes them excellent candidates for the development of multiplex assays for individual identification and paternity testing.