Forensic validation and population genetic evaluation of an MPS-based integrated microhaplotype and Y-SNP/STR (MY)...

Microhaplotypes (MHs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) are highly informative genetic markers that complement the limitations of conventional autosomal forensic markers. We evaluated an integrated MH and Y-SNP/STR (MY) system based on massively parallel sequencing (MPS), which incorporates 114 Y-SNPs, 45 Y-STRs, and 22 MHs. These 22 MHs were selected based on high effective number of alleles (mean global A_e > 8.3) and substantial ancestry informativeness (I_n > 0.185), suggesting their utility in mixture deconvolution and ancestry inference. In this study, we performed a comprehensive forensic validation of the MY system, demonstrating high sensitivity to 0.25 ng gDNA under the present experimental conditions, PCR inhibitor resistance (100 μM EDTA, 50 μM hemoglobin, 50 μM humic acid, and 25 μM indigo), species specificity (successfully distinguishing humans from 10 non-human species), repeatability (100%), and concordance (100% for 240 Y-STR alleles). In addition, the global forensic efficacy and ancestry inference of the 22 MHs were evaluated through forensic parameters and population genetic analyses, including principal component analysis (PCA), multidimensional scaling (MDS), F _ST , phylogenetic tree, and STRUCTURE, based on data from 26 populations in the 1000 Genomes Project (1KGP) and a Guangdong Han (GDH) cohort. The results indicate that the integrated MH and Y-SNP/Y-STR panel provides complementary information for forensic mixture analysis, paternal-lineage characterization, and biogeographic ancestry inference, while further population-scale and inter-laboratory studies will be valuable for broader implementation.