Analysis of Y chromosome haplogroups in Japanese population using short amplicons and its application in forensic analysis

We designed three mini multiplex PCR systems using single-base extension reactions to identify Japanese Y chromosome haplogroups. We selected a group of 22 Y chromosome single nucleotide polymorphisms (SNPs) from the haplogroups most commonly reported in East Asia. To make the systems more useful in analyzing degraded DNA samples, we designed primers to render amplicons of ⩽150 bp. Applying these systems, we classified the Japanese population into major haplogroups and confirmed the applicability of these systems in forensic DNA analysis.