Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM)

Massively parallel sequencing (MPS) technology is gaining interest in the forensic community. The capabilities of high throughput and simultaneously analyses of many markers enable MPS as an attractive method for human forensics. Recent studies have demonstrated the successful application of the MPS system to short tandem repeat (STR) typing. However, not only DNA sequence variations in the repeat regions of STR but also in flanking regions are required to facilitate profiles sharing with capillary electrophoresis (CE)-based typing method. In this study, we constructed a multiplex PCR system for the MPS analysis of 10 autosomal STR loci (D13S317, D16S539, D19S433, D2S441, D3S1358, D5S818, D6S1043, D7S820, TH01, TPOX) by designing amplicons in the size range of 168-273 base pairs. Sequencing results from 165 Chinese unrelated individuals demonstrated 11 variations in the flanking regions between amplification primer binding sites and core repeat motifs. In addition, three loci, D13S317, D5S818, and D7S820, displayed variants adjacent to the core repeats and caused discordances between sequence-based and length-based typing results. Four loci (D3S1358, D2S441, D19S433 and D7S820) demonstrated an increased allele number using MPS-based typing. This study demonstrated that STR typing by MPS could provide more genetic information from both repeat and flanking regions of STR loci, thus improving the diversity and discrimination power of the system in forensic detection.