Evaluation of HID-Ion Ampliseq™ panel in HAN population

Abstract Second generation sequencing offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted fragments. 124 SNPs included in HID-Ion Ampliseq™ panel for human identification were evaluated on the Ion torrent PGM Sequencer System this time. Reference sample of 9948 and blood samples of 45 unrelated individuals were involved for study. Concordance study was performed with reference sample of 9948 between NGS and Sanger sequencing. Full concordance were obtained, however, 3 SNP loci (rs7520386, rs214955 and rs4530059) were detected with F MAR (%) values above 60% for heterozygote. In the SGS data analysis, F MAR values for accurate heterozygotes should be range from 50% to 60%, for homozygotes or Y-SNP should be above 90%. SNPs of rs7520386, rs4530059, rs214955, rs1523537, rs2342747, rs576261 and rs12997453 were recognized as poorly performing loci, either with allelic imbalance or with lower coverage. For the genetic analysis, 8 SNPs (rs2056277, rs1886510, rs740910, rs717302, rs251934, rs938283, rs729172 and rs733164) with lower polymorphism in HAN population (PIC −23 with the 90 auto-SNPs in HAN population of China. And when using the Variant Caller plug-in, variants close to target sites of rs1490413, rs12997453, rs727811, rs6955448, rs1015250, rs10776839, rs2342747 and rs430046 were observed. This preliminary study has demonstrated considerable potential of Ion Torrent PGM as a low to medium throughput SGS platform for SNP detection and HID-Ion Ampliseq™ panel as a commercial tool for human identification in HAN population from China.