Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. (July 2016) - Guo, Fei
Highlights: The Early Access STR Kit v1 is designed to detect 25-plex loci with NGS technology on the Ion Torrent PGM™ platform. Analytical thresholds of 10×, 50× and 100× were assessed to the influence on the confirmation of alleles and on the filtration of noises. Data quality was evaluated on constituent ratio, allele coverage and heterozygous balance at each locus. Series experiments demonstrated that the Early Access STR Kit v1 system is a robust, reliable and reproducible system. Full profile was obtained from 100 pg. Mixtures were easily detected at 9:1 and 1:9 ratios. It could be adapted to case-type and degraded samples. Abstract: The Early Access STR Kit v1 is designed to detect 25-plex loci with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 16 of 20 expanded Combined DNA Index System (CODIS) core loci (CSF1PO, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D13S317, D16S539, D19S433, D21S11, TH01, TPOX and vWA), 8 non-CODIS core loci (D1S1677, D2S1776, D4S2408, D5S2500.AC008791, D6S1043, D6S474, D9S2157 and D14S1434) and Amelogenin. In this study, we compared the Early Access STR Kit v1 with the Ion Torrent™ HID STR 10-plex to find out its improvements and explored an appropriate analytical threshold to enhance the performance. In addition, seven experiments were conducted to evaluate the Early Access STR Kit v1 such as studies of repeatability, concordance, sensitivity, mixtures, degraded samples, case-type samples and pedigrees. Other than a little discordance (0.95%) with CE-STR results observed at D21S11, NGS-STR results correctly reflected the sample being tested. Repeatable results were obtained from both initial PCRs and emPCRs aside from a few variations of allele coverage. Full profiles could be obtained from 100 pg input DNA and >48.84% profiles from 10 pg input DNA. Mixtures were easily detected at 9:1 and 1:9 ratios. This system could be adapted to case-type samples and degraded samples. As a whole, the Early Access STR Kit v1 is a robust, reliable and reproducible assay for NGS-STR typing and a potential tool for human identification.