title: Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform.
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 100pg input DNA and >48.84% profiles from 10pg 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.
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China; Department of Forensic Medicine, National Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Guo
authors.affiliation: China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.
authors.forename: Yishu
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Yu
authors.affiliation: China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.
authors.forename: He
authors.initials: H
authors.lastname: Song
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Hongying
authors.initials: H
authors.lastname: Shen
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Jia
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.
authors.forename: Guangwei
authors.initials: G
authors.lastname: Hou
authors.affiliation: Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China; China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China. Electronic address: jiangxianhua_2006@aliyun.com.
authors.forename: Xianhua
authors.initials: X
authors.lastname: Jiang
mesh_terms: D000483:Alleles; D053836:DNA Degradation, Necrotic; D016172:DNA Fingerprinting / Q000295:instrumentation*; D053803:Forensic Genetics / Q000295:instrumentation / Q000379:methods; D005838:Genotype; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018895:Microsatellite Repeats; D010375:Pedigree; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods
keywords: Degraded samples; Early Access STR Kit v1; Evaluation; Ion Torrent PGM™; Next generation sequencing (NGS); Short tandem repeat (STR)