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Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform.
Forensic Sci Int Genet. 2016 07; 23:111-120.FS

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+Show Affiliations

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.China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.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.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China.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.

Pub Type(s)

Comparative Study
Evaluation Study
Journal Article

Language

eng

PubMed ID

27082757

Citation

Guo, Fei, et al. "Evaluation of the Early Access STR Kit V1 On the Ion Torrent PGM™ Platform." Forensic Science International. Genetics, vol. 23, 2016, pp. 111-120.
Guo F, Zhou Y, Liu F, et al. Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. Forensic Sci Int Genet. 2016;23:111-120.
Guo, F., Zhou, Y., Liu, F., Yu, J., Song, H., Shen, H., Zhao, B., Jia, F., Hou, G., & Jiang, X. (2016). Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. Forensic Science International. Genetics, 23, 111-120. https://doi.org/10.1016/j.fsigen.2016.04.004
Guo F, et al. Evaluation of the Early Access STR Kit V1 On the Ion Torrent PGM™ Platform. Forensic Sci Int Genet. 2016;23:111-120. PubMed PMID: 27082757.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. AU - Guo,Fei, AU - Zhou,Yishu, AU - Liu,Feng, AU - Yu,Jiao, AU - Song,He, AU - Shen,Hongying, AU - Zhao,Bin, AU - Jia,Fei, AU - Hou,Guangwei, AU - Jiang,Xianhua, Y1 - 2016/04/04/ PY - 2015/12/23/received PY - 2016/03/12/revised PY - 2016/04/02/accepted PY - 2016/4/16/entrez PY - 2016/4/16/pubmed PY - 2017/6/15/medline KW - Degraded samples KW - Early Access STR Kit v1 KW - Evaluation KW - Ion Torrent PGM™ KW - Next generation sequencing (NGS) KW - Short tandem repeat (STR) SP - 111 EP - 120 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 23 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27082757/Evaluation_of_the_Early_Access_STR_Kit_v1_on_the_Ion_Torrent_PGM™_platform_ DB - PRIME DP - Unbound Medicine ER -