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Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM).
Forensic Sci Int Genet. 2016 11; 25:34-38.FS

Abstract

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.

Authors+Show Affiliations

Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, North Zhongshan No.1 Road 803, Shanghai 200083, China. Electronic address: xiaoxuexx588@126.com.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, North Zhongshan No.1 Road 803, Shanghai 200083, China.Institute of Forensic Medicine, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, North Zhongshan No.1 Road 803, Shanghai 200083, China.Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, North Zhongshan No.1 Road 803, Shanghai 200083, China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27497643

Citation

Zhao, Xueying, et al. "Massively Parallel Sequencing of 10 Autosomal STRs in Chinese Using the Ion Torrent Personal Genome Machine (PGM)." Forensic Science International. Genetics, vol. 25, 2016, pp. 34-38.
Zhao X, Li H, Wang Z, et al. Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet. 2016;25:34-38.
Zhao, X., Li, H., Wang, Z., Ma, K., Cao, Y., & Liu, W. (2016). Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM). Forensic Science International. Genetics, 25, 34-38. https://doi.org/10.1016/j.fsigen.2016.07.014
Zhao X, et al. Massively Parallel Sequencing of 10 Autosomal STRs in Chinese Using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet. 2016;25:34-38. PubMed PMID: 27497643.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM). AU - Zhao,Xueying, AU - Li,Hui, AU - Wang,Zheng, AU - Ma,Ke, AU - Cao,Yu, AU - Liu,Wenbin, Y1 - 2016/07/30/ PY - 2016/03/03/received PY - 2016/07/13/revised PY - 2016/07/27/accepted PY - 2016/10/23/pubmed PY - 2017/6/15/medline PY - 2016/8/8/entrez KW - Autosomal STRs KW - Forensic genetics KW - Ion torrent personal genome machine (PGM) KW - Massively parallel sequencing (MPS) SP - 34 EP - 38 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 25 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27497643/Massively_parallel_sequencing_of_10_autosomal_STRs_in_Chinese_using_the_ion_torrent_personal_genome_machine__PGM__ DB - PRIME DP - Unbound Medicine ER -