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Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM).
Forensic Sci Int Genet. 2015 Nov; 19:192-196.FS

Abstract

Massively parallel sequencing (MPS) technologies allow parallel sequencing analyses of many targeted regions of multiple samples at desirable depth of coverage. Routine use of MPS for forensic genetics is on the horizon. In this study, we explore the application of MPS technology in forensic Y-STR analysis. We designed a multiplex assay with 13 Y-STR loci (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS437, DYS438, DYS439, DYS448, DYS456, DYS635, GATA-H4) for the purpose of MPS. The multiplex Y-STR assay was amplified in 42 unrelated male individuals and amplicons were sequenced simultaneously using the ion torrent personal genome machine (PGM) system. All loci were detected successfully, except for DYS389 II that exhibited a failure rate of 1.8% due to the relatively long amplicon sizes. We observed 7, 3, 2, 6 and 5 new alleles, respectively in DYS389 II, DYS390, DYS437, DYS448 and DYS635 due to the presence of sub-repeat composition differences, and a new allele in DYS438 because of nucleotide substitution. One allele of DYS390 was inconsistent with allele call from conventional capillary electrophoresis (CE) because of 4 bp deletions upstream of the core repeat unit. This study demonstrates that Y-STR typing by MPS can provide more genetic information, holding the promise for high discriminatory power.

Authors+Show Affiliations

Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, North Zhongshan No. 1 Road 803, 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, Shanghai 200083, China.Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, 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, North Zhongshan No. 1 Road 803, Shanghai 200083, China. Electronic address: pingyuan803@126.com.

Pub Type(s)

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

Language

eng

PubMed ID

26247785

Citation

Zhao, Xueying, et al. "Multiplex Y-STRs Analysis Using the Ion Torrent Personal Genome Machine (PGM)." Forensic Science International. Genetics, vol. 19, 2015, pp. 192-196.
Zhao X, Ma K, Li H, et al. Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet. 2015;19:192-196.
Zhao, X., Ma, K., Li, H., Cao, Y., Liu, W., Zhou, H., & Ping, Y. (2015). Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM). Forensic Science International. Genetics, 19, 192-196. https://doi.org/10.1016/j.fsigen.2015.06.012
Zhao X, et al. Multiplex Y-STRs Analysis Using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet. 2015;19:192-196. PubMed PMID: 26247785.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM). AU - Zhao,Xueying, AU - Ma,Ke, AU - Li,Hui, AU - Cao,Yu, AU - Liu,Wenbin, AU - Zhou,Huaigu, AU - Ping,Yuan, Y1 - 2015/07/16/ PY - 2015/02/06/received PY - 2015/06/25/revised PY - 2015/06/28/accepted PY - 2015/8/7/entrez PY - 2015/8/8/pubmed PY - 2016/7/19/medline KW - Forensic genetics KW - Ion torrent personal genome machine (PGM) KW - Massively parallel sequencing (MPS) KW - Y-STR SP - 192 EP - 196 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 19 N2 - Massively parallel sequencing (MPS) technologies allow parallel sequencing analyses of many targeted regions of multiple samples at desirable depth of coverage. Routine use of MPS for forensic genetics is on the horizon. In this study, we explore the application of MPS technology in forensic Y-STR analysis. We designed a multiplex assay with 13 Y-STR loci (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS437, DYS438, DYS439, DYS448, DYS456, DYS635, GATA-H4) for the purpose of MPS. The multiplex Y-STR assay was amplified in 42 unrelated male individuals and amplicons were sequenced simultaneously using the ion torrent personal genome machine (PGM) system. All loci were detected successfully, except for DYS389 II that exhibited a failure rate of 1.8% due to the relatively long amplicon sizes. We observed 7, 3, 2, 6 and 5 new alleles, respectively in DYS389 II, DYS390, DYS437, DYS448 and DYS635 due to the presence of sub-repeat composition differences, and a new allele in DYS438 because of nucleotide substitution. One allele of DYS390 was inconsistent with allele call from conventional capillary electrophoresis (CE) because of 4 bp deletions upstream of the core repeat unit. This study demonstrates that Y-STR typing by MPS can provide more genetic information, holding the promise for high discriminatory power. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/26247785/Multiplex_Y_STRs_analysis_using_the_ion_torrent_personal_genome_machine__PGM__ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(15)30033-8 DB - PRIME DP - Unbound Medicine ER -