title: Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM).
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.affiliation: Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
authors.forename: Xueying
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
authors.forename: Ke
authors.initials: K
authors.lastname: Ma
authors.affiliation: Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Yu
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Huaigu
authors.initials: H
authors.lastname: Zhou
authors.affiliation: 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.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ping
mesh_terms: D041322:Chromosomes, Human, Y; D053803:Forensic Genetics; D015894:Genome, Human; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*
keywords: Forensic genetics; Ion torrent personal genome machine (PGM); Massively parallel sequencing (MPS); Y-STR