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Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing.
Forensic Sci Int Genet. 2016 11; 25:132-141.FS

Abstract

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories.

Authors+Show Affiliations

Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea. Electronic address: kjshin@yuhs.ac.

Pub Type(s)

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

Language

eng

PubMed ID

27591816

Citation

Kwon, So Yeun, et al. "Investigation Into the Sequence Structure of 23 Y Chromosomal STR Loci Using Massively Parallel Sequencing." Forensic Science International. Genetics, vol. 25, 2016, pp. 132-141.
Kwon SY, Lee HY, Kim EH, et al. Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. Forensic Sci Int Genet. 2016;25:132-141.
Kwon, S. Y., Lee, H. Y., Kim, E. H., Lee, E. Y., & Shin, K. J. (2016). Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. Forensic Science International. Genetics, 25, 132-141. https://doi.org/10.1016/j.fsigen.2016.08.010
Kwon SY, et al. Investigation Into the Sequence Structure of 23 Y Chromosomal STR Loci Using Massively Parallel Sequencing. Forensic Sci Int Genet. 2016;25:132-141. PubMed PMID: 27591816.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing. AU - Kwon,So Yeun, AU - Lee,Hwan Young, AU - Kim,Eun Hye, AU - Lee,Eun Young, AU - Shin,Kyoung-Jin, Y1 - 2016/08/28/ PY - 2016/02/24/received PY - 2016/08/23/revised PY - 2016/08/27/accepted PY - 2016/10/23/pubmed PY - 2017/6/15/medline PY - 2016/9/5/entrez KW - Gene diversity KW - Massively parallel sequencing KW - Noise KW - Sequence variation KW - Stutter KW - Y-SNP KW - Y-STR SP - 132 EP - 141 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 25 N2 - Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27591816/Investigation_into_the_sequence_structure_of_23_Y_chromosomal_STR_loci_using_massively_parallel_sequencing_ DB - PRIME DP - Unbound Medicine ER -