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Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing

Authors
 So Yeun Kwon  ;  Hwan Young Lee  ;  Eun Hye Kim  ;  Eun Young Lee  ;  Kyoung-Jin Shin 
Citation
 FORENSIC SCIENCE INTERNATIONAL-GENETICS, Vol.25 : 132-141, 2016 
Journal Title
FORENSIC SCIENCE INTERNATIONAL-GENETICS
ISSN
 1872-4973 
Issue Date
2016
MeSH
Alleles ; Asian Continental Ancestry Group/genetics ; Chromosomes, Human, Y* ; DNA Fingerprinting* ; Electrophoresis, Capillary ; Genetic Markers ; High-Throughput Nucleotide Sequencing* ; Humans ; Male ; Microsatellite Repeats* ; Multiplex Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Republic of Korea
Keywords
Gene diversity ; Massively parallel sequencing ; Noise ; Sequence variation ; Stutter ; Y-SNP ; Y-STR
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.
Full Text
http://www.sciencedirect.com/science/article/pii/S1872497316301624?via%3Dihub
DOI
10.1016/j.fsigen.2016.08.010
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
Yonsei Authors
Shin, Kyoung Jin(신경진) ORCID logo https://orcid.org/0000-0002-1059-9665
Lee, Eun Young(이은영)
Lee, Hwan Young(이환영)
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/152446
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