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Sequence-based diversity of 23 autosomal STR loci in Koreans investigated using an in-house massively parallel sequencing panel

Authors
 Eun Hye Kim  ;  Hwan Young Lee  ;  So Yeun Kwon  ;  Eun Young Lee  ;  Woo Ick Yang  ;  Kyoung-Jin Shin 
Citation
 FORENSIC SCIENCE INTERNATIONAL-GENETICS, Vol.30 : 134-140, 2017 
Journal Title
 FORENSIC SCIENCE INTERNATIONAL-GENETICS 
ISSN
 1872-4973 
Issue Date
2017
MeSH
Asian Continental Ancestry Group/genetics* ; Genotype ; High-Throughput Nucleotide Sequencing* ; Humans ; INDEL Mutation* ; Microsatellite Repeats* ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide* ; Republic of Korea ; Sequence Analysis, DNA*
Keywords
Discrimination power ; Koreans ; Massively parallel sequencing ; MiSeq ; Sequence variation ; Short tandem repeat
Abstract
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles. However, high-throughput analysis has rarely been reported for forensic DNA databasing. In this study, we present the sequencing results from 250 Korean samples at 23 commonly used STR loci (D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045) using an in-house assay designed for MPS. All amplicons in the multiplex exhibited a size range of 77 to 217 base pairs, and the barcoded library for the MPS run was easily prepared using a PCR-based library preparation method followed by sequencing on a MiSeq System (Illumina). We compared the STR genotyping results with those obtained using CE and scrutinized the sequence variations in both the targeted STR and flanking regions. MPS results of 23 autosomal STRs were 99.97% concordant with those of CE results. D12S391 and D21S11 exhibited, respectively, the highest number of alleles and genotypes by the MPS analysis. Single nucleotide polymorphisms and insertion and deletions (Indels) were observed in the flanking regions of D1S1656, D2S441, D5S818, D7S820, D13S317, D16S539, D21S11, and Penta D. Consequently, an MPS analysis of an expanded set of STRs, as demonstrated in the population statistics of a Korean population, will be of great practical use in forensic genetics.
Full Text
https://www.sciencedirect.com/science/article/pii/S1872497317301436
DOI
10.1016/j.fsigen.2017.07.001
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers
Yonsei Authors
Shin, Kyoung Jin(신경진) ORCID logo https://orcid.org/0000-0002-1059-9665
Yang, Woo Ick(양우익) ORCID logo https://orcid.org/0000-0002-6084-5019
Lee, Eun Young(이은영)
Lee, Hwan Young(이환영)
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/161220
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