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Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

Authors
 Eun Hye Kim  ;  Hwan Young Lee  ;  In Seok Yang  ;  Sang-Eun Jung  ;  Woo Ick Yang  ;  Kyoung-Jin Shin 
Citation
 FORENSIC SCIENCE INTERNATIONAL-GENETICS, Vol.22 : 1-7, 2016 
Journal Title
 FORENSIC SCIENCE INTERNATIONAL-GENETICS 
ISSN
 1872-4973 
Issue Date
2016
MeSH
Amelogenin/genetics* ; DNA/analysis ; DNA/genetics ; DNA Fingerprinting/methods* ; Female ; Forensic Anthropology ; Forensic Genetics/methods* ; Genotype ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Male ; Microsatellite Repeats* ; Multiplex Polymerase Chain Reaction/methods ; Nucleic Acid Amplification Techniques/methods
Keywords
Autosomal STR ; Degraded DNA ; Mixture ; Next-generation sequencing ; Sequence variation ; Small-sized amplicon
Abstract
The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples.
Full Text
http://www.sciencedirect.com/science/article/pii/S1872497316300011
DOI
10.1016/j.fsigen.2016.01.001
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
Yang, In Seok(양인석) ORCID logo https://orcid.org/0000-0001-5224-2587
Lee, Hwan Young(이환영)
Jung, Sang Eun(정상은)
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/146986
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