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Info. Vol.9 - No.2 (2015.06.20)
Title Characterization of Human Short Tandem Repeats (STRs) for Individual Identification Using the Ion Torrent
Authors Seri Lim1,3, Jong Pil Youn1, Sang Ok Moon2, Youn Hyung Nam2, Seung Bum Hong2, Dongho Choi2, Myunsoo Han2,*& Seung Yong Hwang1,3,*
Institutions 1Biocore Co. Ltd., Guro-gu, Seoul, Korea
2Forensic DNA Division, National Forensic Service, Korea
3Department of Molecular and Life Science, Hanyang University, Korea
Abstract Human genomic short tandem repeats (STRs) are specific gene sequences containing base pairs that are repeatedly arranged. From the various methods available for identifying individuals, STR analysis is the method most widely used in forensic science. Conventional polymerase chain reaction (PCR) was used for STR typing, and the PCR products, consisting of amplified STR loci (amplicons) were electrophoresed with a DNA analysis device. About ten STR markers were used as standards for STR characterization and analysis of size. Extensive efforts are currently being made to explore the STR sequence diversity by analyzing multiple chromosomal loci using next generation sequencing (NGS). NGS greatly facilitates STR marker analysis for individual identification and the complete sequencing of any given sample through concurrent high-throughput sequencing of multiple loci. As a result, NGS data are more accurate and comprehensive compared to that in a conventional database. In order to overcome the limitations of the currently used size-based STR analysis method, we have typed the DNA of 13 combined DNA index system (CODIS) STR markers using Ion PGM. This kit, developed by Ion Torrent, enables the analysis of STR alleles and the sequencing of corresponding genes. We then analyzed the alleles using the HID_STR_Genotyper plugin. Through this, we determined the sequence of the allele type 15 at the D3S1358 locus in all NIST SRM 2391b samples. This allowed for the verification of the exact type of allele, which the conventional size-based STR typing methods could not resolve.
Keyword Short tandem repeats, Forensic DNA typing, Massively parallel sequencing, Ion PGM, HID_ STR_Genotyper plugin
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