Tags

Type your tag names separated by a space and hit enter

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing.
Sci Rep. 2020 07 22; 10(1):12225.SR

Abstract

Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases.

Authors+Show Affiliations

Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. 812811596@qq.com. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China. 812811596@qq.com.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. wurg3@mail.sysu.edu.cn. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China. wurg3@mail.sysu.edu.cn.Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China. sunhy@mail.sysu.edu.cn. Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China. sunhy@mail.sysu.edu.cn.

Pub Type(s)

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

Language

eng

PubMed ID

32699278

Citation

Peng, Dan, et al. "Identification of Sequence Polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan Population Using Massively Parallel Sequencing." Scientific Reports, vol. 10, no. 1, 2020, p. 12225.
Peng D, Zhang Y, Ren H, et al. Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing. Sci Rep. 2020;10(1):12225.
Peng, D., Zhang, Y., Ren, H., Li, H., Li, R., Shen, X., Wang, N., Huang, E., Wu, R., & Sun, H. (2020). Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing. Scientific Reports, 10(1), 12225. https://doi.org/10.1038/s41598-020-69137-1
Peng D, et al. Identification of Sequence Polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan Population Using Massively Parallel Sequencing. Sci Rep. 2020 07 22;10(1):12225. PubMed PMID: 32699278.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing. AU - Peng,Dan, AU - Zhang,Yinming, AU - Ren,Han, AU - Li,Haixia, AU - Li,Ran, AU - Shen,Xuefeng, AU - Wang,Nana, AU - Huang,Erwen, AU - Wu,Riga, AU - Sun,Hongyu, Y1 - 2020/07/22/ PY - 2020/01/19/received PY - 2020/06/16/accepted PY - 2020/7/24/entrez PY - 2020/7/24/pubmed PY - 2020/12/2/medline SP - 12225 EP - 12225 JF - Scientific reports JO - Sci Rep VL - 10 IS - 1 N2 - Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/32699278/Identification_of_sequence_polymorphisms_at_58_STRs_and_94_iiSNPs_in_a_Tibetan_population_using_massively_parallel_sequencing_ L2 - https://doi.org/10.1038/s41598-020-69137-1 DB - PRIME DP - Unbound Medicine ER -