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Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population.
Electrophoresis. 2018 11; 39(21):2725-2731.E

Abstract

Massively parallel sequencing (MPS) has been used in forensic genetics in recent years owing to several advantages, e.g. MPS can provide precise descriptions of the repeat allele structure and variation in the repeat-flanking regions, increasing the discriminating power among loci and individuals. However, it cannot be fully utilized unless sufficient population data are available for all loci. Thus, there is a pressing need to perform population studies providing a basis for the introduction of MPS into forensic practice. Here, we constructed a multiplex PCR system with fusion primers for one-directional PCR for MPS of 15 commonly used forensic autosomal STRs and amelogenin. Samples from 554 unrelated Chinese Northern Han individuals were typed using this MPS assay. In total, 313 alleles obtained by MPS for all 15 STRs were observed, and the corresponding allele frequencies ranged between 0.0009 and 0.5162. Of all 15 loci, the number of alleles identified for 12 loci increased compared to capillary electrophoresis approaches, and for the following six loci more than double the number of alleles was found: D2S1338, D5S818, D21S11, D13S317, vWA, and D3S1358. Forensic parameters were calculated based on length and sequence-based alleles. D21S11 showed the highest heterozygosity (0.8791), discrimination power (0.9865), and paternity exclusion probability in trios (0.7529). The cumulative match probability for MPS was approximately 2.3157 × 10-20 .

Authors+Show Affiliations

Forensic Science Service, Beijing Public Security Bureau, Beijing, P. R. China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China.IPE Biotechnology, Beijing, P. R. China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China. University of Chinese Academy of Sciences, Beijing, P. R. China.IPE Biotechnology, Beijing, P. R. China.College of forensic medicine, Shanxi Medical University, Taiyuan, P. R. China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China.Forensic Science Service, Beijing Public Security Bureau, Beijing, P. R. China.Forensic Science Service, Beijing Public Security Bureau, Beijing, P. R. China. College of forensic medicine, Shanxi Medical University, Taiyuan, P. R. China.CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China. University of Chinese Academy of Sciences, Beijing, P. R. China. College of forensic medicine, Shanxi Medical University, Taiyuan, P. R. China.

Pub Type(s)

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

Language

eng

PubMed ID

29772597

Citation

Zhang, Qing-Xia, et al. "Development of a Massively Parallel Sequencing Assay for Investigating Sequence Polymorphisms of 15 Short Tandem Repeats in a Chinese Northern Han Population." Electrophoresis, vol. 39, no. 21, 2018, pp. 2725-2731.
Zhang QX, Yang M, Pan YJ, et al. Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis. 2018;39(21):2725-2731.
Zhang, Q. X., Yang, M., Pan, Y. J., Zhao, J., Qu, B. W., Cheng, F., Yang, Y. R., Jiao, Z. P., Liu, L., & Yan, J. W. (2018). Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis, 39(21), 2725-2731. https://doi.org/10.1002/elps.201800071
Zhang QX, et al. Development of a Massively Parallel Sequencing Assay for Investigating Sequence Polymorphisms of 15 Short Tandem Repeats in a Chinese Northern Han Population. Electrophoresis. 2018;39(21):2725-2731. PubMed PMID: 29772597.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. AU - Zhang,Qing-Xia, AU - Yang,Meng, AU - Pan,Ya-Jiao, AU - Zhao,Jing, AU - Qu,Bao-Wang, AU - Cheng,Feng, AU - Yang,Ya-Ran, AU - Jiao,Zhang-Ping, AU - Liu,Li, AU - Yan,Jiang-Wei, Y1 - 2018/06/04/ PY - 2018/02/10/received PY - 2018/04/11/revised PY - 2018/05/07/accepted PY - 2018/5/18/pubmed PY - 2019/10/8/medline PY - 2018/5/18/entrez KW - Chinese Northern Han KW - Forensic science KW - Massively parallel sequencing KW - Sequence variants KW - Short tandem repeats SP - 2725 EP - 2731 JF - Electrophoresis JO - Electrophoresis VL - 39 IS - 21 N2 - Massively parallel sequencing (MPS) has been used in forensic genetics in recent years owing to several advantages, e.g. MPS can provide precise descriptions of the repeat allele structure and variation in the repeat-flanking regions, increasing the discriminating power among loci and individuals. However, it cannot be fully utilized unless sufficient population data are available for all loci. Thus, there is a pressing need to perform population studies providing a basis for the introduction of MPS into forensic practice. Here, we constructed a multiplex PCR system with fusion primers for one-directional PCR for MPS of 15 commonly used forensic autosomal STRs and amelogenin. Samples from 554 unrelated Chinese Northern Han individuals were typed using this MPS assay. In total, 313 alleles obtained by MPS for all 15 STRs were observed, and the corresponding allele frequencies ranged between 0.0009 and 0.5162. Of all 15 loci, the number of alleles identified for 12 loci increased compared to capillary electrophoresis approaches, and for the following six loci more than double the number of alleles was found: D2S1338, D5S818, D21S11, D13S317, vWA, and D3S1358. Forensic parameters were calculated based on length and sequence-based alleles. D21S11 showed the highest heterozygosity (0.8791), discrimination power (0.9865), and paternity exclusion probability in trios (0.7529). The cumulative match probability for MPS was approximately 2.3157 × 10-20 . SN - 1522-2683 UR - https://www.unboundmedicine.com/medline/citation/29772597/Development_of_a_massively_parallel_sequencing_assay_for_investigating_sequence_polymorphisms_of_15_short_tandem_repeats_in_a_Chinese_Northern_Han_population_ L2 - https://doi.org/10.1002/elps.201800071 DB - PRIME DP - Unbound Medicine ER -