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Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics.
Electrophoresis. 2020 12; 41(23):2029-2035.E

Abstract

Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.

Authors+Show Affiliations

National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China. School of Forensic Medicine, Kunming Medical University, Kunming, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China. Public Security Bureau of Ximeng County in Pu'er City, Pu'er, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.School of Forensic Medicine, Kunming Medical University, Kunming, P. R. China.National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.

Pub Type(s)

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

Language

eng

PubMed ID

32770833

Citation

Wu, Hao, et al. "Massively Parallel Sequencing of STRs Using a 29-plex Panel Reveals Stutter Sequence Characteristics." Electrophoresis, vol. 41, no. 23, 2020, pp. 2029-2035.
Wu H, Ji AC, Liu YC, et al. Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics. Electrophoresis. 2020;41(23):2029-2035.
Wu, H., Ji, A. C., Liu, Y. C., Kang, K. L., Zhang, C., Li, Z. W., Ji, A. Q., Ye, J., Nie, S. J., & Wang, L. (2020). Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics. Electrophoresis, 41(23), 2029-2035. https://doi.org/10.1002/elps.202000093
Wu H, et al. Massively Parallel Sequencing of STRs Using a 29-plex Panel Reveals Stutter Sequence Characteristics. Electrophoresis. 2020;41(23):2029-2035. PubMed PMID: 32770833.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics. AU - Wu,Hao, AU - Ji,Ai-Cen, AU - Liu,Yi-Cheng, AU - Kang,Ke-Lai, AU - Zhang,Chi, AU - Li,Zhi-Wen, AU - Ji,An-Quan, AU - Ye,Jian, AU - Nie,Sheng-Jie, AU - Wang,Le, Y1 - 2020/09/06/ PY - 2020/04/20/received PY - 2020/06/20/revised PY - 2020/08/05/accepted PY - 2020/8/10/pubmed PY - 2021/4/2/medline PY - 2020/8/10/entrez KW - Forensic genetics KW - Next-generation sequencing KW - STR KW - Stutter sequence KW - Yunnan Bai population SP - 2029 EP - 2035 JF - Electrophoresis JO - Electrophoresis VL - 41 IS - 23 N2 - Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution. SN - 1522-2683 UR - https://www.unboundmedicine.com/medline/citation/32770833/Massively_parallel_sequencing_of_STRs_using_a_29_plex_panel_reveals_stutter_sequence_characteristics_ L2 - https://doi.org/10.1002/elps.202000093 DB - PRIME DP - Unbound Medicine ER -