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Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population.
Mol Genet Genomic Med. 2021 Apr; 9(4):e1626.MG

Abstract

BACKGROUND

Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence-based STR genotypes.

METHODS

In this study, we report the characterization of sequence-based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE-based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared.

RESULTS

The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A-STRs was 2.04 × 10-29 , 1.93 × 10-31 , and 9.56 × 10-33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y-STR loci were observed when using length-based and sequence-based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs.

CONCLUSIONS

Our data suggest that MPS- and CE-derived alleles are compatible. MPS-based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger-scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework.

Authors+Show Affiliations

Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China. Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, China.Center for Material Evidence, Tibet Autonomous Region Public Security, Lhasa, Tibet, China.Laboratory of Forensic Evidence and Science Technology, Xianyang Municipal Public Security Bureau, Xianyang, Shaanxi, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, China.Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, China.National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China.Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.

Pub Type(s)

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

Language

eng

PubMed ID

33630413

Citation

Li, Hui, et al. "Concordance and Characterization of Massively Parallel Sequencing at 58 STRs in a Tibetan Population." Molecular Genetics & Genomic Medicine, vol. 9, no. 4, 2021, pp. e1626.
Li H, Zhang C, Song G, et al. Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population. Mol Genet Genomic Med. 2021;9(4):e1626.
Li, H., Zhang, C., Song, G., Ma, K., Cao, Y., Zhao, X., Yang, Q., & Xie, J. (2021). Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population. Molecular Genetics & Genomic Medicine, 9(4), e1626. https://doi.org/10.1002/mgg3.1626
Li H, et al. Concordance and Characterization of Massively Parallel Sequencing at 58 STRs in a Tibetan Population. Mol Genet Genomic Med. 2021;9(4):e1626. PubMed PMID: 33630413.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population. AU - Li,Hui, AU - Zhang,Cheng, AU - Song,Guoqing, AU - Ma,Ke, AU - Cao,Yu, AU - Zhao,Xueying, AU - Yang,Qinrui, AU - Xie,Jianhui, Y1 - 2021/02/25/ PY - 2021/1/17/revised PY - 2020/12/14/received PY - 2021/2/10/accepted PY - 2021/2/26/pubmed PY - 2021/12/15/medline PY - 2021/2/25/entrez KW - MPS KW - STR KW - flanking region KW - forensic genetics KW - population genetics SP - e1626 EP - e1626 JF - Molecular genetics & genomic medicine JO - Mol Genet Genomic Med VL - 9 IS - 4 N2 - BACKGROUND: Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence-based STR genotypes. METHODS: In this study, we report the characterization of sequence-based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE-based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared. RESULTS: The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A-STRs was 2.04 × 10-29 , 1.93 × 10-31 , and 9.56 × 10-33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y-STR loci were observed when using length-based and sequence-based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs. CONCLUSIONS: Our data suggest that MPS- and CE-derived alleles are compatible. MPS-based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger-scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework. SN - 2324-9269 UR - https://www.unboundmedicine.com/medline/citation/33630413/Concordance_and_characterization_of_massively_parallel_sequencing_at_58_STRs_in_a_Tibetan_population_ DB - PRIME DP - Unbound Medicine ER -