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Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system.
Forensic Sci Int Genet. 2021 05; 52:102490.FS

Abstract

Massively parallel sequencing (MPS), or next generation sequencing (NGS), is a promising methodology for the detection of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) in forensic genetics. Here, the prototype SifaMPS Panel is designed to simultaneously target 87 STRs and 294 SNPs with forensic interest in a single multiplex in conjunction with the TruSeq™ Custom Amplicon workflow and MiSeq FGx™ System. Two in-house python scripts are adopted for the fastq-to-genotype interpretation of MPS data concerning STR and SNP, respectively. In the present study, by sequencing 50 Chinese Hans and many other DNA samples involved in validation studies, system parameters including the depth of coverage (DoC), heterozygote balance (Hb) and sequence coverage ratios (SCRs), as well as different forensic parameters of STRs and SNPs in a population study, were calculated to evaluate the overall performance of this new panel and its practicality in forensic application. In general, except for two STRs (DYS505 and DYS449) and one SNP (rs4288409) that performed poorly, the other 85 STRs and 293 SNPs in our panel had good performance that could strengthen efficiency for human identification and paternity testing. In addition, discordant STR genotype results between those generated from capillary electrophoresis (CE) and from the MPS platform were clearly illustrated, and these results could be a useful reference for applying these particular non-CODIS STRs in forensic practice.

Authors+Show Affiliations

Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325035, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China. Electronic address: zhangsh@ssfjd.cn.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China. Electronic address: lichengtaohla@163.com.

Pub Type(s)

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

Language

eng

PubMed ID

33689955

Citation

Tao, Ruiyang, et al. "Parallel Sequencing of 87 STR and 294 SNP Markers Using the Prototype of the SifaMPS Panel On the MiSeq FGx™ System." Forensic Science International. Genetics, vol. 52, 2021, p. 102490.
Tao R, Wang S, Chen A, et al. Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system. Forensic Sci Int Genet. 2021;52:102490.
Tao, R., Wang, S., Chen, A., Xia, R., Zhang, X., Yang, Q., Qu, Y., Zhang, S., & Li, C. (2021). Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system. Forensic Science International. Genetics, 52, 102490. https://doi.org/10.1016/j.fsigen.2021.102490
Tao R, et al. Parallel Sequencing of 87 STR and 294 SNP Markers Using the Prototype of the SifaMPS Panel On the MiSeq FGx™ System. Forensic Sci Int Genet. 2021;52:102490. PubMed PMID: 33689955.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system. AU - Tao,Ruiyang, AU - Wang,Shouyu, AU - Chen,Anqi, AU - Xia,Ruocheng, AU - Zhang,Xiaochun, AU - Yang,Qi, AU - Qu,Yiling, AU - Zhang,Suhua, AU - Li,Chengtao, Y1 - 2021/03/04/ PY - 2020/05/19/received PY - 2021/02/26/revised PY - 2021/03/02/accepted PY - 2021/3/11/pubmed PY - 2021/8/6/medline PY - 2021/3/10/entrez KW - Forensic genetics KW - Human identification KW - Massively parallel sequencing (MPS) KW - MiSeq FGx™ system KW - Short tandem repeats (STRs) KW - Single nucleotide polymorphisms (SNPs) SP - 102490 EP - 102490 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 52 N2 - Massively parallel sequencing (MPS), or next generation sequencing (NGS), is a promising methodology for the detection of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) in forensic genetics. Here, the prototype SifaMPS Panel is designed to simultaneously target 87 STRs and 294 SNPs with forensic interest in a single multiplex in conjunction with the TruSeq™ Custom Amplicon workflow and MiSeq FGx™ System. Two in-house python scripts are adopted for the fastq-to-genotype interpretation of MPS data concerning STR and SNP, respectively. In the present study, by sequencing 50 Chinese Hans and many other DNA samples involved in validation studies, system parameters including the depth of coverage (DoC), heterozygote balance (Hb) and sequence coverage ratios (SCRs), as well as different forensic parameters of STRs and SNPs in a population study, were calculated to evaluate the overall performance of this new panel and its practicality in forensic application. In general, except for two STRs (DYS505 and DYS449) and one SNP (rs4288409) that performed poorly, the other 85 STRs and 293 SNPs in our panel had good performance that could strengthen efficiency for human identification and paternity testing. In addition, discordant STR genotype results between those generated from capillary electrophoresis (CE) and from the MPS platform were clearly illustrated, and these results could be a useful reference for applying these particular non-CODIS STRs in forensic practice. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/33689955/Parallel_sequencing_of_87_STR_and_294_SNP_markers_using_the_prototype_of_the_SifaMPS_panel_on_the_MiSeq_FGx™_system_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(21)00029-6 DB - PRIME DP - Unbound Medicine ER -