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Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system.
Forensic Sci Int Genet. 2019 11; 43:102147.FS

Abstract

With the continuous development of massively parallel sequencing (MPS), increasing numbers of laboratories have utilized this method for forensic genomic analyses. When sequencing common short tandem repeats (STRs), MPS does have many advantages over the length-based genotyping method that uses traditional capillary electrophoresis (CE) technology. The Precision ID GlobalFiler™ NGS STR Panel v2 was recently released to simultaneously target 31 autosomal STRs (20 expanded Combined DNA Index System (CODIS) core loci and 11 non-CODIS loci) and 4 gender determination loci (Amelogenin, DYS391, SRY and Y-indel (rs2032678)) with the Ion S5™ System. In the current study, we performed a preliminary validation for this novel MPS-STR panel that included the following analyses: repeatability, concordance, stutter and balance, sensitivity, case-type sample testing, stability, mixture and a population investigation. Complete and reliable profiles were obtained using 125 pg of positive control DNA. The commonly encountered types of case samples and artificial mixtures with ratios of 1:1, 1:3 and 3:1 were also fully genotyped. Additional allele sequence variations were detected in samples from 50 unrelated individuals, and subsequently, an increased power of discrimination and power of exclusion were achieved. However, the average depth of coverage (DoC) of the Penta D locus was detected to be dramatically lower than those of other loci, which caused an interlocus imbalance; this could be one of the reasons for the intralocus imbalance of this locus and the 0.18% inconsistent results in the concordance study. Although certain flaws were observed, the informative metrics, including the DoC, sequence coverage ratios (SCRs) and heterozygote balance (Hb), of the novel MPS multiplex in our study were sufficient for reliable sequencing results that were 99.61% in concordance with the capillary electrophoresis (CE) results. In general, the Precision ID GlobalFiler™ NGS STR Panel v2 was demonstrated to be sensitive, reliable and robust and could be a powerful tool for human identification and kinship analyses. Additionally, we look forward to its updated version.

Authors+Show Affiliations

Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.Minhang Criminal Police, Shanghai Public Security Bureau, Shanghai 200199, PR China.Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, 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 Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, PR China.Minhang Criminal Police, Shanghai Public Security Bureau, Shanghai 200199, 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.Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, 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: lichengtaohla@163.com.

Pub Type(s)

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

Language

eng

PubMed ID

31437781

Citation

Tao, Ruiyang, et al. "Pilot Study for Forensic Evaluations of the Precision ID GlobalFiler™ NGS STR Panel V2 With the Ion S5™ System." Forensic Science International. Genetics, vol. 43, 2019, p. 102147.
Tao R, Qi W, Chen C, et al. Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system. Forensic Sci Int Genet. 2019;43:102147.
Tao, R., Qi, W., Chen, C., Zhang, J., Yang, Z., Song, W., Zhang, S., & Li, C. (2019). Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system. Forensic Science International. Genetics, 43, 102147. https://doi.org/10.1016/j.fsigen.2019.102147
Tao R, et al. Pilot Study for Forensic Evaluations of the Precision ID GlobalFiler™ NGS STR Panel V2 With the Ion S5™ System. Forensic Sci Int Genet. 2019;43:102147. PubMed PMID: 31437781.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system. AU - Tao,Ruiyang, AU - Qi,Wenjie, AU - Chen,Chong, AU - Zhang,Jingyi, AU - Yang,Zihao, AU - Song,Wei, AU - Zhang,Suhua, AU - Li,Chengtao, Y1 - 2019/08/15/ PY - 2019/03/02/received PY - 2019/08/14/revised PY - 2019/08/14/accepted PY - 2019/8/23/pubmed PY - 2019/12/27/medline PY - 2019/8/23/entrez KW - Forensic science KW - GlobalFiler™ NGS STR Panel v2 KW - Ion S5™ system KW - Massively parallel sequencing (MPS) KW - Short tandem repeats (STRs) SP - 102147 EP - 102147 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 43 N2 - With the continuous development of massively parallel sequencing (MPS), increasing numbers of laboratories have utilized this method for forensic genomic analyses. When sequencing common short tandem repeats (STRs), MPS does have many advantages over the length-based genotyping method that uses traditional capillary electrophoresis (CE) technology. The Precision ID GlobalFiler™ NGS STR Panel v2 was recently released to simultaneously target 31 autosomal STRs (20 expanded Combined DNA Index System (CODIS) core loci and 11 non-CODIS loci) and 4 gender determination loci (Amelogenin, DYS391, SRY and Y-indel (rs2032678)) with the Ion S5™ System. In the current study, we performed a preliminary validation for this novel MPS-STR panel that included the following analyses: repeatability, concordance, stutter and balance, sensitivity, case-type sample testing, stability, mixture and a population investigation. Complete and reliable profiles were obtained using 125 pg of positive control DNA. The commonly encountered types of case samples and artificial mixtures with ratios of 1:1, 1:3 and 3:1 were also fully genotyped. Additional allele sequence variations were detected in samples from 50 unrelated individuals, and subsequently, an increased power of discrimination and power of exclusion were achieved. However, the average depth of coverage (DoC) of the Penta D locus was detected to be dramatically lower than those of other loci, which caused an interlocus imbalance; this could be one of the reasons for the intralocus imbalance of this locus and the 0.18% inconsistent results in the concordance study. Although certain flaws were observed, the informative metrics, including the DoC, sequence coverage ratios (SCRs) and heterozygote balance (Hb), of the novel MPS multiplex in our study were sufficient for reliable sequencing results that were 99.61% in concordance with the capillary electrophoresis (CE) results. In general, the Precision ID GlobalFiler™ NGS STR Panel v2 was demonstrated to be sensitive, reliable and robust and could be a powerful tool for human identification and kinship analyses. Additionally, we look forward to its updated version. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/31437781/Pilot_study_for_forensic_evaluations_of_the_Precision_ID_GlobalFiler���������_NGS_STR_Panel_v2_with_the_Ion_S5���������_system_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(19)30091-2 DB - PRIME DP - Unbound Medicine ER -