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Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing.
Int J Legal Med. 2022 Mar; 136(2):447-464.IJ

Abstract

Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.

Authors+Show Affiliations

Institute of Archaeological Science, Fudan University, Shanghai, 200433, China. School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China. School of Basic Medicine and Life Science, Hainan Medical University, Haikou, 571199, China.Institute of Archaeological Science, Fudan University, Shanghai, 200433, China.School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.Institute of Archaeological Science, Fudan University, Shanghai, 200433, China.Institute of Archaeological Science, Fudan University, Shanghai, 200433, China.Institute of Archaeological Science, Fudan University, Shanghai, 200433, China.School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China. liuchaogzf@163.com.Institute of Archaeological Science, Fudan University, Shanghai, 200433, China. wenshaoqing@fudan.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34741666

Citation

Fan, Haoliang, et al. "Development and Validation of a Novel 133-plex Forensic STR Panel (52 STRs and 81 Y-STRs) Using Single-end 400 Bp Massive Parallel Sequencing." International Journal of Legal Medicine, vol. 136, no. 2, 2022, pp. 447-464.
Fan H, Wang L, Liu C, et al. Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. Int J Legal Med. 2022;136(2):447-464.
Fan, H., Wang, L., Liu, C., Lu, X., Xu, X., Ru, K., Qiu, P., Liu, C., & Wen, S. Q. (2022). Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. International Journal of Legal Medicine, 136(2), 447-464. https://doi.org/10.1007/s00414-021-02738-1
Fan H, et al. Development and Validation of a Novel 133-plex Forensic STR Panel (52 STRs and 81 Y-STRs) Using Single-end 400 Bp Massive Parallel Sequencing. Int J Legal Med. 2022;136(2):447-464. PubMed PMID: 34741666.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. AU - Fan,Haoliang, AU - Wang,Lingxiang, AU - Liu,Changhui, AU - Lu,Xiaoyu, AU - Xu,Xuding, AU - Ru,Kai, AU - Qiu,Pingming, AU - Liu,Chao, AU - Wen,Shao-Qing, Y1 - 2021/11/06/ PY - 2021/08/17/received PY - 2021/10/25/accepted PY - 2021/11/7/pubmed PY - 2022/4/7/medline PY - 2021/11/6/entrez KW - Forensic genetics KW - Massive parallel sequencing KW - Multiplex PCR KW - Next-generation sequencing KW - STR KW - Single-end 400 bp KW - Validation study KW - Y-STR SP - 447 EP - 464 JF - International journal of legal medicine JO - Int J Legal Med VL - 136 IS - 2 N2 - Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/34741666/Development_and_validation_of_a_novel_133_plex_forensic_STR_panel__52_STRs_and_81_Y_STRs__using_single_end_400_bp_massive_parallel_sequencing_ L2 - https://dx.doi.org/10.1007/s00414-021-02738-1 DB - PRIME DP - Unbound Medicine ER -