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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

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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.

Highlights

  • A novel MPS-based panel of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) was developed based on multiplex PCR and single-end 400 bp sequencing strategy.

  • A reasonably large number of ~2200 MPS-based and ~2500 CE-based DNA profiles were generated to comprehensively validated the novel 133-plex forensic STR panel according to SWGDAM.

  • The concordance rate reached to 99.98% between 41900 MPS-based and CE-based genotypes at 100 STR markers (52 STRs and 48 Y-STRs).

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Data availability

The raw data of this article is available upon reasonable requests to the corresponding authors.

Code availability

The in-house Python scripts for length-based and sequence-based allele frequencies are available from the corresponding authors.

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Acknowledgements

First, we would like to thank all donors for this study. In addition, especially, we would like to thank DeepReads Biotech, Guangzhou, Guangdong, China for their technical assistance in support of this work.

Funding

This study was supported by the Program of Hainan Association for Science and Technology Plans to Youth R&D Innovation (QCXM201705), the Science and Technology Program of Guangzhou, China (No. 2019030016), the National Undergraduate Innovation and Entrepreneurship Training Program (No. 201911810008 and No. 201911810023), and the National Natural Science Foundation of China (NSFC, No. 32070576).

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  1. Haoliang Fan, Lingxiang Wang, and Changhui Liu These authors contribute equal to this work.

Authors and Affiliations

  1. Institute of Archaeological Science, Fudan University, Shanghai, 200433, China

    Haoliang Fan, Lingxiang Wang, Xiaoyu Lu, Xuding Xu, Kai Ru & Shao-Qing Wen

  2. School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China

    Haoliang Fan, Changhui Liu, Pingming Qiu & Chao Liu

  3. School of Basic Medicine and Life Science, Hainan Medical University, Haikou, 571199, China

    Haoliang Fan

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  1. Haoliang Fan
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Correspondence to Chao Liu or Shao-Qing Wen.

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This study was approved by the Ethics Committee of Fudan University of Life Sciences (No. 14012) and in accordance with the standards of the Declaration of Helsinki. All participants had signed the informed consent form.

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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 136, 447–464 (2022). https://doi.org/10.1007/s00414-021-02738-1

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