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Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit

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Abstract

Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E−31 and 1.53E−34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.

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Acknowledgements

The authors would like to thank the volunteers who provided the biological samples used in the study. This study was supported by grants from the National Natural Science Fund of China (82293654, 81930056, 82202080) and the Shanghai Science and Technology Innovation Fund (21DZ2202700). The funders had no role in study design, data analysis, publishing decisions, or manuscript preparation.

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Author notes

  1. Ruiyang Tao and Xinyu Dong have contributed equally to this work.

Authors and Affiliations

  1. Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China

    Ruiyang Tao, Xinyu Dong, Xiaoyuan Zhen, Ruocheng Xia, Yiling Qu & Chengtao Li

  2. Shanghai Medical College, Fudan University, Shanghai, 200032, China

    Suhua Zhang & Chengtao Li

  3. Minhang Branch of Shanghai Public Security Bureau, Shanghai, 201108, China

    Xinyu Dong

  4. Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China

    Xiaoyuan Zhen

  5. Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China

    Yiling Qu

  6. Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, 100088, China

    Shiquan Liu

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  1. Ruiyang Tao
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Contributions

RY, SH, and CT conceived this study. XY Dong collected the samples. RC and YL finished the investigation. XY Dong, YL, and SQ contributed to formal analysis. RY, XY Dong, and SQ wrote the draft. XY Zhen revised the draft. All authors have read and agreed to publish the manuscript.

Corresponding authors

Correspondence to Shiquan Liu, Suhua Zhang or Chengtao Li.

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The authors have no relevant financial interests to disclose.

Compliance with ethical standards

The studies involving human participants were reviewed and approved by the Ethics Committee at the Academy of Forensic Science, Ministry of Justice, China. The participants provided their written informed consent to participate in this study.

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Communicated by Shuhua Xu.

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Tao, R., Dong, X., Zhen, X. et al. Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit. Mol Genet Genomics 299, 9 (2024). https://doi.org/10.1007/s00438-024-02121-w

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