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A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples

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Abstract 

Short tandem repeats (STRs) are the most widely used genetic markers in forensic application, but they are not ideal genetic markers for the analysis of forensic challenging samples such as highly degraded or unbalanced mixed samples because of their relatively large amplicons and stutter peaks. In this study, we developed a set of short microhaplotypes based on non-binary SNPs with molecular extent sizes no longer than 60 bases and genotyped 100 unrelated individuals from northern Han groups. Our results showed this panel has similar discrimination power to STR kits, as the combined random match probability (CMP) reached 1.396 × 10−22 and mean effective number of alleles (Ae) was 3.59. The cumulative probability of exclusion for duos (CPE-duos) was 0.999919 and the cumulative probability of exclusion for trios (CPE-trios) was 0.9999999987, suggesting this panel could be applied for forensic personal identification and parentage testing independently. Population differentiation in 26 populations from the 1000 Genomes Project indicated this panel could distinguish populations from Africa, East Asia, South Asia, America, and Europe. These microhaplotypes based on non-binary SNPs have short amplicons, good discrimination power, no stutter artifacts, and have great potential in detection of highly degraded and unbalanced mixtures for personal identification, paternity testing, and ancestry inference.

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Acknowledgements

The authors would like to thank all volunteers who contributed samples to this study.

Funding

This project was supported by the National Key R&D Program of China (No. 2017YFC0803508) and China Postdoctoral Science Foundation (No. 2020M682591).

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Authors and Affiliations

  1. School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, China

    Xingchun Zhao & Zichun Hua

  2. National Engineering Laboratory for Forensic Science, Beijing, 100038, China

    Xingchun Zhao & Yang Fan

  3. Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan Province, 410013, People’s Republic of China

    Moutanou Modeste Judes Zeye, Wei He, Dan Wen, Chudong Wang & Jienan Li

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  1. Xingchun Zhao
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  2. Yang Fan
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Corresponding authors

Correspondence to Jienan Li or Zichun Hua.

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Ethics approval

This study was performed according to Helsinki guidelines and approved by the Ethics Committee of the Third Xiangya Hospital of Central South University (Changsha, China) with the ethics approval code, 2018-S194.

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All volunteers provided informed consent before inclusion in this study.

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Supplementary Fig. 1

Neighbor-joining (NJ) tree constructed based on genetic distance (Fst values) between the studied population and 26 populations (PNG 235 KB)

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Zhao, X., Fan, Y., Zeye, M.M.J. et al. A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples. Int J Legal Med 136, 43–53 (2022). https://doi.org/10.1007/s00414-021-02719-4

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  • DOI: https://doi.org/10.1007/s00414-021-02719-4

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