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Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection

  • Author Footnotes
    1 The author contributed equally to this work and should be considered co-first author.
    Jing Liu
    Footnotes
    1 The author contributed equally to this work and should be considered co-first author.
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Author Footnotes
    1 The author contributed equally to this work and should be considered co-first author.
    Lirong Jiang
    Footnotes
    1 The author contributed equally to this work and should be considered co-first author.
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Mengyao Zhao
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Weian Du
    Affiliations
    School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
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  • Yufeng Wen
    Affiliations
    School of Life Sciences, Jilin University, Changchun 130012, China
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  • Suyu Li
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Shuyuan Zhang
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Fengfei Fang
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Jian Shen
    Affiliations
    Anhui Hopegenerich Biotechnology, Hefei 230031, China
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  • Guanglin He
    Affiliations
    Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
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  • Mengge Wang
    Affiliations
    Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
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  • Hao Dai
    Affiliations
    Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Yiping Hou
    Correspondence
    Corresponding authors.
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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  • Author Footnotes
    2 ORCID: 0000-0003-3419-1741.
    Zheng Wang
    Correspondence
    Corresponding authors.
    Footnotes
    2 ORCID: 0000-0003-3419-1741.
    Affiliations
    Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
    Search for articles by this author
  • Author Footnotes
    1 The author contributed equally to this work and should be considered co-first author.
    2 ORCID: 0000-0003-3419-1741.
Published:October 08, 2022DOI:https://doi.org/10.1016/j.fsigen.2022.102786

      Highlights

      • This novel Y-SNP panel contains 256 Y-SNPs and allows inferring 253 Y haplogroups.
      • This Y-SNP MPS panel could provide an achievable high-resolution in the Chinese populations.
      • This Y-SNP MPS panel performs highly accurate, is sensitive, reliable, specific and robust.

      Abstract

      Y-chromosomal haplogroups determined by Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal biogeographic ancestry inference, which has attracted a lot of interest in the forensic community. Recently, a comprehensive Y-SNP tool with dominant markers targeting haplogroups in R, E and I branches has been reported, which allows the inference of 640 Y haplogroups. It had a very good performance and could provide a high level of Y haplogroup resolution in most populations. However, the predominant haplogroups in the Chinese populations are O, C and N, suggesting that more Y-SNPs under these clades are needed to achieve the population-specific high resolution. Herein, aiming at the Chinese population, we presented a largely improved custom Y-SNP MPS panel that contains 256 carefully ascertained Y-SNPs based on our previous studies, and evaluated this panel via a series of tests, including the tests for concordance, repeatability, sensitivity, specificity, and stability, as well as the mixture, degraded and case-type sample analysis. The preliminary developmental validation demonstrated that this panel was highly reliable, sensitive, specific, and robust. In the sensitivity test, even when the DNA input was reduced to as low as 0.5 ng, the sample could still be assigned to the correct Y haplogroup. For mixture analysis, even the 1:99 (Male: Female) mixtures had no effects on the assignation of the Y haplogroup of the male contributor. In summary, this assay has provided a high-resolution Y-chromosomal haplogrouping workflow to determine a male’s paternal lineage and/or paternal biogeographic ancestry and could be widely used for Chinese Y-chromosomal haplogroups dissection.

      Keywords

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