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Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations

  • Ruiyang Tao
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
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  • Min Li
    Affiliations
    School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
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  • Siyu Chai
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China

    Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China
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  • Ruocheng Xia
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
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  • Yiling Qu
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China

    Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
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  • Chunyan Yuan
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China

    Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
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  • Guangyuan Yang
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China

    Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
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  • Xinyu Dong
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China

    School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
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  • Yingnan Bian
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
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  • Suhua Zhang
    Correspondence
    Corresponding authors.
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
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  • Chengtao Li
    Correspondence
    Corresponding authors.
    Affiliations
    Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
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Published:October 29, 2022DOI:https://doi.org/10.1016/j.fsigen.2022.102803

      Highlights

      • The SifaMPS 381 Y-SNP panel was designed to simultaneously target 381 Y-SNPs using the Illumina MiSeq System.
      • A high-resolution haplogroup tree defining 359 different haplogroups aimed at Chinese males was built.
      • High-resolution SifaMPS 381 Y-SNP panel could facilitate paternal lineage classification, familial searching and so forth.

      Abstract

      Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications.

      Keywords

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