Development and evaluation of a panel of newly screened Y chromosome InDels for inferring paternal ancestry information in Southwest China.

IF 2.2 3区 医学 Q1 MEDICINE, LEGAL International Journal of Legal Medicine Pub Date : 2024-10-08 DOI:10.1007/s00414-024-03344-7
Zefei Wang, Mengyuan Song, Qiang Lyu, Jun Ying, Qian Wu, Feng Song, XinDi Wang, Lanrui Jiang, Yuxiang Zhou, Chaoran Sun, Shuangshuang Wang, Hewen Yao, Zhirui Zhang, Xingbo Song, Haibo Luo
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Abstract

Y-InDels (insertions/deletions) are genetic markers which are extremely understudied. It is unknown whether this type of markers can be utilized for genetic ancestry inference. We have developed an innovative Y chromosome ancestry inference system tailored for forensic applications. This panel amplifies 21 Y chromosome loci, encompassing Y-InDels and Y-SNPs (Single Nucleotide Polymorphism), utilizing the capillary electrophoresis (CE) platform. The system performed well at DNA concentrations greater than 0.125 ng/ul and produced accurate results at a 1:100 mixing ratio of male and female DNA. The Cumulative probability of matching (CPM) was between 0.95 and 0.97 in the experimental population. The system's efficacy in inferring ancestral origins was demonstrated through intercontinental population discrimination, revealing high discrimination power between African and East Asian populations. Population genetic analyses conducted on Han, Qiang and Hui populations in Southwest China, where the smallest FST value was 0.0002 between Han Chinese in Beijing (from 1000 Genomes Project) and Qiang Chinese from Sichuan (CQSC). Phylogenetic tree construction further illuminated distinct haplotypes among populations, with ethnically unique haplotypes observed in 34.6% of Hui and 7.1% of Qiang populations. K-fold cross-validation show the system's inference abilities at the intercontinental level. In addition, our investigations identified potential associations between the Y-InDel locus Y: 15,385,547 (GRCh37) and haplogroup R1a1a1b2a2- Z2124, as well as locus Y: 13,990,180 (GRCh37) and haplogroup F-M89. In conclusion, we have established a Y-chromosome inference system tailored for grassroots-level application, underscoring the value of incorporating Y-InDel markers in forensic analyses.

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开发和评估用于推断中国西南地区父系祖先信息的新筛选 Y 染色体 InDels 小组。
Y-InDels(插入/缺失)是一种研究极少的遗传标记。这类标记是否可用于遗传祖先推断尚不得而知。我们为法医应用开发了一种创新的 Y 染色体祖先推断系统。该小组利用毛细管电泳(CE)平台扩增了 21 个 Y 染色体位点,包括 Y-InDels 和 Y-SNP(单核苷酸多态性)。该系统在 DNA 浓度大于 0.125 ng/ul 时性能良好,在男女 DNA 混合比为 1:100 时结果准确。实验人群的累积匹配概率(CPM)介于 0.95 和 0.97 之间。该系统在推断祖先起源方面的功效通过洲际种群鉴别得到了证明,显示了非洲和东亚种群之间的高鉴别力。对中国西南地区的汉族、羌族和回族人群进行的人群遗传分析显示,北京汉族(来自千人基因组计划)和四川羌族(CQSC)之间的最小 FST 值为 0.0002。系统发生树的构建进一步揭示了不同人群之间不同的单倍型,在 34.6% 的回族人群和 7.1% 的羌族人群中观察到了独特的单倍型。K 倍交叉验证显示了该系统在洲际水平上的推断能力。此外,我们的研究还发现了 Y-InDel 基因座 Y: 15,385,547 (GRCh37) 与单倍群 R1a1a1b2a2- Z2124 之间的潜在联系,以及基因座 Y: 13,990,180 (GRCh37) 与单倍群 F-M89 之间的潜在联系。总之,我们建立了一个适合基层应用的 Y 染色体推断系统,强调了将 Y-InDel 标记纳入法医分析的价值。
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来源期刊
CiteScore
5.80
自引率
9.50%
发文量
165
审稿时长
1 months
期刊介绍: The International Journal of Legal Medicine aims to improve the scientific resources used in the elucidation of crime and related forensic applications at a high level of evidential proof. The journal offers review articles tracing development in specific areas, with up-to-date analysis; original articles discussing significant recent research results; case reports describing interesting and exceptional examples; population data; letters to the editors; and technical notes, which appear in a section originally created for rapid publication of data in the dynamic field of DNA analysis.
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