Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection
Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection
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开发和验证包含 256 个 Y-SNP 的定制面板，用于中国 Y 染色体单倍群解剖
DOI：
10.1016/j.fsigen.2022.102786
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发表时间：
2022-10-12
影响因子：
3.1
通讯作者：
Wang, Zheng
中科院分区：
文献类型：
--
作者：
Liu, Jing;Jiang, Lirong;Wang, Zheng
利用Y染色体单核苷酸多态性（Y-SNPs）确定Y染色体单倍群，可以进行父系谱系鉴定和父系家系推断，这一研究在法医学领域引起了广泛的兴趣。最近，一个全面的Y-SNP工具与显性标记靶向单倍群在R，E和I分支，它允许推断640 Y单倍群已被报道。它具有非常好的性能，可以在大多数群体中提供高水平的Y单倍型群分辨率。然而，中国人群中的优势单倍型群是O，C和N，这表明需要更多的Y-SNPs在这些分支下，以实现群体特异性的高分辨率。在此，我们针对中国人群，在前期研究的基础上，提出了一个经过大幅改进的定制Y-SNP MPS面板，包含256个精心确定的YSNPs，并通过一系列测试，包括一致性，重复性，灵敏度，特异性和稳定性测试，以及混合，降解和病例类型样本分析，对该面板进行了评估。初步开发验证表明，该面板具有高度可靠性、灵敏度、特异性和耐用性。在灵敏度测试中，即使当DNA输入降低到低至0.5 ng时，样品仍然可以被分配到正确的Y单倍型组。对于混合物分析，即使是1：99（男性：女性）的混合物上的分配的男性贡献者的Y单倍型群没有影响。总之，该测定提供了高分辨率Y染色体单倍群工作流程，以确定男性的父系谱系和/或父系遗传学祖先，并且可广泛用于中国Y染色体单倍群解剖。
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 YSNPs 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.