MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
Forensic Sci Int Genet. 2024 Jul;71:103029. doi: 10.1016/j.fsigen.2024.103029. Epub 2024 Mar 5.
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
Y 染色体短串联重复序列多态性（Y-STRs）和 Y 染色体单核苷酸多态性（Y-SNPs）是用于父系鉴定和群体遗传学的有价值的遗传标记。目前，缺乏一种有效的面板，将 Y-STRs 和 Y-SNPs 整合到研究父系的研究中，特别是在东亚人群中。因此，我们基于多重 PCR 和单端 400 大规模平行测序（MPS）策略，开发了一种名为 YARN（Y 染色体祖先和区域网络）的新型 Y 染色体靶向面板，该面板由 44 个父系 Y-STRs 和 260 个进化 Y-SNPs 组成。根据 SWGDAM 验证指南，共验证了 386 个反应来验证 YARN 的有效性和适用性，包括灵敏度（最小输入 gDNA 为 0.125ng）、混合物识别（范围为 1:1-1:10）、PCR 抑制剂测试（使用 50μM 血红素、100μM 血红蛋白、100μM 腐殖酸和 2.5mM 靛蓝染料等物质）、种特异性（成功将人类与其他动物区分开来）、重复性研究（达到 100%的准确性）和一致性研究（对于 1121 个 Y-STR 等位基因的准确率为 99.91%）。此外，我们在中国广东省肇庆市怀集县的 484 名汉族男性中进行了 YARN 的试点研究（GDZQHJ 队列）。在该队列中，我们鉴定出 52 个不同的 Y 单倍群和 73 个不同的姓氏。我们发现 Y 单倍群、中国姓氏和 GDZQHJ 队列的地理位置之间存在弱到中度相关性（λ 值范围为 0.050 至 0.340）。然而，当我们将两个不同的类别组合成一个新的独立变量时，我们观察到更强的相关性（λ 值范围为 0.617 至 0.754）。总体而言，YARN 面板结合了 Y-STR 和 Y-SNP 遗传标记，符合法医 DNA 质量保证指南，并且具有推断东亚地理起源和父系分析的潜力。
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