Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
Genes (Basel). 2021 Aug 22;12(8):1284. doi: 10.3390/genes12081284.
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.
我们详细介绍了构成 VISAGE Basic Tool（BT）一部分的祖先信息单核苷酸多态性（SNP）面板的开发，该面板将 41 个外观预测 SNP 和 112 个祖先预测 SNP（两组之间共享三个 SNP）组合在一个大规模平行测序（MPS）多重检测中，而基于血液的年龄分析则使用甲基化标记在平行的 MPS 分析管道中运行。BT 祖先面板的 SNP 选择侧重于已建立的法医标记，这些标记在 MPS 中已经具有良好测序性能的可靠记录，并且总体 SNP 多重检测规模与现有的法医 MPS 检测非常匹配。选择 SNP 来区分来自非洲、欧洲、东亚、美洲和大洋洲这五个主要大陆人群组的个体，并扩展到包括区分南亚个体。从这六个人群组的 1000 个基因组和 HGDP-CEPH 样本的分析中，使用在线分析门户的贝叶斯似然计算器显示 BT 祖先面板没有分类错误。BT 中各祖先 SNP 的分化能力尽可能平衡，以避免在混合背景个体中共同祖先比例估计的偏差。平衡过程导致非洲、欧洲、美洲和大洋洲的累积群体特异性差异值非常相似，东亚略低于平均值，而南亚则与其他群体不同。使用 BT 祖先面板 SNP 和 572,000 个 Affymetrix Human Origins 芯片 SNP，比较了六个混合 1000 个基因组群体中的非洲、欧洲和美洲估计的共同祖先比例。观察到非常相似的共同祖先比例，最低值为 10%，低于该值，BT SNP 并不总是可靠地检测到低水平的共同祖先。分析门户提供了 BT 祖先面板 SNP 的综合人群数据集，包括一个 520 个样本的标准化参考数据集；来自 1000 个基因组、HGDP-CEPH、西蒙斯基金会和爱沙尼亚生物中心基因组多样性项目的 3445 个额外样本；以及来自中东、北非和东非地区个体的 167 个六个群体样本，这些样本来自其他多样性项目的抽样方案，补充了这些样本。
