我们详细介绍了构成VISAGE基本工具(BT)一部分的祖先信息单核苷酸多态性(SNP)小组的发展,它在一个大规模平行测序(MPS)多重中结合了41个外观预测性SNP和112个祖先预测性SNP(在集合之间共享的三个SNP),而使用甲基化标记的基于血液的年龄分析是在平行的MPS分析管道中运行的。BT祖先小组的SNP选择集中在已建立的法医标记上,这些标记已经在MPS中具有良好的测序性能,整体SNP多重量表与现有的法医MPS检测方法非常匹配。选择SNP来区分来自非洲五个主要大陆人口群体的个体,欧洲,东亚,美国,大洋洲,延伸到包括来自南亚的个体的分化。通过对这六个群体的1000个基因组和HGDP-CEPH样本的分析,使用Snipper在线分析门户的Bayes似然计算器,BT祖先小组没有分类错误.尽可能平衡BT的组成祖先SNP的分化能力,以避免在具有混合背景的个体中估计共同祖先比例时出现偏差。平衡过程导致非洲非常相似的累积人口特定差异值,欧洲,美国,大洋洲,东亚略低于平均水平,南亚是其他群体的异类。对非洲人进行了比较,欧洲,和美洲原住民在六个混合的1000个基因组种群中估计的共同祖先比例,使用BT祖先面板SNP和572,000Affymetrix人类起源阵列SNP。观察到非常相似的共同祖先比例下降到10%的最小值,下面,BTSNP并不总是可靠地检测到低水平的共同血统。Snipper分析门户为BT祖先小组SNP提供了一个全面的人口数据集,包含520个样本的标准化参考数据集;来自1000个基因组的3445个额外样本,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;以及来自中东个体内部基因分型的六个种群的167个样本,北非和东非区域补充了其他多样性项目的抽样制度。
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 Snipper 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 Snipper 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.