Zeng Xiangpei, Chakraborty Ranajit, King Jonathan L, LaRue Bobby, Moura-Neto Rodrigo S, Budowle Bruce
Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.
Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
Int J Legal Med. 2016 Mar;130(2):341-52. doi: 10.1007/s00414-015-1297-9. Epub 2015 Dec 8.
Ancestry informative markers (AIMs) can be used to detect and adjust for population stratification and predict the ancestry of the source of an evidence sample. Autosomal single nucleotide polymorphisms (SNPs) are the best candidates for AIMs. It is essential to identify the most informative AIM SNPs across relevant populations. Several informativeness measures for ancestry estimation have been used for AIMs selection: absolute allele frequency differences (δ), F statistics (F ST), and informativeness for assignment measure (In). However, their efficacy has not been compared objectively, particularly for determining affiliations of major US populations. In this study, these three measures were directly compared for AIMs selection among four major US populations, i.e., African American, Caucasian, East Asian, and Hispanic American. The results showed that the F ST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did the δ panel and both performed better than the In panel. Therefore, the 23 AIMs selected by the F ST measure were used to characterize the four major American populations. Genotype data of nine sample populations were used to evaluate the efficiency of the 23-AIMs panel. The results indicated that individuals could be correctly assigned to the major population categories. Our AIMs panel could contribute to the candidate pool of AIMs for potential forensic identification purposes.
祖先信息标记（AIMs）可用于检测和校正群体分层，并预测证据样本来源的祖先。常染色体单核苷酸多态性（SNP）是AIMs的最佳候选者。识别相关群体中最具信息性的AIM SNP至关重要。几种用于祖先估计的信息性度量已被用于AIMs选择：绝对等位基因频率差异（δ）、F统计量（F ST）和分配度量信息性（In）。然而，它们的功效尚未得到客观比较，尤其是在确定美国主要群体的归属方面。在本研究中，直接比较了这三种度量在美国四个主要群体（即非裔美国人、白种人、东亚人和西班牙裔美国人）中进行AIMs选择的情况。结果表明，基于主成分分析（PCA）聚类，F ST面板在群体分辨率方面的表现略优于δ面板，且两者均优于In面板。因此，由F ST度量选择的23个AIMs用于表征美国四个主要群体。九个样本群体的基因型数据用于评估23个AIMs面板的效率。结果表明，个体能够被正确地归入主要群体类别。我们的AIMs面板可为潜在法医鉴定目的的AIMs候选库做出贡献。
