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01-03-2016 | Original Article

Selection of highly informative SNP markers for population affiliation of major US populations

Authors: Xiangpei Zeng, Ranajit Chakraborty, Jonathan L. King, Bobby LaRue, Rodrigo S. Moura-Neto, Bruce Budowle

Published in: International Journal of Legal Medicine | Issue 2/2016

Abstract

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.

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Title: Selection of highly informative SNP markers for population affiliation of major US populations
Authors: Xiangpei Zeng
Ranajit Chakraborty
Jonathan L. King
Bobby LaRue
Rodrigo S. Moura-Neto
Bruce Budowle
Publication date: 01-03-2016
Publisher: Springer Berlin Heidelberg
Published in: International Journal of Legal Medicine / Issue 2/2016
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI: https://doi.org/10.1007/s00414-015-1297-9

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Selection of highly informative SNP markers for population affiliation of major US populations

Abstract

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