title: Selection of highly informative SNP markers for population affiliation of major US populations.
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.
authors.affiliation: 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. Xiangpei.Zeng@live.unthsc.edu.
authors.forename: Xiangpei
authors.initials: X
authors.lastname: Zeng
authors.affiliation: 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.
authors.forename: Ranajit
authors.initials: R
authors.lastname: Chakraborty
authors.affiliation: 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.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: King
authors.affiliation: 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.
authors.forename: Bobby
authors.initials: B
authors.lastname: LaRue
authors.affiliation: Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.|Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias, Brazil.
authors.forename: Rodrigo S
authors.initials: RS
authors.lastname: Moura-Neto
authors.affiliation: 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.|Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
mesh_terms: D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population; D005838:Genotype; D060148:HapMap Project; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D044469:Racial Groups / Q000235:genetics*; D014481:United States
chemical_list: D005819:Genetic Markers
keywords: 1000 Genomes; Ancestry informative markers (AIMs); F ST; HapMap; Population differentiation; Single nucleotide polymorphisms (SNPs)