title: PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations.
abstract: Identifying ancestry along each chromosome in admixed individuals provides a wealth of information for understanding the population genetic history of admixture events and is valuable for admixture mapping and identifying recent targets of selection. We present PCAdmix (available at https://sites.google.com/site/pcadmix/home ), a Principal Components-based algorithm for determining ancestry along each chromosome from a high-density, genome-wide set of phased single-nucleotide polymorphism (SNP) genotypes of admixed individuals. We compare our method to HAPMIX on simulated data from two ancestral populations, and we find high concordance between the methods. Our method also has better accuracy than LAMP when applied to three-population admixture, a situation as yet unaddressed by HAPMIX. Finally, we apply our method to a data set of four Latino populations with European, African, and Native American ancestry. We find evidence of assortative mating in each of the four populations, and we identify regions of shared ancestry that may be recent targets of selection and could serve as candidate regions for admixture-based association mapping.
authors.affiliation: Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY, USA. abrisbin@gmail.com
authors.forename: Abra
authors.initials: A
authors.lastname: Brisbin
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Bryc
authors.forename: Jake
authors.initials: J
authors.lastname: Byrnes
authors.forename: Fouad
authors.initials: F
authors.lastname: Zakharia
authors.forename: Larsson
authors.initials: L
authors.lastname: Omberg
authors.forename: Jeremiah
authors.initials: J
authors.lastname: Degenhardt
authors.forename: Andrew
authors.initials: A
authors.lastname: Reynolds
authors.forename: Harry
authors.initials: H
authors.lastname: Ostrer
authors.forename: Jason G
authors.initials: JG
authors.lastname: Mezey
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human; D003198:Computer Simulation; D023281:Genomics; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D025341:Principal Component Analysis / Q000379:methods*; D044469:Racial Groups / Q000235:genetics*; D014481:United States