PCAdmix: Principal Components-based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations

Overview

Journal Hum Biol

Specialty Social Sciences

Date 2012 Dec 20

PMID 23249312

Citations 108

Authors

Abra Brisbin

Katarzyna Bryc

Jake Byrnes

Fouad Zakharia

Larsson Omberg

Jeremiah Degenhardt

Andrew Reynolds

Harry Ostrer

Jason G Mezey

Carlos D Bustamante

Affiliations

Soon will be listed here.

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.

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