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PCAdmix: Principal Components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations

Authors :
Brisbin, Abra
Bryc, Katarzyna
Byrnes, Jake
Zakharia, Fouad
Omberg, Larsson
Degenhardt, Jeremiah
Reynolds, Andrew
Ostrer, Harry
Mezey, Jason G.
Bustamante, Carlos D.
Source :
Human Biology. August 1, 2012, Vol. 84 Issue 4, p343, 22 p.
Publication Year :
2012

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. KEY WORDS: ADMIXTURE, PRINCIPAL COMPONENTS ANALYSIS (PCA), LOCAL ANCESTRY DECONVOLUTION, HAPLOTYPE-BASED, FORWARD-BACKWARD ALGORITHM.<br />There is increasing awareness that admixed individuals such as African Americans or Latinos may have a broad range of ancestry proportions, with varying ancestry proportions throughout the genome even within [...]

Details

Language :
English
ISSN :
00187143
Volume :
84
Issue :
4
Database :
Gale General OneFile
Journal :
Human Biology
Publication Type :
Academic Journal
Accession number :
edsgcl.313345711