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

Document Type

Open Access Article

Authors

Abra Brisbin, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NYFollow
Katarzyna Bryc, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY
Jake Byrnes, Department of Genetics, Harvard Medical School, Boston, MA
Fouad Zakharia, Department of Genetics, Stanford University, Stanford, CA
Larsson Omberg, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY
Jeremiah Degenhardt, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY
Andrew Reynolds, Department of Pathology and Genetics, Albert Einstein College of Medicine, Bronx, NY
Harry Ostrer, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY
Jason G. Mezey, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NY
Carlos D. Bustamante, Department of Biostatistics and Computational Biology, Cornell University, Ithaca, NYFollow

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 Componentsbased 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.

Recommended Citation

Brisbin, Abra; Bryc, Katarzyna; Byrnes, Jake; Zakharia, Fouad; Omberg, Larsson; Degenhardt, Jeremiah; Reynolds, Andrew; Ostrer, Harry; Mezey, Jason G.; and Bustamante, Carlos D. (2012) "PCAdmix: Principal Components-Based Assignment of Ancestry along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations," Human Biology: Vol. 84: Iss. 4, Article 5.
Available at: https://digitalcommons.wayne.edu/humbiol/vol84/iss4/5