TY - JOUR
T1 - Pcadmix
T2 - Principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations
AU - Brisbin, Abra
AU - Bryc, Katarzyna
AU - Byrnes, Jake
AU - Zakharia, Fouad
AU - Omberg, Larsson
AU - Degenhardt, Jeremiah
AU - Reynolds, Andrew
AU - Ostrer, Harry
AU - Mezey, Jason G.
AU - Bustamante, Carlos D.
PY - 2012/8
Y1 - 2012/8
N2 - 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.
AB - 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.
KW - Admixture
KW - Forward-backward algorithm
KW - Haplotype-based
KW - Local ancestry deconvolution
KW - Principal components analysis (PCA)
UR - http://www.scopus.com/inward/record.url?scp=84872074517&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84872074517&partnerID=8YFLogxK
U2 - 10.3378/027.084.0401
DO - 10.3378/027.084.0401
M3 - Article
C2 - 23249312
AN - SCOPUS:84872074517
SN - 0018-7143
VL - 84
SP - 343
EP - 364
JO - Human Biology
JF - Human Biology
IS - 4
ER -