Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations.
Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
Bryc
Katarzyna
K
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA.
Velez
Christopher
C
Karafet
Tatiana
T
Moreno-Estrada
Andres
A
Reynolds
Andy
A
Auton
Adam
A
Hammer
Michael
M
Bustamante
Carlos D
CD
Ostrer
Harry
H
D001499:Bayes Theorem; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D005828:Genetics, Population; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006630:Hispanic or Latino; D006801:Humans; D008297:Male; D025341:Principal Component Analysis; D012737:Sex Factors; D014481:United States
D004272:DNA, Mitochondrial
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