Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

Katarzyna Bryc, Christopher Velez, Tatiana Karafet, Andres Moreno-Estrada, Andy Reynolds, Adam Auton, Michael F Hammer, Carlos D. Bustamante, Harry Ostrer

Research output: Contribution to journalArticle

220 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)8954-8961
Number of pages8
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue numberSUPPL. 2
DOIs
StatePublished - May 11 2010

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Hispanic Americans
Genome
North American Indians
Population
Single Nucleotide Polymorphism
Dominican Republic
Ecuador
Sexism
Puerto Rico
Colombia
Genetic Structures
Y Chromosome
Genome-Wide Association Study
Linkage Disequilibrium
Population Dynamics
X Chromosome
Principal Component Analysis
Mitochondrial DNA
African Americans
Haplotypes

Keywords

  • Hispanic/Latino
  • Human genomics
  • Population genetics

ASJC Scopus subject areas

  • General

Cite this

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. / Bryc, Katarzyna; Velez, Christopher; Karafet, Tatiana; Moreno-Estrada, Andres; Reynolds, Andy; Auton, Adam; Hammer, Michael F; Bustamante, Carlos D.; Ostrer, Harry.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. SUPPL. 2, 11.05.2010, p. 8954-8961.

Research output: Contribution to journalArticle

Bryc, Katarzyna ; Velez, Christopher ; Karafet, Tatiana ; Moreno-Estrada, Andres ; Reynolds, Andy ; Auton, Adam ; Hammer, Michael F ; Bustamante, Carlos D. ; Ostrer, Harry. / Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. SUPPL. 2. pp. 8954-8961.
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