Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations

Proc Natl Acad Sci U S A. 2010 May 11;107 Suppl 2(Suppl 2):8954-61. doi: 10.1073/pnas.0914618107. Epub 2010 May 5.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bayes Theorem
  • Chromosome Mapping
  • Cluster Analysis
  • Computational Biology / methods
  • DNA, Mitochondrial / genetics
  • Female
  • Genetics, Population*
  • Genome, Human*
  • Genome-Wide Association Study
  • Hispanic Americans
  • Humans
  • Male
  • Principal Component Analysis
  • Sex Factors
  • United States

Substances

  • DNA, Mitochondrial