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

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

Research output: Chapter in Book/Report/Conference proceedingChapter

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 SN P 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 disequi- libria 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)
Title of host publicationThe Human Condition
PublisherNational Academy of Sciences
Pages147-166
Number of pages20
Volume4
ISBN (Print)030910405X, 9780309156578
DOIs
StatePublished - Dec 30 2010
Externally publishedYes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Bryc, K., Velez, C., Karafet, T., Moreno-Estrada, A., Reynolds, A., Auton, A. J., Hammer, M., Bustamante, C. D., & Ostrer, H. (2010). Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. In The Human Condition (Vol. 4, pp. 147-166). National Academy of Sciences. https://doi.org/10.17226/12931