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Genetic Admixture and Population Substructure in Guanacaste Costa Rica

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Listed:
  • Zhaoming Wang
  • Allan Hildesheim
  • Sophia S Wang
  • Rolando Herrero
  • Paula Gonzalez
  • Laurie Burdette
  • Amy Hutchinson
  • Gilles Thomas
  • Stephen J Chanock
  • Kai Yu

Abstract

The population of Costa Rica (CR) represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs) genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU), East Asians (JPT+CHB), West African Yoruba (YRI), as well as Native Americans (NA) from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD) measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS) could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.

Suggested Citation

  • Zhaoming Wang & Allan Hildesheim & Sophia S Wang & Rolando Herrero & Paula Gonzalez & Laurie Burdette & Amy Hutchinson & Gilles Thomas & Stephen J Chanock & Kai Yu, 2010. "Genetic Admixture and Population Substructure in Guanacaste Costa Rica," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-10, October.
    • Handle: RePEc:plo:pone00:0013336
    DOI: 10.1371/journal.pone.0013336
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    References listed on IDEAS

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    1. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    2. Gil McVean, 2009. "A Genealogical Interpretation of Principal Components Analysis," PLOS Genetics, Public Library of Science, vol. 5(10), pages 1-10, October.
    3. Kai Yu & Zhaoming Wang & Qizhai Li & Sholom Wacholder & David J Hunter & Robert N Hoover & Stephen Chanock & Gilles Thomas, 2008. "Population Substructure and Control Selection in Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 3(7), pages 1-14, July.
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    1. Ani Manichaikul & Walter Palmas & Carlos J Rodriguez & Carmen A Peralta & Jasmin Divers & Xiuqing Guo & Wei-Min Chen & Quenna Wong & Kayleen Williams & Kathleen F Kerr & Kent D Taylor & Michael Y Tsai, 2012. "Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis," PLOS Genetics, Public Library of Science, vol. 8(4), pages 1-14, April.

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