Original Investigation

Human Genetics

, Volume 128, Issue 2, pp 145-153

Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape

  • Erika de WitAffiliated withMolecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University
  • , Wayne DelportAffiliated withDepartment of Pathology, Antiviral Research Center, University of CaliforniaInstitute of Infectious Disease and Molecular Medicine, University of Cape Town
  • , Chimusa E. RugamikaAffiliated withInstitute of Infectious Disease and Molecular Medicine, University of Cape Town
  • , Ayton MeintjesAffiliated withInstitute of Infectious Disease and Molecular Medicine, University of Cape Town
  • , Marlo MöllerAffiliated withMolecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University
  • , Paul D. van HeldenAffiliated withMolecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University
  • , Cathal SeoigheAffiliated withSchool of Mathematics, Statistics and Applied Mathematics, National University of Ireland
  • , Eileen G. HoalAffiliated withMolecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University Email author 

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Abstract

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32–43%), Bantu-speaking Africans (20–36%), European (21–28%) and a smaller Asian contribution (9–11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.