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

Molecular 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, PO Box 19063, Tygerberg, 7505, South Africa.
Human Genetics (Impact Factor: 4.82). 08/2010; 128(2):145-53. DOI: 10.1007/s00439-010-0836-1
Source: PubMed


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.

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    • "Race distribution was as follows: mixed ancestry (n = 82, 77%), black (n = 15, 14%) and white (n = 10, 9%). The South African mixed ancestry population, or socalled South African Coloured population, is a unique population with a complex genetic history that is largely made up of Khoisan genes admixed with African, European and a smaller Asian contribution [11]. Patients who self-identified as South African Coloured were included under mixed ancestry category. "

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    • "The older Khoisan populations based in the South-Western parts of Africa make up the remaining African population. In South Africa, there is also a Cape mixed ancestry population, which originated from the sub-Saharan African Bantu-speakers, with influences from both Europe and Asia (de Wit et al., 2010). When two Bantu-speaking populations from Cameroon and South Africa were compared, they were found to be genetically similar with regard to CYP2A6 and CYP2B6. "
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    • "Briefly, Bellville South is predominantly a mixed ancestry township located in the northern suburb of Cape Town in the Tygerberg subdistrict. The mixed ancestry, commonly referred to as coloured, is a South African population group with 32–43% Khoisan, 20–36% Bantu-speaking African, 21–28% European, and 9–11% Asian ancestry [14]. All participants received a standardized interview and physical examination during which blood pressure was measured according to the World Health Organisation (WHO) guidelines [15] using a semiautomated digital blood pressure monitor (Rossmax PA, USA) on the right arm in a sitting position. "
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