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

@article{Wit2010GenomewideAO,
  title={Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape},
  author={Erika de Wit and Wayne Delport and Chimusa E. Rugamika and Ayton Meintjes and Marlo M{\"o}ller and Paul D. van Helden and Cathal Seoighe and Eileen G. Hoal},
  journal={Human Genetics},
  year={2010},
  volume={128},
  pages={145-153}
}
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… 
View on Springer
ncbi.nlm.nih.gov
197 Citations
Highly Influential Citations
16
Background Citations
77
Methods Citations
5
Results Citations
5

197 Citations

A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population
TLDR
It is shown that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population.
Genetic diversity in black South Africans from
TLDR
The most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg), indicated that Sowetan population structure appears unique compared to other black Africans, and may have clinical implications.
Genetic diversity in black South Africans from Soweto
TLDR
Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources.
Patterns of African and Asian admixture in the Afrikaner population of South Africa
TLDR
In a genome-wide study of 77 Afrikaners, it was found their majority ancestry came from Europeans, but almost all Afrikaans had admixture from non-Europeans, and despite their small founding population, there was no sign of a recent bottleneck in theAfrikaner compared to other European populations.
Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
TLDR
It is demonstrated that the genetic contribution to TB risk varies between continental populations, and the value of including admixed populations in studies of TB risk and other complex phenotypes is illustrated, and case-only admixture mapping is currently impractical in multi-way admixture populations due to spurious deviations in average local ancestry generated by current local ancestry inference methods.
Genetic-substructure and complex demographic history of South African Bantu speakers
TLDR
There is strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny in South Eastern Bantu-speaking groups, and simulated trait genome-wide association studies show that the observed population structure could have major implications for biomedical genomics research in South Africa.
Genetic substructure and complex demographic history of South African Bantu speakers
TLDR
There is strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny in South Eastern Bantu-speaking groups, and simulated trait genome-wide association studies show that the observed population structure could have major implications for biomedical genomics research in South Africa.
Extensive Population Structure in San, Khoe, and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes
TLDR
The present study made use of 220 autosomal SNP markers (in the format of both haplotypes and genotypes) to examine the population structure of various San and Khoe groups and their relationship to other neighboring groups.
Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
TLDR
Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification, and illustrated the importance of African genomic diversity in understanding human evolutionary history.
Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa
TLDR
High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1, so it is compelling to assess genome-wide contribution of ancestry to HIV- 1 infection.
...
...

References

SHOWING 1-10 OF 52 REFERENCES
Strong maternal Khoisan contribution to the South African coloured population: a case of gender-biased admixture.
The Genetic Structure and History of Africans and African Americans
TLDR
A detailed genetic analysis of most major groups of African populations is provided, suggesting that Africans represent 14 ancestral populations that correlate with self-described ethnicity and shared cultural and/or linguistic properties.
Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.
  • P. Mckeigue
  • Biology
    American journal of human genetics
  • 1997
TLDR
The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture.
A second generation human haplotype map of over 3.1 million SNPs
TLDR
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
Implications of biogeography of human populations for 'race' and medicine
TLDR
It is shown that racial classifications are inadequate descriptors of the distribution of genetic variation in the authors' species and whether or not populations cluster according to the popular concept of 'race'.
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
TLDR
Although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HAPMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.
African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping.
TLDR
This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.
Investigation of chromosome 17 candidate genes in susceptibility to TB in a South African population.
Genetic analysis of African populations: human evolution and complex disease
Africa is one of the most ethnically and genetically diverse regions of the world. It is thought to be the ancestral homeland of all modern humans, and is the homeland of millions of people of the…
Statistical tests for admixture mapping with case-control and cases-only data.
TLDR
New statistical methods for analyzing multipoint data from admixture-mapping studies to detect "ancestry association" are described, and it is shown that, although "ANCestry informative markers" (AIMs) are superior to random single-nucleotide polymorphisms (SNPs), random SNPs can perform quite well when AIMs are not available.
...
...