A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population

Abstract

Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al's -statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show 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.

A post-GWAS analysis of predicted regulatory variants and tuberculosis susceptibility

“…The admixed SAC population has genetic contributions from five ancestral populations. On average, Bantu-speaking populations contribute ~30%, the KhoeSan ~30%, Europeans 12–18% South Asian ~15%, and East Asian <10% [23–25]. Genotyping of ancestry informative markers (AIMS) was previously performed by Daya et al (2013).…”

“…Genotyping of ancestry informative markers (AIMS) was previously performed by Daya et al (2013). These AIMS were used to infer admixture proportions using ADMIXTURE [25,26]. …”

Population differences in the postcrania of modern South Africans and the implications for ancestry estimation

“…In South Africa the term "coloured" refers to a self-identified social group that exhibits highly diverse origins [14]. Because South African coloureds constitute such a complex combination of continental populations, the group typically presents with some of the highest degrees of genetic variation in the world [15,16]. Parental populations are inclusive of (1) indigenous Khoesan, (2) descendants of slaves brought from countries such as Malaysia, Indonesia and 4 India, (3) Europeans and (4) Bantu-speaking groups [14,[17][18][19].…”

The identification of novel genetic variants associated with antipsychotic treatment response outcomes in first-episode schizophrenia patients

“…To allow for correction for population stratification, 100 ancestry informative markers (AIMs), which were designed specifically for the SAC population [29], were included in the genotyping assay (Supplementary materials, Supplemental digital content 1, http://links.lww.com/FPC/A995). After the successful genotyping of these AIMs, ancestry proportions were estimated by ADMIXTURE utilizing the genotype data obtained for the FES cohorts as well as the data obtained from the five populations from which the AIMS were designed.…”

“…After the successful genotyping of these AIMs, ancestry proportions were estimated by ADMIXTURE utilizing the genotype data obtained for the FES cohorts as well as the data obtained from the five populations from which the AIMS were designed. This procedure is described in further detail by Daya and colleagues [29].…”