title: 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 In-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.
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Michelle
authors.initials: M
authors.lastname: Daya
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa ; Biostatistics Unit, Medical Research Council, Tygerberg, South Africa ; Statistics Department, University of Western Cape, Cape Town, South Africa.
authors.forename: Lize
authors.initials: L
authors.lastname: van der Merwe
authors.affiliation: Biostatistics Unit, Medical Research Council, Tygerberg, South Africa.
authors.forename: Ushma
authors.initials: U
authors.lastname: Galal
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Marlo
authors.initials: M
authors.lastname: Möller
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Muneeb
authors.initials: M
authors.lastname: Salie
authors.affiliation: Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Cape Town, South Africa.
authors.forename: Emile R
authors.initials: ER
authors.lastname: Chimusa
authors.affiliation: University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Galanter
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
authors.affiliation: Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Brenna M
authors.initials: BM
authors.lastname: Henn
authors.affiliation: University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Chris R
authors.initials: CR
authors.lastname: Gignoux
authors.affiliation: Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Eileen
authors.initials: E
authors.lastname: Hoal
mesh_terms: D044383:Black People / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics; D005788:Gene Pool; D005789:Genealogy and Heraldry; D005819:Genetic Markers; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D013019:South Africa
chemical_list: D005819:Genetic Markers