A panel of ancestry informative markers for the complex five-way admixed South African Coloured population

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dc.contributor.authorDaya, Michelleen_ZA
dc.contributor.authorMerwe, Lize van deren_ZA
dc.contributor.authorGalal, Ushmaen_ZA
dc.contributor.authorMöller, Marloen_ZA
dc.contributor.authorSalie, Muneeben_ZA
dc.contributor.authorChimusa, Emile Ren_ZA
dc.contributor.authorGalanter, Joshua Men_ZA
dc.contributor.authorHelden, Paul D vanen_ZA
dc.contributor.authorHenn, Brenna Men_ZA
dc.contributor.authorGignoux, Chris Ren_ZA
dc.date.accessioned2015-12-28T06:47:27Z
dc.date.available2015-12-28T06:47:27Z
dc.date.issued2013en_ZA
dc.description.abstractAdmixture 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.en_ZA
dc.identifier.apacitationDaya, M., Merwe, L. v. d., Galal, U., Möller, M., Salie, M., Chimusa, E. R., ... Gignoux, C. R. (2013). A panel of ancestry informative markers for the complex five-way admixed South African Coloured population. <i>PLoS One</i>, http://hdl.handle.net/11427/16027en_ZA
dc.identifier.chicagocitationDaya, Michelle, Lize van der Merwe, Ushma Galal, Marlo Möller, Muneeb Salie, Emile R Chimusa, Joshua M Galanter, Paul D van Helden, Brenna M Henn, and Chris R Gignoux "A panel of ancestry informative markers for the complex five-way admixed South African Coloured population." <i>PLoS One</i> (2013) http://hdl.handle.net/11427/16027en_ZA
dc.identifier.citationDaya, M., Van Der Merwe, L., Galal, U., Möller, M., Salie, M., Chimusa, E. R., ... & Hoal, E. (2013). A panel of ancestry informative markers for the complex five-way admixed South African Coloured population, PLoS ONE, 8(12), e82224. doi:10.1371/journal.pone.0082224en_ZA
dc.identifier.ris TY - Journal Article AU - Daya, Michelle AU - Merwe, Lize van der AU - Galal, Ushma AU - Möller, Marlo AU - Salie, Muneeb AU - Chimusa, Emile R AU - Galanter, Joshua M AU - Helden, Paul D van AU - Henn, Brenna M AU - Gignoux, Chris R AB - 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. DA - 2013 DB - OpenUCT DO - 10.1371/journal.pone.0082224 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2013 T1 - A panel of ancestry informative markers for the complex five-way admixed South African Coloured population TI - A panel of ancestry informative markers for the complex five-way admixed South African Coloured population UR - http://hdl.handle.net/11427/16027 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16027
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0082224
dc.identifier.vancouvercitationDaya M, Merwe Lvd, Galal U, Möller M, Salie M, Chimusa ER, et al. A panel of ancestry informative markers for the complex five-way admixed South African Coloured population. PLoS One. 2013; http://hdl.handle.net/11427/16027.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_ZA
dc.rights.holder© 2013 Daya et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plosoneen_ZA
dc.subject.otherPopulation geneticsen_ZA
dc.subject.otherGenetic association studiesen_ZA
dc.subject.otherGenotypingen_ZA
dc.subject.otherComparative genomicsen_ZA
dc.subject.otherGenome complexityen_ZA
dc.subject.otherChromosomesen_ZA
dc.subject.otherPermutationen_ZA
dc.subject.otherSouth Africaen_ZA
dc.titleA panel of ancestry informative markers for the complex five-way admixed South African Coloured populationen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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