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

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dc.contributor.authorDaya, Michelle
dc.contributor.authorVan der Merwe, Lize
dc.contributor.authorUshma Galal
dc.contributor.authorMöller, Marlo
dc.contributor.authorSalie, Muneeb
dc.contributor.authorChimusa, Emile R.
dc.contributor.authorGalanter, Joshua M.
dc.contributor.authorVan Helden, Paul D.
dc.contributor.authorHenn, Brenna M.
dc.contributor.authorGignoux, Chris R.
dc.contributor.authorHoal, Eileen
dc.date.accessioned2014-02-11T09:03:11Z
dc.date.available2014-02-11T09:03:11Z
dc.date.issued2013-12
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.en_ZA
dc.descriptionThe original publication is available at http://www.plosone.org/en_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 falsepositive 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.en_ZA
dc.description.sponsorshipStellenbosch Universityen_ZA
dc.description.sponsorshipNational Research Foundation (NRF) National Bioinformatics Functional Programme (http://hicd.nrf.ac.za/ ?q = node/11) and NRF DAAD Scholarships (http://www.nrf.ac.za/funding_overview.php?fid = 190)
dc.description.versionPublishers' versionen_ZA
dc.format.extent11 p. : col. ill.
dc.identifier.citationDaya, M. et al. 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.0082224.en_ZA
dc.identifier.issn1932-6203 (print)
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0082224
dc.identifier.urihttp://hdl.handle.net/10019.1/86136
dc.language.isoen_ZAen_ZA
dc.publisherPLoSen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectColoured peoples -- South Africa -- Genetics -- Researchen_ZA
dc.subjectGenome wide ancestry -- Researchen_ZA
dc.subjectAncestry informative markers (AIMS)en_ZA
dc.titleA panel of ancestry informative markers for the complex five-way admixed South African Coloured populationen_ZA
dc.typeArticleen_ZA
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