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

 

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dc.contributor.author Daya, Michelle en_ZA
dc.contributor.author Merwe, Lize van der en_ZA
dc.contributor.author Galal, Ushma en_ZA
dc.contributor.author Möller, Marlo en_ZA
dc.contributor.author Salie, Muneeb en_ZA
dc.contributor.author Chimusa, Emile R en_ZA
dc.contributor.author Galanter, Joshua M en_ZA
dc.contributor.author Helden, Paul D van en_ZA
dc.contributor.author Henn, Brenna M en_ZA
dc.contributor.author Gignoux, Chris R en_ZA
dc.date.accessioned 2015-12-28T06:47:27Z
dc.date.available 2015-12-28T06:47:27Z
dc.date.issued 2013 en_ZA
dc.identifier.citation Daya, 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.0082224 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16027
dc.identifier.uri http://dx.doi.org/10.1371/journal.pone.0082224
dc.description.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. en_ZA
dc.language.iso eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights This 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.uri http://creativecommons.org/licenses/by/4.0 en_ZA
dc.source PLoS One en_ZA
dc.source.uri http://journals.plos.org/plosone en_ZA
dc.subject.other Population genetics en_ZA
dc.subject.other Genetic association studies en_ZA
dc.subject.other Genotyping en_ZA
dc.subject.other Comparative genomics en_ZA
dc.subject.other Genome complexity en_ZA
dc.subject.other Chromosomes en_ZA
dc.subject.other Permutation en_ZA
dc.subject.other South Africa en_ZA
dc.title A panel of ancestry informative markers for the complex five-way admixed South African Coloured population en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2013 Daya et al en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image
dc.identifier.apacitation Daya, 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/11427/16027 en_ZA
dc.identifier.chicagocitation Daya, 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/11427/16027 en_ZA
dc.identifier.vancouvercitation Daya 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.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


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This 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. Except where otherwise noted, this item's license is described as This 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.