Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method

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dc.contributor.authorChimusa, Emile Ren_ZA
dc.contributor.authorDaya, Michelleen_ZA
dc.contributor.authorMöller, Marloen_ZA
dc.contributor.authorRamesar, Rajen_ZA
dc.contributor.authorHenn, Brenna Men_ZA
dc.contributor.authorvan Helden, Paul Den_ZA
dc.contributor.authorMulder, Nicola Jen_ZA
dc.contributor.authorHoal, Eileen Gen_ZA
dc.date.accessioned2015-12-28T06:47:34Z
dc.date.available2015-12-28T06:47:34Z
dc.date.issued2013en_ZA
dc.description.abstractAdmixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes.en_ZA
dc.identifier.apacitationChimusa, E. R., Daya, M., Möller, M., Ramesar, R., Henn, B. M., van Helden, P. D., ... Hoal, E. G. (2013). Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method. <i>PLoS One</i>, http://hdl.handle.net/11427/16035en_ZA
dc.identifier.chicagocitationChimusa, Emile R, Michelle Daya, Marlo Möller, Raj Ramesar, Brenna M Henn, Paul D van Helden, Nicola J Mulder, and Eileen G Hoal "Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method." <i>PLoS One</i> (2013) http://hdl.handle.net/11427/16035en_ZA
dc.identifier.citationChimusa, E. R., Daya, M., Möller, M., Ramesar, R., Henn, B. M., Van Helden, P. D., ... & Hoal, E. G. (2013). Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method. PloS one, 8(9), e73971. doi:10.1371/journal.pone.0073971en_ZA
dc.identifier.ris TY - Journal Article AU - Chimusa, Emile R AU - Daya, Michelle AU - Möller, Marlo AU - Ramesar, Raj AU - Henn, Brenna M AU - van Helden, Paul D AU - Mulder, Nicola J AU - Hoal, Eileen G AB - Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes. DA - 2013 DB - OpenUCT DO - 10.1371/journal.pone.0073971 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2013 T1 - Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method TI - Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method UR - http://hdl.handle.net/11427/16035 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16035
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pone.0073971
dc.identifier.vancouvercitationChimusa ER, Daya M, Möller M, Ramesar R, Henn BM, van Helden PD, et al. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method. PLoS One. 2013; http://hdl.handle.net/11427/16035.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 Chimusa 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.otherSimulation and modelingen_ZA
dc.subject.otherPopulation geneticsen_ZA
dc.subject.otherHaplotypesen_ZA
dc.subject.otherPrincipal component analysisen_ZA
dc.subject.otherSouth Africaen_ZA
dc.subject.otherAfricansen_ZA
dc.subject.otherGenome-wide association studiesen_ZA
dc.subject.otherGene poolen_ZA
dc.titleDetermining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection methoden_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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