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

 

Show simple item record

dc.contributor.author Chimusa, Emile R en_ZA
dc.contributor.author Daya, Michelle en_ZA
dc.contributor.author Möller, Marlo en_ZA
dc.contributor.author Ramesar, Raj en_ZA
dc.contributor.author Henn, Brenna M en_ZA
dc.contributor.author van Helden, Paul D en_ZA
dc.contributor.author Mulder, Nicola J en_ZA
dc.contributor.author Hoal, Eileen G en_ZA
dc.date.accessioned 2015-12-28T06:47:34Z
dc.date.available 2015-12-28T06:47:34Z
dc.date.issued 2013 en_ZA
dc.identifier.citation Chimusa, 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.0073971 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16035
dc.identifier.uri http://dx.doi.org/10.1371/journal.pone.0073971
dc.description.abstract 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. 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 Simulation and modeling en_ZA
dc.subject.other Population genetics en_ZA
dc.subject.other Haplotypes en_ZA
dc.subject.other Principal component analysis en_ZA
dc.subject.other South Africa en_ZA
dc.subject.other Africans en_ZA
dc.subject.other Genome-wide association studies en_ZA
dc.subject.other Gene pool en_ZA
dc.title Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2013 Chimusa 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


Files in this item

This item appears in the following Collection(s)

Show simple item record

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.