A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

 

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dc.contributor.author Chimusa, Emile R en_ZA
dc.contributor.author Meintjies, Ayton en_ZA
dc.contributor.author Tchanga, Milaine en_ZA
dc.contributor.author Mulder, Nicola en_ZA
dc.contributor.author Seoighe, Cathal en_ZA
dc.contributor.author Soodyall, Himla en_ZA
dc.contributor.author Ramesar, Rajkumar en_ZA
dc.date.accessioned 2015-12-28T06:47:30Z
dc.date.available 2015-12-28T06:47:30Z
dc.date.issued 2015 en_ZA
dc.identifier.citation Chimusa, E. R., Meintjies, A., Tchanga, M., Mulder, N., Seioghe, C., Soodyall, H., & Ramesar, R. (2015). A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations. PLoS genetics, 11(3), e1005052-e1005052. doi:10.1371/journal.pgen.1005052 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16030
dc.identifier.uri http://dx.doi.org/10.1371/journal.pgen.1005052
dc.description.abstract We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. 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 Genetics en_ZA
dc.source.uri http://journals.plos.org/plosgenetics en_ZA
dc.subject.other Population genetics en_ZA
dc.subject.other Africa en_ZA
dc.subject.other Linkage disequilibrium en_ZA
dc.subject.other Genomic databases en_ZA
dc.subject.other Drug metabolism en_ZA
dc.subject.other Alleles en_ZA
dc.subject.other Haplotypes en_ZA
dc.subject.other Metabolic pathways en_ZA
dc.title A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2015 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
dc.identifier.apacitation Chimusa, E. R., Meintjies, A., Tchanga, M., Mulder, N., Seoighe, C., Soodyall, H., & Ramesar, R. (2015). A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations. <i>PLOS Genetics</i>, http://hdl.handle.net/11427/16030 en_ZA
dc.identifier.chicagocitation Chimusa, Emile R, Ayton Meintjies, Milaine Tchanga, Nicola Mulder, Cathal Seoighe, Himla Soodyall, and Rajkumar Ramesar "A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations." <i>PLOS Genetics</i> (2015) http://hdl.handle.net/11427/16030 en_ZA
dc.identifier.vancouvercitation Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, et al. A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations. PLOS Genetics. 2015; http://hdl.handle.net/11427/16030. en_ZA
dc.identifier.ris TY - Journal Article AU - Chimusa, Emile R AU - Meintjies, Ayton AU - Tchanga, Milaine AU - Mulder, Nicola AU - Seoighe, Cathal AU - Soodyall, Himla AU - Ramesar, Rajkumar AB - We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. DA - 2015 DB - OpenUCT DO - 10.1371/journal.pgen.1005052 DP - University of Cape Town J1 - PLOS Genetics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2015 T1 - A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations TI - A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations UR - http://hdl.handle.net/11427/16030 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.