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

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dc.contributor.authorChimusa, Emile Ren_ZA
dc.contributor.authorMeintjies, Aytonen_ZA
dc.contributor.authorTchanga, Milaineen_ZA
dc.contributor.authorMulder, Nicolaen_ZA
dc.contributor.authorSeoighe, Cathalen_ZA
dc.contributor.authorSoodyall, Himlaen_ZA
dc.contributor.authorRamesar, Rajkumaren_ZA
dc.date.accessioned2015-12-28T06:47:30Z
dc.date.available2015-12-28T06:47:30Z
dc.date.issued2015en_ZA
dc.description.abstractWe 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.identifier.apacitationChimusa, 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/11427/16030en_ZA
dc.identifier.chicagocitationChimusa, 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/11427/16030en_ZA
dc.identifier.citationChimusa, 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.1005052en_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
dc.identifier.urihttp://hdl.handle.net/11427/16030
dc.identifier.urihttp://dx.doi.org/10.1371/journal.pgen.1005052
dc.identifier.vancouvercitationChimusa 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.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© 2015 Chimusa et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLOS Geneticsen_ZA
dc.source.urihttp://journals.plos.org/plosgeneticsen_ZA
dc.subject.otherPopulation geneticsen_ZA
dc.subject.otherAfricaen_ZA
dc.subject.otherLinkage disequilibriumen_ZA
dc.subject.otherGenomic databasesen_ZA
dc.subject.otherDrug metabolismen_ZA
dc.subject.otherAllelesen_ZA
dc.subject.otherHaplotypesen_ZA
dc.subject.otherMetabolic pathwaysen_ZA
dc.titleA Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populationsen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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