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Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape
Includes bibliographical references.
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| Other Authors: | |
| Format: | Thesis |
| Language: | English |
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Institute of Infectious Disease and Molecular Medicine
2014
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| _version_ | 1867613343293898752 |
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| access_status_str | Open Access |
| author | Rugamika, Emile Chimusa |
| author2 | Mulder, Nicola |
| author_browse | Mulder, Nicola Rugamika, Emile Chimusa |
| author_facet | Mulder, Nicola Rugamika, Emile Chimusa |
| author_sort | Rugamika, Emile Chimusa |
| collection | Thesis |
| description | Includes bibliographical references. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/10691 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:34:38.153Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | Institute of Infectious Disease and Molecular Medicine |
| publisherStr | Institute of Infectious Disease and Molecular Medicine |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/10691 Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape Rugamika, Emile Chimusa Mulder, Nicola Price, Alkes Van Helden, Eileen Hoal Computational Biology Includes bibliographical references. The South Africa Coloured population of the Western Cape is the result of unions between Europeans, Africans (Bantu and Khoisan), and various other populations (Malaysian or Indonesian descent). The world-wide burden of tuberculosis remains an enormous problem, and is particularly severe in this population. In general, admixed populations that have arisen in historical times can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Despite numerous successful genome-wide association studies, detecting variants that have low disease risk still poses a challenge. Furthermore, admixture association studies for multi-way admixed populations pose constant challenges, including the choice of an accurate ancestral panel to infer ancestry and for imputing missing genotypes to identify possible genetic variants causing susceptibility to disease. This thesis addresses some of these challenges. We first developed PROXYANC, an approach to select the best proxy ancestral populations for admixed populations. From the simulation of a multi-way admixed population, we demonstrated the ability and accuracy of PROXYANC in selecting the best proxy ancestry and illustrated the importance of the choice of ancestries in both estimating admixture proportions and imputing missing genotypes. We applied this approach to the South African Coloured population, to refine both the choice of ancestral populations and their genetic contributions. We also demonstrated that the ancestral allele frequency differences correlated with increased linkage disequilibrium in the SAC, and that the increased LD originates from admixture events rather than population bottlenecks. Secondly, we conducted a study to determine whether ancestry-specific genetic contributions affect tuberculosis risk. We additionally conducted imputation genome-wide association studies and a meta-analysis incorporating previous genome-wide association studies of tuberculosis. 2014-12-31T19:29:46Z 2014-12-31T19:29:46Z 2013 Doctoral Thesis Doctoral PhD http://hdl.handle.net/11427/10691 eng application/pdf Institute of Infectious Disease and Molecular Medicine Faculty of Health Sciences University of Cape Town |
| spellingShingle | Computational Biology Rugamika, Emile Chimusa Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| thesis_degree_str | Doctoral |
| title | Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| title_full | Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| title_fullStr | Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| title_full_unstemmed | Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| title_short | Mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the South African coloured population of the Western Cape |
| title_sort | mapping genes underlying ethnic differences in tuberculosis risk by linkage disequilibrium in the south african coloured population of the western cape |
| topic | Computational Biology |
| url | http://hdl.handle.net/11427/10691 |
| work_keys_str_mv | AT rugamikaemilechimusa mappinggenesunderlyingethnicdifferencesintuberculosisriskbylinkagedisequilibriuminthesouthafricancolouredpopulationofthewesterncape |