Thesis (MScMedSc)--Stellenbosch University, 2012. / Bibliography / ENGLISH ABSTRACT: South Africa is ranked amongst the top tuberculosis (TB) burden countries in the world and the Western Cape has a particularly high incidence of the disease. Previous studies have showed that several genes may play crucial roles in susceptibility to TB. In this study, we investigated the role of three genes previously associated with susceptibility to TB and progression to disease. These genes were Surfactant protein D (SFTPD), Macrophage receptor with collagenous structure (MARCO) and CD14. The proteins from these genes bind M. tuberculosis and are involved in the uptake of the bacteria into macrophages. The study investigated the role of ten polymorphisms from SFTPD and MARCO within a South African Coloured (SAC) population, where tuberculosis is highly prevalent. A casecontrol study design was used and polymorphisms were genotyped with Taqman® genotyping assays and amplification refractory mutation system polymerase chain reaction (ARMS-PCR). The results were analysed for association with disease, linkage disequilibrium, haplotypes and gene-gene interactions. Allele and genotype frequencies were also determined which allowed for comparisons to other populations. Five SNPs were associated with TB: two in SFTPD (rs1923537; rs2255326) and three in MARCO (rs1318645; rs3943679; rs2119112). The associated SNPs were located in regions other than exons and the effects of polymorphisms in these regions are not well understood but studies in other genes have shown them to play a functional role. Gene-gene interaction analysis showed that polymorphisms interacted with each other within and between genes, illustrating the importance of epistasis and the complexity of the genetic influences on TB. In addition to the case-control association studies, the role of the rs2569190 promoter SNP in CD14 was assessed. Gene-expression analysis was conducted with qPCR and a reporter gene assay and results from both of these approaches showed that individuals with the TT genotype had a twofold greater expression level than individuals with the CC genotype. Previously, the TT genotype has been associated with stronger promoter activity and expression of soluble CD14 in serum. Since the TT genotype was present at a higher frequency in the control group, we speculate that greater expression of CD14 may contribute to a more TB resistant phenotype. The work presented in this study illustrates the importance of the host genetic component of TB. Genetic studies will eventually revolutionize the current treatment regime as the identification of vulnerable individuals and populations will aid in the development of personalised medicines. / AFRIKAANSE OPSOMMING: Suid-Afrika is een van die top tuberkulose (TB) lande in die wêreld en die Wes-Kaap het veral ‘n hoë insidensie van die siekte. Vorige studies het gewys dat verskeie gene bydra to die vatbaarheid vir tuberkulose. In hierdie studie het ons drie gene, wat voorheen vir vatbaarheid vir tuberkulose en progressie na die siekte ondersoek is, bestudeer. Hierdie gene is Surfactant protein D (SFTPD), Macrophage receptor with collagenous structure (MARCO) en CD14. Die proteïene van hierdie gene bind M. tuberculosis en is betrokke in die opname van die bakterieë in die makrofages. Hierdie studie het tien polimorfismes van SFTPD en MARCO in die Suid-Afrikaanse Kleurlingbevolking (SAK), wat ‘n hoë TB insidensie het, getoets. Pasiënt-kontrole assosiasie studies is gedoen en polimorfismes is gegenotipeer met Taqman® genotiperingsisteem en die amplifikasie refraktoriese mutasie sisteem polimerase ketting reaksie (ARMS-PCR). Die resultate is geanaliseer vir assosiasies met TB, koppelings disekwilibrium, haplotipes en geen-geen interaksies. Alleel en genotype frekwensies is ook bepaal en vergelyk met die van ander bevolkings. Vyf enkel nukleotied polimorfismes (ENPs) is met TB geassosieer: twee in SFTPD (rs1923537; rs2255326) en drie in MARCO (rs1318645; rs3943679; rs2119112). Die geassosieerde ENPs was nie in eksons nie. Die effek van polimorfismes in areas anders as eksons word nie goed verstaan nie, maar studies het bewys dat hulle wel ‘n funksionele rol kan hê. Geen-geen interaksie analise het gewys dat polimorfismes interaksies met mekaar binne sowel as tussen gene gehad het, wat die belangrikheid van epistase en die kompleksiteit van genetiese invloede op TB illustreer. Tesame met die pasiënt-kontrole assosiasie studies is die rol van die rs2569190 promoter ENP in CD14 ook ondersoek. Geenuitdrukkingsanalise is gedoen met qPKR en rapporteerder geen toetse. Die resultate van beide hierdie benaderings het gewys dat individue met die TT genotipe twee keer soveel uitdrukkingsvlakke gehad het as individue met die CC genotipe. Die TT genotipe is voorheen geassosieer met sterk promoter aktiwiteit en die uitdrukking van oplosbare CD14 in serum. Aangesien die TT genotipe meer in die kontrolegroep gevind is, spekuleer ons dat die hoër uitdrukking van CD14 kan bydra tot ‘n meer TB weerstandbiedende fenotipe. Hierdie werk illustreer die belangrikheid van die gasheer genetiese komponent in TB. Genetiese studies sal in die toekoms die huidige behandeling regime revolusioneer, aangesien die identifikasie van individue en bevolkings met ‘n hoë risiko om TB te ontwikkel sal bydra tot die ontwikkeling van persoonlike medisynes. / The National Research Foundation (NRF); the South African Medical Research Council (MRC); Stellenbosch University and the Harry Crossley Foundation.