Genetic diversity of the Organic Cation Transporter 1 gene within the Cape Coloured Population

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dc.contributor.advisorBenjeddou, Mongi
dc.contributor.authorPearce, Brendon
dc.contributor.otherDept. of Biotechnology
dc.date.accessioned2014-03-28T10:39:29Z
dc.date.accessioned2024-05-09T07:45:06Z
dc.date.available2013/07/11
dc.date.available2013/07/11 15:45
dc.date.available2014-03-28T10:39:29Z
dc.date.available2024-05-09T07:45:06Z
dc.date.issued2012
dc.descriptionMagister Scientiae - MScen_US
dc.description.abstractThe aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South Africa; a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot® and Multiplex AS-PCR genotyping assays, and also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the Cape Metropolitan area. Two SNaPshot® Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific – PCR (MAS-PCR) genotyping system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan large numbers of samples for novel genetic variations.en_US
dc.description.countrySouth Africa
dc.identifier.urihttps://hdl.handle.net/10566/13287
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderCopyright: University of the Western Capeen_US
dc.subjectPharmacogeneticsen_US
dc.subjectPolymerase Chain Reaction (PCR)en_US
dc.subjectOrganic Cation Transporter (OCT)en_US
dc.subjectHigh-resolution melten_US
dc.subjectSingle nucleotide polymorphismen_US
dc.subjectAllele-specific PCRen_US
dc.subjectGenotypingen_US
dc.subjectMultiplex PCRen_US
dc.subjectInternal validationen_US
dc.subjectPopulation studiesen_US
dc.subjectAllele frequenciesen_US
dc.titleGenetic diversity of the Organic Cation Transporter 1 gene within the Cape Coloured Populationen_US

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