Van der Merwe, N .C.Visser, B.Schneider, Sue-Rica2015-11-062015-11-062011-12http://hdl.handle.net/11660/1520English: The aim of the study was to elucidate the variation in phenotypic expression observed within BRCA2 c.8162delG mutation positive families. The study attempted to identify possible genetic factors that contribute to the residual risk conferred by the BRCA2 founder mutation. As BC is a polygenetic disorder, polymorphisms within various low penetrance genes may contribute to the expression of the disease. The selection of the SNPs were based on the results of the CIMBA consortium and have been proven to be associated with an increased BC risk in the general population (Easton et al., 2007) and in BRCA2 mutation carriers specifically (Antoniou et al., 2008). Two SNPs (rs2234693 [PvuII] and rs9340799 [XbaI]) present within ESR1 as well as SNPs present in TNRC9 (rs3803662), LSP1 (rs3817198), MAP3K1 (rs889312) and FGFR2 (rs2981582) identified by GWAS have been implicated in BC risk. These six polymorphisms have been selected to evaluate the risk within the Afrikaner BRCA2 8162delG (c.7934del, p.Arg2645AsnfsX3) mutation carriers specifically. Genotyping of rs2234693 (PvuII) and rs9340799 (XbaI) was done by PCR-RFLP analysis whereas Taqman® assays were used for genotyping rs3803662 (TNRC9), rs3817198 (LSP1), rs889312 (MAP3K1) and rs2981582 (FGFR2). Automated allelic discrimination using the BioRad CFX Manager v1.1.308.1111 software were compared to manual discrimination methods to ensure robust genotyping. Cohen’s kappa analysis suggested a combination of automated (Method 1) and manual (Method 3) genotyping was best suited for accurate allelic discrimination except for LSP1. Due to an putative SNP detected within LSP1, the validity of the LSP1 results should be treated cautiously as no information on the frequency of the second putative SNP in white European individuals is available. Of the six polymorphisms analyzed, only rs2234693 (PvuII), indicated a possible association with BC (P-value = 0.0896), which should be explored within a larger study group. For FGFR2, the HWE results indicated that the deviation observed in the BRCA2 mutation carrier group could possibly be associated with BC. Haplotypes compiled for rs2234693 (PvuII) and rs9340799 (XbaI) as well as the remaining four SNPs were uninformative as it revealed no differences between the BC patients and the Cases. These results may have been due to the high allelic heterogeneity observed within the Afrikaner population, as well as the small test group used.. Although the results of this study did not deliver significant results, it did provide insight into allelic distributions of the SNPs in the Afrikaner BRCA2 8162delG (c.7934del, p.Arg2645AsnfsX3) mutation carriers specifically. Larger scale genotyping could lead to more significant findings to help elucidate the polygenetic nature of BC with the Afrikaner.Afrikaans: Die doel van hierdie studie was om die variasie waargeneem in die fenotipiese uitdrukking onder BRCA2 k.8162delG mutasie positiewe families toe te lig. Die studie het gepoog om verskeie genetiese faktore wat moontlik kan bydra tot die gesamentlike risiko wat toegeken word deur die BRCA2 stigtersmutasie, te identifiseer. Aangesien borskanker ʼn poligeniese siekte is, kan polimorfismes binne verskeie lae-penetrasie gene tot die uitdrukking van die siekte bydra. Die seleksie van die polimorfismes was gebaseer op die resultate van die CIMBA konsortium wat bewys het dat diè polimorfismes met verhoogde borskanker risiko in die algemene populasie (Easton et al., 2007) sowel as in die BRCA2 stigtersmutasie draers spesifiek geassosieerd is (Antoniou et al., 2008). Twee polimorfismes (rs2234693 [PvuII] en rs9340799 [XbaI]) teenwoordig in ESR1 asook die polimorfismes teenwoordig in TNRC9 (rs3803662), LSP1 (rs3817198), MAP3K1 (rs889312) en FGFR2 (rs2981582) wat deur GWAS geidentifiseer is, word met ‘n verhoogde borskanker risiko geassosieer. Die ses polimorfismes is gekies om die addisionele risiko in die Afrikaner BRCA2 k. 8162delG (k.7934del, p.Arg2645AsnfsX3) mutasie draers spesifiek te ondersoek. Genotipering van rs2234693 (PvuII) en rs9340799 (XbaI) is uitgevoer met behulp van ensiem snydings (RFLP), terwyl Taqman® analises gebruik is om rs3803662 (TNRC9), rs3817198 (LSP1), rs889312 (MAP3K1) en rs2981582 (FGFR2) te genotipeer. Outomatiese alleliese diskriminasie gedoen deur die BioRad CFX Manager v1.1.308.1111 sagteware is vergelyk met semi- en nie-outomatiese diskriminasie metodes om sodoende robuuste genotipering te verseker. Cohen se kappa analises het die datastelle vergelyk en aangedui dat die metode van analise van Metode 1 en Metode 3 die meeste ooreenstem, met LSP1 as die uitsondering. Die teenwoordigheid van ‘n addisionele polimorfisme binne dieselfde gebied, impliseer dat die data ingewin vir LSP1 met versigtigheid geïnterpreteer moet word. Geen inligting rakende die frekwensie van hierdie polimorfisme was vir die Europese individue beskikbaar nie. Van die ses polimorfismes geanaliseer, het slegs rs2234693 (PvuII) ʼn moontlike assosiasie met borskanker getoon (P-waarde = 0.0896) wat in ‘n toekomstige groter studie verder ondersoek moet word. Die HWE resultate het aangedui dat die afwyking waargeneem vir FGFR2 in die BRCA2 mutasie draer groep, moontlike assosiasie met borskanker kan beteken. Saamgestelde haplotipes vir rs2234693 (PvuII) en rs9340799 (XbaI) asook die oorblywende vier polimorfismes was oninsiggewend omdat daar geen verkil tussen die borskanker pasiënte en gevalle opgemerk is nie. Die bevindinge kan moontlik die gevolg wees van die hoë alleliese variasie waargeneem in die Afrikaner populasie, sowel as die klein toetsgroep wat gebruik is. Alhoewel die bevindinge van die studie nie statisties betekenisvolle resultate opgelewer het nie, dui dit die alleliese verpreiding van die polimorfimses in die Afrikaner BRCA2 k.8162delG (k.7934del, p.Arg2645AsnfsX3) mutasie draers aan. Grootskaalse genotipering kan lei tot meer insiggewende bevindige.enFGFR2LSP1MAP3K1TNRC9Taqman®ESR1HaplotypePenetranceFamilial breast cancerGenetic modifiersSNPsBreast -- CancerBreast -- Cancer -- Genetic aspectsDissertation (M.Med.Sc. (Human Genetics))--University of the Free State, 2011DissertationUniversity of the Free State