Abstracts Category : Other

Identification of rare gene variants in South African breast cancerfamilies through next generation sequencing

by Juliet Lewie Mentoor

Breast cancer (BC) has become the leading canceramongst women in South Africa. The overall life time risk fordeveloping this disease is one in 12 (National Cancer registry,2000- 2011). A strong family history (3 affected) is an importantfactor for inherited predisposition to BC that accounts forapproximately 10% of cases worldwide. Mutations in several high-and moderate risk breast cancer genes have been associated withfamilial BC and includes BRCA1, BRCA2, TP53, PALB2, and CHEK2.Individuals that carry germline mutations in BRCA1 and BRCA2possess an 80% lifetime risk for BC. Mutations in BRCA1 and BRCA2are responsible for 29% and 25% of familial BC worldwide. In SouthAfrica BRCA1 mutations account for 19% and BRCA2 for 47% offamilial breast cancer. Mutations associated with a moderate riskfor BC account for ~1% of cases. This data suggests that ~30% ofSouth African BC families are not characterised by pathogenicmutations in known breast/ovarian (BC/OVC) genes. The purpose ofthe present study was to identify gene variants that may predisposeto breast cancer. Next generation sequencing was performed toinvestigate the germline DNA of highrisk BC/OVC families that havepreviously tested negative for premature truncating mutations inBRCA1/2, PALB2 and RAD51C. Paired-end whole exome sequencing wasperformed with nine index cases, selected from six families with astrong background for BC/OVC. This resulted in the discovery of anaverage of 26 000 coding variants in index cases. Geneprioritisation strategies were incorporated to filter all exomevariants and identify high-priority genes for further analysis.After sequence verification, three high-priority genes wereselected for further analysis. The three genes coded for; a novelputative tumour suppressor (TCHP) that is pro-apoptotic; theXPF-endonuclease homolog, EME2; and a POLQ like helicase enzyme(HELQ). Prioritised genes were screened in a total of 61 high-riskfamilies and cohorts of patients with BC or OVC without a familyhistory for their disease. Two potentially damaging variants(stop-gain & inframe amino acid deletion) were identified inTCHP, four (frameshift, nonsense & two in-frame deletions) inEME2 and one frameshift mutation in HELQ in high-risk families andcases that were without a family history for BC/OVC. The analysesperformed in the last section of this project was aimed atidentifying other potential genes of interest by making use of alist of 516 well recognised and putative DNA repair genes. Throughthis approach, one additional truncating mutation in POLN(p.Q837SfsX7) was highlighted as a potential gene of interest forfuture investigation. Despite the key roles that the high-prioritygenes play in their respective processes, the present study couldnot verify that the potential loss of function variants discoveredmake an appreciable contribution towards BC/OVC susceptibility inour setting. Further investigation is necessary to validate theirinvolvement in breast/ovarian cancerAdvisors/Committee Members: Jansen van Rensburg, Elizabeth (advisor), Joubert, Fourie (coadvisor).