Establishing Cancer Genomics Registry to Support Implementation of Personalised Medicine
Project ended 31 March 2018
Prof Maritha Kotze
Title of the project
Establishing a cancer genomics registry to support the implementation of personalised medicine.
A database resource for translational oncogenomic research was established during the introduction of a microarray-based gene expression profiling test for early-stage breast carcinoma in South Africa. The on-going development of this resource has facilitated the development of eligibility criteria and reimbursement policies for this service (MammaPrint). This is comparable to existing referral guidelines for familial breast cancer screening programs focused on high-penetrance BRCA1/2 mutations, using risk assessment tools such as the Manchester score. This study investigated the rationale for incorporating actionable low-moderate penetrance mutations into a novel pre-screen algorithm for selection of breast cancer patients eligible for whole exome sequencing, which is currently lacking in the local setting. Our experience in cancer genetics provided the basis for establishment of a cancer genomics database/registry as a valuable resource for ongoing oncogenomic research.
How the project was of value in the struggle against cancer:
Use of the CANSA grant helped to develop the conceptual framework for clinical application of whole exome sequencing (WES) in SA breast cancer patients. Many pathogenic mutations that remained undetected with previous used of tests focused on a limited number of mutations/gene were identified and provided targets for treatment and disease prevention in affected studies.
Our pathology-supported genetic testing (PSGT) platform was used to develop an exome pre-screen algorithm (EPA) for selection of genetically uncharacterised patients for WES. First, diagnostic BRCA testing is offered as a routine service according to standard referral guidelines, or the chronic disease risk screen is offered to patients receiving hormone therapy, are at high risk for tumour recurrence, or are required to take potentially competing antidepressants. In certain cases, combined diagnostic and pharmacogenetics testing is performed to explain the presence of comorbidities or predict drug response/recurrence risk. Finally, where extended mutation analysis of the entire BRCA1 and 2 genes as well as the CYP2D6 gene is unable to explain breast cancer or the occurrence of drug side effects/failure, WES is performed to identify potential novel causative genes/mutations.
WES preceded by PSGT facilitates the identification and clinical interpretation of genetic risk factors of relevance to both cancer development and tailored therapeutic intervention in a single test.