A R3 million grant from the South African Medical Research Council (SAMRC) will enable Stellenbosch University (SU) scientists to test the efficacy of a novel gene-based point-of-care screening tool that will help clinicians determine the best course of cancer treatment.
Professor Maritha Kotze, principal medical scientist in the Department of Pathology at SU's Faculty of Medicine and Health Sciences, will spearhead this interdisciplinary research project entitled Development and validation of a pharmacogenomics platform using point-of-care screening tests and application of whole genome sequencing in cancer treatment.
This award relates to the recent launch by the SAMRC of a cutting-edge, national research facility that will refine the science of genomics for implementation of personalised medicine.
The facility aims to unlock Africa's diverse gene pool and to grow capacity for whole genome sequencing as the most comprehensive testing strategy available in South Africa. "Prof Kotze's project will facilitate the reporting of complex whole genome sequencing data to patients using a multi-disciplinary team approach," said Mrs Rizwana Mia, Program Manager for Precision Medicine and the SAMRC Genomics Centre. She also noted that the project addressed critical data warehousing and data dissemination tools to enable a secure clinical workflow. Kotze said a major focus of this initiative is to match the medication administered to cancer patients with their genetics based on both host (germline) and tumour gene profiles.
Novel point-of-care assays recently developed by Kotze and co-workers under the SAMRC Strategic Health Innovation Partnership (SHIP) program and the Innovate UK Newton Fund initiative in Precision Medicine, will be used as a first-line screen to determine the need for whole genome sequencing at the SAMRC Genomics Centre. An important focus will be to identify the cause of cancer and treatment failure or medication side effects, as well as explain cardiovascular or other co-morbidities found to be most common in the study database developed. This resource was developed over more than a decade with support from the Cancer Association of South Africa. "The database informs development of an adaptive pathology-supported genetic testing algorithm, which is continuously modified and refined to minimise the chance that something is missed that could benefit a patient. We are motivated by a desire to not only treat the cancer, but the person as a whole," Kotze said.
The pharmacogenomics platform, once developed in collaboration with both the public and private sectors, will help to reduce the burden of cancer and other non-communicable diseases (NCDs). "For selection of patients for whole genome sequencing we start with an NCD/wellness screen to help resolve complex cases step-by-step. In many cancer patients it remains uncertain whether genetic or lifestyle factors, or a combination of both, is involved," she said in an interview.
Kotze indicated that the planned pharmacogenomics platform may also support responsive research and development as required during pandemics like COVID-19 that affects cancer treatment. "For me, innovation is about bridging the knowledge gaps as they arise. It is our duty as scientists to ensure that what we discover will, in the end, be useful to clinicians and could empower them to provide the best care to their patients." The platform will help scientists to return their research results to eligible cancer patients, by making use of an adaptive report template currently developed under the Open Genome Project supported by the Technology Innovation Agency of South Africa. These reports are subject to approval by an expert review panel for clinical use by the referring clinician, supported by genetic counsellors. Co-investigator, Dr Nicole van der Merwe, will play a key role in this context by using a three-tier approach from sample to result, starting with 1) a questionnaire-based assessment to inform appropriate use of 2) point-of-care DNA testing of key NCD pathways that are evaluated during or after a genetic counselling session to 3) inform the need for whole exome/genome sequencing in uninformative cases. For the first time, South Africa's burden of cancer and other NCDs will be addressed by simultaneously assessing risk factors associated with disease development, recurrence risk and response to treatment considered relevant to each individual patient.
Kotze said her research team was honoured to be awarded the grant. "I am very excited about the opportunities that opened up as a result of this project. I see it as a recognition of the effort I've put in during my scientific career to find the place where genetic testing can add value to existing pathology results, thereby overcoming the limitations of each when used in isolation. This platform will help to bridge the remaining communication gaps and implementation barriers as we move from single- to multi-gene testing and full genome-scale data generation."
Mia concluded that this is a culmination of long-term persistence as the SAMRC SHIP Program has supported the development of the breast cancer and NCD testing solutions developed by Kotze and her team from 2014. It is indeed a complement to the team for progressing these precision medicine solutions along the innovation value chain from applied basic research to a tangible African-centric solution. She added that Kotze's project is amoung nine recipients with a total investment of R25 million made by the SAMRC SHIP Program in collaboration with the Distributed Platform in OMICS (DIPLOMICS) to invest in the development of pharmacogenomics research and innovation that address treatment-associated risk in the South African population affected by prevelant NCDs.
