​​​The integration of genomic research and routine clinical service delivery became a reality when co-investigators Prof Maritha Kotze and Prof Karin Baatjes received a Strategic Health Innovation Partnership grant from the South African Medical Research Council. 

Kotze is the principal medical scientist in the Division of Chemical Pathology at SU and the National Health Laboratory Service (NHLS) at Tygerberg Academic Hospital; Baatjes is the head of clinical anatomy and a consultant surgeon in the Division of Surgery and Clinical Anatomy at SU.

Combining the skills and experience gained from working in different health disciplines as a human geneticist and surgeon, respectively, enabled the establishment of a dynamic, clinically enriched breast cancer genomics database that can also be used in other studies.

Additional support from the Cancer Association of South Africa provided a solid foundation for further research capacity building, as evidenced by a case study described atwww.cansa.org.za/cancergeneti…. Screening of the two major breast cancer genes, BRCA1 and BRCA2, is usually the starting point to distinguish familial risk from lifestyle-triggered multi-factorial disease in patients with breast or ovarian cancer.

Aligning data from different spheres

 When genetic data already stored in the genomics database of clinical cases at Tygerberg Academic Hospital, established during the doctoral study of Baatjes, become clinically relevant to a patient, this could be flagged for the clinician to re-contact the patient. These alerts include the development of therapy-associated co-morbidities, metastasis or a second cancer. The process that follows involves support from a genetic counsellor and medical scientists registered with the Health Professions Council of South Africa. Everyone works together as a team to return research results to study participants. 

Earlier this year, experience with this research translation model was described by postdoctoral fellow Rispah Torrorey-Sawe, in the journal Frontiers in Genetics. This was the first study performed in Kenya to determine the cause of familial breast cancer in patients using whole exome sequencing (WES). This advanced methodology allows for extended data analysis beyond BRCA1/2, at no additional cost in uninformative cases who may also experience treatment failure or medication side effects. 

As a direct result of these findings, a rapid point-of-care (POC) BRCA1/2 DNA test was recently developed under the South Africa-UK Newton Collaborative Research Development Programme in Precision Medicine. Given the potential lack of understanding of the meaning of a negative test result, POC testing was pro-actively positioned as a first-tier screening step for WES. The genetic results are integrated into a differential diagnosis or treatment algorithm that combines medical history, response to medication and lifestyle factors into an adaptive report for clinical decision-making. Use of this pathology supported genetic platform by an increasing number of postgraduate students – including master's student Lwando Mampunye at the Cape Peninsula University of Technology and Dr Abisola Okunola from Nigeria who graduated in April 2020 – has already proved its value for patient care. 

The doctoral study by Baatjes concluded that aligning the clinical, biochemical and genetic information could merge the fragmented clinical service delivery and research silos. The goal is to fuse multi-disciplinary research in the clinical setting with next-generation sequencing technologies such as WES to inform risk management of patients across the continuum of care, ranging from early-stage to metastatic disease and cancer survivorship.    

* This article featured in the latest edition of Stellenbosch University (SU)'s  multi-award winning publication Research at Stellenbosch University . Produced annually by SU's Division for Research Development (DRD), this flagship publication offers the national and international research community as well as other interested parties a comprehensive, yet accessible overview of innovative and interesting research being done at the institution.The theme of the edition is Research for Impact which is one of SU's core strategic themes from its Vision 2040 and Strategic Framework 2019–2024.

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