1
|
Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. Mutat Res Rev Mutat Res 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
Collapse
Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| |
Collapse
|
2
|
Miao DNR, Ladha F, Lyle SM, Olivier DW, Ahmed S, Drögemöller BI. Current Perspectives on Data Sharing and Open Science in Pharmacogenomics. Clin Pharmacol Ther 2024; 115:408-411. [PMID: 38087986 DOI: 10.1002/cpt.3115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 02/17/2024]
Affiliation(s)
- Deanne Nixie R Miao
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Feryal Ladha
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sarah M Lyle
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel W Olivier
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Samah Ahmed
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Paul Albrechtsen Research Institute CancerCare Manitoba Research, Winnipeg, Manitoba, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Centre on Aging, Winnipeg, Manitoba, Canada
| |
Collapse
|