Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings

Nicole Van Der Merwe; Raj Ramesar; Jantina De Vries

doi:10.3389/fgene.2022.864822

Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings

Front Genet. 2022 Jun 8:13:864822. doi: 10.3389/fgene.2022.864822. eCollection 2022.

Authors

Nicole Van Der Merwe^{1

2}, Raj Ramesar¹, Jantina De Vries^{3

4}

Affiliations

¹ UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa.
² Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
³ Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁴ Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa.

Abstract

The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA. Semi-structured interviews were conducted, and the transcripts analysed using the framework approach for data analysis. Current roadblocks for the clinical adoption of WES in SA include a lack of standardised guidelines; complexities relating to variant interpretation due to lack of functional studies and underrepresentation of people of African ancestry in the reference genome, population and variant databases; lack of resources and skilled personnel for variant confirmation and follow-up. Suggestions to overcome these barriers include obtaining funding and buy-in from the private and public sectors and medical insurance companies; the generation of a locally relevant reference genome; training of health professionals in the field of genomics and bioinformatics; and multidisciplinary collaboration. Participants emphasised the importance of upscaling the accessibility to and training of GCs, as well as upskilling of clinicians and genetic nurses for return of genetic data in collaboration with GCs and medical geneticists. Future research could focus on exploring the development of stakeholder partnerships for increased access to trained specialists as well as community engagement and education, alongside the development of guidelines for result disclosure.

Keywords: South Africa; genetic counselling; incidental findings; return of results; secondary findings; whole exome sequencing.