Next generation sequencing (NGS) technologies using gene panels screen for mutations in a limited number of pre-selected genes. NGS using WES enables a more comprehensive analysis that covers the protein coding regions and exon-intron boundaries of all human genes. Exons of genes contain more than 80% of disease-causing mutations.
Coverage may not be uniform in all the genes tested and large rearrangements cannot be reliably detected by these NGS methods. Therefore, sophisticated bioinformatics tools are used to detect copy number changes. Additional testing using long-range nanopore sequencing may also be required as part of a research programme in mutation-negative patients.
WES usually takes 3-6 weeks before a report is provided since the medical scientists who perform the test as part of a multi-disciplinary team also evaluate previous pathology reports, and other information relevant to the genes prioritised for WES. All causative gene variants identified are furthermore confirmed with a second method called Sanger sequencing, to ensure accuracy of positive genetic results.
WES is evaluated in a clinical context to distinguish between monogenic and polygenic familial breast cancer, or multifactorial disease caused by gene-environment interaction. This is necessary to identify patients with different treatment requirements. Our pathology-supported genetic testing approach enables the generation of a comprehensive report, which highlights both genetic and modifiable lifestyle risk factors relevant to the clinical profile of the tested individual.
Management of patients can be extended beyond familial risk using WES, to also assess the role of genetics in (treatment-related) co-morbidities and medication side effects, if clinically indicated. The report will be customised according to the information provided by the clinician and patient in the questionnaire at referral, integrated with the genetic findings.
In some patients, due to their unique genetic blueprint, variants of uncertain clinical significance are identified. This is why the WES service is linked to the generation of a research database. The WES data is stored with approval of the patient and may be re-analysed on request if new information becomes available of relevance to the patient or to address a new health concern or family condition that may present in future.
Tools developed for WES (to select genes for variant calling and to facilitate clinical interpretation):
Step 1: Genecare pre-screen report
· BRCA1/2 checklist (available on the CANSA website), and/or
· Questionnaire-based lifestyle assessment
Step 2: Pathway panel screen
· BRCA1/2 family-specific single mutation, population-specific founder mutation, or full gene screen, and/or
· Chronic disease screen (Wellness GeneScreen / GenePro performed by MDS lab in Durban)
Step 3: Gknowmix knowledge database
· Data integration for translation into adaptable reports: from pre-screen assessment to panel-based testing to WES in genetically uncharacterised cases.
Lifestyle-related cancers and other non-communicable diseases (NCDs) have many symptoms and signs in common due to similar underlying metabolic abnormalities. We have therefore implemented a pathway-based wellness screen / NCD assay developed as a starting point when pathology-supported genetic testing (PSGT) is performed. PSGT is a novel concept developed in South Africa to help distinguish between genetic and lifestyle-related conditions that may require different treatment strategies. When there is uncertainty or the information obtained is insufficient to address the individual’s health concerns, extended genetic testing using WES is performed to evaluate multiple gene variants for clinical relevance to familial risk and lifestyle- or therapy-induced medical conditions. The WES reports include a summary page focused on the indication for testing, supported by a detailed description of familial and personal risk implications that may be of current or future concern.