Hereditary predispositions to breast & ovarian cancer: focus on interpretation

This may appear paradoxical: at a time when very high throughput sequencing allows rapid sequencing of a large number of genes in a large number of people, there have never been as many identifications of gene variants whose biological - and therefore medical - significance is unknown. Understanding what these variants mean would be very useful for the patient. This is a major challenge for medical genetics. The findings of the two studies by the Genetics department from the Hospital Group, conducted on gene variants predisposing to BRCA1 and BRCA2 breast and ovarian cancer, signal progress in the issue of classification. 

In order to classify certain variants of unknown significance (VSI) of genes predisposing to BRCA1 and BRCA2 breast and/or ovarian cancer, the Genetics department (anatomo-pathological department of the Hospital Group), led by Prof. Dominique Stoppa-Lyonnet, conducted two studies. "One looked at the functional modifications caused by the change in BRCA1 amino acid," explains Sandrine Caputo, Biological engineer (PhD). "The other focused on a specific group of variants of the BRCA2 gene and combined functional tests and family analyses."

Usually, tools for classifying variants as "pathogens" or as "neutral" are based on keeping a nucleotide (structural unit of a gene) or an amino acid (structural unit of the corresponding protein) through the evolution of species, the physical and chemical change of an amino acid replaced by another, the high frequency of the variant in the group of cases compared with the controls. But these observations are often insufficient for us to draw conclusions.

Using the national database of BRCA1 variants and in collaboration with the CEA-Saclay and Gustave Roussy, the team developed various functional cellular tests in order to

• measure the ability of VSIs to repair DNA breakage by homologous recombination
• test their ability to relocate to the nucleus after addition of alkylating agent
• measure the thermo-stability of certain domains of BRCA1 concerning these VSIs (BRCT domains)
• and study their interactions with a broad range of phosphorylated peptides from various partners of BRCA1 (ACC1, BACH1, CtiP and Abraxas).

These tests described in the first study, combining all the techniques, have allowed a certain number of these variants to be classified as probable pathogens and others as probably neutral.

In the second multicentric study, the team's goal was to classify VSIs of the BRCA2 gene that may lead to partial skipping in phase of the BRCA2 protein, indeed the part coded by exon 3. "Firstly, we conducted functional tests that examined the stability of the skipped BRCA2 protein in collaboration with Dr Aura Carreira from Institut Curie," explains Sandrine Caputo, leading author of the study, "and secondly, we looked at the association in families of the presence of otherwise of the variant, and the diagnosis of breast and/or ovarian cancer (co-segregation studies)." Thirty-nine families, with a total of 293 patients, were tested in France, Portugal, Sweden and Denmark. "We were able to conclude that all the variants causing complete exon 3 skipping of BRCA2 were pathogens, and thus associated with a high risk of breast and ovarian cancer," explains Dr Carreira.

Supported by the Inca (French national cancer institute), these two studies are based on the contribution of genetics consultations and French laboratories together, through the COVAR study, in the Genetics and Cancer group led by Unicancer  They illustrate the important of collaborative work and the need for patients and their families to participate.

Find out more

• Combining Homologous Recombination and Phosphopeptide-binding Data to predict the impact of BRCA1 BRCT variants on cancer risk. Molecular Cancer Research (27 September 2018)
• Full in-frame exon 3 skipping of BRCA2 confers high risk of breast and/or ovarian cancer. Oncotarget (3 April 2018)
• Presentation of the COVAR study