Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families.

BACKGROUND: In the majority of familial breast cancer (BC) families, the etiology of the disease remains unresolved. To identify missing BC heritability resulting from relatively rare variants (minor allele frequency ≤ 1%), we have performed whole exome sequencing followed by variant analysis in a virtual panel of 492 cancer-associated genes on BC patients from BRCA1 and BRCA2 negative families with elevated BC risk. METHODS: BC patients from 54 BRCA1 and BRCA2-negative families with elevated BC risk and 120 matched controls were considered for germline DNA whole exome sequencing. Rare variants identified in the exome and in a virtual panel of cancer-associated genes [492 genes associated with different types of (hereditary) cancer] were compared between BC patients and controls. Nonsense, frame-shift indels and splice-site variants (strong protein-damaging variants, called PDAVs later on) observed in BC patients within the genes of the panel, which we estimated to possess the highest probability to predispose to BC, were further validated using an alternative sequencing procedure. RESULTS: Exome- and cancer-associated gene panel-wide variant analysis show that there is no significant difference in the average number of rare variants found in BC patients compared to controls. However, the genes in the cancer-associated gene panel with nonsense variants were more than two-fold over-represented in women with BC and commonly involved in the DNA double-strand break repair process. Approximately 44% (24 of 54) of BC patients harbored 31 PDAVs, of which 11 were novel. These variants were found in genes associated with known or suspected BC predisposition (PALB2, BARD1, CHEK2, RAD51C and FANCA) or in predisposing genes linked to other cancer types but not well-studied in the context of familial BC (EXO1, RECQL4, CCNH, MUS81, TDP1, DCLRE1A, DCLRE1C, PDE11A and RINT1) and genes associated with different hereditary syndromes but not yet clearly associated with familial cancer syndromes (ABCC11, BBS10, CD96, CYP1A1, DHCR7, DNAH11, ESCO2, FLT4, HPS6, MYH8, NME8 and TTC8). Exome-wide, only a few genes appeared to be enriched for PDAVs in the familial BC patients compared to controls. CONCLUSIONS: We have identified a series of novel candidate BC predisposition variants/genes. These variants/genes should be further investigated in larger cohorts/case-control studies. Other studies including co-segregation analyses in affected families, locus-specific loss of heterozygosity and functional studies should shed further light on their relevance for BC risk.

The impact of an interventional counselling procedure in families with a BRCA1/2 gene mutation: efficacy and safety.

BACKGROUND: Predictive genetic testing has high impact on cancer prevention for BRCA carriers and passing this information in BRCA families is important. Mostly, this is proband-mediated but this path is defective and denies relatives lifesaving information. OBJECTIVE: To assess the efficacy/safety of an intervention, in which relatives are actively informed. DESIGN: Sequential prospective study in new BRCA families. The proband informed relatives about predictive testing (phase I). After 6 months, a letter was sent to adult relatives who had not been reached (phase II). Then a phone call was made to obtain a final notion of their wishes. All subjects received psychometric testing (State-Trait Anxiety Inventory, STAI), an interview and routine counselling. RESULTS: Twenty families were included. Twenty-four of the relatives could not be reached, 59 were 'decliners', 47 participated by the proband and 42 by the letter. Predictive testing was performed in 98% of the participants of which 30 were mutation carriers. The intervention is psychologically safe: the 95% CI for the estimated mean difference in STAI DY1 between phase II/I subjects (mean difference -1.07, 95% CI -4.4 to 2.35, p = 0.53) shows that the mean STAI DY1 score (measured at first consult) for phase II is no more than 2.35 units higher than for phase I, which is not relevant. CONCLUSIONS: A protocol directly informing relatives nearly doubles the number of relatives tested and is psychologically safe. This should lead to a change in counselling guidelines in families with a strong germline predisposition for cancer.