Double heterozygous pathogenic variants prevalence in a cohort of patients with hereditary breast cancer

Abstract

Hereditary breast cancer (BC) corresponds to 5% of all BC and a larger parcel of early-onset disease. The incorporation of next-generation sequencing (NGS) techniques reduced the cost of molecular testing and allowed the inclusion of additional cancer predisposition genes in panels that are more comprehensive. This enabled the identification of germline pathogenic variants in carriers and the introduction of risk-reducing strategies. It also resulted in the identification of the co-occurrence of more than one germline pathogenic variant in BC genes in some families. This is a rare event, and there are few reports on its impact on cancer risk. We conducted a single-institution retrospective study in which 1,156 women with early onset BC and/or a family history of cancer were tested by a germline multi-gene hereditary cancer panel. Germline pathogenic variants in high- and/or moderate-penetrance BC genes were identified in 19.5% of the individuals (n = 226). The most frequent variants were found in TP53 (69 of 226; 55 of them represented by p.R337H), BRCA1 (47 of 226), and BRCA2 (41 of 226). Double heterozygous (DH) variants were detected in 14 cases, representing 1.2% of all individuals assessed. There were no significant differences in age of BC onset and risk for bilateral BC in DH carriers when compared with those with one germline variant.

Keywords: NGS; breast cancer; double heterozygous variants; germline panels; hereditary breast cancer.

Figure 1

Flowchart summarizing the cohort included in the study. From 3,030 individuals screened from the Hereditary Cancer Registry-Hospital Sírio-Libanês for germline variants by NGS panels, 1,156 had BC and 226 were positive for a pathogenic/likely pathogenic variant in BC-risk genes, 14 of them presented two or more variants.

Figure 2

Germline variants detected in BC-risk genes in the 226 patients with BC from the Brazilian Hereditary Cancer Registry. (A) Proportion of germline P and LP variants in TP53, BRCA1, and BRCA2 (35%) was the most frequent, followed by ATM, PALB2, and CHEK2. (B) Frequency and distribution of pathogenic germline variants identified in BC genes, and associations with age at BC diagnosis and occurrence of multiple primary tumors (diagram implemented with Oncoprinter, available at: https://www.cbioportal.org/oncoprinter).

Figure 3

(A) Chord diagram illustrating the BC-risk genes combinations among germline DH pathogenic variants. (B) Violin plot diagram showing the distribution, interquartile range, and median age of BC diagnosis from cases with no variant (white), one variant (green), and two or more variants (blue) detected. ***P < 0.001; *P < 0.05; NS, not significant (Dunn’s post hoc test). Chord diagram and violin plot were implemented with the circlize and plotly R packages, respectively.

Figure 4

Triple pathogenic variant carriers in BC-risk genes. In family 02114, two individuals with early onset breast cancers are both carriers of three pathogenic variants in three cancer predisposing genes, BRCA1 c.5266dup (p.Gln1756fs), TP53 c.1010G>A (p.Arg337His) and PALB2 c.3271C>T (p.Gln1091Ter).