Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer families

Abstract

Background: Multigene panels are routinely used to assess for predisposing germline mutations in families at high breast cancer risk. The number of variants of unknown significance thereby identified increases with the number of sequenced genes. We aimed to determine whether tumor sequencing can help refine the analysis of germline variants based on second somatic genetic events in the same gene. Methods: Whole-exome sequencing (WES) was performed on whole blood DNA from 70 unrelated breast cancer patients referred for genetic testing and without a BRCA1, BRCA2, TP53, or CHEK2 mutation. Rare variants were retained in a list of 735 genes. WES was performed on matched tumor DNA to identify somatic second hits (copy number alterations (CNAs) or mutations) in the same genes. Distinct methods (among which immunohistochemistry, mutational signatures, homologous recombination deficiency, and tumor mutation burden analyses) were used to further study the role of the variants in tumor development, as appropriate. Results: Sixty-eight patients (97%) carried at least one germline variant (4.7 ± 2.0 variants per patient). Of the 329 variants, 55 (17%) presented a second hit in paired tumor tissue. Of these, 53 were CNAs, resulting in tumor enrichment (28 variants) or depletion (25 variants) of the germline variant. Eleven patients received variant disclosure, with clinical measures for five of them. Seven variants in breast cancer-predisposing genes were considered not implicated in oncogenesis. One patient presented significant tumor enrichment of a germline variant in the oncogene ERBB2, in vitro expression of which caused downstream signaling pathway activation.(Continued on next page) Conclusion: Tumor sequencing is a powerful approach to refine variant interpretation in cancer-predisposing genes in high-risk breast cancer patients. In this series, the strategy provided clinically relevant information for 11 out of 70 patients (16%), adapted to the considered gene and the familial clinical phenotype.

Cyclin B2 (CCNB2) Stimulates the Proliferation of Triple-Negative Breast Cancer (TNBC) Cells In Vitro and In Vivo

“…Due to the lack of effective targeted therapy drugs, TNBC was an aggressive malignant tumor [ 15 ]. Also, the survival rates of TNBC patients are still the shortest among all breast cancer subtypes [ 16 ].…”

Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness

“…Further studies are required to investigate if BRCAness at the RNA level exists due to other mechanisms than mutational patterns. Molecular signature analysis has previously been shown to be useful in the characterisation of variants [ 24 ], and the identification of high HRDetect and LOH in the tumour carrying the spliciogenic variant c.202G > A and LOH at the RAD51D locus illustrate this.…”

An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes

“…Currently, a systematic evidence-based approach for a joint interpretation of germline and somatic data does not exist. Both tumor-derived genomic signatures and pathology examination of tumor biopsies are unique to cancer types ( 45 ) or cancer subtypes ( 41 ). The tumor-derived somatic evidence has a variable degree of relevance in different cancers, and one generalized approach of variant assessment is not practical for all cancer types.…”

“…Indeed, the full extent of the consequence of germline findings can often be appreciated when examined with somatic genetic data in unison. Several approaches have been reported to manage germline findings in cancer by integrated analyses of germline and somatic data (39)(40)(41)(42)(43)(44). Some of these strategies use a one-forall approach in cancers (39,40) or assign ACMG criteriadeveloped for germline disease -to somatic data (e.g., somatic hotspots) (39,42).…”