Imprecise Medicine: BRCA2 Variants of Uncertain Significance (VUS), the Challenges and Benefits to Integrate a Functional Assay Workflow with Clinical Decision Rules

Abstract

Pathological mutations in homology-directed repair (HDR) genes impact both future cancer risk and therapeutic options for patients. HDR is a high-fidelity DNA repair pathway for resolving DNA double-strand breaks throughout the genome. BRCA2 is an essential protein that mediates the loading of RAD51 onto resected DNA breaks, a key step in HDR. Germline mutations in BRCA2 are associated with an increased risk for breast, ovarian, prostate, and pancreatic cancer. Clinical findings of germline or somatic BRCA2 mutations in tumors suggest treatment with platinum agents or PARP inhibitors. However, when genetic analysis reveals a variant of uncertain significance (VUS) in the BRCA2 gene, precision medicine-based decisions become complex. VUS are genetic changes with unknown pathological impact. Current statistics indicate that between 10-20% of BRCA sequencing results are VUS, and of these, more than 50% are missense mutations. Functional assays to determine the pathological outcome of VUS are urgently needed to provide clinical guidance regarding cancer risk and treatment options. In this review, we provide a brief overview of BRCA2 functions in HDR, describe how BRCA2 VUS are currently assessed in the clinic, and how genetic and biochemical functional assays could be integrated into the clinical decision process. We suggest a multi-step workflow composed of robust and accurate functional assays to correctly evaluate the potential pathogenic or benign nature of BRCA2 VUS. Success in this precision medicine endeavor will offer actionable information to patients and their physicians.

Keywords: BRCA2; BRCAness; DNA repair; hereditary breast and ovarian cancer (HBOC); homologous recombination; variants of uncertain significance.

Figure 1

Percentages of lifetime breast and ovarian cancer risks in BRCA germline carriers.

Figure 2

Schematic of BRCA2 domains. DBD: DNA binding domain; CTD: C-terminal domain. DOG illustrator of protein domain structure [50].

Figure 3

Pie charts representing the percentages of BRCA2 germline and somatic variants grouped into clinical significance (left) or molecular consequences (right) as reported in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/?term=BRCA2%5Bgene%5D, accessed on 10 April 2021).

Figure 4

cBioPortal for Cancer Genomics display of the (A) percentage of BRCA2 germline and somatic alterations and (B) spectrum of BRCA2 germline and somatic mutations in the different protein domains. The curated set of non-redundant studies of cBioPortal for Cancer Genomics was used. Combined study with 48,081 samples and 184 studies. Graphs display BRCA2 somatic mutation frequency of 3% and BRCA2 germline mutation frequency of <0.1.

Figure 5

Pie charts representing the percentages of BRCA2 germline and somatic genetic variants grouped into driver mutations (left) and VUS (right) as reported in cBioPortal for Cancer Genomics database (https://www.cbioportal.org/results/cancerTypesSummary?tab_index=tab_visualize&Action=Submit&session_id=607f022de4b0242bd5d49461, accessed on 10 April 2021). The curated set of non-redundant studies of cBioPortal for Cancer Genomics was used. A total of 48,081 samples and 184 studies. The total number of driver mutations and variants of uncertain significance (1934) corresponds to 3% of the samples with BRCA2 somatic mutations and <0.1% of the samples with BRCA2 germline mutations.

Figure 6

BRCA2 Management Strategies.

Figure 7

IARC proposed a classification system for BRCA2 sequence variants identified by genetic testing.

Figure 8

Workflow to analyze BRCA2 variants of uncertain significance.