Precision screening facilitates clinical classification of BRCA2-PALB2 binding variants with benign and pathogenic functional effects.

BACKGROUND Decoding the clinical impact of genetic variants is particularly important for precision medicine in cancer. Genetic screening of mainly breast and ovarian cancer patients has identified numerous BRCA1/BRCA2 'variants of uncertain significance' (VUS) that remain unclassified due to a lack of pedigrees and functional data. METHODS Here, we used CRISPR-Select - a technology that exploits unique inbuilt controls at the endogenous locus - to assess 54 rare ClinVar VUS located in the PALB2-binding domain (PBD) of BRCA2. Variant deleteriousness was examined in the absence and presence of PARPi, Cisplatin, or Mitomycin C. RESULTS Marked functional deficiency was observed for variants in the exon 2-donor splice region (A22 = (c.66A>C), A22 = (c.66A>G), A22 = (c.66A>T), and D23H) and Trp31 amino acid (W31G, W31L, and W31C), both critical for BRCA2 function. Moreover, T10K and G25R resulted in an intermediate phenotype, suggesting these variants are hypomorphic in nature. Combining our functional results with the latest ClinGen BRCA1/2 Variant Curation Expert Panel recommendations, we could classify 49 of the 54 VUS as either likely benign (n = 45) or likely pathogenic (n = 4). CONCLUSION Hence, CRISPR-Select is an important tool for efficient variant clinical classification. Application of this technology in the future will ultimately improve patient care. FUNDING Danish Cancer Society, Novo Nordisk Foundation, Sygeforsikring Danmark, Børnecancerfonden, Neye-Fonden, Roche, Novartis, Pfizer, AstraZeneca, MSD, and Daiichi Sankyo Europe GmbH.