Saturation genome editing of <i>BARD1</i> resolves VUS and provides insight into BRCA1-BARD1 tumor suppression

Abstract

Abstract BARD1 encodes a dimeric partner of BRCA1 and is required for homology-directed double strand DNA break repair 1–5 . Germline loss-of-function variants in BARD1 are linked to elevated risk for breast cancer and neuroblastoma 6–8 and PARP inhibitors have shown effectiveness against BARD1-deficient tumors. However, the majority of BARD1 variants identified by genetic testing for cancer risk are variants of uncertain significance (VUS) 9 limiting clinical utility. We used saturation genome editing 10 to assess the impact of nearly 11,000 single-nucleotide variants and three base-pair deletions across all 11 coding exons of BARD1 on cellular fitness and gene expression. The cellular fitness data are nearly perfectly concordant with known pathogenic and benign BARD1 variants 9 (AUC &gt; 0.99) and loss-of-function missense variants in all three functional domains were associated with elevated risk for breast cancer 6,8 . When used for clinical variant classification, our data resolved 95.4% of existing BARD1 variants of uncertain significance. Comparison of cellular fitness data to known structures 11–14 , further solidifies that BARD1’s role in homology-directed repair is required for tumor suppression in humans 15 . These results will immediately improve clinical genetic testing and decision-making for patients with BARD1 variants and deepen our understanding of BARD1’s role in maintaining genome integrity.