Variant-Specific Landscape of Mutual Exclusivity Among BRAF, EGFR, and KRAS Oncogenes Reveals Overlap With Functionally Antagonistic Mutant Pairs.

Mutual exclusivity (ME) and co-occurrence (CO) of oncogenic mutations reflect functional antagonism or dependence and may inform therapeutic strategies.

However, most studies overlook variant-level patterns. We performed a comprehensive, cross-cohort analysis of BRAF, KRAS, and EGFR mutation subtypes using 64,807 cBioPortal tumor samples, 1570 cancer cell lines, and 2714 Belgian clinical cases. Across all datasets, CO was rare among class I BRAF, hydrolysis KRAS, and classical-like EGFR mutations. Pairwise variant-level analyses revealed novel ME interactions, including atypical variants, some overlapping with previously reported synthetically lethal pairs.

We functionally validated the ME findings by inducing the expression of EGFRA289V or BRAFV600E in cell lines harboring KRASG12D or EGFRexon19del, respectively, resulting in growth inhibition. Overall survival analysis showed no consistent prognostic disadvantage for CO, except in EGFR-KRAS co-mutant NSCLC.

These findings further refine the ME landscape of BRAF, KRAS, and EGFR variants, offering a variant-level reference to support mutation-informed precision oncology.