Integrative analysis with RM2 identified 41 significant interactions between genomic features and site-specific elevations in mutation frequencies in nine cancer types, including five driver genes (ARID1A, BRAF, CTNNB1, HIST1H1C, SETD2), 25 recurrently amplified loci and one locus with genomic loss (RM2 FDR < 0.05, interaction P < 0.05) (Fig. 5a) (Additional file 2: Table S1H). Here, ARID1A is linked to cancer.