APC and breast carcinoma: Our method was capable of identifying well-known genes in pan-cancer and 26 cancer-specific types including KRAS, NRAS, TP53, BRAF, and PIK3CA in missense alteration, ERBB2, CDK4, and FLT3 as amplification driver genes, and well-recognized non-missense driver genes such as TP53, TOP2A, APC, and GATA3. Additionally, in cancer-specific analyses, our method was able to identify well-known genes such as KRAS and PIK3CA as missense driver genes, NRAS and EGFR as amplification driver genes in breast carcinoma.