Contingency table.

Effective identification of oncogenic mutations is essential for diagnosis, forecasting resistance, and metastasis in remission. It is required for an optimal drug regimen. We develop a framework to discover mutations that co-exist in different oncoproteins, and those that are excluded, likely encoding oncogene-induced senescence. First, mapping the proteins onto pathways assists combinatorial drug selections and helps to detect metastases. Second, it provides the molecular basis for synthetic lethality, to date investigated at the genome level. Our pan-cancer profiles of ~60,000 tumor sequences, detect 3424 co-existing tumor-specific mutations. Mapping them onto pathways indicates that they preferentially promote specific primary tumors. We uncover metastatic mutations and provide metastatic breast-cancer markers. This work not only clarifies the mechanistic basis of intratumor mutational diversity but usefully reveals markers for metastasis in patients’ genomes and introduces a novel computational framework for detecting metastasis based on tumor mutational profiles. Mapping the mutations onto pathways provides an invaluable metastasis-targeting resource, guiding drug combinations.