With prospective clinical sequencing of tumors emerging as a mainstay in cancer care, there is an urgent need for clinical support tools that aid clinicians in their decision making. To this end, we are developing tools for the visualization and interpretation of genomic variants in the context of clinical annotation.
To this end, we have developed OncoKB, a precision oncology knowledge base that annotates the effects and treatment implications of somatic mutations in cancer. OncoKB annotations are available for research use via oncokb.org, and the database is used to annotate the sequencing reports of of tumor samples from patients at Memorial Sloan Kettering Cancer Center.
We are also co-developers of the cBioPortal for Cancer Genomics. The cBioPortal is an open source software tool that provides intuitive visualization and analysis of cancer genomics data, allowing cross-cohort analyses but also the viewing and interpretation of individual tumor samples. The public site at cbioportal.org provides access to published sequencing data from more than 25,000 tumor samples, and private instances of cBioPortal are installed at multiple academic research centers, in hospitals, and pharmaceutical companies. Annotations from OncoKB as well as other sources, such as COSMIC, CIViC, and cancerhotspots.org, are integrated into cBioPortal to facilitate the interpretation of variants in cancer cohorts and individual patient samples.
This presentation will summarize the challenges of precision oncology and cancer genomics research and will present how OncoKB and the cBioPortal for Cancer Genomics can be used to overcome some of these challenges.