New FDA Recognized MSK Database Makes 5600 Mutations Searchable to Researchers


A new database organizes information on driver mutations for researchers.

The FDA has granted partial recognition status to OncoKB, a precision oncology knowledge database of somatic cancer variants, according to a press release by Memorial Sloan Kettering (MSK) Cancer Center.

OncoKB is the first database of somatic variations to be recognized the FDA. The database contains information over 5600 genomic changes in over 680 cancer-associated genes. It is designed to assist in cataloging precision oncology knowledge.

“Part of the mission of precision oncology is empowering the clinical community to leverage the cancer genome of a patient’s tumor to guide treatment,” said Debyani Chakravarty, PhD, lead scientist of OncoKB and assistant attending in MSK’s Department of Pathology, in a press release. “Currently, there are hundreds of targeted therapies that are either FDA-approved or being tested in clinical trials. What sets OncoKB apart is its active curation by disease experts and scientists at MSK who are at the forefront of cancer treatment and research. With the FDA partial recognition of OncoKB, the agency credentials our knowledge base as providing accurate, reliable, and clinically meaningful information to the medical and scientific communities.”

The database is a collaboration between software engineers and oncologists. The database collects knowledge of specific mutations from publicly available resources. Treatment-specific guidelines from the National Comprehensive Cancer Network and FDA drug labels are also included. Scientific literature was collected from the American Society of Clinical Oncology and the American Association for Cancer Research.

The database separates driver mutation, meaning those that are responsible for tumor initiation or growth, from passenger variants, which do not contribute to tumorigenesis. OncoKB identifies which driver mutations are actionable, adding to its clinical value. A built-in feature known as the Therapeutic Levels of Evidence scale differentiates FDA-approved and NCCN-guideline listed biomarkers from those that are investigational and associated with drug sensitivity currently being investigated in clinical trials. Information on drug resistance are also collected. The database is updated monthly in order to reflect new research.

“Precision medicine has changed the way we treat cancer, and OncoKB is a key resource as it helps ensure that each patient receives the treatments most likely to be effective for their specific cancer,” said David B. Solit, MD, director of the Marie-Josée and Henry R. Kravis Center for Molecular Oncology at MSK, in a press release.

The database is freely available for academic research use and can also be licensed commercially. A clinical trial matching system along with the annotation of germline alterations are in development. At MSK, OncoKB is used to annotate sequencing reports of over 12000 patients a year.

“Today, tumor genomic profiling is performed for almost every MSK patient with advanced cancer to ensure that we administer the cancer therapy most likely to be effective for that person,” Solit, in the press release. “Each tumor profiled is likely to have several mutations, and it can be challenging for clinicians to memorize which mutations are predictive of response to FDA-approved and experimental therapies or are important for understanding a patient’s prognosis or cancer subtype. OncoKB solves this dilemma by providing an expertly curated database of the biologic and clinical implications of thousands of cancer-associated mutations.”

FDA grants partial recognition status to Memorial Sloan Kettering Cancer Center Precision Oncology Knowledge Database. Press release. Memorial Sloan Kettering. October 7, 2021. Accessed October 12, 2021.
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