General
What is OncoKB™?
OncoKB (https://www.oncokb.org) is a precision oncology knowledge base that annotates the biological consequences and clinical implications (therapeutic, diagnostic, and prognostic) of genetic variants in cancer.
Does OncoKB™ curate both somatic and germline variants?
Currently, OncoKB’s focus is on the curation of somatic variants in cancer. However, we plan to expand our database to include annotation of germline variants.
What are the differences between OncoKB™ and cBioPortal?
The cBioPortal for Cancer Genomics hosts cancer genomics data, including genetic variants in patients from published sequencing efforts such as TCGA. OncoKB contains manually curated information about specific genetic alterations in cancer and provides an API for annotating variants in patients (although OncoKB itself does not contain any data from patients). For example, the cBioPortal utilizes OncoKB API to annotate cancer variants in this database. In other words, cBioPortal contains information about which mutations are observed in individual tumor samples (and by aggregating data from multiple patients, cBioPortal contains information about gene and variant alteration frequencies), and OncoKB contains information about the effects and treatment implications of variants. Both can be combined together, but information from OncoKB can also be applied to any other data set not in cBioPortal.
I am preparing a manuscript for publication and I am including OncoKB™ data. How should I cite OncoKB™?
When using OncoKB, please cite: Chakravarty et al., JCO PO 2017 and Suehnholz et al., Cancer Discovery 2023.
Is OncoKB™ a medical product?
No, OncoKB is not a medical product. OncoKB contains information about the effects and treatment implications of specific cancer gene alterations. OncoKB content is not intended as a substitute for professional medical help, judgment or advice. A physician or other qualified health provider should always be consulted for any health problem or medical condition.
However, we have partial FDA recognition as a public human genetic variant database to support clinical validity for genetic and genomic-based in vitro diagnostics. Under this guidance, a subset of leveled OncoKB variants have FDA recognition.
Do you provide clinical trial matching?
We are currently working on matching clinical trials based on OncoKB annotated drugs and the patient cancer type. We will make matched trials available through our API.
What variant-level information do you have?
OncoKB annotates allele-specific variants found in cancer with their biological effect, oncogenicity and clinical implications, if applicable, based on peer-reviewed published literature. OncoKB does not contain or report on the prevalence of cancer variants. For prevalence data, we recommend using cBioPortal.
OncoKB provides the following variant-level information:
Mutation effect: indicates whether the variant is gain/loss/switch-of-function, likely gain/loss/switch-of-function, neutral, or inconclusive. A detailed description of the evidence that supports this assertion is also included with citations.
Oncogenic effect: indicates whether the variant is oncogenic, likely oncogenic, likely neutral, or inconclusive.
Whether the variant has been identified as a statistically significant hotspot.
Whether the variant is a variant of unknown significance (VUS) based on the current knowledge.
Tumor type-specific diagnostic implications, if available (currently hematological malignancies only).
Tumor type-specific prognostic implications, if available (currently hematological malignancies only).
If OncoKB is listed in a Local Coverage Determination (LCD), does this mean OncoKB will review my company’s Laboratory-Developed Test (LDT) to determine if it will be covered by insurance?
No. OncoKB does not review LDTs. LDTs are not enforced by or regulated by OncoKB. OncoKB is a comprehensive database that annotates the oncogenic effects and clinical actionability of somatic alterations in cancer. Specifically, OncoKB utilizes its Levels of Evidence system (Therapeutic, Diagnostic and Prognostic) to categorize variants based on their tumor type-specific predictive value of sensitivity or resistance to targeted therapies, or based on their diagnostic or prognostic potential (for hematological malignancies only). Select alterations are assigned an OncoKB Level of Evidence based on the validity and strength of peer-reviewed data to support the leveled assertion and in accordance with the OncoKB Standard Operating Procedure and OncoKB Tx, Dx and Px Levels of Evidence. The inclusion of OncoKB in an LCD strictly means that test developers may use OncoKB-leveled variants as valid biomarkers in their LDTs.
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