UPDATE: We recently updated our Level of Evidence, please see Levels of Evidence section for more information

UPDATE: API token required, please see OncoKB API section for more information

oncokb-annotator

Annotates variants in MAF with OncoKB annotation. Supports both python2 and python3.

Please try

• python MafAnnotator.py -h
• python FusionAnnotator.py -h
• python CnaAnnotator.py -h
• python ClinicalDataAnnotator.py -h
• python OncoKBPlots.py -h

Example input files are under data. An example script is here: example.sh

We recommend processing MAF files by vcf2maf with MSK override isoforms before using the MafAnnotator here.

Levels of Evidence

Introducing Simplified OncoKB Levels of Evidence:

• New Level 2, defined as “Standard care biomarker recommended by the NCCN or other expert panels predictive of response to an FDA-approved drug in this indication” (formerly Level 2A).
• Unified Level 3B, defined as “Standard care or investigational biomarker predictive of response to an FDA-approved or investigational drug in another indication” (combination of previous Levels 2B and 3B).

We have implemented these changes for 2 reasons:

• To be consistent with the Joint Consensus Recommendation by AMP, ASCO and CAP and the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)
• To reflect the clinical data that demonstrates patients with investigational predictive biomarkers for a specific tumor type based on compelling clinical evidence (currently Level 3A) are more likely to experience clinical benefit compared to patients with predictive biomarkers that are considered standard care in a different tumor type (previously Level 2B, now combined into Level 3B).

If you want to annotate your files with previous Levels of Evidence, please git checkout v1.

OncoKB API

When you run MafAnnotator.py, FusionAnnotator.py and CnaAnnotator.py, you need a token before accessing the OncoKB data via its web API. Please visit OncoKB Data Access Page for more information about how to register an account and get an OncoKB API token.
With the token listed under OncoKB Account Settings Page, you could use it in the following format.

python ${FILE_NAME.py} -i ${INPUT_FILE} -o ${OUTPUT_FILE} -b ${ONCOKB_API_TOKEN}

Columns added in the annotation files

Column	Possible Values	Description
mutation_effect	Gain-of-function, Likely Gain-of-function, Loss-of-function, Likely Loss-of-function, Switch-of-function, Likely Switch-of-function, Neutral, Likely Neutral, Inconclusive, Unknown	The biological effect of a mutation/alteration on the protein function that gives rise to changes in the biological properties of cells expressing the mutant/altered protein compared to cells expressing the wildtype protein.
oncogenic	Oncogenic, Likely Oncogenic, Likely Neutral, Inconclusive Unknown	In OncoKB, “oncogenic” is defined as “referring to the ability to induce or cause cancer” as described in the second edition of The Biology of Cancer by Robert Weinberg (2014).
Level_*	LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4, LEVEL_R1, LEVEL_R2	The treatments available for a mutation/alteration giving a tumor type.
Highest_level	LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4, LEVEL_R1, LEVEL_R2	The highest level across all available treatments giving a tumor type.
citations	PMID, Abstract, Website Link	All citations related to a mutation/alteration

FAQs

• How to get the subversion of the ensembl transcript ID?
  vcf2maf is designed to work with all Ensembl releases and reference genomes, that is the reason the subversion is not included.

  Within MSK, we are using GRCh37 which corresponding to the Ensembl release 75. You can get the full list of versioned transcript IDs here http://grch37.ensembl.org/biomart/martview/40d921c6ab6956144cf6fb2e9a8ca093?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id_version&FILTERS=&VISIBLEPANEL=attributepanel.