Clinical-Genomics
Add oncoKB annotation
Need
oncoBB annotation in BALSAMIC output.
Information:
https://www.oncokb.org/
Suggested approach
A few sentences about the intended solution
Considered alternatives
Were there alternative approaches which have been rejected?
Requests/suggestions/bugs solved by the feature
Came as a request by Emma Tham in a user meeting regarding an unrelated topic
Can be closed when
Blockers
Could this perhaps be a Scout feature?
Also, is this for research or clinical use?
Check with Emma Tham
Adding just in case we forget, it's probably https://www.oncokb.org/ not oncodb
Yes, oncoKB is correct. I'll update the title and body
See here the reply from Emma regarding this:
Hello!
When we manually corroborate the significance of somatic variants, we use cbioportal which links to onkoKB (which I've understood as the biggest and best), but also to the following databases which are also interesting:
https://www.oncokb.org/ https://www.mycancergenome.org/ https://civicdb.org/welcome https://www.cancerhotspots.org/#/home
We use these for both research and clinical purposes.
If one wants to set up a ranking of cancer variants in SCOUT, they should get a much higher rank if they are known hotspots on https://www.cancerhotspots.org/#/home and known pathogenic (called oncogene) in onkoKB. If that database is too complicated, one can use CIVIC and/or my cancergenome.
Best regards, Emma