Support CIViC annotation for somatic mutations

[muabnezor]

CIViC (Clinical Interpretation of Variants in Cancer) is an open-access, community-driven resource for the clinical interpretation of cancer variants. To enhance Scout’s functionality for somatic variants, it would be beneficial to see this information in scout.

One way to achieve this would before loading the variants into scout annotate the vcf against the CIViC database, and add support in scout to load the relevant civic annotations into scout.

[dnil]

If you have a VCF with CiViC annotations and a key for those this should be really simple and useful! Perfect!

Do they provide a VEP plugin or annotation track for use perhaps?

As I'm sure you know, Scout has a CiViC gene level linkout - that was the API level we were comfortable with last time this was on the table.

[dnil]

If their API has matured to allow confident variant lookups (eg using transcript qualifiers for aa changes) we can also make a variant level linkout, but I get the feeling this is still a bit rough around the edges?

[muabnezor]

Hi, no currently no vep plugin, so this is something that needs to be solved. I have started looking at this https://docs.civicpy.org/en/latest/, but have not yet tested it. But yes this will be a matter of first confidently annotate variants, before submitting loading them to scout.