Cbioportal: MYD88 mutations are being reporting in Non-canonical transcript (1 study only)

[ecerami]

Reported by user:

In this study (and only this study): "Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)", MYD88 mutations are being reported based on transcript: ENST00000417037.

But, all other studies are using the default UniProt https://raw.githubusercontent.com/mskcc/vcf2maf/master/data/isoform_overrides_uniprot transcript, e.g. ENST00000396334.

This results in a non-standard L273P mutation, versus the commonly report L265P mutation.

Is is possible that this specific study is not being pre-processed by our standard pipeline?

[ecerami]

Discussed with @ritikakundra and assigning to her to resolve.

[ritikakundra]

Data files on datahub (https://github.com/cBioPortal/datahub/tree/master/public/pcnsl_mayo_2015) look correct. Going to reimport to see if that solves this issue

[jjgao]

cc'ing @inodb here: maybe it's another case that is related to genome nexus.

[jjgao]

@ritikakundra if it's the same tomorrow, please notify @inodb .

[ritikakundra]

Re-import on triage shows the correct annotations

[ritikakundra]

@ecerami Resolved: http://www.cbioportal.org/index.do?session_id=5b6898c1498eb8b3d56742ce&show_samples=false&clinicallist=PROFILED_IN_pcnsl_mayo_2015_mutations

[ecerami]

Awesome! thanks @ritikakundra!!

[ecerami]

Ethan reported status back to user.