Calculating Tumor Mutation Burden from CbioPortal

[Mysona, David]

Hi!

My name is David Mysona and I am an OBGYN at University of North Carolina Chapel Hill. Thank you so much for the work you all have done putting together the cBioportal!

For a current project, I am trying to calculate tumor mutation burden. I was wondering if there was a simple way to do this from any of the TCGA panCancer Atlas studies from the explore page or if I. will need to download the data and perform the analysis separately in R? 

Thanks!

Sincerely,

   David Mysona

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[Nikolaus Schultz]

Hi David,

We do not yet have the TMB values in cBioPortal, but we should really add those values to the TCGA PanCancer cohort (cc’ing Ritika to make her aware, but it is probably already on the list to be curated).

You can download TMB values here:

https://gdc.cancer.gov/about-data/publications/PanCan-CellOfOrigin

The following file has the numbers you are looking for:

• Mutation Load - mutation-load-updated.txt

Using the new custom data feature, you can probably add these data to the cBioPortal study view. See the News item from January 12th here:

https://www.cbioportal.org/news

Niki.

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[kun...@mskcc.org]

Hi David,

We are working on computing TMB scores for all cBioPortal studies (including TCGA PanCan), which we are planning on releasing very soon (https://github.com/cBioPortal/datahub/pull/1292).

Thanks,

Ritika

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