Clarification Regarding TCGA Dataset Fields

[Francisco Penonori]

To whom it may concern,

My name is Francisco Peñoñori. I am part of the data science group working on a research project related to thyroid cancer, and we are currently using one of the datasets kindly provided by your site.

The reason for this email concerns certain fields in the "Thyroid Carcinoma (TCGA, Firehose Legacy)" dataset, specifically the columns "Mutation count" and "TMB (nonsynonymous)" in the clinical file. Both fields are important for our analysis but contain a considerable number of missing values. I was wondering if it is possible to compute these values with a calculation that I am not aware of.

For instance, the patient with ID TCGA-J8-A3YG shows a positive BRAF mutation in the "BRAF mutation" column, but the "Mutation count" field is left empty.

I would greatly appreciate any clarification you can provide regarding the calculation and interpretation of these fields, perhaps with available resources or documentation that I am not aware of.

Thank you in advance for your time and support.

Kind regards,
Francisco Peñoñori

[JJ Gao]

Hi Francisco,

Thanks for reporting this to us. I have logged the issue here: https://github.com/cBioPortal/datahub/issues/2208. Please note that it might take us some time to investigate this issue and see if we have a solution.

At the same time, would switching your analysis to the pancancer study (https://www.cbioportal.org/study/summary?id=thca_tcga_pan_can_atlas_2018) a feasible solution for you?

Best,

-JJ

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