TCGA melanoma clinical data

[Stephen Barron]

 

Hi there

 

I have a question about the clinical data included in the TCGA melanoma data (skcm_tcga_pan_can_atlas_2018) available on cBioPortal. I have read papers based on this study (with data downloaded from cBioPortal, see https://www.nature.com/articles/s41467-021-21207-2 for a recent example), that report information on Breslow thickness and Ulceration, but neither seem to be included in the data that I downloaded?

 

Just to provide a little more detail:

1. I downloaded the file “skcm_tcga_pan_can_atlas_2018.tar.gz”, and successfully extracted the text files.
2. There seems to be two files with clinical data: “data_clinical_patient.txt” and “data_clinical_sample.txt”. However, neither of these files include data on Breslow thickness or Ulceration.

 

I’d be very grateful if you could let me know if data on Breslow thickness and Ulceration are available for TCGA melanoma and how I might access it?

 

Thank you for your help and apologies if I’m missing something obvious.

Stephen

 

 

[JJ Gao]

Hi Stephen,

The study they used is likely to be this one (https://www.cbioportal.org/study/summary?id=skcm_tcga_pub_2015). Both Breslow and Ulceration were included there.

Best,

-JJ

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[Stephen Barron]

Hi JJ, thanks for your help and quick response, much appreciated.

 

Stephen