How to download primary site data from TCGA?

Question

[randalljellis]

I'm aware that on the https://portal.gdc.cancer.gov/ portal you can download a JSON file that contains metadata, but it doesn't contain the primary site of the sample, or whether the sample was malignant or benign, outcome, etc. Is this data available?

Answer 1

[Kevin Blighe]

It is possible to distinguish malignant / benign from the TCGA barcode ( A: Meaning letters in TCGA sample barcode field ). In your JSON file, if you don't have barcodes, you will likely have a UUID or filename - these can be converted easily to barcodes, if needed:

• https://seandavi.github.io/post/2017-12-29-genomicdatacommons-id-mapping/
• C: Sample names for TCGA data from GDC-legacy archive

Kevin

[Tran]

This is interesting. Would you please explain more how to distinguish malignant / benign from the TCGA barcode? I am new to the GDC data.

Thank you.