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How to download primary site data from TCGA?

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?

tcga
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updated by Tran • Tran • written by randalljellis randalljellis

1 answer

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:

Kevin

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written by Kevin Blighe Kevin Blighe

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.

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written by Tran • Tran

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