I was wondering if anyone knew the best place to find the most up-to date clinical data for all TCGA projects?
My thoughts would be that using the GDC/TCGAbiolinks would be best, but then I find that neither have progression/remission data.
cBioportal does have progression/remission data but I thought the GDC was the official place to find TCGA-associated data so I am a bit confused.
Any suggestions would be much appreciated, thanks in advance.
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jack.henry •
See https://gdc.cancer.gov/about-data/publications/pancanatlas -- "TCGA-Clinical Data Resource (CDR) Outcome"
It states "It is strongly recommended that this file be used for clinical elements and survival outcome data first"; and there is a Cell paper ( https://www.cell.com/cell/fulltext/S0092-8674(18)30229-0 ) describing it in more detail.
This is true when the paper was first published. But many of such information were later gradually submitted to GDC by TCGA, together with even more updated clinical data. So in the long run, I would suggest you to use GDC.
The Genomic Data Commons is the primary source of TCGA data: https://portal.gdc.cancer.gov/
Using the filters, under Data Format, toggle the boxes for bcr biotab and xlsx.
Survival data is available, where possible. Keep in mind that not all patients will attend follow-up.
Kevin
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