Question: TCGA clinical data, info about treatment_id / drug
3
gravatar for Siha
18 months ago by
Siha30
Siha30 wrote:

From literature I know that a few TCGA samples have also information about treatment. It isn't clear to me how to obtain that information. After downloading the clinical data sets with TCGAbiolinks package I see one column "treatment_id". Each TCGA sample has a code in this column, looking like this: dbf26982-97b4-59f7-b165-d3889623bc21.

I can't figure out what that means, or how I can translate the code into drug name. Any ideas? Or is there an other way, how to obtain the treatment information outside the "clinical data information"?

tcga R • 1.1k views
ADD COMMENTlink modified 13 months ago by Chris Miller20k • written 18 months ago by Siha30
1
gravatar for Chris Miller
13 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

None of the TCGA tumors were treated prior to sequencing:

Neoadjuvant treatment was not allowable TCGA's goal was to accelerate the understanding of the underlying genomics of primary, untreated tumors. Cancer treatment can involve mutagens or carcinogens which could cloud the origin of the cancer.

https://cancergenome.nih.gov/cancersselected/biospeccriteria

If you're looking to use the clinical outcomes data, I'll leave a warning that it's often incomplete and/or of short duration. Nonetheless, there should be associated metadata files alongside the clinical data that describe the allowable entries in those fields and provide keys.

ADD COMMENTlink modified 13 months ago • written 13 months ago by Chris Miller20k
0
gravatar for bioInfo
13 months ago by
bioInfo0
bioInfo0 wrote:

Hi, did you find a solution? I now have the same problem: I couldn't find a way for getting useful treatment information.

ADD COMMENTlink written 13 months ago by bioInfo0
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