Question: TCGA clinical data, info about treatment_id / drug
gravatar for Siha
3.7 years ago by
Siha50 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 • 3.4k views
ADD COMMENTlink modified 17 months ago by borauyar198540 • written 3.7 years ago by Siha50

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

ADD REPLYlink written 3.3 years ago by bioInfo0
gravatar for borauyar1985
17 months ago by
borauyar198540 wrote:

The treatment/drug information can be downloaded using the TCGAbiolinks package. Here is the command from the vignette:

query <- GDCquery(project = "TCGA-COAD", 
              data.category = "Clinical", 
              file.type = "xml", 
              barcode = c("TCGA-RU-A8FL","TCGA-AA-3972"))
clinical <- GDCprepare_clinic(query, = "drug")

You can extract other kinds of clinical data such as "radiation" therapy using the same command. Just set argument with radiation.

ADD COMMENTlink written 17 months ago by borauyar198540
gravatar for Chris Miller
3.3 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k 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.

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 3.3 years ago • written 3.3 years ago by Chris Miller21k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1549 users visited in the last hour