Question: TCGA clinical data, info about treatment_id / drug
4
gravatar for Siha
2.5 years ago by
Siha40
Siha40 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 • 2.0k views
ADD COMMENTlink modified 10 weeks ago by borauyar198510 • written 2.5 years ago by Siha40

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 2.1 years ago by bioInfo0
1
gravatar for borauyar1985
10 weeks ago by
borauyar198510
borauyar198510 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"))
GDCdownload(query)
clinical <- GDCprepare_clinic(query, clinical.info = "drug")

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

ADD COMMENTlink written 10 weeks ago by borauyar198510
2
gravatar for Chris Miller
2.1 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.

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 2.1 years ago • written 2.1 years ago by Chris Miller21k
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