Question: Find Information about TCGA samples from GDC data portal
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gravatar for lawarde.ankita1
3 months ago by
lawarde.ankita120 wrote:

Hello Sir/ma'am,

I have one question regarding the sample information from GDC (Genomic Data Commons) data portal. I am working on transcriptome profiling data of LUAD. My question is regarding to the drug treatments given to the patients.

  1. when is the drug treatment given, before or after the sample is taken for RNA sequencing?
  2. And how to find this information from the GDC?

Your valuable suggestions would really help me.

Thanks, Ankita

ADD COMMENTlink modified 3 months ago by svlachavas480 • written 3 months ago by lawarde.ankita120
1
gravatar for svlachavas
3 months ago by
svlachavas480
Greece
svlachavas480 wrote:

Dear Ankita,

consider that from my personal search and email one or two years ago, to the main contributors and directors of the TCGA project-which "evolved" to GDC, i got the following answer : "The criterion used for all of the TCGA projects, is that samples be obtained from the primary tumor site from patients who have not received any prior treatment"-

moreover, consider the fact that it would not make any impact, if for the initial characterization of primary cancers of different origins, specimens used from patients that had any type of therapy-

however, i don't know about extra information, adjuvant therapy that applied after initial treatment (that is surgery), etc. I think all is included in the clinical tab information in GDC, which is available for every project.

Also, you should have also checked firstly the relative publication:

https://www.nature.com/articles/nature13385#s1 - it has a section as every similar TCGA paper, describing the patient cohorts and characteristics.

Best,

Efstathios

ADD COMMENTlink modified 3 months ago • written 3 months ago by svlachavas480

Thank you so much for information and the reference.

ADD REPLYlink written 3 months ago by lawarde.ankita120
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