GDC portal : search by drug

Question

[guillaume.rbt]

Hi all,

I'm currently looking for public RNAseq datasets from biopsies prior to anti-PD1 or anti-PDL1 treatment.

I'm trying to find this kind of data on the GDC portal (https://portal.gdc.cancer.gov), but I haven't been able to make selection based on the given drug.

Does anyone know a way to filter for a specific treatment in this portal?

Thank you in advance

Answer 1

[Kevin Blighe]

I have provided a previous answer here: C: TCGA immunotherapy treated melanoma data

In short, you must be aware of the official drug names for these for the purpose of searching, i.e., Nivolumab or Pembrolizumab

Kevin

[guillaume.rbt]

Thanks for your reply, sorry I've missed this previous post.

I fear I still haven't been able to understand where I should look for the drug names.

I've selected RNAseq data with sequencing reads available :

https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%5B%22Aligned%20Reads%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.experimental_strategy%22%2C%22value%22%3A%5B%22RNA-Seq%22%5D%7D%7D%5D%7D&searchTableTab=cases

I've download the clinical data tsv file associated with those 13704 cases, but there is no field indicating which drug was given, am I missing something?

[Kevin Blighe]

Hey, I am unsure which data you downloaded, but therapeutic agent ('drug') information is there. You need to use these filters:

1. Data Category > Clinical
2. Data Format > BCR Biotab

Then, in the Files tab, you'll see TXT files for each cohort. One of these has 'drug' in the name, and it is this file that contains information about the therapeutic agent that was taken.

Here it is for UCEC:

[guillaume.rbt]

Ok great I found it, thanks a lot for your explanations !