Question: TCGA immunotherapy treated melanoma data
2
gravatar for Pin.Bioinf
12 months ago by
Pin.Bioinf260
Malaga
Pin.Bioinf260 wrote:

Hello,

I need to download melanoma TCGA mutation data for patients that have been treated with anti PD1 immunotherapy.

I have found the TCGA melanoma data, but when I looked at the clinical data, treatment information is not provided. Where can I find which treatment was applied to each patient? I have seen articles that use this type of information, so it must be available somewhere.

Thank you

download snp mutation tcga • 863 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Pin.Bioinf260

There are many clinical data files. The treatment used is definitely there. From where did you download the clinical data?

ADD REPLYlink written 12 months ago by Kevin Blighe48k
1

For example, the Biotab files on the GDC Legacy contain some information:

  • history_neoadjuvant_tx_type
  • fn_tx_90_days_prior_to_resection
  • radiation_treatment_adjuvant
  • pharmaceutical_tx_adjuvant
  • new_tumor_event_dx_indicator

Source: https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=...

ADD REPLYlink written 12 months ago by Kevin Blighe48k

Is there any way I can also find if that immunotherapy treatment was anti PD1 ? (more detailed info on treatments)

ADD REPLYlink modified 12 months ago • written 12 months ago by Pin.Bioinf260
1

I solved it by looking at the medicine name (nivolumab, etc.) Thank you. EDIT: I had not seen your response, even better. Thank you again

ADD REPLYlink modified 12 months ago • written 12 months ago by Pin.Bioinf260

I downloaded it from here: https://portal.gdc.cancer.gov/projects/TCGA-SKCM, and the files I downloaded did not have any annotation in those fields: all were 'Not available', but I saw now that there is some files with immunotherapy annotations. Thank you!

ADD REPLYlink written 12 months ago by Pin.Bioinf260
4
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe48k
Kevin Blighe48k wrote:

Yes, there is more detailed information in this file: https://portal.gdc.cancer.gov/legacy-archive/files/6011a7f8-5880-42b3-8e64-909b9715c29f (GDC Legacy)

It shows that a few patients were taking anti PD1 (Nivolumab or Pembrolizumab).

The equivalent on the main GDC Data Portal is: https://portal.gdc.cancer.gov/files/8da29d73-2299-49f0-9740-d04b3793fd8d

To configure this search, I did:

  1. Primary Site --> Skin
  2. Program --> TCGA
  3. Data Category --> Clinical
  4. Data Format --> BCR Biotab / Biotab
ADD COMMENTlink written 12 months ago by Kevin Blighe48k
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