Question: TCGA immunotherapy treated melanoma data
2
gravatar for Pin.Bioinf
6 months ago by
Pin.Bioinf240
Malaga
Pin.Bioinf240 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 • 464 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Pin.Bioinf240

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

ADD REPLYlink written 6 months ago by Kevin Blighe39k
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 6 months ago by Kevin Blighe39k

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

ADD REPLYlink modified 6 months ago • written 6 months ago by Pin.Bioinf240
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 6 months ago • written 6 months ago by Pin.Bioinf240

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 6 months ago by Pin.Bioinf240
4
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k 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 6 months ago by Kevin Blighe39k
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