Question: TCGA immunotherapy treated melanoma data
2
gravatar for Pin.Bioinf
17 months ago by
Pin.Bioinf270
Malaga
Pin.Bioinf270 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 • 1.5k views
ADD COMMENTlink modified 5 days ago by inesdesantiago170 • written 17 months ago by Pin.Bioinf270

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

ADD REPLYlink written 17 months ago by Kevin Blighe54k
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 17 months ago by Kevin Blighe54k

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

ADD REPLYlink modified 17 months ago • written 17 months ago by Pin.Bioinf270
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 17 months ago • written 17 months ago by Pin.Bioinf270

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 17 months ago by Pin.Bioinf270

This is an old post and I'm not sure if I'll get an answer on a related point, but here it goes... Is there a way of figuring out when the tumor samples were collected and when the immunotherapy started? I'm trying to understand if these patient samples are pre- or post-immunotherapy treatment.

ADD REPLYlink written 4 months ago by atakanekiz190
1

Please take a look at the related answer, here: A: GDC portal : search by drug

Please also sift through the other clinical data tables to see if you can find what you need. I just took a quick look and it is possible to, for example, infer from the data things such as:

  • date of birth
  • date of first pathologic diagnosis
  • date of treatment start
  • date of relapse
  • date of death

Take a look through the available BCR Biotab files for each cancer cohort

ADD REPLYlink written 4 months ago by Kevin Blighe54k

I've downloaded all available clinical data about treatment, and search for anti-PD1 and anti-PDL1 drugs. There are very few patients treated with this type of immunotherapy. Hence TCGA doesn't seem the go to option for finding anti-PD1/anti-PDL1 datasets. I've been more successful on ENA and GEO.

ADD REPLYlink modified 4 months ago • written 4 months ago by guillaume.rbt770

Thank you for that feedback.

ADD REPLYlink written 4 months ago by Kevin Blighe54k
7
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

Edit 18th October 2019: A related answer: A: GDC portal : search by drug

--------------------------

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 modified 4 months ago • written 17 months ago by Kevin Blighe54k
1
gravatar for inesdesantiago
5 days ago by
United Kingdom
inesdesantiago170 wrote:

Hi I use this:

# Get all metadata 

metadata_clean <- recount::all_metadata("tcga")

# Get only SKCM project

x <- metadata_clean[metadata_clean$gdc_cases.project.project_id == "TCGA-SKCM",]
dim(x)

[1] 473 271

Now you can see 14 patients with Ipilimumab and 1 with nivolumab. Also note that there are many typos (e.g. small caps, lower caps..) in the table.

> library(knitr)
> kable(table(toupper(x$cgc_drug_therapy_drug_name)))

    |Var1               | Freq|
|:------------------|----:|
|2B3-101            |    1|
|ACTINOMYCIN-D      |    1|
|AFLIBERCEPT        |    2|
|ALKERAN            |    1|
|AVASTIN            |    1|
|AXITINIB           |    1|
|BLEOMYCIN          |    1|
|BRAF INHIBITOR     |    1|
|CANCER VAX         |    1|
|CARBOPLATIN        |    2|
|CICLOSPORIN        |    1|
|CISPLATIN          |    3|
|DABRAFENIB         |    2|
|DACABARZINE        |    1|
|DACARBAZINE        |   13|
|DIPHENCYPRONE      |    1|
|DTIC               |    2|
|FARESTON           |    1|
|FOTEMUSTINE        |    2|
|GM-CSF             |    1|
|GP-100             |    1|
|IL-18              |    1|
|IMIQUIMOD          |    1|
|INTERFERON         |   17|
|INTERFERON ALFA    |    1|
|INTERFERON ALFA-2B |    1|
|INTERFERON ALPHA   |    6|
|INTERFERON-ALFA    |    1|
|INTERLEUKIN - 2    |    1|
|INTERLEUKIN-2      |    2|
|IPILIMUMAB         |   14|
|LAFERON            |    2|
|LOMUSTINE          |    1|
|MAGE A3            |    1|
|MAGE-3             |    1|
|MEL-44             |    2|
|MELPHALAN          |    2|
|NIVOLUMAB          |    1|
|PACLITAXEL         |    1|
|PEMBROLIZUMAB      |    2|
|PI88               |    1|
|PNU-159548         |    1|
|PV-10              |    1|
|RECMAGE- A3        |    2|
|SYLATRON           |    3|
|TAMOXIFEN          |    1|
|TEMODAL            |    2|
|TEMODAR            |    3|
|TEMOZOLOMIDE       |    1|
|TRAMETINIB         |    1|
|VEMURAFENIB        |    5|
|VINBLASTINE        |    2|
|VMCL               |    1|
|YERVOY             |    2|
ADD COMMENTlink written 5 days ago by inesdesantiago170
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