TCGA immunotherapy treated melanoma data

Question

[Pin.Bioinf]

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

[Kevin Blighe]

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

[Kevin Blighe]

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=...

[Pin.Bioinf]

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

[Pin.Bioinf]

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

[Pin.Bioinf]

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!

[atakanekiz]

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.

[Kevin Blighe]

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

[guillaume.rbt]

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.

[Kevin Blighe]

Thank you for that feedback.

Answer 1

[Kevin Blighe]

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

Answer 2

[inesdesantiago]

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|