Querying all samples within cBio portal with a specific mutation

[Jeremy Ng]

Hi everyone,

I spent quite some time reading through the cBioPortal API documentations but am still feeling a little lost, so am hoping to for some advice on what is a suitable end point (if at all) for my use case.

What I would like to do is to search for all samples across all projects which contain a specific mutation. From this search, I would like to be able to calculate how many samples with the mutation are of a specific cancer type (e.g. breast cancer).

Could anyone point me in the right direction on how do I go about accomplishing this?

Thanks in advance!

Jeremy

[pr...@ds.dfci.harvard.edu]

Hi Jeremy,

You should be able to run this query from cBioPortal webpage by selecting “Curated list of non-redundant studies” and “Query by gene” option. You can use OQL to query for specific mutation (Example BRAF: MUT=V600E). 

Is there any specific reason you want to use the API?

Thanks,

Priti 

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[Ino de Bruijn]

Hi Jeremy,

Thanks for reaching out!

How it currently works on the website if you e.g. search for BRAF V600E across the list of non-redundant curated studies. You would pull all BRAF mutations for all samples across the list of non-redundant curated studies. Then filter by V600E programmatically. For each of the remaining samples you can get the CANCER_TYPE or CANCER_TYPE_DETAILED clinical attribute.

It's currently not possible to pull the list of non-redundant studies from the API, but you can find the study ids here:

https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/blob/a0885b44eb8fe5cd7e42bf9e4e169b1f1492c445/cbioportal/cbioportal_spring_boot.yaml#L80

Does that help?

Note that the calculation can become quite complex if you want to take into account which samples were profiled for that gene. In that case you would also want to pull the gene panel info for each sample.

Best wishes,

Ino

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[Jeremy Ng]

Hi Ino,

Great thanks, that was very helpful! I'd implement it using your suggestion then!

Jeremy 

On 16 Sep 2021, at 2:18 AM, Ino de Bruijn <i...@ino.pm> wrote:



[Ryan Abo]

Hi Ino,

I am interested in the gene panel info for each sample to have a better resolution of mutation frequencies. How do I obtain this information using the API?

Thank you,

Ryan

[Sjoerd van Hagen]

Hi Ryan,

Adding Ino on CC so he will get your message.

Best,

Sjoerd.

---

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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[debr...@mskcc.org]

Hi Ryan,

 

Thanks for reaching out! Apologies for the delay

 

There is the /api/gene-panel-data endpoint. E.g. for the mskimpact 2017 study:

 

curl 'https://www.cbioportal.org/api/gene-panel-data/fetch'    -H 'accept: application/json'      -H 'content-type: application/json'               --data-raw '{"molecularProfileIds":["msk_impact_2017_cna","msk_impact_2017_mutations","msk_impact_2017_fusion"]}'   --compressed

 

This will return what sample is profiled for what panel. And then you can use /api/gene-panels to see what genes are profiled in that panel.

 

For an example you can open the network tab for this query and look for gene-panel* endpoints (see screenshot):

 

https://bit.ly/3HUfpeY

 

Hope that helps!

 

Best wishes,

Ino

 

From: Sjoerd van Hagen <sjo...@thehyve.nl>
Date: Monday, May 30, 2022 at 9:17 AM
To: Ryan Abo <ryan...@gmail.com>
Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>, "de Bruijn, Ino/Sloan Kettering Institute" <debr...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] Querying all samples within cBio portal with a specific mutation

 

Hi Ryan,

 

Adding Ino on CC so he will get your message.

 

Best,

 

Sjoerd.

 

---

 

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

 

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

 

    

 

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