cBioPortal Pathways tab

[Aaron Atkinson]

Hello cBioPortal group,

I would just like to confirm that the data that populates the “pathways" tab takes only from the somatic variants loaded. In other words, that no germline data is incorporated even if exposed due to LoH etc. 

Thanks in advance for the confirmation. 

Aaron

[JJ Gao]

Hi Aaron,

In the public cBioPortal (cbioportal.org), we only have somatic variants with a few rare exceptions (BRCA1/2 in ovariant TCGA).

Best,

-JJ

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[Aaron Gmail]

Okay. Thanks. 

For added clarity, would a private cBio instance loaded with WES germline results be the same as the largely somatic variants in the public data?

Cheers!  Aaron. 

On Sep 15, 2023, at 9:01 AM, JJ Gao <jianji...@gmail.com> wrote:



[JJ Gao]

If germline mutations are imported in the private instance, they will be used in the pathways tab and other places. If they are properly annotated as germline, you'll see them in the Mutations tab, e.g. https://bit.ly/3PI3zLv

[Aaron Atkinson]

I wonder if the germline notation could be extended to the pathway analysis so people would be aware of germline vs somatic indications there…perhaps even suggestions of LoH as cBio already does. 

Thanks for the clarifications. 

Have a great weekend, Aaron. 

On Sep 15, 2023, at 9:48 AM, JJ Gao <jianji...@gmail.com> wrote:

If germline mutations are imported in the private instance, they will be used in the pathways tab and other places. If they are properly annotated as germline, you'll see them in the Mutations tab, e.g. https://bit.ly/3PI3zLv

<image.png>

[JJ Gao]

That's something that we may not be able to prioritize given that most of our public data are somatic. The issue is that we only display one number per gene in the pathway tab. A proper germline notation would require two numbers (one for somatic and one for germline). Adding a asterisk when there may be more doable but it would be hard to prioritize based on our current workload. If you have coding experience and would like to contribute, please feel free to create an issue and pull request :)

Also, when querying, you can exclude germline mutations, or use OQL to indicate that you only want to look at germline or somatic: https://docs.cbioportal.org/user-guide/oql/#oql-modifiers.