Re: gene query and TMB data

[annart...@gmail.com]

Hello,

I have two questions about the database and would appreciate direction:

1. Is there a way to query 2 concurrent genes? For example, I would like to see EGFR and SPEN coexist samples in non-small cell lung cancer
2. Can we request TMB and MSI status if we offer the unique sample ID?

 

Thank you!

 

Sincerely,

 

Zhaohui (Ann) Arter, MD

Hematology/Oncology Fellow

Email: annart...@gmail.com

 

[Tali Mazor]

Hi Ann,

You can query more than one gene at a time, see this example where I've queried for both EGFR & SPEN: https://www.cbioportal.org/results/oncoprint?cancer_study_list=luad_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=luad_tcga_pan_can_atlas_2018_cnaseq&gene_list=EGFR%2520SPEN&geneset_list=%20&tab_index=tab_visualize&Action=Submit&comparison_selectedGroups=%5B%22EGFR%22%2C%22SPEN%22%5D

You can see in the OncoPrint that there are a small number of samples with alterations in both genes, and you can use the Comparison tab/Overlap subtab to create & save that group of samples (saving requires logging in; for more detailed instructions, see our user docs: https://docs.cbioportal.org/user-guide/overview/)

You can also select samples with mutations in both EGFR & SPEN on the study view page by applying filters for both genes: https://bit.ly/3FgdrGn

As for TMB & MSI status, we include that information for any study for which it is available to us. If we don't have that data for a particular sample, it is likely because the original publication did not provide it.

-Tali

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[Tali Mazor]

Hi Ann,

The Group Comparison Tutorial slides show how to create a new group, see slide 26. You can also use the Download tab to download a list of samples with alterations in each gene, and with some sorting in excel, you can get the set of samples with alterations in both genes.

-Tali

PS Please keep the google group cc'ed so others can benefit from this conversation.

On Mon, Mar 13, 2023 at 7:24 PM <annart...@gmail.com> wrote:

Hi Tali,

Thank you for the instructions.

 

I can see under “ OncoPrint” that there are a small number of samples with alterations in both genes, but how to create that list? Or do you know which Docs explained the steps?

 

Sincerely,

 

Ann