Obtaining patient survival data for specific gene mutations

[Rohan CHIPPALKATTI]

Hello,

I am a postdoc at the University of Luxembourg and for my current project, I need to compile data for KRAS gene mutations and the effect on patient survival.

I tried to input a query as suggested on the cbioportal webpage where I wrote KRAS: MUT=G12V (where G12V is the amino acid change). In the oncoprint tab, I do see data for each patient but when I click the 'plot' tab, I am not able to visualize the proportion of deceased vs surviving patients for this specific G12V mutation. Instead I see this data for all type of KRAS mutations combined. Is it possible to visualize for e.g. the KRAS missense mutations G12V, G12D, G12C etc on the X axis and on the Y axis the proportion of deceased vs surviving patients?

I would really appreciate your advice on this..

Regards,

Rohan

Rohan Chippalkatti, PhD

Post-Doctoral Researcher

Department of Life Sciences and Medicine (DLSM)

Cancer Cell Biology and Drug Discovery (CCBDD) Laboratory

UNIVERSITÉ DU LUXEMBOURG 

Belval campus, BT1 
7, avenue des Hauts-Fourneaux 
L-4362 Esch-sur-Alzette 
Tel +352 46 66 44 5886
rohan.chi...@uni.lu

[Sowmiyaa Kumar]

Hi Rohan, 

Thank you for reaching out to us. I believe you are right about the fact that you cannot view each individual (missense) mutation on the x-axis along with their overall survival status (or patient vital status) in the Plots tab. However, you can view the missense mutations separately by grouping the mutations by mutation type in the same tab.

Another way to view the proportion of deceased to living for individual mutations would be to query the required mutations (i.e. G12V, G12D, G12C, etc.) and use the Comparison/Survival tab to select your required groups (the mutations you specify in your case) on the top of the page and then selecting the survival sub-tab. The graph should look something like the attached. You can also choose your preferred clinical attribute (in this case, Patient Vital Status) in the clinical sun-tab and view a bar graph of the same. I have attached another screenshot to show you how to do that. Please note that while selecting the groups in the Comparison/Survival tab, the altered and unaltered groups will be selected by default so you may have to unselect those two and select the specific missense mutations that you queried.

Hope this helps and do not hesitate to ask for further assistance if not. Please remember to "Reply All" while responding to this thread. 

Thanks and regards, 

Sowmiyaa

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Sowmiyaa Senthil Kumar

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[Rohan CHIPPALKATTI]

Dear Sowmiyaa,

Thanks a lot for you detailed response.

I tried to search with the steps that you suggested and was able to get survival curves for all mutants of interest.

This really enables me to draw connections to clinical data with my own experimental results.

Thanks again!

Regards,

Rohan

Rohan Chippalkatti, PhD

Post-Doctoral Researcher

Department of Life Sciences and Medicine (DLSM)

Cancer Cell Biology and Drug Discovery (CCBDD) Laboratory

UNIVERSITÉ DU LUXEMBOURG 

Belval campus, BT1 
7, avenue des Hauts-Fourneaux 
L-4362 Esch-sur-Alzette 
Tel +352 46 66 44 5886
rohan.chi...@uni.lu

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From: Sowmiyaa Kumar <sowm...@thehyve.nl>
Sent: Monday, October 16, 2023 4:47 PM
To: Rohan CHIPPALKATTI <rohan.chi...@uni.lu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Obtaining patient survival data for specific gene mutations