Aqsa Arshad
I am new to cBioportal. I want to know how to select specific cancer samples but only MSS samples?
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debr...@mskcc.org
Hi Aqsa Arshad,
Thanks for reaching out!
Not all studies in cBioPortal have MSS information. We do have it for the TCGA pancan studies. If you go to the pancan study view you can see there are two charts (see attached) with MSI information from two different algorithms (MANTIS and MSISensor).
For MSISensor they recommend to set the MSS threshold at <10. You can select those cases using the chart
Since not all studies have the same MSI algorithm data, you’ll have to look in the study view if you see any attributes with the name MSI. E.g. in this MSK MetTropism study the attribute has a different name:
https://www.cbioportal.org/study/summary?id=msk_met_2021
The attribute is called “MSI Type” and has categorical values. There you can select all MSS cases like this:
Hope that helps!
Best wishes,
Ino
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