cbioportal/GENIE data to aid histopathology diagnosis

[Owen Prall]

Hi, I am an anatomical pathologist and use cbioportal and GENIE data frequently to aid diagnosis of difficult to classify tumours. I do this by interrogating relative frequencies across different cancer subtypes of the mutations/CN/SV changes that we detect by large panel NGS or WGS.  This is somewhat analogous to how we have used immunohistochemistry for sometime now. The genomic changes are now an incredibly valuable addition to diagnostics.. However, in it's current form, the cbioportal/GENIE websites can be difficult to easily visualise this data, e.g. for combinations of specific variants. Is there any chance of a simplified "pathologist" interface, bearing in mind that histopathologists in general have less molecular and informatics skills than many cBioportal users ?  

[JJ Gao]

Hi Owen,

Thanks for contacting us. 

For looking at combinations of genes and variants, one option is to query them, e.g. https://youtu.be/uJsp9kd2jIk?t=1931. You can also query directly: https://www.youtube.com/watch?v=JId304dp3tc. Please let me know if that works for your use case.

Would you please also let us know if there are any specific features  you are looking for?

FYI, when there are detailed longitudinal data, the patient view page is really useful for analyzing one patient at a time, e.g. https://genie.cbioportal.org/patient?studyId=nsclc_public_genie_bpc&caseId=GENIE-DFCI-004022

Best,

-JJ

On Thu, Jul 21, 2022 at 11:48 PM Owen Prall <owen....@gmail.com> wrote:

Hi, I am an anatomical pathologist and use cbioportal and GENIE data frequently to aid diagnosis of difficult to classify tumours. I do this by interrogating relative frequencies across different cancer subtypes of the mutations/CN/SV changes that we detect by large panel NGS or WGS.  This is somewhat analogous to how we have used immunohistochemistry for sometime now. The genomic changes are now an incredibly valuable addition to diagnostics.. However, in it's current form, the cbioportal/GENIE websites can be difficult to easily visualise this data, e.g. for combinations of specific variants. Is there any chance of a simplified "pathologist" interface, bearing in mind that histopathologists in general have less molecular and informatics skills than many cBioportal users ?  

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