[cBioPortal] hg38 CNA data is not showing

[She, Ruicong]

Hello,

 

My name is Ruicong She, from Henry Ford Health System. While setting up our local cBioPortal server, I have a small question regarding the reference genome version.

 

Our data is hg38, so I specified it in meta_study.txt with reference_genome: hg38. Our study seemed to be uploaded successfully, but the problem is with CNA data, which is not showing in the interface. Attached please find a screenshot of the interface. As you could see, the mutation data is showing correctly, but the CNA data box is just empty.

One solution I thought of is to convert our data to hg37, but I am wondering if there is a better and more convenient solution. I appreciate if you could offer any suggestion.

 

Please let me know if any information is needed.

 

Thanks much,

Ruicong

 

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[Benjamin Gross]

Hi Ruicong,

I don’t think the reference genome should affect the displaying of CNA data.  I imagine you didn’t have any errors importing the CNA data - actually I see that your screen capture shows that 286 samples were imported with CNA data.  What happens if you select those samples in the Genomic Profile Sample Counts table and then query for a gene - do you successfully get to the query results page?

Can you open up your browser debugger and show us if any error are occurring when the study view page is loading (you can see this information in Chrome under the network tab)

Let me know how it goes.

-Benjamin

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<HFHS_Study_CNA_missing.PNG>

[She, Ruicong]

Hi Benjamin,

 

Thank you so much for the quick reply.

I did as you instructed but the CNA box is still empty (CAN_missing.PNG). The screenshot of the debugger is also attached.

 

To rule out the causes of this problem, I also tried simply removing reference_genome: hg38 when importing the study. Thus our data would be treated as hg37 (although it is not). This time the CNA query page showed up with no problem (Fake_hg37_Version.PNG)…

 

 

Best,

Ricky