Discrete CNA Table

[Bullen, Catherine (NIH/NCI) [C]]

Hello cBio team,

 

We are running into issues with trying to load in discrete CNA gene data for a given study, whereby the table of discrete CNAs is empty on study summary page but the data is successfully loaded in as we can see in sample view list of Deep Deletions and Amplified genes.

 

 

Data shows on sample level but does not show cytoband information:

 

• Confirmed not due to toggling OncoKB gene list filter
• Reinstalled and insured using most up to date version of cbioportal-docker-compose and seed database and ensured that most recent seed db with hg38 was loaded (as per suggestions here: https://github.com/cBioPortal/cbioportal/issues/7262 and here: https://groups.google.com/g/cbioportal/c/gO-TMtLL88U/m/4fQPHCDtAAAJ )
• Confirmed that meta_study.txt file to specify ref genome is hg38
• Remove -1 and 1 discrete CNA annotations as suggested by a comment in this GitHub issue (https://github.com/cBioPortal/cbioportal/issues/7262), did not yield results in CNA table
• Checked validation report of data load, only validation flags were that a small subset of genes had Hugo_Symbol not recognized:

 

Other context:

• We have case_lists for _cna, _seq and _cnaseq
• Also have loaded in segment data and continuous (log2) CNA data in same instance for same study

 

We also looked thru past posts with the similar issue and could not get same result unfortunately.

 

Any insight or ideas on how to resolve would be much appreciated!

 

Thanks,
Catie

 

 

Catherine Bullen, Ph.D. [c]

Manager I, Bioinformatics, CTOS

Bioinformatics and Computational Sciences Directorate (BACS)

Frederick National Laboratory for Cancer Research

National Institutes of Health

office: 240-620-0843

catherin...@nih.gov [c]

 

 

[de Bruijn, Ino]

Hi Catie,

 

Thanks for reaching out!

 

Can you check what network request is failing (if any)? In Chrome:

 

• View > Developer > Developer Tools
• Go to Network Tab
• Search for the can:

 

 

If you do see a response, you can check what the data content looks like in the preview column:

 

 

This will help us debug whether the problem is on the server side or the frontend of the application

 

It might also be good to try with a different example study (e.g. a TCGA pancan study) to check if that does work (i.e. is your issue study-specific or instance-specific). There’s also a hg38 version of the same study if you want to see if the issue is hg38 specific

Hope that helps in narrowing it down!

 

Best wishes,

Ino

 

 

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[Bullen, Catherine (NIH/NCI) [C]]

Hi Ino,

 

Thanks so much for the help. I loaded in both example TCGA studies (hg19 and hg38) as suggested and both do not appear to be displaying the discrete CNA table in my local instance:

 

 

In looking at the developer tools in Chrome, it looks like there is a response:

 

 

The Preview does not display any info:

 

Here’s screenshots from Payload and Header as well:

 

 

 

It looks to me that the requests are being made ok but no data is returned. Any ideas?

 

Thanks,

Catie

 

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[Bullen, Catherine (NIH/NCI) [C]]

Hi Ino and team,

 

Following up if you have any ideas or additional things we can try related to issue below? I reinstalled the docker-compose repo and reset the docker installations and still was not able to get the discrete CNA table to visualize in our local instance. Appreciate any additional troubleshooting insights!

 

Thanks,

Catie

[Aaron L]

Hi Catie, 

Can you tell us what the stable_id is for the cna genetic profile is? 

look in the genetic profile table stable_id column.

Thanks!

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/SA0PR09MB6652BBC6630721DB6CDF88E59C48A%40SA0PR09MB6652.namprd09.prod.outlook.com.

[Aaron L]

Actually, scratch that. Can you tell me if there are any rows in the cna_event table of the database?

[Bullen, Catherine (NIH/NCI) [C]]

Hi Aaron, 

Thanks for reaching out! We do see data loaded into the cna_event table:

We did notice that the total count of cna_events was much lower than expected, we were expecting >200k cna_events for amplification and homozygous deletion events, but observed that only 35,058 were loaded in: 

We did not note any major errors during loading aside from a few Gene Symbol not recognized errors:

Any ideas? Appreciate the help!

Thanks, 

Catie 

[Aaron L]

Hi Catie, 

Perhaps a zoom debugging session would be the best way to get to the bottom of this.  Can we schedule something later this week? I'm very flexible during the day.

--Aaron

[Bullen, Catherine (NIH/NCI) [C]]

Hi Aaron, 

Thanks that would be great! I am free Thursday morning until 1PM ET or Friday afternoon after 2PM ET.

[Aaron L]

I send you an invite for thursday at 11am.  We will need access to database and your application running in a browser.