Issue with Discrete CNA Not Showing in Mutations Tab (CGHcall, sWGS)

[Ji Hen Lau]

Hi all,

I’m currently importing discrete copy number alteration (CNA) data into a local cBioPortal instance. My CNA calls were generated using CGHcall within the QDNAseq package. My data are shallow WGS (sWGS) data and since GISTIC is not optimized for sWGS, so I’m using CGHcall’s output instead.

I’ve formatted my CNA file (data_cna.txt) as gene-level, with the structure:

Hugo_Symbol ID1 ID2 ID3 ID4
PLEKHN1 0 -2 -1 1
TP53 1 2 -1 -2
...

My meta_cna.txt looks like this:

cancer_study_identifier: my_study_id
genetic_alteration_type: COPY_NUMBER_ALTERATION
datatype: DISCRETE
stable_id: cna
show_profile_in_analysis_tab: true
profile_name: Copy-number alteration from CGHcall
profile_description: Copy-number from CGHcall: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral; 1 = gain; 2 = high level amplification.
data_filename: data_cna.txt

While doing gene query, the import passes validation and displays CNAs correctly in the OncoPrint tab (Deep Deletion and Amplification). However, I noticed:

• CNAs do not show up in the Mutations tab

• Changing the stable_id to gistic did seem to make CNAs visible in that tab.

I’ve also attached a screenshot of the section I’m referring to (highlighted in red). It’s a public dataset on cBioPortal, where different CNA statuses like DeepDel and ShallowDel are shown under the “Mutations” tab.

However, for my case, the entire CNA column have no entry.

So my questions are:

1. Is there any difference in downstream behavior or analysis depending on what stable_id is used (e.g., cna vs gistic)?

2. Is it okay to use stable_id: gistic for CNA data not produced by GISTIC (in my case, CGHcall)?

3. Are there other configurations or metadata settings I might be missing?

Thank you for your time and help!

Best,
Ji Hen

[Priti Kumari]

Hi Ji Hen,

Can you try adding Entrez ID in your data files (mutation and Copy number) and see if that works?

Thank you,

Priti

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[Ji Hen Lau]

Hi,

Sorry for the delay in response. I've tried to add the Entrez ID and the CNA are still not showing up.

Regards,

Ji Hen

[Ji Hen Lau]

Hi,

I think I kind of sorted the issue out. It seems there's some internal data structure error at my end. I've fix the error and the CNA is now showing. Sorry that I did not figure it out sooner!

Thanks again!

Regards,

Ji Hen