Question about Gastric Cancer (OncoSG, 2018) dataset in cBioPortal

[Florian Andersch]

Dear cBioPortal team,

First, I would like to thank you for providing cBioPortal as such an amazing resource for the research community. It has been extremely helpful in my work.

While browsing the data, I noticed something unusual in the study Gastric Cancer (OncoSG, 2018). A large set of X-chromosomal genes (almost all) are marked as homozygous deleted in nearly 100% of the samples. Since these genes include essential ones, and this phenomenon was not mentioned in the linked publication, I was wondering whether this might reflect an experimental or computational artifact.

Could you please share your thoughts or recommendations on how best to handle this dataset? Specifically:

• Have any steps been taken to ensure the validity of these CNA calls?

• Were any bias correction or data normalization procedures applied that might explain this pattern?

• Do you suggest treating these data points with caution when performing downstream analyses?

I would greatly appreciate your insights on this, as well as any advice on best practices for handling such anomalies.

Thank you again for all your efforts in maintaining and improving cBioPortal.

With best regards,
Florian Andersch

[Prasanna Jagannathan]

Hi Florian

Thanks for your email. The issue is present in the underlying dataset files of the study. The cBioPortal DataHub team will be looking into the issue and reply back with a suitable solution.

Please reply back only to cBioPortal google group.

thanks

Jag

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[Florian Andersch]

Hi, 

thank you for your response! Do you have any further information regarding this issue? 

Looking forward to hear from you. 

Best,

Florian

[Anu Vijay]

Hi Florian,

We are currently working on updating the cohort. The updates will be in by tomorrow .

Best,

Baby Anusha.

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/fff79fdd-8399-4f30-ae93-05926f651cd1n%40googlegroups.com.

[Nikolaus Schultz]

Hi Florian,

Thank you for flagging this issue and following up. 

I suggest that we remove the x chromosome genes from the copy-number data. I have cc’d Anders, the senior author of the study, to make him aware. 

Niki.

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/fff79fdd-8399-4f30-ae93-05926f651cd1n%40googlegroups.com.

[Kundra, Ritika]

Thanks everyone. We will remove the chrX data from copy number data and release it ASAP.

 

Ritika

 

From: SKANDERUP Anders Martin Jacobsen <skande...@a-star.edu.sg>
Date: Thursday, October 16, 2025 at 9:06 AM
To: Nikolaus Schultz <nsch...@gmail.com>, Florian Andersch <fl.an...@gmail.com>
Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>, Kundra, Ritika <kun...@mskcc.org>
Subject: [EXTERNAL] Re: [cbioportal] Question about Gastric Cancer (OncoSG, 2018) dataset in cBioPortal

ARES PRIVATE Thanks, Yes, this issue has been flagged previously – caused by the copy number caller we used at the time. Good idea to remove chrX from the cbioportal dataset. -Anders From: Nikolaus Schultz <nschultz@ gmail. com> Date: Thursday,

ARES PRIVATE

 

Thanks,

 

Yes, this issue has been flagged previously – caused by the copy number caller we used at the time. Good idea to remove chrX from the cbioportal dataset.

 

-Anders

 

From: Nikolaus Schultz <nsch...@gmail.com>
Date: Thursday, 16 October 2025 at 8:14 PM
To: Florian Andersch <fl.an...@gmail.com>
Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>, SKANDERUP Anders Martin Jacobsen <skande...@a-star.edu.sg>, Kundra, Ritika <kun...@mskcc.org>
Subject: Re: [cbioportal] Question about Gastric Cancer (OncoSG, 2018) dataset in cBioPortal

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