Suggestion

[Mehta, Nikita]

Hello,

 

With COSMIC becoming pay-to-view, I wanted to suggest turning on the MS column by default in the Mutation list so that people can easily tell what has confirmed somatic status when known.  Would that be possible?

 

Thanks,

Nikita

 

Nikita Mehta, MS, CGC

Genetic Analysis Specialist, Sr

Diagnostic Molecular Genetics Laboratory, Department of Pathology

 

Memorial Sloan Kettering Cancer Center

1250 First Ave., New York, NY 10065

Schwartz Building

Meh...@mskcc.org

 

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[Nikolaus Schultz]

Hi Nikita,

Thank you for reaching out to us. 

Can you please explain what the utility of showing the MS status would be in this context? With a few exception, this would show “Somatic” or “Unknown” (which is in most cases presumed to be somatic). So I am not sure it really replaces the value of the COSMIC column. But maybe I misunderstood and you can elaborate?

Thanks,

Niki.

P.S.: If this is something specific to our MSK-internal instance, please respond privately.

On Sep 17, 2025, at 3:52 PM, Mehta, Nikita <Meh...@mskcc.org> wrote:

Hello,

 

With COSMIC becoming pay-to-view, I wanted to suggest turning on the MS column by default in the Mutation list so that people can easily tell what has confirmed somatic status when known.  Would that be possible?

 

Thanks,

Nikita

 

Nikita Mehta, MS, CGC <image001.png>

Genetic Analysis Specialist, Sr

Diagnostic Molecular Genetics Laboratory, Department of Pathology

 

Memorial Sloan Kettering Cancer Center

1250 First Ave., New York, NY 10065

Schwartz Building

Meh...@mskcc.org

 

Please consider the environment before printing this page or its attachments.

 

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[Mehta, Nikita]

Hi,

 

Most of the somatic variant curation experts groups in ClinGen require knowing somatic status for sure to count cases towards an oncogenicity classification per Horak et al., 2021.  Many of these groups rely on the assessment by the databases; historically, this was COSMIC who used Confirmed Somatic to indicate true somatic status.  In reality, this was often presumed somatic status also (based on VAF), but it’s the closest/quickest assessment that users had.  Given COSMIC is now pay-to-view, I thought cBioPortal (has significant overlap) could replace COSMIC in this sense.  ClinGen biocurators could now identify “true” somatic cases and/or go to the papers to verify somatic status (assumptions would not be made).

 

If you don’t think this column is properly reflective of somatic status, then I agree it wouldn’t be very useful.  However, if it is accurate – and perhaps even more accurate than COSMIC’s assessment – then it could be useful and a timesaver.

 

Does that help clarify the use situation?

 

Thanks,

Nikita

 

Nikita Mehta, MS, CGC

Genetic Analysis Specialist, Sr

Diagnostic Molecular Genetics Laboratory, Department of Pathology

 

Memorial Sloan Kettering Cancer Center

1250 First Ave., New York, NY 10065

Schwartz Building

Meh...@mskcc.org

 

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