MSK METtropism data inconsistency

[Daniel Boiarsky]

Hi,

I found an inconsistency in the MSK METtropism data that I wanted to get your thoughts on.

As per documentation, OS_MONTHS refers to OS from time of diagnosis (which I assume means initial diagnosis). What I am seeing though is if you calculate the age of diagnosis as (age of death or last contact - OS), this age often happens to be greater than age of mets in cases of metastatic disease and in cases of non-metastatic disease is often greater than age of surgery. 

Could you help clarify from what OS_MONTHS refers to?

Thanks,
Daniel

[David Higgins]

Hi Daniel,

 

Thanks for reaching out about the MSK METtropism dataset. I took a look at a couple participants (1, 2, 3) and tried to repeat your math. When I did <AGE AT DEATH> - 12 * <OVERALL SURVIVAL (MONTHS)>, my calculations were matching or getting pretty close to <AGE AT SEQUENCING>, which is typically later than <AGE AT FIRST METS DX> and also logically later than age at original DX that you’re trying to infer.  

 

This doesn’t seem like its consistent with our definition of OS_MONTHS as “overall survival in months since initial diagnosis.”

 

I put in a ticket for one of our curators to take a look.

 

If you have any follow-up questions, please Reply All so that our continued conversation is captured on the cBioPortal Google Group.

 

Best,

 

David M. Higgins, Ph.D. | (he/him)
Informatics Program Manager
Center for Data-Driven Discovery in Biomedicine (D3b)
Children’s Hospital of Philadelphia, USA

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[Nikolaus Schultz]

Thank you David!

I just want to confirm that OS MONTHS in this data set refers to time since sequencing, not initial diagnosis. 

Niki.

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[Nikolaus Schultz]

Yes, surgery or biopsy… depending on what kind of sample was used.

On Dec 19, 2022, at 11:07 AM, Daniel Boiarsky <boiar...@gmail.com> wrote:

Thank you both very much for the quick replies and clarification. 

One additional question — in the field “Age at surgery”, does surgery mean biopsy?

Thanks!