Likely oncogenic

[Marcelino Ghafari]

Hello, I hope this email finds you well.

I have a question regarding " Likely oncogenic". What do you scientifically mean by it? based on what it is decided to be likely oncogenic? thank you 

[Tali Mazor]

Hi Marcelino,

Are you referring to the designation of 'Likely oncogenic' in the OncoKB tooltip? If so, that is a classification made by the OncoKB team. You can learn more about their curation process on their website: https://www.oncokb.org/about. That page includes links to their manuscript and SOP which will provide additional detail about exactly how variants are classified.

If that's not what you're referring to, can you please provide some additional explanation?

-Tali

On Thu, Apr 22, 2021 at 6:26 AM Marcelino Ghafari <marcelino...@gmail.com> wrote:

Hello, I hope this email finds you well.

I have a question regarding " Likely oncogenic". What do you scientifically mean by it? based on what it is decided to be likely oncogenic? thank you 

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[Tali Mazor]

Hi Marcelino,

That content is coming directly from OncoKB - if you look at the lower left of the tooltip, you can see it says OncoKB. All of the content in that Annotation column is pulled in from outside knowledgebases/resources. You can actually click on that OncoKB logo in the lower left corner and it will bring you to the OncoKB page for that specific mutation. For more information about how OncoKB classifies mutations, see their website: https://www.oncokb.org/about

-Tali

P.S. Please keep the google group cc'ed so others can benefit from your question.

On Thu, Apr 22, 2021 at 9:17 AM Marcelino Ghafari <marcelino...@gmail.com> wrote:

Thank you for the reply. I meant the likely oncogenic in the lollipop model  ( attached below) what does it mean?  thanks 

[Nikolaus Schultz]

Hi Marcelino,

You can find all rules about how OncoKB annotates variants in this document:

https://sop.oncokb.org/

Please feel free to reach out to the OncoKB team directly if you have any more questions.

I hope this is helpful.

Niki

On Apr 22, 2021, at 9:40 AM, Tali Mazor <tma...@ds.dfci.harvard.edu> wrote:

Hi Marcelino,

That content is coming directly from OncoKB - if you look at the lower left of the tooltip, you can see it says OncoKB. All of the content in that Annotation column is pulled in from outside knowledgebases/resources. You can actually click on that OncoKB logo in the lower left corner and it will bring you to the OncoKB page for that specific mutation. For more information about how OncoKB classifies mutations, see their website: https://www.oncokb.org/about

-Tali

P.S. Please keep the google group cc'ed so others can benefit from your question.

On Thu, Apr 22, 2021 at 9:17 AM Marcelino Ghafari <marcelino...@gmail.com> wrote:

Thank you for the reply. I meant the likely oncogenic in the lollipop model  ( attached below) what does it mean?  thanks 

<Screen Shot 2021-04-22 at 5.12.56 PM.png>

On Thu, 22 Apr 2021 at 4:26 PM Tali Mazor <tma...@ds.dfci.harvard.edu> wrote:

Hi Marcelino,

Are you referring to the designation of 'Likely oncogenic' in the OncoKB tooltip? If so, that is a classification made by the OncoKB team. You can learn more about their curation process on their website: https://www.oncokb.org/about. That page includes links to their manuscript and SOP which will provide additional detail about exactly how variants are classified.

If that's not what you're referring to, can you please provide some additional explanation?

-Tali

On Thu, Apr 22, 2021 at 6:26 AM Marcelino Ghafari <marcelino...@gmail.com> wrote:

Hello, I hope this email finds you well.

I have a question regarding " Likely oncogenic". What do you scientifically mean by it? based on what it is decided to be likely oncogenic? thank you 

-- 
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CANmvuSJYpiLDMGCGxQFG_53nSEUSPdHhmQ-vMhc5K_tf9DodXw%40mail.gmail.com.

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You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
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