Questions about putative driver/passenger

[Piao, Wenying]

To whom it may concern,

I would like to enquire about definition of putative driver/passenger mutations on cBioPortal.

After I submitted queries on cBioPortal, I found that in the OncoPrint session, some mutations are classified as putative driver whereas some others are putative passenger. Please, may I know how do you define or classify a certain mutation as driver/passenger? Is is based on published studies or based on prediction of the mutations' effect on protein structural changes or any other criteria?

I would be grateful if you would kindly answer my questions! Thank you so much for your time!

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Sincerely,

Piao Wenying

[Nikolaus Schultz]

Hi Wenying,

Driver and passenger information is based on prior knowledge (from oncokb.org) or statistical recurrence (cancerhotspots.org).

We do not take the predicted effect into account.

Niki.

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[Pieter Lukasse]

Hi Wenying,

we are working on a solution to allow custom annotations to be used in the oncoprint. See https://docs.google.com/document/d/1pZq2_geY5yuCRd43tsrKOjQ8EJ9u4RIh3KmJXADy9Mc/edit and 
https://github.com/cBioPortal/cbioportal/pull/2896

Best regards,

Pieter

On Tuesday, August 1, 2017 at 6:29:15 PM UTC+2, Nikolaus Schultz wrote:

Hi Wenying,

Driver and passenger information is based on prior knowledge (from oncokb.org) or statistical recurrence (cancerhotspots.org).

We do not take the predicted effect into account.

Niki.

On Aug 1, 2017, at 1:59 AM, Piao, Wenying <wyp...@connect.hku.hk> wrote:

To whom it may concern,

I would like to enquire about definition of putative driver/passenger mutations on cBioPortal.

After I submitted queries on cBioPortal, I found that in the OncoPrint session, some mutations are classified as putative driver whereas some others are putative passenger. Please, may I know how do you define or classify a certain mutation as driver/passenger? Is is based on published studies or based on prediction of the mutations' effect on protein structural changes or any other criteria?

I would be grateful if you would kindly answer my questions! Thank you so much for your time!

--

Sincerely,

Piao Wenying

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[Piao, Wenying]

Dear Dr. Schultz,

Thank you so much for your kind reply! I'm very very sorry for the late reply due to some personal reasons.

I checked the mutations on both websites that you sent me, OncoKB and Cancer Hotspots. Whereas I could find most of the putative driver mutations on these websites, I couldn't find many of the mutations that were defined as putative passenger. From another email reply from Mr. Pieter Lukasse, the "custom annotation of driver and passenger mutations" is explained in a github link. After reading the documentation, I found that apart from database such as OncoKB and Cacner Hotspots, the frequency of a certain mutation in the patient population is also taken into consideration for defining driver or passenger. So I am wondering, for those putative passenger mutations that I could not find reference in OncoKB or Cancer Hotspots, are they defined so due to low occurrence in a certain patient cohort?

Best Regards!

Wenying

On Wed, Aug 2, 2017 at 12:29 AM, Nikolaus Schultz <nsch...@gmail.com> wrote:

Hi Wenying,

Driver and passenger information is based on prior knowledge (from oncokb.org) or statistical recurrence (cancerhotspots.org).

We do not take the predicted effect into account.

Niki.

On Aug 1, 2017, at 1:59 AM, Piao, Wenying <wyp...@connect.hku.hk> wrote:

To whom it may concern,

I would like to enquire about definition of putative driver/passenger mutations on cBioPortal.

After I submitted queries on cBioPortal, I found that in the OncoPrint session, some mutations are classified as putative driver whereas some others are putative passenger. Please, may I know how do you define or classify a certain mutation as driver/passenger? Is is based on published studies or based on prediction of the mutations' effect on protein structural changes or any other criteria?

I would be grateful if you would kindly answer my questions! Thank you so much for your time!

--

Sincerely,

Piao Wenying

--
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For more options, visit https://groups.google.com/d/optout.

--

Sincerely,

Piao Wenying