Methods for assessing and comparing variant databases and AI technologies

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Methods for assessing and comparing variant databases and AI technologies #37

Closed stryxvaria closed 2 years ago

stryxvaria commented 5 years ago

I'm interested in methods for testing the accuracy of information in variant databases, with an eye to developing ways to assess the accuracy and utility of AI technologies for variant interpretation. Hoping to find other folks interested in these issues as well, and to share ideas about how to approach this both conceptually and technically.

Ian King, University Health Network (Toronto)

malachig commented 5 years ago

Sounds very interesting @stryxvaria. The plan is to have a largely "unconference" format where some topics for discussion will be decided in the moment. With that in mind, we would welcome you to prepare a 2-3 minute "elevator pitch" on this idea to help identify those attendees that are specifically interested in this area.

stryxvaria commented 5 years ago

Will be happy to! -Ian

From: Malachi Griffith notifications@github.com Sent: Friday, October 5, 2018 1:12 PM To: griffithlab/civic-meeting Cc: stryxvaria; Mention Subject: Re: [griffithlab/civic-meeting] Methods for assessing and comparing variant databases and AI technologies (#37)

Sounds very interesting @stryxvariahttps://github.com/stryxvaria. The plan is to have a largely "unconference" format where some topics for discussion will be decided in the moment. With that in mind, we would welcome you to prepare a 2-3 minute "elevator pitch" on this idea to help identify those attendees that are specifically interested in this area.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/griffithlab/civic-meeting/issues/37#issuecomment-427485483, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ApxdfJlrpwIPOPpn5pZtNi0uVKyJpSZLks5uh700gaJpZM4XFO_b.

malachig commented 5 years ago

Selected for discussion in the afternoon session. Participants shared experiences with AI technologies. 12 participants attended this session. Examples uses:

Use Watson to find variants with evidence on OncoKB
Use machine learning to identify false positive rare variants (benign variants)
Is there good value to these technologies today (is it worth the real cost for what you get today).
Bringing AI into molecular tumor boards. Does it add value given the constraints within a health care system that is not unlimited in treatment options.
For discussion purposes we reviewed a Watson example report.
Do any of these AI system evaluate variant combinations in predicting treatments.
Is there anything that resources like CIViC can do to help evaluate the effectiveness of AI platforms.
Analysis proposal. Start with the GENIE variant results. Compare what you get for these variants/cases using Watson to what you get from CIViC for the VICC aggregator.

bpitel12 commented 5 years ago

Summary - AI session.pptx