Stream: genomics
Topic: Liquid Biopsies and Reporting in our IG
Arthur Hermann (Nov 04 2020 at 20:16):
We may have this covered already and it is equally possible that we can't address this in our current scope for the IG going to ballot - but liquid biopsies are becoming a significant part of genomics.. this article points out some issues of how two different companies are presenting their information from a ligquid biopsy, which makes me think that we will need to allow a lot of leeway in any attempt to enable reporting of such results through our IG - https://www.360dx.com/liquid-biopsy/regulatory-documents-newly-approved-liquid-biopsy-ngs-panels-detail-diverse-test?utm_source=Sailthru&utm_medium=email&utm_campaign=360Cancer%20Wed%202020-11-04&utm_term=360Dx%20Cancer%20Bulletin
Kevin Power (Nov 04 2020 at 20:31):
@Arthur Hermann - Would you be willing to put together some examples based on what you see? My guess is we should be able to support at some/most of it, but was there something specific you were wondering about?
Arthur Hermann (Nov 04 2020 at 20:35):
@Kevin Power I would like to look at a report from either, both of these companies so that we can ensure that our IG can appropriately handle the content.. if anyone has access to such reports that would help.. I can try to reach out to someone I know at Foundation. Again, my goal is to ensure that our IG can appropriately handle the information in the liquid biopsy reports
Kevin Power (Nov 04 2020 at 23:26):
Once we find some examples, we can find out :smile:
Patrick Werner (Dec 01 2020 at 16:20):
I recently got contacted by Guarduant Europe. We are already using liquid biopsy in Heilbronn.
Patrick Werner (Dec 01 2020 at 16:21):
From my experience the data ist similar to tumor-normal-testing
Patrick Werner (Dec 01 2020 at 16:21):
example guarduant reports:
http://www.sequenca.nz/guardant/assets/new---lung---sample-report-1-time-point.pdf
http://www.sequenca.nz/guardant/assets/new---lung---sample-report-2-time-points.pdf
Arthur Hermann (Dec 02 2020 at 00:51):
Thanks @Patrick Werner . I am meeting with foundation tomorrow and should be able to provide a few more examples. Have you tried to develop a report for liquid biopsy of for any tumor testing using our FHIR IG? If so, can it handle all of the information in the samples you linked to?
Arthur Hermann (Dec 07 2020 at 21:18):
I met with a few folks from Foundation Medicine and they provided two samples of their Liquid Cdx reports which I uploaded to our google drive repository. They can be found here:
https://drive.google.com/file/d/1Yww9xEuD9dneVE5ua-S5BcOi775NdY2f/view?usp=sharing
https://drive.google.com/file/d/1gvLx7iOIT2LFwi5w6-KcX6iA9cvkuldL/view?usp=sharing
They are also interested in joining our Genomics Working Group... either on a weekly basis, or at a minimum at one of our codethon's to use our IG in relation to their reports.. I will provide more information when I have it.
May Terry (Mar 31 2022 at 14:41):
Quite a bit of time since we last discussed this, but I was reading through this thread and noticed that the FM liquid Cdx example links are broken. Any reason why? Did it change location, been deleted, or other?
Arthur Hermann said:
I met with a few folks from Foundation Medicine and they provided two samples of their Liquid Cdx reports which I uploaded to our google drive repository. They can be found here:
https://drive.google.com/file/d/1Yww9xEuD9dneVE5ua-S5BcOi775NdY2f/view?usp=sharing
https://drive.google.com/file/d/1gvLx7iOIT2LFwi5w6-KcX6iA9cvkuldL/view?usp=sharingThey are also interested in joining our Genomics Working Group... either on a weekly basis, or at a minimum at one of our codethon's to use our IG in relation to their reports.. I will provide more information when I have it.
Kevin Power (Mar 31 2022 at 14:57):
Here is the link to our Example Report folder anyway:
https://drive.google.com/drive/folders/18T4RS0VnrJdLS3k79skbrZ0cYyL1U53t
Arthur Hermann (Mar 31 2022 at 17:32):
May Terry said:
Quite a bit of time since we last discussed this, but I was reading through this thread and noticed that the FM liquid Cdx example links are broken. Any reason why? Did it change location, been deleted, or other?
Arthur Hermann said:
I met with a few folks from Foundation Medicine and they provided two samples of their Liquid Cdx reports which I uploaded to our google drive repository. They can be found here:
https://drive.google.com/file/d/1Yww9xEuD9dneVE5ua-S5BcOi775NdY2f/view?usp=sharing
https://drive.google.com/file/d/1gvLx7iOIT2LFwi5w6-KcX6iA9cvkuldL/view?usp=sharingThey are also interested in joining our Genomics Working Group... either on a weekly basis, or at a minimum at one of our codethon's to use our IG in relation to their reports.. I will provide more information when I have it.
May - I cannot find those documents either. I don't know where they went - however the best source for some sample Foundation reports is to go here: https://www.foundationmedicine.com/test/foundationone-cdx - then scroll down to "real world results" and you can see PDFs of various reports... I also added an "overview" document of Foundation Medicine reports in the repository which Kevin highlighted. Hope this helps
Last updated: Apr 12 2022 at 19:14 UTC
