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Chair:  Bob Milius

Scribe: Bob Milius



HL7 Clinical Genomics Weekly Call - 15 Sep 2020 11:00 AM (US Eastern)

...

Find your local number: https://zoom.us/u/adNIRW2P8J 


Agenda

Table of Contents


Attendees Sign-in

Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org

  1. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org 
  2. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  3. Jamie Jones - BCH - james.jones.bch@gmail.com 
  4. Dora Walter - MOLIT Institut - dora.walter@molit.eu
  5. Liz Amos - NLM - liz.amos@nih.gov 
  6. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io  
  8. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  9.  Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com 
  10.  Kevin Power - Cerner - kpower@cerner.com 
  11.  JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  12.  May Terry - MITRE - mayT@mitre.org 
  13.  Bret Heale


Standing Informational Items

Agendas and Important Dates 

CG Call Date

Co-Chair

Agenda https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings

Important Dates

5/19/20

Bob F

Sync for Genes


5/21/20


Joint call with OO @ 10 am ET (no IM call)


5/26/20

Bob M


6/2/20

Bob F

  • vote on extending co-chair position
  • Use of LOINC in IG orders and reports (Swapna Abhyankar) [30+ min]

6/9/20

Patrick

  • Tumor Normal Testing
  • Example of real life lab data
  • Continue Discussion on Use of LOINC in IG orders and reports

6/16/20


Canceled


6/23/20

Bob M

  • DiagnosticReport.code
  • Virtual WGM in September

6/30/20

Kevin P

  • LOINC in IG orders and reports (continued)

7/7/20

Bob M

  • Virtual WGM in Sep
  • Implication Examples
  • IM work

7/14/20

Patrick

  • Moving away from spreadsheets for our IG
  • Molecular consequence

7/21/20

Bob M

  • Connectathon
  • WGM
  • Moving away from spreadsheets for our IG
  • MSI LOINC

7/28/20

Patrick

  • MSI LOINC
  • mCODE alignment with CG IG STU2 (20-30 minutes minimum)

8/4/20

Patrick

  • Scheduling WGM Sessions (Kevin)
  • Update & Announcing Voting on:
    • Build Issues
    • Updating callable region profile

8/11/20

Bob M

  • Scheduling WGM
  • Genomics Reporting IG STU2 - Template
  • Block vote preview
  • Missing items in the CG DR
  • Uncallable regions (cont discussion)

8/18/20

Bob M

  • Block vote
  • Scheduling WGM
  • Missing items in the CG DR
  • Uncallable regions (cont discussion)

8/25/20

Jamie

  • Uncallable subregions
  • WGM topics

9/1/20

Kevin

  • WGM planning

9/8/20

Patrick

Canceled


9/15/20

Bob M



Connectathon Sep 9-11, 2020

Virtual WGM Sep 21-25, 2020

External efforts

Subgroup reports

...

WG projects and outreach

  • NMDP/CIBMTR hosting virtual Data Standards Symposium and Hackathon (DaSSH) - Thu morning will be focused on FHIR efforts.

Topic 0: Approval of Minutes from Last Meeting


Sep 1


Topic 1: WGM Sessions (cont)

Time slots and proposed topics

...

From chat.fhir.org: Sep 2020 WGM Topics 

Topic 2: Jira Issues

Future Topics

Orders for genetic testing

  • How to define ServiceRequest.code
  • Multiple tests per report?

LOINC changes for Level of Evidence / Clinical Significance

...

  • Motion B: Consider creating new codes for diagnostic, therapeutic, and prognostic significance (see Quest screenshot, LabCorp report) and/or type of evidence (see Baylor report)
    • 1st/2nd -
    • Discussion -
    • Abstain/Nay/Yea -  / /
    • Result - 
  • Need to create an example to understand the meaning of this change/concepts.
  • Need a caretaker for this topic.

Clinical Genomics Reference Docs


Chat:

  • From Arthur Hermann to Everyone: (10:04 AM)
  • From Me to Everyone: (10:04 AM)
  • From may terry to Everyone: (10:19 AM)
  • From Anand Kulanthaivel to Everyone: (10:22 AM)
  • From may terry to Everyone: (10:26 AM)
    • 
Great find, Anand! It’s not on their typical OncotypeDx report, but definitely good to know. Thanks!

  • From Bret H to Everyone: (10:28 AM)
    • 
so the info is definitional. I wonder if the patent captures the current state
or if other variants are used today

  • From Kevin Power to Everyone: (10:30 AM)
    • 
Hey all - I am going to be away for a few minutes.

  • From Bret H to Everyone: (10:30 AM)
    • 
the point being that genetic tests change quickly. be useful to have a location where a profile on the test definition can be found, programmatically, with a REST http get request. obviously, the test vendor would maintain this information to keep it up to date

  • From Bret H to Everyone: (10:31 AM)
    • 
I prefer this to sending a fully specified regions targeted profile with every test report instance

  • From Anand Kulanthaivel to Everyone: (10:31 AM)
    • 
If the patent is the only place this is available, it's a good indication they don't feel like sharing it :-\ so yes, there is a practicality issue.  and I don't know if they even generate a variant specific report.

  • From may terry to Everyone: (10:33 AM)
    • 
Exactly. So it goes back to the question of whether at least for mCODE, it should be considered a Genomics report that aligns with the IG, or a more general lab report that has components for ER, PR, HER2 results and a recurrence score.
anyway…I suppose stay tuned for the WGM discussion. :-)

  • From Bret H to Everyone: (10:35 AM)
    • 
be pragmatic. allow for both, indicate the preference. customers are where the demand comes from

  • From Liz Amos to Everyone: (10:37 AM)
  • From Bob Dolin to Everyone: (10:41 AM)
    • 
Thanks @liz. Maybe we can help make sure it gets discussed during the Monday WGM session ;-)

  • From Kevin Power to Everyone: (10:42 AM)
    • 
I am back (sorry all)

  • From Bret H to Everyone: (10:45 AM)
    • 
anyone follow up on the r4 menu pointing to the our old guidance using sequence resource instead of our current IG?
ideally it would point to the current IG
it causes confusion and delay

  • From Kevin Power to Everyone: (10:46 AM)
    • 
“R4 menu” ?

  • From James Jones to Everyone: (10:46 AM)
    • 
FHIR main page

  • From James Jones to Everyone: (10:46 AM)
    • 
We have a link to the IG right from the genomics page, but it isn’t linked from the r4 main page

  • From Kevin Power to Everyone: (10:46 AM)
    • 
Ahh.  We can bring it up to FHIR-I again, but Grahame didn’t support doing a technical correction like this before.

  • From James Jones to Everyone: (10:47 AM)
    • 
There’s always r5 ;)

  • From Kevin Power to Everyone: (10:47 AM)
    • 
And yes it is better in R5 (I hope, I would suggest everyone review the genomics page in R5 and provide feedback)

  • From James Jones to Everyone: (10:47 AM)
    • 
Honestly I don’t think the google search issue is nearly as bad as we think it is — folks have recently found our IG just fine
WE see the old stuff first because WE used to go to it ;)
It isn’t as heavily weighted for others

  • From Kevin Power to Everyone: (10:50 AM)
    • 
I have said it before, and I will say it here - if someone only does a Google search to decide the standard they build a system like on, that is, well, wrong?

  • From Bob Dolin to Everyone: (10:50 AM)
    • 
Ah, Jamie I hadn't realized that. I was just wondering if we might, for instance, just add some language to the genomics page linked from the r4 main page, and include that in the next ballot?

  • From James Jones to Everyone: (10:51 AM)
    • 
Similar issue if they can’t read the Trial-Use note, they are likely not able to read our IG even if they do find their way there

  • From James Jones to Everyone: (10:51 AM)
    • 
(The trial use note directs folks to the IG, though it could be worded more stongly)

  • From Bob Dolin to Everyone: (10:52 AM)
    • 
Right, perhaps we can just word it more strongly for now

  • From Kevin Power to Everyone: (10:52 AM)
  • From Liz Amos to Everyone: (10:53 AM)
    • 
just saying - for someone who is new to FHIR, it is confusing. it's a complex topic

  • From Kevin Power to Everyone: (10:54 AM)
    • 
R5 was slimmed down, but still includes a lot about MolecularSequence, which perhaps can be moved to the MolecularSequence resource page

  • From Bret H to Everyone: (10:54 AM)
    • 
yeah,I'd splash a popover that has to be clicked to remove

  • From James Jones to Everyone: (10:54 AM)
    • 
Overview slides presentation with good updated links will help :)

  • From Kevin Power to Everyone: (10:54 AM)
    • 
Feel free to bring ideas and concerns to the FHIR-I joint session
Any changes to R4 will require them to sign off

  • From Bret H to Everyone: (10:55 AM)
    • 
I'm unlikely to be able to attend so I'm relying on the kindness of the co-chairs and fellow members

  • From Bob Freimuth to Everyone: (10:56 AM)
    • 
+1 Kevin. Developing based on a spec found after a single google search but not engaging with the spec owners seems like a less-than-optimal approach.
I need to drop - thanks all (and sorry for the early exit)

  • From Liz Amos to Everyone: (10:56 AM)
    • 
but it is a reality that people do!

  • From Dora Finkeisen to Everyone: (10:57 AM)
    • 
Patrick will contact you

  • From Joel Schneider to Everyone: (10:57 AM)
    • 
There has also been some discussion of an R4b release.  If that happens, it may be possible to do something there.

  • From Dora Finkeisen to Everyone: (10:57 AM)
    • 
says sorry for not beeing here

  • From Kevin Power to Everyone: (10:58 AM)
    • 
We can ask about including something in R4B, but I think it will be very targetted

  • From Bob Dolin to Everyone: (10:58 AM)
    • 
I was suggesting we address this during the Monday WGM session - I would guess we could come up with a light-weight interim solution

  • From Bob Dolin to Everyone: (10:59 AM)
    • 
(e.g. just a more strongly worded caveat at the top of the page)

  • From Bret H to Everyone: (10:59 AM)
    • 
see ya