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HL7 Clinical Genomics Weekly Call - 02 June 2020 11:00 AM (US Eastern)


Minutes

http://tinyurl.com/HL7CGGroupCall 

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

Archive of minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=25559917&src=contextnavpagetreemode



Agenda

Attendees Sign-in

Standing Informational Items

Agendas and Important Dates

External efforts

Subgroup reports

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Topic 1: OO call recap

Topic 2: Project Update on #460 - CDA IG for Genetic Testing Reports

Topic 3: Co-chair elections

Topic 4: Update to FHIR core genomic specific and extensions

Topic 5: Update - Stress testing IG implications with examples

Chat

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

Clinical Genomics Reference Docs

Attendees Sign-in

Presiding Co-Chair (Bob Freimuth) 

  1. Patrick Werner - MOLIT Institut - pw@molit.eu
  2. Arthur Hermann - Kaiser Permanente - arhur.hermann@kp.org 
  3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu 
  4. Kevin Power - Cerner - kpower@cerner.com  
  5. Daniel Rutz - Epic - drutz@epic.com 
  6. Michelle Barry-Availity, LLC michelle.barry@availity.com 
  7. Swapna Abhyankar - sabhyank@regenstrief.org
  8. Jami Deckard - Regenstrief/LOINC - jkdeckar@regenstrief.org 
  9. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  10. James Jones - BCH - james.jones.bch@gmail.com 
  11. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  12. May Terry - MITRE - mayT@mitre.org 
  13. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 
  14. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  15. Ning Xie - BWH - nxie1@bwh.harvard.edu
  16. Bob Dolin - Elimu Informatics - bdolin@elimu.io  
  17. Rachel Kutner - epic - rkutner@epic.com 
  18. Liz Amos - NLM - liz.amos@nih.gov
  19. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  20. Bret Heale - Intermountain - bheale@gmail.com 


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



6/16/20




6/23/20

Bob M



6/30/20




7/7/20

Patrick



7/14/20

Bob M



7/21/20




7/28/20

Bob M



8/4/20

Patrick



8/11/20




8/18/20

Bob M



8/25/20

Patrick



9/1/20

Bob M



9/8/20

Patrick



9/15/20




WGM?? Sept 18-25, 2020

External efforts

  • GA4GH (Global Alliance for Genomics and Health)
    •  
    • Variant Representation subgroup (lead by Larry Babb/Alex Wagner/Reece Hart)
    • GA4GH news
    • Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)

Subgroup reports


  • FHIR (Jamie)
    • Minutes:

https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/

  • Reviewing JIRA items for STU2

New simplified implications live on CI build 

http://build.fhir.org/ig/HL7/genomics-reporting

WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

May 19 

        • Clem: frustrated with the visibility of the Implementation Guidance page and navigation to the official IG
        • Lloyd: FMG is considering a 4.1 release early next year, we may be able to add descriptive text to our Guidance page at that time
        • Arthur: come back to this topic later
      • Vote: (Abstain / Opposed / In Favor): Bret H, Swapna, Dan R, Clem, Jami D (5)  / 0  /  14
      • Result: motion passes


See chat:

  • From Kevin Power to Everyone:  10:24 AM


Topic 1: Vote on extending co-chair position

  •     Clinical Genomics - electing three co-chairs to fill the positions currently held by Gil Alterovitz, James Jones (Interim), and Bob Milius (all of whom may be re-elected)


Background:  Our original intention was to have Jamie’s new position co-chair position expire at the end of 2020 (see minutes when this seat was approved here: https://confluence.hl7.org/display/CGW/CG-2019-11-19).  It was originally term-limited as a trial period after which the WG would evaluate whether or not retaining the seat is merited.


The CG WG has two options:

  • Inform HL7 HQ that the seat opened last fall (when Jamie was elected as a co-chair) should NOT be permanent, and therefore CG has only two spots available for election.
  • CG votes to make that co-chair seat permanent, so we will have 3 seats available for the upcoming election.


  • Last week's discussion
    • Arthur - not in best interest of group to remove a co-chair position; should keep the extra position
    • Bob M - CG will vote on this next week
    • Jamie: nomination deadline for co-chair elections is June 15
  • Discussion
    • Clem: opened to reward Jamie for contributions?
    • Arthur, Bob M: no, that was not the stimulus
    • Bob M: we have 6 cochair seats, only 5 active cochairs
    • Bob M: one cochair has not been active (Gil)
    • Bob M: 2 year terms, end at calendar year, 3 would be open if this vote passes
    • Bob F: each meeting requires a cochair to preside if a decision is made (ANSI/HL7 rules)
    • Bob M: yes, we need the extra position, plenty of work to do
    • JD: even at 8, we find ourselves strapped in terms of bandwidth; lots of need for administrative and technical/scientific expertise; 6+ seems right for CG
    • Bob F: please lobby HL7 HQ!
    • Arthur: please announce when “chunks of work” can be done by non-cochairs
    • Bob M: example - Eric H in OO is driving FHIR work but isn’t cochair
    • Bob M: stimulus for opening the seat was to help with the workload among the chairs
    • Arthur: too much work among the co-chairs, need more hands
    • Bob M: having the extra seat has been a relief to the co-chairs, lots of work outside of leading the calls, administrative work needs to get done, having this seat gives more people access to the tooling that is used to administer the CG WG, very helpful
    • Clem: have we had 6 active cochairs?
    • Bret H: why only 5 active?
    • Arthur: Q on terms and length of cochair positions
    • Jamie: there are also other mechanisms to “give credit” to active contributors (e.g., project facilitators on PSSs)
    • May: seems to be a need for multiple subcommittees within the CG WG
    • Bob D: what do the cochairs think? Do we need this extra seat?
    • May: please summarize roles and responsibilities of cochairs
    • Bob M: 6 cochairs is not unusual (OO has 8)
    • Clem: we spend a lot of time on process, can we focus more and do less?
    • Bret H: there are ways people can contribute to the WG even if not a cochair
  • Motion: make permanent the co-chair seat that was added in Nov 2019
    •  None (see above)
    • Move / 2nd: Bob M / Arthur
    • Discussion:
    • Vote: (Abstain / Opposed / In Favor): Jami D, Swapna / 0 / 18
    • Result: motion passes


Topic 2: Use of LOINC in IG orders and reports (Swapna Abhyankar, interim director of LOINC)

  • Context: LOINC being used incorrectly in genomics
  • 2016: labs requesting LOINC codes for reporting the same set of results, not interoperable
  • Existing codes
    • 81247-9: master HL7 genetic variant reporting panel (updated version)
    • Genes
    • Study types
  • 81247-9 should NOT be used for ordering or for results reporting (only used to group results together)
  • Example
    • 79571-6: used for the order
    • 81247-9 is attached to the order, within which can be reported the discrete results
    • See slides for details
  • Coding challenges in 2020
    • Still getting overlapping requests from labs for new codes
    • 81247-9 is still being used incorrectly
  • Use in CG’s FHIR IG
    • DiagnosticReport. ???
    • Examples in the HLA reporting section - ambiguous use/interpretation
  • Recommendations for genetics reporting (example)
    • See slides
  • Discussion
    • 81247-9 would not go on the penultimate slide
    • Example: coding for 81247-9 (master panel) + coding for gene name
    • Need a post-coordinated approach because cannot get pre-coordinated codes for everything that will be reported
    • May: this is a design pattern for multiple IGs
    • Bret: please clarify examples on slides - last slide vs penultimate slide
    • Bob M: HLA example contains an error, idea was because only 1 code is allowed in a CC, can use codings to provide additional info that isn’t captured in the generic master panel code
    • Clem: large labs want an approach that works with existing systems
    • Swapna: using the panel code for the report is incorrect
    • Clem: look at order catalogs to see what they’re already doing
  • This topic will be continued on a future meeting
    • See chat log for additional comments
    • Please continue this discussion on JIRA


Chat

  • From Kevin Power to Everyone:  10:24 AM
  • From Kevin Power to Everyone:  10:38 AM
  • From Patrick to Everyone:  10:57 AM
    • I agree with Swabna. Our Codes are messy.
    • I don’t think Loinc Panels will help us. We just need proper code for our concepts.
  • From Bret H to Everyone:  10:57 AM
    • they're very clear. we are postcoordinated
  • From James Jones to Everyone:  10:57 AM
  • From Bret H to Everyone:  10:58 AM
    • our codes are clear we are postcoordinated
    • loinc panels have a place but loinc is precoordinated as bob m is saying
  • From Patrick to Everyone:  10:58 AM
    • I like to postcoordinate. But some of our codes are not correct
  • From James Jones to Everyone:  10:58 AM
    • It seems we may need a better-coordinated code for the report itself
  • From Bret H to Everyone:  10:58 AM
    • the code is specific
  • From Patrick to Everyone:  10:58 AM
    • yes jamie
  • From Jamalynne Deckard to Everyone:  10:59 AM
    • Not all are as precoordinated
    • LOINC codes are based on actual requests from labs
  • From Bret H to Everyone:  11:00 AM
    • "using something other than panel code" hmm interesting hope we continue from there
  • From Patrick to Everyone:  11:00 AM
    • +1
  • From Bret H to Everyone:  11:00 AM
    • loinc codes are based on a precoordinated paradigm sufficient in the past. in FHIR we are post coirdinating. if you're using fhir maybe we need a specific FhIr genome report  code
  • From Jamalynne Deckard to Everyone:  11:01 AM
    • It would help to look at Mayo, etc. They are mapping their orders to LOINC
    • And using "generic" codes (post coordinated) for results
  • From Bret H to Everyone:  11:02 AM
    • FHIR genetic report code






Clinical Genomics Reference Docs


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