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Chair:  Kevin Power

Scribe: Kevin Power



HL7 Clinical Genomics Weekly Call - 27 Oct 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

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Agenda

Attendees Sign-in

Presiding Co-Chair (Kevin Power - Cerner - kpower@cerner.com

  1. Arthur Hermann, Kaiser Permanente, arthur.hermann@kp.org
  2. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu 
  3. Jamie Jones - BCH - james.jones.bch@gmail.com 
  4. Rachel Kutner - Epic - rkutner@epic.com 
  5. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com 
  6. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
  7. Kevin Roberg-Perez, Bioi, krp@bioi.com
  8. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  9. Alex Mankovich - Philips - alex.mankovich@philips.com 
  10. Daniel Rutz - Epic - drutz@epic.com
  11. Anand Kulanthaivel, Clinical Architecture, anand_kulanthaivel@clinicalarchitecture.com
  12. Mullai Murugan, Baylor College of Medicine, murugan@bcm.edu
  13. Liz Amos - NLM - liz.amos@nih.gov 
  14. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  15. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 

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

6-Oct

Kevin

WGM Review

R4B: JIRA (Dragon Warning)

R5: Genomics Guidance updates


13-Oct

Bob M

CDA publishing
R5: Genomics Guidance updates

Oct 18 - “FHIR IG Proposals Due”

20-Oct

Jamie

IG JIRA proposals


27-Oct

Kevin

Topic 1: NIB

Topic 2: Updates to background section of FHIR Genomics Guidance

Topic 3: FSH Migration Update

Topic 4: eMERGE updates

Nov 1 - NIB deadline for January cycle

3-Nov

Kevin



10-Nov

Patrick


Nov 15 - Initial Content Deadline

17-Nov

Bob M


Nov 17 - Connectathon Proposals Due

24-Nov

Patrick



1-Dec



Dec 6 - Final Content Deadline

8-Dec

Kevin



15-Dec

Bob M



22-Dec

Patrick



29-Dec




5-Jan

Bob M



12-Jan

Kevin



19-Jan

Patrick



Connectathon Jan 13-15, 2021

Virtual WGM Jan 25-29, 2021

External efforts

Subgroup reports



WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

Oct 20

Topic 1: NIB

  1. http://www.hl7.org/Special/committees/tsc/ballotmanagement/EditNIB.cfm?ballot_document_sdo_id=953&Action=Create 
    1. Official name: HL7 FHIR® Implementation Guide: Clinical Genomics, Release 2
    2. Remain UV rather than any realm specific changes
    3. Primary Work Group Contact: 
    4. Publishing Facilitator: not required - Grant Wood
    5. Project insight: 1217 - outdated details but correct id
      1. Projects for our WG: http://www.hl7.org/Special/committees/clingenomics/projects.cfm 
  2. Limit of 500 characters: Please provide a description of the proposed document. This description will be used in both the Announcement of Formation of Ballot Pools and Announcement of Ballot Openings documents.
    1. Brief description, what it does, why we are re-balloting


Genomics is a rapidly evolving area of healthcare that involves complex data structures. There is significant value in sharing this information in a way that is consistent, computable and that can accommodate ongoing evolution of medical science and practice. This guide covers all aspects of human genomic genomics-reporting. At present, this implementation guide focuses solely on data structures - what data should be/might be present and how it should be organized.

  1. Provide a summary of changes of material interest (including all substantive changes) in this document since its last ballot. This description will be used in both the Announcement of Formation of Ballot Pools and Announcement of Ballot Openings documents.
      1. Jamie volunteered to enumerate the substantive changes:


The updated version of this Implementation Guide incorporates community feedback and accomplishes the following:


  • Provides Increased textual guidance and example instances, particularly on the “Variant” and “Region Studied” profiles;
  • Reduces the number of defined “Implication” Observation profiles from 11 down to 3, aligning pharmacogenomic and cancer use cases;
  • Removes the former requirement of a single fixed code for genomics on DiagnosticReport, allowing for more granular codes;
  • Removes some of the least-used components on the “Variant” Observation profile; and
  • Provides an OperationDefinition for “$find-subject-variants”, a standardized way to query and retrieve a subject’s known variants with precise breakpoints in a specified region.



  1. Motion: Approve NIB as stated 
    • Move / 2nd: Arthur / Bob M 
    • Discussion:
      1. None
    • Vote: (Abstain / Opposed / In Favor): 0 / 0 / 15
    • Result: motion passes

Topic 2: Updates to background section of FHIR Genomics Guidance

https://docs.google.com/document/d/139W4FZ2U2w7fk2zcjqT15-_PdgBgiql_bswlXXu3nmo/edit#heading=h.ogvgzwyoicd3

Reminder, here is the current (R5) page:

http://build.fhir.org/genomics.html 

  • Discussion:
    • No major updates since last week, need further review
  • Next Steps:
    • Confirm items that need a home in the IG
    • Bob M to review and elaborate

Topic 3: FSH Migration Update


Topic 4: eMERGE updates use cases for text in clinical genetic reports

Mullai:

<links to overview and example report>

Proposed Recommendation: associated to DiagnosticReport, specific to patient (even if canned). 

Implemented as extension from DR.extension[recommendedAction] -> Task

Interp Summary Text (aka Variant Interp) text: canned text describing variant/gene and associated phenotype (not specific to patient, specific to the variant/gene)

Implemented as custom extension on the Inherited Dis Path profile.

Overall Interp Summary Text: at the level of the entire report, specific to the patient

Implemented as custom extension on Overall Interp profile

Report Comment Text: General comments about the case

Implemented as additional Observation Result on DiagnosticReport with LOINC to indicate comment - would prefer to have on report itself

Chat:

Future Topics

Orders for genetic testing

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

LOINC changes for Level of Evidence / Clinical Significance



Need to consider the following two new motions:

    • Motion A: Use 53037-8 for both germline and somatic variant clinical significance reporting, and add information to the Term description about the different guidelines for somatic and germline variants;  Keep the Answer list the same, but update the type from Preferred to Example


  • 1st/2nd -
  • Discussion -
  • Abstain/Nay/Yea -  / /
  • Result -


(Notes from Jamie:)

  • Want to separate clinical significance from level of evidence.
  • 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