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Chair:  James Jones

Scribe: James Jones


HL7 Clinical Genomics Weekly Call - 20 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 (James Jones - BCH/SMART Health IT - james.jones.bch@gmail.com

  1. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  2. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  4. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  5. Rachel Kutner - Epic - rkutner@epic.com 
  6. Ling teng -BWH - lteng@bwh.harvard.edu
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  8. Dora Walter - MOLIT Institut - dora.walter@molit.eu 
  9. May Terry - MITRE - mayT@mitre.org 
  10. Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu

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


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 13

    • https://confluence.hl7.org/display/CGW/CG-2020-10-13 
    • Motion: Approve minutes as written 
      • Move / 2nd: Dora / Lloyd
      • Discussion:
        •      Need someone to update the ‘Agenda’ links to confluence
      • Vote: (Abstain / Opposed / In Favor):  2 / 0 / 7
      • Result: motion passes

Topic 1: CDA IG for Genetic Testing Reports - Publication Request Document to Move Forward

Background:

This CDA IG originally passed ballot in the September 2012 ballot cycle and published as a DSTU. But because we had no plans on moving this to Normative, we were told it was going to expire after 5yrs. So, we wanted to re-ballot it as Informative to inform any future work in this domain. Amnon Shabo took the lead on this as he was the principal author. It passed the May 2018 ballot, but the reconciliation spreadsheet was never submitted.

This was identified as something we needed to finish off for our WG health metric. Because it was balloted, we could not simply withdraw it. We had to submit the reconciliation spreadsheet so we did.

Reconciliation spreadsheet:
http://www.hl7.org/documentcenter/public/ballots/2018JAN/reconciliation/recon_cdar2_ig_gentestrpt_r1_i1_2018jan.xls

The CG WG already voted to submit this CDA IG for publication:

https://confluence.hl7.org/display/CGW/CG-2020-05-26 

Now we needed to submit a Publication Request document. Bob M started this and Grant Wood completed it. 

The Publication Request document is found here:

https://confluence.hl7.org/display/CGW/CDA+Implementation+Guide+for+Genetic+Testing+Reports+-+Publication+Request 

  1. CG WG reviews the contents of the form. It adds any keywords (if any, not required) to Question 48.
  2. Need to ensure document has note from May vote:


“Please note that this document reflects work done by the Clinical Genomics Work Group (CG WG) prior to the development of FHIR.  It is considered a historical document that is published as an informative artifact, and is not an actively maintained product of the CG WG.”

  • To do:
    • Motion: Approve Publication Document with the above comment starting the “description (element 49)”
    • Move / 2nd:   Bob D / Dora 
    • Discussion:
      •      WG had voted in May to include a note:
        • “Please note that this document reflects work done by the Clinical Genomics Work Group (CG WG) prior to the development of FHIR.  It is considered a historical document that is published as an informative artifact, and is not an actively maintained product of the CG WG.”
        • We will add this note to the description before sending to CDA management
    • Vote: (Abstain / Opposed / In Favor):  0  / 0 / 9      
    • Result: motion passes

Next steps:

  1. Grant has pre-populated Questions 37 and 38. Change date on 38 if needed and add comment to 49
  2. Send Confluence form link to the CDA Management Group (CMG) co-chair Linda Michaelsen linda.michaelsen@optum.com. Their next meeting is November 4th. They may or may not ask for a CGWG rep to answer questions about the request on the call.
  3. When approved by the CMG, send the Confluence form link to Anne Wizauer anne@hl7.org. She will present it to the TSC for final approval. We do not know the date of the TSC call at this time.

Topic 3: 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 4: FSH Migration Update

Topic 5: IG Trackers

  1. FHIR-20978 Ability to include interpretation text/findings and recommendations to Observation 
    1. Discussion:
      1. (from eMERGE work - see tracker notes)
      2. Pending updates to DR from OO - composition text is likely a great candidate here
        1. ‘Canned comments’ not necessarily interpretation
      3. Mullai: Every variant we report on has a comment, and the report itself has separate entered text
      4. JD: that text likely attached to an electronic signature - already in DR. 
      5. Mullai: interpretation text (beside from the overall interpretation), secondary finding text - a few other use cases could go over next week
      6. Frank Genova: is this related to recommendation text? I.e. do not recommend follow-up sequencing on family members. 
      7. Rachel: hoping for examples of these types of comments in FHIR - in relation to the overall order result. Need to keep the verbosity from the labs. Line between human and other sources of interpretation varies between implementations, and may all be sent to the same place.
      8. Mullai: in eMERGE, we had it split up, overall-interpretation obs carried physician text, variant interpretations went (in extensions on) variants and implications
    2. Next Steps:
      1. Define (guidance on and where they go) stock comments vs interpretation
        1. Database hits/code sets from a knowledge source vs
        2. A (either human or CDS)-made interpretation of a number of elements, resulting into something of clinical importance
        3. Agenda item next week
  2. FHIR-19829 - Inclusion of Sanger confirmation information
    1. Discussion:
      1. Previously marked “considered for future use”
      2. eMerge used Observation.note, could be upgraded to a more structured data element. Could be a flag, component, or even a parallel obs-
      3. Currently, labs are implied to only send variants they are confident in
      4. Labelling this confirmation quality would allow labs to send info that may be used for follow-up testing/etc - use case question
    2. Next Steps:
      1. Include guidance if no other element is identified.
  3. FHIR-28403 Provide clear guidance on how to use the IG - Within Content Pages, Detailed Description Pages, and by adding an Examples Page 
    1. Discussion:
      1. (Jamie begun proposal work with volunteers)
      2. Proposal:
        1. Every profile will have a canonical example and a lay-terms introduction
        2. Every defined component & codeableconcept will be represented meaningfully in at least one example
        3. Increase guidance on components that should or should not be used together, as seen in both text and links to examples using alternative supported patterns
        4. Examples will be updated to reflect latest guidance
        5. Additional use case examples:
          1. tumor/normal and/or trio testing (track multiple specimens)
          2. Uncallable regions?
        6. Glossary to be updated prior to publication (not necessarily prior to ballot)
    2. Next Steps:
      1. Continue work!~
  4. FHIR-27864 - DR codes update (Patrick and Liz previously investigating, didn’t cover today)
    1. Discussion:
    2. Next Steps:

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