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HL7 Clinical Genomics Weekly Call - 13 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

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: WGM Minutes review

Topic 2: O&O JIRA for R4B updates

Topic 3: Updates to background section of FHIR Genomics Guidance

Chat:

Future Topics

Orders for genetic testing

LOINC changes for Level of Evidence / Clinical Significance

Clinical Genomics Reference Docs

Attendees Sign-in

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

  1. Patrick Werner - MOLIT Institut - pw@molit.eu  
  2. Dora Walter - MOLIT Institut - dora.walter@molit.eu
  3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  4. Jamie Jones - BCH - james.jones.bch@gmail.com 
  5. Kevin Power - Cerner - kpower@cerner.com 
  6. May Terry - MITRE - mayT@mitre.org
  7. Bob Dolin  Elimu Informatics - bdolin@elimu.io 
  8.  Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com 
  9.  Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  10.  Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu
  11.  Liz Amos - NLM - liz.amos@nih.gov  
  12.  Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  13.  Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu (at x:12 during CDA)
  14. 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

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



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

Sep 15

Topic 1: Oct 18 - “FHIR IG Proposals Due”

  • Discussion -  
  • Probably doesn't apply to us - new IGs, radically changes 
  • Ours is a STU2 of Genomics Reporting IG

Topic 2: CDA IG for Genetic Testing Reports - Publication

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 

Next steps:

  1. CG WG reviews the contents of the form. It adds any keywords (if any, not required) to Question 48.
  2. If approved on the next CGWG call, Grant has pre-populated Questions 37 and 38. Change date on 38 if needed.
  3. 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.
  4. 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.


  • To do next week:
    • Motion: Approve Publication Document as written 
    • Move / 2nd:   /  
    • Discussion:
      •      
    • Vote: (Abstain / Opposed / In Favor):    /   /       
    • Result: motion  


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 

  • Bob D: 
    • keep the page short
    • highlight groups using it
  • Bob M: highlight that we are actively engaged with external genomics groups to inform the IG
    • Bob M will write up description of actively working with external groups to inform IG
    • Focus of this page should be pointing to the IG. It should be the primary message learned by the reader
  • Kevin -
    • Diagnostic Module
      • update "Genomics Implementation Guidance" to "Overview of Genomics"
      • (bare minimum to update the name and update figure to rename Sequence to MolecularSequence)
      • New JIRA if other changes should be considered

Topic 4: FSH update

  • May: could use more contributors (either dev/authoring or at QA level)
  • Bret: technical dependencies
  • May: no, spreadsheet is used for tracking
  • Kevin:  Sushi 1.0 and Publisher and text editor for developers
  • Jamie: Any plan for doing examples in FSH?
  • Bob: will do Genotype, Haplotype, and HLA examples in FSH
  • Patrick: will this be usable with GoFSH? (StructureDef-->FSHd
  • May: still limited, no support for valuesets, etc


Chat:

  • From Bret H to Everyone: (10:43 AM)
  • 
the rules on FHIR from onc are important drivers.
genetic reporting for what? make sure that is defined

  • From Bret H to Everyone: (10:47 AM)
  • 
it's for exchange that supports clinical decision making, right? not only research transmission of data

  • From Patrick Werner to Everyone: (10:51 AM)
  • 
all use cases: CDS, research, daily care





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



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