Clinical Genomics
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Chair:  Patrick Werner

Scribe: Patrick Werner


HL7 Clinical Genomics Weekly Call - 10 Nov 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

Presiding Co-Chair (Patrick Werner - MOLIT Institut - pw@molit.eu ) 

  1. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 
  2. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  3. Rachel Kutner - Epic - rkutner@epic.com 
  4. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  5. Kevin Roberg-Perez - Bioi - krp@bioi.com
  6. Jamie Jones - BCH - james.jones.bch@gmail.com 
  7. Liz Amos - NLM - liz.amos@nih.gov  
  8. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  9. May Terry - MITRE - mayT@mitre.org 
  10. Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu
  11. Bret Heale - intermountain - bheale@gmail.com 
  12. Dora Walter - MOLIT Institut - dora.walter@molit.eu
  13. Bob Dolin - Elimu Informatics - bdolin@elimu.io
  14. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org

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

Topic 1: Updates to background section of FHIR Genomics Guidance

Topic 2: FSH Migration Update

...


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



  • OO Work (JD)
    • DiagnosticReport work to handle complex reports 
      • Proposal to use Composition to handle the sections (the style) and connect this to DiagnosticReport via presentedForm <- in R5
      • https://jira.hl7.org/browse/FHIR-29258 
      • Talking about this on OO on FHIR calls (Tuesdays 2PM EDT)
        • Question on inclusion of multiple DRs here (and not just multiple Obs)
        • Composition approach may assist interpretation/notes


WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

Nov 03

Topic 1: Sign-In Sheets/Minutes

  • We are currently capturing the minutes and participants with google docs, with a manual migration to confluence.
  • To reduce the workload the Minutes and attendance could be captured directly in confluence. 
  • This implies that every participant must have a confluence login to sign in.
  • Discussion:
    • Joel: Host can also sign-in participants
    • Joel: Viewers cannot see edits live (?)
    • Bret: Capturing email addresses and institutions is important (could be captured in confluence as well?)
    • Bob M: CDA management group uses pre-populated table of regular attendees (with names, institution, email), simple check box to indicate when present; guests added manually
    • Jamie: concurrent editing is much better in confluence, but live edits can only be viewed in editing mode. Participants not in edit mode will see the updates after a “save”.
    • No anticipated major issues (by those in attendance) to moving to confluence

Topic 2: Updates to background section of FHIR Genomics Guidance

Last Week next Steps included:


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: -
  • Next Steps: 
    • Applying the new text the R5 build, create PR 

Topic 3: QA Feedback: FSH'ism update


  • Discussion:
    • Jamie: Looking good, examples are creating errors, most major errors are addressed now

Topic 4: open Issues to be applied

These issues are already voted on, ready to be applied:

https://jira.hl7.org/issues/?filter=12415&jql=project%20%3D%20%22FHIR%20Specification%20Feedback%22%20AND%20(Specification%20%3D%20%22Genomics%20Reporting%20(FHIR)%20%5BFHIR-genomics-reporting%5D%22%20OR%20%22Work%20Group%22%20%3D%20%22Clinical%20Genomics%20%5Bcg%5D%22)%20AND%20status%20in%20(%22Resolved%20-%20change%20required%22)%20ORDER%20BY%20cf%5B11302%5D%20DESC%2C%20created%20DESC

Discussion:

https://jira.hl7.org/browse/FHIR-24906 

Bret: ist this meant for computational use or human consumption?

Meant to display to humans, codings still useful for translations. Will include guidance (with the how to identify a variant guidance)

Bob D.:

Jira Ticket about wild-type, Bob volunteers to create/update the guidance text.

Topic 5: Sync for Genes Phase 4 Call for Demonstration Sites

The ONC is seeking health IT companies, genomic medicine organizations, researchers, and clinical institutions such as academic medical centers, ambulatory clinics and hospitals to participate as demonstration sites in Sync for Genes Phase 4.

For questions or to be considered as a site, complete the Demonstration Site Profile and submit to becky.angeles@carradora.com by Friday, January 8, 2021.

See full announcement and other program information at https://www.healthit.gov/topic/sync-genes

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



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