CG-2023-10-31

HL7 Clinical Genomics Weekly Call - Oct 31, 2023 11:00 AM (US Eastern)

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Minutes

Attending the meeting

https://us02web.zoom.us/j/2980068716?pwd=eG9VOXdjTU43VGpJVGNNNGtqbW1qQT09 

Meeting ID: 298 006 8716 // Passcode: 2020

Agenda

Attendees Sign-in

Presiding Co-Chair (Kevin Power - CMH - kmpower@cmh.edu  —- May Terry - MITRE - mayT@mitre.org ) 

1. Patrick Werner - MOLIT Insitut - pw@molit.eu  
2. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
3. Patrick McCormick - IMO - pmccormick@imohealth.com
4. Raja Kathirvel - Philips - raja.kathirvel@philips.com
5. Bob Freimuth - Mayo Clinic - freimuth.robert @ mayo.edu
6. Srikar
7. Soyean Kim CIDGOH, SFU ska8@sfu.ca
8. Shahim Essaid CU shahim@essaid.com
9. Michael Watkins - UChicago - michaelwatkins@bsd.uchicago.edu 
10. Walter Sujansky - FDA  walter.sujansky@fda.hhs.gov 
11. Willie Chang - Epic
12. Aly Khalifa - Mayo Clinic - khalifa.aly@mayo.edu (:30)
13. May Terry - MITRE - mayT@mitre.org (:30)

Agendas and Important Dates 

https://confluence.hl7.org/display/HL7/2024+January+Cycle 

Subgroup reports

• Information Modeling (IM) (Bob F)
• Minutes:
• HL7 CG Information Modeling - Minutes for Oct 2023 to present
• FHIR (Jamie)
• Minutes:
• FHIR SubGroup Meetings Doc
• tinyurl.com/fhirgenomics 
• Review of biomarker proposal
• OO Work (JD)
• https://jira.hl7.org/browse/FHIR-22147 - Should a reference to device be added as a performer for both Observation and DiagnosticReport 
• More chatter on the above: https://confluence.hl7.org/display/OO/2023-10-16+OO+-+Specimen
• https://jira.hl7.org/browse/FHIR-24863 Ok to reject? 
• IG Maturity (Bret H)
• https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Maturity.20group 
• First meeting held, updating proposed plan. Next step is review within subgroup and finalize. Then there will be a request to present to WG. 

Topic 0: Approval of Minutes from Last Meeting

• https://confluence.hl7.org/display/CGW/CG-2023-10-24   

"You have received the minutes. Are there any corrections to the minutes? (pause) Hearing none, if there are no objections, the minutes are approved"

• Minutes are Approved

Topic 0.5: Congrats Michael Watkins as co-chair elect

Background in clinical genomics, has implemented versions of the IG

Topic 0.75: Discussion with Patient Care RE: ‘genetics profile’ of FamilyMemberHistory

Shahim - in the meeting with PC, we reviewed the profile (extensions for parents, siblings, genetic observations). The PC group was not aware of any usage of the profiles, extensions, value sets (etc …). No decisions yet, but suggestions to ask the community for implementor usage, and if little or none, perhaps we will remove the profile, extensions, value sets. Other discussion - where should these kinds of features (pedigree, linked observations) go in the future? Phenomics IG? New IG? Genomics Reporting? Still unknown.

Patrick: not aware of any implementations

Joel: perhaps we should check with Grant Wood.

Kevin: PC will reach out to the community

Bob F: Not aware of implementations, but we need a champion or driver

Shahim: focus now is what to do with current, then can consider what to do in the future

Patrick: little technical concerns

Topic 1: Review and Vote on the NIB (Kevin)

Changes:

New profile for Molecular Consequences. New profile and guidance for Biomarkers and removing of old TMB and MSI profiles. New artifacts to backport GenomicStudy from R5. New category (genetics) required for all Observation profiles. Terminology updates adopt THO approved URIs and required prefixes. Improve binding on GenomicsReport.code. New operations with more extensive guidance. Updates to all for repeat expansion representation. Reorganize several extensions to reuse base extensions and better align some extensions.

Vote: Accept the NIB as reviewed on the call

Mover/Seconder: Bob F / Patrick W

Discussion: none

For-Against-Abstain – 13-0-0

Motion passes

CHAT:

Helpful info

Vote template

Vote: <describe the motion here>

Mover/Seconder: <makes the motion/second:: Name1/Name 2>

Discussion: <ask for and document discussions>

For-Against-Abstain – <document vote: X-Y-Z>

Motion <passes/fails>

chat.fhir.org (zulip) comments

• Genomics
• If you would like to bring up a topic for discussion, Zulip is the platform and the stream is genomics - https://chat.fhir.org/#narrow/stream/179197-genomics 

Future proposed agenda topics/requests 

• WG members: please use this section to request topics to cover on our WG calls

https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings Needs review/clean up

Jira for change requests

• If you like to open a ticket, Jira is the platform - https://jira.hl7.org/secure/Dashboard.jspa?selectPageId=12002 

External efforts (updates welcome)

• GenomeX/CodeX Accelerator (hosted through CodeX) (Arthur Hermann)
• Arthur to provide updates as needed https://confluence.hl7.org/display/COD/Genomics 
• GA4GH (Global Alliance for Genomics and Health)
• Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
• Variant Representation subgroup (lead by Larry Babb/Alex Wagner)
• See ongoing project board at https://github.com/orgs/ga4gh/projects/5
• VRS 1.3 (structural variation) anticipated by Dec 2021
• Variant Annotation subgroup (lead by Matt Brush and Javi Lopez)
• Working on statements about therapeutic interventions and variant pathogenicity
• https://docs.google.com/spreadsheets/d/1zQU-Yv7gB7IHKIOVsTh-74BwdtgB9KQpKcWkSHZOa-Q/edit
• V0 release: 4 core substatement types + generalized model
• Due "soon"
• Sequence Annotation subgroup (lead by Karen Eilbeck and Shawn Rynearson)
• Clinical & Phenotypic Data Capture Work Stream
• Pedigree Activity (Grant Wood)
• help GA4GH community to understand HL7 Pedigree standards
• https://docs.google.com/spreadsheets/d/1AxRufaSICADO_f9CAhbkVh5dChT4FjHZgvGFFdC-2WI/edit
• Phenopackets
• Under continuous development
• Currently going through the ISO
• G2MC (Grant Wood)
• Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
• Create KB on G2MC website 
• ClinGen/ClinVar (Larry Babb)
• Data Exchange/Platform WG, major driver project of GA4GH GKS
• will discuss further when Larry in on a call
• ONC Sync for Genes (Bob Freimuth)
• ONC website: https://www.healthit.gov/topic/sync-genes
• Phase 5 briefing from Bob Dolin here.
• ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob F)
• Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
• The technical experts group just convened to work on this (mid Aug)
• Since Phenopackets is implementing the GA4GH VR spec, which we are attempting to keep aligned with the CG IM, this work will be of interest to the CG WG
• Arthur to review for other standards that might overlap with CG
• Bob M / Bob F: Liaison through HL7
• Cannot share documents, but we can talk about them
• mCODE (May Terry)
• mCODE STU3 passed ballot approval. Currently in reconciliation with publication ETA in Sept 2023.

WG projects and outreach