CG-2023-10-10

HL7 Clinical Genomics Weekly Call - Oct 3, 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 (Patrick Werner - MOLIT Institut - pw@molit.eu) 

1. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
2.  Soyean Kim- CIDGOH -ska8@sfu.ca
3. JD Nolen - CMH - jlnolen@cmh.edu
4. Walter Sujansky - FDA
5. May Terry - MITRE - mayT@mitre.org 
6. Bob Freimuth - Mayo Clinic - freimuth.robert @ mayo.edu
7. James Patterson - MITRE - jpatterson@mitre.org
8. Aly Khalifa - Mayo Clinic - khalifa.aly@mayo.edu 
9. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org (until :30)
10. Omar Khan - NHS England - omar.khan2@nhs.net 
11. Kevin Power - CMH - kmpower@cmh.edu (joined at :15)
12. Lloyd McKenzie - Dogwood - lloyd@lmckenzie.com (joined at :18)
13. Patrick McCormick - IMO - pmccormick@imohealth.com (joined at :20) 

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 2019 to Jan 2020+ 
• Several weeks off .. will bring back more discussion next time
• FHIR (Jamie)
• Minutes:
• https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/edit?pref=2&pli=1#heading=h.p1e5sxbkjxz9
• 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 
• 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-2023-09-26  
• https://confluence.hl7.org/display/CGW/CG-2023-10-03 

"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 1: Discuss Jan 2024 Connectathon

Use Cases:

1. Genomics Reporting IG (Jan 2024 will be similar to May 2023):

https://confluence.hl7.org/display/FHIR/2023+-+05+Clinical+Genomics

& Operations 

• Improve return Parameters to possibly use IM created resources
• Combining R5(+) with Operations

→ are our tracks “connected” or independent sub-tracks?

→ who will facilitate this ?

Who is interested in attending? Being a track lead?

https://confluence.hl7.org/display/FHIR/Track+Lead+Resources 

1. FHIR Core resources (table below is from last Thursday IM call):

Three ‘tracks’ / use cases:

IG - Genomics Data Exchange

IG - Genomics Operations

FHIR Core - R5+ IM

Who is interested in attending?

James P

Patrick

May

Bob D

Raja

Aly

Soyean

Bob F

Kevin

( Tempus and Epic have expressed interest )

Can we express it as an Ecosystem?

<diagram from May Terry>

Bob F:

Would like to explore some of the overlap in these use cases and the work coming out of IM (updated MolSeq + GenStudy + MolVar + new profiles)

Patrick:

I’d like to talk about technical implications. r5+ needs custom server & client builds, which is not easy to do. So I expect no participation outside of this group

R5 would also need our IG ported to R5 (and published). And im still happy to support the connectathon with servers (hapi servers with IGs preloaded, and a configuration to not give errors for known issues of validation)

May:

R5+ could be less about ‘connections’ and more about exploring and evaluating?

Bob F:

Could we take R4 use cases and map into an R5+ world?

https://docs.google.com/document/d/1A4Uf5wcIr1OvOc62m3guvMjZZKtPo6tr4a_xILjTwYg/edit#heading=h.sw7c803rr3xf

CHAT:

May Terry (MITRE) to Everyone (Oct 10, 2023, 10:18 AM)

https://confluence.hl7.org/display/FHIR/Track+Lead+Resources

Aly Khalifa to Everyone (Oct 10, 2023, 10:19 AM)

I can see black screen

May Terry (MITRE) to Everyone (Oct 10, 2023, 10:22 AM)

https://confluence.hl7.org/display/HL7/HL7+Calendars#514e5f8f-68b1-4d3e-9ff2-00f4eafe7422-156543454

Soyean Kim to Everyone (Oct 10, 2023, 10:31 AM)

I am driving but please count me in

Patrick to Everyone (Oct 10, 2023, 10:50 AM)

I’d like to talk about technical implications.

r5+ needs custom server & client builds, which is not easy to do. So I expect no participation outside of this group

R5 would also need our IG ported to R5 (and published)

And im still happy to support the connectathon with servers (hapi servers with IGs preloaded, and a configuration to not give errors for known issues of validation)

May Terry (MITRE) to Everyone (Oct 10, 2023, 11:00 AM)

https://docs.google.com/document/d/1A4Uf5wcIr1OvOc62m3guvMjZZKtPo6tr4a_xILjTwYg/edit

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