CG-2023-10-03

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 ) 

1. Kevin Power - CMH - kmpower@cmh.edu  
2. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
4. Raja Kathirvel - Philips - raja.kathirvel@philips.com
5. Arthur Hermann - Kaiser Permanente
6. Patrick McCormick - IMO - pmccormick@imohealth.com
7. Willie Chang - Epic - willie@epic.com 
8.  Aly Khalifa - Mayo Clinic - khalifa.aly@mayo.edu
9. Lloyd McKenzie - Dogwood - lloyd@lmckenzie.com
10. May Terry- MITRE - mayT@mitre.org 
11. Bob Freimuth - Mayo Clinic - freimuth.robert @mayo.edu (x: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-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  

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

• (PW) Confluence was down, has to be voted on next week

Topic 1: Block Vote

Vote: Accept the proposed resolutions

Mover/Seconder: Kevin P. / Bob D.

Discussion: mCODE might not be able to adopt the biomarker profile quickly as mCODE already has its own profiles which are not 100% compatible (BM.component:biomarker-category is not included in mCODEs profiles).

Component:biomarker-category could be made 0..*, allowing downstream profiles to ignore it.

→ item pulled from block after discussion

For-Against-Abstain – 10 - 0 - 0

Motion passes

Pulled from the block vote, requested by Bob D.

• Variant has currently 29 components, many components can confuse implementers. Transcripts could be included in the protein and transcript hgvs. This would mean to remove the existing transcript-ref-seq component.

• The component is already in active usage. Wchang will ask for the use case of having the component in usage.
• There is value in having the transcript in a separate field. 
• Problem: HGVS Strings “don’t have to” include the transcript id, hgvs can’t be validated easily by the current tooling
• Issue was brought up during the May connectathon, motivated by consistency of the profile
• Tempus uses the transcript id components, epic uses them as well.

Motion to vote: Willie C. / May T

Motion approved (in Jira)

Component:biomarker-category should be made 0..*, allowing downstream profiles to ignore it.

Kevin will apply the cardinality change before merging to main.

Motion passes (JIRA)

Topic 2: Review somatic guidance updates

Review next draft of ‘somatic guidance’ (Srikar)

Draft branch should be available mid/end October.

Topic 3: current zulip topics

FHIR profile metadata anyone confused?

Variant Category

Validation issue for HGVS/HGNC code

Would a Filter for unknown CS errors help?
Problem: Might lead to consequential validation errors (e.g. slicing by profile)

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