HL7 Clinical Genomics Weekly Call - Oct 3, 2023 11:00 AM (US Eastern)
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Attending the meeting
Meeting ID: 298 006 8716 // Passcode: 2020
Presiding Co-Chair (Patrick Werner )
- Kevin Power - CMH - email@example.com
- Bob Dolin - Elimu Informatics - firstname.lastname@example.org
- JD Nolen - Children’s Mercy Hospital - email@example.com
- Raja Kathirvel - Philips - firstname.lastname@example.org
- Arthur Hermann - Kaiser Permanente
- Patrick McCormick - IMO - email@example.com
- Willie Chang - Epic - firstname.lastname@example.org
- Aly Khalifa - Mayo Clinic - email@example.com
- Lloyd McKenzie - Dogwood - firstname.lastname@example.org
- May Terry- MITRE - mayT@mitre.org
- Bob Freimuth - Mayo Clinic - freimuth.robert @mayo.edu (x:20)
Agendas and Important Dates
CG Call Date
Review and approve WGM minutes (Kevin)
Review draft of ‘somatic guidance’ (Srikar)
Block Vote (Kevin)
Review draft of ‘somatic guidance’ (Srikar)
Review Connectathon Proposals and ideas
Review of pathogen genomics (Soyean)
Review and vote on NIB (Kevin)
Connectathon Track Proposal Review
Nov 12 - NIB deadline
November 17 - 2024JAN FHIR Connectathon Proposals Due
Dec 5 - Content freeze (STU3 IG)
Dec 19 - Content QA complete
Dec 22 - Ballot opens
HL7 FHIR Connectathon
Jan 16, 2024 to Jan 18, 2024 - Online/Virtual
January Working Group Meeting
Jan 29, 2024 to Feb 2, 2024 - Virtual Event
- Information Modeling (IM) (Bob F)
- HL7 CG Information Modeling - Minutes for Oct 2019 to Jan 2020+
- Several weeks off .. will bring back more discussion next time
- FHIR (Jamie)
- OO Work (JD)
- https://jira.hl7.org/browse/FHIR-24863 Ok to reject?
- IG Maturity (Bret H)
- 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
"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
HGVS should be string, not code
Proposing to keep HGVS as a CodeSystem to allow for validation (which is not functional currently, but we hope will be again soon).
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
Pulled from the block vote, requested by Bob D.
protein-hgvs is missing an equivalent protein-ref-seq component.
There isn't a LOINC code that accurately describes this, so we need a tbd-code and separately submit a LOINC code request for new term.
- 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)
More guidance on biomarkers
New CodeSystem for MolecularBiomarkerCategory
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
Would a Filter for unknown CS errors help?
Problem: Might lead to consequential validation errors (e.g. slicing by profile)
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>
chat.fhir.org (zulip) comments
- 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
- 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
- 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
- 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)
- 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.