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


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 


CG Call Date


Agenda https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings

Important Dates



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

Subgroup reports

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

Issue Type





Resolution Description

Change Request


Mark Kramer

HGVS should be string, not code

Not Persuasive

Proposing to keep HGVS as a CodeSystem to allow for validation (which is not functional currently, but we hope will be again soon).

There are other CodeSystems that have grammer options:



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.

Change Request


May Terry

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.
Add it as a new component slice to the Variant profile with tbd-code.

  • 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)

Change Request


James Jones

More guidance on biomarkers


New CodeSystem for MolecularBiomarkerCategory

New ValueSet for MolecularBiomarkerCategory CodeSystem.

New ValueSet for MolecularBiomarkerCodes (with example LOINC codes)

New profile for MolecularBiomarker (MB)

Remove TMB and MSI profiles

GenomicImplication can deriveFrom MB

New examples of MolecularBiomarker for TMB, MSI, Implication that refers to MB, and more

Update general page guidance (replacing TMB and MSI with MB)

Update diagrams that refer to TMB/MSI to refer to MB instead

See exact changes here:


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)


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

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

External efforts (updates welcome)

  • GenomeX/CodeX Accelerator (hosted through CodeX) (Arthur Hermann)
  • GA4GH (Global Alliance for Genomics and Health)
  • 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.

WG projects and outreach

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