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Chair:  Patrick Werner




HL7 Clinical Genomics Weekly Call - 24 Nov 2020 11:00 AM (US Eastern)

Agenda

Attendees Sign-in

Presiding Co-Chair (Patrick Werner - MOLIT Institut - pw@molit.eu

  1. Jamie Jones - BCH - james.jones.bch@gmail.com   
  2. Liz Amos - NLM - liz.amos@nih.gov  
  3. Rachel Kutner - epic - rkutner@epic.com 
  4. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  5. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  6. Kim Peifer - Flatiron Health - kim.peifer@flatiron.com
  7. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu (at x:40)


Standing Informational Items

Agendas and Important Dates 

CG Call Date

Co-Chair

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

Important Dates

6-Oct

Kevin

WGM Review

R4B: JIRA (Dragon Warning)

R5: Genomics Guidance updates


13-Oct

Bob M

CDA publishing
R5: Genomics Guidance updates

Oct 18 - “FHIR IG Proposals Due”

20-Oct

Jamie

IG JIRA proposals


27-Oct

Kevin

Topic 1: NIB

Topic 2: Updates to background section of FHIR Genomics Guidance

Topic 3: FSH Migration Update

Topic 4: eMERGE updates

Nov 1 - NIB deadline for January cycle

3-Nov

Kevin

Topic 1: Updates to background section of FHIR Genomics Guidance

Topic 2: FSH Migration Update

...


10-Nov

Patrick


Nov 15 - Initial Content Deadline

17-Nov

Bob M


Nov 19 - Connectathon Proposals Due

Bob D: pharmacogenomics pipeline connectathon track?

24-Nov

Patrick



1-Dec



Dec 6 - Final Content Deadline

8-Dec

Kevin



15-Dec

Bob M



22-Dec

Patrick



29-Dec




5-Jan

Bob M



12-Jan

Kevin



19-Jan

Patrick



Connectathon Jan 13-15, 2021

Virtual WGM Jan 25-29, 2021

External efforts

  • GA4GH (Global Alliance for Genomics and Health)
    • GA4GH news
    • Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
    • Clinical & Phenotypic Data Capture Work Stream
  • 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)
    • 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
    • Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
    • https://emerge-fhir-spec.readthedocs.io/en/latest/ 
    • Pilot project has completed
    • Manuscript in preparation
    • eMERGE 4 sites have been announced, will focus on polygenic risk scores
    • NHGRI will continue to support work with FHIR and our IG
    • Mullai: mostly wrapped up, just have to do the manuscript (almost done)
  • mCODE (May Terry)
    • Better representation of prognostic factors, including serum tumor markers  in the Genomics related elements.
    • STU1 published - http://hl7.org/fhir/us/mcode/
    • Initial feedback from some reviewers (UCSF, Princess Margaret of Toronto) for mCODE enhancements:
    • working on STU2 version, would like to better align with CG IG next release
    • WGM - mCode update, would like to move time slot to later in the week
    • Someone created a genomics report using mCode, made some assumptions. It would be good to see how they interpret it;  perhaps discuss at WGM as an example; test based on 21 gene panel, but it doesn't report variants; should this be treated a genomics report? or as a tumor marker test? actually a gene expression test. Should gene expression test be considered a genetic test?
    • May T: last internal sprint, going through FSH migration; evaluating roadmap to mCODE STU2 release to use Genomics Reporting IG more directly; should there be an interim release of Genomics Reporting IG after STU2 ballot? mCODE can't derive from an IG that won't validate. Needs a published snapshot, this could be a ballot snapshot. Genomics Reporting IG needs to become more stable. Revisit in Jan 2021.

Subgroup reports


  • OO Work (JD)


WG projects and outreach

  • Guardant Health interested in CG on FHIR

Topic 0: Approval of Minutes from Last Meeting

Nov 17

Topic 1:  hotfix for IG Creator:

Unofficial release:

https://1drv.ms/u/s!AiblQ6yMWNkSm5oPQozBJAEJYY7QGA?e=hPtwEF

Topic 1.5:  Ballot Timeline and options

Freeze for January ballot is December 6

Have been aiming to submit this cycle (knew we may not make it)

Published version:

http://hl7.org/fhir/uv/genomics-reporting/general.html

Current version:

http://build.fhir.org/ig/HL7/genomics-reporting/general.html 

+$find-subject-variants Operation

+reduction in number of implication profiles (still need review)

+pending changes… (IG lite needs more attention as well)

Bob D:
What would be missing if we ballot in January compared to May?

Jamie:
the already vote on tracker items should be able to make it in. Implications and “annotations” (e.g. effects) are not as stable as intended.

Decision is up to the WG.

Bob D:
Still a lot unfinished parts in the IG, is there a pressure to ballot? 

Topic 2:  Tracker items to vote on

https://jira.hl7.org/browse/FHIR-29780  update variant-inheritance list

  • Discussion: aligning this request with the variant-inheritance component, whose answer list is currently sequence ontology (but a broader sense of ‘inheritance’ than we’d like as it overlaps with genomic source class). Remains a TBD-coded component

Resolution Description:
Update the answer list for Variant component 'variant-inheritance' to the last 4 terms of https://loinc.org/LL4025-4/ , less 'Other', with an extensible binding

Resolution Vote: Jamie Jones / Anand Kulanthaivel : 7 - 0 - 1


https://jira.hl7.org/browse/FHIR-29781  update allelic phase list guidance - structures are unchanged

  • Discussion:

Bob F: will the VS binding be changed?

Jamie: no, same VS

Resolution Description:

  1. create an illustrative example of sequence phase relation using our defined list http://build.fhir.org/ig/HL7/genomics-reporting/ValueSet-seq-phase-relationship.html
  2. remove old list from glossary + documentation, point out that we don't use the example list on the code.
  3. reach out to LOINC to request a corresponding new answer list to https://loinc.org/82120-7/ for allelic phase.

Resolution Vote: Jamie Jones / Bob Freimuth : 7 - 0 - 0


https://jira.hl7.org/browse/FHIR-28403  add better examples + "IG Lite" variant guidance

  • Discussion:
    Liz: maybe the proposal should be more concrete and/or include action items
  • Current draft: Variant component groups v2 
    • May started on examples
    • Jamie started on the Variant component groups
    • Patrick will add/update onco examples
    • specific disease screening with ACMG secondary findings: ?
    • PGx panel reporting : ?
  • Bob F: Tracker is more an objective than a concrete proposal, should wait for concrete PRs before voting
    • NOT VOTED ON TODAY

=== END OF CALL ===

https://jira.hl7.org/browse/FHIR-26945  clarify 'context' vs 'risk-of' for associated phenotype & associated cancer components

  • Discussion:

https://jira.hl7.org/browse/FHIR-27747  New Component for Functional Effect

  • Discussion:

Chat:

Me to Everyone (5:01 PM)

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit#heading=h.llov6sxiaux3

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit#heading=h.llov6sxiaux3

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit#heading=h.llov6sxiaux3

Liz Amos (NLM) to Everyone (5:06 PM)

do we need a quorum to be able to vote?

James Jones to Everyone (5:12 PM)

(Co-chair +2 = quorum in our SOPs)




Future Topics

Orders for genetic testing

  • How to define ServiceRequest.code
  • Multiple tests per report?

LOINC changes for Level of Evidence / Clinical Significance



Need to consider the following two new motions:

    • Motion A: Use 53037-8 for both germline and somatic variant clinical significance reporting, and add information to the Term description about the different guidelines for somatic and germline variants;  Keep the Answer list the same, but update the type from Preferred to Example


  • 1st/2nd -
  • Discussion -
  • Abstain/Nay/Yea -  / /
  • Result -


(Notes from Jamie:)

  • Want to separate clinical significance from level of evidence.
  • Motion B: Consider creating new codes for diagnostic, therapeutic, and prognostic significance (see Quest screenshot, LabCorp report) and/or type of evidence (see Baylor report)
    • 1st/2nd -
    • Discussion -
    • Abstain/Nay/Yea -  / /
    • Result - 
  • Need to create an example to understand the meaning of this change/concepts.
  • Need a caretaker for this topic.

Clinical Genomics Reference Docs







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