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HL7 Clinical Genomics Weekly Call - 07 Apr 2020 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall 

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

Archive of minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=25559917&src=contextnavpagetreemode

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Agenda

Attendees Sign-in

Standing Informational Items

Agendas and Important Dates

External efforts

Subgroup reports

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Topic 1: Ability to include interpretation text/findings and recommendations to Observation (FHIR-20978)

Topic 2 : cont from FHIR subgroup meeting

Chat

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

FHIR-25296 Uncallable subregions in a region studied

FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

FHIR-19844 PGx High Risk Allele Medication Impact is confusing

Clinical Genomics Reference Docs

Attendees Sign-in

Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org): 

  1. Patrick Werner - MOLIT Institut - patrick.werner@molit.eu 
  2. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu 
  3. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  4.  Kevin Power - Cerner - kpower@cerner.com 
  5.  Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  6. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  7. JD Nolen - Children’s Mercy Hospital -  jlnolen@cmh.edu 
  8.  Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  9.  Liz Amos - NLM - liz.amos@nih.gov 
  10.  Stephen Schwartz - Epic - sschwart@epic.com
  11. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  12. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  13.  
  14.  
  15.  
  16.  
  17.  


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

2/18/20

Patrick



2/25/20

Kevin

Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)

Topic 2: Update/Discussion on Implication Profiles (Jamie)


3/3/20

Kevin

CG IG Lite: Liz & Clem
Attachments from 1/28 email


3/10/20

Bob M

1: CMS/ONC rules 

2: Vote on operations for IG

3: STU2 of IG


3/17/20

Kevin

1: Reminder - CMS/ONC rules 

2: STU2 of IG (cont...)


3/24/20

Bob M

Tumor/normal examples to review 


3/31/20

Patrick



4/7/20

Bob M



4/14/20

Patrick



4/21/20

Bob M



4/28/20

Patrick



5/5/20

Bob M



5/12/20

Patrick



Working Group Meeting

Cancelled! May 16-22, 2020   • San Antonio, Texas

Register Today!

CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday

External efforts

  • GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)
    • Having virtual connect meeting starting today,
      • agenda has changed, still hope to include some working sessions
      • Bob will report back after the meeting
      • help GA4GH community to understand HL7 Pedigree standards
      • Many researchers currently using PED format - family history statement, simple, not as robust as FHIR
      • Grant is co-chairing that effort
      • Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
      • Create KB on G2MC website 
      • Driver project = GEM Japan
      • Modeling and exchanging HLA results in the Japanese population
      • HLA nomenclature vs discovery of new alleles
      • Connecting to the HLA work done by NMDP within this WG
      • GA4GH news
      • Variant Representation (formerly VMC) (lead by Larry Babb/Alex Wagner/Reece Hart)
      • Variant Annotation
      • Phenopackets on FHIR
      • Pedigree Activity (Grant Wood)
      • G2MC (Grant Wood)
      • HLA reporting (Bob F)
    • ClinGen/ClinVar (Larry Babb, Bob Freimuth)
      • Data Exchange/Platform WG, major driver project of GA4GH GKS
      • will discuss further when Larry in on a call
    • CDISC PGx (Dorina B.)
      • CDISC involved in standardizing reporting of data to regulatory bodies. E.g. Pharma communication to FDA - looking to include genomics in research reporting.
      • Clem: no specific insight - Transcelerate Biopharma (https://transceleratebiopharmainc.com) group fairly active in FHIR. FDA has active interest in FHIR.
    • ONC Sync for Genes (Bob Freimuth)
      • ONC website: https://www.healthit.gov/topic/sync-genes
      • Final report for Sync for Genes Phase 2 has been finalized and approved (in the process of being)
      • ACI manuscript is in press
      • Phase 3 has started - more details to be announced soon
    • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob)
      • March 30 - April 3, 2020 in Arlington, VA
      • Looks to be virtual only
      • Bob F - attended, alike to HL7 meeting for first time, mostly status reports, at end a number of proposals were voted on by different countries and adopted
      • Meetings
    • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
    • MCODE

    Subgroup reports

    • Information Modeling (IM) (Bob F)
      • Ideally would like to computationally derive it from the conceptual model, but will likely have to create most of it manually
      • Scott is evaluating options
      • Conceptual model => logical model => physical model
      • FHIR profiles/IGs would be expressed as a physical model
      • Logical: language-neutral model for implementation, specifies relationships, cardinalities, data types that will map down to the physical layer
      • Logical model provides a traceable link between our conceptual IM and the physical layer (e.g., FHIR)
      • Bob F: No, just trying to illustrate more explicitly how our conceptual model maps into the FHIR space
    • FHIR (Jamie, Patrick)
      • Minutes:

    https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/

    WG projects and outreach

      Topic 0: Approval of Minutes from Last Meeting

      March 31 

      Topic 1: Ability to include interpretation text/findings and recommendations to Observation (FHIR-20978)


        • "As highlighted in the attached test reports, we include textual findings/interpretations and recommendations in a genetic report. For the eMERGE reports, while mapping to draft CG IG spec, these textual interpretations span multiple FHIR Observation profiles in our implemention e.g. Referencing file "highlighted..." test report, text highlighted in grey and yellow would be a fit for general profiles like obs-overall and obs-inh-dis-path; text highlighted in green would be a fit for PGx profiles and the recommendations text highlighted in blue is a recommendation for the provider but not exactly a recommended action; it would be up to the provider to decide on the recommended action.
          Considering the need for including this kind of interpretative/summary text (this is not the same as the "text" narrative element) spans multiple Observation resources, it would be very helpful if Interpretation Text and Recommendations were added as Narrative or String elements to the obs-base resource itself."

          • This was submitted last year (2019-04-25)
          • Deferred to after publication of STU1 of IG, now re-opened
          • Options mentioned in issue comments
            • human readable summary of entire resource instance
            • not really appropriate
            • KP  - not sure if this is where it should go
            • Clem - why is doesn't work?
            • KP - implementation issues?
            • JD - are we overloading it? should it move to DR?
            • see above for ob.text
            • concerned with if this appropriate
            • use case is generalizable and will be used by others, so OO should address this.
            • suggest propose to OO a poison pill that forces them to fix it.
            • Observation.text (Narrative)
            • Observation.note (0..* Annotation)
            • DR.text
            • DR.presentedForm
            • new component under observation with valueString
            • could this just be the value of the observation? 
            • extension - add when needed
            • Need for distinct requirements for each use case, may be appropriate for components
            • KP: addition guidance may be included as a standalone observation and can be derivedFrom in another observation. Patrick agrees this is viable.
            • Patrick: do we need additional qualifier? e.g., method info, guidance info
            • Clem: maybe use Patrick's suggestion of complex extension.
            • KP: not in favor of using .note, unless we can distinguish what kinds of notes are included
            • include extension in our IG until OO decides on including it as a base extension.
            • extension - would NOT have to create codes for each type of note
            • component - would need to have a separate code for each type of note
            • Patrick - complex extension would have a type with a valueString. Can be reused.
            • KP - keep it unbound, provide guidance how to use (narrative? annotation? string?)
            • KP - .note has datatype of annotation
            • Proposed motion: KP will write up a proposed motion to use complex extension on zulip for comments, will vote on this next week.
            • Bob F raises his hand (and a shield for the rotten veggies that are about to be hurled at him)
          • discussed in this recent thread
          • related zulip thread on methodology 


          Topic 2 : cont from FHIR subgroup meeting

          Would be done via Zoom, 24/7 Connectathon. Official Information to come

          https://confluence.hl7.org/display/FHIR/2020-05+Connectathon+24


          from CG FHIR subgroup minutes:

        • Connectathon track review  https://confluence.hl7.org/display/FHIR/2020-05+Genomics
        • Jamie: Important to check query ability as well

          Bob M: wants to test out his HLA IG, or provide insight on how to constrain our IG to make a use-case specific IG.

          Bob D: testing subject-variant operation could be an option. Could provide a server which supports the operation. 

          Bret: A Scenario: searching for the same Variant  with different Variant Identifiers (ClinVar, hgvs, …) on the Repository would be nice.

          • Bob D - will go forward and make the Genetic Data Server to test operation. Would be great to have a partner to test this. Jamie & Bret are interested
          • Patrick - evaluate use cases of current build IG, how east to query information, eg need all driver mutations displayed for practitioners.
          • Bob M - working on profiling CG IG for more constrained use cases - issues?

          Chat


          Future Topics

          LOINC changes for Level of Evidence / Clinical Significance

          See these notes from Swapna: LOINC Significance vs Evidence and TMB code proposal.pdf

          Level of evidence 

          https://loinc.org/93044-6/

          https://loinc.org/LL5356-2/

          See these previous call notes for earlier discussion:  CG-2019-08-27

          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
        • https://r.details.loinc.org/AnswerList/LL4034-6.html
        •        o  1st/2nd -

                 o  Discussion -

                 o  Abstain/Nay/Yea -  / /

                 o  Result -

          (Notes from Jamie:)

          Want to separate clinical significance from level of evidence.

          Sites want to continue to use the tier system as well.

          Ask: a therapeutic somatic variant: 

          E.g. from http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncologyexamples-r4.xml

          (note, this example uses placeholder value “AMP Guidelines” instead of a tier)

          Profile: http://build.fhir.org/ig/HL7/genomics-reporting/somatic-predictive.html

          Code: somatic-predictive (TBD LOINC)

          Value: E.g. Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response

          Component: Level of evidence - 

          Code: 93044-6, 

          Value: from LOINC Answer List LL5356-2 (preferred) CAN USE TIER SYSTEM HERE

          Component: medication

          Component: cancer

          • 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)

                 o  1st/2nd -

                 o  Discussion -

                 o  Abstain/Nay/Yea -  / /

                 Result - 

          Need to create an example to understand the meaning of this change/concepts.
          Need a caretaker for this topic.

          FHIR-25296 Uncallable subregions in a region studied

          FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

          FHIR-19844 PGx High Risk Allele Medication Impact is confusing

          Clinical Genomics Reference Docs

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