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HL7 Clinical Genomics Weekly Call - 24 Mar 2020 11:10 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

Attending the meeting

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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: Tumor/normal examples for review (Patrick)

Topic 2: STU 2 of Genomics Reporting IG (Continued …)

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. Rachel Kutner - Epic - rkutner@epic.com
  2. Patrick Werner - MOLIT Institut - patrick.werner@molit.eu
  3. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu
  4. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  5.  Stephen Schwartz - Epic - sschwart@epic.com
  6. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  7. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org 
  8.  Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  9. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  10.  Peter Muir - Peter@PjmConsultingLLC.com
  11. Liz Amos - NLM - liz.amos@nih.gov 
  12.  Kevin Power - Cerner - kpower@cerner.com 
  13.  Jamie Jones - BCH - james.jones.bch@gmail.com
  14. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  15.  
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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




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)
    • GA4GH news
      • Having virtual connect meeting starting today,
        • agenda has changed, still hope to include some working sessions
        • Bob will report back after the meeting
    • Variant Representation (formerly VMC) (lead by Larry Babb/Alex Wagner/Reece Hart)
    • Variant Annotation
    • Phenopackets on FHIR
    • Pedigree Activity (Grant Wood)
      • 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
    • G2MC (Grant Wood)
      • Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
      • Create KB on G2MC website 
    • HLA reporting (Bob)
      • 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
  • 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 (but not posted yet)
    • ACI manuscript is in press
    • Phase 3 has started - more details to be announced soon
  • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob)
    • Meetings
      • March 30 - April 3, 2020 in Arlington, VA
      • Liz will check to see whether the meeting is open or ISO members only
      • Scott R: must be a member of a national member organization to attend
      • Clem - request from them to sign-off for transmission of big data (eg BAMs), may have problems with use case.
      • Looks to be virtual only
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • MCODE

Subgroup reports

  • Information Modeling (IM) (Bob F)
    • Minutes: https://docs.google.com/document/d/15kBa3HqxQfwwe0Uwgx3UNashTIanpGRiyRVbimE_j3A/edit#
    • Draft model docs: https://docs.google.com/document/d/1Wys14HNJAEB_YJ-EeDPAKX50_oxiDqAKi3WD4wlfjbk/edit
    • Export of model (http://gcds.mayo.edu/HL7CG/IM_190604/model.html)
    • Currently looking at tooling to develop a logical model from our conceptual model
      • 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
    • Model-Driven Architecture (MDA)
      • 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)
    • Arthur: does this mean people will have trouble implementing IG will have trouble because it isn't aligned with model?
      • Bob F: No, just trying to illustrate more explicitly how our conceptual model maps into the FHIR space
  • FHIR (Jamie, Gil)
    • Minutes:

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

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

March 10 


Topic 1: Tumor/normal examples for review (Patrick)

  • https://gist.github.com/patrick-werner/5d715f00c4c0e096be35debcb0962267#file-first-demo
  • New extension on Observation (multi-specimen), multiple instances of the extension (references tumor and normal), and then Observation.specimen references tumor
  • Could use .focus() ?
    • Still need to know which specimen is which (tumor / normal)
  • What about multiple Observations?
    • Could do 3 (one of tumor, one for normal, one for ‘both’)?
    • Typically only send 1 result (related to the tumor)
  • Questions outstanding:
    • What are these observations saying?
    • Are they associated with the specimens correctly?
    • Concerns about ‘true nature’ of how the specimens are linked versus some real world ‘how is it done today’
    • Conversation can continue on Zulip

No Topics after this line were discussed.

Topic 2: STU 2 of Genomics Reporting IG (Continued …)

  • copied from last week, possibly continue discussion...
  • Review of discussion from FHIR subgroup:

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

Specific topics from FHIR subgroup to point out:


  • Next steps:
  • Jamie: Log a tracker to update guidance on index.html
  • Bob M draw up draft based on ‘newcomer’ slides from Sydney
  • Keep it to items unique to our IG where possible
  • Address “what’s necessary for me to read?” issue
  • More narrative isn’t necessarily better narrative
  • Bob D: can we point out ‘conformance narrative’ vs framework information… flag pages and sort them based on that
  • Joel: more guidance around our examples and use cases - a cookbook
  • Bob M: examples with descriptive narrative
  • Jamie: Log a tracker to classify and separate guidance between “conformance” and more unnecessary items



Tooling support for “required” genomic code system bindings - to test at connectathons

    • Possible validators for HGVS
    • Online tools are difficult for many stakeholders to integrate with and support…
      • Lloyd: 1 Concern is performance, doing validation directly within terminology server is much preferred
    • Bob M: Grahamme had shown support for including clinvar in particular, effort was previously made to integrate
    • Joel: HAPI 5 supposed to have better integration with external terminology services


  • Next steps:


    • Collect popular online (and offline if we can find any) tools and review


  • Definitional vs Observational:
    • Our findings are all observational information, though they log definitional information in various values and components.
      • Need to strengthen arguments here and make a stronger position
      • Collapsing multiple reference sequences and/or HGVS components??
        • Group to review pros and cons offline and circle back with Clem
  • Implications
    • Show how current examples will look under change



  • Ballot for Jan 2021 Timeline
    • This will be continue to be based on FHIR R4
    • Oct 16 -- IG Proposals due (probably doesn't apply?)
    • Nov 1 -- NIB due, IG substantially complete
    • Nov 14 -- submit initial content
    • Nov 22 - Dec 4 -- QA
    • Dec 4-8 -- Content change QA application
    • Need to settle on STU2 content




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



       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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