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HL7 Clinical Genomics Weekly Call - 14 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


Agenda

Attendees Sign-in

Presiding Co-Chair (Patrick Werner - MOLIT Institut - patrick.werner@molit.eu): 

  1.  Dora Finkeisen - MOLIT Institut - Dora.Finkeisen@molit.eu 
  2.  Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  4. Liz Amos - NLM - liz.amos@nih.gov 
  5. Stephen Schwartz - Epic - sschwart@epic.com
  6. Bob Milius - NMDP/CBMTR - bmilius@nmdp.org 
  7. Kevin Power - Cerner - kpower@cerner.com
  8. Jamie Jones - BCH - james.jones.bch@gmail.com
  9. Scott Robertson - Kaiser Permanente - scott.m.robertson@kp.org
  10. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  11. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  12. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  13. Lloyd McKnezie - Gevity - lmckenzie@gevityinc.com


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



5/19/20

Bob F

Sync for Genes


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 F)
      • 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 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)
    • Meetings
      • 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
  • 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
    • recently looked into tooling for logical models. Scott and Lloyd have worked on this.
  • FHIR (Jamie, Patrick)
    • Minutes:

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

WG projects and outreach

  • nothing new

Topic 0: Approval of Minutes from Last Meeting

April 7 


Topic 1: Abandoned WG projects



NMD069

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

Connection with Decision Support

564

Next Milestone Date Is: 2014 Jan WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

NMD070

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

Family Health History and Pedigree standard, Release 2

844

Next Milestone Date Is: 2014 Jan WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

NMD072

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

CDA Implementation Guide for Genetic Testing Reports

460

Next Milestone Date Is: 2018 May WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

Bob F: closing these project doesn’t remove the current content, only cleaning up administratively as we are not actively working on them (and haven’t for some time)

Topic 1: Update: 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."


 

I brought the note vs. component topic up on the OO on FHIR call. After a 20 minute debate about things, the group landed on the suggestion of making an extension on Observation.note so you could add in more of a structure (codeableConcept and text) to the information beyond just the free text that Observation.note currently has.

Thoughts?

And other OO related questions at bottom of these minutes (JD)

JD: too complex for complex component/extension. Should be an extension on Obs.note, could evolve into in its own resource in the future.  Using our work as a pilot to show its value.

Kevin: would this still be a complex extension?

JD: would be an Extension on Observation.note to add a code to the Observation.note?

Jamie: note is 0..*, this would be an Extension on Observation itself?

JD: no an Extension on Observation

Lloyd: Extension on Annotation is possible. Comments are often created AFTER the Observation was made. If we are thinking that this should be included in the same Observation and have agreement in the group fitting it into the same Obs would be ok.

Jamie: it is more qualifying methodology, e.g. describing the test which was done. 

Example:

"Heterozygous germline NF2 loss or inactivation is associated with neurofibromatosis type 2 syndrome, which results in the development of vestibular schwannomas, meningiomas, ependymomas, and ocular disturbances (65,66,67). Prevalence for this disorder in the general population is estimated to be 1:25,00067."

Lloyd: could do this as a complex extension, or different simple extension (one per extension type) or giving context through its nesting.
Deep nested extensions are more robust if a user/computer doesn’t know the extension.

Could point to ObservationDefinition from Variant to capture the methodology
Jamie: emerge uses currently PlanDefinition for this
Lloyd: because of the event pattern you can have a Reference to PlanDefinition, a PDF or other describing file. (http://hl7.org/fhir/extension-workflow-instantiatescanonical.html)

As long as we can draw a clear line between Extension.String and the actual value (method, component, etc.) we can use Extensions. Having the Extension on Element would make it hard to to give it a scope, better to have Extension on the specific elements in the Observation.

Next steps: look through requested extensions from use cases and get a short list of where they need to go so we can draw clear lines between method.text, component.interpretation, etc.

eMERGE examples (older, multiple extensions included): https://docs.google.com/spreadsheets/d/1n_u1RQWHmAm8tafIFioR0g3HFLqKdvZF/edit#gid=2105486159

https://emerge-fhir-spec.readthedocs.io/en/latest/ (latest public guidance)

Bonus Topic 1.5 Specimen:

V2 to FHIR Mapping 

Questions from OO Specimen Call for CG about SpecimenPurity and subTypeCode

https://confluence.hl7.org/display/OO/Specimen+Call+Notes+April+13%2C+2020

OO: Adding specimen.purity, other additions

Seeking CG perspective for specimen subtypes:

Clem: might be presumptive to know what should go here depending on where in the workflow this resource is generated. A lot of concepts that might go here are actually results of multiple tests… 

Next steps: review possible specimen subtypes, prepare some guidance on what shouldn’t go here, or at least how to tie these “results” to observations that explain them if needed.

Topic 2: Observation.derivedFrom 

Currently:

There is no slice to point from Obs.derivedFrom to MolecularSequence. Slice should be added?

Discussion:

Bob M: deriving from MolSeq currently throws a warning as we don’t have a slice for MolecularSequence. Also there is no easy way to link to a profiled version of MolSeq in a derived Profile.

Patrick: We have to seperate the two issues: 1) adding a slice 2) deriving an IG and enforce a reference to a profiled MolSeq. We are currently discussing 2) on zulip in the IG commiter stream, should probably take this to a public stream.

Jamie: the missing slice was related to technical errors while creating the IG.

THE FOLLOWING TOPICS WERE NOT DISCUSSED:

Topic 3: how to link to region studied?

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

Discussion:

Topic 4: Uncallable subregions in a region studied

FHIR-25296 Uncallable subregions in a region studied

Discussion:

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.



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