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Chair:  Kevin Power

Scribe: Kevin Power



HL7 Clinical Genomics Weekly Call - 25 Feb 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

Attending the meeting

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Agenda


Attendees Sign-in

Presiding Co-Chair: Kevin Power - Cerner - kpower@cerner.com 

  1.  Arthur Hermann, Kaiser Permanente, Arthur.hermann@kp.org
  2. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  3. Liz Amos - NLM - liz.amos@nih.gov
  4. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  5. Jamie Jones - BCH - james.jones.bch@gmail.com
  6. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  7. Patrick Werner - MOLIT Institut - pw@molit.eu
  8. Stephen Schwartz - Epic - sschwart@epic.com
  9. Bijal Amin - Montefiore/Columbia - bamin@montefiore.org
  10. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  11. Wendy Ver Hoef - NCI/Samvit Solutions - verhoefw@nih.gov 
  12. Bret Heale - Intermountain Healthcare  - bheale@gmail.com 
  13. Grant Wood - Intermountain Healthcare - grant.wood@imail.org
  14. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  15. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 

 

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


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


3/10/20




3/17/20




3/24/20




3/31/20




4/7/20




4/14/20




4/21/20




4/28/20




5/5/20




5/12/20




Working Group Meeting

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

Subgroup reports


  • FHIR (Jamie, Gil)
    • Minutes:

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

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Feb 18 


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

  1. Proposal: include 
    1. http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/find-variants.html and
    2. http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/operations.html

Into the CI of our IG (Jira Ticket: https://jira.hl7.org/browse/FHIR-25250)

Questions:

    • Operation.out uses data type canonical should be Observation?
      • Bob D - Canonical used for a profile of an Observation?
      • Lloyd - No, used for infrastructure, URL as the identifier
      • Patrick - Use OperationDefinition.parameter.targetProfile
      • Bob D - We are using that, but doesn’t render
        • Change the type to Observation
        • Target profile only works if type is a reference (need to ask on IG Creation) - creating an operation, it has an out param that is a resource, how do I declare the resource might meet?
    • What is the appropriate context?
      • [base]/$find-variants
        • Perhaps this makes the most sense for the ‘genomic data server’ use cases.
        • Most flexible.  Consensus is to start here for our first operation.


  • [base]/Observation/$find-variants


        • Returning observations, so this makes sense.  Servers following our IG should have Observations.
        • What is the server is not storing Observations, a VCF only repo for example?  Just a facade to an existing system?


  • [base]/Patient/$find-variants


      • May not be available on all genomic servers, so maybe not a good match.
  • Related - if current operation ‘requires’ a subject (Patient) identifier, perhaps it makes sense to be under Patient, and be called ‘find-subject-variants’ ?  And in the future, an operation that doesn’t require Patient can be under Observation and be called ‘find-?
    • Appropriate name: find-subject-variants
    • Conformance ?  Will systems want to declare conformance differently?  If so, different operations.
    • Consensus is that finding ‘patient’ variants versus ‘all’ are different operations

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


Consensus: This simplification is a good first step, likely will need adjustments going forward.  Ready to vote on combining existing profiles/components into the smaller set of profiles indicated in the attachment.  This will likely trigger an additional set of questions/concerns that will need to be addressed.


  • Genomic Implication (Abstract guidance and components for both types of implication)
  • derivedFrom (reference: Observation/Variant/Haplotype/Genotype)
  • Method (should give guidance on how link to knowledge was obtained)
  • Component: 0..1 93044-6 | Level of Evidence / “clinical validity”
  • ...


   


  • Diagnostic Implication Profile
  • code: TBD | Diagnostic implication
  • Value 0..0
  • Component: 0..1 53037-8 | LL4034-6 (clinical significance)
  • Pathogenic, Likely pathogenic, Uncertain significance, Likely benign, Benign
  • Component: 0..* 81259-4 | unbound (Associated phenotype)
  • Component: 0..* TBD | unbound (Associated cancer)




  • Component 0..1 TBD | (prognosis) May still warrant a separate profile
  • Better Outcome, Poorer Outcome




  • Therapeutic Implication Profile 
  • code: TBD | Therapeutic implication
  • Value 0..0
  • Component: 0..* 51963-7 | unbound (medication-assessed)
  • Component: 0..* TBD | unbound (non-medicinal-therapy-assessed)




  • Component: 0..1 51961-1 | Genetic variation's effect on drug efficacy
  • Component: 0..1 TBD | (Transporter phenotype)
  • Increased function, Normal function, Decreased function, Poor function
  • Component: 0..1 53040-2 | LL3856-3 (Metabolizer phenotype)
  • Component: 0..1 TBD | (High Risk phenotype)
  • Component: 0..* TBD | unbound (contextual cancer type/condition)







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.

Genomics Reporting "Lite" 0.2 ???

Clem

"Focus is on the variant.  Pharmacogenomics and HLA type stuff is out. They add a lot of complexity and tend to be reported on their own and already have a pretty good start.

 

I treated all variants (big/little 0 the same). Did not model either genotype or haplotype. They get in the way of simplicity (but I may get fired because of that).

 

I focused on the 5 ways of specifying a variant.  Some of our fields are convenience fields – don’t add real information, but people like them-so segregated them"

Attachments from 1/28 email

https://docs.google.com/document/d/1eVBvUsezw69qlylWnPAz5bVQpATJ3g_F-gm4dD1ENsU/edit

https://docs.google.com/spreadsheets/d/1UAphpeYuyiQ1ANwusaculVt2vFmSvmaju1TfMv67RU8/edit#gid=1509314707


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