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Chair:  Bob Milius

Scribe: Bob Milius



HL7 Clinical Genomics Weekly Call - 10 Dec 2019 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: Bob Milius - CIBMTR/NMDP - bmilius@nmdp.org  )

  1. Arthur Herman - Kaiser Permanente - arthur.hermann@kp.org  
  2. Scott Robertson - Kaiser Permanente - scott.m.robertson@kp.org
  3. Liz Amos - NLM - liz.amos@nih.gov 
  4. Jamie Jones - Boston Children’s Hospital - james.jones.bch@gmail.com
  5. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu
  6. Bret Heale - Intermountain Healthcare - bheale@gmail.com 
  7. Stephen Schwartz - Epic - sschwart@epic.com 
  8. Bob Dolin - Elimu Informatics - bdolin@elimu.io  
  9. May Terry - MITRE - mayT@mitre.org 
  10.  Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  11. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  12.  Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu (at x:20)
  13. Kevin Power - Cerner - kpower@cerner.com (at 20 after the hour - after vote on minutes approval)
  14. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.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

10/1/19

Patrick W

Last Trackers before publication


10/8/19

Kevin P

Updates before publication


10/15/19

Kevin P

Finalize request and vote to publish!

MCode / Genomics Reporting IG Alignment


10/22/19

Kevin P

How do we want to manage engagement with other genomics related initiatives?

  • MCode
  • EMERGE
  • Phenopackets

Review of discussion from FHIR subgroup


10/29/19

Bob M

Using Draft CG FHIR Spec for AoU: Larry Babb / Mullai Murugan


11/5/19

Bob M

Larry Babb / Mullai Murugan

continue AoU discussion

eMERGE - IG debrief

Tentative:

LOINC updates:

Issue #1: Level of Evidence versus Clinical Significance

Issue #2: Tumor Mutation Burden (TMB) concept


11/12/19

Patrick W



11/19/19

Kevin P

Topic 0: STU2 Themes - Feedback requested

Topic 1: New temporary co-chair

Topic 2: Level of Evidence / Clinical Significance

Topic 3: Tumor Mutation Burden (TMB) concept


11/26/19

Bob F

Topic 0: Bob Dolin: GACS FHIR Operations

Topic 1: STU2 Themes (Feedback requested)


12/3/19

Bob F

Topic 1: PGx implications

Topic 2: Phenopackets on FHIR

Topic 3: STU2 themes


12/10/19

Bob M

Topic 1: PGx implications (cont)

Topic 2: Phenopackets on FHIR

Topic 3: STU2 themes


12/17/19

Kevin P

Topic 1: Larry Babb / Mullai Murugan -  eMERGE IG
Topic 2: Bob F - Phenopackets on FHIR (?)


12/24/19


CANCELED


12/31/19


CANCELED


1/7/20

Bob M



1/14/20

Patrick W



1/21/20

Jamie



1/28/20

Bob M



International Conference & Working Group Meeting

Sydney, Australia | February 2 - 7, 2020

Register Today

CG WG will be meeting Tue Q3 & Q4, and all-day Wed and Thu

External efforts

Subgroup reports


  • FHIR (Jamie, Gil)
    • Minutes:

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

WG projects and outreach

from previous meetings:


  • Dev Days in Amsterdam
  • Press Release for HL7 newsletter
  • Group should identify better criteria for how individual names get listen on the IG itself in the future.
  • Should also get help from Grant Wood to get more exposure for the IG once out.


Topic 0: Approval of Minutes from Last Meeting

Nov 26

Topic 1: Continue from last week… Adequate PGx (Bret Heale, Kevin Power)


  • See slides sent to the CG listserv on Dec 2, 2019
  • Reviewed current IG structure on slide 5, which ties Medication Implications (Observation) to Medication Usage Implications (Task)
  • Attached to variant, haplotype, or genotype
  • Task resource has reasonReference, hard coded to cardinality 1; we submitted a tracker to have this changed
  • Slide 9: RelatedArtifact can be a link to a service (e.g., Infobutton)
  • Slide 10: discussion about creating LOINC codes and extensible value sets for level of evidence
  • Slide 11: discussion about the Narrative element, specifically level of effort by the lab to produce this and potential differences between how the lab wants to use the field vs. FHIR intentions for it
  • Slides 12-13: proposed changes: use components instead of profiles for Medication Implication
  • Action: review Med Transporter (is this needed if we don’t have values for it?)
  • We should structure statements, not model biology
  • Why is Med Impl an Observation?  Does O&O agree with this usage?
  • It works for current reporting
  • Action: follow up with O&O
  • Slide 15: this proposal simplifies implementation as it is only a single profile


  • Start at slide 16
    • Implementation - Querying Efficiency
      • Can search easily for all medication implications
    • Other semantic simplification opportunities
      • “One place” to put all therapeutic annotations, “one place” to put all diagnostic
    • Semantic concern on keeping the profile names as values, leaving value blank and only populating the components may be clearer.
    • Discussed opportunity for more granular medication-assessed modelling. Do we need to add drug class? May need input from pharmacy wg. 
    • Bob M: profound comment re: scope (genomics reporting vs workflow or downstream uses such as CDS)


Topic 2: Phenopackets on FHIR (Bob Freimuth)

  • DEFERRED


Topic 3: STU2 Themes - Feedback requested

Themes: 

https://docs.google.com/document/d/17r-HNm-gyqthepU40gqh39uYK9PV3HmBl1VM-vW6TuY/edit 

Brain dump: https://docs.google.com/document/d/1SYdzxanCgkwzhhBJCBrguZ6H8HdjQFjG_l2nufAkCGU/edit#

  • Collecting themes and volunteers to work on them.

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.

Clinical Genomics Reference Docs