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Chair: Bob Milius

Scribe: 



HL7 Clinical Genomics Weekly Call - 7 Jan 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

Join the online meeting (VoIP available with this):

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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: WGM Agenda

Topic 2: eMERGE updates (continued)

Topic 3: Phenopackets on FHIR

Topic 4: STU2 Themes - Feedback requested

Chat

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

Clinical Genomics Reference Docs

Attendees Sign-in

(Presiding co-chair: Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org  )

  1. Michael Stevens - Optum - jmichael.stevens@optum.com
  2. Kevin Power - Cerner - kpower@cerner.com 
  3. Arthur Herman - KP
  4. Daniel Rutz - Epic - drutz@epic.com 
  5. Jamie Jones - BCH - james.jones.bch@gmail.com
  6. Grant Wood - Intermountain Healthcare - grant.wood@imail.org  
  7. Scott Bauer - Mayo - bauer.scott@mayo.edu 
  8.  Stephen Schwartz - Epic - sschwart@epic.com
  9.  Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  10.  Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu
  11. JD Nolen - CMH
  12. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  13. Larry Babb - Broad
  14. Bret Heale - Intermountain Healthcare - bheale@gmail.com 
  15. Bob Dolin - Elimu Informatics - bdolin@elimu.io 



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 (deferred)

Topic 3: STU2 themes


12/10/19

Bob M

Topic 1: PGx implications (cont)

Topic 2: Phenopackets on FHIR (deferred)

Topic 3: STU2 themes


12/17/19

Kevin P

Topic 1: Larry Babb / Mullai Murugan -  eMERGE IG


12/24/19


CANCELED


12/31/19


CANCELED


1/7/20

Bob M

Topic 1: WGM agenda

Topic 2: Larry Babb / Mullai Murugan -  eMERGE IG (continued)

Topic 3: Bob F - Phenopackets on FHIR (deferred)

Topic 4: STU2 Themes - Feedback requested


1/14/20

Patrick W

TMB & MSI


1/21/20

Jamie

Bob F - Phenopackets on FHIR


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.
  • Still pending (Dec 17)


Topic 0: Approval of Minutes from Last Meeting

Dec 17 


Topic 1: WGM Agenda

Topic 2: eMERGE updates (continued)

Larry B / Mullai

Slide Deck

eMERGE FHIR Specification and Implementation Project


Previous notes:


  • Project Review
  • Working on a pilot with JHU / NU - will push report to common server, pilot sites will develop their own dashboard for viewing the details (including PGx CDS with NU)
  • Gap Analysis
  • Review of issue resolutions (completed and pending)
  • Adoption and Direction of IG
  • Other groups/labs/EHRs adopting
  • NMDP - utilize it for HLA, with some additional constraints 
  • Cerner plans to implement subset of IG by late summer of 2020
  • Others listed on Use Case driven implementations
  • Elimu, Phillips, MOLIT (no other comments)
  • Do we need additional, more constrained versions of the IG?
  • Perhaps, NMDP follows a similar strategy
  • The ‘find-variants’ operation is an example of this sort of thing
  • Other gaps
  • Summary text to DR and Observations
  • Take the narrative report and break down into a structured report? eMERGE approach was to ensure this.
  • Current eMERGE approach is an extension (interpretation-summary-text on both DR and Observation).  Is there a better way?
  • Prefer to have a ‘real’ element
  • DR.conclusion (string)?  Not on Observation, need something similar at level of Observation as well.
  • Bret H - statement is like conclusion in diagnostic report, but to be placed in variant observation. 'bundle of interpreted knowledge' will need provenance. The link to a resource like ClinVar is considered not sufficient for this purpose.
  • Concern with extension - is an extra ‘text string’ really structured?
  • If it needs to be included, and not a natural place in the base resource or profile, extension is fine.  Everything relevant gets collapsed into Narrative.
  • Other gaps (not discussed in detail)
  • Disclaimer text (DR extension)
  • Management of secondary findings (may want a simple Yes/No)
  • Validation/Confirmation testing 
  • Definitional Variant Data Types
  • Adding chromosome as a component
  • Representation of Gene coverage (attached BED as related artifact on DR
  • Management of coding systems



Topic 3: Phenopackets on FHIR

Bob F


Topic 4: 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


  • [Jan 7, 2020 at 10:02:45 AM] Bob Milius: 
  • [Jan 7, 2020 at 10:13:04 AM] Kevin Power: 
  • [Jan 7, 2020 at 10:18:14 AM] Kevin Power: 
    • Others can volunteer to scribe :) 
  • [Jan 7, 2020 at 10:23:02 AM] Larry Babb: 
  • [Jan 7, 2020 at 10:39:03 AM] Bret Heale: 
    • what preparation did they do with regards to learning FHIR before looking at the CGIG?
  • [Jan 7, 2020 at 10:39:03 AM] Bret Heale: 
    • for example, there were questions with regards to data types that would have been taught as part of the HL7 courses on FHIR
  • [Jan 7, 2020 at 10:40:45 AM] Bret Heale: 
    • There was also a DSTU3 FHIR proficiency  exam to demonstrate for oneself their preparedness to adopt FHIR
  • [Jan 7, 2020 at 10:50:03 AM] Jamie Jones: 
    • our first draft outlines many optional ways to represent the same information, to encourage users from each subculture to be able to send what they currently have
  • [Jan 7, 2020 at 10:50:03 AM] Jamie Jones: 
    • those different shapes should be presented separately
  • [Jan 7, 2020 at 10:51:53 AM] Jamie Jones: 
    • we should be able to model one off of eMerge, as a starting point
  • [Jan 7, 2020 at 10:53:58 AM] Bret Heale: 
    • +1
  • [Jan 7, 2020 at 10:54:49 AM] Bob Freimuth: 
    • Preach it, Larry!
  • [Jan 7, 2020 at 10:55:19 AM] Bret Heale: 
    • +1...does that mean we don't have to send clinvarIDs?
  • [Jan 7, 2020 at 10:55:19 AM] Bret Heale: 
    • or that the clinvarID is now additional helpful information
  • [Jan 7, 2020 at 10:56:53 AM] Bret Heale: 
    • totally able to replace HGVS with use of the correct data fields in our current IG
  • [Jan 7, 2020 at 11:02:33 AM] Jamie Jones: 
    • thanks all



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