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Chair:  Kevin Power

Scribe: Kevin Power



HL7 Clinical Genomics Weekly Call - 17 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

Join the online meeting (VoIP available with this):

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Agenda


Attendees Sign-in

(Presiding co-chair: Kevin Power - Cerner - kpower@cerner.com  )

  1. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  2. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  3. Bret Heale - Intermountain Healthcare - bheale@gmail.com  
  4. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  5. May Terry - MITRE - mayT@mitre.org
  6. Bob Dolin - Elimu Informatics - bdolin@Elimu.io
  7. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
  8. Jamie Jones - BCH - james.jones.bch@gmail.com
  9. Larry Babb - Broad - lbabb@broadinstitute.org
  10. Mullai Murugan - BCM - murugan@bcm.edu
  11. 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


12/24/19


CANCELED


12/31/19


CANCELED


1/7/20

Bob M


Topic X: Bob F - Phenopackets on FHIR (?)


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.
  • Still pending (Dec 17)


Topic 0: Approval of Minutes from Last Meeting

Dec 10 

Topic 1: eMERGE updates

Larry B / Mullai

Slide Deck

https://docs.google.com/presentation/d/16ED3p4_1NSd7KAW0R-YeCDys8gYnuG045tuawj3T3v0/edit?usp=sharing

  1. Project Review
    1. https://emerge-fhir-spec.readthedocs.io/ - not complete, but in process documentation that shows details about how eMERGE has used the IG
    2. 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)
  2. Gap Analysis
    1. Review of issue resolutions (completed and pending)
  3. Adoption and Direction of IG
    1. Other groups/labs/EHRs adopting
      1. NMDP - utilize it for HLA, with some additional constraints 
      2. Cerner plans to implement subset of IG by late summer of 2020
      3. Others listed on Use Case driven implementations
        1. Elimu, Phillips, MOLIT (no other comments)
    2. Do we need additional, more constrained versions of the IG?
      1. Perhaps, NMDP follows a similar strategy
      2. The ‘find-variants’ operation is an example of this sort of thing
  4. Other gaps
    1. Summary text to DR and Observations
      1. Take the narrative report and break down into a structured report? eMERGE approach was to ensure this.
      2. Current eMERGE approach is an extension (interpretation-summary-text on both DR and Observation).  Is there a better way?
        1. Prefer to have a ‘real’ element
          1. DR.conclusion (string)?  Not on Observation, need something similar at level of Observation as well.
            1. 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.
        2. Concern with extension - is an extra ‘text string’ really structured?
        3. 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.
    2. Other gaps (not discussed in detail)
      1. Disclaimer text (DR extension)
      2. Management of secondary findings (may want a simple Yes/No)
      3. Validation/Confirmation testing 
      4. Definitional Variant Data Types
      5. Adding chromosome as a component
      6. Representation of Gene coverage (attached BED as related artifact on DR
      7. Management of coding systems


Topic 2: Phenopackets on FHIR

Bob F

DEFERRED TO JAN 7

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

[Dec 17, 2019 at 10:45:37 AM] Jamie Jones: it is one of the themes on our list

[Dec 17, 2019 at 10:45:37 AM] Jamie Jones: but no proposals have come up yet

[Dec 17, 2019 at 10:50:13 AM] Jamie Jones: Kevin and I were recently thinking about using it as Observation. value for the implications

[Dec 17, 2019 at 10:51:16 AM] mullai: Jamie - are you referring to the simplified IG subset

case studies

[Dec 17, 2019 at 10:52:00 AM] Jamie Jones: we are currently considering proposals to simplify/improve/combine our implication profiles

[Dec 17, 2019 at 10:52:19 AM] Bret Heale: also there is the string field conclusion in diagnostic report

[Dec 17, 2019 at 10:52:34 AM] Jamie Jones: specifically, the current values may move into components, freeing up the observation.value for other use

[Dec 17, 2019 at 10:52:36 AM] mullai: we actually needed to input the text for Observations

[Dec 17, 2019 at 10:52:36 AM] mullai: our options were Narrative and Notes and this summary interpretation text was not a good fit

[Dec 17, 2019 at 10:56:12 AM] Jamie Jones: could consider repurposing overall interpretation.value for this, or a text component on that profile. each grouper may have one interpretation

[Dec 17, 2019 at 10:56:13 AM] Bret Heale: "bundle the package of knowledge" needs provanance

[Dec 17, 2019 at 10:57:26 AM] mullai: isn't the grouper more of a navigational resource

[Dec 17, 2019 at 11:01:32 AM] Jamie Jones: yes, would rather have it on the implications themselves

[Dec 17, 2019 at 11:02:24 AM] mullai: Jamie - re your comment - we are currently considering proposals to simplify/improve/combine our implication profiles

[Dec 17, 2019 at 11:02:24 AM] mullai: we will have as

 use case

[Dec 17, 2019 at 11:03:23 AM] Jamie Jones: I'll be on zulip!



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