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Chair:  Kevin Power

Scribe: Kevin Power



HL7 Clinical Genomics Weekly Call - 21 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

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

  1. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  2. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu
  3. Michael Stevens - Optum - jmichael.stevens@optum.com
  4. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
  5. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  6. James Jones - BCH - james.jones.bch@gmail.com
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  8. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  9.  Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  10. Grant Wood - Intermountain - grant.wood@imail.org
  11. Bret Heale - Intermountain Healthcare  - bheale@gmail.com 
  12. Arthur Hermannn - Kaiser Permanente - arthur.hermann@kp.org
  13. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  14. Mullai Murugan - BCM - murugan@bcm.edu
  15. May Terry - MITRE - mayT@mitre.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

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

Kevin P

WGM Agenda

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


WG projects and outreach

from previous meetings:


  • 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

Jan 14 


Topic 1: WGM Agenda

https://confluence.hl7.org/display/CGW/2020-01+CG+WGM+Agenda 

Joint with BRR - Phenopackets

May not have FHIR-I rep on Tuesday Q4

No session Thursday Q3/Q4

Topic 2:  Include chromosome as a component to Variant 


Motion: Add new component for ‘chromosome-identifier’ as component to Variant profile

  • LOINC code for the component: 48000-4, AnswerList VS: LL2938-0

    Move / 2nd:  May / Mualli

    Discussion: None

    Vote (Abstain / Opposed / In Favor): 0 / 0 / 14 

    Result: Motion Passes

Topic 3: Update/Discussion on Implication Profiles (Jamie)

https://docs.google.com/document/d/1SYdzxanCgkwzhhBJCBrguZ6H8HdjQFjG_l2nufAkCGU/edit#heading=h.n5eokak2o6ca


Skipping

Topic 4: Phenopackets on FHIR (Bob F)

Bob F

https://drive.google.com/open?id=1Yj4zauf6tlbl37s0nh9oBvv6zUfmuvoR 

What is it?

  • Schema from GA4GH, links Patient info, Disease, Detailed phenotypic descriptions, genetic data


Goal - exchange detailed phenotypic data across clinical and research systems

Clinical Testing/Interp - labs receive little/no phenotypic info

Define a common exchange format for other DBs

Computable metadata for Publications

Patient Matchmaking - distributed query to find similar patients

Exchange data from Research → Clinical

Schema: https://phenopackets-schema.readthedocs.io/en/latest/index.html 

    Not modeling genetic variants specifically, refers to VR spec 

VR Spec: https://vr-spec.readthedocs.io/en/1.0/ 

NIH/NLM Award to GA4GH - support development Phenopackets on FHIR

  • Community engagement
  • Use Cases and Requirements
  • FHIR IG
  • Evaluation


Project led by GA4GH Clin/Pheno and GKS Work Streams

Anyone is welcome to join the effort.

Current Phenopackets on FHIR IG draft

https://aehrc.github.io/fhir-phenopackets-ig/profiles.html

Chat

[Jan 21, 2020 at 10:09:57 AM] Bob Dolin: Grant, here is the link to NHGRI site: https://www.genome.gov/Health/Genomics-and-Medicine/Polygenic-risk-scores

[Jan 21, 2020 at 10:16:36 AM] Liz Amos: https://confluence.hl7.org/display/BRR/2020+02+WGM+Agenda

[Jan 21, 2020 at 10:18:43 AM] Bret Heale: notes of each quarter will be online?

[Jan 21, 2020 at 10:43:06 AM] Bret Heale: the phenotype data needs to exist in a computable format in the EMR to begin with

[Jan 21, 2020 at 10:44:20 AM] Bret Heale: does that mean micorganisms and viruses are in scope?

[Jan 21, 2020 at 10:47:01 AM] Bret Heale: I think we should put our resources together with the G4GH phenopacket effort and be more tightly part of their effort

[Jan 21, 2020 at 10:47:52 AM] Arthur: Brett - Bob is doing that - but I think you are saying that this needs to become a larger effort for the entire working group

[Jan 21, 2020 at 10:47:54 AM] Bret Heale: we're struggling with impact statements, as Jamie alluded to the phenopacket effort overlaps with this.

[Jan 21, 2020 at 10:49:08 AM] Bret Heale: Yes. I think that our limited development resources (Bob, Bob, Kevin, Patrick, Jamie, myself) should be actively working on the Phenopackets team

[Jan 21, 2020 at 10:49:08 AM] Bret Heale: or something like that : ^ )

[Jan 21, 2020 at 10:49:08 AM] Bret Heale: a little radical, but developing together should be better than alignment

[Jan 21, 2020 at 10:49:08 AM] Bret Heale: I mean easier

[Jan 21, 2020 at 10:49:56 AM] Kevin Power: Schema: https://phenopackets-schema.readthedocs.io/en/latest/index.html

    Not modeling genetic variants specifically, refers to VR spec

VR Spec: https://vr-spec.readthedocs.io/en/1.0/

[Jan 21, 2020 at 10:50:14 AM] Bret Heale: phenopackets effort is better resourced than we are, right? : ^ )

[Jan 21, 2020 at 10:50:23 AM] May Terry: agree with Bret on putting our resources into working with the Phenopackets team.  This is indeed a hot-topic and one I'd like to further explore for extending mCODE.

[Jan 21, 2020 at 10:50:23 AM] May Terry: I'd like to help in any way if possible. :-)

[Jan 21, 2020 at 10:52:14 AM] Jamie: VR spec itself may be an easier target for alignment while they get this rolling

[Jan 21, 2020 at 10:52:46 AM] Bret Heale: @jamie VR spec? variant...: ^ )

[Jan 21, 2020 at 10:52:46 AM] Bret Heale: i'm more concernd about lab based phenotyping information. and knowledge resources. but i guess we gotta be willing to give : ^ )

[Jan 21, 2020 at 10:54:22 AM] Jamie: One issue is Phenopackets seem to point to GA4GH variant representations, which we haven’t gone over in terms of FHIR integration

[Jan 21, 2020 at 10:54:54 AM] Bret Heale: some of us have looked ; ^ ) largely mappable

[Jan 21, 2020 at 10:54:54 AM] Bret Heale: not too worried about the most fundamental parts

[Jan 21, 2020 at 11:01:35 AM] Bret Heale: thanks!

[Jan 21, 2020 at 11:01:55 AM] Jamie: Do we have a Link for the working FHIR IG doc?

[Jan 21, 2020 at 11:01:55 AM] Jamie: We CSIRO’s version back in Atlanta

[Jan 21, 2020 at 11:01:55 AM] Jamie: We saw*

[Jan 21, 2020 at 11:02:28 AM] Kevin Power: https://aehrc.github.io/fhir-phenopackets-ig/profiles.html

[Jan 21, 2020 at 11:02:41 AM] Jamie: Great!


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