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Chair:  Kevin Power

Scribe: Kevin Power

HL7 Clinical Genomics Weekly Call - 21 Jan 2020 11:00 AM (US Eastern)


Archive of minutes:

Attending the meeting

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(Presiding co-chair:  Kevin Power - Cerner - )

  1. Bob Freimuth - Mayo Clinic -
  2. Dora Finkeisen - MOLIT Institut -
  3. Michael Stevens - Optum -
  4. Bob Milius - NMDP/CIBMTR -
  5. JD Nolen - Children’s Mercy Hospital -
  6. James Jones - BCH -
  7. Bob Dolin - Elimu Informatics - 
  8. Joel Schneider - NMDP/CIBMTR -
  9.  Perry Mar - Health Catalyst - 
  10. Grant Wood - Intermountain -
  11. Bret Heale - Intermountain Healthcare  - 
  12. Arthur Hermannn - Kaiser Permanente -
  13. Lloyd McKenzie - Gevity -
  14. Mullai Murugan - BCM -
  15. May Terry - MITRE - 




Standing Informational Items

Agendas and Important Dates 

CG Call Date



Important Dates


Patrick W

Last Trackers before publication


Kevin P

Updates before publication


Kevin P

Finalize request and vote to publish!

MCode / Genomics Reporting IG Alignment


Kevin P

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

  • MCode
  • Phenopackets

Review of discussion from FHIR subgroup


Bob M

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


Bob M

Larry Babb / Mullai Murugan

continue AoU discussion

eMERGE - IG debrief


LOINC updates:

Issue #1: Level of Evidence versus Clinical Significance

Issue #2: Tumor Mutation Burden (TMB) concept


Patrick W


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


Bob F

Topic 0: Bob Dolin: GACS FHIR Operations

Topic 1: STU2 Themes (Feedback requested)


Bob F

Topic 1: PGx implications

Topic 2: Phenopackets on FHIR (deferred)

Topic 3: STU2 themes


Bob M

Topic 1: PGx implications (cont)

Topic 2: Phenopackets on FHIR (deferred)

Topic 3: STU2 themes


Kevin P

Topic 1: Larry Babb / Mullai Murugan -  eMERGE IG






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


Patrick W



Kevin P

WGM Agenda

Bob F - Phenopackets on FHIR


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 

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)


Topic 4: Phenopackets on FHIR (Bob F)

Bob F 

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


    Not modeling genetic variants specifically, refers to VR spec 

VR Spec: 

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

  • Community engagement
  • Use Cases and Requirements
  • Evaluation

Project led by GA4GH Clin/Pheno and GKS Work Streams

Anyone is welcome to join the effort.

Current Phenopackets on FHIR IG draft


[Jan 21, 2020 at 10:09:57 AM] Bob Dolin: Grant, here is the link to NHGRI site:

[Jan 21, 2020 at 10:16:36 AM] Liz Amos:

[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:

    Not modeling genetic variants specifically, refers to VR spec

VR Spec:

[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:

[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

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

    (note, this example uses placeholder value “AMP Guidelines” instead of a tier)


    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