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Chair:  Robert Freimuth

Scribe: Robert Freimuth  

HL7 Clinical Genomics Weekly Call - 26 Nov 2019 11:00 AM (US Eastern)


Archive of minutes:

Attending the meeting

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(Presiding co-chair: Bob Freimuth - Mayo Clinic - )

  1. Bret Heale - Intermountain Healthcare -
  2. Arthur Hermann - KP -
  3. Jamie Jones - BCH -
  4. Liz Amos - NLM - 
  5. Patrick Werner - MOLIT Institut - 
  6. Dora Finkeisen - MOLIT Institut - 
  7. Bob Dolin - Elimu Informatics - 
  8. Joel Schneider - NMDP/CIBMTR -
  9. Bob Milius - NMDP/CIBMTR -
  10. Scott Robertson - Kaiser Permanente -
  11. Kevin Power - Cerner - (joined at :20 after the hour, just after minutes approval)
  12. Deepak Sharma - Mayo Clinic -

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


Bob M


Larry Babb / Mullai Murugan

eMERGE - IG debrief






Bob M


Patrick W



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:

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.
  • Potential new sponsored products:
  • Bob D - Set of API (FHIR based) for a Genomics Data Server.  What is the process to bring this to the WG?
  • Motivation: Not all servers will have FHIR backend, want to define set of standardized operations for how to interact with genomic servers, similar to products put out by terminology
  • Question: scope - should this be balloted as separate a separate item/IG or included in current IG
  • on agenda in November, Bob D will share proposal ahead of time
  • possibly have subgroup for this effort

Topic 0: Approval of Minutes from Last Meeting

Nov 19 

Topic 1: FHIR Operations for a Genomic Data Server (Bob Dolin)

  • Slides: GACS API Dolin.pdf
  • Link to Jira ticket related to this topic FHIR-25250
  • Proposal: add a set of FHIR operations into the next version of the IG
  • Historical context
    • Many discussions during scientific conferences leading up to that publication… this concept has been around for a long time!
    • Starren 2013 (one of the first publications describing an ancillary genomics system)
    • GACS: similar to PACS for radiology images
    • Walton (Geisinger): presentation at HIMSS: GACS + phenotypes
  • FHIR operations
    • E.g., BAM/VCF processing on the fly
    • Server may need to play more active role informulating response content (not a simple query and retrieval)
    • Supports data normalization
    • Bret: align to GA4GH service standards (see posting for public comment today)
    • Patrick: “GACS” as a name - did we agree on it?
  • Analogy to terminology servers
    • Need “higher order conceptual model” for underlying data structures (e.g., IM subgroup) and metadata as well as for operations
    • Correct. Need to be very prescriptive about query params and return structures. How the server performs that operation can be a black box.
    • Code systems can have their own rules about how to implement things
    • Currently undefined
    • Abstract away from the underlying data
    • Implicit in the operations (e.g., retrieve concept code) is an underlying data model
    • How do we know what is supported by the GACS when the data (e.g., files, content, annotation) changes so frequently?
    • Bob M: operations describe an API, not logic?
    • Joel S: terminology services can be complex (e.g., value set expansions)
    • Patrick: we must also describe the logic behind the operation
    • Patrick: “extract variants” operation - what is the scope?
  • See slides for examples of possible use cases and starting points

Topic 2: STU2 Themes - Feedback requested


Brain dump:

  • Collecting themes and volunteers to work on them.


[11/26/2019 10:28:17 AM] Bret Heale: G4GH operations as part of the proposed work? as in writing a FHIR query 

[11/26/2019 10:29:14 AM] Patrick: did we ever agree on “GACS” as a name? An EHR also could include FHIR Endpoints supporting our IG, including these operations.

[11/26/2019 10:35:36 AM] Bob Milius: When defining an operation, we are basically describing the API, not the logic/code to do the operation, correct?

[11/26/2019 10:38:26 AM] Bret Heale: too Bob M. Yes

[11/26/2019 10:38:26 AM] Bret Heale: but example implementations are pretty useful. Not sure if an example implmentation is included

[11/26/2019 10:40:18 AM] Joel Schneider: terminology service is not necessarily a small space - can get weird when talking about value set expansions, closures, or even subsumption

[11/26/2019 10:40:18 AM] Joel Schneider: concept maps ...

[11/26/2019 10:43:05 AM] Patrick: @Bob M:

We also have to describe the logic behind the operation.

[11/26/2019 10:46:20 AM] Kevin Power: Just a note to everyone ~ 14 mins left :) 

[11/26/2019 10:46:32 AM] Bret Heale: +1

[11/26/2019 10:46:38 AM] Bob Freimuth to Kevin Power: have we ever been known to end early?

[11/26/2019 10:46:39 AM] Bret Heale: to practical implementation

[11/26/2019 10:50:32 AM] Bob Milius: Can fhir operations be federated to multiple fhir servers and their local genomic data?

[11/26/2019 10:50:32 AM] Bob Milius: I’m thinking of collaborative work

[11/26/2019 10:56:54 AM] Bret Heale: interesting question. I would say yes, but to me that would be under the hood of the specific API server

[11/26/2019 10:57:21 AM] Bob Dolin: GA4GH's htsget operation is an example of a federated API

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