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HL7 Clinical Genomics Weekly Call - 10 Mar 2020 11:00 AM (US Eastern)


Archive of minutes:

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Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - 

  1. James Jones - BCH - 
  2. Liz Amos - NLM - 
  3. Bob Dolin - Elimu Informatics - 
  4. Bob Freimuth - Mayo Clinic -
  5. Dan Rutz - Epic -
  6. Arthur Hermann - Kaiser Permanente - 
  7. Lloyd McKenzie - Gevity -
  8. Ling teng -
  9. Rachel Kutner - Epic - 
  10. Joel Schneider - NMDP/CIBMTR -
  11. JD Nolen - Children’s Mercy Hospital -
  12. Scott Bauer - Mayo Clinic -
  13.  Kevin Power - Cerner - (:17)

Standing Informational Items

Agendas and Important Dates 

CG Call Date



Important Dates





Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)

Topic 2: Update/Discussion on Implication Profiles (Jamie)



CG IG Lite: Liz & Clem
Attachments from 1/28 email


Bob M

1: CMS/ONC rules 

2: Vote on operations for IG

3: STU2 of IG






Bob M






Bob M


Working Group Meeting

May 16-22, 2020   • San Antonio, Texas

Register Today!

CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday

External efforts

Subgroup reports

WG projects and outreach

  • MOLIT will start a inter-institutional virtual tumor board project with 5 hospitals 2020/04/01 the whole persistence layer is FHIR with extensive usage of our IG. Our lab partner CEGAT ( will send the Diagnostic Reports using our profiles.

Topic 0: Approval of Minutes from Last Meeting

March 3 

Topic 1: Request regarding interoperability and information blocking rules released by CMS and ONC

"This is a request for your review of new regulations incorporating HL7 standards, and your feedback to the HL7 Policy Advisory Committee. 

Final interoperability and information blocking rules were released by CMS and ONC today. Please read the rules and consider 

(1) their impact on your work group and HL7; 

(2) any clarification of the rules that HL7 should request; and 

(3) how the relevant content should be presented to your work group and its stakeholders. Your input is important, and we look forward to receiving this feedback from you within 10 days, by 19 March 2020.

CMS Final Rule

Medicare and Medicaid Programs; Patient Protection and Affordable Care Act; Interoperability and Patient Access for Medicare Advantage Organization and Medicaid Managed Care Plans, State Medicaid Agencies, CHIP Agencies and CHIP Managed Care Entities, Issuers of Qualified Health Plans in the Federally Facilitated Exchanges and Health Care Providers 

Rule Text:

Fact Sheet:

ONC Final Rule

21st Century Cures Act: Interoperability, Information Blocking, and the ONC Health IT Certification Program

Rule Text:

Fact Sheet:

HL7 and its standards -- such as FHIR® -- are central to these proposed rules

CMS and ONC seek to:

  • Improve the interoperability of electronic health information, primarily through standards-based APIs;
  • Enhance care coordination;
  • Foster innovation that promotes patient access to and control over their health information; and
  • Put forward a framework for implementing the information blocking provisions of the 21st Century Cures Act.

Initial comments?

Topic 2: Vote -- Genomics FHIR Operations

  • Description
    • Proposal that the next version of the IG include FHIR Operations for a genomic data server (as further described here:
    • (An example would be an '$extract-variants' operation, which takes patient ID, chromosome, and region as input, and returns a FHIR Genomics diagnostic report containing variants in the requested region. This proposal is to include operations in the next IG. The specific operations to be included will be subsequently fleshed out).
  • Proposed Resolution
    • Resolution is to merge the $find-subject-variants operation ( into the Master branch. (Additional change proposals to the operation are still welcome, and will be managed in the Master branch).
    • Description of $find-subject-variants operation:
      • Use this operation to retrieve variants with precise endpoints from a specified genomic region for a specified patient. If the range in question has been studied, the operation returns variants overlapping the region. If the patient or the specified region has not been studied, the operation returns a 404 error.
    • IN Parameters:
      • subject [1..1]
      • genomicRefSeq [1..1]
      • range (numeric within the ref seq) [1..1]
    • OUT Parameters:
      • regionStudied [0..1]
      • variant [0..*]
      • sequencePhaseRelationships [0..*]
    • Additional resolutions include:
      • operation name: $find-subject-variants
      • context: [base]/$find-subject-variants
      • include discussion of normalization and liftover, including expectations of the server
    • Details of the operation are here:
  • Motion : see Proposed Resolution above
    • 1st/2nd:  Bob D/ Kevin P
    • Discussion
      • Arthur: Is this on the server or branch?
      • Jamie: this is moved into the master branch (proposed for including into next version), re genomic server, this a capability that a server might support.
      • Kevin P: what is being proposed is a good starting point.
      • Bob F: we may want to get additional feedback, something on the operations page itself
      • Jamie: a lot of our content should be flagged on the next version for highlighted changes for comment
      • Bob M: reminder that this is a specification for an api, not the logic/code to carry them out
      • Kevin: hesitant to flag all changes in the new STU, might be overwhelming?
    • Vote (Abstain / Opposed / In Favor):   0 / 0 / 13
    • Motion passes

Topic 3: STU 2 of Genomics Reporting IG

    • Ballot for Jan 2021 (?)
      • Bob M asked for guidance on when to ballot next STU2 for a FHIR IG. Lloyd replied
        • Primarily one of two things: 
          • there's been a significant enough set of changes, that community review is again warranted
          • you want to boost the ballot level
          • Also, there's an expectation for 2 full STU cycles before you can take something normative.
      • This will be continue to be based on FHIR R4
      • Oct 16 -- IG Proposals due (probably doesn't apply?)
      • Nov 1 -- NIB due, IG substantially complete
      • Nov 14 -- submit initial content
      • Nov 22 - Dec 4 -- QA
      • Dec 4-8 -- Content change QA application
      • Need to settle on STU2 content
      • Dan Rutz
        • people talking about going past genomic results and including biomarkers

  • groups of variants?

      • assessment based biomarker?
      • may include in next round of the IG
    • Jamie
      • including groups of variants as biomarker
      • discussed a bit in Atlanta, what was tested vs what was found
    • Arthur
      • look at real world reports how they do it
    • Dan
      •  need to look at this now before it gets too fractured
    • Bob D
      • can groups for variants a biomarker
    • Dan
      • would like to model a Condition.evidence that references a biomarker
      • Additional level of authority for a statement
    • JD
      • yes, agree
    • Bob D
      • do we need pre coordinated codes for evidence of condition?
    • Bob M
      • Does this belong in the Genomics Reporting IG, or should it be a new IG describing CDS and workflow how lab results are used.
    • Dan
      • will submit a tracker on this


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.

FHIR-25296 Uncallable subregions in a region studied

FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

FHIR-19844 PGx High Risk Allele Medication Impact is confusing

Clinical Genomics Reference Docs

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