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HL7 Clinical Genomics Weekly Call - 17 Mar 2020 11:00 AM (US Eastern)


Archive of minutes:

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Presiding Co-Chair (Kevin Power - Cerner - ): 

  1. Patrick Werner - MOLIT Institut - 
  2. Bret Heale - Intermountain HealthCare - 
  3. Jamie Jones - BCH -
  4. Liz Amos - NLM - 
  5. Lloyd McKenzie - Gevity -
  6. Joel Schneider - NMDP/CIBMTR -
  7. Bob Milius - NMDP/CIBMTR -
  8. Bob Freimuth - Mayo Clinic - 
  9. Rachel Kutner - Epic - 
  10.  Clem McDonald - NLM - 
  11.  Scott Bauer - Mayo -
  12.  May Terry - MITRE - 
  13.  Stephen Schwartz - Epic -
  14. Bob Dolin - Elimu Informatics - 
  15.  Ning Xie - BWH -
  16. Perry Mar - Health Catalyst - 

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



1: Reminder - CMS/ONC rules 

2: STU2 of IG (cont...)


Bob M




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 10 

Topic 1: Reminder - 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: STU 2 of Genomics Reporting IG (Continued …)

  • Review of discussion from FHIR subgroup: 

Specific topics from FHIR subgroup to point out:

  • Next steps:
  • Jamie: Log a tracker to update guidance on index.html
  • Bob M draw up draft based on ‘newcomer’ slides from Sydney
    • Newcomer slides here: 
  • Keep it to items unique to our IG where possible
  • Address “what’s necessary for me to read?” issue
  • More narrative isn’t necessarily better narrative
  • Bob D: can we point out ‘conformance narrative’ vs framework information… flag pages and sort them based on that
  • Joel: more guidance around our examples and use cases - a cookbook
  • Bob M: examples with descriptive narrative
  • Jamie: Log a tracker to classify and separate guidance between “conformance” and more unnecessary items

Tooling support for “required” genomic code system bindings - to test at connectathons

    • Possible validators for HGVS
    • Online tools are difficult for many stakeholders to integrate with and support…
      • Lloyd: 1 Concern is performance, doing validation directly within terminology server is much preferred
    • Bob M: Grahamme had shown support for including clinvar in particular, effort was previously made to integrate
    • Joel: HAPI 5 supposed to have better integration with external terminology services

  • Next steps:

    • Collect popular online (and offline if we can find any) tools and review

  • Definitional vs Observational:
    • Our findings are all observational information, though they log definitional information in various values and components.
      • Need to strengthen arguments here and make a stronger position
      • Collapsing multiple reference sequences and/or HGVS components??
        • Group to review pros and cons offline and circle back with Clem
  • Implications
    • Show how current examples will look under change

  • 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


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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