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Chair:  Bob Milius

Scribe: Bob Milius

HL7 Clinical Genomics Weekly Call - 23 June 2020 11:00 AM (US Eastern)


Archive of minutes:

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Meeting ID: 298 006 8716

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Meeting ID: 298 006 8716

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Attendees Sign-in

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

  1.  Bob Freimuth - Mayo Clinic -
  2.  Liz Amos - NLM - 
  3. Arthur Hermann, Kaiser Permanente,
  4. Bob Dolin - Elimu Informatics -  
  5.  Rachel Kutner - Epic
  6.  Jamie Jones - BCH - 
  7.  Clem McDonald - NLM - 
  8.  Lloyd McKenzie - Gevity - 
  9.  May Terry - MITRE - 

Standing Informational Items

Agendas and Important Dates 

CG Call Date



Important Dates


Bob F

Sync for Genes


Joint call with OO @ 10 am ET (no IM call)


Bob M


Bob F

  • vote on extending co-chair position
  • Use of LOINC in IG orders and reports (Swapna Abhyankar) [30+ min]



  • Tumor Normal Testing
  • Example of real life lab data
  • Continue Discussion on Use of LOINC in IG orders and reports




Bob M

  • DiagnosticReport.code
  • Virtual WGM in September


  • LOINC in IG orders and reports (continued)




Bob M


Bob M





Bob M


Bob M







Bob M

Connectathon Sep 9-11, 2020

Virtual WGM Sep 21-25, 2020

External efforts

  • GA4GH (Global Alliance for Genomics and Health)
    • GA4GH news
      • will likely have new draft standards to review in the next few weeks
      • Clem - GA4GH has standards that can be shared, Liz will share
        • Variant annotation
    • Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
      • Variant Representation subgroup (lead by Larry Babb/Alex Wagner/Reece Hart)
      • Variant Annotation subgroup
        • Working on statements about therapeutic interventions and variant pathogenicity
      • Sequence Annotation subgroup
        • Brand new activity, more will be announced soon
        • Open to all participants!
    • Clinical & Phenotypic Data Capture Work Stream
      • Pedigree Activity (Grant Wood)
        • help GA4GH community to understand HL7 Pedigree standards
        • Many researchers currently using PED format - family history statement, simple, not as robust as FHIR
        • Grant is co-chairing that effort
      • Phenopackets
        • May Terry gave an overview of mCode to GA4GH Phenopackets
  • Phenopackets on FHIR (NLM funded) (Bob Freimuth and others in GA4GH)
  • G2MC (Grant Wood)
    • Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
    • Create KB on G2MC website 
  • ClinGen/ClinVar (Larry Babb)
    • Data Exchange/Platform WG, major driver project of GA4GH GKS
    • will discuss further when Larry in on a call
  • CDISC PGx (Dorina B.)
    • CDISC involved in standardizing reporting of data to regulatory bodies. E.g. Pharma communication to FDA - looking to include genomics in research reporting.
    • Clem: no specific insight - Transcelerate Biopharma ( group fairly active in FHIR. FDA has active interest in FHIR.
  • ONC Sync for Genes (Bob Freimuth)
  • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob F)
    • Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • mCODE (May Terry)
    • STU1 published -
    • Initial feedback from some reviewers (UCSF, Princess Margaret of Toronto) for mCODE enhancements:
      • Better representation of prognostic factors, including serum tumor markers  in the Genomics related elements.
      • gave update to GA4GH

Subgroup reports

  • FHIR (Jamie)
    • Minutes:

  • Working on JIRA Trackers
  • MolecularSequence use-case evaluation
  • Variant annotation discussions - continued, looking for feedback, looking at GA4GH space

WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

June 9 

Topic 1: DiagnosticReport.code: Continue Discussion: Use of LOINC in IG orders and reports (Swapna Abhyankar)

From June 2:

  • Context: LOINC being used incorrectly in genomics
  • 2016: labs requesting LOINC codes for reporting the same set of results, not interoperable
  • Existing codes
  • 81247-9: master HL7 genetic variant reporting panel (updated version)
  • Genes
  • Study types
  • 81247-9 should NOT be used for ordering or for results reporting (only used to group results together)
  • Example
  • 79571-6: used for the order
  • 81247-9 is attached to the order, within which can be reported the discrete results
  • See slides for details
  • Coding challenges in 2020
  • Still getting overlapping requests from labs for new codes
  • 81247-9 is still being used incorrectly
  • Use in CG’s FHIR IG
  • DiagnosticReport.
  • Examples in the HLA reporting section - ambiguous use/interpretation
  • Recommendations for genetics reporting (example)
  • See slides
  • Discussion
  • Bret: please clarify examples on slides - last slide vs penultimate slide
  • 81247-9 would not go on the penultimate slide
  • Bob M: HLA example contains an error, idea was because only 1 code is allowed in a CC, can use codings to provide additional info that isn’t captured in the generic master panel code
  • Example: coding for 81247-9 (master panel) + coding for gene name
  • Need a post-coordinated approach because cannot get pre-coordinated codes for everything that will be reported
  • Clem: large labs want an approach that works with existing systems
  • Swapna: using the panel code for the report is incorrect
  • Clem: look at order catalogs to see what they’re already doing
  • May: this is a design pattern for multiple IGs
  • This topic will be continued on a future meeting
  • See chat log for additional comments: 
  • Please continue this discussion on JIRA




  • Mullai Murugan: Is the usage of the LOINC code 81247-9 as a code value for the code field in the DiagnosticReport resource applicable for all types of genetics tests e.g. Whole Exome Sequencing, Whole Genome Sequencing, Exome Panels etc.?
  • Swapna: 81247-9 should not be the code value used in the DiagnosticReport code field. It is a panel code and panel codes should not be used for result reporting.
  • Any observation LOINC can be used as appropriate to represent the testing being done and the collection of information resulted.
  • Some examples in the genetics space:
  • 86206-0 Whole genome sequence analysis in Blood or Tissue by Molecular genetics method
  • 86205-2 Whole exome sequence analysis in Blood or Tissue by Molecular genetics method
  • 38404-0 CFTR gene targeted mutation analysis in Blood or Tissue by Molecular genetics method
  • 93201-2 Coronary heart disease multigene analysis in Blood or Tissue by Molecular genetics method
  • Kevin's proposal - "On the FHIR subgroup call today (8-Jun-2020), we decided that this JIRA would focus on remove the required fixed value from code, but make the category fixed value required. Patrick Werner will be logging a follow-up JIRA for tracking the appropriate way for us to change the binding on DiagnosticReport.code for our own purposes."
  • Bob M: Seems we could have some kind of fixed value that could be further defined with more granularity with an additional coding. I think I heard Swapna said the code we're using isn't appropriate, but another general code for documents (perhaps yet to be defined/created) could be.

Further discussion with Swapna needed(available next week). Discussion about not using panel codes for DR codes. Generally agree to make DR.code bound to LOINC, but not a specific code. Require DR.category to be fixed to GE.

Jamie: searched Jira tracker, Patrick hasn't started a new tracker yet. 

Liz will submit. Follow up JIRA: 

  • Motion? Key members not present, vote not taken.
    • Remove required fixed value from DR.code. Make DR.category required. ?
    • Move / 2nd:   Kevin? /   
    • Discussion:
      • -
    • Vote: (Abstain / Opposed / In Favor):   /    /    
    • Result: motion  

Topic 2: Virtual WGM - September 2020 

    • FHIR Connectathon: 
      • Wednesday, September 9 - Friday, September 11
    • Plenary Meeting: 
      • Monday, September 21 (morning)
    • Work Group Meetings: 
      • Monday, September 21 (afternoon) - Thursday, September 24 

  • TSC recognizes challenges of individual availability on a virtual basis and is reviewing options that better accommodate those in international time zones

  • Comments:
    • WGM days/times?
      • probably not have full quarters
      • Will be an HL7, so there will be a cost to participate
        • will likely be organized like how virtual DevDays was done
    • WGM topics?
      • probably focus on joint calls, which can't be on regular calls
        • e.g., OO, 
        • FHIR-I (Josh/Lloyd) may not be critical since Lloyd comes to most weekly calls
        • may want to have a joint with CDS, BRR?
      • whatever WG feels they need to do is completely up to them
    • Connectathon topics?
      • MolecularSequence
      • IG STU2
      • other?
    • Arthur: If we have a pile of work to do, are there sets of items we need to do together. This is what works well for us at WGMs in the. Make sure that people who are attending are truly attending. Need to be focused as if they actually traveled to the WGM.
    • Where are the cookies

Future Topics

Update - Stress testing IG implications with examples

  • Bret H, Arthur H, Rachel K
  • zulip thread: 
  • Arthur: We have our spreadsheet updated (I have added the input from our Kaiser Oncologists and added a single Strata report which they like very much
  • Rachel: I still need to upload the example reports I have to the spreadsheet. I'm not the most well-versed with FHIR, but it sounded like the next part we wanted to do was to try and model the pertinent pieces of each report using the different methods and get feedback on how well it represents the information in the report.
  • Jamie:  If we can get folks to select a short list of individual statements of interest I would have no problem doing a lift to FHIR, which we can then comment on more broadly (I think we'll see there will be some room for decision-making in the encoding)

    After I've posted a couple in FHIR and patterns for the encoding are more obvious, folks should be able to easily edit them "Mad Lib" style and we can see if we run into problems from there

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