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Chair:  Robert Freimuth

Scribe: Robert Freimuth  

HL7 Clinical Genomics Weekly Call - 19 May 2020 11:00 AM (US Eastern)


Archive of minutes:

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Meeting ID: 298 006 8716

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Attendees Sign-in

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

Bob Freimuth - Mayo Clinic -

  1. Bob Milius - NMDP/CIBMTR - 
  2. May Terry - MITRE - 
  3. Joel Schneider -
  4. Mullai Murugan - BCM -
  5. Arthur Hermann- Kaiser Permanente -
  6. Daniel Rutz - Epic -
  7. Liz Amos - NLM - 
  8. Clem McDonald - NLM - 
  9. Kevin Power  - Cerner - 
  10. Perry Mar - Health Catalyst - 
  11. Bob Dolin - Elimu Informatics - 
  12. Stephen Schwartz - Epic - 
  13. JD Nolen - Childrens Mercy Hospital -
  14. Jamie Jones - BCH -
  15. Ning Xie - BWH -

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

Tumor/normal examples to review 




Bob M




Bob M

1: old projects

2: connecathon

3: emerge extensions




Bob M

  • Co-chair elections
  • Connectathon - Scenarios
  • "Associated" phenotype/cancer component discussion from FHIR subgroup
  • appropriate way to structure our 'additional text' extension?
  • how to link to region studied?
  • Uncallable subregions in a region studied




Bob F

Sync for Genes



  • Use of LOINC in IG orders and reports (Swapna Abhyankar) [30+ min]

Working Group Meeting

Joint call with OO

External efforts

Subgroup reports

New simplified implications live on CI build

WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

May 12 

Topic 1: Sync for Genes

  • Overview of the ONC Sync for Genes program - Kevin Chaney
  • eMERGE FHIR Specification and Pilot Implementatation - Mullai Murugan (Baylor)
    • Slides: 0519 S4G_CG Update.pdf
    • Goal: develop FHIR spec for eMERGE research network, POC implementation (pilot), evaluate feasibility of FHIR genomics data with EHRs
    • Milestones:  localized eMERGE draft spec, publish reports for emerge samples
    • Example reports from Baylor and LMM labs, mapped each component into a hierarchical structure that links to FHIR components
    • Draft spec:
      • See this site for info about how FHIR genomics worked for eMERGE!
    • Pilot implementation
      • 200 reports selected from the emerge work, instantiated in FHIR format
      • Pushed to Northwestern (Microsoft) and JHU (Azure) FHIR servers
      • NW and JHU are implementing data elements of interest from the emerge FHIR spec into their local back ends, extracting data from FHIR reports
      • Both sites working on implementing CDS using the FHIR data
    • Collaboration with HL7 CG
      • See slides for a list of major issues (both resolved and pending)
        • Short term solutions have been found for most
        • Longer term (more robust) solutions still need to be developed
      • Lots of extensions were implemented...
  • HLA reporting with FHIR - Bob Milius (NMDP)
    • Slides:  HL7CG_S4G_NMDP_20200519.pdf
    • Scope of NMDP/Be the Match: world’s largest and most diverse volunteer donor registry for treating blood cancers, international partners
      • Be the Match: matches patients with donors
      • CIBMTR: performs research on transplant outcomes, results improve matching at BTM
    • Nearly 26,000 HLA alleles have been defined in the IMGT database
    • Current matching occurs based on nomenclature
      • Future matching may occur instead using the actual HLA sequence
    • MIRING implementation guide for NGS of HLA/KIR in HML
      • HML not used outside of HLA community, makes integration with healthcare systems difficult => need FHIR
    • Developing HLA reporting FHIR IG, lab partner = Versiti
    • See slides 21-22 for an overview of how FHIR transaction bundles will be used for HLA, including using Observations for specifying HLA nomenclature
    • First draft of HLA reporting IG is available, derived from FHIR genomics IG but is not a direct child of it
    • Slide 24: overview of the components in the HLA IG
    • Engaging two software vendors to convert


From Bret H to Everyone:  10:23 AM

did onc given us domain specific remit, update fhir genomics with us core version?

From Kevin Chaney to Everyone:  10:25 AM

From Bret Heale to Everyone:  10:30 AM

just a thank you to Mullai and Larry for their patient collaboration.  : ^ ) 

From Dan Rutz (Epic) to Everyone:  10:38 AM

Would it be possible to get the presentation that Mullai is using, especially since it seems to have links to relevant other content?

From Kevin Chaney to Everyone:  10:38 AM

From may terry to Everyone:  10:39 AM

+1 on requesting the eMERGE presentation slides.

From Mullai Murugan to Everyone:  10:46 AM

Thank you for opportunity! I learnt a lot from this group during this process

From Arthur Hermann to Everyone:  10:46 AM

There is great information in this slides. I would like for the work group to review the comments (please send link to the slides)  and map back to current iG - see which of these need attention.. 

From Bret Heale to Everyone:  10:51 AM

There are many notes, comments, interpretative guidance, disclaimer topics. When one dissects examples of these statements, you can find descrete elements. However, the statements vary in their presentation of the information. Essentially styles. I'd suggest that using extension is a reasonable way to add text to your report. However, the Oberservation.text element is an important narrative section. It would be good to outline what the clinical, laboratory, regulatory, business needs are for the information.  

once the purpose of the statements are defined we can work to place them appropriately. But part of the issue is that we're moving from a nearly fully narrative document (PDF) to a computable data structure. one might expect to need to parse and rebuild the 'clinical' statements in a UI rather than in the data structure.

oh and is there a place where the artifacts can be examined? 

From Arthur Hermann to Everyone:  10:52 AM

Bret - can I suggest we move this discussion to Zulip or bring this up in a mtg within the next few weeks? 

From Dan Rutz (Epic) to Everyone:  10:56 AM

That may end up being part of the discussion with OO on Thursday too.

From Bret Heale to Everyone:  11:00 AM

we could think about a value set for DiagnosticReport.Code

but it gets messy to try to have a code for every 'type' of report

Bob's action here seems like a fair approach

to give both a 'known' code that everyone should know and a secondary code that is specific to the business use case. But will the recipient system know what to do with it...

From may terry to Everyone:  11:00 AM

The O&O call…what time is it? I see 2… one at 10a and one at 1p.

From Bret Heale to Everyone:  11:01 AM

I would like to see an example what a recipient system does - Very cool Work! 

From Dan Rutz (Epic) to Everyone:  11:01 AM

Special joint session 1.5 hours, starting at 10a Eastern

From may terry to Everyone:  11:01 AM

Great, thanks!

From Bret Heale to Everyone:  11:01 AM

OandO joint session is in the ListServ