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Chair:  Robert Freimuth

Scribe: Robert Freimuth  




HL7 Clinical Genomics Weekly Call - 3 Dec 2019 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall 

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

Archive of minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=25559917&src=contextnavpagetreemode

Attending the meeting

Join the online meeting (VoIP available with this):

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Agenda

Attendees Sign-in

(Presiding co-chair: Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu )

  1. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  2. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  3. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  4. May Terry - MITRE - mayT@mitre.org
  5. Jamie Jones - Boston Children’s Hospital - james.jones.bch@gmail.com
  6. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 
  7. Stephen Schwartz - Epic - sschwart@epic.com
  8. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  9. Liz Amos - NLM - liz.amos@nih.gov 
  10. Bret Heale - Intermountain Healthcare - bheale@gmail.com 
  11. Deepak Sharma - Mayo Clinic - sharma.deepak2@mayo.edu
  12. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 



Standing Informational Items

Agendas and Important Dates 

CG Call Date

Co-Chair

Agenda https://confluence.hl7.org/display/CGW/Future+Topics+for+Weekly+Meetings

Important Dates

10/1/19

Patrick W

Last Trackers before publication


10/8/19

Kevin P

Updates before publication


10/15/19

Kevin P

Finalize request and vote to publish!

MCode / Genomics Reporting IG Alignment


10/22/19

Kevin P

How do we want to manage engagement with other genomics related initiatives?

  • MCode
  • EMERGE
  • Phenopackets

Review of discussion from FHIR subgroup


10/29/19

Bob M

Using Draft CG FHIR Spec for AoU: Larry Babb / Mullai Murugan


11/5/19

Bob M

Larry Babb / Mullai Murugan

continue AoU discussion

eMERGE - IG debrief

Tentative:

LOINC updates:

Issue #1: Level of Evidence versus Clinical Significance

Issue #2: Tumor Mutation Burden (TMB) concept


11/12/19

Patrick W



11/19/19

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


11/26/19

Bob F

Topic 0: Bob Dolin: GACS FHIR Operations

Topic 1: STU2 Themes (Feedback requested)


12/3/19

Bob F

Topic 1: PGx implications

Topic 2: Phenopackets on FHIR

Topic 3: STU2 themes


12/10/19

Bob M



12/17/19


Larry Babb / Mullai Murugan

eMERGE - IG debrief


12/24/19


CANCELED


12/31/19


Canceled??


1/7/20

Bob M



1/14/20

Patrick W



1/21/20




1/28/20

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:

https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/

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.


Topic 0: Approval of Minutes from Last Meeting

Nov 26

    • https://confluence.hl7.org/display/CGW/CG-2019-11-26
    • Motion: Approve minutes as written
      • Bob M: upload slides to confluence, avoid external links
        • Bob F - DONE 12/4/19
      • Move / 2nd: Jamie / Bret
      • Discussion:
      • Vote: (Abstain / Opposed / In Favor): 0 / 0 / 11
      • Result: Motion passes, minutes approved as written (pending embedding of slides)

Topic 1: Adequate PGx (Bret Heale, Kevin Power)


  • Current guidance: http://build.fhir.org/ig/HL7/genomics-reporting/pharmacogenomics.html
  • Reviewed current IG structure on slide 5, which ties Medication Implications (Observation) to Medication Usage Implications (Task)
    • Attached to variant, haplotype, or genotype
  • Task resource has reasonReference, hard coded to cardinality 1; we submitted a tracker to have this changed
  • Slide 9: RelatedArtifact can be a link to a service (e.g., Infobutton)
  • Slide 10: discussion about creating LOINC codes and extensible value sets for level of evidence
  • Slide 11: discussion about the Narrative element, specifically level of effort by the lab to produce this and potential differences between how the lab wants to use the field vs. FHIR intentions for it
  • Slides 12-13: proposed changes: use components instead of profiles for Medication Implication
  • Action: review Med Transporter (is this needed if we don’t have values for it?)
  • We should structure statements, not model biology
  • Why is Med Impl an Observation?  Does O&O agree with this usage?
    • It works for current reporting
    • Action: follow up with O&O
  • Slide 15: this proposal simplifies implementation as it is only a single profile
  • RAN OUT OF TIME at slide 16, will start here at a future date


Topic 2: Phenopackets on FHIR (Bob Freimuth)

  • DEFERRED


Topic 3: STU2 Themes - Feedback requested

Themes: 

https://docs.google.com/document/d/17r-HNm-gyqthepU40gqh39uYK9PV3HmBl1VM-vW6TuY/edit 

Brain dump: https://docs.google.com/document/d/1SYdzxanCgkwzhhBJCBrguZ6H8HdjQFjG_l2nufAkCGU/edit#

  • Collecting themes and volunteers to work on them.


Chat


[12/3/2019 10:34:54 AM] Bob Freimuth: https://www.pharmgkb.org/page/clinAnnLevels

[12/3/2019 10:48:38 AM] Jamie: PGx lists came from 

[12/3/2019 10:48:38 AM] Jamie: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/

[12/3/2019 10:49:56 AM] Jamie: Specifically, as defined in this table: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/table/tbl2/


Clinical Genomics Reference Docs