Skip to end of metadata
Go to start of metadata

Chair: Patrick Werner

Scribe: 



HL7 Clinical Genomics Weekly Call - 14 Jan 2020 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):

Dial into the conference:


Agenda

Attendees Sign-in

Standing Informational Items

Agendas and Important Dates

External efforts

Subgroup reports

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Topic 1:  Presentation/Discussion/Vote of MSI/TMB profile drafts (Patrick)

Topic 2: Discuss: Need to include chromosome as a component to ObsVariant

Topic 3: Update/Discussion on Implication Profiles (Jamie)

Topic 4: STU2 Themes - Feedback requested

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

Clinical Genomics Reference Docs

Attendees Sign-in

(Presiding co-chair: Patrick Werner - Molit Institut - pw@molit.eu )

  1. Michael Stevens (Optum) - jmichael.stevens@optum.com
  2. Kevin Power - Cerner - kpower@cerner.com 
  3. Dora Finkeisen - MOLIT Institut - Dora.Finkeisen@molit.eu
  4. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  5. Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu
  6. Jamie Jones - BCH - james.jones.bch@gmail.com
  7. Grant Wood - Intermountain Healthcare - grant.wood@imail.org
  8. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com
  9. Rachel Kutner - Epic - rkutner@epic.com
  10. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  11. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
  12. Bret Heale - Intermountain Healthcare - bheale@gmail.com
  13. JD Nolen - Children’s Mercy Hosptial - jlnolen@cmh.edu



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 (deferred)

Topic 3: STU2 themes


12/10/19

Bob M

Topic 1: PGx implications (cont)

Topic 2: Phenopackets on FHIR (deferred)

Topic 3: STU2 themes


12/17/19

Kevin P

Topic 1: Larry Babb / Mullai Murugan -  eMERGE IG


12/24/19


CANCELED


12/31/19


CANCELED


1/7/20

Bob M

Topic 1: WGM agenda

Topic 2: Larry Babb / Mullai Murugan -  eMERGE IG (continued)

Topic 3: Bob F - Phenopackets on FHIR (deferred)

Topic 4: STU2 Themes - Feedback requested


1/14/20

Patrick W

TMB & MSI


1/21/20

Kevin P

WGM Agenda

Bob F - Phenopackets on FHIR


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:


  • 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.
  • Still pending (Dec 17)


Topic 0: Approval of Minutes from Last Meeting

Dec 17 


Topic 1:  Presentation/Discussion/Vote of MSI/TMB profile drafts (Patrick)


  • Motion: Approve Profiles 
    • How do we determine which tests should be given profiles from us in the CG space?
        • Case by case analysis based on what we see included/requested in reports and deemed to be domain-specific to genomics
      • Jamie: We never used interpretation in our profiles, do we want to include referenceRanges as well? Do we provide a way to mark if the Observation is calculated using synonymous versus nonsynonymous mutations? 
      • Patrick: leaving that up to Observation.method. Will add guidance for that.
      • Should MSI/TMB derive from Finding or


MSI: give guidance that MSI is derived from Variants, these Variants could be included in Observation(MSI).derived

  • Motion: Include Profiles with added guidance on method/derived (see discussion) to the IG. Guidance will be added to general reporting, especially Fig.1 and 3. (Fig3.: replace Finding with GenomicsBase)
  • Move / 2nd: Jamie / Bret   
  • Discussion: -
  • Vote: (Abstain / Opposed / In Favor): 2 / 0 / 11 
  • Result: Motion passes


Topic 2: Discuss: Need to include chromosome as a component to ObsVariant 



Topic 3: Update/Discussion on Implication Profiles (Jamie)

https://docs.google.com/document/d/1SYdzxanCgkwzhhBJCBrguZ6H8HdjQFjG_l2nufAkCGU/edit#heading=h.n5eokak2o6ca

Topic 4: STU2 Themes - Feedback requested

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 

https://loinc.org/93044-6/

https://loinc.org/LL5356-2/

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 http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncologyexamples-r4.xml

(note, this example uses placeholder value “AMP Guidelines” instead of a tier)

Profile: http://build.fhir.org/ig/HL7/genomics-reporting/somatic-predictive.html

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