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Chair:  Bob Milius

Scribe: Bob Milius



HL7 Clinical Genomics Weekly Call - 28 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

(Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org  )

  1. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org 
  2. Liz Amos - NLM - liz.amos@nih.gov 
  3. Michael Stevens - Optum - jmichael.stevens@optum.com 
  4. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  5. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  6. Kevin Power - Cerner - kpower@cerner.com 
  7. Bret Heale - Intermountain Healthcare - bheale@gmail.com  
  8. Jamie Jones - BCH - james.jones.bch@gmail.com
  9. Grant Wood - Intermountain Healthcare - grant.wood@imail.org
  10. Alex Mankovich - Philips - alex.mankovich@philips.com 
  11. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  12. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  13.  Stephen Schwartz - Epic - sschwart@epic.com 
  14. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  15. Mullai Murugan - BCM - murugan@bcm.edu
  16. Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com

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

WGM Agenda


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.


Topic 0: Approval of Minutes from Last Meeting

Jan 21 


Topic 1: WGM Agenda

https://confluence.hl7.org/display/CGW/2020-01+CG+WGM+Agenda 

Topic 2: Genomics Reporting "Lite" 0.2

  • Clem

"Focus is on the variant.  Pharmacogenomics and HLA type stuff is out. They add a lot of complexity and tend to be reported on their own and already have a pretty good start.

 

I treated all variants (big/little 0 the same). Did not model either genotype or haplotype. They get in the way of simplicity (but I may get fired because of that).

 

I focused on the 5 ways of specifying a variant.  Some of our fields are convenience fields – don’t add real information, but people like them-so segregated them"

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


Topic 4: Update/Discussion on find-variants Operation (Bob D & Jamie)

Chat

[1/28/2020 10:15:02 AM] Bret Heale: this is the phenopackets implementation guide git hub: https://github.com/phenopackets/phenopacket-schema-fhir-implementation-guide

 [1/28/2020 10:17:20 AM] Bret Heale: here's the phenopackets FHIR implementation guide documentation: https://phenopackets-schema.readthedocs.io/en/latest/fhir.html

[1/28/2020 10:19:17 AM] Bret Heale: this is the Phenopackets IG as you might be used to looking at IGs: https://aehrc.github.io/fhir-phenopackets-ig/

 [1/28/2020 10:19:36 AM] Bret Heale: as of dec 2 2019

[1/28/2020 10:25:29 AM] Bret Heale: regards lite. Could the mission be accomplished with simply giving examples of implementing with the current IG, rather than develop a new IG?

[1/28/2020 10:27:56 AM] Bret Heale: thanks Clem : ^ )

[1/28/2020 10:30:23 AM] Kevin Power: I would like to request that we get and document the specific people/organizations that are complaining about the complexity of what we have - and what they have done to understand and review the IG

[1/28/2020 10:33:09 AM] Bob Freimuth: +1 Kevin. Anonymous and indirect feedback is difficult to make actionable.

[1/28/2020 10:34:56 AM] Arthur Hermann: I agree.. i would also like Clem to be cear about the use case he is solving for. Then we need to understand if we are ching the ig or simply providing a specific use case in terms impact to ig

[1/28/2020 10:34:56 AM] Arthur Hermann: Changing IG i meant

[1/28/2020 10:38:15 AM] Bob Freimuth: It seems there are at least 2 targets that this group is trying to meet. 1) Create a simple structure to move data around; focus is on standardizing the container. 2) Create a more in-depth structure that adds deeper semantics by requiring greater specificity in the data itself; requires more complexity. #1 will help move data around, #2 will help those data be interpretable more independently and consistently. These two solutions may co-exist, but we need to acknowledge the difference in objectives.

[1/28/2020 10:40:14 AM] Arthur Hermann: Thanks .. i think you may be right.. but we need clarity on the target groups and what should be included

 [1/28/2020 10:41:59 AM] Arthur Hermann: My 2 cents.. this is not an efficient way to discuss this issue. We need to work this offline

[1/28/2020 10:41:59 AM] Arthur Hermann: Perhaps it could be discussed at working group mtg in Sydney

 [1/28/2020 10:59:37 AM] Bret Heale: The proposal is to "merge the operation branch into Build for further development as part of the work for version 2 of our IG"?

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