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Chair: Patrick Werner

Scribe: Patrick Werner



HL7 Clinical Genomics Weekly Call - 18 Feb 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

Working Group Meeting

External efforts

Subgroup reports

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Topic 1: WGM Review

Topic 2: Update/Discussion on Implication Profiles (Jamie)

Chat

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

Genomics Reporting "Lite" 0.2 ???

find-variant operation (updates from yesterday's discussion)

FHIR-25296 Uncallable subregions in a region studied

FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

FHIR-19844 PGx High Risk Allele Medication Impact is confusing

Clinical Genomics Reference Docs

Attendees Sign-in

Presiding Co-Chair: Patrick Werner

  1. Arthur Hermann, Kaiser Permanente, arthur.hermann@kp.org
  2. Daniel Rutz, Epic, drutz@epic.com
  3. JD Nolen, Children’s Mercy Hospital, jlnolen@cmh.edu
  4. Liz Amos, NLM, liz.amos@nih.gov
  5. Perry Mar, Health Catalyst, perry.mar@healthcatalyst.com 
  6. Jamie Jones, BCH, james.jones.bch@gmail.com
  7. Lloyd McKenzie, Gevity, lmckenzie@gevityinc.com
  8. Rachel Kutner, Epic, rkutner@epic.com
  9. Bob Dolin, Elimu Informatics, bdolin@elimu.io 
  10. Joel Schneider, NMDP/CIBMTR, jschneid@nmdp.org (:20)
  11. Kevin Power - Cerner - kpower@cerner.com (:25)
  12. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu (:30)

 

 

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

2/18/20

Patrick



2/25/20




3/3/20


CG IG Lite: Liz & Clem
Attachments from 1/28 email


3/10/20




3/17/20




3/24/20




3/31/20




4/7/20




4/14/20




4/21/20




4/28/20




5/5/20




5/12/20




Working Group Meeting

May 16-22, 2020   • San Antonio, Texas

Register Today!

CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday

External efforts

Subgroup reports


  • FHIR (Jamie, Gil)
    • Minutes:

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

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Jan 28 


Topic 1: WGM Review

https://confluence.hl7.org/display/CGW/2020-02+CG+WGM+Minutes 

Recap by Bob F.:

  • FHIR Shorthand (FHIS): a lot of people interested in FHIS. FHIS is a simple way to model Profiles and IGs. http://build.fhir.org/ig/HL7/fhir-shorthand/
  • R5 Updates:
    • Release Will be moved from May -> September 2021 (due to regulations, mostly US regulations)
    • Expectation is that most of the Resources used by US Core will be normative in R5

Pending: recap by Bob M (Wed Q4)


Topic 2: Update/Discussion on Implication Profiles (Jamie) 

Arthur: Is this related to the IG Lite?

Jamie: Clem’s recent discussions are about simplifying Variant itself, this is about implications. Both could potentially be looked at as approaches to simplify the structure and presentation of the IG and its guidance

Arthur: I’m in contact with industry partners to implement PDF reports with our IG. If we “hit a wall” who should be contacted? 

Patrick: Zulip or email list.


Jamie: Will create examples in the new format and we should vote on this rather soon. Will gather user stories. Please report 


For technical questions and concerns, send everyone (come chat!) to:

Zulip CG discussion threads: https://chat.fhir.org/#narrow/stream/179197-genomics




Chat



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.

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"

Attachments from 1/28 email

https://docs.google.com/document/d/1eVBvUsezw69qlylWnPAz5bVQpATJ3g_F-gm4dD1ENsU/edit

https://docs.google.com/spreadsheets/d/1UAphpeYuyiQ1ANwusaculVt2vFmSvmaju1TfMv67RU8/edit#gid=1509314707

find-variant operation (updates from yesterday's discussion)

  1. Proposal: include 
    1. http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/find-variants.html and
    2. http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/operations.html

Into the CI of our IG (Jira Ticket: ?? )

  • Operation.out uses data type canonical should be Observation?
  • context: [base]/$find-variants correct?


FHIR-25296 Uncallable subregions in a region studied


FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations


FHIR-19844 PGx High Risk Allele Medication Impact is confusing


Clinical Genomics Reference Docs