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HL7 Clinical Genomics Weekly Call - 31 Mar 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


Agenda

Attendees Sign-in

Presiding Co-Chair (Patrick Werner - MOLIT Institut - patrick.werner@molit.eu): 

  1. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  2. Rachel Kutner - Epic - rkutner@epic.com 
  3. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  4. Stephen Schwartz - Epic - sschwart@epic.com
  5. Kevin Power - Cerner - kpower@cerner.com 
  6. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
  7. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  8. Liz Amos - NLM - liz.amos@nih.gov
  9. Scott Robertson - Kaiser Permanente - scott.m.robertson@kp.org
  10. Clem McDonald - NLM - clemmcdonald@mail.nih.gov
  11. Bret Heale - Intermountain
  12. Jamie Jones - BCH - james.jones.bch@gmail.com
  13. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  14. Bob Dolin - Elimu Informatics - bdolin@elimu.io
  15. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu

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

Kevin

Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)

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


3/3/20

Kevin

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


3/10/20

Bob M

1: CMS/ONC rules 

2: Vote on operations for IG

3: STU2 of IG


3/17/20

Kevin

1: Reminder - CMS/ONC rules 

2: STU2 of IG (cont...)


3/24/20

Bob M

Tumor/normal examples to review 


3/31/20

Patrick



4/7/20

Bob M



4/14/20

Patrick



4/21/20




4/28/20

Patrick



5/5/20

Bob M



5/12/20

Patrick



Working Group Meeting

Cancelled! 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

  • GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)
    • GA4GH news
      • Having virtual connect meeting starting today,
        • agenda has changed, still hope to include some working sessions
        • Bob will report back after the meeting
    • Variant Representation (formerly VMC) (lead by Larry Babb/Alex Wagner/Reece Hart)
    • Variant Annotation
    • Phenopackets on FHIR
    • Pedigree Activity (Grant Wood)
      • help GA4GH community to understand HL7 Pedigree standards
      • Many researchers currently using PED format - family history statement, simple, not as robust as FHIR
      • Grant is co-chairing that effort
    • G2MC (Grant Wood)
      • Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
      • Create KB on G2MC website 
    • HLA reporting (Bob)
      • Driver project = GEM Japan
      • Modeling and exchanging HLA results in the Japanese population
      • HLA nomenclature vs discovery of new alleles
      • Connecting to the HLA work done by NMDP within this WG
  • ClinGen/ClinVar (Larry Babb, Bob Freimuth)
    • Data Exchange/Platform WG, major driver project of GA4GH GKS
    • will discuss further when Larry in on a call
  • CDISC PGx (Dorina B.)
    • CDISC involved in standardizing reporting of data to regulatory bodies. E.g. Pharma communication to FDA - looking to include genomics in research reporting.
    • Clem: no specific insight - Transcelerate Biopharma (https://transceleratebiopharmainc.com) group fairly active in FHIR. FDA has active interest in FHIR.
  • ONC Sync for Genes (Bob Freimuth)
    • ONC website: https://www.healthit.gov/topic/sync-genes
    • Final report for Sync for Genes Phase 2 has been finalized (but not posted yet)
    • ACI manuscript is in press
    • Phase 3 has started - more details to be announced soon
  • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob)
    • Meetings
      • March 30 - April 3, 2020 in Arlington, VA
      • Liz will check to see whether the meeting is open or ISO members only
      • Scott R: must be a member of a national member organization to attend
      • Clem - request from them to sign-off for transmission of big data (eg BAMs), may have problems with use case.
      • Looks to be virtual only
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • MCODE

Subgroup reports

WG projects and outreach

  • nothing new

Topic -1 : Virtual Connectathon Track -24/7 Friday to Sunday

Would be done via Zoom, 24/7 Connectathon. Official Information to come


https://confluence.hl7.org/display/FHIR/2020-05+Connectathon+24

Brainstorm scenarios!

  1. Create and consume full reports using new structures
    1. Tumor-normal test report
    2. WES trio report
    3. eMerge-style report (with gap analysis)
    4. mCODE-style report (with gap analysis)
  2. $find-subject-variants


Bob M.: focus on IG STU2 themes for this connectathon, test already implemented STU2 profiles. Identify missing items/profiles in/for STU2.

Bob D.: has an implementation of $find-subject-variants on a VCF FHIR Facade server.Won’t be ready for the may connectathon. Might be ready in september.

Kevin.: even only the first 2 topics would be ok for the connectathon track.

Topic 0: Approval of Minutes from Last Meeting

March 10 

Topic 1: Tumor/normal examples for review (continued discussion) (Patrick) 

FROM LAST WEEK:

  • https://gist.github.com/patrick-werner/5d715f00c4c0e096be35debcb0962267#file-first-demo
  • New extension on Observation (multi-specimen), multiple instances of the extension (references tumor and normal), and then Observation.specimen references tumor
  • Could use .focus() ?
    • Still need to know which specimen is which (tumor / normal)
  • What about multiple Observations?
    • Could do 3 (one of tumor, one for normal, one for ‘both’)?
    • Typically only send 1 result (related to the tumor)
  • Questions outstanding:
    • What are these observations saying?
    • Are they associated with the specimens correctly?
    • Concerns about ‘true nature’ of how the specimens are linked versus some real world ‘how is it done today’
    • Conversation can continue on Zulip

NEW Discussion:

(Zulip thread: https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Representing.20tumor-normal.20sequencing.20tests.3F)

  • Just link in DiagnosticReport?

JD: Specimen Resource is suitable to handle needed specimen concepts. Question is if DiagnosticReport is a Composition or stand alone.

Bob F.: could you add trio study to the “ultimate example report”. What is a specimen? If digital pathology is a specimen what is NGS data?

Bob F.: would it be helpful that someone from O&O will present their ideas about specimen, DR, Observation, etc.

Patrick: yes!

JD: should we do a meeting in may to exchange ideas O&O < -- > CG? (keep in touch in zulip, do a doodle poll)

Bob D.: JD could describe what O&O is currently doing in the lab space, and this then can be applied/transferred to the IM group

  • Specimen.type

Bret: you could use tumor-normal testing, but then lose the ability to type the Specimen (Blood/tissue type)

Bob D.: specimen is important, but methodology is also important. 

https://www.hl7.org/fhir/family-member-history-genetics.html 

Bret: There are some older slides explaining this profile. 

Bob F.: Topic is also coming up in G4GH at the moment.

Bret: is trio analysis comparable to tumor-normal testing?

Bob F.: could us relations between specimen or Observations

Will ask May and other Stakeholder for Feedback, continue the discussion after consolidating feedback.

From May via zulip:

https://zulip-uploads.s3.amazonaws.com/10155/-ltSSSyB_EcbV4rHkvqZGcyY/sample-tempus-ngs.pdf?Signature=W%2FZsxjCF0awNYX0fDeNJCiDdHxY%3D&Expires=1585670112&AWSAccessKeyId=AKIAIEVMBCAT2WD3M5KQ

Topic 2: Implication Profiles: Merge components?

Branch link: http://build.fhir.org/ig/HL7/genomics-reporting/branches/kpower_SomaticImplication/artifacts.html

Current Zulip discussion: https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Associated.20Phenotype.20Nomenclature 

Questions from the discussion:

  • Can we merge associated-phenotype and associated-cancer? 
  • In both profiles? (Diagnostic & Therapeutic)

Before we can answer the question if these can be merged, we should define what this component states, provide examples, what is inside and outside of scope. 

Chat

10:08:30 From Clinical Genomics Work Group : https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit#

10:20:22 From Kevin Power : https://confluence.hl7.org/display/FHIR/2020-05+Connectathon+24

10:42:33 From Bret Heale : awesome. what's data and what's style

10:42:38 From Bret Heale : +1

10:45:12 From Bret Heale : please let's record that session

10:45:21 From Bret Heale : and make it cannon

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.

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

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