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HL7 Clinical Genomics Weekly Call - 1 Sep 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 (Kevin Power - Cerner - kpower@cerner.com

  1. Rachel Kutner - Epic - rkutner@epic.com
  2. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  3. Patrick Werner - MOLIT Institut - pw@molit.eu
  4. Dora Walter - MOLIT Institut - dora.walter@molit.eu
  5. Michelle Barry-Availity michelle.barry@availity.com 
  6. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  8. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  9. Liz Amos - NLM - liz.amos@nih.gov 
  10. James Jones - BCH - james.jones.bch@gmail.com 
  11. May Terry - MITRE - mayT@mitre.org 
  12. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  13. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  14. Ling teng -BWH -tenglingling@gmail.com
  15. Bret Heale

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

5/19/20

Bob F

Sync for Genes


5/21/20


Joint call with OO @ 10 am ET (no IM call)


5/26/20

Bob M


6/2/20

Bob F

  • vote on extending co-chair position
  • Use of LOINC in IG orders and reports (Swapna Abhyankar) [30+ min]

6/9/20

Patrick

  • Tumor Normal Testing
  • Example of real life lab data
  • Continue Discussion on Use of LOINC in IG orders and reports

6/16/20


Canceled


6/23/20

Bob M

  • DiagnosticReport.code
  • Virtual WGM in September

6/30/20

Kevin P

  • LOINC in IG orders and reports (continued)

7/7/20

Bob M

  • Virtual WGM in Sep
  • Implication Examples
  • IM work

7/14/20

Patrick

  • Moving away from spreadsheets for our IG
  • Molecular consequence

7/21/20

Bob M

  • Connectathon
  • WGM
  • Moving away from spreadsheets for our IG
  • MSI LOINC

7/28/20

Patrick

  • MSI LOINC
  • mCODE alignment with CG IG STU2 (20-30 minutes minimum)

8/4/20

Patrick

  • Scheduling WGM Sessions (Kevin)
  • Update & Announcing Voting on:
    • Build Issues
    • Updating callable region profile

8/11/20

Bob M

  • Scheduling WGM
  • Genomics Reporting IG STU2 - Template
  • Block vote preview
  • Missing items in the CG DR
  • Uncallable regions (cont discussion)

8/18/20

Bob M

  • Block vote
  • Scheduling WGM
  • Missing items in the CG DR
  • Uncallable regions (cont discussion)

8/25/20

Jamie

  • Uncallable subregions
  • WGM topics

9/1/20

Kevin



9/8/20

Patrick



9/15/20

Bob M



Connectathon Sep 9-11, 2020

Virtual WGM Sep 21-25, 2020

External efforts

  • GA4GH (Global Alliance for Genomics and Health)
    • GA4GH news
      • working group meeting (virtual plenary) coming up this fall
    • Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
      • Variant Representation subgroup (lead by Larry Babb/Alex Wagner/Reece Hart)
      • Variant Annotation subgroup (lead by Matt Brush and Javi Lopez)
        • Working on statements about therapeutic interventions and variant pathogenicity
      • Sequence Annotation subgroup (lead by Karen Eilbeck and Shawn Rynearson)
        • Brand new activity, more will be announced soon
        • Open to all participants!
    • Clinical & Phenotypic Data Capture Work Stream
      • Pedigree Activity (Grant Wood)
        • help GA4GH community to understand HL7 Pedigree standards
      • Phenopackets
        • Under continuous development, expanding to COVID and cancer use cases
        • Phenopackets on FHIR (NLM funded) (Bob Freimuth and others in GA4GH): translation of the GA4GH standard to HL7 FHIR
  • G2MC (Grant Wood)
    • Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
    • Create KB on G2MC website 
  • ClinGen/ClinVar (Larry Babb)
    • 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
    • Phase 3 is in progress, wrapping up this fall
    • Phase 4 was just awarded, will share more info ASAP (intend to provide an update at the WGM, so attend to learn more!)
  • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob F)
    • Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
      • The technical experts group just convened to work on this (mid Aug)
      • Since Phenopackets is implementing the GA4GH VR spec, which we are attempting to keep aligned with the CG IM, this work will be of interest to the CG WG
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • mCODE (May Terry)
    • STU1 published - http://hl7.org/fhir/us/mcode/
    • Initial feedback from some reviewers (UCSF, Princess Margaret of Toronto) for mCODE enhancements:
      • Better representation of prognostic factors, including serum tumor markers  in the Genomics related elements.
    • working on STU2 version, would like to better align with CG IG next release

Subgroup reports


WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting


Aug 25

Topic 1: WGM Sessions

Time slots and proposed topics

November 1st = NIB deadline for January 2021 ballot

November 15th = Initial content deadline

Dec 6th = Final Content deadline


Update on joint sessions

  • FHIR-I
  • O&O (JD Nolen)
    • Diagnostic report...I think it is time for a cross-domain (AP, CG, etc.) IG. We need to take what we have on a test drive to see where the gaps are. 
      • What to use for DiagnosticReport.code (removing fixed LOINC panel code, guidance on which LOINC codes are appropriate)
      • Should be a ‘starter’ list, should be extensible
    • Further discussion/plans on the use of "notes" or something else for extra information on genetic findings that we talked about a few months ago. 
    • Discuss the ability / guidance around delivering biomarker observations
    • Merging DocRef/Media - updates on current status
    • Alignment of Observation.category and DiagnosticReport.category valueSets?
    • FYI update on OO/PA work on a new "task"-like resource to handle the movement of specimens and other procedural things


From chat.fhir.org: Sep 2020 WGM Topics 

Topic 2: Missing items in the CG DR (review only)

Currently Missing Coded Items which are contained in PDF Reports:


Past Discussion


  • Patrick introduced topic - will have full discussion next week
  • Bret - don't see this from Intermountain genetic reports
  • Arthur - only in somatic?
  • Patrick - for breast cancer
  • Anand - found in panel, not any one gene
  • Bob D - variant profile may not be good for reporting loss of heterozygosity


Topic 3: Uncallable Regions (review only)

Indeterminates via region-studied FHIR-25296


  • Group had determined to do subtraction before reporting
  • Needs guidance
  • Uncallable regions were still “studied”
  • Add guidance and examples to not use Variant to convey a non-callable gene
  • Proposal B: allow Observation.value to convey callability
  • “No Call different from Absent” on variant answer list




  • Add in extensible binding to 
  • (Present LA9633-4 | No Call LA18198-4 | Unknown LA4489-6)




  • Future extensible Options for value
  • ( Callable | uncallable ) | high-quality | intermediate quality
  • Proposal C: separate profile for listing uncallable regions
  • Proposal A: add uncallable sub-region component
  • Hard to convey uncallable whole genes



FHIR-25296

Persuasive with Modification

Uncallable subregions in a region studied

Bob Dolin

To allow full use of the current profile's components, add in a required [1..1] value for region-studied (currently 0..0) with an extensible binding to a local answer list with the 3 LOINC answer codes: (Present LA9633-4 | No Call LA18198-4 | Unknown LA4489-6). Add in textual guidance for this value, along the lines of:  'When reporting regions of study, the value field is used to filter regions by callability. A value of "Present" shall accompany components describing a region fully called by the lab, so that omission of variant results within that region implies wildtype calls in the sample, compared to a specified reference. A value of "No Call" shall accompany components describing a region explicitly deemed uncallable by the lab. A value of "Unknown" shall accompany components describing a region where callability varies, for example the full list of genes studied in a panel. Omission of variants within a "No Call" or "Unknown" region shall not be used to imply wildtype calls in the sample.'


Discussion:
Jamie: Goal is to clarify the profile.

Bob M.: There is a difference between region targeted vs found

BoB F.: Targeted regions should also be included. 3 concepts:  intended to be targeted, what was assayed, what was the call

Uncallable would be option 3(what was the call), A gene panel is 1(intended to be targeted),  

Possibly breaking examples: target gene, find pseudogene. Target gene, which isn’t actually present.

Targeting gene which is often not present. This could be a Variant: absent only filling out the gene id.

Target Gene: ServiceRequest? Order specific genes/mutations to look at. Standard screening panel - may be planDefinition/etc. 

Bob M.: We need guidance on ServiceRequest, “if you want to find the target gene, it has to be included in the ServiceRequest.”

PlanDefinition used by eMerge

What was assayed? Region-studied
Make sure guidance text reflects the meaning.

(what was found? Findings: variant/haplotype/genotype)

Component:gene-mutations is a duplication of parts of the variant profile?

Revisit code of region-studied profile: 53041-0 DNA region of interest panel → which isn’t representing the callability of a region.

Discussion

  • http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-region-studied.html
  • change Present to Callable to answer list
  • get proper code with clear definition
  • use code/answer-list for a new component (rather than observation.value)
  • create temporary answer list
  • https://chat.fhir.org/#narrow/stream/179197-genomics/topic/STU2.20Theme.3A.20Uncallable.20subregions.20in.20a.20region.20studied
    • Graphical example of SNPs in regions studied vs not studied
    • Concerns of definition(s) of callability - 
      • Test limitations as separate observation/model
  • Bob F: when reporting variant results, there’s 
      • a list of variants in context of a reference
      • Statements about the variants (eg heterozygous)
    • The subject of this (region studied) is not a variant - subject of the statement is closely related to the assaying (and the interrogated sequence)
      • Target of the $find-subject-variants operation is not necessarily a database of variants, could be a server storing raw sequencing data (or FHIRized Observations)
  • Liz: suggest we look at eMerge’s usage (or lack thereof) of the region-studied structure
    • relatedArtifact for gene-coverage
    • https://emerge-fhir-spec.readthedocs.io/en/latest/design.html#example-reports
      • Issue 8: request from eMerge to support multiple regions on one instance (possible now, bound to 1 max reference sequence: could be 23 callable region studied observations -- and potentially 23 uncallable region studied observations)
    • Bret: Reports do not NEED to include regions studied, could have (or be able to have) them as needed -- just send details for how/where to find them - architecture around implementing the IG
  • Bob D: reports often come back with read depth and % coverage across the entire studied region - not able to do when limited to 1 reference seq per instance


Future Topics

Orders for genetic testing

  • How to define ServiceRequest.code
  • Multiple tests per report?

LOINC changes for Level of Evidence / Clinical Significance



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


  • 1st/2nd -
  • Discussion -
  • Abstain/Nay/Yea -  / /
  • Result -


(Notes from Jamie:)

  • Want to separate clinical significance from level of evidence.
  • 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)
    • 1st/2nd -
    • Discussion -
    • 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


Chat:

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