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Chair:  Bob Milius

Scribe: Bob Milius



HL7 Clinical Genomics Weekly Call - 18 August 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

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Meeting ID: 298 006 8716

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Agenda

Attendees Sign-in

Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org

  1. Patrick Werner - MOLIT Institut - pw@molit.eu
  2. Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com 
  3. Jamie Jones - BCH - james.jones.bch@gmail.com
  4. May Terry - MITRE - mayT@mitre.org 
  5. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  6. Bob Dolin - Elimu Informatics - bdolin@elimu.io   
  7.  Ling teng -BWH -tenglingling@gmail.com
  8.  Michael Hultner - Optum - michael.hultner@optum.com
  9.  Daniel Rutz - Epic - drutz@epic.com
  10.  Rachel Kutner - Epic - rkutner@epic.com
  11.  Ning Xie - BWH - nxie1@bwh.harvard.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

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




9/1/20




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)
    • working group meeting (virtual plenary) coming up this fall
    • 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!
    • 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
    • GA4GH news
    • Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
    • Clinical & Phenotypic Data Capture Work Stream
  • 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)
    • 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
    • Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • mCODE (May Terry)
    • Better representation of prognostic factors, including serum tumor markers  in the Genomics related elements.
    • STU1 published - http://hl7.org/fhir/us/mcode/
    • Initial feedback from some reviewers (UCSF, Princess Margaret of Toronto) for mCODE enhancements:
    • working on STU2 version, would like to better align with CG IG next release

Subgroup reports


WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting


Aug 11


Topic 1: Block vote

Link to JIRA Query for the block vote items.

https://jira.hl7.org/issues/?filter=13081

See chat at https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Block.20Vote.3A.20Tuesday.2C.20August.2018th 

From yesterday's FHIR subgroup meeting, FHIR-27146 is pulled from block.

Discussion

Current Block:

Key

Resolution

Summary

Reporter

Resolution Description

Not Persuasive

Do we need an introductions for Background of IG and before 1.1?

Gil Alterovitz

FHIR-20165

Persuasive

Once the IG is finished ask O&O to remove our deprecated artifacts from core for R5

Patrick Werner

Persuasive - Removed profiles, extensions, examples for genomics under Observation, DiagnosticReport, and ServiceRequest. Streamlined genomics.html (Implementation Guidance).

FHIR-22802

Persuasive

set StructureDefinition.abstract true on all abstract profiles

Patrick Werner

Now that we have plain text StructureDefintions, we can make this change.

FHIR-22829

Persuasive

secondary-finding has Observation Category Codes as name & title

Pascal Pfiffner

Correct the Name and Title of the Secondary Findings code system and value set.

FHIR-25187

Persuasive

CG IG TaskRecFollowup profile code should be extensible

Larry Babb

Change the binding to extensible.

FHIR-25241

Persuasive with Modification

Missing LOINC codes in Variant profile (but are in UML)

Liz Amos

Fix the codes in the UML diagram as indicated.

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.'

FHIR-25418

Persuasive

Require "Genetics" category on report

James Jones

Change cardinality of .category to 1..*, and the fixed value slice of GE to 1..1

FHIR-26905

Persuasive

HGVS is misspelled

Liz Amos

Correct spelling

FHIR-27942

Persuasive

Convert IG from spreadsheets to StructureDefinitions

Kevin Power

Persuasive. Work group will cease reliance on spreadsheet templating and will move to editing profile structure definitions directly. We will explore free or open source tooling (e.g., Forge, FSH) for future development. NOTE - This is a backend change and will only impact the technology stack for applying future updates to our structure definitions.


  • FHIR-25296 pulled from block
  • Motion: Accept proposed resolutions as written 
    •   none   
    • Move / 2nd:  Patrick  /    Anand
    • Discussion:
    • Vote: (Abstain / Opposed / In Favor):   0 /  0   / 10     
    • Result:   motion passes 

Topic 2: Scheduling WGM Sessions

Proposed time slots


From chat.fhir.org: Sep 2020 WGM Topics 

  • Jamie Jones: Adding to one point that came up further in the notes--we could go through intro slides covering the IG and some major use cases and examples for newcomers. We could build it out from materials we've presented at DevDays in the past and may even want to add a link to a slidedeck to the IG itself--the bulk data IG does this, though we may want to host it on confluence rather than somebody's google account.
    Also we still need to cover how our joint with O&O and FHIR-I are structured - who is hosting, is anything else happening in 'our room' during, and talking points


Topic 3: Uncallable Regions (continued discussion)

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.”

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

Clinical Genomics Reference Docs


Chat:

  • From Bret H to Everyone: (11:00 AM)
    • 
Patrick's question on HRD score brings up the point of where the threshold is between extension vs adding a new component. there are very many types of scores, and there will be many in the future. perhaps the score is an observation