CG-2020-11-03

Chair:  Kevin Power

Scribe: Kevin Power

HL7 Clinical Genomics Weekly Call - 03 Nov 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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Agenda

Attendees Sign-in

Presiding Co-Chair (Kevin Power - Cerner - kpower@cerner.com ) 

1. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
2. Arthur Hermann- Kaiser Permanente - arthur.hermann@kp.org
3. JD Nolen = Children’s Mercy Hospital - jlnolen@cmh.edu 
4. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com 
5. Liz Amos - NLM - liz.amos@nih.gov 
6. Jamie Jones - BCH - james.jones.bch@gmail.com 
7. Rachel Kutner - Epic - rkutner@epic.com 
8. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
9. Bob Dolin - Elimu Informatics - bdolin@elimu.io  
10. Ling teng - BWH - lteng@bwh.harvard.edu
11. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
12.  

Standing Informational Items

Agendas and Important Dates 

External efforts

• GA4GH (Global Alliance for Genomics and Health)
• GA4GH news
• working group meeting (virtual plenary) was Sept 29-30
• https://broadinstitute.swoogo.com/ga4gh-8th-plenary/455678
• Recordings available!
• Genomic Knowledge Standards (GKS) Work Stream (leads: Bob Freimuth, Andy Yates)
• Variant Representation subgroup (lead by Larry Babb/Alex Wagner/Reece Hart)
• VRS 1.1 released: https://vr-spec.readthedocs.io/en/1.1/
• Added support for ChromosomeLocation, Haplotype, VariantSet
• See ongoing project board at https://github.com/orgs/ga4gh/projects/5
• Variant Annotation subgroup (lead by Matt Brush and Javi Lopez)
• Working on statements about therapeutic interventions and variant pathogenicity
• https://docs.google.com/spreadsheets/d/1zQU-Yv7gB7IHKIOVsTh-74BwdtgB9KQpKcWkSHZOa-Q/edit
• Sequence Annotation subgroup (lead by Karen Eilbeck and Shawn Rynearson)
• Brand new activity
• Open to all participants!
• Minutes: https://docs.google.com/document/d/1izgaIy925xQf3opiU_O5Ru9IwlXrjOdfXS542s8QJG4/edit
• Clinical & Phenotypic Data Capture Work Stream
• Pedigree Activity (Grant Wood)
• help GA4GH community to understand HL7 Pedigree standards
• https://docs.google.com/spreadsheets/d/1AxRufaSICADO_f9CAhbkVh5dChT4FjHZgvGFFdC-2WI/edit
• 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
• https://phenopackets-analysis.readthedocs.io/en/latest/
• 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
• 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 (an update was shared at the WGM)
• 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)
• https://emerge-fhir-spec.readthedocs.io/en/latest/ 
• Pilot project has completed
• Manuscript in preparation
• eMERGE 4 sites have been announced, will focus on polygenic risk scores
• NHGRI will continue to support work with FHIR and our IG
• 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
• WGM - mCode update, would like to move time slot to later in the week
• Someone created a genomics report using mCode, made some assumptions. It would be good to see how they interpret it;  perhaps discuss at WGM as an example; test based on 21 gene panel, but it doesn't report variants; should this be treated a genomics report? or as a tumor marker test? actually a gene expression test. Should gene expression test be considered a genetic test?
• https://www.oncotypeiq.com/en-US/breast-cancer/healthcare-professionals/oncotype-dx-breast-recurrence-score/interpreting-the-results
• https://patentimages.storage.googleapis.com/39/50/d7/962c1e8f62250f/WO2014130617A1.pdf 

Subgroup reports

• Information Modeling (IM) (Bob F)
• Minutes:
• https://docs.google.com/document/d/15kBa3HqxQfwwe0Uwgx3UNashTIanpGRiyRVbimE_j3A/edit#
• slides in minutes
• Draft model docs:
• https://docs.google.com/document/d/1Wys14HNJAEB_YJ-EeDPAKX50_oxiDqAKi3WD4wlfjbk/edit [outdated]
• Export of model (http://gcds.mayo.edu/HL7CG/IM_190604/model.html) [outdated]
• Developed tooling to convert EA XMI to FHIR XML
• Developing a logical model from our conceptual model
• Finished discussing elements related to Variant from our IG, will pull into the IM
• Draft model of definitional variant - in progress
• Attempting to align with GA4GH VR (as usual)
• Working on structural variants next

• FHIR (Jamie)
• Minutes:
• https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/
• Discussed remaining steps and deadlines to ballot our FHIR IG in Jan 2021 cycle
• Looking for volunteers to help propose new/better examples:
• example modeling stu2 genomics reporting IG 
• FSH migration updates
• LOINC TBD submission
• OO Work (JD)
• DiagnosticReport work to handle complex reports 
• Proposal to use Composition to handle the sections (the style) and connect this to DiagnosticReport via presentedForm 
• https://jira.hl7.org/browse/FHIR-29258 
• Talking about this on OO on FHIR calls (Tuesdays 2PM EDT)
• Question on inclusion of multiple DRs here (and not just multiple Obs)
• Composition approach may assist interpretation/notes

WG projects and outreach

• none

Topic 0: Approval of Minutes from Last Meeting

Oct 27

• https://confluence.hl7.org/display/CGW/CG-2020-10-27 
• Motion: Approve minutes as written 
• Move / 2nd: Bob F / Bob M
• Discussion:
• none
• Vote: (Abstain / Opposed / In Favor):  0 / 0 / 9
• Result: motion passes

Topic 1: Updates to background section of FHIR Genomics Guidance

https://docs.google.com/document/d/139W4FZ2U2w7fk2zcjqT15-_PdgBgiql_bswlXXu3nmo/edit#heading=h.ogvgzwyoicd3

Reminder, here is the current (R5) page:

http://build.fhir.org/genomics.html 

• Discussion:
• Bob M - Priorities:
• IG stu2 content
• R5 guidance page content
• R5 molecularSequence updates
• Next Steps:
• Send draft to listserv, vote next week to update R5 page 
• Log separate tracker for adding appropriate narrative content to molecularSequence for R5

Topic 2: FSH Migration Update

• Tracking sheet for FSH migration issues: CGReportingIG-to-FSH-MigrationTracker.xlsx
• Goal: 
• Discussion of issues