Chair: Bob Milius
Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - email@example.com )
- Mullai Murugan - Baylor College of Medicine - firstname.lastname@example.org
- Bob Dolin - Elimu Informatics - email@example.com
- JD Nolen - Children’s Mercy Hospital - firstname.lastname@example.org
- Rachel Kutner - Epic - email@example.com
- Jamie Jones - BCH - firstname.lastname@example.org
- May Terry - MITRE - mayT@mitre.org
- Kevin Roberg-Perez - Bioi - email@example.com
- Joel Schneider - NMDP/CIBMTR - firstname.lastname@example.org (:44)
Standing Informational Items
Agendas and Important Dates
CG Call Date
R4B: JIRA (Dragon Warning)
R5: Genomics Guidance updates
Oct 18 - “FHIR IG Proposals Due”
IG JIRA proposals
Topic 1: NIB
Topic 2: Updates to background section of FHIR Genomics Guidance
Topic 3: FSH Migration Update
Topic 4: eMERGE updates
Nov 1 - NIB deadline for January cycle
Topic 1: Updates to background section of FHIR Genomics Guidance
Topic 2: FSH Migration Update
Nov 15 - Initial Content Deadline
Nov 19 - Connectathon Proposals Due
Bob D: pharmacogenomics pipeline connectathon track?
Dec 6 - Final Content Deadline
Connectathon Jan 13-15, 2021
Virtual WGM Jan 25-29, 2021
- GA4GH (Global Alliance for Genomics and Health)
- GA4GH news
- working group meeting (virtual plenary) was Sept 29-30
- 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
- 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
- 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
- May T: not necessarily aligning to CG IG; talking about biosamples, regimen data, not that active right now
- Jamie: Are they looking at composition?
- May T: not really looking at IG at all, or even looking at FHIR
- Bob M: so closer to modeling work? Not implementation
- May T: Yes
- 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 complete, final report under review by ONC
- Phase 4 has started; call for demonstration sites has been announced, submissions due Jan 8, 2021
- 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)
- 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
- Mullai: mostly wrapped up, just have to do the manuscript (almost done)
- 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?
- May T: last internal sprint, going through FSH migration; evaluating roadmap to mCODE STU2 release to use Genomics Reporting IG more directly; should there be an interim release of Genomics Reporting IG after STU2 ballot? mCODE can't derive from an IG that won't validate. Needs a published snapshot, this could be a ballot snapshot. Genomics Reporting IG needs to become more stable. Revisit in Jan 2021.
- Information Modeling (IM) (Bob F)
- slides in minutes
- Draft model docs:
- 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
- Expanding draft model of definitional variant - in progress
- Attempting to align with GA4GH VR (as usual)
- Working on structural variation, including copy number/abundance
- FHIR (Jamie)
- Initial content deadline - all set
- Connectathon proposals
- Currently we don’t have a proposal. If we don’t get a proposal ready, we have to skip our own track (again).
- Bob D: potential topic: pharmacogenomic converter: FHIR DR -> VCF -> pharmcat (Mullai interested)
- Remaining JIRA CG JIRAs November 2020, Variant component groups v2
- Jira trackers have to be voted on before the end of November.
- Github merge
- 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 <- in R5
- Updated discussion on Friday’s LAB call: https://confluence.hl7.org/display/OO/2020-11-13+LAB
- JD: discussion continuing, see "diagnosticReport/composition" section of confluence page above.
- Mullai: nested diagnosticreports?
- JD: still working on it
WG projects and outreach
Topic 0: Approval of Minutes from Last Meeting
- Motion: Approve minutes as written
- Move / 2nd: Clem / Jamie
- Vote: (Abstain / Opposed / In Favor): 0 / 0 / 6
Result: motion passes
Topic 1: CDA status
- Reconciliation spreadsheet:
- The CG WG already voted to submit this CDA IG for publication:
- The Publication Request document is found here:
- Bob M met with CDA Mgmt group to discuss publication of the Genetics Reporting CDA as informative. Bob's report:
- "I just finished the call with the CDA mgmt group re our IG. They were very confused about the history, especially when the document we were publishing identifies itself as a DSTU and includes language such as SHALL and SHOULD. Informative documents would not have those. If someone downloads an Informative document, it shouldn't be presented as a DSTU which is what the PDF says it is. They thought that the original DSTU should just be relabeled as Retired which would accomplish what we really want, that the IG would live on and be retrievable in the future. I emphasized that that would be fine with us, but we don't want more work, and are not sure about what are the next steps. We tried to abandon it, but we were told that since It already has been balloted we had to submit the reconciliation spreadsheet and finish the process. So now what? The CDA mgmt group said they would contact the TSC on our behalf to figure out the best way forward, hopefully without more work for us."
- Email from Lisa Nelson:
Hello! After meeting with Lynn Lasko, we wanted to follow up regarding your publication request to publish the Clinical Genomics Report IG as an Informative resource.
We can publish this as an Informative resource, but you need to remake the publication with the following changes:
- Include the balloted reconciled artifact using the same cover page as was used in the January 2018 ballot. This should be include in the zip file in Word format.
- Include a _readme.txt file. Do not include the CDA.xsl style sheet. The _readme.txt explains where to get the CDA stylesheet. Attached is a draft _readme.txt file based on the package that was submitted to CMG. Please review and make any needed changes.
- Update the Publication Request accordingly. This is Genetic Testing Report, Release 1 and it is Informative. (Example: CDAR2_IG_GENTESTRPT_R1_I1_2020NOV) The URL of publication material / SVN repository on the Publication request points to the initial material from 2013 and not the updated material. Please update to the correct link for the package material that includes the Informative information on cover page, title of document, footer, etc. It may be needed to include the updated publication date of 2020NOV.
After those changes are complete, have your Workgroup vote to approve to publish the updated Publication Package, then return the new Publication Package and the link to the Publication Request before the next CMG meeting on November 18th, and we will get your request approved.
- Won't get done by Nov 18.
Topic 2: Inclusion of Genetic Test Results to FHIR Core Resources
- "I would like to propose adding a summary of genetic test results to a patient’s EHR. Information such as a patient’s germline genetic test results or Polygenic Risk Scores typically do not change over time (barring variant reclassification) and could be considered as possible candidates to be part of the patient’s primary health information along with demographics, family history or allergy information."
- Came from eMerge project
- How can test results be pushed to EHR?
- Part of patient's record (PDF aren't transferred?)
- Use Condition?
- Clem: problem with putting problem list in report is "which problem list?" And lab report don't include this kind of information -not portable
- Bob D: using problem list is complicated
- JD: using problem list can be thorny. Makes problem list unusable.
- Rachel: Epic has a genomic flavored problem list.
- JD: is Epic capturing HPO codes?
- Rachel: Epic solution isn't generalizable
- May T: +1 with Clem’s comments. Problem lists are a snapshot and in some cases could be relative to the specialist or even encounter.
- May T: +1 on Bob’s proposal. Site-specific logic could enable the provider to add or prioritize it.
- What is found in the report? vs what needs to pushed to EHR? Our IG is focussed on lab report, not on workflow to use the report.
- Jamie: Sounds like a good use for Observation.category
- Clem: define what can be in the report that could segue to problem list
- JD: where is the EHR is the blood type? Observation? or should it be part of patient demographics?
- Clem: will always be retyped before any transfusion or need for it.
- May: Condition has an evidence data element that can reference Any (e.g., DiagnosticReport)
- Jamie: Regarding Polygenic Risk Scores, we really haven’t discussed them much. We do have some support for referencing RiskAssessment resources on the DiagnosticReport. Don’t think we’ve done our homework on how to model them there yet though. Bob F left good comments on the linked doc, in my opinion
- From Bob M to Everyone: (10:03 AM)
- From may terry to Everyone: (10:39 AM)
- +1 with Clem’s comments. Problem lists are a snapshot and in some cases could be relative to the specialist or even encounter. +1 on Bob’s proposal. Site-specific logic could enable the provider to add or prioritize it.
- From James Jones to Everyone: (10:48 AM)
- Sounds like a good use for Observation.category
- From may terry to Everyone: (10:51 AM)
- In agreement with Clem.
- From James Jones to Everyone: (10:57 AM)
- Regarding Polygenic Risk Scores, we really haven’t discussed them much. We do have some support for referencing RiskAssessment resources on the DiagnosticReport. Don’t think we’ve done our homework on how to model them there yet though. Bob F left good comments on the linked doc, in my opinion
- From Rachel Kutner (Epic) to Everyone: (11:02 AM)
- Yeah, thank you Mullai - this is definitely a clinical issue that needs solving
- From may terry to Everyone: (11:02 AM)
- From Mullai Murugan to Everyone: (11:03 AM)
- thank you! This was very helpful to me as well!