HL7 Clinical Genomics Weekly Call - 07 Apr 2020 11:00 AM (US Eastern)
Attending the meeting
Join Zoom Meeting
Meeting ID: 298 006 8716
One tap mobile
+16699006833,,2980068716# US (San Jose)
+19294362866,,2980068716# US (New York)
Dial by your location
+1 669 900 6833 US (San Jose)
+1 929 436 2866 US (New York)
+1 253 215 8782 US
+1 301 715 8592 US
+1 312 626 6799 US (Chicago)
+1 346 248 7799 US (Houston)
Meeting ID: 298 006 8716
Find your local number: https://zoom.us/u/adNIRW2P8J
Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - email@example.com):
- Patrick Werner - MOLIT Institut - firstname.lastname@example.org
- Dora Finkeisen - MOLIT Institut - email@example.com
- Joel Schneider - NMDP/CIBMTR - firstname.lastname@example.org
- Kevin Power - Cerner - email@example.com
- Lloyd McKenzie - Gevity - firstname.lastname@example.org
- Bob Dolin - Elimu Informatics - email@example.com
- JD Nolen - Children’s Mercy Hospital - firstname.lastname@example.org
- Bob Freimuth - Mayo Clinic - email@example.com
- Liz Amos - NLM - firstname.lastname@example.org
- Stephen Schwartz - Epic - email@example.com
- Clem McDonald - NLM - firstname.lastname@example.org
- Perry Mar - Health Catalyst - email@example.com
Standing Informational Items
Agendas and Important Dates
CG Call Date
Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)
Topic 2: Update/Discussion on Implication Profiles (Jamie)
CG IG Lite: Liz & Clem
1: CMS/ONC rules
2: Vote on operations for IG
3: STU2 of IG
1: Reminder - CMS/ONC rules
2: STU2 of IG (cont...)
Tumor/normal examples to review
Working Group Meeting
Cancelled! May 16-22, 2020 • San Antonio, Texas
CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday
- GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)
- Having virtual connect meeting starting today,
- agenda has changed, still hope to include some working sessions
- Bob will report back after the meeting
- V1 RC was approved by GA4GH
- 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
- Looking to develop AI tool for literature review for poly-genetic risk, generate guidance
- Create KB on G2MC website
- 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
- GA4GH news
- Variant Representation (formerly VMC) (lead by Larry Babb/Alex Wagner/Reece Hart)
- Variant Annotation
- Phenopackets on FHIR
- Pedigree Activity (Grant Wood)
- G2MC (Grant Wood)
- HLA reporting (Bob F)
- 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 and approved (in the process of being)
- ACI manuscript is in press
- Phase 3 has started - more details to be announced soon
- ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob)
- March 30 - April 3, 2020 in Arlington, VA
- Looks to be virtual only
- Bob F - attended, alike to HL7 meeting for first time, mostly status reports, at end a number of proposals were voted on by different countries and adopted
- eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
- Kevin P: mostly completed their work, have not broadly shared yet. Need to finalize some details.
- Clem: is there a document summarizing their FHIR work?
- Kevin: something presented in past meetings
- Mullai: still work in progress
- STU1 published - http://hl7.org/fhir/us/mcode/
- Information Modeling (IM) (Bob F)
- Ideally would like to computationally derive it from the conceptual model, but will likely have to create most of it manually
- Scott is evaluating options
- Conceptual model => logical model => physical model
- FHIR profiles/IGs would be expressed as a physical model
- Logical: language-neutral model for implementation, specifies relationships, cardinalities, data types that will map down to the physical layer
- Logical model provides a traceable link between our conceptual IM and the physical layer (e.g., FHIR)
- Bob F: No, just trying to illustrate more explicitly how our conceptual model maps into the FHIR space
- Minutes: https://docs.google.com/document/d/15kBa3HqxQfwwe0Uwgx3UNashTIanpGRiyRVbimE_j3A/edit#
- Draft model docs: https://docs.google.com/document/d/1Wys14HNJAEB_YJ-EeDPAKX50_oxiDqAKi3WD4wlfjbk/edit
- Export of model (http://gcds.mayo.edu/HL7CG/IM_190604/model.html)
- Currently looking at tooling to develop a logical model from our conceptual model
- Model-Driven Architecture (MDA)
- Arthur: does this mean people will have trouble implementing IG will have trouble because it isn't aligned with model?
- recently looked into tooling for logical models. Scott and Lloyd have worked on this.
- FHIR (Jamie, Patrick)
- Identifying priority FHIR topics for next cycle
- Discussion split off into brainstorming doc for Implications https://docs.google.com/document/d/1SYdzxanCgkwzhhBJCBrguZ6H8HdjQFjG_l2nufAkCGU/edit#heading=h.n5eokak2o6ca
- Preparing proposals
- Reducing annotation/implication profiles Simplications IG STU2
- IG LITE companion - preparing to tighten guidance on Variant - better highlighting/comparing definitional components vs observational, showing which concepts may be derived from/related to others
- Looked at examples for Implications, compared old way vs new way.
- Implication migration spreadsheet of notes from migrating examples
- discussed connectathon track, IG Lite (use of invariants), implications text
WG projects and outreach
Topic 0: Approval of Minutes from Last Meeting
- Motion: Approve minutes as written
- Move / 2nd: BobF/Patrick
- Vote: (Abstain / Opposed / In Favor): 0 / 0 / 10
- Result: motion passes
Topic 1: Ability to include interpretation text/findings and recommendations to Observation (FHIR-20978)
- "As highlighted in the attached test reports, we include textual findings/interpretations and recommendations in a genetic report. For the eMERGE reports, while mapping to draft CG IG spec, these textual interpretations span multiple FHIR Observation profiles in our implemention e.g. Referencing file "highlighted..." test report, text highlighted in grey and yellow would be a fit for general profiles like obs-overall and obs-inh-dis-path; text highlighted in green would be a fit for PGx profiles and the recommendations text highlighted in blue is a recommendation for the provider but not exactly a recommended action; it would be up to the provider to decide on the recommended action.
Considering the need for including this kind of interpretative/summary text (this is not the same as the "text" narrative element) spans multiple Observation resources, it would be very helpful if Interpretation Text and Recommendations were added as Narrative or String elements to the obs-base resource itself."
- This was submitted last year (2019-04-25)
- Deferred to after publication of STU1 of IG, now re-opened
- Options mentioned in issue comments
- human readable summary of entire resource instance
- not really appropriate
- KP - not sure if this is where it should go
- Clem - why is doesn't work?
- KP - implementation issues?
- JD - are we overloading it? should it move to DR?
- see above for ob.text
- concerned with if this appropriate
- use case is generalizable and will be used by others, so OO should address this.
- suggest propose to OO a poison pill that forces them to fix it.
- Observation.text (Narrative)
- Observation.note (0..* Annotation)
- new component under observation with valueString
- could this just be the value of the observation?
- extension - add when needed
- Need for distinct requirements for each use case, may be appropriate for components
- KP: addition guidance may be included as a standalone observation and can be derivedFrom in another observation. Patrick agrees this is viable.
- Patrick: do we need additional qualifier? e.g., method info, guidance info
- Clem: maybe use Patrick's suggestion of complex extension.
- KP: not in favor of using .note, unless we can distinguish what kinds of notes are included
- include extension in our IG until OO decides on including it as a base extension.
- extension - would NOT have to create codes for each type of note
- component - would need to have a separate code for each type of note
- Patrick - complex extension would have a type with a valueString. Can be reused.
- KP - keep it unbound, provide guidance how to use (narrative? annotation? string?)
- KP - .note has datatype of annotation
- Proposed motion: KP will write up a proposed motion to use complex extension on zulip for comments, will vote on this next week.
- Bob F raises his hand (and a shield for the rotten veggies that are about to be hurled at him)
- discussed in this recent thread
- related zulip thread on methodology
Topic 2 : cont from FHIR subgroup meeting
Would be done via Zoom, 24/7 Connectathon. Official Information to come
from CG FHIR subgroup minutes:
- Connectathon track review https://confluence.hl7.org/display/FHIR/2020-05+Genomics
Jamie: Important to check query ability as well
Bob M: wants to test out his HLA IG, or provide insight on how to constrain our IG to make a use-case specific IG.
Bob D: testing subject-variant operation could be an option. Could provide a server which supports the operation.
Bret: A Scenario: searching for the same Variant with different Variant Identifiers (ClinVar, hgvs, …) on the Repository would be nice.
- Bob D - will go forward and make the Genetic Data Server to test operation. Would be great to have a partner to test this. Jamie & Bret are interested
- Patrick - evaluate use cases of current build IG, how east to query information, eg need all driver mutations displayed for practitioners.
- Bob M - working on profiling CG IG for more constrained use cases - issues?
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
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:
(note, this example uses placeholder value “AMP Guidelines” instead of a tier)
Code: somatic-predictive (TBD LOINC)
Value: E.g. Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response
Component: Level of evidence -
Value: from LOINC Answer List LL5356-2 (preferred) CAN USE TIER SYSTEM HERE
- 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 - / /
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
- Mission & Charter
- Currently displayed here:
- Edit here:
- Approved in Sep 2019 WGM
- Review complete as of Aug 1, 2017
- Approved in Sep 2019 WGM
- Decision Making Process
- New DMP: http://www.hl7.org/documentcenter/public/procedures/Default_HL7_WG_DMP_2018.pdf
- DMP Addendum template: http://www.hl7.org/documentcenter/public/procedures/DMP_Modification_Template_2018.docx
- We will review/edit/approve by Sep 2019 WGM