CG-2020-10-13

Patrick Werner - MOLIT Institut - pw@molit.eu
Dora Walter - MOLIT Institut - dora.walter@molit.eu
JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
Jamie Jones - BCH - james.jones.bch@gmail.com
Kevin Power - Cerner - kpower@cerner.com
May Terry - MITRE - mayT@mitre.org
Bob Dolin Elimu Informatics - bdolin@elimu.io
Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
Mullai Murugan - Baylor College of Medicine - murugan@bcm.edu
Liz Amos - NLM - liz.amos@nih.gov
Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu (at x:12 during CDA)
Bret Heale - Intermountain - bheale@gmail.com

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
6-Oct	Kevin	WGM Review R4B: JIRA (Dragon Warning) R5: Genomics Guidance updates
13-Oct	Bob M	CDA publishing R5: Genomics Guidance updates	Oct 18 - “FHIR IG Proposals Due”
20-Oct	Jamie
27-Oct	Kevin		Nov 1 - NIB deadline for January cycle
3-Nov	Kevin
10-Nov	Patrick		Nov 15 - Initial Content Deadline
17-Nov	Bob M		Nov 17 - Connectathon Proposals Due
24-Nov	Patrick
1-Dec			Dec 6 - Final Content Deadline
8-Dec	Kevin
15-Dec	Bob M
22-Dec	Patrick
29-Dec
5-Jan	Bob M
12-Jan	Kevin
19-Jan	Patrick
Connectathon Jan 13-15, 2021 Virtual WGM Jan 25-29, 2021

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

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 (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?

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)

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

WG projects and outreach

none

Topic 0: Approval of Minutes from Last Meeting

Sep 15

https://confluence.hl7.org/display/CGW/CG-2020-10-06
Motion: Approve minutes as written

Move / 2nd: Jamie J / Patrick W
Discussion:

none

Vote: (Abstain / Opposed / In Favor): 0 / 0 / 11
Result: motion passes

Topic 1: Oct 18 - “FHIR IG Proposals Due”

Discussion -
Probably doesn't apply to us - new IGs, radically changes
Ours is a STU2 of Genomics Reporting IG

Topic 2: CDA IG for Genetic Testing Reports - Publication

Background:

This CDA IG originally passed ballot in the September 2012 ballot cycle and published as a DSTU. But because we had no plans on moving this to Normative, we were told it was going to expire after 5yrs. So, we wanted to re-ballot it as Informative to inform any future work in this domain. Amnon Shabo took the lead on this as he was the principal author. It passed the May 2018 ballot, but the reconciliation spreadsheet was never submitted.

This was identified as something we needed to finish off for our WG health metric. Because it was balloted, we could not simply withdraw it. We had to submit the reconciliation spreadsheet so we did.

Reconciliation spreadsheet:
http://www.hl7.org/documentcenter/public/ballots/2018JAN/reconciliation/recon_cdar2_ig_gentestrpt_r1_i1_2018jan.xls

The CG WG already voted to submit this CDA IG for publication:

https://confluence.hl7.org/display/CGW/CG-2020-05-26

Now we needed to submit a Publication Request document. Bob M started this and Grant Wood completed it.

The Publication Request document is found here:

https://confluence.hl7.org/display/CGW/CDA+Implementation+Guide+for+Genetic+Testing+Reports+-+Publication+Request

Next steps:

CG WG reviews the contents of the form. It adds any keywords (if any, not required) to Question 48.
If approved on the next CGWG call, Grant has pre-populated Questions 37 and 38. Change date on 38 if needed.
Send Confluence form link to the CDA Management Group (CMG) co-chair Linda Michaelsen linda.michaelsen@optum.com. Their next meeting is November 4th. They may or may not ask for a CGWG rep to answer questions about the request on the call.
When approved by the CMG, send the Confluence form link to Anne Wizauer anne@hl7.org. She will present it to the TSC for final approval. We do not know the date of the TSC call at this time.

To do next week:

Motion: Approve Publication Document as written
Move / 2nd: /
Discussion:

Vote: (Abstain / Opposed / In Favor): / /
Result: motion

Topic 3: 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

Bob D:

keep the page short
highlight groups using it

Bob M: highlight that we are actively engaged with external genomics groups to inform the IG

Bob M will write up description of actively working with external groups to inform IG
Focus of this page should be pointing to the IG. It should be the primary message learned by the reader

Kevin -

Diagnostic Module

update "Genomics Implementation Guidance" to "Overview of Genomics"
(bare minimum to update the name and update figure to rename Sequence to MolecularSequence)
New JIRA if other changes should be considered

Topic 4: FSH update

May: could use more contributors (either dev/authoring or at QA level)
Bret: technical dependencies
May: no, spreadsheet is used for tracking
Kevin: Sushi 1.0 and Publisher and text editor for developers
Jamie: Any plan for doing examples in FSH?
Bob: will do Genotype, Haplotype, and HLA examples in FSH
Patrick: will this be usable with GoFSH? (StructureDef-->FSHd
May: still limited, no support for valuesets, etc

Chat:

From Bret H to Everyone: (10:43 AM)
 the rules on FHIR from onc are important drivers. genetic reporting for what? make sure that is defined 
From Bret H to Everyone: (10:47 AM)
 it's for exchange that supports clinical decision making, right? not only research transmission of data 
From Patrick Werner to Everyone: (10:51 AM)
 all use cases: CDS, research, daily care

Future Topics

Orders for genetic testing

How to define ServiceRequest.code
Multiple tests per report?

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
https://loinc.org/93044-6/

https://loinc.org/LL5356-2/

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

https://r.details.loinc.org/AnswerList/LL4034-6.html

1st/2nd -

Discussion -

Abstain/Nay/Yea - / /

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:
E.g. from http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncologyexamples-r4.xml

(note, this example uses placeholder value “AMP Guidelines” instead of a tier)
Profile: http://build.fhir.org/ig/HL7/genomics-reporting/somatic-predictive.html
Code: somatic-predictive (TBD LOINC)
Value: E.g. Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response
Component: Level of evidence -

Code: 93044-6,
Value: from LOINC Answer List LL5356-2 (preferred) CAN USE TIER SYSTEM HERE

Component: medication
Component: cancer

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)