CG-2020-10-06

HL7 Clinical Genomics Weekly Call - 6 Oct 2020 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

Agenda

Attendees Sign-in

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

Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org
Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
Kevin Roberg-Perez - Bioi - krp@bioi.com
Anand Kulanthaivel - Clinical Architecture - anand_kulanthaivel@clinicalarchitecture.com
JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
Jamie Jones - BCH - james.jones.bch@gmail.com
Liz Amos - NLM - liz.amos@nih.gov
Bob Dolin - Elimu Informatics - bdolin@elimu.io
May Terry - MITRE - mayT@mitre.org
Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
Bret Heale - Intermountain - bheale@gmail.com
Mullai Murugan - Baylor College of Medicine - murugan@bcm.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
6-Oct	Kevin	WGM Review R4B: JIRA (Dragon Warning) R5: Genomics Guidance updates
13-Oct	Bob M		Oct 18 - “FHIR IG Proposals Due”
20-Oct
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

NMDP/CIBMTR hosting virtual Data Standards Symposium and Hackathon (DaSSH) - Thu morning will be focused on FHIR efforts.

Topic 0: Approval of Minutes from Last Meeting

Sep 15

https://confluence.hl7.org/display/CGW/CG-2020-09-15
Motion: Approve minutes as written

Move / 2nd: Jamie J / Arthur H
Discussion:

Vote: (Abstain / Opposed / In Favor): 1 / 0 / 9
Result: motion passes

Topic 1: WGM Minutes review

Co-Chair Elections:

Bob Milius

Jamie Jones

Mullai Murugan

https://confluence.hl7.org/display/CGW/CG-2020-09+WGM+Minutes

Topic 2: O&O JIRA for R4B updates

https://jira.hl7.org/browse/FHIR-28620

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

Chat:

10:01:49 From Kevin Power : https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit

10:21:38 From Bob Milius : We use the CG IG and MolecularSequence in our implementation. It works well and would be disappointed if it were deprecated.

10:22:12 From Bret H : it's been used in smartonfhir apps too

10:30:30 From Bret H : simplification through reducing named data elements will lead to a large reliance on terminology to provide contextual meaning of data. not a problem but a facet. think about both sending the data and querying the data. I prefer more specific operations for genomics to solve querying across variant representations. but this requires additional build over a base FHIR server. again a caveat not a barrier

10:32:56 From Bret H : using condition makes it hard to find unless everyone does it....

10:33:22 From Bret H : the old adage as long as we all do it wrong, we'll all be good 😁

10:36:19 From Bret H : @May, you've got some great input on biomarkers. sorry I could not attend the meeting.

10:39:16 From Bret H : thanks May for clarifying.

10:42:17 From Bret H : it's related to us core as well

10:43:01 From Bret H : but the elements used in mcode are asubset of the ig elements . you could support both mcode and our ig

10:47:26 From James Jones : Just logged https://jira.hl7.org/browse/FHIR-28943, all are encouraged to comment there

10:48:13 From James Jones : re: biomarker guidance

10:50:25 From Bret H : does the mcode kb have a link? sounds interesting and a great strategy to encourage adoption of your ig.

10:54:17 From may terry : https://confluence.hl7.org/display/COD/Knowledge+Base+-+mCODE

11:02:16 From James Jones : Gotta drop, thanks all!

11:02:21 From Anand Kulanthaivel : I vote "Genes on FHIR". It just has that ring to it.

11:02:55 From Kevin Roberg-Perez : Excellent …. although in Dad joke zone

11:03:06 From Bret H : awesome

11:04:47 From Kevin Roberg-Perez : Bye all

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)