Skip to end of metadata
Go to start of metadata

Chair:  Kevin Power

Scribe: Kevin Power
 


HL7 Clinical Genomics Weekly Call - October 30, 2018 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall

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

Attending the meeting

Join the online meeting (VoIP available with this):

Dial into the conference:


Agenda



Attendees Sign-in

(Presiding co-chair: Kevin Power - Cerner - kpower@cerner.com )

  1. Deepak Sharma - Mayo Clinic - sharma.deepak2@mayo.edu

  2. Caterina Lasome - iON Informatics - cat@ioninformatics.com

  3. Andrea Pitkus - apitkus@gmail.com

  4. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org

  5. Patrick Werner - MOLIT Institut/ Heilbronn University - patrick.werner@molit.eu  

  6. Mullai Murugan BCM murugan@bcm.edu

  7. Jamie Jones - BCH - james.jones.bch@gmail.com

  8. Liz Amos - NLM - liz.amos@nih.gov

  9. Clem McDonald - NLM - clemmcdonald@mail.nih.gov

  10. Jamie Parker - Carradora Health - jamie.parker@carradora.com

  11. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org

  12. Ning Xie - BCH - ningxie2018@gmail.com

  13. Arthur Hermann - Kaiser Permanente - arthur.hermann @kp.org

  14. JD Nolen - Children’s Mercy - jlnolen@cmh.edu

  15. Bob Dolin - Elimu Informatics - bdolin@elimu.io

  16. Gideon Giacomelli - Berlin Institute of Health - gideon.giacomelli@charite.de

  17. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com

  18. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu

  19. Scott Robertson - Kaiser Permanente - scott.m.robertson@kp.org

  20. Gil Alterovitz - BCH- gil.alterovitz@gmail.com

  21. Bret Heale - Intermountain Healthcare - bheale@gmail.com




Previous Minutes Approval

Agendas and Important Dates


Date

Co-Chair

Agenda

Important Dates

9-Oct-18


No Meeting


16-Oct-18

Kevin P

WGM Review

2-to-FHIR PSS - vote

Committers channel on Zulip

NIB for IG - vote

Code Systems / Value Sets


23-Oct-18

Kevin P

FHIR IG Block Vote - vote

Committers channel on Zulip

Code Systems / Value Sets


30-Oct-18

Kevin P

Tracker 19453 - Rename Sequence -> MolecularSequence

Tracker 19440 - Update to ‘stu note’ on FHIR Core profiles and artifacts

Tracker 1900 - Relax cardinality for reference.windowStart/windowEnd

Previous FHIR Core Trackers with no or inadequate resolution documented

Code Systems / Value Sets (Discussion: Patrick/Julian)

Oct 31: All R4 STU comments reconciled in gForge with votes and no “tracker issues”

Oct 28: NIBs due - IG must be “feature complete” and building in HL7’s continuous integration environment.  If not, the NIB will be refused

6-Nov-18




13-Nov-18



Nov 18: IG Content deadline – only QA changes after this point

Nov 18: IG Ballot reconciliation due

20-Nov-18




27-Nov-18




4-Dec-18



Dec. 2: IG Final freeze deadline

11-Dec-18



Dec 7 - Ballots opened

18-Dec-18




25-Dec-18




1-Jan-19




8-Jan-19



Jan 7 - Ballots closed

2019 January Working Group Meeting

Health Level Seven International January 2019 Working Group Meeting, San Antonio, TX

  • Location: San Antonio, TX United States

  • Start Date: January 12, 2019

  • End Date: January 18, 2019

External efforts

  • GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)

  • DIGITiZe (aka National Academies)  (Grant Wood, JD Nolen)

    • Stilling planning, Working to get a planning call on the schedule to move things forward (JD)

  • ClinGen/ClinVar (Larry Babb, Bob Freimuth)

    • no report

  • CDISC PGx (Dorina B.)

    • no report

  • ONC Sync for Genes (Bob Freimuth)

    • Pilot sites are planning/implementing their respective use cases.  ONC will be encouraging their participation in both the Sept 2018 and Jan 2019 FHIR Connectathons.

Subgroup reports

Topic 1: Tracker 19453 - Rename Sequence -> MolecularSequence (recommendation of FHIR subgroup) (VOTE)


Notes from FHIR subgroup call

Tracker

19453

N/A

Bob Milius

Summary

change name of Sequence resource to MolecularSequence or BioSequence,

Links

http://build.fhir.org/sequence.html

Resolution

Notes

Persuasive:

Rename Sequence to MolecularSequence

Details

I've met programmers confused by the Sequence resource, thinking it was for a sequence of events. Yes, they can go to the spec and figure out what it really is, but I suggest clarifying it's name to MolecularSequence or BiologicalSequence or BioSequence to avoid initial confusion.

Follow-ups


Discussion

not persuasive (at the moment) - no consensus on terms yet in chat, must have very good idea to change from something that already aligns with SO/VMC/etc

Consider for future use? Comment not attached to a ballot so have time

Bob M: prefer BioSequence (but would be open to other) and prefer changing it for R4. Precedence of resource name changes with every version as long as it’s for good reason.

I would make that motion to change the name to something more specific to differentiate (Lloyd would second, provided the original 2 terms are the only ones in the motion)

Bob W: I think MolecularSequence is more accurate

Bob M: since we are in a clinical healthcare setting, we should expect to have to provide more context for molecular biology terms.

Deepak: vote for MolecularSequence

Liz: Clem prefers some version of genomic sequence

Bob D: AnnotatedMolecularSequence is an option

Andrea: like GeneticSequence

Options so far:

BioSequence

MolecularSequence

GeneticSequence - but what about AA

GenomicSequence - but what about AA

Does anyone have a problem with eliminating the last 2 specific options as they seem to exclude AA?

Main options:

BioSequence  - shorter,

MolecularSequence - potentially more accurate

Does anyone hate either option? Strong arguments against?

BioSequence has some conflicting search results, seems too general & can apply to plants, animals, and non human subjects…

Kevin: +1 for MolecularSequence

Bob M /Lloyd : recommend to Tuesday call for name change to MolecularSequence:

Discussion:

Abstain/Nay/Yay:

0/0/14

Passes






Motion: Accept recommendation of FHIR subgroup and rename Sequence to MolecularSequence

Move / Second: Jamie / Bob M  

Discussion:

Patrick - deadline is close, so why now?  

Generally some confusion around the name.  Plus R4 release is 18 months or so out.

Clem - not the biggest issue we have to address

Vote (Abstain / Against / For): Clem,Patrick / 0 /  17

Result - Motion Passes.


Topic 2: Tracker 19440 - Update to ‘stu note’ on FHIR Core profiles and artifacts (note - NOT Sequence, different change already applied for Sequence) (VOTE)

Notes from FHIR subgroup below:

Tracker

19440

N/A

Kevin Power

Summary

Update CG FHIR Core artifacts - observation-genetics and Genomics Guidance,

Links

N/A

Resolution

Notes

Persuasive (for all CG profiles that had the previous note):

http://build.fhir.org/observation-genetic.html

http://build.fhir.org/diagnosticreport-genetic.html

 

The material on this page is currently undergoing work to be refactored or potentially removed in a future release as further analysis is done as part of the [Genomics Reporting Implementation Guide].

 

 

Or

 

(for the Genomics Guidance):http://build.fhir.org/genomics.html

 

The material on this page is currently undergoing work to be refactored in a future release as further analysis is done, for example as part of the [Genomics Reporting Implementation Guide].

Details

http://build.fhir.org/observation-genetic.htmland http://build.fhir.org/genomics.html

Currently has this note:

This profile is slated for deprecation. It is included in this ballot for comparison purposes but is not expected to be included in the FHIR R4 published specification. This material is being refactored into an Implementation Guide (IG) for clinical genomics reporting, which can be found here .

We either need to deprecate it or update the R4 reference to R5.

Follow-ups

-Thu, 18 Oct 2018 - by Bob Milius-While I would like to deprecate it, since the IG isn't published, I think we probably should say R5.-Unless we can be confident that the IG will be very published soon after the R4 is published, and given the sense of urgency that Grant conveyed, that seems pretty likely (yeah, wishy-washy answer)

Disposition

Persuasive with mod - recently proposed wording on Listserv:

The material on this page is currently undergoing work to be refactored in a future release as further analysis is done as part of the [Genomics Reporting Implementation Guide].

Could also mention Breast Cancer IG? Should we make this clear or keep it set to our own group’s scope?

Kevin: move to recommend the proposed wording for vote tomorrow. I would believe the Breast cancer IG would point to us. Since they haven’t done work on these resources/profiles with us.

“The material on this page is currently undergoing work to be refactored in a future release as further analysis is done, for example as part of the [Genomics Reporting Implementation Guide].”

Lloyd: there will be national guides/etc but they will be proper subsets of our international guide, against calling our IG an example as it should be THE WAY to implement genomics in FHIR.

Bob M the strength of this is the concreteness of placing our work on the

Gil: Acknowledge the fact that there are other ones out there today

Gil will send thinking of including references to others via email routing in prep for tomorrow (Tuesday) call.

Vote on Tuesday (Oct 30)


Final Proposed Wording:

Persuasive (for all CG profiles that had the previous note):

http://build.fhir.org/observation-genetic.html

http://build.fhir.org/diagnosticreport-genetic.html

 

The material on this page is currently undergoing work to be refactored or potentially removed in a future release as further analysis is done as part of the [Genomics Reporting Implementation Guide].

 

 

(for the Genomics Guidance):http://build.fhir.org/genomics.html

 

The material on this page is currently undergoing work to be refactored in a future release as further analysis is done, for example as part of the [Genomics Reporting Implementation Guide].


Motion: Accept proposed wording

Move / Second: Clem / Jamie  

Discussion: None

Vote (Abstain / Against / For): 0 / 0 /  20

Result: Motion passes

Topic 3: Tracker 1900 - Relax cardinality for reference.windowStart/windowEnd (VOTE)


Tracker

19000

N/A

Bob Milius

Summary

relax cardinality for reference.windowStart and windowEnd,

Links

http://build.fhir.org/sequence.html

Resolution

Notes

Persuasive:

Change cardinality.

Details

currently, if referenceSeq is used, then referenceSeq.windowStart and windowEnd are required.

These should be supplied, but not always available.

Some of our current lab reports supply a reference sequence, but not a window into that sequence, so we don't have the start or end.

so, proposed changed is to cardinality from 1..1 to 0..1 for each of these.

Follow-ups


Disposition

Vote on Tuesday (Oct 30)


Motion: Accept proposed disposition

Move / Second: Bob M / Patrick  

Discussion:

Bret - Not always available for the variation?

Bob M - No, the window on the reference.  Base resource should be more open, and perhaps future profiles can constrain further.

Bob D - Clarify definitions in the future

Vote (Abstain / Against / For): 0 / 0 /  21

Result: Motion passes

Topic 4: Previous FHIR Core Trackers with no or inadequate resolution documented

Tracker

13623



Summary

Add capability to capture genetic ancestry, partial ancestries, and sources.,

Links

N/A

Resolution

Notes

N/A

Details

Add capability to capture genetic ancestry, partial ancestries, and sources.

Follow-ups

-Sun, 28 Oct 2018 - by Patrick Werner-this tracker was voted on without giving a resolution. It is unclear what changes sould be applied.-Sun, 28 Oct 2018 - by Patrick Werner-related document:https://drive.google.com/file/d/0B-0YtCs_i_-eMnB6OUJrY05HMGs/view-there is already: http://build.fhir.org/extension-observation-geneticsancestry.html-Zulip discussion:https://chat.fhir.org/#narrow/stream/43-genomics/subject/GF13623.20has.20no.20resolution

Discussion






Tracker

13626



Summary

Capture genetic references for profile of diagnostic report.,

Links

N/A

Resolution

Notes

N/A

Details

Capture genetic references for profile of diagnostic report.

Follow-ups

-Sun, 28 Oct 2018 - by Patrick Werner-resolution is missing, there is: http://build.fhir.org/extension-observation-geneticsphaseset.htmlalready.-Sun, 28 Oct 2018 - by Patrick Werner-please ignore my last follow up, it was entered by mistake.-This balloted item has not resolution. There already is: http://build.fhir.org/extension-diagnosticreport-geneticsreferences.html

Disposition






Tracker

13622



Summary

Capture phaseset which sequence links and phase set id.,

Links

N/A

Resolution

Notes

N/A

Details

Capture phaseset which sequence links and phase set id.

Follow-ups

-Sun, 28 Oct 2018 - by Patrick Werner-resolution is missing, there is: http://build.fhir.org/extension-observation-geneticsphaseset.html already.-  

Disposition






Tracker

13624



Summary

Hierarchical structure for genetics profile names,

Links

N/A

Resolution

Notes

N/A

Details

Hierarchical structure for genetics profile names

Disposition



Proposed to mark as applied?

Jamie - might be missing some of the textual guidance wasn’t finished, might want to document some Resolution notes.

No objections.

Topic 5: Code Systems / Value Sets (Discussion: Patrick/Julian)

Discussed at WGM (and vote taken on tracker):

https://confluence.hl7.org/display/CGW/2018-09+CG+WGM+Minutes#id-2018-09CGWGMMinutes-Quarter:Q3.2

WIP (Patrick / Julian):

https://docs.google.com/spreadsheets/d/14sIVVED2rI0Ab2ZQ3oV6v8njzX-sRezkIWcgkkepUUg/edit#gid=0

Zulip Chat:

https://chat.fhir.org/#narrow/stream/43-genomics/subject/CodeSystem.20URIs.20for.20genomics

RE: HGNC codes

Patrick - not supportive of relaxing to example binding from required binding.

Lloyd - required can be 1..1, or binding of required. Either way, must be cautious.

Value Set can be validated by a Terminology server.  If it can’t find the code is legal or not, it might

Patrick - Value Set points to HGNC, but can’t resolve the codes.

Possible the validator should report a warning at most if the code can’t be validated by the Terminology server.

Clem - not all genes are in HGNC

Perhaps needs to be Preferred or maybe Extensible to cover the genes that are not in HGNC.

Does the Code System cover everything, and does the Lab always have it.

Add a “good practice” invariant to encourage HGNC?

HGNC Value Set -> Preferred seems to make the most sense for now.

Extensible can only be validated by a human.


Chat

none recorded


Clinical Genomics Docs