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HL7 Clinical Genomics Weekly Call - 27 Nov 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

Previous Minutes Approval

Agendas and Important Dates

External efforts

Subgroup reports

Topic 0: Ballot Sign Up

Topic 1: Remaining non-ballot tracker items from Mon FHIR call (yesterday)

Chat

Attendees Sign-in

(Presiding co-chair:  Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org  )

  1. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  2. Andrea Pitkus - apitkus@gmail.com
  3. Kevin Power - Cerner - kpower@cerner.com
  4. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu
  5. Patrick Werner - MOLIT Institut - patrick.werner@molit.eu
  6. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  8. Joel Schneider - NMDP/CIBMTR - jschneid@nmpd.org
  9. Deepak Sharma - Mayo Clinic - sharma.deepak2@mayo.edu        
  10.  James Jones - BCH - james.jones.bch@gmail.com
  11.  Ning Xie - BCH- ningxie2018@gmail.com
  12.  Scott Robertson  - Kaiser Permanente  - scott.m.robertson@kp.org
  13.  Jungang Zou - XMU- jungang.zou@gmail.com
  14. Mullai Murugan - BCM - murugan@bcm.edu
  15.  Clem McDonald - NLM - clemmcdonald@mail.nih.gov
  16.  Liz Amos - NLM - liz.amos@nih.gov 

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

Bob M

 

 

13-Nov-18

Bob M

 

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

Nov 18: IG Ballot reconciliation spreadsheet due - two ballot items left to reconcile

20-Nov-18

Kevin P

Topic 0: Ballot Sign Up

Topic 1: May 2018 Ballot Reconciliation Complete

Topic 2: Non-ballot tracker items still remaining

 

Topic 3: Code Systems / Value Sets (Discussion: Patrick/Julian - Clem/Liz)

  Nov 23: Co-Chair Nominations Close at 5:00 pm Eastern (email nominations to NOMINATIONS@HL7.ORG)

27-Nov-18

Bob M

 

Dec. 2: IG Final freeze deadline

4-Dec-18

Bob F

 

Dec 6 - Consensus pool signup closed

Dec 7 - Ballots opened

 

Dec 7: Co-Chair election statements due to HQ

11-Dec-18

Bob M

 

 Dec 14: Deadline to post your WGM agenda on the WGM information page (WG Health metric)

18-Dec-18

Kevin P

 

 

25-Dec-18

Holiday

meeting cancelled

 

1-Jan-19

Holiday

meeting cancelled

 

8-Jan-19

Bob M

 

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)
    • Still attempting to schedule a follow-up meeting (Sandy, JD, Grant) for next steps.
  • ClinGen/ClinVar (Larry Babb, Bob Freimuth)
    • In-person modeling meeting was held Nov 12-14, focused on CNVs for ClinGen, ClinVar, and ClinGen Allele Registry
    • Internal follow-up on outcomes of the in-person modeling meeting, vetting ideas
    • Significant consideration given to GKS/VR approaches, may help drive that work
  • CDISC PGx (Dorina B.)
    • no report       
  • ONC Sync for Genes (Bob Freimuth)
    • Collected example genetic test reports from each pilot site, mapping to FHIR profiles
    • Planning for Jan WGM Connectathon
    • S4G will conduct a number of tests under Scenario 10 of the CG genomics track 

Subgroup reports

 

Topic 0: Ballot Sign Up

Announcement of ballot openings for early January 2019 Ballot Cycle

Ballot Period Open/Close Dates

Voting for consensus group members in most ballots in this document will open and close on the following dates. Exceptions for a specific ballot are listed with that ballot description.

 

Ballot Open Date: Friday, December 7, 2018

Ballot Close Date: Monday, January 7, 2019

 

Consensus Group

Enrollment Period Important Note:

Consensus group signup closes when ballot voting begins. Consensus group enrollment will be available from a date at least four weeks preceding the ballot vote opening date and will continue until the opening of voting. While the exact dates are dependent upon individual ballot open and close dates, in general the consensus group sign up period dates are as follows:

 

Consensus Group Sign-Up Open Date: Monday, November 5, 2018

Consensus Group Sign-Up Close Date: Thursday, December 6, 2018

Please be aware that these dates may not be accurate for all consensus groups.

 

To sign up, point your browser to

http://www.hl7.org/ctl.cfm?action=ballots.home

 

Important Note:

Consensus group signup will close when ballot voting begins. This is also the final date non-members can sign up for Non-Member Participation in the ballot.


Additional Information:
http://www.hl7.org/documentcenter/public_temp_87AEFCD4-1C23-BA17-0CEC7A7FE30214CE/ballots/2019JAN/Announcements/Formation%20of%20Consensus%20Groups%20for%202019%20January%20Ballot%20Cycle.pdf


Topic 1: Remaining non-ballot tracker items from Mon FHIR call (yesterday)

 

Tracker

16387

N/A

David Poloway

Summary

LOINC reference for HLA,

Links

http://build.fhir.org/ig/HL7/genomics-reporting/transplants.html

Resolution

Notes

Persuasive with Mod (pending discussion re: GL String)

Details

Do we need to add LOINC reference for HLA in FHIR STU4? Perhaps consider adding LOINC coding system here.

Follow-ups

-Tue, 20 Nov 2018 - by Andrea Pitkus-Concur it would be great to add LOINC as a preferred terminology/code system for HLA test results in FHIR.

- No mention of LOINC on recently updated http://build.fhir.org/ig/HL7/genomics-reporting/histocompatibility.html, which pushes for GLString. Do we want to mention LOINC as a backup?

Bob M: depends on the HLA they are reporting, especially resolution - issue of picking. There is a set of LOINC we can use or we can redefine a set that is more in line with what NMDP uses. If we can get a LOINC code for HLA allele names then we can be more prescribed about how to use them in the IG.

Currently dozens of LOINC codes that could be used for different concepts in HLA reporting. Narrowing down these LOINCs would be helpful.

Clem: historically there were a ton of codes

Bob D: I imagine there’s a consistent way across genes to list these, rather than wrangling in the old code, looking at being consistent moving forward seems like a more useful approach.

Bob M: There is a standard way this group has determined we’d like to do that but labs will be using older codes, etc in their own standards. We want them to have to report along our guidelines but also be able to send their internal codes.

Andrea (from chat):

looks like the Nominal responses for [Type] which are the result values are missing.  The LOINC 57290-9 and LOINC 78014-8 low resolution could use them to guide users.

Are low and high resolution the only methods used for HLA A?

https://www.labcorp.com/test-menu/28041/hla-abc-intermediate-resolution

LabCorp has an intermediate resolution which would need it's own LOINC reflecting this method.  Also they map to the generic methodless LOINC which is not low or high…

if these other methods are applicable we will want to request and/or clarify codes for them in LOINC as well

 

Bob M: would be nice to get a unified HLA loinc code and then separate out the method information. We’ve been trying to accomplish this with the GL String, which can be used in multiple scopes (allele/haplotype/genotype). We want to also encode the method

 

Clem: does GL String cover method?

 

Bob M: no, it provides the database and the result, including ambiguity. Generally a lower resolution test could be probes or serology but this won’t necessarily be captured in the result. Would prefer a separate approach in capturing the methods.

 

Andrea: pre-coordinated (LOINC) vs post-coordinated is an ongoing question in places like SIMI etc. translation from pre-to-post is an extra layer of complexity in the model, re: queries etc. Since V2 is required for MU2 aspects, many systems will be supporting LOINC here. US-specific issues here as well.

 

Bob D:

Next steps:

Do we want to add guidance for which LOINC codes to use on http://build.fhir.org/ig/HL7/genomics-reporting/histocompatibility.html (in addition to our required Genotype/Haplotype codes)?

Seems like it is nontrivial and guidance would be appreciated but need to iron out what that guidance is.

 

 

 

Tracker

16413

 

 

Summary

Clarify in IG that other reporting guides for specific areas may exist,

Links

N/A

Resolution

Notes

Not persuasive - can incorporate/point to other IGs as they are finished and published, no need to dedicate space to them before that

Details

Make IG guide be clear that there may be other reporting guides for specific areas (e.g. HLA, clinical research, etc) in the title somehow (e.g. clinical molecular lab reporting or similar) and text. Have section that can be used to point to other domain-specific guides. This will help distinguish from other guides (e.g. HLA) that may be complimentary.

Follow-ups

-Mon, 07 May 2018 - by Lloyd McKenzie-I believe the current intention is that HLA reporting will be part of the scope of this IG.  (There's already a section for it.)  Insofar as a research IG would be focused on reporting of genetic results, that would also fall within the scope of this IG.-Wed, 21 Nov 2018 - by Kevin Power-As stated by Lloyd in his comment, HLA is included in the IG at this point.  We have discussed the Breast Cancer IG in the past, but I think our WGs position is that they should align with our IG when it comes to reporting genomics results, and we should make sure to support their use cases.

  • Motion to accept resolution - ie.  not persuasive - Clem M/Kevin P
  • discussion
    • ■      Scott R -
    • ■      "considered for future use" allows use of tracker a reminder to do it later. Just a comment, not advocating to change the motion
  • abstain - Scott
  • nay - 0
  • yea - 15
  • motion passes

Tracker

15893

N/A

Kevin Power

Summary

Decide what examples to bring across from existing profiles and convert them,

Links

N/A

Resolution

Notes

Persuasive

Details

Decide what examples to bring across from existing profiles and convert them (with narrative explanation)

Follow-ups

#N/A

  • motion to accept persuasive - Kevin P/Patrick W
  • discussion - none
  • abstain - 0
  • nay - 0
  • yea - 16
  • motion passes

Tracker

16411

 

 

Summary

Explain rationale for differences in term names,

Links

http://build.fhir.org/ig/HL7/genomics-reporting/general.html

Resolution

Notes

Persuasive with Mod - should be taken care of with deferred “Glossary” tracker

Details

If term names and/or definitions are different from community consensus (e.g. VMC) and kept, explain rationale and differences so various users are not confused. (e.g. allele vs variant, etc)

Follow-ups

 

  •  

Tracker

16410

N/A

David Poloway

Summary

Reconsider term names if inconsistent,

Links

http://build.fhir.org/ig/HL7/genomics-reporting/general.html

Resolution

Notes

Persuasive with Mod - should be taken care of with deferred “Glossary” tracker

Details

If term names and/or definitions are different from community consensus (e.g. VMC), reconsider

Follow-ups

#N/A

  • 16411 and 16410 appear to be addressed by glossary tracker item (deferred).
  • motion: comment the glossary tracker with these two, and mark these two as duplicate
    • Kevin P/Bob F
  • discussion - none
  • abstain - 0
  • nay - 0
  • yeas - 16
  • motion passes

Tracker

16405

 

 

Summary

add mappings to R4,

Links

http://build.fhir.org/ig/HL7/genomics-reporting/general.html

Resolution

Notes

Not persuasive - out of scope

Details

Mappings developed could go in the R4 differences so people can see that.

Follow-ups

 

Mon, 07 May 2018

byLloyd McKenzieThis specification is based on R4, so not clear how it could map to R4...

  • motion: not persuasive
    • James J / Kevin P
  • discussion - none
  • abstain - 0
  • nay - 0
  • yea - 16
  • motion passes

Chat

  • Joel Schneider - 10:18AM
    • +1 for using method-less HLA LOINC codes
  • Andrea - 10:18AM
    • do have a comment after others have a chance to chime in....
  • Anonymous - 10:19AM
    • Ideally, these codes should all be post-coordinated
  • Andrea - 10:20AM
    • LOINC is a precoordinated terminology by nature of its design...
  • Anonymous - 10:20AM
    • Yeah. I know. :-)
  • Kevin Power Host - 10:21AM
    • Someone making comments is showing up as Anonymous - Can you identify yourself for our notes?
  • Anonymous - 10:22AM
    • If it’s me, I thought I was signed in. Bob F.
  • Kevin Power Host - 10:23AM
    • Thanks Bob F.
  • Kevin Power Host - 10:27AM
    • We have spent a lot of time on this one - should we move on to cover other topics?
  • Andrea - 10:39AM
    • one resolution would be to request LOINC codes for the intermediate resolution so they are available for labs that report them.
  • James Jones - 10:39AM
    • I think we should add some text to the page highlighting these issues
  • Andrea - 10:39AM
    • right Clem.
  • Andrea - 10:40AM
    • 74720-4  Device name
  • James Jones - 10:40AM
    • I don't know of anywhere in the IG that points out that you can/should use multiple codes for value
  • Andrea - 10:40AM
    • looks like some of the items where LOINC is available, need to be updated in tracker....
  • Andrea - 10:41AM
    • 74719-6  Manufacturer name
  • Andrea - 10:41AM
    • 62376-9  Microarray platform version number Narrative
  • Andrea - 10:42AM
    • 62375-1  Microarray platform [Identifier] Narrative
  • Andrea - 10:43AM
    • would it be consider for future use?

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