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HL7 Clinical Genomics Weekly Call - 27 Aug 2019 11:00 AM (US Eastern)

Minutes

http://tinyurl.com/HL7CGGroupCall 

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

Archive of minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=25559917&src=contextnavpagetreemode

Attending the meeting

Join the online meeting (VoIP available with this):

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Agenda

Attendees Sign-in

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

 

  1.  James Jones - BCH - James.jones.bch@gmail.com
  2.  Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  3.  JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  4.  Swapna Abhyankar - Regenstrief Institute - sabhyank@regenstrief.org 
  5. Liz Amos - NLM - liz.amos@nih.gov  
  6. Joel Schneider - NMNP/CIBMTR - jschneid@nmdp.org
  7. Michael Stevens - Optum - jmichael.stevens@optum.com
  8. Jami Deckard - Regenstrief Institute - jkdeckar@regenstrief.org
  9.  David Baorto - Regenstrief Institute - dmbaorto@regenstrief.org
  10. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  11. Deepak Sharma - Mayo Clinic - sharma.deepak2@mayo.edu
  12. Kevin Power - Cerner - kpower@cerner.com (joined at :12 after the hour)
  13. Bret Heale - Intermountain HealthCare - bheale@gmail.com 



Standing Agenda Items

Previous Minutes Approval

Agendas and Important Dates 


CG Call Date

Co-Chair

Agenda

Important Dates

5/21/19

Patrick

Topic 1: WGM Minutes

Topic 2: How to search for SNV vs SV?

Topic 3: Functional Class

Topic 4: Tracker Voting


5/28/19

Kevin

Topic 1: WGM Minutes

Topic 2: Tracker Voting

Topic 3: How to search for SNV vs SV?

Topic 4: Functional Class


6/4/19

Kevin

Topic 1: Tracker Voting

Topic 2: Review proposal from last week

Topic 3: How to search for SNV vs SV?

Topic 4: Functional Class


6/11/19

Kevin

Topic 1: Tracker Voting

Topic 2: Review pending trackers

Topic 3: How to search for SNV vs SV?

Topic 4: Functional Class


6/18/19

Bob M

Topic 1: DevDays Update

Topic 2: Tracker Voting

Topic 3: Pending Tracker Update

Topic 4: NIB for IM

Topic 5: July Harmonization cycle

Topic 6: WG health - doc review

Topic 7: How to search for SNV vs SV?

Topic 8: Functional Class


6/25/19

Bob F

Topic -3: GA4GH VR - v1 RC released

Topic -2: ISO Genomics SC

Topic -1: Connectathon planning

Topic 0: NIB for IM

Topic 1: Tracker Voting

Topic 2: Pending Tracker Update

June 30: NIB due

July 31: Connectathon track proposals due

7/2/19

Kevin

GA4GH VR spec

Tracker Voting


7/9/19

Patrick



7/16/19

Bob M

WG docs review

FHIR issues

  • Variant type
  • Functional class
  • Start-end

7/23/19

Bob F

Topic 1: Workgroup documents

Topic 2: Sanger confirmation info (gforge 19829)

Topic 3: TBD LOINC codes (gforge 22815)

July 31: Connectathon track proposals due

7/30/19

Patrick


July 31: Connectathon track proposals due

8/6/19

Kevin

1st draft WGM Agenda (Bob M)

Topic 0: WGM Agenda

Topic 0.5: Sep ballots!

Topic 1: TBD LOINC codes (carry over)

Topic 2: Functional Class (gforge 22815) (carry over)

Topic 3: FHIR subgroup voting (carry over)


8/13/19

Bob M

Topic 0: WGM Agenda


8/20/19

Kevin

Topic 0: WGM Agenda

Topic 1: Sep ballots!

Topic 2: Docs

Topic 3: FHIR subgroup voting

Topic 4: FHIR subgroup voting (continuation from previous weeks)

Topic 5: TBD LOINC codes (carry over)

Aug 24: Early bird deadline for WGM

8/27/19

Bob M



9/3/19




9/10/19

Bob M



33rd Annual Plenary & Working Group Meeting

September 14-20, 2019   • Atlanta, GA

Early bird registration ends Aug 24


External efforts

  • GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)
    • GA4GH 7th Plenary @ Boston, MA, Oct 21-23, 2019
    • https://www.ga4gh.org/events/
    • Bob F: very busy, half dozen candidate projects being evaluated, going to a steering committee to be ready by plenary meeting
    • Bob D: question about phenopacket?
    • Bob F: set future meeting to discuss this
    • Phenopackets group - Clem understands they are working on FHIR, we should see what they are doing.
    • Working on v1 of spec, target release Sept 2019
    • V1 RC was released for internal review on June 24, 2019
    • WG is working on edits in response to comments
    • Working on population frequency
    • nothing in review, continuing in modeling activities
    • GA4GH news
    • Variant Representation (formerly VMC) (lead by Larry Babb/Tristan Nelson)
    • Variant Annotation
  • DIGITiZe (aka National Academies)  (Grant Wood, JD Nolen)
    • Grant and JD talked at WGM and have a plan. Looking to plan a DIGITiZe pilot team call to recap and set the stage for what is next (date TBD). 
    • No response from Gil...consider this item inactive for now.
    • no response, no activity 
    • will take this off standing agenda 
  • ClinGen/ClinVar (Larry Babb, Bob Freimuth)
    • Bob F: schedule a meeting after the WGM, perhaps late Sep
    • Data Exchange/Platform WG
    • will discuss further when Larry in on a call
    • could be folded up into GA4GH summary
    • no report
  • 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.
    • nothing new (Dorina not present)
  • ONC Sync for Genes (Bob Freimuth)
  • ISO TC/215 Genomics Subcommittee (Liz, Clem)
    • complete next week (23rd) - will report later call
    • November 4-8,  2019 in Daegu, South Korea  First for SC01
    • March 30 - April 3, 2020 in Arlington, VA
    • Liz will check to see whether the meeting is open or ISO members only
    • Scott R: must be a member of a national member organization to attend
    • Meeting coming up in October 3 in Arlington, VA - Liz to get more info
    • ISO/TC 215/SC 01 "Genomics Informatics" has been formed
    • Secretariat assigned to Korea
    • Chair: voting in progress
    • Meetings
  • 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 talked to Larry Babb, asked Larry to present and share in future call.

Subgroup reports

WG projects and outreach

Topic 0: WGM Agenda

WGM - September 14-20, 2019, Atlanta, GA

https://confluence.hl7.org/display/CGW/2019-09+CG+WGM+Agenda

Please review and propose agenda items!

Topic 1: Sep ballots!

Balloting is open 

Topic 2: Docs

reminder to read workgroup docs

(see below)

Topic 3: Should we push to publish IG or wait until WGM?

  • Don't need to vote at WGM, just need to get it done
  • Clem: get it done
  • Kevin: no new items, just apply all resolutions
  • Jamie: we can get it done this week, but have build issues.
  • Bob M: working on HLA changes
  • Jamie: get everything in place by the deadline (week from today), then use the time to the WGM for final QA.

Topic 4: Level of evidence and clinical significance

  • from the listserv…

from Bret:

To me Swapna's proposals seem sound. Level of evidence and clinical significance are different concepts. Also seems reasonable to treat somatic and germline differently.  But would suggest not expanding past somatic and germline as categories for clinical significance, if possible. Clinical significance is a tricky topic for germline variants as clinical significance of germline variants can be context dependent.

Take care to limit the number of level of Evidence codes. I think the LOINC observation (slot to fill) is the same weather the answer is a Baylor value or not. The answer list choice can be more or less informative depending on choice. By using only one LOINC code we push complexity to the answer level. Meaning I'll have to write software to handle different values differently and normalize. To me this is preferable to needing to maintain a list of LOINC codes for searching and still have the normalization problem. But I'm assuming that the answers would be represented with their code system (which would help in normalizing). If I'm in a LOINC only world then I'd find multiple LOINC codes useful for normalization, however multiple, non-overlapping, LOINC answer lists might help in a LOINC only world. We're hard pressed to find a single best solution due to the variation in reporting.

#4 looks good to me for TMB handling. Codes are needed. Hope something drives the community to a standard approach to TMB, the LOINC codes will help.

But that is just my opinion.

On Mon, Aug 26, 2019, 5:41 PM Jones, James <clingenomics@lists.hl7.org> wrote:

Great insight into the lists and concepts we recently requested!

I agree we have to separate clinical significance from level of evidence, that was a bit of a sloppy inclusion from the AMP "table" graphic.

I personally don't see how diagnostic significance in the cancer space is any different than pathological significance in germline variants, but we still need to consider bindings for our diagnostic somatic implication values (not mentioned in the attachment) so would favor splitting the concepts.

Similarly, I'd really prefer that level of evidence was objective of intended use, but looking at the different use cases for diagnostic/prognostic/predictive evidence may likewise help us create bindings for the remaining somatic profiles' value concepts, at least for prignostic (i.e. "better outcome predicted from XX", rather than just "better outcome").

For the Predictive case I would love to see it mirror the PGx efficacy profile.

Thanks,

Jamie

On Mon, Aug 26, 2019, 2:04 PM Amos, Liz <clingenomics@lists.hl7.org> wrote:

Sending this attached on behalf of Swapna for discussion tomorrow.

Thanks!

Liz Amos, MLIS

  • Motion 1: Remove the text about AMP from the description of 93044-6 so that the Level of Evidence concept is
    distinct from Level of clinical significance
    • motion/2nd: Swapna/Clem
    • discusion - none
    • abstains 0
    • nay 0
    • yeas 13 
    • motion passes

No Time for further voting

  • Motion 2: Use 53037-8 for both germline and somatic variant clinical significance reporting, and
    a. Add information to the Term description about the different guidelines for somatic and germline
    variants;
    b. Keep the Answer list the same, but update the Update the type from Preferred to Example
    • 1st/2nd -
    • Discussion -
    • Abstain/Nay/Yea -  / /
    • Result - 

  • Motion 3: Consider creating new codes for diagnostic, therapeutic, and prognostic significance (see Quest
    screenshot, LabCorp report) and/or type of evidence (see Baylor report)
    • 1st/2nd -
    • Discussion -
    • Abstain/Nay/Yea -  / /
    • Result -   

Topic 5: TBD LOINC codes (carry over)

Currently we have a lot of todo/tbd Loinc codes creating errors if they are used to validate instances. 

Proposal:

Create a temporary LOINC system and AnswerLists:

https://docs.google.com/spreadsheets/d/1qqVHlVPBcS7bQfSV_PARB862YMG2Q-Q9lJeTo3qzzz4/edit?usp=sharing

(TBD items from Jamies CodeSystem binding list: https://docs.google.com/document/d/1E-nal_OPhJ8SSaIN_f9XqiLI5lyuGyhTIbUae8MWLMU/edit )

---updates July 30---

Clem: objects temporary LOINC codes as it could create a mess. Prefers to not create them.

Andrea: could violate LOINC trademarks shouldn’t be done

Is this proposal compliant with LOINC licensing requirements?  May not be… (See #1, 4 of LOINC license)  

Have the LOINC Answers be requested so they can hopefully be in the next LOINC release in Dec 2019?

Patrick: i don’t think so, the original tracker doesn’t contain this information

Arthur: we could do a temporary solution and ask LOINC for the correct codes 

Clem: where do these codes come from?

Patrick: from reviewing the current state of our IG, collecting all TBD codes which can’t be used to validate and are creating errors in the IG build.

Clem: Just delete all TBD codes

Patrick: makes large parts of our IG useless

Arthur: maybe send out the list to the group and discuss afterwards

DEFERRED FOR NOW 

---updates Aug 6---

Get more opinions, vote or send to group.

  • Group Consensus: Go with temporary CG specific ValueSets and codes (from the google doc), don’t include “LOINC” in the URIs and ensure the name clearly implies these are temporary.  Will at the same time continue to refine the list, potentially find existing LOINC codes that might fit (but must understand original intention). Continue to review existing reports and make proposals to change the IG.


--- updates to Group Consensus on Aug 20 ---

  • Include an additional note on all profiles using the TBD codes to further call out that these codes are “TBD” are not well specified and might be wrong/removed in the future.  Discuss on where it should go and what it should say will occur on Zulip.

Chat Log:

Clinical Genomics Reference Docs

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