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HL7 Clinical Genomics Weekly Call - 28 Apr 2020 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

Agenda

Attendees Sign-in

Presiding Co-Chair (Patrick Werner - Molit Institut - pw@molit.eu  ): 

  1. Liz Amos - NLM - liz.amos@nih.gov 
  2. Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org 
  3. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  4. Kevin Power - Cerner - kpower@cerner.com 
  5. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  6. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  7. James Jones - BCH - james.jones.bch@gmail.com 
  8. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  9.  Michelle Barry-Availity, LLC- michelle.barry@availity.com 
  10.  Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  11.  Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  12.  Ning Xie - BWH- nxie1@bwh.harvard.edu
  13. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 
  14.  Perry Mar - Health Catalyst - perry.mar@healthcatalyst.com 
  15.  May Terry - mayt@mitre.org
  16. Rachel Kutner - Epic - rkutner@epic.com
  17. 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

2/18/20

Patrick



2/25/20

Kevin

Topic 1: ‘find-variant’ operation - outstanding questions (Bob D / Patrick)

Topic 2: Update/Discussion on Implication Profiles (Jamie)


3/3/20

Kevin

CG IG Lite: Liz & Clem
Attachments from 1/28 email


3/10/20

Bob M

1: CMS/ONC rules 

2: Vote on operations for IG

3: STU2 of IG


3/17/20

Kevin

1: Reminder - CMS/ONC rules 

2: STU2 of IG (cont...)


3/24/20

Bob M

Tumor/normal examples to review 


3/31/20

Patrick



4/7/20

Bob M



4/14/20

Patrick



4/21/20

Bob M

1: old projects

2: connecathon

3: emerge extensions


4/28/20

Patrick



5/5/20

Bob M



5/12/20

Patrick



5/19/20

Bob F

Sync for Genes


Working Group Meeting

Cancelled! May 16-22, 2020   •   San Antonio, Texas

Register Today!

CG WG will be meeting Monday Q3 & Q4, and all-day Tuesday and Wednesday

Register Connectathon: 


Other workgroups (eg OO) will meet several times during that week. Should we do likewise?

topics/times?

JD: Monday stuffed, Wednesday would be preferred, in the morning because of european call-ins

Kevin: Have normal calls, and then schedule other/extra calls around it.

JD: should discuss: DiagnosticReport, (multiple) Specimen, Observation (10min presentation what are we doing how with OO resources)

Arthur: What is the current Phenopackets status?
Bob: Not sure if ready to show in May, but for the Sept. WGM

External efforts

Subgroup reports

https://docs.google.com/document/d/1FGCQRtxJKyHhnC1uB_t4sJZ9yXbLMGOqPXHPr5tSLLQ/

WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

April 21 

Topic 2: Connectathon - Scenarios

  • Cancer Screening (without risk screening) (Patrick, Alex)
    • Including tumor-normal testing
    • Tumor only testing
  • ACMG screening (Bob D, Bret)
    • Expose $find-subject-variants API (genomic data server with 300 1000-Genomes patients)
    • Use variants in an ACMG screening pipeline
    • Reassess ACMG screening after genomic data changes

Topic 2.5: Block Vote


Key

Resolution

Summary

Reporter

Created

Resolution Description

 




FHIR-16871

Persuasive with Modification

Specialization for somatic variant might not be necessary - 2018-May Genomics #56

Clement McDonald

5/12/18

Remove all current Implication profiles except abstract base, add 2 new profiles restructuring our current components and codes as *Diagnostic Implication* and *Therapeutic Implication*

*Genomic Implication Profile*

Extension: RelatedArtifact (0..*)

derivedFrom (reference: Observation/Variant/Haplotype/Genotype) (1..*)

Component: 93044-6 | Level of Evidence / “clinical validity” (0..1)

Binding: [LOINC Answer List LL5356-2|https://r.details.loinc.org/AnswerList/LL5356-2.html] ([preferred|http://hl7.org/fhir/terminologies.html#preferred])

Component: TBD code | prognosis (0..1)

E.g. Better outcome, poorer outcome

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])


*Diagnostic Implication Profile*

code: TBD code | Diagnostic implication

Value 0..0

 Component: [53037-8|https://r.details.loinc.org/LOINC/53037-8.html?sections=Comprehensive] | LL4034-6 (clinical significance) (0..1)

Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign

Binding: [LOINC Answer List LL4034-6|https://r.details.loinc.org/AnswerList/LL4034-6.html] ([extensible|http://hl7.org/fhir/terminologies.html#extensible])

Component: [81259-4|https://r.details.loinc.org/LOINC/81259-4.html?sections=Comprehensive] | (Associated phenotype) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

Component: TBD code | (Associated cancer) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

Component [79742-3|https://r.details.loinc.org/LOINC/79742-3.html?sections=Comprehensive] | [LL3731-8|http://r.details.loinc.org/AnswerList/LL3731-8.html] (Mode of inheritance) (0..1)

Autosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial

Binding: [LOINC Answer List LL3731-8|https://r.details.loinc.org/AnswerList/LL3731-8.html] ([preferred|http://hl7.org/fhir/terminologies.html#preferred])

 

*Therapeutic Implication* *Profile* 

code: TBD | Therapeutic implication

Value 0..0

 

Component: [81259-4|https://r.details.loinc.org/LOINC/81259-4.html?sections=Comprehensive] | (Associated phenotype) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

Component: TBD code | (Associated cancer) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

 

Component: [51963-7|https://loinc.org/51963-7/] |  (medication-assessed) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

Component: TBD |  (therapy-assessed) (0..*)

Binding: [(unbound)|http://hl7.org/fhir/terminologies.html#unbound] ([example|http://hl7.org/fhir/terminologies.html#example])

Component: 53040-2 |  (effect-medication-metabolism) (0..1)

Ultrarapid metabolizer | Rapid metabolizer | Normal metabolizer | Intermediate metabolizer | Poor metabolizer

Binding: [LOINC Answer List LL3856-3|https://r.details.loinc.org/AnswerList/LL3856-3.html] ([preferred|http://hl7.org/fhir/terminologies.html#preferred])

Component: 83009-1 | (effect-medication-high-risk) (0..1)

Low risk | High risklogies.html#example])

Component: 51961-1 | LL3856-3 (effect-medication-efficacy) (0..1)

Resistant | Responsive | Presumed resistant | Presumed responsive | Unknown significance | Non-Responsive | Presumed non-responsive

Binding: [LOINC Answer List LL539-8|https://r.details.loinc.org/AnswerList/LL539-8.html] ([preferred|http://hl7.org/fhir/terminologies.html#preferred])

 



FHIR-21635

Not Persuasive

Variant.code shouldn't be fixed

Patrick Werner

5/6/19

Comment from Patrick: after some discussions at the WGM, it would be better to leave this fixed, but to introduce a variant type component



FHIR-24883

Not Persuasive

Link to Genomics Reporting IG is dead

Pascal Pfiffner

10/1/19

The link ([http://hl7.org/fhir/uv/genomics-reporting/index.html]) appears to have fixed itself as part of the IG publication process.



 

    • Motion: Approve proposed resolutions 
      • Move / 2nd: Kevin / Bob M.  
      • Discussion: - 
      • Vote: (Abstain / Opposed / In Favor):  3 / 0 / 13 
      • Result:  motion passes


Kevin: will remove the ne complex note extension before merging

Topic 3: Update: Discriminator derivedFrom on Haplotype

  • https://chat.fhir.org/#narrow/stream/179304-genomics.2Fcommitters/topic/fixing.20haplotype 
  • Bob M.: just want to make sure that derived profiles can add profiled MolecularSequences to their profiles.
  • Patrick: With the proposed change this can be dobe with reslicing. Will test as soon the IG publisher works again on our IG
  • Bret: Was there an update on deriving from multiple IGs?
  • May: mix-ins in FSH could possibly solve the diamond of death problem.
  • Bob M.: could we have a new release of our IG with the TC?
  • Patrick: Technical correction could be introduced as a snapshot of the IG (frozen version of the ci build)
  • Bret: will this technical correction then be seen on our IG?
  • Patrick: will ask for guidance on this, if we can upgrade to STU1: 1.0.1 without voting
  • Lloyd: can be done with a technical correction, no voting required


NO TOPICS WERE DISCUSSED AFTER THIS 

Topic 4: how to link to region studied?

FHIR-24598 How to reference a region studied observation from genotype, haplotype, variant observations

Discussion:

Topic 5: Uncallable subregions in a region studied

FHIR-25296 Uncallable subregions in a region studied

Discussion:

Chat


Future Topics

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



       o  1st/2nd -

       o  Discussion -

       o  Abstain/Nay/Yea -  / /

       o  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)

       o  1st/2nd -

       o  Discussion -

       o  Abstain/Nay/Yea -  / /

       Result - 

Need to create an example to understand the meaning of this change/concepts.
Need a caretaker for this topic.


Clinical Genomics Reference Docs


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