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HL7 Clinical Genomics Weekly Call - 28 Apr 2020 11:00 AM (US Eastern)


Archive of minutes:


Attendees Sign-in

Presiding Co-Chair (Patrick Werner - Molit Institut -  ): 

  1. Liz Amos - NLM - 
  2. Bob Milius - NMDP/CIBMTR - 
  3. Bob Freimuth - Mayo Clinic -
  4. Kevin Power - Cerner - 
  5. JD Nolen - Children’s Mercy Hospital -
  6. Arthur Hermann - Kaiser Permanente -
  7. James Jones - BCH - 
  8. Bob Dolin - Elimu Informatics - 
  9.  Michelle Barry-Availity, LLC- 
  10.  Joel Schneider - NMDP/CIBMTR -
  11.  Arthur Hermann - Kaiser Permanente -
  12.  Ning Xie - BWH-
  13. Clem McDonald - NLM - 
  14.  Perry Mar - Health Catalyst - 
  15.  May Terry -
  16. Rachel Kutner - Epic -
  17. Bret Heale - Intermountain - 

Standing Informational Items

Agendas and Important Dates 

CG Call Date



Important Dates





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

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



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


Bob M

1: CMS/ONC rules 

2: Vote on operations for IG

3: STU2 of IG



1: Reminder - CMS/ONC rules 

2: STU2 of IG (cont...)


Bob M

Tumor/normal examples to review 




Bob M




Bob M

1: old projects

2: connecathon

3: emerge extensions




Bob M




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?


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

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






Resolution Description



Persuasive with Modification

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

Clement McDonald


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|] ([preferred|])

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

E.g. Better outcome, poorer outcome

Binding: [(unbound)|] ([example|])

*Diagnostic Implication Profile*

code: TBD code | Diagnostic implication

Value 0..0

 Component: [53037-8|] | LL4034-6 (clinical significance) (0..1)

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

Binding: [LOINC Answer List LL4034-6|] ([extensible|])

Component: [81259-4|] | (Associated phenotype) (0..*)

Binding: [(unbound)|] ([example|])

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

Binding: [(unbound)|] ([example|])

Component [79742-3|] | [LL3731-8|] (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|] ([preferred|])


*Therapeutic Implication* *Profile* 

code: TBD | Therapeutic implication

Value 0..0


Component: [81259-4|] | (Associated phenotype) (0..*)

Binding: [(unbound)|] ([example|])

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

Binding: [(unbound)|] ([example|])


Component: [51963-7|] |  (medication-assessed) (0..*)

Binding: [(unbound)|] ([example|])

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

Binding: [(unbound)|] ([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|] ([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|] ([preferred|])



Not Persuasive

Variant.code shouldn't be fixed

Patrick Werner


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


Not Persuasive

Link to Genomics Reporting IG is dead

Pascal Pfiffner


The link ([]) 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

  • 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


Topic 4: how to link to region studied?

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


Topic 5: Uncallable subregions in a region studied

FHIR-25296 Uncallable subregions in a region studied



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

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

(note, this example uses placeholder value “AMP Guidelines” instead of a tier)


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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