Skip to end of metadata
Go to start of metadata

Chair:  Patrick Werner

Scribe: Patrick Werner



HL7 Clinical Genomics Weekly Call - 12 May 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

Attending the meeting

Join Zoom Meeting

https://zoom.us/j/2980068716 

Meeting ID: 298 006 8716

One tap mobile

+16699006833,,2980068716# US (San Jose)

+19294362866,,2980068716# US (New York)

Dial by your location

        +1 669 900 6833 US (San Jose)

        +1 929 436 2866 US (New York)

        +1 253 215 8782 US

        +1 301 715 8592 US

        +1 312 626 6799 US (Chicago)

        +1 346 248 7799 US (Houston)

Meeting ID: 298 006 8716

Find your local number: https://zoom.us/u/adNIRW2P8J 


Agenda

Attendees Sign-in

Presiding Co-Chair (Patrick Werner - MOLIT Institut - patrick.werner@molit.eu): 

  1. Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  2. May Terry - MITRE - mayT@mitre.org
  3. Stephen Schwartz - Epic - sschwart@epic.com 
  4. Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  5. Jamie Jones - BCH - james.jones.bch@gmail.com
  6. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  7. Kevin Power - Cerner - kpower@cerner.com
  8. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  9. Liz Amos - NLM - liz.amos@nih.gov 
  10. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  11. Rachel Kutner - Epic - rkutner@epic.com 
  12. Bret Heale

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

  • Co-chair elections
  • Connectathon - Scenarios
  • "Associated" phenotype/cancer component discussion from FHIR subgroup
  • appropriate way to structure our 'additional text' extension?
  • how to link to region studied?
  • Uncallable subregions in a region studied

5/12/20

Patrick



5/19/20

Bob F

Sync for Genes


5/26/20




6/2/20


  • Use of LOINC in IG orders and reports (Swapna Abhyankar) [30+ min]

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: https://www.hl7.org/events/fhir/connectathon/2020/05/

Joint call with OO

  • JD Nolen: Would May 21th, Thursday, 10-11:30 ET work for CG? 
  • during the normal IM call
  • Topics
    • DR (lab report) - likely main topic
    • Specimen
    • plans for MolecularSequence?
    • Device
    • Deprecated genomics parts FHIR core
  • other groups may be invited (BRR, II) but likely just CG and OO
  • Send out request for more/missed topics to the list/zulip

External efforts

Subgroup reports

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

New simplified implications live on CI build 

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

WG projects and outreach

  • none

Topic 0: Approval of Minutes from Last Meeting

May 5 

Topic 1: Functional Annotation vs. Variant Consequence
(Rachel Kutner)

https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Update.20on.20TBD.20Code.20Systems.20for.20FHIR


For Mode of Inheritance, there's a LOINC code suggested in the link I originally included, but the LOINC's answer list isn't fully inclusive of the terms we're wanting to create. Would the best approach be to submit a request to update the LOINC code to include the full list of terms we're interested in? The list is here: https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Mode_of_inheritance.txt

Or is there some reason a new LOINC code might be warranted if we want to expand the scope?

For Functional Annotation, we have a few questions. Based on the description of the term in the link, it points to a SO code which indicates Structural_Variant, which seems incorrect. http://sequenceontology.org/browser/current_svn/term/SO:0001537

It possibly intended to reference the Functional Effect list here, which corresponds to our concept of "Functional Effect": http://sequenceontology.org/browser/current_svn/term/SO:0001536

If it did intend to reference the Structural_Variant SO, that is what we're considering "Variant Consequence" in our own data structure: https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html

Which term is intended to be referenced by "Functional Annotation"?

Is the WG considering including one or both of these concepts (our 'Variant Consequence' and 'Functional Effect') in future Variant Specs, either for FHIR or HL7v2?

Rachel: Functional Annotation points to Variant Consequence (clinvar)

Jamie: do we need two concepts?

Bret: depends on the usage context, is used in different places in our IG.

Jamie: IG currently has: Functional Annotation, DNA Change Type, AA Change Type

Rachel: currently implemented v2 LRI, want to extend with Var Consequences and Functional Effect

Bret: The concepts under: functional_effect_variant are not really consistent.

Patrick: could open the binding to allow both

May: would dilute the component

Rachel: if we want to defer this we can invite an expert to one of this calls (via Rachel)

Kevin: just invite someone during the next weeks?

Rachel: can we provide an agenda to an invitee?

Arthur: if we look at real life reports wouldn’t we find an answer for this issue?

Jamie: maybe add a component for “all SO concepts”

Rachel: doesn’t help here

Jamie: could be outside of Variant, we currently have 3 groups of components: definitional, observational, additional annotations carrying annotations/”implication”

Kevin: G4GH has two groups: Variant Representation and Variant Annotation


Topic 2: appropriate way to structure our 'additional text' extension?

FHIR-20978 - Ability to include interpretation text/findings and recommendations to Observation (Mullai Murugan) 

"As highlighted in the attached test reports, we include textual findings/interpretations and recommendations in a genetic report. For the eMERGE reports, while mapping to draft CG IG spec, these textual interpretations span multiple FHIR Observation profiles in our implemention e.g. Referencing file "highlighted..." test report, text highlighted in grey and yellow would be a fit for general profiles like obs-overall and obs-inh-dis-path; text highlighted in green would be a fit for PGx profiles and the recommendations text highlighted in blue is a recommendation for the provider but not exactly a recommended action; it would be up to the provider to decide on the recommended action.

Considering the need for including this kind of interpretative/summary text (this is not the same as the "text" narrative element) spans multiple Observation resources, it would be very helpful if Interpretation Text and Recommendations were added as Narrative or String elements to the obs-base resource itself."

Resolution: Analysis in Progress

"Resolution Description:
Next steps: look through requested extensions from use cases and get a short list of where they need to go so we can draw clear lines between method.text, component.interpretation, etc.

Previous proposal

Add a new complex Extension (AdditionalGuidance) (0..*), with two attributes:


  • type (CodeabeConcept), binding = example, unbound
  • content (Annotation)


Associate extension to GenomicsBase profile, making it available on any Observation profiles."


**From Tuesday Apr 14:
Next steps: look through requested extensions from use cases and get a short list of where they need to go so we can draw clear lines between method.text, component.interpretation, etc.**

  • Discussion
  • Motion: ? 
    • Move / 2nd:  /   
    • Further Discussion:
    • Vote: (Abstain / Opposed / In Favor):     /   /  
    • Result:  


Topic 3: how to link to region studied?

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

"I have a DR with multiple result (Observations). Each Observation could have different Region Studied. While I can add each Region Studied to the DR, this doesn't allow me to associate a specifc Genotype/Haplotype/Variant to a specific region studied. I'm looking for guidance how to do this. Observation.derivedFrom? I used to be able to use a component for "Description of ranges of DNA sequences examined".

  • Discussion:
    • Bob M: There is a lack of documentation around how to use region-studied at different levels. Is it only at the DR?  I understand that observation.component[gene-studied] allows me to see what found, and that region-studied tells me what was looked for, and that mostly answers my question. But I use gene-studied as a qualifier for Genotype or Haplotype observations. It tells me that I'm reporting a genotype (or haplotype) for a particular gene. So it's telling me not only what found, but also what was looked for. Basically I'm looking for more specific guidance on how to associate what was looked for for each separate observation. 
  • Motion: ? 
    • Move / 2nd:  /   
    • Discussion:
    • Vote: (Abstain / Opposed / In Favor):     /   /  
    • Result:  

Topic 3: Uncallable subregions in a region studied

FHIR-25296 Uncallable subregions in a region studied (Bob Dolin)

 "Would like to consider a new 'no call region' component for the region-studied profile. With this component, in response to a query for variants in a given region, a server can provide a report that also enumerates non-callable subregions, potentially enabling one to differentiate non-callable vs. true negatives.

 

(The main use case we based this on was the need to include wildtype variant calls for PharmGKB's PharmCAT (https://github.com/PharmGKB/PharmCAT) software).

 

The attached example is a set of variants found for 1000 Genomes patient HG00403 in range chr1:1000000-1100000 that includes non-callable subregions. (It's based on a slightly outdated pre-publication version of the IG)."

  • Discussion:
  • Motion: ? 
    • Move / 2nd:  /   
    • Discussion:
      •    
    • Vote: (Abstain / Opposed / In Favor):     /   /  
    • Result:   



Chat

From Me to Everyone: (05:05 PM)

https://docs.google.com/document/d/12-uBrMmav71a3_c9h_FXQteJo_I5Kt72NEBYXZuwhFg/edit#heading=h.wq4fomhpfyys

From Rachel Kutner (Epic) to Everyone: (05:24 PM)


We've reached out to some Oncology Genomics labs to see if there are examples we can use, specifically with our focus in mind.


From James Jones to Everyone: (05:24 PM)


:) Thanks Rachel!


From Arthur Hermann to Everyone: (05:25 PM)


Thanks Rachel - as you heard, I am compiling some info from different oncologists at Kaiser


From Liz Amos to Everyone: (05:35 PM)


The old tracker re: Functional Annotation https://jira.hl7.org/browse/FHIR-22815

From Arthur Hermann to Everyone: (05:38 PM)


link to clinvar example fyi: https://www.ncbi.nlm.nih.gov/clinvar/?term=APC[gene]+AND+(clinsig_pathogenic[prop]+OR+clinsig_likely_pathogenic[prop])+AND+%22single+gene%22[prop]


From Bob Freimuth to Me: (Privately) (05:47 PM)


Patrick: the presiding chair can express opinions, you just need to ensure that everyone has a chance to be heard and that the consensus view is followed if that differs from your own. We need everyone's perspective and expertise, so please don't hold back if you have something to add!


From Me to Bob Freimuth: (Privately) (05:51 PM)


thanks!


From Rachel Kutner (Epic) to Everyone: (05:59 PM)


I have to drop off early, but thank you for the interesting conversation. I'll post in the Zulip thread to ask how we want to follow up on this.


From Bret H to Everyone: (06:01 PM)


great topic and convo. thanks for bringing it up. it would take the ig deeper into the molecular characterization of a variant, which is something



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