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HL7 Clinical Genomics Weekly Call - 21 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

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Agenda

Attendees Sign-in

Standing Informational Items

Agendas and Important Dates

External efforts

Subgroup reports

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

Topic 1: Abandoned WG projects

Topic 2: Connectathon - track leaders

Topic 3: Update: Ability to include interpretation text/findings and recommendations to Observation (FHIR-20978)

Topic 4: how to link to region studied?

Topic 5: Uncallable subregions in a region studied

Chat

Future Topics

LOINC changes for Level of Evidence / Clinical Significance

Clinical Genomics Reference Docs

Attendees Sign-in

Presiding Co-Chair (Bob Milius - NMDP/CIBMTR - bmilius@nmdp.org ): 

  1. Patrick Werner - MOLIT Institut - patrick.werner@molit.eu 
  2. Dora Finkeisen - MOLIT Institut - dora.finkeisen@molit.eu 
  3. Liz Amos - NLM - liz.amos@nih.gov 
  4. Bret Heale - Intermountain Healthcare - bheale@gmail.com Bob Freimuth - Mayo Clinic - freimuth.robert@mayo.edu
  5.  Stephen Schwartz - Epic - sschwart@epic.com
  6. Kevin Power - Cerner - kpower@cerner.com 
  7. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  8. JD Nolen - Children’s Mercy Hospital - jlnolen@cmh.edu
  9.  Arthur Hermann - Kaiser Permanente - arthur.hermann@kp.org
  10.  James Jones - BCH - james.jones.bch@gmail.com 
  11.  Rachel Kutner - Epic - rkutner@epic.com
  12.  Ling Teng -BWH- tenglingling@gmail.com
  13.  
  14.  
  15.  
  16.  
  17.  
  18.  
  19.  


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

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

Arthur - we should start working on agenda for more meetings

Kevin - poll group, what time frames are available? put them on the agenda and then fill with topics

Bob F - figure out topics, then pick times

Kevin - either works, but available time is smaller set and start there.

Bob F - find topic leaders and find out when they are available

Patrick - may incorporate an extended hackathon

Arthur - find out most important things to talk about

Bob M - co-chairs to discuss and propose something in email/zulip, decide next week

External efforts

  • GA4GH Genomic Knowledge Standards (GKS) (leads: Bob Freimuth, Andy Yates)
  • ClinGen/ClinVar (Larry Babb, Bob Freimuth)
    • Data Exchange/Platform WG, major driver project of GA4GH GKS
    • will discuss further when Larry in on a call
  • 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.
    • Clem: no specific insight - Transcelerate Biopharma (https://transceleratebiopharmainc.com) group fairly active in FHIR. FDA has active interest in FHIR.
  • ONC Sync for Genes (Bob Freimuth)
    • ONC website: https://www.healthit.gov/topic/sync-genes
    • Final report for Sync for Genes Phase 2 has been finalized and approved (in the process of being)
    • ACI manuscript is in press
    • Phase 3 has started - more details to be announced soon
  • ISO TC/215 Genomics Subcommittee (Liz, Clem, Bob F)
    • Canada is sponsoring a phenopackets spec in ISO, will be based on the GA4GH spec that was approved fall 2019
  • eMERGE FHIR adoption (Larry Babb, Mullai Murugan, Kevin Power)
  • MCODE

Subgroup reports

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

WG projects and outreach

Topic 0: Approval of Minutes from Last Meeting

April 14 


Topic 1: Abandoned WG projects



NMD069

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

Connection with Decision Support

564

Next Milestone Date Is: 2014 Jan WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

NMD070

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

Family Health History and Pedigree standard, Release 2

844

Next Milestone Date Is: 2014 Jan WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

NMD072

Pjt Insight Next Milestone Behind>120 Days

Clinical Genomics Work Group

CDA Implementation Guide for Genetic Testing Reports

460

Next Milestone Date Is: 2018 May WGM/Ballot

Determine when the next deliverable will be (the tgt date can be a WGM or Ballot Cycle); send dates to pmo@HL7.org.

Bob F: closing these project doesn’t remove the current content, only cleaning up administratively as we are not actively working on them (and haven’t for some time)

There was a question on where info about these can be found:


For us to continue any of these projects, we need someone to take on ownership for one or more of them (preferably someone with a particular interest in them).

Motion: To request to close these projects (all listed above)

  • 1st/2nd:  Bob F /  Patrick
  • discussion: 
    • Kevin - we will request that these be closed, but caveat will be HL7 leadership re how to close. There may be process we need to follow. We will respond back to group with final status.
  • Vote: (Abstain / Opposed / In Favor):    0 / 0 / 12
  • Result: motion passes



Topic 2: Connectathon - Scenarios

Scenarios that have 2 or more interested participants

  1. Cancer Screening (Patrick, Alex)
    1. Including tumor-normal testing
    2. Bob M: what about non-cancerous tumors - is there any data to contribute?
    3. Bob D: publically available breast cancer data set may help here as well-could mock up some clinical data in mCode and combine to match a patient to a clinical trial - not easy, but very interesting
    4. Clem: COSMIC could easily be used for extra cancer variant data
  2. ACMG screening (Bob D, Bret)
    1. Bob D - will make available 1k genome project GACS - could create an ACMG screening scenario. Bret would like to collab as well
    2. Canhouse raw genomic data in a server and export in FHIR
    3. Resulting FHIR data can be part of a decision support pipeline
      1. ACMG screening
      2. Other PGx

Other topics mentioned:

  1. WES Trio (Jamie)
  2. HLA/Profiling the CG IG (Bob M, also may be working on FHIR shorthand track)
    1. test proposed fixes for derivedFrom
  3. Clem is bringing some developers and others may be around as well


Arthur - Invitae interested in developing one or more standard clinical health care reports. Arthur can lead this (not as a technical lead). Arthur will follow up and get an answer as soon as possible (end of next week).

Bob D - interested in helping this

Jamie - number of different levels they can participate (bring reports, files) and we can help them navigate through FHIR. Maybe they can fit in existing tracks.

Bob D - PGx screening would have a 1k genome server and they may want to help using this.

Patrick and BobD will be identified as track leads.

Topic 3: Update: Ability to include interpretation text/findings and recommendations to Observation (FHIR-20978)


We will finish work on Implications before continuing this work


From last week:
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.

eMERGE examples (older, multiple extensions included): https://docs.google.com/spreadsheets/d/1n_u1RQWHmAm8tafIFioR0g3HFLqKdvZF/edit#gid=2105486159

https://emerge-fhir-spec.readthedocs.io/en/latest/ (latest public guidance)

  1. Reviewing emerge extensions - discussion for tomorrow
    1. https://emerge-fhir-spec.readthedocs.io/en/latest/artifacts/index.html
    2. https://docs.google.com/spreadsheets/d/1n_u1RQWHmAm8tafIFioR0g3HFLqKdvZF/edit?dls=true#gid=1008959679

A heterozygous c.1552C>T (p.Arg518*) pathogenic variant in the KCNQ1 (NM_000218.2) gene was detected in this individual, which was confirmed by Sanger sequencing. Defects i...

Confirmation should be modelled if possible, as should be computable...

This individual is homozygous for the functional allele of the DPYD gene. This genotype information can be used by patients and clinicians as part of the shared decision-making process for fluoropyrimidines (capecitabine, fluorouracil, tegafur). Based on the genotype result, this patient is predicted to have a normal DPD activity phenotype. Individuals with this diplotype are expected to have "normal" risk for fluoropyrimidine toxicity. Recommendations include the use of label recommended dosage and administration. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for-fluoropyrimidines-and-dpyd/


This individual is homozygous for the rs4149056 T/T allele in the SLCO1B1 gene. This genotype information can be used by patients and clinicians as part of the shared decision-making process for simvastatin and other drugs affected by SLCO1B1. Based on the genotype result, this patient is predicted to have normal SLCO1B1 function. This means that there is no reason to adjust the dose of most medications that are affected by SLCO1B1 (including simvastatin) on the basis of SLCO1B1 genetic status. Refer to current guidelines for dosage and recommendations at https://cpicpgx.org/guidelines/guideline-for-simvastatin-and-slco1b1/.




      Below was not discussed

      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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