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Notes from FHIR subgroup meeting (2020-05-18)

FHIR Subgroup Meeting MAY 18th, 2020

We are ZOOMing away from FCC. New coordinates:

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Quick link to this sign-in/notes document: tinyurl.com/fhirgenomics 

Sign In: (presiding co-chair - Jamie Jones )

  1. Kevin Power - Cerner - kpower@cerner.com 
  2. May Terry - MITRE - mayT@mitre.org 
  3. Liz Amos - NLM - liz.amos@nih.gov 
  4. Bret Heale - Intermountain - bheale@gmail.com
  5. Bob Dolin - Elimu Informatics - bdolin@elimu.io 
  6. Daniel Rutz - Epic - drutz@epic.com
  7. Hayden Bader - Epic - hbader@epic.com
  8. Lloyd McKenzie - Gevity - lmckenzie@gevityinc.com
  9. Patrick Werner - MOLIT - pw@molit.eu 
  10. Joel Schneider - NMDP/CIBMTR - jschneid@nmdp.org
  11. Scott Isaac - Epic - scisaac@epic.com
  12. Clem McDonald - NLM - clemmcdonald@mail.nih.gov 

Agenda:

  1. Connectathon review
  2. Next steps
  3. JIRA (didn’t cover)

Discussion:

  1. Connectathon review
    1. CAT 24 Report out
    2. CG connectathon 24 links
      1. Representing variants in apps (https://molit.eu/variant-viewer/) Still very beta, configurable rewrite is done at the moment.
        1. Webcomponents contained here: https://github.com/molit-institute/fhir-components
        2. Docs here: https://docs.molit.eu/fhir-components/#/components/MolecularReport
        3. Currently - Need to support ALL possible configurations/representations to display. Choosing only one method may not be sufficient 
        4. Producing reusable open source web components
          1. Patrick is a gift
        5. Clem’s group working on GUI questionnaire with some bioinformatic logic built in
          1. SPDI as a partial check on validity, hoping to integrate with mutalyzer
      2. $find-subject-variants
        1. Syntactic normalization - use API to display variants using the same components regardless of how it was provided to server
        2. Semantic normalization - aligning different representations of the ‘same variant’ e.g CCC > CC vs CC > C.
          1. SPDI effective tool for indels that look like this
      3. STU2 implication reporting
        1. http://hapi.fhir.org/baseR4/DiagnosticReport/1167557

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      1. FSH - FHIR shorthand for creating structureDefinitions
        1. Current Beta version of sushi pulls all IG configurations into one yaml file, does more than just create structure definitions, can initialize a whole IG with template - open questions on long term support and scope in that regard (question of whether it should just restrict itself to structureDefinitions)
          1. https://github.com/FHIR/sushi/releases/tag/v0.13.0-beta.1
        2. Technical concerns around lack of round tripping from structure definitions. Proof of concept work in progress
      2. QA - outdated artifacts pull request for R5
        1. Review current core build for straggling references to old profiles
        2. Guidance on MolecularSequence remains for now (no other guidance on it exists)
        3. Merits full review
  1. Next steps:
    1. Looking ahead
      1. https://www.devdays.com/us/schedule/
      2. Sept Connectathon
      3. Content freeze?
    2. Priorities before STU2 freeze
      1. Variant components
        1. 3 JIRAs
      2. Finalize implication update
        1. associated phenotype/cancer stress test
        2. 10 JIRAs
      3. TBD-LOINCs
        1. 1 JIRA, may need more
      4. TMB, MSI
        1. Example validation
      5. Region Studied
        1. 3 JIRAs, examples needed
      6. MolecularSequence??
        1. 2 JIRAs, may need more
  2. JIRA (37 open issues)

Grouping

Key

Summary

Reporter

Notes

variant

FHIR-27146

Remove components from Variant Profile

Kevin Power


variant

FHIR-27137

Clarify the representation of wild type in variant profile

Bob Dolin


variant

FHIR-19829

Inclusion of Sanger confirmation information

Mullai Murugan


Tech correction?

FHIR-25742

Change LOINC Codesets

Mullai Murugan


Tech correction?

FHIR-25418

Require "Genetics" category on report

James Jones


Tech correction?

FHIR-22802

set StructureDefinition.abstract true on all abstract profiles

Patrick Werner


Tech correction?

FHIR-19966

Fix slicings in obs profiles

Patrick Werner


Tech correction?

FHIR-19964

Check all slicings if we want to have open vs closed

Patrick Werner


Tech correction?

FHIR-17341

Error in Description & Constrains for Genetic Observation Common Properties

Bob Milius


Tech correction?

FHIR-26905

HGVS is misspelled

Liz Amos


tbd-loincs

FHIR-25241

Missing LOINC codes in Variant profile (but are in UML)

Liz Amos


TASK

FHIR-25187

CG IG TaskRecFollowup profile code should be extensible

Larry Babb


semantics

FHIR-16390

Enhance terminology of Genetic Impact

Gil Alterovitz


reporting

FHIR-19828

FHIR representation of a genetics test with multiple test components/results

Mullai Murugan


reporting

FHIR-26362

What is an appropriate resource and element to include addendum text?

Mullai Murugan


reporting

FHIR-19831

Usage of LOINC code 81247-9 for Genetic tests

Mullai Murugan


region studied

FHIR-25296

Uncallable subregions in a region studied

Bob Dolin


region studied

FHIR-24598

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

Bob Milius


region studied

FHIR-20314

Ideal strategy for handling a large amount of genomic results. Method needed to describe what things you looked at and didn't touch.

Apurva Dharia


new guidance

FHIR-16406

Add plans for future mappings to R4

Gil Alterovitz


new guidance

FHIR-16404

Add group doc STU3 to STU4

Gil Alterovitz


new guidance

FHIR-16402

Add material from guidance document

Gil Alterovitz


molSeq

FHIR-24682

MolecularSequence.referenceSeq.genomeBuld should align with obsGenFinding.component.ref-sequence.assembly

Larry Babb


molSeq

FHIR-19373

Consider support for sending VCF data in Sequence

Gil Alterovitz


molSeq

FHIR-16398

Add detail to quality matrix

Gil Alterovitz


implications

FHIR-26945

clarifying 'context' vs 'risk-of' for associated phenotype and/or associated cancer component

Bret Heale


implications

FHIR-26426

Add new component for 'Potential Clinical Trial Match'

Kevin Power


implications

FHIR-26380

describe adverse effects on Implication

James Jones


implications

FHIR-26379

Support for detailed lab text on Implications

James Jones


implications

FHIR-25170

relatedArtifact extension on Obesrvation.component

James Jones


implications

FHIR-20198

Medication Impact profile obs-med-impact (CG IG)

Larry Babb


implications

FHIR-19844

PGx High Risk Allele Medication Impact is confusing

Larry Babb


implications

FHIR-19244

Level of Evidence CodeableConcept should have some kind of binding

Patrick Werner


implications

FHIR-16175

Genetic Impact - Add ACMG reference for level of evidence

Kevin Power


implications

FHIR-16082

PGx Impact - Allele functional status

Kevin Power


family member history

FHIR-15886

Missing the Ancestry profile in the IG

Xin Liu


duplicate

FHIR-16493

Relation of PgX Example to Specimen analyzed to produce Diagnostic Report results

Andrea Pitkus



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See the following notes for other calls that happened during the Virtual WGM for CG

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