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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. Patrick is a gift
        1. SPDI as a partial check on validity, hoping to integrate with mutalyzer
        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
        1. Clem’s group working on GUI questionnaire with some bioinformatic logic built in
    3. SPDI as a partial check on validity, hoping to integrate with mutalyzer
      1. $find-subject-variants
        1. SPDI effective tool for indels that look like this
        1. Syntactic normalization - use API to display variants using the same components regardless of how it was provided to server
        2. Semantic normalization - aligning different representations of the ‘same variant’ e.g CCC > CC vs CC > C.
    4. SPDI effective tool for indels that look like this
      1. STU2 implication reporting
        1. http://hapi.fhir.org/baseR4/DiagnosticReport/1167557
      1. CAT 24 Report out
      2. CG connectathon 24 links
          1. http://hapi.fhir.org/baseR4/Observation/?component-code-value-concept=http://loinc.org|81252-9$https://www.ncbi.nlm.nih.gov/clinvar|653974&_revinclude=Observation:derived-from
            1. Questions over integration with problem list
            2. Condition.evidence?
          2. This example can trigger some interesting discussion around our usage of ‘Associated Phenotype’
Ties back to this JIRA: https://jira.hl7.org/browse/FHIR-26945
 And the Zulip discussion here: https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Stress.20Testing.20IG.20Implications.20with.20Examples
        1. FSH - FHIR shorthand for creating structureDefinitions
          1. https://github.com/FHIR/sushi/releases/tag/v0.13.0-beta.1
          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)
          2. https://github.com/FHIR/sushi/releases/tag/v0.13.0-beta.1
          3. 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
          TBD

    -

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    1. 1 JIRA, may need more

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    1. Example validation

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    1. 3 JIRAs, examples needed

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    1. 2 JIRAs, may need more

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    Grouping

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    Key

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    Summary

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    Reporter

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    Notes

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    variant

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    -

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    Remove components from Variant Profile

    ...

    Kevin Power

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    variant

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    FHIR-27137

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    Clarify the representation of wild type in variant profile

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    Bob Dolin

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    variant

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    FHIR-19829

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    Inclusion of Sanger confirmation information

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    Mullai Murugan

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    Tech correction?

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    FHIR-25742

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    Change LOINC Codesets

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    Mullai Murugan

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    Tech correction?

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    -

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    Require "Genetics" category on report

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    ...

    Tech correction?

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    FHIR-22802

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    set StructureDefinition.abstract true on all abstract profiles

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    Patrick Werner

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    Tech correction?

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    FHIR-19966

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    Fix slicings in obs profiles

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    Patrick Werner

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    Tech correction?

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    FHIR-19964

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    Check all slicings if we want to have open vs closed

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    Patrick Werner

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    Tech correction?

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    FHIR-17341

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    Error in Description & Constrains for Genetic Observation Common Properties

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    Bob Milius

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    Tech correction?

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    FHIR-26905

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    HGVS is misspelled

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    Liz Amos

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    tbd-loincs

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    FHIR-25241

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

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    Liz Amos

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    TASK

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    FHIR-25187

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    CG IG TaskRecFollowup profile code should be extensible

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    Larry Babb

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    semantics

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    FHIR-16390

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    Enhance terminology of Genetic Impact

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    Gil Alterovitz

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    reporting

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    FHIR-19828

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

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    Mullai Murugan

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    reporting

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    FHIR-26362

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

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    Mullai Murugan

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    reporting

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    FHIR-19831

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    Usage of LOINC code 81247-9 for Genetic tests

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    Mullai Murugan

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    region studied

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    FHIR-25296

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    Uncallable subregions in a region studied

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    Bob Dolin

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    region studied

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    FHIR-24598

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

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    Bob Milius

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    region studied

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    FHIR-20314

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

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    Apurva Dharia

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    new guidance

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    FHIR-16406

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    Add plans for future mappings to R4

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    Gil Alterovitz

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    new guidance

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    FHIR-16404

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    Add group doc STU3 to STU4

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    Gil Alterovitz

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    new guidance

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    FHIR-16402

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    Add material from guidance document

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    Gil Alterovitz

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    molSeq

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    FHIR-24682

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

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    Larry Babb

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    molSeq

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    FHIR-19373

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    Consider support for sending VCF data in Sequence

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    Gil Alterovitz

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    molSeq

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    FHIR-16398

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    Add detail to quality matrix

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    Gil Alterovitz

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    implications

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    FHIR-26945

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

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    Bret Heale

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    implications

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    FHIR-26426

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    Add new component for 'Potential Clinical Trial Match'

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    Kevin Power

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    implications

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    FHIR-26380

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    describe adverse effects on Implication

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    James Jones

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    implications

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    FHIR-26379

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    Support for detailed lab text on Implications

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    James Jones

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    implications

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    FHIR-25170

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    relatedArtifact extension on Obesrvation.component

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    James Jones

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    implications

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    FHIR-20198

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

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    Larry Babb

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    implications

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    FHIR-19844

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    PGx High Risk Allele Medication Impact is confusing

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    Larry Babb

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    implications

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    FHIR-19244

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    Level of Evidence CodeableConcept should have some kind of binding

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    Patrick Werner

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    implications

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    FHIR-16175

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    Genetic Impact - Add ACMG reference for level of evidence

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    Kevin Power

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    implications

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    FHIR-16082

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    PGx Impact - Allele functional status

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    Kevin Power

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    family member history

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    FHIR-15886

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    Missing the Ancestry profile in the IG

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    Xin Liu

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    duplicate

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    FHIR-16493

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

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    Andrea Pitkus

    ---

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

    CG-2020-05-19

    OO Conf Call Minutes - 2020-05-21 OO/CG/II