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  1. FHIR Specification Feedback
  2. FHIR-35864

Add study-level metadata capabilities into the FHIR Genomics IG

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    • Icon: Change Request Change Request
    • Resolution: Persuasive
    • Icon: Medium Medium
    • Genomics Reporting (FHIR)
    • 1.0.0
    • Clinical Genomics
    • General Genomic Reporting
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      Backport R5 GenomicStudy features to our R4 based implementation guide.

      Resolution based mostly on this proposal: https://docs.google.com/document/d/1N9JsMW3OXVO1VVipIYs-Cz6J0zpWEx51yvigMGlINOo/edit

      High level:

      • GenomicStudy profile of Procedure (for R5 GenomicStudy)
      • GenomicStudyAnalysis profile of Procedure (for R5 GenomicStudy.analysis[] backbone element)
      • Create CodeSystems and ValueSets defined for GenomicStudy
      • Map elements to existing attributes where appropriate
      • New extensions for elements that do not map
      • Additional extension for 'uncallable regions' (not an element in GenomicStudy)
      • Create guidance and refer to R5 GenomicStudy
      • Create references to GenomicStudy from GenomicsReport and GenomicsBase observation profile.
      • Update the general reporting page to provide an introduction to the new profiles, and to update the 'Attaching Genomic Files' section to reflect the expectation to use the GenomicStudy profiles as the way to attach files instead of the STU2 approach of using an extension on GenomicsReport.
      • Remove the GenomicsReport.result[] slice that refers to Region Studied observations, and use that feature of GenomicStudy profile instead.¬†
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      Backport R5 GenomicStudy features to our R4 based implementation guide. Resolution based mostly on this proposal: https://docs.google.com/document/d/1N9JsMW3OXVO1VVipIYs-Cz6J0zpWEx51yvigMGlINOo/edit High level: GenomicStudy profile of Procedure (for R5 GenomicStudy) GenomicStudyAnalysis profile of Procedure (for R5 GenomicStudy.analysis[] backbone element) Create CodeSystems and ValueSets defined for GenomicStudy Map elements to existing attributes where appropriate New extensions for elements that do not map Additional extension for 'uncallable regions' (not an element in GenomicStudy) Create guidance and refer to R5 GenomicStudy Create references to GenomicStudy from GenomicsReport and GenomicsBase observation profile. Update the general reporting page to provide an introduction to the new profiles, and to update the 'Attaching Genomic Files' section to reflect the expectation to use the GenomicStudy profiles as the way to attach files instead of the STU2 approach of using an extension on GenomicsReport. Remove the GenomicsReport.result[] slice that refers to Region Studied observations, and use that feature of GenomicStudy profile instead. 
    • Bob Dolin / Srikar Chamala: 9-0-1
    • Enhancement
    • Non-compatible

    Description

      Several lines have now raised the need for study-level meta-data (including 3 Jiras: JIRA #32084 'Create Study Level subtype for Genomics Base'; JIRA #19829 'FHIR representation of a genetics test with multiple test components/results'; JIRA #24598 'How to reference a region studied observation from genotype, haplotype, variant observations').

      In response to Jira 32084, we drafted a proposal https://docs.google.com/document/d/1N9JsMW3OXVO1VVipIYs-Cz6J0zpWEx51yvigMGlINOo/edit

      Subsequent discussion with O&O, and within the HL7 CG IM group has identified additional options.

      This tracker is meant to address JIRA 32084, 19829, and 24598 and the other requirements called out in the draft proposal, so that we have an active ticket to guide the WG to solidify a final disposition.

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            cerkyp Kevin Power
            bob.dolin Bob Dolin
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              Created:
              Updated:
              Resolved: