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  1. FHIR Specification Feedback
  2. FHIR-43744

GenomicStudyAnalysis needs additional metadata

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    • Icon: Change Request Change Request
    • Resolution: Persuasive with Modification
    • Icon: Highest Highest
    • Genomics Reporting (FHIR)
    • 3.0.0-ballot
    • Clinical Genomics
    • Genomic Study Analysis
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      Add genomic-source-class as an extension to genomic study analysis, (currently only available as Observation.component[genomic-source-class].

      valueCodeeableConcept &  LOINC Answer List LL378-1 (extensible)

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      Add genomic-source-class as an extension to genomic study analysis, (currently only available as Observation.component [genomic-source-class] . valueCodeeableConcept &   LOINC Answer List LL378-1  ( extensible )
    • Bob D / Kevin P : 9 - 0 - 0
    • Enhancement
    • Compatible, substantive

    Description

      When attempting to parse a referenced VCF file, it might be possible for GenomicStudyAnalysis to contain sufficient metadata to enable a safe parse. In particular, we use genomic source class (e.g. does the VCF file contain only germline variants, only somatic variants, or a mix) and VCF sample column (e.g. in a multi-sample VCF such as a tumor-normal VCF, which sample column in the VCF contains the patient variants) when converting VCF to FHIR. 

      While it might make sense to add a genomicSourceClass metadata field, it may also be that we need a flexible key-value mechanism that allows a lab to include test specific parameters. 

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            Unassigned Unassigned
            bob.dolin Bob Dolin
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              Updated:
              Resolved: