Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: GenomicReport - Detailed Descriptions

Active as of 2024-12-12

Definitions for the genomic-report resource profile.

Guidance on how to interpret the contents of this table can be found here

0. DiagnosticReport
2. DiagnosticReport.extension
SlicingThis element introduces a set of slices on DiagnosticReport.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
  • value @ url
  • 4. DiagnosticReport.extension:recommended-action
    Slice Namerecommended-action
    Control0..*
    TypeExtension(Recommended Action) (Extension Type: Reference(Medication Recommendation, Followup Recommendation))
    6. DiagnosticReport.extension:genomic-risk-assessment
    Slice Namegenomic-risk-assessment
    Control0..*
    TypeExtension(Genomic Risk Assessment) (Extension Type: Reference(RiskAssessment))
    8. DiagnosticReport.extension:coded-note
    Slice Namecoded-note
    ShortComments about the report that also contain a coded type
    Comments

    May include general statements about the report, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation. The CodedAnnotation data type, while not allowing for or intending to make the content computable, does allow the author to indicate the type of note. This does not replace the use of results or conclusion or conclusionCode. One important note is that Annotation is a FHIR data type, this is NOT about annotations in the genomic context.

    Control0..*
    TypeExtension(Genomic Report Note) (Extension Type: Annotation(Coded Annotation))
    Requirements

    Need to be able to provide free text additional information. Notes SHALL NOT contain information which can be captured in a structured way.

    10. DiagnosticReport.extension:supporting-info
    Slice Namesupporting-info
    Control0..*
    TypeExtension(Supporting info) (Extension Type: Reference(Resource))
    12. DiagnosticReport.extension:genomic-study
    Slice Namegenomic-study
    ShortReference to full details of an genomic study associated with the diagnostic report
    Control0..*
    TypeExtension(Genomic Study Reference) (Extension Type: Reference(Genomic Study))
    14. DiagnosticReport.extension:hla-genotyping-results-allele-database
    Slice Namehla-genotyping-results-allele-database
    Control0..1
    TypeExtension(allele-database) (Extension Type: CodeableConcept)
    16. DiagnosticReport.extension:hla-genotyping-results-glstring
    Slice Namehla-genotyping-results-glstring
    Control0..1
    TypeExtension(glstring) (Complex Extension)
    18. DiagnosticReport.extension:workflow-relatedArtifact
    Slice Nameworkflow-relatedArtifact
    Comments

    Note that in contrast this extension, the supportingInfo extension references other resources from the patient record that were used in creating the resource.

    Control0..*
    TypeExtension(Related artifact) (Extension Type: RelatedArtifact)
    20. DiagnosticReport.category
    Control1..?
    SlicingThis element introduces a set of slices on DiagnosticReport.category. The slices areUnordered and Open, and can be differentiated using the following discriminators:
    • value @ coding
    • 22. DiagnosticReport.category:Genetics
      Slice NameGenetics
      Control1..1
      24. DiagnosticReport.category:Genetics.coding
      Control1..1
      Pattern Value{
        "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
        "code" : "GE"
      }
      26. DiagnosticReport.code
      Pattern Value{
        "coding" : [{
          "system" : "http://loinc.org",
          "code" : "51969-4"
        }]
      }
      28. DiagnosticReport.effective[x]
      TypedateTime, Period
      [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
      Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
      30. DiagnosticReport.result
      SlicingThis element introduces a set of slices on DiagnosticReport.result. The slices areUnordered and Open, and can be differentiated using the following discriminators:
      • profile @ resolve()
      • 32. DiagnosticReport.result:diagnostic-implication
        Slice Namediagnostic-implication
        ShortDiagnostic Implication
        Control0..*
        TypeReference(Diagnostic Implication)
        34. DiagnosticReport.result:therapeutic-implication
        Slice Nametherapeutic-implication
        ShortTherapeutic Implication
        Control0..*
        TypeReference(Therapeutic Implication)
        36. DiagnosticReport.result:molecular-consequence
        Slice Namemolecular-consequence
        ShortMolecular Consequence
        Control0..*
        TypeReference(Molecular Consequence)
        38. DiagnosticReport.result:variant
        Slice Namevariant
        ShortVariant
        Control0..*
        TypeReference(Variant)
        40. DiagnosticReport.result:sequence-phase-relation
        Slice Namesequence-phase-relation
        ShortSequence Phase Relationship
        Control0..*
        TypeReference(Sequence Phase Relationship)
        42. DiagnosticReport.result:genotype
        Slice Namegenotype
        ShortGenotype
        Control0..*
        TypeReference(Genotype)
        44. DiagnosticReport.result:haplotype
        Slice Namehaplotype
        ShortHaplotype
        Control0..*
        TypeReference(Haplotype)
        46. DiagnosticReport.result:biomarker
        Slice Namebiomarker
        ShortMolecularBiomarker
        Control0..*
        TypeReference(Molecular Biomarker)
        48. DiagnosticReport.conclusion
        ShortAssessment of overall results
        50. DiagnosticReport.conclusionCode
        ShortCoarse overall interpretation of the genomic results