Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build 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 4.0.0-cibuild 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: Genomic Report

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report Version: 4.0.0-cibuild
Standards status: Trial-use Maturity Level: 2 Computable Name: GenomicReport

Genomic profile of DiagnosticReport.

Scope and Usage

The genomic report is the focus of all genomic reporting. It conveys metadata about the overall report (what kind of report it was, when it was written, who wrote it, final vs. draft, etc.). It also typically includes a rendered version for review by a clinician. It also groups together all relevant information found as part of the genomic analysis (Rules for relevancy will depend on the type of testing ordered, the reason for testing and the policies of the lab). Most of the structured genomic information is expressed as FHIR Observations. Any recommendations that come with the report are expressed as FHIR Tasks. The report can be organized into sub-reports using core DiagnosticReport extensions like extends or summaryOf, which is especially useful for later analysis steps. Additionally, an observation can be used to group content for viewing purposes or to indicate a higher-level panel (with a specific LOINC panel code in the Observation.code for example).

Class diagram showing the high-level categories of the component parts in a genomic diagnostic report

Genomic Report Overview

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
DiagnosticReport.status This element is a modifier element. This element is included in summaries. 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
DiagnosticReport.Slices for category This element is included in summaries. 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics This element is included in summaries. 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.code This element is included in summaries. 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.effective[x] This element is included in summaries. 0..1 dateTime Clinically relevant time/time-period for report
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📍4.0.1 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍4.0.1 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from DiagnosticReport

NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.Slices for category 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
DiagnosticReport.Slices for category.category:Genetics 1..1 CodeableConcept Service category
DiagnosticReport.Slices for category.category:Genetics.coding 1..1 Coding Code defined by a terminology system
Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.code 1..1 CodeableConcept Name/Code for this diagnostic report
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.id This element is included in summaries. 0..1 id Logical id of this artifact
DiagnosticReport.meta This element is included in summaries. 0..1 Meta Metadata about the resource
DiagnosticReport.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
DiagnosticReport.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
DiagnosticReport.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
DiagnosticReport.contained 0..* Resource Contained, inline Resources
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
DiagnosticReport.identifier This element is included in summaries. 0..* Identifier Business identifier for report
DiagnosticReport.basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) What was requested
DiagnosticReport.status This element is a modifier element. This element is included in summaries. 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
DiagnosticReport.Slices for category This element is included in summaries. 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics This element is included in summaries. 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics.id 0..1 string Unique id for inter-element referencing
DiagnosticReport.Slices for category.category:Genetics.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for category.category:Genetics.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.Slices for category.category:Genetics.text This element is included in summaries. 0..1 string Plain text representation of the concept
DiagnosticReport.code This element is included in summaries. 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) The subject of the report - usually, but not always, the patient
DiagnosticReport.encounter This element is included in summaries. 0..1 Reference(Encounter) Health care event when test ordered
DiagnosticReport.effective[x] This element is included in summaries. 0..1 dateTime Clinically relevant time/time-period for report
DiagnosticReport.issued This element is included in summaries. 0..1 instant DateTime this version was made
DiagnosticReport.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Responsible Diagnostic Service
DiagnosticReport.resultsInterpreter This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
DiagnosticReport.specimen 0..* Reference(Specimen) Specimens this report is based on
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
DiagnosticReport.media This element is included in summaries. 0..* BackboneElement Key images associated with this report
DiagnosticReport.media.id 0..1 string Unique id for inter-element referencing
DiagnosticReport.media.extension 0..* Extension Additional content defined by implementations
DiagnosticReport.media.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
DiagnosticReport.media.comment 0..1 string Comment about the image (e.g. explanation)
DiagnosticReport.media.link This element is included in summaries. 1..1 Reference(Media) Reference to the image source
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.
DiagnosticReport.presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base preferred Common Languages 📍4.0.1 FHIR Std.
DiagnosticReport.status Base required DiagnosticReportStatus 📍4.0.1 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍4.0.1 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from DiagnosticReport

Summary

Mandatory: 3 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of DiagnosticReport.category
  • The element 1 is sliced based on the value of DiagnosticReport.result

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
DiagnosticReport.status This element is a modifier element. This element is included in summaries. 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
DiagnosticReport.Slices for category This element is included in summaries. 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics This element is included in summaries. 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.code This element is included in summaries. 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.effective[x] This element is included in summaries. 0..1 dateTime Clinically relevant time/time-period for report
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📍4.0.1 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍4.0.1 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Differential View

This structure is derived from DiagnosticReport

NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.Slices for category 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
DiagnosticReport.Slices for category.category:Genetics 1..1 CodeableConcept Service category
DiagnosticReport.Slices for category.category:Genetics.coding 1..1 Coding Code defined by a terminology system
Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.code 1..1 CodeableConcept Name/Code for this diagnostic report
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.effective[x] 0..1 dateTime Clinically relevant time/time-period for report
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
DiagnosticReport.id This element is included in summaries. 0..1 id Logical id of this artifact
DiagnosticReport.meta This element is included in summaries. 0..1 Meta Metadata about the resource
DiagnosticReport.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
DiagnosticReport.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
DiagnosticReport.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
DiagnosticReport.contained 0..* Resource Contained, inline Resources
DiagnosticReport.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for extension.extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
DiagnosticReport.Slices for extension.extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
DiagnosticReport.Slices for extension.extension:coded-note 0..* CodedAnnotation Comments about the report that also contain a coded type
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note
DiagnosticReport.Slices for extension.extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
DiagnosticReport.Slices for extension.extension:genomic-study 0..* Reference(Genomic Study) Reference to full details of an genomic study associated with the diagnostic report
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
DiagnosticReport.Slices for extension.extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
DiagnosticReport.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
DiagnosticReport.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
DiagnosticReport.identifier This element is included in summaries. 0..* Identifier Business identifier for report
DiagnosticReport.basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) What was requested
DiagnosticReport.status This element is a modifier element. This element is included in summaries. 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
DiagnosticReport.Slices for category This element is included in summaries. 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics This element is included in summaries. 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.
DiagnosticReport.Slices for category.category:Genetics.id 0..1 string Unique id for inter-element referencing
DiagnosticReport.Slices for category.category:Genetics.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
DiagnosticReport.Slices for category.category:Genetics.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern:
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
DiagnosticReport.Slices for category.category:Genetics.text This element is included in summaries. 0..1 string Plain text representation of the concept
DiagnosticReport.code This element is included in summaries. 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.
Required Pattern:
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51969-4"
    }
  ]
}
DiagnosticReport.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) The subject of the report - usually, but not always, the patient
DiagnosticReport.encounter This element is included in summaries. 0..1 Reference(Encounter) Health care event when test ordered
DiagnosticReport.effective[x] This element is included in summaries. 0..1 dateTime Clinically relevant time/time-period for report
DiagnosticReport.issued This element is included in summaries. 0..1 instant DateTime this version was made
DiagnosticReport.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Responsible Diagnostic Service
DiagnosticReport.resultsInterpreter This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
DiagnosticReport.specimen 0..* Reference(Specimen) Specimens this report is based on
DiagnosticReport.Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
DiagnosticReport.Slices for result.result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
DiagnosticReport.Slices for result.result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
DiagnosticReport.Slices for result.result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
DiagnosticReport.Slices for result.result:variant 0..* Reference(Variant) Variant
DiagnosticReport.Slices for result.result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
DiagnosticReport.Slices for result.result:genotype 0..* Reference(Genotype) Genotype
DiagnosticReport.Slices for result.result:haplotype 0..* Reference(Haplotype) Haplotype
DiagnosticReport.Slices for result.result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
DiagnosticReport.imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
DiagnosticReport.media This element is included in summaries. 0..* BackboneElement Key images associated with this report
DiagnosticReport.media.id 0..1 string Unique id for inter-element referencing
DiagnosticReport.media.extension 0..* Extension Additional content defined by implementations
DiagnosticReport.media.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
DiagnosticReport.media.comment 0..1 string Comment about the image (e.g. explanation)
DiagnosticReport.media.link This element is included in summaries. 1..1 Reference(Media) Reference to the image source
DiagnosticReport.conclusion 0..1 string Assessment of overall results
DiagnosticReport.conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.
DiagnosticReport.presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base preferred Common Languages 📍4.0.1 FHIR Std.
DiagnosticReport.status Base required DiagnosticReportStatus 📍4.0.1 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍4.0.1 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍4.0.1 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from DiagnosticReport

Summary

Mandatory: 3 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of DiagnosticReport.category
  • The element 1 is sliced based on the value of DiagnosticReport.result

Maturity: 2

 

Other representations of profile: CSV, Excel, Schematron

Notes:

Overall Interpretation and Conclusion

On the report, it is important to answer the question "Did you find anything when you did the test I asked you to do?" The data sender can use attributes of conclusionCode and conclusion to represent the summary result of the test (e.g., Positive, Negative, Unknown) and a textual summary. These are typically used when the genomic test was looking for a particular genomically-based disease. It allows indication of whether genomic results known to be associated with the disease were found or not.

Linking To Genomic Observations

Results observation profiles, like genomic observations, are typically referenced directly by a Genomic Report. The genetic findings and implication profiles all contain links to computably define their composite relationships (e.g., the variant observation is referenced within the implication profile using derivedFrom). However, observations could be organized into groups by other observations. See this grouping guidance for an overview with examples and considerations for processing reports. Be aware that consumers of Genomic Diagnostic Report MUST navigate through all hasMember relations and navigate through derivedFrom relationships to ensure processing of all clinically relevant information.

Risk Assessments

In some cases, the lab or other reporting organization may generate risk assessments as part of their reports. These are referenced from a report or an observation from the Genomic Risk extension.

Presented Form

When sending a copy of the report (e.g., PDF or other document containing the written report), use presentedForm. Note this is different from the Related Artifact extension, which is used to reference citations, evidence and other supporting documentation for the observation or report. Another approach which should be avoided (at least for this current release) is the DiagnosticReport.media attribute. Its definition focuses on "Key images associated with this report" which does not align well with this use case.

Complex Reports

If needed, large or complex genomic reports may be broken down into sub-reports using core DiagnosticReport extensions like extends or summaryOf. This approach is particularly useful when different labs or services are performing later steps in the analysis, for example. Or a panel Observation.code can be used.