Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot 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-ballot 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-ballot
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: Filtersdoco
.. DiagnosticReport C 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
Constraints: dgr-1
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... status ?!Σ 1..1 code registered | partial | preliminary | modified | final | amended | corrected | appended | cancelled | entered-in-error | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
..... coding 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): LOINC Codes for Diagnostic Reports
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for the results that are included in the report
... Slices for result C 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication C 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication C 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence C 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant C 0..* Reference(Variant) Variant
.... result:sequence-phase-relation C 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype C 0..* Reference(Genotype) Genotype
.... result:haplotype C 0..* Reference(Haplotype) Haplotype
.... result:biomarker C 0..* Reference(Molecular Biomarker) MolecularBiomarker
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): SNOMED CT Clinical Findings

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required Diagnostic Report Status 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍6.0.0-ballot3 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dgr-1 error DiagnosticReport When a Composition is referenced in `DiagnosticReport.composition`, all Observation resources referenced in `Composition.entry` must also be referenced in `DiagnosticReport.result` or in the `Observation.hasMember` references. composition.exists() implies (composition.resolve().section.entry.reference.where(resolve() is Observation) in (result.reference|result.reference.resolve().hasMember.reference))
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... Slices for category 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
.... category:Genetics 1..1 CodeableConcept Service category
..... coding 1..1 Coding Code defined by a terminology system
Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code 1..1 CodeableConcept Name/Code for this diagnostic report
Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
... Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant 0..* Reference(Variant) Variant
.... result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype 0..* Reference(Genotype) Genotype
.... result:haplotype 0..* Reference(Haplotype) Haplotype
.... result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport C 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
Constraints: dgr-1
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: AllLanguages (required): IETF language tag for a human language
Additional BindingsPurpose
CommonLanguages Starter
... 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
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business identifier for report
... basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) What was requested
... status ?!Σ 1..1 code registered | partial | preliminary | modified | final | amended | corrected | appended | cancelled | entered-in-error | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
..... id 0..1 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): LOINC Codes for Diagnostic Reports
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Practitioner | Medication | Substance | BiologicallyDerivedProduct) The subject of the report - usually, but not always, the patient
... relatesTo 0..* RelatedArtifact Related DiagnosticReports
... encounter Σ 0..1 Reference(Encounter) Encounter associated with the DiagnosticReport
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for the results that are included in the report
... issued Σ 0..1 instant DateTime this version was made
... procedure Σ 0..* Reference(Procedure) The procedure(s) from which the report was produced
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | HealthcareService | Device) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(Specimen) Specimens this report is based on
... Slices for result C 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication C 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication C 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence C 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant C 0..* Reference(Variant) Variant
.... result:sequence-phase-relation C 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype C 0..* Reference(Genotype) Genotype
.... result:haplotype C 0..* Reference(Haplotype) Haplotype
.... result:biomarker C 0..* Reference(Molecular Biomarker) MolecularBiomarker
... note 0..* Annotation Comments about the diagnostic report
... study 0..* Reference(GenomicStudy | ImagingStudy) Reference to full details of an analysis associated with the diagnostic report
... supportingInfo 0..* BackboneElement Additional information supporting the diagnostic report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... type 1..1 CodeableConcept Supporting information role code
Binding: hl7VS-VS-observationType (example): The code value for the role of the supporting information in the diagnostic report.
.... reference 1..1 Reference(ImagingStudy | Procedure | Observation | DiagnosticReport | Citation | FamilyMemberHistory | AllergyIntolerance | DeviceUsage | Condition | GenomicStudy) Supporting information reference
... media Σ 0..* BackboneElement Key images or data associated with this report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... comment 0..1 string Comment about the image or data (e.g. explanation)
.... link Σ 1..1 Reference(DocumentReference) Reference to the image or data source
... composition C 0..1 Reference(Composition) Reference to a Composition resource for the DiagnosticReport structure
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): SNOMED CT Clinical Findings
... recomendation Σ 0..* CodeableReference(Resource) Recommendations based on findings and interpretations
... presentedForm 0..* Attachment Entire report as issued
... communication 0..* Reference(Communication) Communication initiated during the reporting process

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.status Base required Diagnostic Report Status 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.supportingInfo.​type Base example hl7VS-VS-observationType 📦2.0.0 THO v6.5
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍6.0.0-ballot3 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dgr-1 error DiagnosticReport When a Composition is referenced in `DiagnosticReport.composition`, all Observation resources referenced in `Composition.entry` must also be referenced in `DiagnosticReport.result` or in the `Observation.hasMember` references. composition.exists() implies (composition.resolve().section.entry.reference.where(resolve() is Observation) in (result.reference|result.reference.resolve().hasMember.reference))
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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: Filtersdoco
.. DiagnosticReport C 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
Constraints: dgr-1
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... status ?!Σ 1..1 code registered | partial | preliminary | modified | final | amended | corrected | appended | cancelled | entered-in-error | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
..... coding 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): LOINC Codes for Diagnostic Reports
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for the results that are included in the report
... Slices for result C 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication C 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication C 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence C 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant C 0..* Reference(Variant) Variant
.... result:sequence-phase-relation C 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype C 0..* Reference(Genotype) Genotype
.... result:haplotype C 0..* Reference(Haplotype) Haplotype
.... result:biomarker C 0..* Reference(Molecular Biomarker) MolecularBiomarker
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): SNOMED CT Clinical Findings

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required Diagnostic Report Status 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍6.0.0-ballot3 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dgr-1 error DiagnosticReport When a Composition is referenced in `DiagnosticReport.composition`, all Observation resources referenced in `Composition.entry` must also be referenced in `DiagnosticReport.result` or in the `Observation.hasMember` references. composition.exists() implies (composition.resolve().section.entry.reference.where(resolve() is Observation) in (result.reference|result.reference.resolve().hasMember.reference))
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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: Filtersdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... Slices for category 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
.... category:Genetics 1..1 CodeableConcept Service category
..... coding 1..1 Coding Code defined by a terminology system
Required Pattern: At least the following
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code 1..1 CodeableConcept Name/Code for this diagnostic report
Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
... Slices for result 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant 0..* Reference(Variant) Variant
.... result:sequence-phase-relation 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype 0..* Reference(Genotype) Genotype
.... result:haplotype 0..* Reference(Haplotype) Haplotype
.... result:biomarker 0..* Reference(Molecular Biomarker) MolecularBiomarker
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport C 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
Constraints: dgr-1
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: AllLanguages (required): IETF language tag for a human language
Additional BindingsPurpose
CommonLanguages Starter
... 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
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... extension:genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... extension:supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... extension:hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... extension:hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business identifier for report
... basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) What was requested
... status ?!Σ 1..1 code registered | partial | preliminary | modified | final | amended | corrected | appended | cancelled | entered-in-error | unknown
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by value:coding
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): HL7 V2 table 0074
..... id 0..1 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): LOINC Codes for Diagnostic Reports
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51969-4
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Practitioner | Medication | Substance | BiologicallyDerivedProduct) The subject of the report - usually, but not always, the patient
... relatesTo 0..* RelatedArtifact Related DiagnosticReports
... encounter Σ 0..1 Reference(Encounter) Encounter associated with the DiagnosticReport
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for the results that are included in the report
... issued Σ 0..1 instant DateTime this version was made
... procedure Σ 0..* Reference(Procedure) The procedure(s) from which the report was produced
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | HealthcareService | Device) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(Specimen) Specimens this report is based on
... Slices for result C 0..* Reference(Observation) Observations
Slice: Unordered, Open by profile:resolve()
.... result:diagnostic-implication C 0..* Reference(Diagnostic Implication) Diagnostic Implication
.... result:therapeutic-implication C 0..* Reference(Therapeutic Implication) Therapeutic Implication
.... result:molecular-consequence C 0..* Reference(Molecular Consequence) Molecular Consequence
.... result:variant C 0..* Reference(Variant) Variant
.... result:sequence-phase-relation C 0..* Reference(Sequence Phase Relationship) Sequence Phase Relationship
.... result:genotype C 0..* Reference(Genotype) Genotype
.... result:haplotype C 0..* Reference(Haplotype) Haplotype
.... result:biomarker C 0..* Reference(Molecular Biomarker) MolecularBiomarker
... note 0..* Annotation Comments about the diagnostic report
... study 0..* Reference(GenomicStudy | ImagingStudy) Reference to full details of an analysis associated with the diagnostic report
... supportingInfo 0..* BackboneElement Additional information supporting the diagnostic report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... type 1..1 CodeableConcept Supporting information role code
Binding: hl7VS-VS-observationType (example): The code value for the role of the supporting information in the diagnostic report.
.... reference 1..1 Reference(ImagingStudy | Procedure | Observation | DiagnosticReport | Citation | FamilyMemberHistory | AllergyIntolerance | DeviceUsage | Condition | GenomicStudy) Supporting information reference
... media Σ 0..* BackboneElement Key images or data associated with this report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... comment 0..1 string Comment about the image or data (e.g. explanation)
.... link Σ 1..1 Reference(DocumentReference) Reference to the image or data source
... composition C 0..1 Reference(Composition) Reference to a Composition resource for the DiagnosticReport structure
... conclusion 0..1 markdown Assessment of overall results
... conclusionCode 0..* CodeableReference(Observation | Condition) Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): SNOMED CT Clinical Findings
... recomendation Σ 0..* CodeableReference(Resource) Recommendations based on findings and interpretations
... presentedForm 0..* Attachment Entire report as issued
... communication 0..* Reference(Communication) Communication initiated during the reporting process

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.status Base required Diagnostic Report Status 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.category:Genetics Base example Diagnostic Service Section Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.code Base preferred LOINC Diagnostic Report Codes 📍6.0.0-ballot3 FHIR Std.
DiagnosticReport.supportingInfo.​type Base example hl7VS-VS-observationType 📦2.0.0 THO v6.5
DiagnosticReport.conclusionCode Base example SNOMED CT Clinical Findings 📍6.0.0-ballot3 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dgr-1 error DiagnosticReport When a Composition is referenced in `DiagnosticReport.composition`, all Observation resources referenced in `Composition.entry` must also be referenced in `DiagnosticReport.result` or in the `Observation.hasMember` references. composition.exists() implies (composition.resolve().section.entry.reference.where(resolve() is Observation) in (result.reference|result.reference.resolve().hasMember.reference))
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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.