Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - 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 3.0.1-SNAPSHOT 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: 3.0.1-SNAPSHOT
Active as of 2024-05-15 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

Usage:

Formal Views of Profile Content

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

This structure is derived from DiagnosticReport

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport DiagnosticReport
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... 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 pattern: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 string Assessment of overall results
... conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


..... coding Σ 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 Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.


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
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for report
... 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 string Assessment of overall results
... 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

PathConformanceValueSet / CodeURI
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
from the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.category:GeneticsexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.codepreferredPattern: LOINC code 51969-4
http://hl7.org/fhir/ValueSet/report-codes
from the FHIR Standard
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings
http://hl7.org/fhir/ValueSet/clinical-findings
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf 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-4errorDiagnosticReportIf 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-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 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 | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.

... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 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 Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe 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) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for report
... issued Σ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) 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 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
... imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
... media Σ 0..* BackboneElement Key images 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 (e.g. explanation)
.... link Σ 1..1 Reference(Media) Reference to the image source
... conclusion 0..1 string Assessment of overall results
... conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.


... presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
DiagnosticReport.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
from the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.category:GeneticsexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.codepreferredPattern: LOINC code 51969-4
http://hl7.org/fhir/ValueSet/report-codes
from the FHIR Standard
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings
http://hl7.org/fhir/ValueSet/clinical-findings
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf 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-4errorDiagnosticReportIf 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-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust 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

Differential View

This structure is derived from DiagnosticReport

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport DiagnosticReport
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... 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 pattern: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 string Assessment of overall results
... conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


..... coding Σ 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 Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports.


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
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for report
... 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 string Assessment of overall results
... 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

PathConformanceValueSet / CodeURI
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
from the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.category:GeneticsexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.codepreferredPattern: LOINC code 51969-4
http://hl7.org/fhir/ValueSet/report-codes
from the FHIR Standard
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings
http://hl7.org/fhir/ValueSet/clinical-findings
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf 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-4errorDiagnosticReportIf 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-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..* DiagnosticReport A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... recommended-action 0..* Reference(Medication Recommendation | Followup Recommendation) Recommended Action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action
.... genomic-risk-assessment 0..* Reference(RiskAssessment) Genomic Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment
.... 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
.... supporting-info 0..* Reference(Resource) Other information that may be relevant to this event.
URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo
.... 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
.... hla-genotyping-results-allele-database 0..1 CodeableConcept Allele Database
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-allele-database
.... hla-genotyping-results-glstring 0..1 (Complex) glstring
URL: http://hl7.org/fhir/StructureDefinition/hla-genotyping-results-glstring
.... workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?! 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 | final +
Binding: DiagnosticReportStatus (required): The status of the diagnostic report.

... Slices for category Σ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:coding
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:Genetics Σ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ 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 Σ 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe 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) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... effective[x] Σ 0..1 dateTime Clinically relevant time/time-period for report
... issued Σ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) 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 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
... imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
... media Σ 0..* BackboneElement Key images 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 (e.g. explanation)
.... link Σ 1..1 Reference(Media) Reference to the image source
... conclusion 0..1 string Assessment of overall results
... conclusionCode 0..* CodeableConcept Coarse overall interpretation of the genomic results
Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report.


... presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
DiagnosticReport.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
DiagnosticReport.statusrequiredDiagnosticReportStatus
http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
from the FHIR Standard
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.category:GeneticsexampleDiagnosticServiceSectionCodes
http://hl7.org/fhir/ValueSet/diagnostic-service-sections
from the FHIR Standard
DiagnosticReport.codepreferredPattern: LOINC code 51969-4
http://hl7.org/fhir/ValueSet/report-codes
from the FHIR Standard
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings
http://hl7.org/fhir/ValueSet/clinical-findings
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDiagnosticReportIf 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-4errorDiagnosticReportIf 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-5errorDiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDiagnosticReportA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust 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

 

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.