HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1
1.0.0 - STU1

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

StructureDefinition: CancerGenomicsReport

Genetic analysis summary report. The report may include one or more tests, with two distinct test types. The first type is a targeted mutation test, where a specific mutation on a specific gene is tested for. The result is either positive or negative for that mutation. The second type is a more general test for variants. This type of test returns the identity of variants found in a certain region of the genome. The identity of non-genomic laboratory tests is typically represented by a LOINC code. However, many genetic tests and panels do not have LOINC codes, although some might have an identifier in NCBI Genetic Testing Registry (GTR), a central location for voluntary submission of genetic test information by providers. To identify the diagnostic report, the name of the report must be in the text sub-field of the code structure. If there is a coded identifier from GTR, LOINC, or other source, then it should be included into the the code sub-field of the code structure. If there is no suitable code, the code can be omitted.

The official URL for this profile is: 

http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-genomics-report

Formal Views of Profile Content

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

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

Summary

Must-Support: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element DiagnosticReport.result is sliced based on the value of pattern:$this.resolve().code

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*USCoreDiagnosticReportProfileLaboratoryReporting
... basedOn 0..*Reference(ServiceRequest | CarePlan)
... category 2..*CodeableConcept
... category:GenomicsCategory 1..1CodeableConceptRequired Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81247-9
... subject 1..1Reference(Cancer Patient)
... specimen S0..*Reference(Genetic Specimen)
... result 0..*(Slice Definition)Slice: Unordered, Open by pattern:$this.resolve().code
.... result:CancerGeneticVariant 0..1Reference(Cancer Genetic Variant)Cancer Genetic Variant
.... result:GenomicRegionStudied 0..1Reference(Genomic Region Studied)Genomic Region Studied

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport I0..*USCoreDiagnosticReportProfileLaboratoryReportingA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness identifier for report
... basedOn I0..*Reference(ServiceRequest | CarePlan)What was requested
... status ?!SΣI1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... category SΣI2..*(Slice Definition)Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (example)
.... category:LaboratorySlice SΣI1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example)

Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: LAB
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
.... category:GenomicsCategory SΣI1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example)

Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
... code SΣI1..1CodeableConceptUS Core Laboratory Report Order Code
Binding: US Core Diagnostic Report Laboratory Codes (extensible)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81247-9
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣI1..1Reference(Cancer Patient)The subject of the report - usually, but not always, the patient
... encounter ΣI0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣI1..1Specimen Collection Datetime or Period
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued SΣI1..1instantDateTime this version was made
... performer SΣI0..*Reference(US Core Practitioner Profile | US Core Organization Profile)Responsible Diagnostic Service
... resultsInterpreter ΣI0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam)Primary result interpreter
... specimen SI0..*Reference(Genetic Specimen)Specimens this report is based on
... result SI0..*(Slice Definition)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:CancerGeneticVariant SI0..1Reference(Cancer Genetic Variant)Cancer Genetic Variant
.... result:GenomicRegionStudied SI0..1Reference(Genomic Region Studied)Genomic Region Studied
... imagingStudy I0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media ΣI0..*BackboneElementKey images associated with this report
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... comment I0..1stringComment about the image (e.g. explanation)
.... link ΣI1..1Reference(Media)Reference to the image source
... conclusion I0..1stringClinical conclusion (interpretation) of test results
... conclusionCode I0..*CodeableConceptCodes for the clinical conclusion of test results
Binding: SNOMEDCTClinicalFindings (example)
... presentedForm I0..*AttachmentEntire report as issued

doco Documentation for this format

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

Summary

Must-Support: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element DiagnosticReport.result is sliced based on the value of pattern:$this.resolve().code

Differential View

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*USCoreDiagnosticReportProfileLaboratoryReporting
... basedOn 0..*Reference(ServiceRequest | CarePlan)
... category 2..*CodeableConcept
... category:GenomicsCategory 1..1CodeableConceptRequired Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81247-9
... subject 1..1Reference(Cancer Patient)
... specimen S0..*Reference(Genetic Specimen)
... result 0..*(Slice Definition)Slice: Unordered, Open by pattern:$this.resolve().code
.... result:CancerGeneticVariant 0..1Reference(Cancer Genetic Variant)Cancer Genetic Variant
.... result:GenomicRegionStudied 0..1Reference(Genomic Region Studied)Genomic Region Studied

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport I0..*USCoreDiagnosticReportProfileLaboratoryReportingA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness identifier for report
... basedOn I0..*Reference(ServiceRequest | CarePlan)What was requested
... status ?!SΣI1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... category SΣI2..*(Slice Definition)Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (example)
.... category:LaboratorySlice SΣI1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example)

Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: LAB
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
.... category:GenomicsCategory SΣI1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example)

Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
... code SΣI1..1CodeableConceptUS Core Laboratory Report Order Code
Binding: US Core Diagnostic Report Laboratory Codes (extensible)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81247-9
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣI1..1Reference(Cancer Patient)The subject of the report - usually, but not always, the patient
... encounter ΣI0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣI1..1Specimen Collection Datetime or Period
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued SΣI1..1instantDateTime this version was made
... performer SΣI0..*Reference(US Core Practitioner Profile | US Core Organization Profile)Responsible Diagnostic Service
... resultsInterpreter ΣI0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam)Primary result interpreter
... specimen SI0..*Reference(Genetic Specimen)Specimens this report is based on
... result SI0..*(Slice Definition)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:CancerGeneticVariant SI0..1Reference(Cancer Genetic Variant)Cancer Genetic Variant
.... result:GenomicRegionStudied SI0..1Reference(Genomic Region Studied)Genomic Region Studied
... imagingStudy I0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media ΣI0..*BackboneElementKey images associated with this report
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... comment I0..1stringComment about the image (e.g. explanation)
.... link ΣI1..1Reference(Media)Reference to the image source
... conclusion I0..1stringClinical conclusion (interpretation) of test results
... conclusionCode I0..*CodeableConceptCodes for the clinical conclusion of test results
Binding: SNOMEDCTClinicalFindings (example)
... presentedForm I0..*AttachmentEntire report as issued

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

Terminology Bindings

PathConformanceValueSet / Code
DiagnosticReport.languagepreferredCommonLanguages
Max Binding: AllLanguages
DiagnosticReport.statusrequiredDiagnosticReportStatus
DiagnosticReport.categoryexampleDiagnosticServiceSectionCodes
DiagnosticReport.category:LaboratorySliceexamplePattern: LAB
DiagnosticReport.category:GenomicsCategoryexamplePattern: GE
DiagnosticReport.codeextensiblePattern: LOINC code 81247-9
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings

Constraints

Constraints

IdPathDetailsRequirements