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

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GenomicsReport

 

The official URL for this profile is:

http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GenomicsReport

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.

Conformance note: To be conformant to US Core, the code attribute must be a LOINC code, if available. If there is no suitable code in LOINC, then a code from an alternative code system (such as GTR) can be used.

Implementation note: The performer of the test (organization or practitioner) should be included in the FHIR profile as the performer.actor.

Conformance note: The category for this profile is set to GE (Genetics), a code from http://hl7.org/fhir/ValueSet/diagnostic-service-sections. This is contrary to the Argonaut and US Core specifications, which require the category 'LAB' in diagnostic reports containing laboratory results. This is assumed to be an oversight in the US Core and Argonaut specifications.

This profile builds on USCoreDiagnosticReportProfileNoteExchange.

This profile was published on Thu Aug 01 00:00:00 EDT 2019 as a active by HL7 International Clinical Interoperability Council.

Summary

Mandatory: 0 element (4 nested mandatory elements)
Must-Support: 4 elements
Fixed Value: 2 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 DiagnosticReport.category.coding is sliced based on the value of value:code
  • The element DiagnosticReport.result is sliced based on the value of value:$this.resolve().code.coding.code

Mapping Source

This structure represents the following mapping definition:

onco.core.GenomicsReport maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.source
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  BasedOn maps to basedOn
  Status maps to status
  Category maps to category
  ObservationSubjectOfRecord maps to subject
  Code maps to code
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  DiagnosticReportPerformer maps to performer
  ResultsInterpreter maps to resultsInterpreter
  Specimen maps to specimen
  Observation maps to result (slice on = $this.resolve().code.coding.code; slice strategy = includes)
  MediaIncluded.CommentOrDescription maps to media.comment
  MediaIncluded.Media maps to media.link
  ConclusionText maps to conclusion
  ConclusionCode maps to conclusionCode
  PresentedForm maps to presentedForm

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... extension Slice: Unordered, Open by value:url
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... basedOn Reference(ServiceRequest | US Core MedicationRequest Profile)
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code Fixed Value: GE
... code Binding: GeneticTestVS (extensible)
... subject Reference(obf-Patient)The subject of an observation
... issued 1..1
... performer 0..1Reference(US Core Practitioner Profile | US Core Organization Profile)
... resultsInterpreter 0..1Reference(US Core Practitioner Profile | US Core Organization Profile)
... result SReference(obf-Observation)Slice: Unordered, Open by value:$this.resolve().code.coding.code
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
... result S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport I0..*onco-core-GenomicsReport
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness identifier for report
... basedOn 0..*Reference(ServiceRequest | US Core MedicationRequest Profile)What was requested
... status ?!SΣ1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... category SΣ1..1CodeableConceptService category
Binding: US Core DiagnosticReport Category (extensible)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: GE
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptUS Core Report Code
Binding: GeneticTestVS (extensible)
... subject SΣ1..1Reference(obf-Patient)The subject of an observation
... encounter SΣ0..1Reference(US Core Encounter Profile)Health care event when test ordered
... effective[x] SΣ1..1dateTime, PeriodTime of the report or note
... issued SΣ1..1instantDateTime this version was made
... performer SΣ0..1Reference(US Core Practitioner Profile | US Core Organization Profile)Responsible Diagnostic Service
... resultsInterpreter Σ0..1Reference(US Core Practitioner Profile | US Core Organization Profile)Primary result interpreter
... specimen 0..*Reference(Specimen)Specimens this report is based on
... result SReference(obf-Observation)Observations
Slice: Unordered, Open by value:$this.resolve().code.coding.code
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
... result S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene
... imagingStudy 0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media SΣI0..*BackboneElementKey images associated with this report
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... comment 0..1stringComment about the image (e.g. explanation)
.... link Σ1..1Reference(Media)Reference to the image source
... conclusion 0..1stringClinical conclusion (interpretation) of test results
... conclusionCode 0..*CodeableConceptCodes for the clinical conclusion of test results
Binding: SNOMEDCTClinicalFindings (example)
... presentedForm S0..*AttachmentEntire report as issued

doco Documentation for this format

Summary

Mandatory: 0 element (4 nested mandatory elements)
Must-Support: 4 elements
Fixed Value: 2 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 DiagnosticReport.category.coding is sliced based on the value of value:code
  • The element DiagnosticReport.result is sliced based on the value of value:$this.resolve().code.coding.code

Mapping Source

This structure represents the following mapping definition:

onco.core.GenomicsReport maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.source
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  BasedOn maps to basedOn
  Status maps to status
  Category maps to category
  ObservationSubjectOfRecord maps to subject
  Code maps to code
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  DiagnosticReportPerformer maps to performer
  ResultsInterpreter maps to resultsInterpreter
  Specimen maps to specimen
  Observation maps to result (slice on = $this.resolve().code.coding.code; slice strategy = includes)
  MediaIncluded.CommentOrDescription maps to media.comment
  MediaIncluded.Media maps to media.link
  ConclusionText maps to conclusion
  ConclusionCode maps to conclusionCode
  PresentedForm maps to presentedForm

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... extension Slice: Unordered, Open by value:url
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... basedOn Reference(ServiceRequest | US Core MedicationRequest Profile)
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code Fixed Value: GE
... code Binding: GeneticTestVS (extensible)
... subject Reference(obf-Patient)The subject of an observation
... issued 1..1
... performer 0..1Reference(US Core Practitioner Profile | US Core Organization Profile)
... resultsInterpreter 0..1Reference(US Core Practitioner Profile | US Core Organization Profile)
... result SReference(obf-Observation)Slice: Unordered, Open by value:$this.resolve().code.coding.code
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
... result S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport I0..*onco-core-GenomicsReport
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"http://hl7.org/fhir/us/mcode/StructureDefinition/obf-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness identifier for report
... basedOn 0..*Reference(ServiceRequest | US Core MedicationRequest Profile)What was requested
... status ?!SΣ1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... category SΣ1..1CodeableConceptService category
Binding: US Core DiagnosticReport Category (extensible)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: GE
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptUS Core Report Code
Binding: GeneticTestVS (extensible)
... subject SΣ1..1Reference(obf-Patient)The subject of an observation
... encounter SΣ0..1Reference(US Core Encounter Profile)Health care event when test ordered
... effective[x] SΣ1..1dateTime, PeriodTime of the report or note
... issued SΣ1..1instantDateTime this version was made
... performer SΣ0..1Reference(US Core Practitioner Profile | US Core Organization Profile)Responsible Diagnostic Service
... resultsInterpreter Σ0..1Reference(US Core Practitioner Profile | US Core Organization Profile)Primary result interpreter
... specimen 0..*Reference(Specimen)Specimens this report is based on
... result SReference(obf-Observation)Observations
Slice: Unordered, Open by value:$this.resolve().code.coding.code
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
... result S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene
... imagingStudy 0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media SΣI0..*BackboneElementKey images associated with this report
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... comment 0..1stringComment about the image (e.g. explanation)
.... link Σ1..1Reference(Media)Reference to the image source
... conclusion 0..1stringClinical conclusion (interpretation) of test results
... conclusionCode 0..*CodeableConceptCodes for the clinical conclusion of test results
Binding: SNOMEDCTClinicalFindings (example)
... presentedForm S0..*AttachmentEntire report as issued

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron

 

Terminology Bindings

PathConformanceValueSet
DiagnosticReport.languagepreferredCommonLanguages
Max Binding: AllLanguages
DiagnosticReport.extension:specimentype.valueCodeableConceptextensibleGeneticSpecimenTypeVS
DiagnosticReport.statusrequiredDiagnosticReportStatus
DiagnosticReport.categoryextensibleUSCoreDiagnosticReportCategory
DiagnosticReport.codeextensibleGeneticTestVS
DiagnosticReport.conclusionCodeexampleSNOMEDCTClinicalFindings

 

Constraints

IdPathDetailsRequirements
dom-2DiagnosticReportIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-4DiagnosticReportIf 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-3DiagnosticReportIf 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-6DiagnosticReportA resource should have narrative for robust management
: text.div.exists()
dom-5DiagnosticReportIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
ele-1DiagnosticReport.mediaAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())