minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.0.0 - STU 2

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Resource Profile: Genomics Report Profile

Defining URL:http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report
Version:2.0.0
Name:GenomicsReport
Title:Genomics Report Profile
Status:Active as of 1/18/22 3:17 AM
Definition:

Genomic 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.

Publisher:HL7 International Clinical Interoperability Council
Source Resource:XML / JSON / Turtle

The official URL for this profile is: 

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

Usage

The identity of non-genomic laboratory tests is typically represented by a LOINC code. However, many genomic tests and panels do not have LOINC codes. Some tests might have an identifier in NCBI Genomic Testing Registry (GTR), a central location for voluntary submission of genomic 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

DiagnosticReport resources associated with an in-scope patient with DiagnosticReport.code LOINC 81247-9 MUST conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.

Formal Views of Profile Content

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

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

Summary

Mandatory: 1 element
Must-Support: 3 elements

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..*USCoreDiagnosticReportProfileLaboratoryReportingA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... category 2..*CodeableConceptService category
... category:GenomicsCategory 1..1CodeableConceptService category
Required 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
... code 1..1CodeableConceptUS Core Laboratory Report Order Code
Required Pattern: At least the following
.... 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
... Slices for result 0..*Reference(US Core Laboratory Result Observation Profile)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:GenomicVariant S0..1Reference(Genomic Variant Profile)Reference to Genomic Variant
.... result:GenomicRegionStudied S0..1Reference(Genomic Region Studied Profile)Reference to Genomic Region Studied

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*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 Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness identifier for report
... basedOn 0..*Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)What was requested
... status ?!SΣ1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ2..*CodeableConceptService category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:LaboratorySlice SΣ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



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 SΣ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



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 SΣ1..1CodeableConceptUS Core Laboratory Report Order Code
Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes


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 SΣ1..1Reference(US Core Patient Profile)The subject of the report - usually, but not always, the patient
... encounter Σ0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣ1..1Clinically relevant time/time-period for report
.... effectiveDateTimedateTime S
.... effectivePeriodPeriod
... issued SΣ1..1instantDateTime this version was made
... performer SΣ0..*Reference(US Core Practitioner Profile S | US Core Organization Profile | US Core CareTeam Profile | US Core PractitionerRole Profile)Responsible Diagnostic Service
... resultsInterpreter Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam)Primary result interpreter
... specimen S0..*Reference(Genomic Specimen Profile)Specimens this report is based on
... Slices for result S0..*Reference(US Core Laboratory Result Observation Profile)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:GenomicVariant S0..1Reference(Genomic Variant Profile)Reference to Genomic Variant
.... result:GenomicRegionStudied S0..1Reference(Genomic Region Studied Profile)Reference to Genomic Region Studied
... imagingStudy 0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media Σ0..*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): Diagnosis codes provided as adjuncts to the report.


... presentedForm 0..*AttachmentEntire report as issued

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*USCoreDiagnosticReportProfileLaboratoryReportingA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... status ?!Σ1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category Σ2..*CodeableConceptService category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:LaboratorySlice Σ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



Required 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: LAB
.... category:GenomicsCategory Σ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



Required 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
... code Σ1..1CodeableConceptUS Core Laboratory Report Order Code
Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes


Required Pattern: At least the following
.... 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
... effective[x] Σ1..1Clinically relevant time/time-period for report
.... effectiveDateTimedateTime
... issued Σ1..1instantDateTime this version was made
... performer Σ0..*Reference(US Core Practitioner Profile)Responsible Diagnostic Service
... specimen 0..*Reference(Genomic Specimen Profile)Specimens this report is based on
... Slices for result 0..*Reference(US Core Laboratory Result Observation Profile)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:GenomicVariant 0..1Reference(Genomic Variant Profile)Reference to Genomic Variant
.... result:GenomicRegionStudied 0..1Reference(Genomic Region Studied Profile)Reference to Genomic Region Studied

doco Documentation for this format

This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting

Summary

Mandatory: 1 element
Must-Support: 3 elements

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..*USCoreDiagnosticReportProfileLaboratoryReportingA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
... category 2..*CodeableConceptService category
... category:GenomicsCategory 1..1CodeableConceptService category
Required 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
... code 1..1CodeableConceptUS Core Laboratory Report Order Code
Required Pattern: At least the following
.... 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
... Slices for result 0..*Reference(US Core Laboratory Result Observation Profile)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:GenomicVariant S0..1Reference(Genomic Variant Profile)Reference to Genomic Variant
.... result:GenomicRegionStudied S0..1Reference(Genomic Region Studied Profile)Reference to Genomic Region Studied

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*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 Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness identifier for report
... basedOn 0..*Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)What was requested
... status ?!SΣ1..1coderegistered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ2..*CodeableConceptService category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.


.... category:LaboratorySlice SΣ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



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 SΣ1..1CodeableConceptService category
Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections.



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 SΣ1..1CodeableConceptUS Core Laboratory Report Order Code
Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes


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 SΣ1..1Reference(US Core Patient Profile)The subject of the report - usually, but not always, the patient
... encounter Σ0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣ1..1Clinically relevant time/time-period for report
.... effectiveDateTimedateTime S
.... effectivePeriodPeriod
... issued SΣ1..1instantDateTime this version was made
... performer SΣ0..*Reference(US Core Practitioner Profile S | US Core Organization Profile | US Core CareTeam Profile | US Core PractitionerRole Profile)Responsible Diagnostic Service
... resultsInterpreter Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam)Primary result interpreter
... specimen S0..*Reference(Genomic Specimen Profile)Specimens this report is based on
... Slices for result S0..*Reference(US Core Laboratory Result Observation Profile)Observations
Slice: Unordered, Open by pattern:$this.resolve().code
.... result:GenomicVariant S0..1Reference(Genomic Variant Profile)Reference to Genomic Variant
.... result:GenomicRegionStudied S0..1Reference(Genomic Region Studied Profile)Reference to Genomic Region Studied
... imagingStudy 0..*Reference(ImagingStudy)Reference to full details of imaging associated with the diagnostic report
... media Σ0..*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): Diagnosis codes provided as adjuncts to the report.


... presentedForm 0..*AttachmentEntire report as issued

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

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