minimal Common Oncology Data Elements (mCODE) Implementation Guide
1.16.0 - STU Release 2 (Ballot Version)
minimal Common Oncology Data Elements (mCODE) Implementation Guide
1.16.0 - STU Release 2 (Ballot Version)
This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v1.16.0: STU 2 Ballot 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 
| Defining URL: | http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-genomics-report |
| Version: | 1.16.0 |
| Name: | CancerGenomicsReport |
| Title: | Cancer Genomics Report |
| Status: | Active as of 2021-04-15T12:44:45+00:00 |
| Definition: | 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. |
| 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-cancer-genomics-report
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. Some tests 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.
DiagnosticReport resources associated with an mCODE 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 mCODE patient that would reasonably be expected to conform to this profile SHOULD be published in this form.
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:
This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  DiagnosticReport | 0..* | USCoreDiagnosticReportProfileLaboratoryReporting | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
  category | 2..* | CodeableConcept | Service category | |
  category:GenomicsCategory | 1..1 | CodeableConcept | Service category 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://terminology.hl7.org/CodeSystem/v2-0074 | |
 code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code | 1..1 | CodeableConcept | US Core Laboratory Report Order Code 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: 81247-9 | |
 subject | 1..1 | Reference(Cancer Patient) | The subject of the report - usually, but not always, the patient | |
| specimen | S | 0..* | Reference(Genetic Specimen) | Specimens this report is based on |
 result | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by pattern:$this.resolve().code | |
 result:CancerGeneticVariant | S | 0..1 | Reference(Cancer Genetic Variant) | Reference to Cancer Genetic Variant |
 result:GenomicRegionStudied | S | 0..1 | Reference(Genomic Region Studied) | Reference to Genomic Region Studied |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | USCoreDiagnosticReportProfileLaboratoryReporting | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
 id | Σ | 0..1 | string | Logical id of this artifact |
 meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) Max Binding: AllLanguages: A human language. | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
| contained | 0..* | Resource | Contained, inline Resources | |
 extension | 0..* | Extension | Additional content defined by implementations | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | Identifier | Business identifier for report |
| basedOn | 0..* | Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | What was requested | |
| status | ?!SΣ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required) |
| category | SΣ | 2..* | (Slice Definition) | Service category Slice: Unordered, Open by pattern:$this Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
 category:LaboratorySlice | SΣ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://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: LAB | |
| 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 | |
 category:GenomicsCategory | SΣ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://terminology.hl7.org/CodeSystem/v2-0074 | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| code | SΣ | 1..1 | CodeableConcept | US Core Laboratory Report Order Code Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes 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: 81247-9 | |
| 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 | SΣ | 1..1 | Reference(Cancer Patient) | 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] | SΣ | 1..1 | Specimen Collection Datetime or Period | |
| effectiveDateTime | dateTime | |||
| effectivePeriod | Period | |||
| issued | SΣ | 1..1 | instant | DateTime this version was made |
| performer | SΣ | 0..* | Reference(US Core Practitioner Profile | US Core Organization Profile) | Responsible Diagnostic Service |
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter |
| specimen | S | 0..* | Reference(Genetic Specimen) | Specimens this report is based on |
| result | S | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by pattern:$this.resolve().code |
| result:CancerGeneticVariant | S | 0..1 | Reference(Cancer Genetic Variant) | Reference to Cancer Genetic Variant |
| result:GenomicRegionStudied | S | 0..1 | Reference(Genomic Region Studied) | Reference to Genomic Region Studied |
| imagingStudy | 0..* | Reference(ImagingStudy) | Reference to full details of imaging associated with the diagnostic report | |
| media | Σ | 0..* | BackboneElement | Key images associated with this report |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| comment | 0..1 | string | Comment about the image (e.g. explanation) | |
| link | Σ | 1..1 | Reference(Media) | Reference to the image source |
| conclusion | 0..1 | string | Clinical conclusion (interpretation) of test results | |
| conclusionCode | 0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |
| presentedForm | 0..* | Attachment | Entire report as issued | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | USCoreDiagnosticReportProfileLaboratoryReporting | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| status | ?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required) |
| category | Σ | 2..* | (Slice Definition) | Service category Slice: Unordered, Open by pattern:$this Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| category:LaboratorySlice | Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://terminology.hl7.org/CodeSystem/v2-0074 | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: LAB | |
| category:GenomicsCategory | Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://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 | US Core Laboratory Report Order Code Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes 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: 81247-9 | |
| subject | Σ | 1..1 | Reference(Cancer Patient) | The subject of the report - usually, but not always, the patient |
| effective[x] | Σ | 1..1 | Specimen Collection Datetime or Period | |
| effectiveDateTime | dateTime | |||
| effectivePeriod | Period | |||
| issued | Σ | 1..1 | instant | DateTime this version was made |
| performer | Σ | 0..* | Reference(US Core Practitioner Profile | US Core Organization Profile) | Responsible Diagnostic Service |
| specimen | 0..* | Reference(Genetic Specimen) | Specimens this report is based on | |
| result | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by pattern:$this.resolve().code | |
| result:CancerGeneticVariant | 0..1 | Reference(Cancer Genetic Variant) | Reference to Cancer Genetic Variant | |
| result:GenomicRegionStudied | 0..1 | Reference(Genomic Region Studied) | Reference to Genomic Region Studied | |
| 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:
Differential View
This structure is derived from USCoreDiagnosticReportProfileLaboratoryReporting
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | USCoreDiagnosticReportProfileLaboratoryReporting | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| category | 2..* | CodeableConcept | Service category | |
| category:GenomicsCategory | 1..1 | CodeableConcept | Service category 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://terminology.hl7.org/CodeSystem/v2-0074 | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code | 1..1 | CodeableConcept | US Core Laboratory Report Order Code 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: 81247-9 | |
| subject | 1..1 | Reference(Cancer Patient) | The subject of the report - usually, but not always, the patient | |
| specimen | S | 0..* | Reference(Genetic Specimen) | Specimens this report is based on |
| result | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by pattern:$this.resolve().code | |
| result:CancerGeneticVariant | S | 0..1 | Reference(Cancer Genetic Variant) | Reference to Cancer Genetic Variant |
| result:GenomicRegionStudied | S | 0..1 | Reference(Genomic Region Studied) | Reference to Genomic Region Studied |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | USCoreDiagnosticReportProfileLaboratoryReporting | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| id | Σ | 0..1 | string | Logical id of this artifact |
| meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) Max Binding: AllLanguages: A human language. | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| 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 | ?!SΣ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required) |
| category | SΣ | 2..* | (Slice Definition) | Service category Slice: Unordered, Open by pattern:$this Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| category:LaboratorySlice | SΣ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://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: LAB | |
| 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 | |
| category:GenomicsCategory | SΣ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. 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://terminology.hl7.org/CodeSystem/v2-0074 | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| code | SΣ | 1..1 | CodeableConcept | US Core Laboratory Report Order Code Binding: US Core Diagnostic Report Laboratory Codes (extensible): LOINC codes 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: 81247-9 | |
| 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 | SΣ | 1..1 | Reference(Cancer Patient) | 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] | SΣ | 1..1 | Specimen Collection Datetime or Period | |
| effectiveDateTime | dateTime | |||
| effectivePeriod | Period | |||
| issued | SΣ | 1..1 | instant | DateTime this version was made |
| performer | SΣ | 0..* | Reference(US Core Practitioner Profile | US Core Organization Profile) | Responsible Diagnostic Service |
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter |
| specimen | S | 0..* | Reference(Genetic Specimen) | Specimens this report is based on |
| result | S | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by pattern:$this.resolve().code |
| result:CancerGeneticVariant | S | 0..1 | Reference(Cancer Genetic Variant) | Reference to Cancer Genetic Variant |
| result:GenomicRegionStudied | S | 0..1 | Reference(Genomic Region Studied) | Reference to Genomic Region Studied |
| 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 | Clinical conclusion (interpretation) of test results | |
| conclusionCode | 0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |
| presentedForm | 0..* | Attachment | Entire report as issued | |
| Documentation for this format | ||||
Other representations of profile: Schematron
| Path | Conformance | ValueSet / Code |
| DiagnosticReport.language | preferred | CommonLanguages Max Binding: AllLanguages |
| DiagnosticReport.status | required | DiagnosticReportStatus |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.category:LaboratorySlice | example | Pattern: LAB |
| DiagnosticReport.category:GenomicsCategory | example | Pattern: GE |
| DiagnosticReport.code | extensible | Pattern: LOINC code 81247-9 |
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindings |
IG © 2019+ HL7 International Clinical Interoperability Council. Package hl7.fhir.us.mcode#1.16.0 based on FHIR 4.0.1. Generated 2021-04-15
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