minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0: STU 3) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomics-report | Version: 3.0.0 | |||
| Draft as of 2023-10-26 | Maturity Level: 1 | Computable Name: GenomicsReport | ||
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.
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.
DiagnosticReport resources associated with an in-scope patient with DiagnosticReport.code LOINC 81247-9 SHALL 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.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from GenomicsReport
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  DiagnosticReport | 0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
  status | S | 1..1 | code | registered | partial | preliminary | final + |
| category | S | 1..* | CodeableConcept | Service category |
  category:Genetics | 1..1 | CodeableConcept | Service category | |
  coding | 1..1 | Coding | Code defined by a terminology system | |
| code | S | 1..1 | CodeableConcept | Name/Code for this diagnostic report |
 subject | S | 0..1 | Reference(Cancer Patient Profile) | The subject of the report - usually, but not always, the patient |
| effective[x] | S | 0..1 | dateTime | Clinically relevant time/time-period for report |
| issued | S | 0..1 | instant | DateTime this version was made |
| performer | S | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service |
| specimen | S | 0..* | Reference(Human Specimen Profile) | Specimens this report is based on |
| result | S | 0..* | Reference(Observation) | Observations |
| result:variant | S | 0..* | Reference(Genomic Variant Profile) | Variant |
 result:region-studied | S | 0..* | Reference(Genomic Region Studied Profile) | Region Studied |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| DiagnosticReport.status | required | DiagnosticReportStatus |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC) |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DiagnosticReport | 0..* | GenomicsReport | 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 | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| 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 | |||||
| genomics-artifact | 0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |||||
| genomics-file | 0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |||||
| recommended-action | 0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |||||
| genomics-risk-assessment | 0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-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 | |||||
 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): The status of the diagnostic report. | ||||
 Slices for category | SΣ | 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 | SΣ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. | ||||
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | 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 | 0..1 | dateTime | Clinically relevant time/time-period for report | ||||
| issued | SΣ | 0..1 | instant | DateTime this version was made | ||||
| performer | SΣ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service | ||||
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter | ||||
| specimen | S | 0..* | Reference(Human Specimen Profile) | Specimens this report is based on | ||||
| Slices for result | S | 0..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | ||||
 result:overall | 0..1 | Reference(Overall Interpretation) | Assessment of overall results | |||||
| result:diagnostic-implication | 0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |||||
| result:therapeutic-implication | 0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |||||
| result:variant | S | 0..* | Reference(Genomic Variant Profile) | Variant | ||||
| result:sequence-phase-relation | 0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |||||
| result:region-studied | S | 0..* | Reference(Genomic Region Studied Profile) | Region Studied | ||||
| result:genotype | 0..* | Reference(Genotype) | Genotype | |||||
 result:haplotype | 0..* | Reference(Haplotype) | Haplotype | |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| DiagnosticReport.language | preferred | CommonLanguages
| ||||
| DiagnosticReport.status | required | DiagnosticReportStatus | ||||
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes | ||||
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodes | ||||
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC) | ||||
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindings |
This structure is derived from GenomicsReport
Summary
Must-Support: 11 elements
Structures
This structure refers to these other structures:
Maturity: 1
Differential View
This structure is derived from GenomicsReport
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| status | S | 1..1 | code | registered | partial | preliminary | final + |
| category | S | 1..* | CodeableConcept | Service category |
| category:Genetics | 1..1 | CodeableConcept | Service category | |
| coding | 1..1 | Coding | Code defined by a terminology system | |
| code | S | 1..1 | CodeableConcept | Name/Code for this diagnostic report |
| subject | S | 0..1 | Reference(Cancer Patient Profile) | The subject of the report - usually, but not always, the patient |
| effective[x] | S | 0..1 | dateTime | Clinically relevant time/time-period for report |
| issued | S | 0..1 | instant | DateTime this version was made |
| performer | S | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service |
| specimen | S | 0..* | Reference(Human Specimen Profile) | Specimens this report is based on |
| result | S | 0..* | Reference(Observation) | Observations |
| result:variant | S | 0..* | Reference(Genomic Variant Profile) | Variant |
| result:region-studied | S | 0..* | Reference(Genomic Region Studied Profile) | Region Studied |
| Documentation for this format | ||||
Key Elements View
| Path | Conformance | ValueSet |
| DiagnosticReport.status | required | DiagnosticReportStatus |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC) |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DiagnosticReport | 0..* | GenomicsReport | 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 | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| 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 | |||||
| genomics-artifact | 0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |||||
| genomics-file | 0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |||||
| recommended-action | 0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |||||
| genomics-risk-assessment | 0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-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 | |||||
| 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): The status of the diagnostic report. | ||||
| Slices for category | SΣ | 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 | SΣ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. | ||||
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | 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 | 0..1 | dateTime | Clinically relevant time/time-period for report | ||||
| issued | SΣ | 0..1 | instant | DateTime this version was made | ||||
| performer | SΣ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service | ||||
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter | ||||
| specimen | S | 0..* | Reference(Human Specimen Profile) | Specimens this report is based on | ||||
| Slices for result | S | 0..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | ||||
| result:overall | 0..1 | Reference(Overall Interpretation) | Assessment of overall results | |||||
| result:diagnostic-implication | 0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |||||
| result:therapeutic-implication | 0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |||||
| result:variant | S | 0..* | Reference(Genomic Variant Profile) | Variant | ||||
| result:sequence-phase-relation | 0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |||||
| result:region-studied | S | 0..* | Reference(Genomic Region Studied Profile) | Region Studied | ||||
| result:genotype | 0..* | Reference(Genotype) | Genotype | |||||
| result:haplotype | 0..* | Reference(Haplotype) | Haplotype | |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| DiagnosticReport.language | preferred | CommonLanguages
| ||||
| DiagnosticReport.status | required | DiagnosticReportStatus | ||||
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes | ||||
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodes | ||||
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC) | ||||
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindings |
This structure is derived from GenomicsReport
Summary
Must-Support: 11 elements
Structures
This structure refers to these other structures:
Maturity: 1
Other representations of profile: CSV, Excel, Schematron
IG © 2019+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.us.mcode#3.0.0 based on FHIR 4.0.1. Generated 2023-10-26
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