minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.1.0 - Pre-STU 3 Development United States of America flag

minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International Clinical Interoperability Council. This is not an authorized publication; it is the continuous build for version 2.1.0). This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions

Resource Profile: Genomic Region Studied Profile

Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-region-studied Version: 2.1.0
Active as of 2023-01-13 Maturity Level: 1 Computable Name: GenomicRegionStudied

A subset of genes or genomic regions of interest in a targeted resequencing study.

Usage

This profile identifies a specific region analyzed for gene mutations or variants in a given genomic test. For example, exome sequencing tests could analyze multiple non-contiguous regions. Each region is designated by a range of start and end location and referencing a coordinate system which is 0-based or 1-based.

RegionStudied is noted at the GenomicsReport level and not directly tied to a given GenomicVariant.

Conformance

Observation resources associated with an in-scope patient with DiagnosticReport.code LOINC 53041-0 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.

Usage:

Formal Views of Profile Content

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

This structure is derived from RegionStudied

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*RegionStudiedRegion Studied
... status S1..1coderegistered | preliminary | final | amended +
... category S1..*CodeableConceptClassification of type of observation
... category:labCategory 1..1CodeableConceptClassification of type of observation
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/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... coding 1..1CodingCode defined by a terminology system
... subject S1..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... effective[x] S0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
... effectiveDateTime S0..1dateTimeClinically relevant time/time-period for observation
... value[x] 0..0Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... dataAbsentReason S0..1CodeableConceptWhy the result is missing
... component S0..*BackboneElementComponent results
... component:gene-studied S0..1BackboneElementGene Studied
.... code S1..1CodeableConcept48018-6
.... value[x] S1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
... component:gene-mutations S0..1BackboneElementGene Mutations ID
.... code S1..1CodeableConcept36908-2
.... value[x] S1..1CodeableConceptActual component result
... component:region-description S0..1BackboneElementRegion Description
.... code S1..1CodeableConcept81293-3
.... value[x] S0..1stringActual component result
... component:ranges-examined S0..*BackboneElementRange(s) of DNA sequence examined
.... code S1..1CodeableConcept51959-5
.... value[x] S0..1RangeActual component result
... component:coordinate-system S0..1BackboneElementCoordinate System
.... code S1..1CodeableConcept92822-6
.... value[x] S1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
... component:genomic-ref-seq S0..1BackboneElementGenomic Reference Sequence
.... code S1..1CodeableConcept48013-7
.... value[x] S1..1CodeableConceptVersioned genomic reference sequence identifier.

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*RegionStudiedRegion Studied
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code SΣ1..1CodeableConcept53041-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 53041-0
... subject SΣ1..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:gene-studied SΣ0..1BackboneElementGene Studied
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48018-6
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:gene-mutations SΣ0..1BackboneElementGene Mutations ID
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept36908-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 36908-2
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:region-description SΣ0..1BackboneElementRegion Description
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81293-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 81293-3
..... value[x] SΣ0..1stringActual component result
.... component:region-coverage Σ0..1BackboneElementRegion Coverage
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptregion-coverage
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: region-coverage
.... component:ranges-examined SΣ0..*BackboneElementRange(s) of DNA sequence examined
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept51959-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 51959-5
..... value[x] SΣ0..1RangeActual component result
.... component:coordinate-system SΣ0..1BackboneElementCoordinate System
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 92822-6
..... value[x] SΣ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:genomic-ref-seq SΣ0..1BackboneElementGenomic Reference Sequence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48013-7
..... value[x] SΣ1..1CodeableConceptVersioned genomic reference sequence identifier.
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:uncallable-regions Σ0..*BackboneElementUncallable Sub-regions
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptuncallable-regions
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: uncallable-regions

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 53041-0
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:gene-mutations.codeexamplePattern: LOINC code 36908-2
Observation.component:gene-mutations.value[x]requiredHGVSVS
Observation.component:region-description.codeexamplePattern: LOINC code 81293-3
Observation.component:region-coverage.codeexamplePattern: region-coverage
Observation.component:ranges-examined.codeexamplePattern: LOINC code 51959-5
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:uncallable-regions.codeexamplePattern: uncallable-regions
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*RegionStudiedRegion Studied
... 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): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... 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/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConcept53041-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 53041-0
..... 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(Cancer Patient Profile)Who and/or what the observation is about
... focus ΣTU0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*CodedAnnotationComments about the Observation that also contain a coded type
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementProvides guide for interpretation
.... 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
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... 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
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... 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
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringSummary conclusion (interpretation/impression)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-studied SΣ0..1BackboneElementGene Studied
..... 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
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-mutations SΣ0..1BackboneElementGene Mutations ID
..... 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
..... code SΣ1..1CodeableConcept36908-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 36908-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:region-description SΣ0..1BackboneElementRegion Description
..... 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
..... code SΣ1..1CodeableConcept81293-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 81293-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ0..1stringActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:region-coverage Σ0..1BackboneElementRegion Coverage
..... 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
..... code Σ1..1CodeableConceptregion-coverage
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: region-coverage
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1QuantityActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ranges-examined SΣ0..*BackboneElementRange(s) of DNA sequence examined
..... 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
..... code SΣ1..1CodeableConcept51959-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 51959-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ0..1RangeActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coordinate-system SΣ0..1BackboneElementCoordinate System
..... 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
..... code SΣ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 92822-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-ref-seq SΣ0..1BackboneElementGenomic Reference Sequence
..... 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
..... code SΣ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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: 48013-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptVersioned genomic reference sequence identifier.
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:uncallable-regions Σ0..*BackboneElementUncallable Sub-regions
..... 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
..... code Σ1..1CodeableConceptuncallable-regions
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: uncallable-regions
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeMust be inside the range given by 'ranges examined' in the given reference sequence and coordinate system.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 53041-0
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
Observation.component:gene-mutations.codeexamplePattern: LOINC code 36908-2
Observation.component:gene-mutations.value[x]requiredHGVSVS
Observation.component:gene-mutations.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-mutations.interpretationextensibleObservationInterpretationCodes
Observation.component:region-description.codeexamplePattern: LOINC code 81293-3
Observation.component:region-description.dataAbsentReasonextensibleDataAbsentReason
Observation.component:region-description.interpretationextensibleObservationInterpretationCodes
Observation.component:region-coverage.codeexamplePattern: region-coverage
Observation.component:region-coverage.dataAbsentReasonextensibleDataAbsentReason
Observation.component:region-coverage.interpretationextensibleObservationInterpretationCodes
Observation.component:ranges-examined.codeexamplePattern: LOINC code 51959-5
Observation.component:ranges-examined.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ranges-examined.interpretationextensibleObservationInterpretationCodes
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:coordinate-system.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coordinate-system.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:genomic-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-ref-seq.interpretationextensibleObservationInterpretationCodes
Observation.component:uncallable-regions.codeexamplePattern: uncallable-regions
Observation.component:uncallable-regions.dataAbsentReasonextensibleDataAbsentReason
Observation.component:uncallable-regions.interpretationextensibleObservationInterpretationCodes

This structure is derived from RegionStudied

Summary

Mandatory: 1 element
Must-Support: 26 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.effective[x] is sliced based on the value of type:$this

Maturity: 1

Differential View

This structure is derived from RegionStudied

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*RegionStudiedRegion Studied
... status S1..1coderegistered | preliminary | final | amended +
... category S1..*CodeableConceptClassification of type of observation
... category:labCategory 1..1CodeableConceptClassification of type of observation
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/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... coding 1..1CodingCode defined by a terminology system
... subject S1..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... effective[x] S0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
... effectiveDateTime S0..1dateTimeClinically relevant time/time-period for observation
... value[x] 0..0Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... dataAbsentReason S0..1CodeableConceptWhy the result is missing
... component S0..*BackboneElementComponent results
... component:gene-studied S0..1BackboneElementGene Studied
.... code S1..1CodeableConcept48018-6
.... value[x] S1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
... component:gene-mutations S0..1BackboneElementGene Mutations ID
.... code S1..1CodeableConcept36908-2
.... value[x] S1..1CodeableConceptActual component result
... component:region-description S0..1BackboneElementRegion Description
.... code S1..1CodeableConcept81293-3
.... value[x] S0..1stringActual component result
... component:ranges-examined S0..*BackboneElementRange(s) of DNA sequence examined
.... code S1..1CodeableConcept51959-5
.... value[x] S0..1RangeActual component result
... component:coordinate-system S0..1BackboneElementCoordinate System
.... code S1..1CodeableConcept92822-6
.... value[x] S1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
... component:genomic-ref-seq S0..1BackboneElementGenomic Reference Sequence
.... code S1..1CodeableConcept48013-7
.... value[x] S1..1CodeableConceptVersioned genomic reference sequence identifier.

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*RegionStudiedRegion Studied
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



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/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code SΣ1..1CodeableConcept53041-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding1..*Coding