Genomics Reporting Implementation Guide (STU1)

Genomics Reporting Implementation Guide, published by HL7 International Clinical Genomics Work Group. This is not an authorized publication; it is the continuous build for version 1.0.0). This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

StructureDefinition: Variant

The official URL for this profile is:

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant

Formal Views of Profile Content

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

This structure is derived from Finding

Summary

Mandatory: 2 elements (61 nested mandatory elements)
Fixed Value: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.component is sliced based on the value of pattern:code

This structure is derived from Finding

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*FindingVariant
... code 1..1CodeableConceptGenetic variant assessment
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: 69548-6
... value[x] 1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... method 0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (extensible)
... component 0..*(Slice Definition)Slice: Unordered, Open by pattern:code
.... component:dna-chg 0..1BackboneElementDNA Change - Transcript (cHGVS)
..... code 1..1CodeableConceptRequired 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: 48004-6
..... value[x] 1..1CodeableConceptBinding: HGVS (required)
.... component:dna-chg-type 0..1BackboneElementDNA change type
..... code 1..1CodeableConceptRequired 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: 48019-4
..... value[x] 1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible)
.... component:functional-annotation 0..*BackboneElementFunctional Annotation
..... code 1..1CodeableConceptRequired 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
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
..... value[x] 1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible)
.... component:variation-code 0..1BackboneElementVariation Code
..... code 1..1CodeableConceptRequired 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: 81252-9
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:dbSNP-id 0..1BackboneElementdbSNP ID
..... code 1..1CodeableConceptRequired 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: 81255-2
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:genomic-dna-chg 0..1BackboneElementDNA Change - Genomic (gHGVS)
..... code 1..1CodeableConceptRequired 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: 81290-9
..... value[x] 1..1CodeableConceptBinding: HGVS (required)
.... component:genomic-source-class 0..1BackboneElementGenomic source class
..... code 1..1CodeableConceptRequired 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: 48002-0
..... value[x] 1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:amino-acid-chg 0..1BackboneElementAmino acid change (pHGVS)
..... code 1..1CodeableConceptRequired 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: 48005-3
..... value[x] 1..1CodeableConceptBinding: HGVS (required)
.... component:amino-acid-chg-type 0..1BackboneElementAmino acid change type
..... code 1..1CodeableConceptRequired 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: 48006-1
..... value[x] 1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
.... component:transcript-ref-seq 0..1BackboneElementTranscript reference sequence ID
..... code 1..1CodeableConceptRequired 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: 51958-7
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:genomic-ref-seq 0..1BackboneElementGenomic reference sequence ID
..... code 1..1CodeableConceptRequired 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] 1..1CodeableConceptBinding: (unbound) (example)
.... component:sample-allelic-frequency 0..1BackboneElementSample Allelic Frequency
..... code 1..1CodeableConceptSample Sample VAF
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: 81258-6
..... value[x] 1..1Quantity
...... value 1..1decimal
...... system 1..1uriFixed Value: http://unitsofmeasure.org
.... component:allelic-read-depth 0..*BackboneElementAllelic read depth
..... code 1..1CodeableConceptRequired 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: 82121-5
..... value[x] 1..1Quantity
.... component:allelic-state 0..1BackboneElementAllelic state
..... code 1..1CodeableConceptRequired 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: 53034-5
..... value[x] 1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:copy-number 0..1BackboneElementGenomic structural variant copy number
..... code 1..1CodeableConceptRequired 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: 82155-3
..... value[x] 1..1Count
.... component:ref-allele 0..1BackboneElementGenomic ref allele
..... code 1..1CodeableConceptRequired 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: 69547-8
..... value[x] 1..1string
.... component:alt-allele 0..1BackboneElementGenomic alt allele
..... code 1..1CodeableConceptRequired 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: 69551-0
..... value[x] 1..1string
.... component:coordinate-system 0..1BackboneElementCoordinate System
..... code 1..1CodeableConceptRequired 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] 1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred)
.... component:exact-start-end 0..1BackboneElementExact start-end
..... code 1..1CodeableConceptRequired 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
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: exact-start-end
..... value[x] 1..1Range
...... low 1..1SimpleQuantityExact Start
...... high 0..1SimpleQuantityExact End
.... component:variant-length 0..1BackboneElementStructural variant length
..... code 1..1CodeableConceptRequired 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: 81300-6
..... value[x] 1..1Count
.... component:outer-start-end 0..1BackboneElementVariant outer start and end
..... code 1..1CodeableConceptRequired 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
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: outer-start-end
..... value[x] 1..1Range
...... low 1..1SimpleQuantity
...... high 1..1SimpleQuantity
.... component:inner-start-end 0..1BackboneElementVariant inner start and end
..... code 1..1CodeableConceptRequired 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
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: inner-start-end
..... value[x] 1..1Range
...... low 1..1SimpleQuantity
...... high 1..1SimpleQuantity
.... component:chromosome-copy-number-change-type 0..1BackboneElementChromosome copy number change type
..... code 1..1CodeableConceptRequired 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: 62378-5
..... value[x] 1..1CodeableConceptCopy number gain | Copy number loss
Binding: LOINC Answer List LL1041-4 (required)
.... component:arrCGH-ratio 0..1BackboneElementStructural variant reported arrCGH [Ratio]
..... code 1..1CodeableConceptRequired 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: 81299-0
..... value[x] 1..1SimpleQuantity
.... component:complex-var-type 0..1BackboneElementComplex variant type
..... code 1..1CodeableConceptRequired 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: 81263-6
..... value[x] 1..1CodeableConceptCompound heterozygous | Double heterozygous | Haplotype | Hemizygous
Binding: LOINC Answer List LL3999-1 (required)
.... component:cytogenomic-nomenclature 0..1BackboneElementCytogenomic Nomenclature
..... code 1..1CodeableConceptVariant ISCN
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: 81291-7
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:variant-inheritance 0..1BackboneElementVariant Inheritance
..... code 1..1CodeableConceptRequired 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
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
..... value[x] 1..1CodeableConceptBinding: Variant Inheritance (extensible)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*FindingVariant
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... language I0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..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)
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness Identifier for observation
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!ΣI1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category I1..*(Slice Definition)Classification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred)
.... category:Laboratory I1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

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
... code ΣI1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example)
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: 69548-6
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject ΣI0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI0..1(Slice Definition)Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime ΣI0..1dateTimeClinically relevant time/time-period for observation
... issued ΣI0..1instantDate/Time this version was made available
... performer ΣI0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... note I0..*AnnotationComments about the observation
... bodySite I0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method I0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen I0..1Reference(Specimen)Specimen examined
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type I0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo I0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age I0..1RangeApplicable age range, if relevant
.... text I0..1stringText based reference range in an observation
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component ΣI0..*(Slice Definition)Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... value[x] ΣI0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:gene-studied ΣI0..*BackboneElementGene studied ID
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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] ΣI1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:cytogenetic-location ΣI0..*BackboneElementCytogenetic (chromosome) location
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48001-2
....... 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] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:ref-sequence-assembly ΣI0..*BackboneElementHuman reference sequence assembly version
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 62374-4
....... 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] ΣI1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:dna-chg ΣI0..1BackboneElementDNA Change - Transcript (cHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48004-6
....... 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] ΣI1..1CodeableConceptActual component result
Binding: HGVS (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:dna-chg-type ΣI0..1BackboneElementDNA change type
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48019-4
....... 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] ΣI1..1CodeableConceptConcepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
Binding: DNA Change Type (extensible)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:functional-annotation ΣI0..*BackboneElementFunctional Annotation
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: functional-annotation
....... 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] ΣI1..1CodeableConceptConcepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
Binding: Functional Annotation (extensible)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:variation-code ΣI0..1BackboneElementVariation Code
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 81252-9
....... 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] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:dbSNP-id ΣI0..1BackboneElementdbSNP ID
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 81255-2
....... 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] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:genomic-dna-chg ΣI0..1BackboneElementDNA Change - Genomic (gHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 81290-9
....... 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] ΣI1..1CodeableConceptActual component result
Binding: HGVS (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:genomic-source-class ΣI0..1BackboneElementGenomic source class
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48002-0
....... 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] ΣI1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:amino-acid-chg ΣI0..1BackboneElementAmino acid change (pHGVS)
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48005-3
....... 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] ΣI1..1CodeableConceptActual component result
Binding: HGVS (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:amino-acid-chg-type ΣI0..1BackboneElementAmino acid change type
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 48006-1
....... 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] ΣI1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:transcript-ref-seq ΣI0..1BackboneElementTranscript reference sequence ID
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
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: 51958-7
....... 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] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... interpretation I0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:genomic-ref-seq ΣI0..1