Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
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:
This structure is derived from Finding
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | 0..* | Variant | ||
  code | 1..1 | CodeableConcept | Genetic variant assessment Required Pattern: At least the following | |
   coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
 system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
| value[x] | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) | |
| method | 0..1 | CodeableConcept | Sequencing | 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..1 | BackboneElement | DNA Change - Transcript (cHGVS) | |
  code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
 coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
 value[x] | 1..1 | CodeableConcept | Binding: HGVS (required) | |
| component:dna-chg-type | 0..1 | BackboneElement | DNA change type | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
| value[x] | 1..1 | CodeableConcept | Concepts 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..* | BackboneElement | Functional Annotation | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |
| value[x] | 1..1 | CodeableConcept | Concepts 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..1 | BackboneElement | Variation Code | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
| value[x] | 1..1 | CodeableConcept | Binding: (unbound) (example) | |
| component:dbSNP-id | 0..1 | BackboneElement | dbSNP ID | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |
| value[x] | 1..1 | CodeableConcept | Binding: (unbound) (example) | |
| component:genomic-dna-chg | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
| value[x] | 1..1 | CodeableConcept | Binding: HGVS (required) | |
| component:genomic-source-class | 0..1 | BackboneElement | Genomic source class | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
| value[x] | 1..1 | CodeableConcept | Germline | 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..1 | BackboneElement | Amino acid change (pHGVS) | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
| value[x] | 1..1 | CodeableConcept | Binding: HGVS (required) | |
| component:amino-acid-chg-type | 0..1 | BackboneElement | Amino acid change type | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |
| value[x] | 1..1 | CodeableConcept | Wild 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..1 | BackboneElement | Transcript reference sequence ID | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
| value[x] | 1..1 | CodeableConcept | Binding: (unbound) (example) | |
| component:genomic-ref-seq | 0..1 | BackboneElement | Genomic reference sequence ID | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
| value[x] | 1..1 | CodeableConcept | Binding: (unbound) (example) | |
| component:sample-allelic-frequency | 0..1 | BackboneElement | Sample Allelic Frequency | |
| code | 1..1 | CodeableConcept | Sample Sample VAF Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
| value[x] | 1..1 | Quantity | ||
| value | 1..1 | decimal | ||
 system | 1..1 | uri | Fixed Value: http://unitsofmeasure.org | |
| component:allelic-read-depth | 0..* | BackboneElement | Allelic read depth | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |
| value[x] | 1..1 | Quantity | ||
| component:allelic-state | 0..1 | BackboneElement | Allelic state | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |
| value[x] | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) | |
| component:copy-number | 0..1 | BackboneElement | Genomic structural variant copy number | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |
| value[x] | 1..1 | Count | ||
| component:ref-allele | 0..1 | BackboneElement | Genomic ref allele | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
| value[x] | 1..1 | string | ||
| component:alt-allele | 0..1 | BackboneElement | Genomic alt allele | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
| value[x] | 1..1 | string | ||
| component:coordinate-system | 0..1 | BackboneElement | Coordinate System | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
| value[x] | 1..1 | CodeableConcept | 0-based interval | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred) | |
| component:exact-start-end | 0..1 | BackboneElement | Exact start-end | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end | |
| value[x] | 1..1 | Range | ||
| low | 1..1 | SimpleQuantity | Exact Start | |
| high | 0..1 | SimpleQuantity | Exact End | |
| component:variant-length | 0..1 | BackboneElement | Structural variant length | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6 | |
| value[x] | 1..1 | Count | ||
| component:outer-start-end | 0..1 | BackboneElement | Variant outer start and end | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end | |
| value[x] | 1..1 | Range | ||
| low | 1..1 | SimpleQuantity | ||
| high | 1..1 | SimpleQuantity | ||
| component:inner-start-end | 0..1 | BackboneElement | Variant inner start and end | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end | |
| value[x] | 1..1 | Range | ||
| low | 1..1 | SimpleQuantity | ||
| high | 1..1 | SimpleQuantity | ||
| component:chromosome-copy-number-change-type | 0..1 | BackboneElement | Chromosome copy number change type | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5 | |
| value[x] | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required) | |
| component:arrCGH-ratio | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0 | |
| value[x] | 1..1 | SimpleQuantity | ||
| component:complex-var-type | 0..1 | BackboneElement | Complex variant type | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6 | |
| value[x] | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required) | |
| component:cytogenomic-nomenclature | 0..1 | BackboneElement | Cytogenomic Nomenclature | |
| code | 1..1 | CodeableConcept | Variant ISCN Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
| value[x] | 1..1 | CodeableConcept | Binding: (unbound) (example) | |
 component:variant-inheritance | 0..1 | BackboneElement | Variant Inheritance | |
| code | 1..1 | CodeableConcept | Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance | |
| value[x] | 1..1 | CodeableConcept | Binding: Variant Inheritance (extensible) | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | I | 0..* | Variant | |
| id | Σ | 0..1 | string | Logical id of this artifact |
| meta | ΣI | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!ΣI | 0..1 | uri | A set of rules under which this content was created |
| language | I | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) Max Binding: AllLanguages |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
 contained | 0..* | Resource | Contained, inline Resources | |
 extension | I | 0..* | Extension | Extension Slice: Unordered, Open by value:url |
| bodySite | I | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite |
| observation-secondaryFinding | I | 0..1 | CodeableConcept | Secondary 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 | ?!I | 0..* | Extension | Extensions that cannot be ignored |
| identifier | ΣI | 0..* | Identifier | Business Identifier for observation |
 basedOn | ΣI | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order |
| partOf | ΣI | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event |
| status | ?!ΣI | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required) |
| category | I | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| code | ΣI | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| subject | ΣI | 0..1 | Reference(Patient | Group | Location) | Who and/or what the observation is about |
| focus | ΣI | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record |
| encounter | ΣI | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made |
| effective[x] | ΣI | 0..1 | (Slice Definition) | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this |
| effective[x]:effectiveDateTime | ΣI | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| issued | ΣI | 0..1 | instant | Date/Time this version was made available |
| performer | ΣI | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation |
| value[x] | ΣI | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible) |
| note | I | 0..* | Annotation | Comments about the observation |
| bodySite | I | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example) |
| method | I | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (extensible) |
| specimen | I | 0..1 | Reference(Specimen) | Specimen examined |
| device | I | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device |
| referenceRange | I | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| low | I | 0..1 | SimpleQuantity | Low Range, if relevant |
| high | I | 0..1 | SimpleQuantity | High Range, if relevant |
| type | I | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred) |
| appliesTo | I | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example) |
| age | I | 0..1 | Range | Applicable age range, if relevant |
| text | I | 0..1 | string | Text based reference range in an observation |
| hasMember | ΣI | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group |
| derivedFrom | ΣI | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from |
| component | ΣI | 0..* | (Slice Definition) | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) |
 value[x] | ΣI | 0..1 | Actual component result | |
| valueQuantity | Quantity | |||
| valueCodeableConcept | CodeableConcept | |||
| valueString | string | |||
| valueBoolean | boolean | |||
| valueInteger | integer | |||
| valueRange | Range | |||
| valueRatio | Ratio | |||
| valueSampledData | SampledData | |||
| valueTime | time | |||
| valueDateTime | dateTime | |||
| valuePeriod | Period | |||
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:gene-studied | ΣI | 0..* | BackboneElement | Gene studied ID |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:cytogenetic-location | ΣI | 0..* | BackboneElement | Cytogenetic (chromosome) location |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:ref-sequence-assembly | ΣI | 0..* | BackboneElement | Human reference sequence assembly version |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:dna-chg | ΣI | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:dna-chg-type | ΣI | 0..1 | BackboneElement | DNA change type |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:functional-annotation | ΣI | 0..* | BackboneElement | Functional Annotation |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:variation-code | ΣI | 0..1 | BackboneElement | Variation Code |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:dbSNP-id | ΣI | 0..1 | BackboneElement | dbSNP ID |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:genomic-dna-chg | ΣI | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:genomic-source-class | ΣI | 0..1 | BackboneElement | Genomic source class |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:amino-acid-chg | ΣI | 0..1 | BackboneElement | Amino acid change (pHGVS) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:amino-acid-chg-type | ΣI | 0..1 | BackboneElement | Amino acid change type |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:transcript-ref-seq | ΣI | 0..1 | BackboneElement | Transcript reference sequence ID |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:genomic-ref-seq | ΣI | 0..1 | BackboneElement | Genomic reference sequence ID |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | ΣI | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example) Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | 0..1 | string | Plain text representation of the concept | |
| value[x] | ΣI | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example) |
| dataAbsentReason | I | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible) |
| referenceRange | I | 0..* | Unknown reference to #Observation.referenceRange Provides guide for interpretation of component result | |
| component:sample-allelic-frequency | ΣI | 0..1 | BackboneElement | Sample Allelic Frequency |
| id | 0..1 | string | Unique id for inter-element referencing |