{ "resourceType": "StructureDefinition", "id": "variant", "meta": { "lastUpdated": "2019-12-20T21:25:08.821+00:00" }, "text": { "status": "generated", "div": "
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\"Observation0..*Variant
\".\"\".\"\".\"code1..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)
\".\"\".\"\".\"method0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (extensible)
\".\"\".\"\".\"component0..*(Slice Definition)Slice: Unordered, Open by pattern:code
\".\"\".\"\".\"\".\"component:dna-chg0..1BackboneElementDNA Change - Transcript (cHGVS)
\".\"\".\"\".\"\".\"\".\"code1..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-type0..1BackboneElementDNA change type
\".\"\".\"\".\"\".\"\".\"code1..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-annotation0..*BackboneElementFunctional Annotation
\".\"\".\"\".\"\".\"\".\"code1..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-code0..1BackboneElementVariation Code
\".\"\".\"\".\"\".\"\".\"code1..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-id0..1BackboneElementdbSNP ID
\".\"\".\"\".\"\".\"\".\"code1..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-chg0..1BackboneElementDNA Change - Genomic (gHGVS)
\".\"\".\"\".\"\".\"\".\"code1..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-class0..1BackboneElementGenomic source class
\".\"\".\"\".\"\".\"\".\"code1..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-chg0..1BackboneElementAmino acid change (pHGVS)
\".\"\".\"\".\"\".\"\".\"code1..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-type0..1BackboneElementAmino acid change type
\".\"\".\"\".\"\".\"\".\"code1..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-seq0..1BackboneElementTranscript reference sequence ID
\".\"\".\"\".\"\".\"\".\"code1..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-seq0..1BackboneElementGenomic reference sequence ID
\".\"\".\"\".\"\".\"\".\"code1..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-frequency0..1BackboneElementSample Allelic Frequency
\".\"\".\"\".\"\".\"\".\"code1..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
\".\"\".\"\".\"\".\"\".\"\".\"value1..1decimal
\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriFixed Value: http://unitsofmeasure.org
\".\"\".\"\".\"\".\"component:allelic-read-depth0..*BackboneElementAllelic read depth
\".\"\".\"\".\"\".\"\".\"code1..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-state0..1BackboneElementAllelic state
\".\"\".\"\".\"\".\"\".\"code1..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-number0..1BackboneElementGenomic structural variant copy number
\".\"\".\"\".\"\".\"\".\"code1..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-allele0..1BackboneElementGenomic ref allele
\".\"\".\"\".\"\".\"\".\"code1..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-allele0..1BackboneElementGenomic alt allele
\".\"\".\"\".\"\".\"\".\"code1..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-system0..1BackboneElementCoordinate System
\".\"\".\"\".\"\".\"\".\"code1..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-end0..1BackboneElementExact start-end
\".\"\".\"\".\"\".\"\".\"code1..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
\".\"\".\"\".\"\".\"\".\"\".\"low1..1SimpleQuantityExact Start
\".\"\".\"\".\"\".\"\".\"\".\"high0..1SimpleQuantityExact End
\".\"\".\"\".\"\".\"component:variant-length0..1BackboneElementStructural variant length
\".\"\".\"\".\"\".\"\".\"code1..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-end0..1BackboneElementVariant outer start and end
\".\"\".\"\".\"\".\"\".\"code1..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
\".\"\".\"\".\"\".\"\".\"\".\"low1..1SimpleQuantity
\".\"\".\"\".\"\".\"\".\"\".\"high1..1SimpleQuantity
\".\"\".\"\".\"\".\"component:inner-start-end0..1BackboneElementVariant inner start and end
\".\"\".\"\".\"\".\"\".\"code1..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
\".\"\".\"\".\"\".\"\".\"\".\"low1..1SimpleQuantity
\".\"\".\"\".\"\".\"\".\"\".\"high1..1SimpleQuantity
\".\"\".\"\".\"\".\"component:chromosome-copy-number-change-type0..1BackboneElementChromosome copy number change type
\".\"\".\"\".\"\".\"\".\"code1..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-ratio0..1BackboneElementStructural variant reported arrCGH [Ratio]
\".\"\".\"\".\"\".\"\".\"code1..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-type0..1BackboneElementComplex variant type
\".\"\".\"\".\"\".\"\".\"code1..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-nomenclature0..1BackboneElementCytogenomic Nomenclature
\".\"\".\"\".\"\".\"\".\"code1..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-inheritance0..1BackboneElementVariant Inheritance
\".\"\".\"\".\"\".\"\".\"code1..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
" }, "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", "version": "1.0.0", "name": "Variant", "title": "Variant", "status": "draft", "experimental": false, "date": "2017-05-20T00:00:00+00:00", "publisher": "HL7 Clinical Genomics WG", "description": "Observation-related profiles", "fhirVersion": "4.0.1", "mapping": [ { "identity": "v2-cg-results", "uri": "http://unknown.org/V2-CG-Results", "name": "V2-CG-Results" }, { "identity": "workflow", "uri": "http://hl7.org/fhir/workflow", "name": "Workflow Pattern" }, { "identity": "sct-concept", "uri": "http://snomed.info/conceptdomain", "name": "SNOMED CT Concept Domain Binding" }, { "identity": "v2", "uri": "http://hl7.org/v2", "name": "HL7 v2 Mapping" }, { "identity": "rim", "uri": "http://hl7.org/v3", "name": "RIM Mapping" }, { "identity": "w5", "uri": "http://hl7.org/fhir/fivews", "name": "FiveWs Pattern Mapping" }, { "identity": "sct-attr", "uri": "http://snomed.org/attributebinding", "name": "SNOMED CT Attribute Binding" } ], "kind": "resource", "abstract": false, "type": "Observation", "baseDefinition": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/finding", "derivation": "constraint", "snapshot": {}, "differential": { "element": [ { "id": "Observation", "path": "Observation", "short": "Variant", "definition": "Details about a set of changes in the tested sample compared to a reference sequence.", "comment": "This change can be simple/discrete (relatively short), structural (potentially very large), or complex (consisting of multiple independent co-occurring variations).", "mustSupport": false }, { "id": "Observation.code", "path": "Observation.code", "short": "Genetic variant assessment", "definition": "Where testing scenarios are intended to assess the prescence or absence of a known set of DNA variants (e.g. tumor profiling using genotyping technology), then the Genetic Variant Assessment is used in conjunction with answer list supports structured communication of these findings. Of note, 'No Call' is different from 'Absent', because 'No Call' did not result in the determination of the marker's presents or absents. This may be due to test failure or specimen specific context which renders the test ineffective.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "69548-6" } ] }, "mustSupport": false }, { "id": "Observation.value[x]", "path": "Observation.value[x]", "short": "Present|Absent|No call|Indeterminate", "definition": "Indicates whether the indicated variation was found or not.", "comment": "If not searching for specific variations and merely reporting what's found, this element should be set to \"Present\".", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "Genetic Variant Assessment", "valueSet": "http://loinc.org/vs/LL1971-2" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.21" } ] }, { "id": "Observation.method", "path": "Observation.method", "short": "Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+", "definition": "Indicates the method of variant analysis.", "min": 0, "max": "1", "mustSupport": false, "binding": { "strength": "extensible", "description": "Variant analysis method type", "valueSet": "http://loinc.org/vs/LL4048-6" } }, { "id": "Observation.component", "path": "Observation.component", "slicing": { "discriminator": [ { "type": "pattern", "path": "code" } ], "rules": "open" }, "mustSupport": false }, { "id": "Observation.component:dna-chg", "path": "Observation.component", "sliceName": "dna-chg", "short": "DNA Change - Transcript (cHGVS)", "definition": "Human Genome Variation Society (HGVS) nomenclature for a single DNA marker.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:dna-chg.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48004-6" } ] }, "mustSupport": false }, { "id": "Observation.component:dna-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.5 (includes A.13 in version)" } ] }, { "id": "Observation.component:dna-chg-type", "path": "Observation.component", "sliceName": "dna-chg-type", "short": "DNA change type", "definition": "Codified type for associated DNA Marker. DNA Marker's use the HGVS notation which implies the DNA Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:dna-chg-type.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48019-4" } ] }, "mustSupport": false }, { "id": "Observation.component:dna-chg-type.value[x]", "path": "Observation.component.value[x]", "short": "Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)", "definition": "Type of DNA variation reported.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "DNA Change type values (Sequence Ontology)", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.7" } ] }, { "id": "Observation.component:functional-annotation", "path": "Observation.component", "sliceName": "functional-annotation", "short": "Functional Annotation", "definition": "Annotated changes to sequence features caused by this variant.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:functional-annotation.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "functional-annotation" } ] }, "mustSupport": false }, { "id": "Observation.component:functional-annotation.value[x]", "path": "Observation.component.value[x]", "short": "Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)", "definition": "Changes to sequence features caused by this variant.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "Functional Annotation (Sequence Ontology)", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-annotation" } }, { "id": "Observation.component:variation-code", "path": "Observation.component", "sliceName": "variation-code", "short": "Variation Code", "definition": "This term is used to report the unique identifier of the simple variant found in this study.", "comment": "If this is present, the components can be omitted but they might be included to avoid a need to look up the information in a registry. Typically only one code would be present, though multiple codings expressing the variant in different code systems are possible.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:variation-code.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81252-9" } ] }, "mustSupport": false }, { "id": "Observation.component:variation-code.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.2, B.16 (A.16 in coding.version)" } ] }, { "id": "Observation.component:dbSNP-id", "path": "Observation.component", "sliceName": "dbSNP-id", "short": "dbSNP ID", "definition": "The unique identifier for the variant represented as a small nucleotide polymorphism (SNP). The dbSNP ID is used routinely as the base identifier in pharmacogenomics as well as arrCGH studies. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the dbSNP ID is 368949613. [http://www.ncbi.nlm.nih.gov/clinvar/variation/30880/].", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:dbSNP-id.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81255-2" } ] }, "mustSupport": false }, { "id": "Observation.component:dbSNP-id.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.15 (includes A.14 in version)" } ] }, { "id": "Observation.component:genomic-dna-chg", "path": "Observation.component", "sliceName": "genomic-dna-chg", "short": "DNA Change - Genomic (gHGVS)", "definition": "The name of a structural variant reported using HGVS nomenclature.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:genomic-dna-chg.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81290-9" } ] }, "mustSupport": false }, { "id": "Observation.component:genomic-dna-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.10 (includes A.13 in version)" } ] }, { "id": "Observation.component:genomic-source-class", "path": "Observation.component", "sliceName": "genomic-source-class", "short": "Genomic source class", "definition": "The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:genomic-source-class.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48002-0" } ] }, "mustSupport": false }, { "id": "Observation.component:genomic-source-class.value[x]", "path": "Observation.component.value[x]", "short": "Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo", "definition": "MG_2_Genetic variant source.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "Genomic source class values", "valueSet": "http://loinc.org/vs/LL378-1" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.18" } ] }, { "id": "Observation.component:amino-acid-chg", "path": "Observation.component", "sliceName": "amino-acid-chg", "short": "Amino acid change (pHGVS)", "definition": "Human Genome Variation Society (HGVS) nomenclature for an amino acid sequence. This value is derivable from the DNA Marker value if available. It is provided for convenience. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:amino-acid-chg.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48005-3" } ] }, "mustSupport": false }, { "id": "Observation.component:amino-acid-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.6 (includes A.13 in version)" } ] }, { "id": "Observation.component:amino-acid-chg-type", "path": "Observation.component", "sliceName": "amino-acid-chg-type", "short": "Amino acid change type", "definition": "Codified type for associated Amino Acid Marker. Amino Acid Marker's use the HGVS notation which implies the Amino Acid Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:amino-acid-chg-type.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48006-1" } ] }, "mustSupport": false }, { "id": "Observation.component:amino-acid-chg-type.value[x]", "path": "Observation.component.value[x]", "short": "Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation", "definition": "MG_4_Amino acid change type.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "Amino acid change type values", "valueSet": "http://loinc.org/vs/LL380-7" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.8" } ] }, { "id": "Observation.component:transcript-ref-seq", "path": "Observation.component", "sliceName": "transcript-ref-seq", "short": "Transcript reference sequence ID", "definition": "This field carries the ID for the transcribed reference sequence, which is the part of the genomic reference sequence that is converted to messenger RNA (i.e., after the introns are removed).", "comment": "Only needed if the transcript sequence or genomic reference sequence versions don't indicate the version.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:transcript-ref-seq.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "51958-7" } ] }, "mustSupport": false }, { "id": "Observation.component:transcript-ref-seq.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.4" } ] }, { "id": "Observation.component:genomic-ref-seq", "path": "Observation.component", "sliceName": "genomic-ref-seq", "short": "Genomic reference sequence ID", "definition": "This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008).\rThe NCI RefSeq genomic IDs are distinguished by a prefix of\"NG\" for genes from the nuclear chromosomes and prefix of \"NC\" for genes from mitochondria. The LRG Identifiers have a prefix of \"LRG_\" Mitochondrial genes are not in the scope of LRG.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:genomic-ref-seq.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48013-7" } ] }, "mustSupport": false }, { "id": "Observation.component:genomic-ref-seq.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.9" } ] }, { "id": "Observation.component:sample-allelic-frequency", "path": "Observation.component", "sliceName": "sample-allelic-frequency", "short": "Sample Allelic Frequency", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:sample-allelic-frequency.code", "path": "Observation.component.code", "short": "Sample Sample VAF", "definition": "The fraction of all reads in a study sample at a given genomic locus that identify the allele (variant) in question.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81258-6" } ] }, "mustSupport": false }, { "id": "Observation.component:sample-allelic-frequency.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity" } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.22, C.4" } ] }, { "id": "Observation.component:sample-allelic-frequency.value[x].value", "path": "Observation.component.value[x].value", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:sample-allelic-frequency.value[x].system", "path": "Observation.component.value[x].system", "min": 1, "max": "1", "type": [ { "code": "uri" } ], "fixedUri": "http://unitsofmeasure.org", "mustSupport": false }, { "id": "Observation.component:allelic-read-depth", "path": "Observation.component", "sliceName": "allelic-read-depth", "short": "Allelic read depth", "definition": "Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:allelic-read-depth.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "82121-5" } ] }, "mustSupport": false }, { "id": "Observation.component:allelic-read-depth.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity" } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.27, C.7" } ] }, { "id": "Observation.component:allelic-state", "path": "Observation.component", "sliceName": "allelic-state", "short": "Allelic state", "definition": "The level of occurrence of a single DNA Marker within a set of chromosomes. Heterozygous indicates the DNA Marker is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Marker is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Marker exists in the only single copy of a gene in a non-homologous chromosome (The male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Maker is present in all of the copies of mitochondrial DNA.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:allelic-state.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "53034-5" } ] }, "mustSupport": false }, { "id": "Observation.component:allelic-state.value[x]", "path": "Observation.component.value[x]", "short": "Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous", "definition": "The relationship between the alleles found at the same locus on different chromosomes.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "Allelic state type values", "valueSet": "http://loinc.org/vs/LL381-5" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.23, C.6" } ] }, { "id": "Observation.component:copy-number", "path": "Observation.component", "sliceName": "copy-number", "short": "Genomic structural variant copy number", "definition": "The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or ISCN fields.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:copy-number.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "82155-3" } ] }, "mustSupport": false }, { "id": "Observation.component:copy-number.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/Count" ] } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.28" } ] }, { "id": "Observation.component:ref-allele", "path": "Observation.component", "sliceName": "ref-allele", "short": "Genomic ref allele", "definition": "Reference values (\"normal\") examined within the Reference Sequence.", "comment": "This is used in a genotyping test to define the reference and variable nucleotide strings. That is if the sequence variation is an insertion, then Reference Nucleotide will be blank and Variable Nucleotide will contain the inserted nucleotides. In contrast, if the sequence variation is a deletion, then the Reference Nucleotide will contain the deleted nucliotieds, and the Variable Nucleotide will be blank.", "min": 0, "max": "1", "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.9" } ] }, { "id": "Observation.component:ref-allele.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "69547-8" } ] }, "mustSupport": false }, { "id": "Observation.component:ref-allele.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "string" } ], "mustSupport": false }, { "id": "Observation.component:alt-allele", "path": "Observation.component", "sliceName": "alt-allele", "short": "Genomic alt allele", "definition": "The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.", "min": 0, "max": "1", "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.11" } ] }, { "id": "Observation.component:alt-allele.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "69551-0" } ] }, "mustSupport": false }, { "id": "Observation.component:alt-allele.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "string" } ], "mustSupport": false }, { "id": "Observation.component:coordinate-system", "path": "Observation.component", "sliceName": "coordinate-system", "short": "Coordinate System", "definition": "Base number of coordinate system either 0-based, with inclusive start and exclusive end (called interval), or 1-based, with inclusive start and end. However, two versions of 1-based are in common use.These systems are HGVS 1-based (called variant method) and VCF 1-based (called alignment method). In general, HGVS recommends right-justification and VCF recommends left-justification. However, these systems further address questions such as wheather or not to place an insertion before or after the nucleotide, and, if always placed before the nucleotide, how to handle insertion after the end of the sequence. Additionally, the systems deal with handling boundary effects of numbers between features. For more details see the HGVS and VCF guides.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:coordinate-system.code", "path": "Observation.component.code", "definition": "This captures the base numbering used to calculate base positions in the reported sequence information.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "92822-6" } ] }, "mustSupport": false }, { "id": "Observation.component:coordinate-system.value[x]", "path": "Observation.component.value[x]", "short": "0-based interval | 0-based character | 1-based character", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "preferred", "description": "Base coordinate systems start and end measurements for variants", "valueSet": "http://loinc.org/vs/LL5323-2" } }, { "id": "Observation.component:exact-start-end", "path": "Observation.component", "sliceName": "exact-start-end", "short": "Exact start-end", "definition": "This location is the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38.", "min": 0, "max": "1", "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.10" } ] }, { "id": "Observation.component:exact-start-end.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "exact-start-end" } ] }, "mustSupport": false }, { "id": "Observation.component:exact-start-end.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Range" } ], "mustSupport": false }, { "id": "Observation.component:exact-start-end.value[x].low", "path": "Observation.component.value[x].low", "short": "Exact Start", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:exact-start-end.value[x].high", "path": "Observation.component.value[x].high", "short": "Exact End", "definition": "Optional since many representations (VCF, SPDI) only provide a single position.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:variant-length", "path": "Observation.component", "sliceName": "variant-length", "short": "Structural variant length", "definition": "Length of the structural variant, which information may be ascertained in some but not all types of structural variants.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:variant-length.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81300-6" } ] }, "mustSupport": false }, { "id": "Observation.component:variant-length.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/Count" ] } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.30" } ] }, { "id": "Observation.component:outer-start-end", "path": "Observation.component", "sliceName": "outer-start-end", "short": "Variant outer start and end", "definition": "The genomic coordinates of the widest genomic range in which the variant might reside.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:outer-start-end.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "outer-start-end" } ] }, "mustSupport": false }, { "id": "Observation.component:outer-start-end.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Range" } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.31" } ] }, { "id": "Observation.component:outer-start-end.value[x].low", "path": "Observation.component.value[x].low", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:outer-start-end.value[x].high", "path": "Observation.component.value[x].high", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:inner-start-end", "path": "Observation.component", "sliceName": "inner-start-end", "short": "Variant inner start and end", "definition": "The genomic coordinates of the narrowest genomic range in which the structural variant might reside.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:inner-start-end.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "inner-start-end" } ] }, "mustSupport": false }, { "id": "Observation.component:inner-start-end.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Range" } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.32" } ] }, { "id": "Observation.component:inner-start-end.value[x].low", "path": "Observation.component.value[x].low", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:inner-start-end.value[x].high", "path": "Observation.component.value[x].high", "min": 1, "max": "1", "mustSupport": false }, { "id": "Observation.component:chromosome-copy-number-change-type", "path": "Observation.component", "sliceName": "chromosome-copy-number-change-type", "short": "Chromosome copy number change type", "definition": "The type of the chromosome copy number change.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:chromosome-copy-number-change-type.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "62378-5" } ] }, "mustSupport": false }, { "id": "Observation.component:chromosome-copy-number-change-type.value[x]", "path": "Observation.component.value[x]", "short": "Copy number gain | Copy number loss", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "Copy Number Change Types", "valueSet": "http://loinc.org/vs/LL1041-4" }, "mapping": [ { "identity": "v2-cg-results", "map": "C.1" } ] }, { "id": "Observation.component:arrCGH-ratio", "path": "Observation.component", "sliceName": "arrCGH-ratio", "short": "Structural variant reported arrCGH [Ratio]", "definition": "todo.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:arrCGH-ratio.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81299-0" } ] }, "mustSupport": false }, { "id": "Observation.component:arrCGH-ratio.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ] } ], "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "B.29" } ] }, { "id": "Observation.component:complex-var-type", "path": "Observation.component", "sliceName": "complex-var-type", "short": "Complex variant type", "definition": "The type of complex variant, for example, compound heterozygous or haplotype.", "comment": "When sending a grouping of non-contiguous variants that are meant to be interpreted together but do not signify a named haplotype, one can send the type of complex variant here (determined by where the individual changes are in relation to each other), and use Observation.hasMember to reference the individual variants, which would then be described as normal.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:complex-var-type.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81263-6" } ] }, "mustSupport": false }, { "id": "Observation.component:complex-var-type.value[x]", "path": "Observation.component.value[x]", "short": "Compound heterozygous | Double heterozygous | Haplotype | Hemizygous", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "Complex variant type", "valueSet": "http://loinc.org/vs/LL3999-1" }, "mapping": [ { "identity": "v2-cg-results", "map": "C.3" } ] }, { "id": "Observation.component:cytogenomic-nomenclature", "path": "Observation.component", "sliceName": "cytogenomic-nomenclature", "short": "Cytogenomic Nomenclature", "definition": "Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:cytogenomic-nomenclature.code", "path": "Observation.component.code", "short": "Variant ISCN", "definition": "ISCN is a syntax for describing cytogenetic findings, from classical karyotypes to details that can be observed with copy number methodologies. Using ISCN nomenclature is highly recommended for reporting structural variants.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81291-7" } ] }, "mustSupport": false }, { "id": "Observation.component:cytogenomic-nomenclature.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "A.11" } ] }, { "id": "Observation.component:variant-inheritance", "path": "Observation.component", "sliceName": "variant-inheritance", "short": "Variant Inheritance", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:variant-inheritance.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "variant-inheritance" } ] }, "mustSupport": false }, { "id": "Observation.component:variant-inheritance.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "Variant Inheritance (Sequence Ontology)", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance" } } ] } }