{ "resourceType": "StructureDefinition", "id": "il-variant-genetics", "language": "he-IL", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-category", "valueString": "Clinical.Diagnostics" }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-security-category", "valueCode": "patient" } ], "url": "http://fhir.health.gov.il/StructureDefinition/il-variant-genetics-survey", "version": "0.1.0", "name": "ILVariantGeneticsInheritedDiseaseSurvey", "title": "IL Observation-Variant Genetics Inherited Disease survey Profile", "status": "draft", "date": "2021-10-04", "publisher": "Israeli Ministry of Health", "description": "Proposed constraints and extensions on the Variant-Genetics Resource", "fhirVersion": "4.0.1", "mapping": [ { "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://fhir.health.gov.il/StructureDefinition/il-core-observation", "derivation": "constraint", "differential": { "element": [ { "id": "Observation", "path": "Observation", "short": "IL Variant Genetics Profile", "definition": "Definitions for the profile Variant-Genetics resource profile." }, { "id": "Observation.identifier", "path": "Observation.identifier", "slicing": { "discriminator": [ { "type": "value", "path": "system" } ], "rules": "open" }, "min": 1 }, { "id": "Observation.identifier.system", "path": "Observation.identifier.system", "min": 1, "mustSupport": true }, { "id": "Observation.identifier.value", "path": "Observation.identifier.value", "short": "The value that is unique within the system.", "min": 1, "mustSupport": true }, { "id": "Observation.status", "path": "Observation.status", "fixedCode": "final" }, { "id": "Observation.category", "path": "Observation.category", "mustSupport": false }, { "id": "Observation.category.coding", "path": "Observation.category.coding", "min": 1, "max": "1" }, { "id": "Observation.category.coding.system", "path": "Observation.category.coding.system", "fixedUri": "http://terminology.hl7.org/CodeSystem/observation-category" }, { "id": "Observation.category.coding.code", "path": "Observation.category.coding.code", "fixedCode": "laboratory" }, { "id": "Observation.category.coding.display", "path": "Observation.category.coding.display", "fixedString": "Laboratory" }, { "id": "Observation.code.coding", "path": "Observation.code.coding", "min": 1, "max": "1" }, { "id": "Observation.code.coding.system", "path": "Observation.code.coding.system", "fixedUri": "http://loinc.org" }, { "id": "Observation.code.coding.code", "path": "Observation.code.coding.code", "fixedCode": "69548-6" }, { "id": "Observation.code.coding.display", "path": "Observation.code.coding.display", "fixedString": "Genetic variant assessment" }, { "id": "Observation.subject", "path": "Observation.subject", "min": 1, "type": [ { "code": "Reference", "targetProfile": [ "http://fhir.health.gov.il/StructureDefinition/il-core-patient" ] } ] }, { "id": "Observation.encounter", "path": "Observation.encounter", "min": 1, "type": [ { "code": "Reference", "targetProfile": [ "http://fhir.health.gov.il/StructureDefinition/il-encounter-genetics-survey" ] } ] }, { "id": "Observation.effective[x]", "path": "Observation.effective[x]", "slicing": { "discriminator": [ { "type": "type", "path": "$this" } ], "ordered": false, "rules": "open" }, "min": 1, "type": [ { "code": "dateTime" } ] }, { "id": "Observation.effectiveDateTime", "path": "Observation.effectiveDateTime", "min": 1, "max": "1" }, { "id": "Observation.issued", "path": "Observation.issued", "min": 1 }, { "id": "Observation.performer", "path": "Observation.performer", "type": [ { "code": "Reference", "targetProfile": [ "http://fhir.health.gov.il/StructureDefinition/il-core-organization" ] } ] }, { "id": "Observation.value[x]", "path": "Observation.value[x]", "min": 1, "type": [ { "code": "CodeableConcept" } ], "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL4034-6" } }, { "id": "Observation.method", "path": "Observation.method", "min": 1, "binding": { "strength": "extensible", "valueSet": "http://loinc.org/vs/LL4048-6" } }, { "id": "Observation.method.coding", "path": "Observation.method.coding", "min": 1, "max": "1" }, { "id": "Observation.specimen", "path": "Observation.specimen", "min": 1, "type": [ { "code": "Reference", "targetProfile": [ "http://fhir.health.gov.il/StructureDefinition/il-specimen-genetics-survey" ] } ] }, { "id": "Observation.derivedFrom", "path": "Observation.derivedFrom", "min": 1, "max": "1", "type": [ { "code": "Reference", "targetProfile": [ "http://fhir.health.gov.il/StructureDefinition/questionnaire-response-genetics-survey" ] } ] }, { "id": "Observation.component", "path": "Observation.component", "slicing": { "discriminator": [ { "type": "value", "path": "code.coding.system" }, { "type": "value", "path": "code.coding.code" } ], "rules": "open" }, "mustSupport": false }, { "id": "Observation.component:associated-phenotype", "path": "Observation.component", "sliceName": "associated-phenotype", "short": "Associated phenotype", "definition": "Associated phenotype caused by this variant.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:associated-phenotype.code", "path": "Observation.component.code", "mustSupport": false }, { "id": "Observation.component:associated-phenotype.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:associated-phenotype.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81259-4" }, { "id": "Observation.component:associated-phenotype.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Associated phenotype" }, { "id": "Observation.component:associated-phenotype.value[x]", "path": "Observation.component.value[x]", "short": "Codes from OMIM", "definition": "Changes to sequence features caused by this variant.", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://www.omim.org", "description": "Associated Phenotype" } }, { "id": "Observation.component:associated-phenotype.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:variant-inheritance.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:variant-inheritance.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "79742-3" }, { "id": "Observation.component:variant-inheritance.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Inheritance pattern based on family history" }, { "id": "Observation.component:variant-inheritance.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "valueSet": "http://loinc.org/vs/LL3731-8", "description": "Variant Inheritance (Sequence Ontology)" } }, { "id": "Observation.component:variant-inheritance.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:dna-chg.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:dna-chg.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48004-6" }, { "id": "Observation.component:dna-chg.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "DNA change (c.HGVS)" }, { "id": "Observation.component:dna-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://fhir.health.gov.il/ValueSet/hgvs-nucleotide", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" } }, { "id": "Observation.component:dna-chg.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:dna-chg-type.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:dna-chg-type.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48019-4" }, { "id": "Observation.component:dna-chg-type.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "DNA change type" }, { "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, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "valueSet": "http://fhir.health.gov.il/ValueSet/dna-chg-type", "description": "DNA Change type values (Sequence Ontology)" } }, { "id": "Observation.component:dna-chg-type.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:functional-annotation.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://sequenceontology.org" }, { "id": "Observation.component:functional-annotation.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "SO:0001537" }, { "id": "Observation.component:functional-annotation.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "A sequence variant that changes one or more structural features." }, { "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, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "valueSet": "http://fhir.health.gov.il/ValueSet/functional-annotation", "description": "Functional Annotation (Sequence Ontology)" } }, { "id": "Observation.component:functional-annotation.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:variation-code.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:variation-code.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81252-9" }, { "id": "Observation.component:variation-code.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Variation Code" }, { "id": "Observation.component:variation-code.value[x]", "path": "Observation.component.value[x]", "comment": "In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code ", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "valueSet": "http://fhir.health.gov.il/ValueSet/clinvar", "description": "Binding not yet defined" } }, { "id": "Observation.component:variation-code.value[x].text", "path": "Observation.component.value[x].text", "comment": "In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code", "min": 1 }, { "id": "Observation.component:variation-code.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:genomic-dna-chg.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:genomic-dna-chg.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81290-9" }, { "id": "Observation.component:genomic-dna-chg.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "DNA Change - Genomic (gHGVS)" }, { "id": "Observation.component:genomic-dna-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" } }, { "id": "Observation.component:genomic-dna-chg.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:genomic-source-class.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:genomic-source-class.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48002-0" }, { "id": "Observation.component:genomic-source-class.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic source class [Type]" }, { "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, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "valueSet": "http://loinc.org/vs/LL378-1", "description": "Genomic source class values" } }, { "id": "Observation.component:genomic-source-class.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:amino-acid-chg.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:amino-acid-chg.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48005-3" }, { "id": "Observation.component:amino-acid-chg.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Amino acid change (pHGVS)" }, { "id": "Observation.component:amino-acid-chg.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" } }, { "id": "Observation.component:amino-acid-chg.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:amino-acid-chg-type.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:amino-acid-chg-type.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48006-1" }, { "id": "Observation.component:amino-acid-chg-type.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Amino acid change type" }, { "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, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL380-7", "description": "Amino acid change type values" } }, { "id": "Observation.component:amino-acid-chg-type.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:transcript-ref-seq.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:transcript-ref-seq.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "51958-7" }, { "id": "Observation.component:transcript-ref-seq.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Transcript reference sequence [ID]" }, { "id": "Observation.component:transcript-ref-seq.value[x]", "path": "Observation.component.value[x]", "comment": "In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" } }, { "id": "Observation.component:transcript-ref-seq.value[x].text", "path": "Observation.component.value[x].text", "comment": "In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code", "min": 1 }, { "id": "Observation.component:transcript-ref-seq.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:genomic-ref-seq.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:genomic-ref-seq.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "48013-7" }, { "id": "Observation.component:genomic-ref-seq.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic reference sequence [ID]" }, { "id": "Observation.component:genomic-ref-seq.value[x]", "path": "Observation.component.value[x]", "comment": "In valueCodebaleConcept.text field, MUST insert value from https://www.ncbi.nlm.nih.gov", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" } }, { "id": "Observation.component:genomic-ref-seq.value[x].text", "path": "Observation.component.value[x].text", "min": 1 }, { "id": "Observation.component:genomic-ref-seq.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:allelic-state.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:allelic-state.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "53034-5" }, { "id": "Observation.component:allelic-state.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Allelic state" }, { "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, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "valueSet": "http://loinc.org/vs/LL381-5", "description": "Allelic state type values" } }, { "id": "Observation.component:allelic-state.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:copy-number.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:copy-number.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "82155-3" }, { "id": "Observation.component:copy-number.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic structural variant copy number" }, { "id": "Observation.component:copy-number.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ] } ], "mustSupport": false }, { "id": "Observation.component:copy-number.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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 }, { "id": "Observation.component:ref-allele.code", "path": "Observation.component.code", "mustSupport": false }, { "id": "Observation.component:ref-allele.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:ref-allele.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "69547-8" }, { "id": "Observation.component:ref-allele.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic ref allele [ID]" }, { "id": "Observation.component:ref-allele.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "string" } ], "mustSupport": false }, { "id": "Observation.component:ref-allele.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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 }, { "id": "Observation.component:alt-allele.code", "path": "Observation.component.code", "mustSupport": false }, { "id": "Observation.component:alt-allele.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:alt-allele.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "69551-0" }, { "id": "Observation.component:alt-allele.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic alt allele [ID]" }, { "id": "Observation.component:alt-allele.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "string" } ], "mustSupport": false }, { "id": "Observation.component:alt-allele.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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.", "mustSupport": false }, { "id": "Observation.component:coordinate-system.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:coordinate-system.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "92822-6" }, { "id": "Observation.component:coordinate-system.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Genomic coordinate system [Type]" }, { "id": "Observation.component:coordinate-system.value[x]", "path": "Observation.component.value[x]", "short": "0-based interval | 0-based character | 1-based character", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "preferred", "valueSet": "http://loinc.org/vs/LL5323-2", "description": "Base coordinate systems start and end measurements for variants" } }, { "id": "Observation.component:coordinate-system.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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 }, { "id": "Observation.component:exact-start-end.code", "path": "Observation.component.code", "mustSupport": false }, { "id": "Observation.component:exact-start-end.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:exact-start-end.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "LP212296-0" }, { "id": "Observation.component:exact-start-end.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Variant exact start-end" }, { "id": "Observation.component:exact-start-end.value[x]", "path": "Observation.component.value[x]", "min": 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, "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.", "mustSupport": false }, { "id": "Observation.component:exact-start-end.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:variant-length.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:variant-length.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81300-6" }, { "id": "Observation.component:variant-length.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Structural variant [Length]" }, { "id": "Observation.component:variant-length.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ] } ], "mustSupport": false }, { "id": "Observation.component:variant-length.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:chromosome-copy-number-change-type.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:chromosome-copy-number-change-type.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "62378-5" }, { "id": "Observation.component:chromosome-copy-number-change-type.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Chromosome copy number change [Type]" }, { "id": "Observation.component:chromosome-copy-number-change-type.value[x]", "path": "Observation.component.value[x]", "short": "Copy number gain | Copy number loss", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL1041-4", "description": "Copy Number Change Types" } }, { "id": "Observation.component:chromosome-copy-number-change-type.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "id": "Observation.component:arrCGH-ratio", "path": "Observation.component", "sliceName": "arrCGH-ratio", "short": "Structural variant reported arrCGH [Ratio]", "definition": "arrCGH ratio", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:arrCGH-ratio.code", "path": "Observation.component.code", "mustSupport": false }, { "id": "Observation.component:arrCGH-ratio.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:arrCGH-ratio.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81299-0" }, { "id": "Observation.component:arrCGH-ratio.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Structural variant reported arrCGH [Ratio]" }, { "id": "Observation.component:arrCGH-ratio.value[x]", "path": "Observation.component.value[x]", "min": 1, "type": [ { "code": "Quantity", "profile": [ "http://hl7.org/fhir/StructureDefinition/SimpleQuantity" ] } ], "mustSupport": false }, { "id": "Observation.component:arrCGH-ratio.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } }, { "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", "mustSupport": false }, { "id": "Observation.component:complex-var-type.code.coding.system", "path": "Observation.component.code.coding.system", "min": 1, "fixedUri": "http://loinc.org" }, { "id": "Observation.component:complex-var-type.code.coding.code", "path": "Observation.component.code.coding.code", "min": 1, "fixedCode": "81263-6" }, { "id": "Observation.component:complex-var-type.code.coding.display", "path": "Observation.component.code.coding.display", "fixedString": "Complex variant type" }, { "id": "Observation.component:complex-var-type.value[x]", "path": "Observation.component.value[x]", "short": "Compound heterozygous | Double heterozygous | Haplotype | Hemizygous", "min": 1, "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL3999-1", "description": "Complex variant type" } }, { "id": "Observation.component:complex-var-type.interpretation", "path": "Observation.component.interpretation", "binding": { "strength": "required", "valueSet": "http://loinc.org/vs/LL604-0" } } ] } }