Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
: RepeatExpansion - TTL Representation
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@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:Observation ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "RepeatExpansion"] ; #
fhir:meta [
( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] )
] ; #
fhir:text [
fhir:status [ fhir:v "extensions" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation RepeatExpansion</b></p><a name=\"RepeatExpansion\"> </a><a name=\"hcRepeatExpansion\"> </a><a name=\"RepeatExpansion-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:8565}\">PABPN1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">chr14</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004643.4}\">NM_004643.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_004643.3:c.3GGC[14]}\">NM_004643.3:c.3GGC[14]</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/clinvar 503634}\">NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 11</p></blockquote></div>"
] ; #
fhir:status [ fhir:v "final"] ; #
fhir:category ( [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ] ] )
] [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ] ] )
] ) ; #
fhir:code [
( fhir:coding [
a loinc:69548-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69548-6" ] ;
fhir:display [ fhir:v "Genetic variant assessment" ] ] )
] ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/ExamplePatient" ]
] ; #
fhir:effective [ fhir:v "2023-06-01"^^xsd:date] ; #
fhir:performer ( [
fhir:reference [ fhir:v "Organization/ExampleLab" ]
] ) ; #
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA9633-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA9633-4" ] ;
fhir:display [ fhir:v "Present" ] ] )
] ; #
fhir:component ( [
fhir:code [
( fhir:coding [
a loinc:48018-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48018-6" ] ;
fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "HGNC:8565" ] ;
fhir:display [ fhir:v "PABPN1" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48001-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48001-2" ] ;
fhir:display [ fhir:v "Cytogenetic (chromosome) location" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
fhir:text [ fhir:v "chr14" ] ]
] [
fhir:code [
( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ] ;
fhir:display [ fhir:v "Transcript reference sequence [ID]" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_004643.4" ] ;
fhir:display [ fhir:v "NM_004643.4" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48004-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48004-6" ] ;
fhir:display [ fhir:v "DNA change (c.HGVS)" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_004643.3:c.3GGC[14]" ] ;
fhir:display [ fhir:v "NM_004643.3:c.3GGC[14]" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:81254-5 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81254-5" ] ;
fhir:display [ fhir:v "Genomic allele start-end" ] ] ) ] ;
fhir:value [
a fhir:Range ;
fhir:low [
fhir:value [ fhir:v "3"^^xsd:decimal ] ] ]
] [
fhir:code [
( fhir:coding [
a loinc:81252-9 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81252-9" ] ;
fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ;
fhir:code [ fhir:v "503634" ] ;
fhir:display [ fhir:v "NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)" ] ] ) ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "1"^^xsd:positiveInteger ] ] ) ;
fhir:code [
( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "repeat-motif" ] ;
fhir:display [ fhir:v "Repeat Expansion Motif" ] ] ) ] ;
fhir:value [ fhir:v "GGC" ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "1"^^xsd:positiveInteger ] ] ) ;
fhir:code [
( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "repeat-number" ] ;
fhir:display [ fhir:v "Number of Repeat Expansions" ] ] ) ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "11"^^xsd:decimal ] ]
] ) . #
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