Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
@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 "MultipleRepeatExpansions"] ; #
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><b>Generated Narrative: Observation</b><a name=\"MultipleRepeatExpansions\"> </a><a name=\"hcMultipleRepeatExpansions\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "MultipleRepeatExpansions" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Patient/ExamplePatient</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization/ExampleLab</a> "Some lab"</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: FMR1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:3775)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48001-2)</span></p><p><b>value</b>: chrx <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_002024.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_002024.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10])</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: Repeat Expansion Motif <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-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>: Number of Repeat Expansions <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 10</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: Repeat Expansion Motif <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: Number of Repeat Expansions <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: Repeat Expansion Motif <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: Number of Repeat Expansions <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 9</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: Repeat Expansion Motif <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: Number of Repeat Expansions <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: Repeat Expansion Motif <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: Number of Repeat Expansions <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 10</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:3775" ] ;
fhir:display [ fhir:v "FMR1" ] ] ) ]
] [
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 "chrx" ] ]
] [
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_002024.5" ] ;
fhir:display [ fhir:v "NM_002024.5" ] ] ) ]
] [
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_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]" ] ;
fhir:display [ fhir:v "NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]" ] ] ) ]
] [
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: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 "10"^^xsd:decimal ] ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "2"^^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 "GGA" ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "2"^^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 "1"^^xsd:decimal ] ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "3"^^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 "3"^^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 "9"^^xsd:decimal ] ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "4"^^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 "GGA" ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "4"^^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 "1"^^xsd:decimal ] ]
] [
( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order"^^xsd:anyURI ] ;
fhir:value [ fhir:v "5"^^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 "5"^^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 "10"^^xsd:decimal ] ]
] ) . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change