Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

## : EGFR-L858R-var - TTL Representation

Page standards status: Informative

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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 rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
    @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 "EGFR-L858R-var"] ; #
      fhir:meta [
        ( fhir:profile [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>     ] )
      ] ; #
      fhir:text [
    fhir:status [ fhir:v "generated" ] ;
    fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation EGFR-L858R-var</b></p><a name=\"EGFR-L858R-var\"> </a><a name=\"hcEGFR-L858R-var\"> </a><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\"/><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>: <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-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><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:\">EGFR L858R</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_005219.2:p.Leu858Arg}\">NP_005219.2:p.Leu858Arg</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</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_005228.4:c.2573T>G}\">NM_005228.4:c.2573T&gt;G</span></p></blockquote><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:3236}\">EGFR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000007.13:g.55259515T>G}\">NC_000007.13:g.55259515T&gt;G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 0.066 decimal</p></blockquote></div>"^^rdf:XMLLiteral ]
      ] ; #
      fhir:status [ fhir:v "final"] ; #
      fhir:category ( [
        ( fhir:coding [
    fhir:system [
    fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ;
    fhir:l <http://terminology.hl7.org/CodeSystem/observation-category>       ] ;
    fhir:code [ fhir:v "laboratory" ]     ] )
      ] [
        ( fhir:coding [
    fhir:system [
    fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ;
    fhir:l <http://terminology.hl7.org/CodeSystem/v2-0074>       ] ;
    fhir:code [ fhir:v "GE" ]     ] )
      ] ) ; #
      fhir:code [
        ( fhir:coding [
    a loinc:69548-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "69548-6" ]     ] )
      ] ; #
      fhir:subject [
    fhir:l fhir:Patient/somaticPatient ;
    fhir:reference [ fhir:v "Patient/somaticPatient" ]
      ] ; #
      fhir:effective [
    a fhir:DateTime ;
    fhir:v "2023-02-01"^^xsd:date
      ] ; #
      fhir:performer ( [
    fhir:l fhir:Practitioner/pathologistPractitioner ;
    fhir:reference [ fhir:v "Practitioner/pathologistPractitioner" ]
      ] ) ; #
      fhir:value [
    a fhir:CodeableConcept ;
        ( fhir:coding [
    a loinc:LA9633-4 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "LA9633-4" ] ;
    fhir:display [ fhir:v "Present" ]     ] )
      ] ; #
      fhir:method [
        ( fhir:coding [
    a loinc:LA26398-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "LA26398-0" ] ;
    fhir:display [ fhir:v "Sequencing" ]     ] )
      ] ; #
      fhir:component ( [
    fhir:code [
          ( fhir:coding [
    a loinc:81252-9 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81252-9" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
    fhir:text [ fhir:v "EGFR L858R" ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48005-3 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48005-3" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
    fhir:l <http://varnomen.hgvs.org>         ] ;
    fhir:code [ fhir:v "NP_005219.2:p.Leu858Arg" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48019-4 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48019-4" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
    fhir:l <http://www.sequenceontology.org>         ] ;
    fhir:code [ fhir:v "SO:0001483" ] ;
    fhir:display [ fhir:v "SNV" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48004-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48004-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
    fhir:l <http://varnomen.hgvs.org>         ] ;
    fhir:code [ fhir:v "NM_005228.4:c.2573T>G" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48018-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48018-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.genenames.org"^^xsd:anyURI ;
    fhir:l <http://www.genenames.org>         ] ;
    fhir:code [ fhir:v "HGNC:3236" ] ;
    fhir:display [ fhir:v "EGFR" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81290-9 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81290-9" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
    fhir:l <http://varnomen.hgvs.org>         ] ;
    fhir:code [ fhir:v "NC_000007.13:g.55259515T>G" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48002-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48002-0" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA6684-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA6684-0" ] ;
    fhir:display [ fhir:v "Somatic" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81258-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81258-6" ]       ] )     ] ;
    fhir:value [
    a fhir:Quantity ;
    fhir:value [ fhir:v 0.066 ] ;
    fhir:unit [ fhir:v "decimal" ] ;
    fhir:system [
    fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
    fhir:l <http://unitsofmeasure.org>       ]     ]
      ] ) . #