Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

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

: somaticReport - TTL Representation

Raw ttl | Download


@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:DiagnosticReport ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "somaticReport"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report>     ] )
  ] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport somaticReport</b></p><a name=\"somaticReport\"> </a><a name=\"hcsomaticReport\"> </a><a name=\"somaticReport-en-US\"> </a><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>When For</td><td>2023-02-02</td></tr><tr><td>Performers</td><td> <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </a> <a href=\"Organization-performingOrganization.html\">Organization My Test Pathology Laboratories</a></td></tr><tr><td>Identifier</td><td> Accession ID/23-0000345</td></tr></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Note</b></td><td><b>When For</b></td><td><b>Reported</b></td></tr><tr><td><a href=\"Observation-NOTCH1-uncertain-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-uncertain-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NOTCH1-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-therapuTrial.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-therapuDrug.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-therapuDrug1.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-therapuDrug2.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-TMB-therapuDrug.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NOTCH1-uncertain-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-uncertain-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-TMBExample.html\"><span title=\"Codes:{http://loinc.org 94076-7}\">Mutations/Megabase [# Ratio] in Tumor</span></a></td><td>29.8</td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSIExample.html\"><span title=\"Codes:{http://loinc.org 81695-9}\">Microsatellite instability [Interpretation] in Cancer specimen Qualitative</span></a></td><td><span title=\"Codes:{http://loinc.org LA26203-2}\">MSI-H</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-PDL1Example.html\"><span title=\"Codes:{http://loinc.org 85147-7}\">PD-L1 by clone 22C3 in Tissue by Immune stain Report</span></a></td><td><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></td><td>Final</td><td>5% tumor proportion score</td><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-HLA-A-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*24:02}\">HLA-A*24:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-A-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*02:06}\">HLA-A*02:06</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-B-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}\">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-B-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}\">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-C-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*03:03}\">HLA-C*03:03</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-C-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*15:02}\">HLA-C*15:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr></table><p>Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications.</p><p><b>Coded Conclusions:</b></p><ul><li><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></li></ul></div>"
  ] ; # 
  fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Procedure/somaticStudy" ] ;
fhir:display [ fhir:v "somaticStudy" ]     ]
  ] ) ; # 
  fhir:identifier ( [
fhir:type [
      ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0203"^^xsd:anyURI ] ;
fhir:code [ fhir:v "ACSN" ] ;
fhir:display [ fhir:v "Accession ID" ]       ] )     ] ;
fhir:value [ fhir:v "23-0000345" ]
  ] ) ; # 
  fhir:basedOn ( [
fhir:reference [ fhir:v "ServiceRequest/somaticServiceRequest" ]
  ] ) ; # 
  fhir:status [ fhir:v "final"] ; # 
  fhir:category ( [
    ( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ] ;
fhir:display [ fhir:v "Genetics" ]     ] )
  ] ) ; # 
  fhir:code [
    ( fhir:coding [
a loinc:51969-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51969-4" ] ;
fhir:display [ fhir:v "Genetic analysis report" ]     ] )
  ] ; # 
  fhir:effective [ fhir:v "2023-02-02"^^xsd:date] ; # 
  fhir:performer ( [
fhir:reference [ fhir:v "Practitioner/pathologistPractitioner" ]
  ] [
fhir:reference [ fhir:v "Organization/performingOrganization" ]
  ] ) ; # 
  fhir:resultsInterpreter ( [
fhir:reference [ fhir:v "Practitioner/supervisorPractitioner" ]
  ] [
fhir:reference [ fhir:v "Organization/performingOrganization" ]
  ] ) ; # 
  fhir:result ( [
fhir:reference [ fhir:v "Observation/NOTCH1-uncertain-var" ]
  ] [
fhir:reference [ fhir:v "Observation/ZFHX3-uncertain-var" ]
  ] [
fhir:reference [ fhir:v "Observation/MSH2-del-var" ]
  ] [
fhir:reference [ fhir:v "Observation/NTHL1-snv-var" ]
  ] [
fhir:reference [ fhir:v "Observation/STAG2-insertion-var" ]
  ] [
fhir:reference [ fhir:v "Observation/ATR-insertion-var" ]
  ] [
fhir:reference [ fhir:v "Observation/EGFR-L858R-var" ]
  ] [
fhir:reference [ fhir:v "Observation/ROS1-Fusion-var" ]
  ] [
fhir:reference [ fhir:v "Observation/NOTCH1-significance" ]
  ] [
fhir:reference [ fhir:v "Observation/ZFHX3-significance" ]
  ] [
fhir:reference [ fhir:v "Observation/MSH2-del-disease" ]
  ] [
fhir:reference [ fhir:v "Observation/NTHL1-snv-disease" ]
  ] [
fhir:reference [ fhir:v "Observation/STAG2-insertion-significance" ]
  ] [
fhir:reference [ fhir:v "Observation/ATR-insertion-significance" ]
  ] [
fhir:reference [ fhir:v "Observation/EGFR-L858R-significance" ]
  ] [
fhir:reference [ fhir:v "Observation/ROS1-Fusion-disease" ]
  ] [
fhir:reference [ fhir:v "Observation/ROS1-Fusion-therapuTrial" ]
  ] [
fhir:reference [ fhir:v "Observation/ROS1-Fusion-therapuDrug" ]
  ] [
fhir:reference [ fhir:v "Observation/EGFR-L858R-therapuDrug1" ]
  ] [
fhir:reference [ fhir:v "Observation/EGFR-L858R-therapuDrug2" ]
  ] [
fhir:reference [ fhir:v "Observation/TMB-therapuDrug" ]
  ] [
fhir:reference [ fhir:v "Observation/NOTCH1-uncertain-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/ZFHX3-uncertain-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/MSH2-del-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/NTHL1-snv-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/STAG2-insertion-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/ATR-insertion-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/EGFR-L858R-molc" ]
  ] [
fhir:reference [ fhir:v "Observation/ROS1-Fusion" ]
  ] [
fhir:reference [ fhir:v "Observation/TMBExample" ]
  ] [
fhir:reference [ fhir:v "Observation/MSIExample" ]
  ] [
fhir:reference [ fhir:v "Observation/PDL1Example" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-A-haplotype1" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-A-haplotype2" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-B-haplotype1" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-B-haplotype2" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-C-haplotype1" ]
  ] [
fhir:reference [ fhir:v "Observation/HLA-C-haplotype2" ]
  ] ) ; # 
  fhir:conclusion [ fhir:v "Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications."] ; # 
  fhir:conclusionCode ( [
    ( fhir:coding [
a loinc:LA6576-8 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6576-8" ] ;
fhir:display [ fhir:v "Positive" ]     ] )
  ] ) . #