Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: PGxGenomicReportEMERGE - 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:DiagnosticReport ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "PGxGenomicReportEMERGE"] ; # 
  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\"><h2><span title=\"Codes: {http://loinc.org 51969-4}, {http://example.org/hgsc.bcm.edu/lab-test-codes/ emerge-seq-ngs-pnl}\">Genetic analysis report</span> (<span title=\"Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>Subject</td><td><b>Adam B. Everyman </b> male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: USUAL))</td></tr><tr><td>When For</td><td>2020-01-01 00:00:00-0500</td></tr><tr><td>Reported</td><td>2020-01-01 00:00:00-0500</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>Note</b></td><td><b>When For</b></td></tr><tr><td><a href=\"Observation-OverallInterpExample2.html\"><span title=\"Codes: {http://loinc.org 51968-6}\">Discrete variation analysis overall interpretation</span></a></td><td><span title=\"Codes: {http://loinc.org LA6576-8}\">Positive</span></td><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp01.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp02.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp03.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp04.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp05.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-TxImp06.html\"><span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-geno-1001.html\"><span title=\"Codes: {http://loinc.org 84413-4}\">Genotype display name</span></a></td><td><span title=\"Codes: {http://www.ncbi.nlm.nih.gov/clinvar 638797}\">CYP2C19*2/*2</span></td><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-geno-1003.html\"><span title=\"Codes: {http://loinc.org 84413-4}\">Genotype display name</span></a></td><td><span title=\"Codes: \">VKORC1 rs9923231 C/T</span></td><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-geno-1002.html\"><span title=\"Codes: {http://loinc.org 84413-4}\">Genotype display name</span></a></td><td><span title=\"Codes: \">CYP2C9*1/*1</span></td><td/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1011.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/><td>2020-01-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1012.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1013.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1014.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1015.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1016.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1017.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1018.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/><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1019.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1020.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr><tr><td><a href=\"Observation-Pgx-var-1021.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr></table></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/PGXGenomicStudy" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Task/PGxRecEx01" ] ;
fhir:display [ fhir:v "No clopidogrel" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Task/PGxRecEx02" ] ;
fhir:display [ fhir:v "No voriconazole" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Task/PGxRecEx03" ] ;
fhir:display [ fhir:v "50% citalopram" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Task/PGxRecEx04" ] ;
fhir:display [ fhir:v "50% escitalopram" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Task/PGxRecEx04" ] ;
fhir:display [ fhir:v "50% amitriptyline" ]     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note"^^xsd:anyURI ] ;
fhir:value [
a fhir:Annotation ;
      ( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code"^^xsd:anyURI ] ;
fhir:value [
a fhir:CodeableConcept ;
          ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "test-disclaimer" ]           ] )         ]       ] ) ;
fhir:text [ fhir:v "This test was developed and its performance determined by this laboratory. It has not been cleared or approved by U.S. Food and Drug Administration.\nSince FDA Approval is not required for clinical use of this test, this laboratory has established and validated the test's accuracy and precision,\npursuant to the requirement of CLIA '88. This laboratory is licensed and/or accredited under CLIA and CAP (CAP# xxxxxxx / CLIA# xxxxxxxxxx)." ]     ]
  ] ) ; # 
  fhir:basedOn ( [
fhir:reference [ fhir:v "ServiceRequest/eMERGEServiceRequest" ]
  ] ) ; # 
  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:code [
    ( fhir:coding [
a loinc:51969-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51969-4" ]     ] [
fhir:system [ fhir:v "http://example.org/hgsc.bcm.edu/lab-test-codes/"^^xsd:anyURI ] ;
fhir:code [ fhir:v "emerge-seq-ngs-pnl" ]     ] )
  ] ; # 
  fhir:subject [
fhir:reference [ fhir:v "Patient/CGPatientExample01" ]
  ] ; # 
  fhir:effective [ fhir:v "2020-01-01T00:00:00-05:00"^^xsd:dateTime] ; # 
  fhir:issued [ fhir:v "2020-01-01T00:00:00-05:00"^^xsd:dateTime] ; # 
  fhir:performer ( [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]
  ] ) ; # 
  fhir:result ( [
fhir:reference [ fhir:v "Observation/OverallInterpExample2" ] ;
fhir:display [ fhir:v "gene-drug interactions found." ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp01" ] ;
fhir:display [ fhir:v "clopidogrel, poor metabolizer" ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp02" ] ;
fhir:display [ fhir:v "voriconazole, poor metabolizer" ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp03" ] ;
fhir:display [ fhir:v "citalopram, poor metabolizer" ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp04" ] ;
fhir:display [ fhir:v "escitalopram, poor metabolizer" ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp05" ] ;
fhir:display [ fhir:v "amitriptyline, poor metabolizer" ]
  ] [
fhir:reference [ fhir:v "Observation/TxImp06" ] ;
fhir:display [ fhir:v "medium sensitivity to warfarin" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-geno-1001" ] ;
fhir:display [ fhir:v "CYP2C19*2/*2" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-geno-1003" ] ;
fhir:display [ fhir:v "VKORC1 rs9923231 C/T" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-geno-1002" ] ;
fhir:display [ fhir:v "CYP2C9*1/*1" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1011" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96521657C=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1012" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96522463A=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1013" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96535173T=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1014" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96535210G=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1015" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96540410G>A" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1016" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96541616G=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1017" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96541756T=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1018" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C19):g.96612495C=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1019" ] ;
fhir:display [ fhir:v "NC_000016.9(VKORC1):g.31096368C>T" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1020" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C9):g.96702047C=" ]
  ] [
fhir:reference [ fhir:v "Observation/Pgx-var-1021" ] ;
fhir:display [ fhir:v "NC_000010.10(CYP2C9):g.96741053A=" ]
  ] ) . #