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

: 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\"><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport PGxGenomicReportEMERGE</b></p><a name=\"PGxGenomicReportEMERGE\"> </a><a name=\"hcPGxGenomicReportEMERGE\"> </a><a name=\"hcPGxGenomicReportEMERGE-en-US\"> </a><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>No display for Patient </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><tr><td>Performer</td><td> <a href=\"Organization-ExampleOrg.html\">Organization some lab</a></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></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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</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>Final</td><td>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr></table><p>Based on the genotype result, this patient is predicted to have a CYP2C19 poor metabolizer phenotype. This genotype information can be used by patients and clinicians as part of the shared decision-making process for several drugs metabolized by CYP2C19 including clopidogrel, voriconazole, amitriptyline, citalopram and escitalopram.</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/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/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=" ]
  ] ) ; # 
  fhir:conclusion [ fhir:v "Based on the genotype result, this patient is predicted to have a CYP2C19 poor metabolizer phenotype. This genotype information can be used by patients and clinicians as part of the shared decision-making process for several drugs metabolized by CYP2C19 including clopidogrel, voriconazole, amitriptyline, citalopram and escitalopram."] ; # 
  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" ]     ] )
  ] ) . #