Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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 sct: <http://snomed.info/id/> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- a fhir:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "bundle-cgexample-withGrouping"] ; # fhir:type [ fhir:v "collection"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "http://example.org/fhir/DiagnosticReport/report-withGrouping"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/DiagnosticReport/report-withGrouping> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Patient/ExamplePatient"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Patient/ExamplePatient> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Specimen/ExampleSpecimen"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Specimen/ExampleSpecimen> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Organization/ExampleLab"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Organization/ExampleLab> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/ServiceRequest/ExampleServiceRequest"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/ServiceRequest/ExampleServiceRequest> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/discrete-variant-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/discrete-variant-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/dis-path-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/dis-path-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-variant-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-variant-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-dis-path-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-dis-path-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-component-D-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-component-D-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-component-E-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-component-E-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/pharmPanel-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/pharmPanel-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/genotype-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/genotype-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/metab-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/metab-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/efficacy-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/efficacy-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/highrisk-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/highrisk-1a> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Task/usage-1a"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Task/usage-1a> ) ] ) . # <http://example.org/fhir/DiagnosticReport/report-withGrouping> a fhir:DiagnosticReport ; fhir:id [ fhir:v "report-withGrouping"] ; # 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\"><a name=\"DiagnosticReport_report-withGrouping\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport report-withGrouping</b></p><a name=\"report-withGrouping\"> </a><a name=\"hcreport-withGrouping\"> </a><a name=\"report-withGrouping-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>Subject</td><td>Anonymous Patient (no stated gender), DoB Unknown</td></tr><tr><td>When For</td><td>2016</td></tr><tr><td>Reported</td><td>2016-09-06 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href=\"Organization-ExampleLab.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></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table><p><b>Coded Conclusions:</b></p><ul><li><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></li><li><span title=\"Codes:{http://snomed.info/sct 10828004}\">Positive</span></li></ul></div>" ] ; # fhir:basedOn ( [ fhir:reference [ fhir:v "ServiceRequest/ExampleServiceRequest" ] ] ) ; # 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:display [ fhir:v "Genetic analysis report" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "Observation/discrete-variant-1a" ] ] [ fhir:reference [ fhir:v "Observation/dis-path-1a" ] ] [ fhir:reference [ fhir:v "Observation/complex-variant-1a" ] ] [ fhir:reference [ fhir:v "Observation/complex-dis-path-1a" ] ] [ fhir:reference [ fhir:v "Observation/pharmPanel-1a" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-1a" ] ] [ fhir:reference [ fhir:v "Observation/genotype-1a" ] ] [ fhir:reference [ fhir:v "Observation/metab-1a" ] ] [ fhir:reference [ fhir:v "Observation/efficacy-1a" ] ] ) ; # 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" ] ] ) ] [ ( fhir:coding [ a sct:10828004 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ; fhir:code [ fhir:v "10828004" ] ; fhir:display [ fhir:v "Positive" ] ] ) ] ) ; # fhir:presentedForm ( [ fhir:contentType [ fhir:v "text/plain" ] ; fhir:data [ fhir:v "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"^^xsd:base64Binary ] ] ) . # <http://example.org/fhir/Patient/ExamplePatient> a fhir:Patient ; fhir:id [ fhir:v "ExamplePatient"] ; # fhir:text [ fhir:status [ fhir:v "additional" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>" ] . # <http://example.org/fhir/Specimen/ExampleSpecimen> a fhir:Specimen ; fhir:id [ fhir:v "ExampleSpecimen"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Specimen_ExampleSpecimen\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen ExampleSpecimen</b></p><a name=\"ExampleSpecimen\"> </a><a name=\"hcExampleSpecimen\"> </a><a name=\"ExampleSpecimen-en-US\"> </a><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>" ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] . # <http://example.org/fhir/Organization/ExampleLab> a fhir:Organization ; fhir:id [ fhir:v "ExampleLab"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_ExampleLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ExampleLab</b></p><a name=\"ExampleLab\"> </a><a name=\"hcExampleLab\"> </a><a name=\"ExampleLab-en-US\"> </a><p><b>name</b>: Some lab</p></div>" ] ; # fhir:name [ fhir:v "Some lab"] . # <http://example.org/fhir/ServiceRequest/ExampleServiceRequest> a fhir:ServiceRequest ; fhir:id [ fhir:v "ExampleServiceRequest"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_ExampleServiceRequest\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest ExampleServiceRequest</b></p><a name=\"ExampleServiceRequest\"> </a><a name=\"hcExampleServiceRequest\"> </a><a name=\"ExampleServiceRequest-en-US\"> </a><p><b>status</b>: Active</p><p><b>intent</b>: Original Order</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonCode</b>: <span title=\"Codes:\">Worried about family planning</span></p></div>" ] ; # fhir:status [ fhir:v "active"] ; # fhir:intent [ fhir:v "original-order"] ; # 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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonCode ( [ fhir:text [ fhir:v "Worried about family planning" ] ] ) . # <http://example.org/fhir/Observation/discrete-variant-1a> a fhir:Observation ; fhir:id [ fhir:v "discrete-variant-1a"] ; # 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 "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_discrete-variant-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation discrete-variant-1a</b></p><a name=\"discrete-variant-1a\"> </a><a name=\"hcdiscrete-variant-1a\"> </a><a name=\"discrete-variant-1a-en-US\"> </a><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-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></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:{http://www.ncbi.nlm.nih.gov/clinvar 30880}\">NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)</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:21497}\">ACAD9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_014049.4}\">NM_014049.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_017064.1}\">NG_017064.1</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_000003.11:g.128625063C>T}\">NC_000003.11:g.128625063C>T</span></p></blockquote><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:{http://www.ncbi.nlm.nih.gov/projects/SNP rs368949613}\">rs368949613</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_014049.4:c.1249C>T}\">NM_014049.4:c.1249C>T</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_054768.2:p.Arg417Cys}\">NP_054768.2:p.Arg417Cys</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://loinc.org LA6690-7}\">Substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 31731-31731</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic alt allele [ID]</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">3q21</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 LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</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>: 47 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code% = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 208 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82155-3}\">Genomic structural variant copy number</span></p><p><b>value</b>: 1 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81301-4}\">Structural variant outer start and end</span></p><p><b>value</b>: 13200589-15592000</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81302-2}\">Structural variant inner start and end</span></p><p><b>value</b>: 14184616-15581544</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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # 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:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:code [ fhir:v "30880" ] ; fhir:display [ fhir:v "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:21497" ] ; fhir:display [ fhir:v "ACAD9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; 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_014049.4" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48013-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48013-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG_017064.1" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81290-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81290-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NC_000003.11:g.128625063C>T" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/projects/SNP"^^xsd:anyURI ] ; fhir:code [ fhir:v "rs368949613" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_014049.4:c.1249C>T" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_054768.2:p.Arg417Cys" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48019-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48019-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6690-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6690-7" ] ; fhir:display [ fhir:v "Substitution" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ] ) ] ; fhir:value [ fhir:v "C" ] ] [ fhir:code [ ( fhir:coding [ a loinc:81254-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81254-5" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "31731"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "31731"^^xsd:decimal ] ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:48001-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48001-2" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; fhir:text [ fhir:v "3q21" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:48002-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48002-0" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:53034-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53034-5" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6706-1 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6706-1" ] ; fhir:display [ fhir:v "Heterozygous" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81258-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81258-6" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "47"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "%" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:82121-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "82121-5" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "208"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:82155-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "82155-3" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "1"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81301-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81301-4" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "13200589"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "15592000"^^xsd:decimal ] ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81302-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81302-2" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "14184616"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "15581544"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/Observation/dis-path-1a> a fhir:Observation ; fhir:id [ fhir:v "dis-path-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_dis-path-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation dis-path-1a</b></p><a name=\"dis-path-1a\"> </a><a name=\"hcdis-path-1a\"> </a><a name=\"dis-path-1a-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_discrete-variant-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6668-3}\">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81259-4}\">Associated phenotype</span></p><p><b>value</b>: <span title=\"Codes:{http://purl.obolibrary.org/obo/mondo.owl MONDO:0012624}\">acyl-CoA dehydrogenase 9 deficiency</span></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 [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "diagnostic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/discrete-variant-1a" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:53037-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53037-8" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6668-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6668-3" ] ; fhir:display [ fhir:v "Pathogenic" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81259-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81259-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://purl.obolibrary.org/obo/mondo.owl"^^xsd:anyURI ] ; fhir:code [ fhir:v "MONDO:0012624" ] ; fhir:display [ fhir:v "acyl-CoA dehydrogenase 9 deficiency" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-variant-1a> a fhir:Observation ; fhir:id [ fhir:v "complex-variant-1a"] ; # 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 "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_complex-variant-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-variant-1a</b></p><a name=\"complex-variant-1a\"> </a><a name=\"hccomplex-variant-1a\"> </a><a name=\"complex-variant-1a-en-US\"> </a><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-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_complex-component-D-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_complex-component-E-1a\">Bundle: type = collection</a></li></ul></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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # 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:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:hasMember ( [ fhir:reference [ fhir:v "Observation/complex-component-D-1a" ] ] [ fhir:reference [ fhir:v "Observation/complex-component-E-1a" ] ] ) . # <http://example.org/fhir/Observation/complex-dis-path-1a> a fhir:Observation ; fhir:id [ fhir:v "complex-dis-path-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_complex-dis-path-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-dis-path-1a</b></p><a name=\"complex-dis-path-1a\"> </a><a name=\"hccomplex-dis-path-1a\"> </a><a name=\"complex-dis-path-1a-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_complex-variant-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6668-3}\">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81259-4}\">Associated phenotype</span></p><p><b>value</b>: <span title=\"Codes:{http://snomed.info/sct 293498008}\">Debrisoquine adverse reaction (disorder)</span></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 [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "diagnostic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/complex-variant-1a" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:53037-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53037-8" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6668-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6668-3" ] ; fhir:display [ fhir:v "Pathogenic" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81259-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81259-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a sct:293498008 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ; fhir:code [ fhir:v "293498008" ] ; fhir:display [ fhir:v "Debrisoquine adverse reaction (disorder)" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-component-D-1a> a fhir:Observation ; fhir:id [ fhir:v "complex-component-D-1a"] ; # 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 "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_complex-component-D-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-component-D-1a</b></p><a name=\"complex-component-D-1a\"> </a><a name=\"hccomplex-component-D-1a\"> </a><a name=\"complex-component-D-1a-en-US\"> </a><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-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></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:{http://www.ncbi.nlm.nih.gov/clinvar 31934}\">NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000106.5}\">NM_000106.5</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_000106.5:c.886C>T}\">NM_000106.5:c.886C>T</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_000097.3:p.Arg296Cys}\">NP_000097.3:p.Arg296Cys</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://loinc.org LA6690-7}\">Substitution</span></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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # 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:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:code [ fhir:v "31934" ] ; fhir:display [ fhir:v "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; 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_000106.5" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5:c.886C>T" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_000097.3:p.Arg296Cys" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48019-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48019-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6690-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6690-7" ] ; fhir:display [ fhir:v "Substitution" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-component-E-1a> a fhir:Observation ; fhir:id [ fhir:v "complex-component-E-1a"] ; # 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 "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_complex-component-E-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-component-E-1a</b></p><a name=\"complex-component-E-1a\"> </a><a name=\"hccomplex-component-E-1a\"> </a><a name=\"complex-component-E-1a-en-US\"> </a><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-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></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:{http://www.ncbi.nlm.nih.gov/clinvar 38486}\">NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000106.5}\">NM_000106.5</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_000106.5:c.1457G>C}\">NM_000106.5:c.1457G>C</span></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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # 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:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:code [ fhir:v "38486" ] ; fhir:display [ fhir:v "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; 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_000106.5" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5:c.1457G>C" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/pharmPanel-1a> a fhir:Observation ; fhir:id [ fhir:v "pharmPanel-1a"] ; # fhir:text [ fhir:status [ fhir:v "extensions" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_pharmPanel-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation pharmPanel-1a</b></p><a name=\"pharmPanel-1a\"> </a><a name=\"hcpharmPanel-1a\"> </a><a name=\"pharmPanel-1a-en-US\"> </a><p><b>Recommended Action</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Task_usage-1a\">Bundle: type = collection</a></p><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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl C43359}\">Group</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_haplotype-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_metab-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_efficacy-1a\">Bundle: type = collection</a></li></ul></div>" ] ; # fhir:extension ( [ 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/usage-1a" ] ] ] ) ; # 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 [ fhir:system [ fhir:v "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"^^xsd:anyURI ] ; fhir:code [ fhir:v "C43359" ] ; fhir:display [ fhir:v "Group" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:hasMember ( [ fhir:reference [ fhir:v "Observation/haplotype-1a" ] ] [ fhir:reference [ fhir:v "Observation/genotype-1a" ] ] [ fhir:reference [ fhir:v "Observation/metab-1a" ] ] [ fhir:reference [ fhir:v "Observation/efficacy-1a" ] ] ) . # <http://example.org/fhir/Observation/haplotype-1a> a fhir:Observation ; fhir:id [ fhir:v "haplotype-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_haplotype-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-1a</b></p><a name=\"haplotype-1a\"> </a><a name=\"hchaplotype-1a\"> </a><a name=\"haplotype-1a-en-US\"> </a><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 84414-2}\">Haplotype name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla *2}\">*2</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_discrete-variant-1a\">Bundle: type = collection</a></p></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:84414-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84414-2" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ebi.ac.uk/ipd/imgt/hla"^^xsd:anyURI ] ; fhir:code [ fhir:v "*2" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/discrete-variant-1a" ] ] ) . # <http://example.org/fhir/Observation/genotype-1a> a fhir:Observation ; fhir:id [ fhir:v "genotype-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_genotype-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation genotype-1a</b></p><a name=\"genotype-1a\"> </a><a name=\"hcgenotype-1a\"> </a><a name=\"genotype-1a-en-US\"> </a><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 84413-4}\">Genotype display name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org CYP2C9*2*5"}\">CYP2C9 *2/*5</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_haplotype-1a\">Bundle: type = collection</a></p><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:2623}\">CYP2C9</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:23663}\">VKORC1</span></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:84413-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84413-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "CYP2C9*2*5\"" ] ; fhir:display [ fhir:v "CYP2C9 *2/*5" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/haplotype-1a" ] ] ) ; # 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:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:23663" ] ; fhir:display [ fhir:v "VKORC1" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/metab-1a> a fhir:Observation ; fhir:id [ fhir:v "metab-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_metab-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation metab-1a</b></p><a name=\"metab-1a\"> </a><a name=\"hcmetab-1a\"> </a><a name=\"metab-1a-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA25390-8}\">Rapid metabolizer</span></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 [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype-1a" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] [ 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 "therapeutic-implication" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA25390-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA25390-8" ] ; fhir:display [ fhir:v "Rapid metabolizer" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/efficacy-1a> a fhir:Observation ; fhir:id [ fhir:v "efficacy-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_efficacy-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation efficacy-1a</b></p><a name=\"efficacy-1a\"> </a><a name=\"hcefficacy-1a\"> </a><a name=\"efficacy-1a-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6676-6}\">Resistant</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</span></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 [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype-1a" ] ] ) ; # fhir:component ( [ 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 "therapeutic-implication" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6676-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6676-6" ] ; fhir:display [ fhir:v "Resistant" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/highrisk-1a> a fhir:Observation ; fhir:id [ fhir:v "highrisk-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_highrisk-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation highrisk-1a</b></p><a name=\"highrisk-1a\"> </a><a name=\"hchighrisk-1a\"> </a><a name=\"highrisk-1a-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA19542-2}\">Low risk</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</span></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 [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype-1a" ] ] ) ; # fhir:component ( [ 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 "therapeutic-implication" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA19542-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA19542-2" ] ; fhir:display [ fhir:v "Low risk" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] ) . # <http://example.org/fhir/Task/usage-1a> a fhir:Task ; fhir:id [ fhir:v "usage-1a"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Task_usage-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Task usage-1a</b></p><a name=\"usage-1a\"> </a><a name=\"hcusage-1a\"> </a><a name=\"usage-1a-en-US\"> </a><p><b>status</b>: Requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LA26423-6}\">May need higher dosage than usual.</span></p><p><b>focus</b>: <a href=\"MedicationStatement-MedicationStatementWarfarin.html\">MedicationStatement: status = unknown; medication[x] = Warfarin</a></p><p><b>for</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>requester</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>reasonReference</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_metab-1a\">Bundle: type = collection</a></p></div>" ] ; # fhir:status [ fhir:v "requested"] ; # fhir:intent [ fhir:v "proposal"] ; # fhir:code [ ( fhir:coding [ a loinc:LA26423-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26423-6" ] ; fhir:display [ fhir:v "Increase dose" ] ] ) ; fhir:text [ fhir:v "May need higher dosage than usual." ] ] ; # fhir:focus [ fhir:reference [ fhir:v "MedicationStatement/MedicationStatementWarfarin" ] ] ; # fhir:for [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:requester [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ; # fhir:reasonReference [ fhir:reference [ fhir:v "Observation/metab-1a" ] ] . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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