Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
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
@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:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "bundle-oncology-diagnostic"] ; # fhir:type [ fhir:v "transaction"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Patient"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Practitioner"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Specimen"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "DiagnosticReport"^^xsd:anyURI ] ] ] ) . # <urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d> a fhir:Patient ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-1"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Patient</b><a name=\"Inline-Instance-for-oncology-diagnostic-1\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Patient "Inline-Instance-for-oncology-diagnostic-1" </p></div><p><b>identifier</b>: id: 1007</p><p><b>name</b>: Carrot John Mr </p><p><b>gender</b>: male</p><p><b>birthDate</b>: 1962-12-31</p><p><b>generalPractitioner</b>: <a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "1007" ] ] ) ; # fhir:name ( [ ( fhir:given [ fhir:v "Carrot" ] [ fhir:v "John" ] [ fhir:v "Mr" ] ) ] ) ; # fhir:gender [ fhir:v "male"] ; # fhir:birthDate [ fhir:v "1962-12-31"^^xsd:date] ; # fhir:generalPractitioner ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) . # <urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef> a fhir:Practitioner ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-2"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Practitioner</b><a name=\"Inline-Instance-for-oncology-diagnostic-2\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Practitioner "Inline-Instance-for-oncology-diagnostic-2" </p></div><p><b>identifier</b>: id: 4654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "4654765876" ] ] ) ; # fhir:name ( [ ( fhir:given [ fhir:v "Akerman" ] [ fhir:v "Philip" ] [ fhir:v "Prof" ] ) ] ) ; # fhir:address ( [ fhir:city [ fhir:v "Castro Valley" ] ; fhir:state [ fhir:v "CA" ] ] ) . # <urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d> a fhir:Specimen ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-3"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Specimen</b><a name=\"Inline-Instance-for-oncology-diagnostic-3\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Specimen "Inline-Instance-for-oncology-diagnostic-3" </p></div><p><b>identifier</b>: id: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: available</p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-diagnostic-1\">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><h3>Collections</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Collector</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></td></tr></table></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "076e1948-2217-11e9-94d8-12e241dc1f66" ] ] ) ; # fhir:status [ fhir:v "available"] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:collection [ fhir:collector [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ] . # <urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-4"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"Inline-Instance-for-oncology-diagnostic-4\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "Inline-Instance-for-oncology-diagnostic-4" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-molecular-biomarker.html\">Molecular Biomarker</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Mutations/Megabase [# Ratio] in Tumor <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#94076-7)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-diagnostic-1\">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>value</b>: 25 Mutations/Megabase<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1/1000000 = '1/1000000')</span></p><p><b>specimen</b>: <a href=\"#Specimen_Inline-Instance-for-oncology-diagnostic-3\">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td>A characterization of a given biomarker observation. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#biomarker-category)</span></td><td>molecular sequence adjacent category <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-molecular-biomarker-ontology-cs.html\">Molecular Biomarker Ontology Codes</a>#molgen)</span></td></tr></table></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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "biomarker-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:94076-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "94076-7" ] ; fhir:display [ fhir:v "Mutations/Megabase [# Ratio] in Tumor" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "25"^^xsd:decimal ] ; fhir:unit [ fhir:v "Mutations/Megabase" ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1/1000000" ] ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # 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 "biomarker-category" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "molgen" ] ; fhir:display [ fhir:v "molecular sequence adjacent category" ] ] ) ] ] ) . # <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-5"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"Inline-Instance-for-oncology-diagnostic-5\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "Inline-Instance-for-oncology-diagnostic-5" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-diagnostic-1\">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26398-0)</span></p><p><b>specimen</b>: <a href=\"#Specimen_Inline-Instance-for-oncology-diagnostic-3\">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000007.13:g.140453136A>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NC_000007.13:g.140453136A>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: Clinvar ID 13961 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-ClinVarV.html\">ClinVar Variant ID</a>#13961)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_004324.2:p.Val600Glu <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NP_004324.2:p.Val600Glu)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: BRAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:1097)</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 "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # 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:method [ ( fhir:coding [ a loinc:LA26398-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26398-0" ] ; fhir:display [ fhir:v "Sequencing" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:62374-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "62374-4" ] ; fhir:display [ fhir:v "Human reference sequence assembly version" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA14029-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA14029-5" ] ; fhir:display [ fhir:v "GRCh37" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81290-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81290-9" ] ; fhir:display [ fhir:v "Genomic DNA change (gHGVS)" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NC_000007.13:g.140453136A>T" ] ; fhir:display [ fhir:v "NC_000007.13:g.140453136A>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: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 "13961" ] ; fhir:display [ fhir:v "Clinvar ID 13961" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ; fhir:display [ fhir:v "Amino acid change (pHGVS)" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_004324.2:p.Val600Glu" ] ; fhir:display [ fhir:v "NP_004324.2:p.Val600Glu" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:1097" ] ; fhir:display [ fhir:v "BRAF" ] ] ) ] ] ) . # <urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-6"] ; # 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 "extensions" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"Inline-Instance-for-oncology-diagnostic-6\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "Inline-Instance-for-oncology-diagnostic-6" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic Implication</a></p></div><p><b>Related Artifact</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-diagnostic-1\">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>method</b>: Computational analysis <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26811-2)</span></p><p><b>specimen</b>: <a href=\"#Specimen_Inline-Instance-for-oncology-diagnostic-3\">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_Inline-Instance-for-oncology-diagnostic-5\">See above (urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Level of Evidence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#93044-6)</span></p><p><b>value</b>: Very strong evidence pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30200-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: melanoma <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote></div>" ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact"^^xsd:anyURI ] ; fhir:value [ a fhir:RelatedArtifact ; fhir:type [ fhir:v "justification" ] ; fhir:display [ fhir:v "https://pmkb.weill.cornell.edu/therapies/103" ] ] ] ) ; # 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:display [ fhir:v "Diagnostic Implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:method [ ( fhir:coding [ a loinc:LA26811-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26811-2" ] ; fhir:display [ fhir:v "Computational analysis" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ] ] ) ; # 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:display [ fhir:v "Genetic variation clinical significance [Imp]" ] ] ) ] ; 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:93044-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "93044-6" ] ; fhir:display [ fhir:v "Level of Evidence" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA30200-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA30200-2" ] ; fhir:display [ fhir:v "Very strong evidence 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:text [ fhir:v "melanoma" ] ] ] ) . # <urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> a fhir:DiagnosticReport ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-7"] ; # 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><b>Generated Narrative: DiagnosticReport</b><a name=\"Inline-Instance-for-oncology-diagnostic-7\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource DiagnosticReport "Inline-Instance-for-oncology-diagnostic-7" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-report.html\">Genomic Report</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-diagnostic-1\">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"#Practitioner_Inline-Instance-for-oncology-diagnostic-2\">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>specimen</b>: <a href=\"#Specimen_Inline-Instance-for-oncology-diagnostic-3\">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_Inline-Instance-for-oncology-diagnostic-5\">See above (urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d: BRAF V600E mutation observed)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-diagnostic-6\">See above (urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524: melanoma implicated)</a></li></ul></div>" ] ; # 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:text [ fhir:v "Genetic analysis report" ] ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:specimen ( [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ] ; fhir:display [ fhir:v "BRAF V600E mutation observed" ] ] [ fhir:reference [ fhir:v "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524" ] ; fhir:display [ fhir:v "melanoma implicated" ] ] ) . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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