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
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"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Patient_Inline-Instance-for-oncology-diagnostic-1\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Patient Inline-Instance-for-oncology-diagnostic-1</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-1\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-1\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-1-en-US\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">Carrot John Mr Male, DoB: 1962-12-31 ( 1007)</p><hr/><table class=\"grid\"><tr><td style=\"background-color: #f3f5da\" title=\"Patient Links\">Links:</td><td colspan=\"3\"><ul><li>General Practitioner: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></li></ul></td></tr></table></div>"
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"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Specimen_Inline-Instance-for-oncology-diagnostic-3\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen Inline-Instance-for-oncology-diagnostic-3</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-3\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-3\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-3-en-US\"> </a><p><b>identifier</b>: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: Available</p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></td></tr></table></div>"
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"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
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"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncology-diagnostic-4\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-4</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-4\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-4\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-4-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}\">A characterization of a given biomarker observation.</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 94076-7}\">Mutations/Megabase [# Ratio] in Tumor</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>value</b>: 25 Mutations/Megabase<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1/1000000 = '1/1000000')</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">Bundle: type = transaction</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><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}\">A characterization of a given biomarker observation.</span></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs molgen}\">molecular sequence adjacent category</span></td></tr></table></div>"
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"component" : [
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{
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"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncology-diagnostic-5",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncology-diagnostic-5\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-5</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-5\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-5\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-5-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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</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_000007.13:g.140453136A>T}\">NC_000007.13:g.140453136A>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/clinvar 13961}\">Clinvar ID 13961</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_004324.2:p.Val600Glu}\">NP_004324.2:p.Val600Glu</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:1097}\">BRAF</span></p></blockquote></div>"
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{
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]
}
},
{
"code" : {
"coding" : [
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"display" : "Discrete genetic variant"
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{
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{
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"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncology-diagnostic-6",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
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},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncology-diagnostic-6\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-6</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-6\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-6\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-6-en-US\"> </a><p><b>Related artifact</b>: No display for RelatedArtifact (type: justification; display: https://pmkb.weill.cornell.edu/therapies/103)</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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26811-2}\">Computational analysis</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">Bundle: type = transaction</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d\">Bundle: type = transaction</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 93044-6}\">Level of Evidence</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30200-2}\">Very strong evidence 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:\">melanoma</span></p></blockquote></div>"
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}
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{
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]
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{
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},
{
"fullUrl" : "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "Inline-Instance-for-oncology-diagnostic-7",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_Inline-Instance-for-oncology-diagnostic-7\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-diagnostic-7</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-7\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-7\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-7-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>Not done yet</td></tr><tr><td>When For</td><td>2019-03-05</td></tr><tr><td>Performer</td><td> <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</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></table></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4"
}
],
"text" : "Genetic analysis report"
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2019-03-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"specimen" : [
{
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
}
],
"result" : [
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
"display" : "BRAF V600E mutation observed"
},
{
"reference" : "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524",
"display" : "melanoma implicated"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
}
]
}
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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