Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
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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🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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"code" : "LA30200-2",
"display" : "Very strong evidence pathogenic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"text" : "Polycythemia vera (PV)"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"text" : "AT9283"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncologyexamples-r4-11",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncologyexamples-r4-11\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-11</b></p><a name=\"Inline-Instance-for-oncologyexamples-r4-11\"> </a><a name=\"hcInline-Instance-for-oncologyexamples-r4-11\"> </a><a name=\"Inline-Instance-for-oncologyexamples-r4-11-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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-04-05</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://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 LA6677-4}\">Responsive</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:\">Polycythemia vera (PV)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed</span></p><p><b>value</b>: <span title=\"Codes:\">SNX-5422</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "therapeutic-implication",
"display" : "Therapeutic Implication"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2023-04-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26811-2",
"display" : "Computational analysis"
}
]
},
"specimen" : {
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
},
"derivedFrom" : [
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "therapeutic-implication"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6677-4",
"display" : "Responsive"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "93044-6",
"display" : "Level of Evidence"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA30200-2",
"display" : "Very strong evidence pathogenic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"text" : "Polycythemia vera (PV)"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"text" : "SNX-5422"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncologyexamples-r4-12",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncologyexamples-r4-12\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-12</b></p><a name=\"Inline-Instance-for-oncologyexamples-r4-12\"> </a><a name=\"hcInline-Instance-for-oncologyexamples-r4-12\"> </a><a name=\"Inline-Instance-for-oncologyexamples-r4-12-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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-04-05</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://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 LA6677-4}\">Responsive</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:\">Polycythemia vera (PV)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed</span></p><p><b>value</b>: <span title=\"Codes:\">TG02</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "therapeutic-implication",
"display" : "Therapeutic Implication"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2023-04-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26811-2",
"display" : "Computational analysis"
}
]
},
"specimen" : {
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
},
"derivedFrom" : [
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "therapeutic-implication"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6677-4",
"display" : "Responsive"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "93044-6",
"display" : "Level of Evidence"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA30200-2",
"display" : "Very strong evidence pathogenic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"text" : "Polycythemia vera (PV)"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"text" : "TG02"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6ecb6",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncologyexamples-r4-14",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncologyexamples-r4-14\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-14</b></p><a name=\"Inline-Instance-for-oncologyexamples-r4-14\"> </a><a name=\"hcInline-Instance-for-oncologyexamples-r4-14\"> </a><a name=\"Inline-Instance-for-oncologyexamples-r4-14-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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-04-05</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>derivedFrom</b>: <a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d\">Bundle: type = transaction</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Extension</b></td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td/><td><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs associated-therapy}\">Associated Therapy</span></td><td><span title=\"Codes:\">Ruxolitinib</span></td></tr></table><hr/><blockquote><p class=\"res-header-id\"><b>Generated Narrative: PlanDefinition #PlanDefRuxolitinib</b></p><a name=\"Inline-Instance-for-oncologyexamples-r4-14/PlanDefRuxolitinib\"> </a><a name=\"hcInline-Instance-for-oncologyexamples-r4-14/PlanDefRuxolitinib\"> </a><a name=\"Inline-Instance-for-oncologyexamples-r4-14/PlanDefRuxolitinib-en-US\"> </a><p><b>name</b>: RuxolitinibPlan</p><p><b>status</b>: Draft</p><p><b>description</b>: </p><div><p>This is not a fully defined resource, just here as a place holder to show how a PlanDefinition could be packaged.</p>\n</div></blockquote></div>"
},
"contained" : [
{
"resourceType" : "PlanDefinition",
"id" : "PlanDefRuxolitinib",
"name" : "RuxolitinibPlan",
"status" : "draft",
"description" : "This is not a fully defined resource, just here as a place holder to show how a PlanDefinition could be packaged."
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "therapeutic-implication",
"display" : "Therapeutic Implication"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2023-04-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"derivedFrom" : [
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"
}
],
"component" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapy-assessed-reference",
"valueReference" : {
"reference" : "#PlanDefRuxolitinib"
}
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "associated-therapy"
}
]
},
"valueCodeableConcept" : {
"text" : "Ruxolitinib"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "Inline-Instance-for-oncologyexamples-r4-13",
"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-oncologyexamples-r4-13\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncologyexamples-r4-13</b></p><a name=\"Inline-Instance-for-oncologyexamples-r4-13\"> </a><a name=\"hcInline-Instance-for-oncologyexamples-r4-13\"> </a><a name=\"Inline-Instance-for-oncologyexamples-r4-13-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>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><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></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"
},
"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" : "SNV analysis for JAK2 variant"
},
{
"reference" : "urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd",
"display" : "SNV analysis for KDR variant"
},
{
"reference" : "urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01",
"display" : "SNV analysis for ERBB4 variant"
},
{
"reference" : "urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f",
"display" : "TMB value analysis"
},
{
"reference" : "urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9",
"display" : "MSI status analysis"
},
{
"reference" : "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524",
"display" : "Therapy match result 1"
},
{
"reference" : "urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b",
"display" : "Therapy match result 2"
},
{
"reference" : "urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20",
"display" : "Therapy match result 3"
},
{
"reference" : "urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4",
"display" : "Therapy match result 4"
}
]
},
"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 2024-11-19
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