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
{
"resourceType" : "Bundle",
"id" : "bundle-oncology-diagnostic",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d",
"resource" : {
"resourceType" : "Patient",
"id" : "Inline-Instance-for-oncology-diagnostic-1",
"text" : {
"status" : "generated",
"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:\u00a01007</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>"
},
"identifier" : [
{
"value" : "1007"
}
],
"name" : [
{
"given" : [
"Carrot",
"John",
"Mr"
]
}
],
"gender" : "male",
"birthDate" : "1962-12-31",
"generalPractitioner" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
]
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef",
"resource" : {
"resourceType" : "Practitioner",
"id" : "Inline-Instance-for-oncology-diagnostic-2",
"text" : {
"status" : "generated",
"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:\u00a04654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>"
},
"identifier" : [
{
"value" : "4654765876"
}
],
"name" : [
{
"given" : [
"Akerman",
"Philip",
"Prof"
]
}
],
"address" : [
{
"city" : "Castro Valley",
"state" : "CA"
}
]
},
"request" : {
"method" : "POST",
"url" : "Practitioner"
}
},
{
"fullUrl" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d",
"resource" : {
"resourceType" : "Specimen",
"id" : "Inline-Instance-for-oncology-diagnostic-3",
"text" : {
"status" : "generated",
"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:\u00a0076e1948-2217-11e9-94d8-12e241dc1f66</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>"
},
"identifier" : [
{
"value" : "076e1948-2217-11e9-94d8-12e241dc1f66"
}
],
"status" : "available",
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"collection" : {
"collector" : {
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
}
},
"request" : {
"method" : "POST",
"url" : "Specimen"
}
},
{
"fullUrl" : "urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncology-diagnostic-4",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
]
},
"text" : {
"status" : "generated",
"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>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "biomarker-category"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "94076-7",
"display" : "Mutations/Megabase [# Ratio] in Tumor"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2019-03-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"valueQuantity" : {
"value" : 25,
"unit" : "Mutations/Megabase",
"system" : "http://unitsofmeasure.org",
"code" : "1/1000000"
},
"specimen" : {
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "biomarker-category"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs",
"code" : "molgen",
"display" : "molecular sequence adjacent category"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncology-diagnostic-5",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"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>"
},
"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://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2019-03-05",
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
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"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
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"specimen" : {
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "62374-4",
"display" : "Human reference sequence assembly version"
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]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA14029-5",
"display" : "GRCh37"
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]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81290-9",
"display" : "Genomic DNA change (gHGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NC_000007.13:g.140453136A>T",
"display" : "NC_000007.13:g.140453136A>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
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]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"code" : "13961",
"display" : "Clinvar ID 13961"
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]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3",
"display" : "Amino acid change (pHGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NP_004324.2:p.Val600Glu",
"display" : "NP_004324.2:p.Val600Glu"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:1097",
"display" : "BRAF"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-oncology-diagnostic-6",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
]
},
"text" : {
"status" : "extensions",
"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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact",
"valueRelatedArtifact" : {
"type" : "justification",
"display" : "https://pmkb.weill.cornell.edu/therapies/103"
}
}
],
"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" : "diagnostic-implication",
"display" : "Diagnostic Implication"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"effectiveDateTime" : "2019-03-05",
"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://loinc.org",
"code" : "53037-8",
"display" : "Genetic variation clinical significance [Imp]"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
}
},
{
"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" : "melanoma"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"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\"><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>"
},
"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-ballot based on FHIR 4.0.1. Generated 2023-12-18
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