Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "Bundle",
"id" : "oncology-diagnostic",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d",
"resource" : {
"resourceType" : "Patient",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>identifier</b>: 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=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">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",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>identifier</b>: 4654765876</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",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>identifier</b>: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: available</p><p><b>subject</b>: <a href=\"urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><h3>Collections</h3><table class=\"grid\"><tr><td>-</td><td><b>Collector</b></td></tr><tr><td>*</td><td><a href=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">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",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>status</b>: final</p><p><b>code</b>: Tumor Mutational Burden <span style=\"background: LightGoldenRodYellow\">(Details )</span></p><p><b>subject</b>: <a href=\"urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: 25.0 somatic variants per megabase of sequenced DNA<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code v/Mb = 'v/Mb')</span></p><p><b>specimen</b>: <a href=\"urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d\">urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d</a></p></div>"
},
"status" : "final",
"code" : {
"text" : "Tumor Mutational Burden"
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"valueQuantity" : {
"value" : 25.0,
"unit" : "somatic variants per megabase of sequenced DNA",
"system" : "http://unitsofmeasure.org",
"code" : "v/Mb"
},
"specimen" : {
"reference" : "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"
}
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
"resource" : {
"resourceType" : "Observation",
"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 with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>subject</b>: <a href=\"urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA26398-0' = 'Sequencing', given as 'Sequencing'})</span></p><p><b>specimen</b>: <a href=\"urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d\">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\">(Details : {LOINC code '62374-4' = 'Human reference sequence assembly version', given as 'Human reference sequence assembly version'})</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA14029-5' = 'GRCh37', given as 'GRCh37'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81290-9' = 'Genomic DNA change (gHGVS)', given as 'Genomic DNA change (gHGVS)'})</span></p><p><b>value</b>: NC_000007.13:g.140453136A>T <span style=\"background: LightGoldenRodYellow\">(Details : {http://varnomen.hgvs.org code 'NC_000007.13:g.140453136A>T' = 'NC_000007.13:g.140453136A>T', given as '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\">(Details : {LOINC code '81252-9' = 'Discrete genetic variant', given as 'Discrete genetic variant'})</span></p><p><b>value</b>: Clinvar ID 13961 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/clinvar code '13961' = '13961', given as 'Clinvar ID 13961'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48005-3' = 'Amino acid change (pHGVS)', given as 'Amino acid change (pHGVS)'})</span></p><p><b>value</b>: p.Val600Glu <span style=\"background: LightGoldenRodYellow\">(Details : {http://varnomen.hgvs.org code 'p.Val600Glu' = 'p.Val600Glu', given as 'p.Val600Glu'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48006-1' = 'Amino acid change [Type]', given as 'Amino acid change type'})</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6698-0' = 'Missense', given as 'Missense'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: BRAF <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code 'HGNC:1097' = 'HGNC:1097', given as 'BRAF'})</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
},
"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"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA14029-5",
"display" : "GRCh37"
}
]
}
},
{
"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"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"code" : "13961",
"display" : "Clinvar ID 13961"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3",
"display" : "Amino acid change (pHGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "p.Val600Glu",
"display" : "p.Val600Glu"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48006-1",
"display" : "Amino acid change type"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6698-0",
"display" : "Missense"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "HGNC:1097",
"display" : "BRAF"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524",
"resource" : {
"resourceType" : "Observation",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/somatic-diagnostic"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: somatic-diagnostic <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'somatic-diagnostic' = 'somatic-diagnostic)</span></p><p><b>subject</b>: <a href=\"urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: Supportive <span style=\"background: LightGoldenRodYellow\">(Details )</span></p><p><b>method</b>: Computational analysis <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA26811-2' = 'Computational analysis', given as 'Computational analysis'})</span></p><p><b>specimen</b>: <a href=\"urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d\">urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d</a></p><p><b>derivedFrom</b>: <a href=\"urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d\">urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Level of Evidence <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '93044-6' = 'Level of evidence', given as 'Level of Evidence'})</span></p><p><b>value</b>: AMP/ASCO/CAP guidelines - Level A <span style=\"background: LightGoldenRodYellow\">(Details )</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: associated-cancer <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'associated-cancer' = 'associated-cancer)</span></p><p><b>value</b>: melanoma <span style=\"background: LightGoldenRodYellow\">(Details )</span></p></blockquote></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/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"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "somatic-diagnostic"
}
]
},
"subject" : {
"reference" : "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"
},
"performer" : [
{
"reference" : "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"
}
],
"valueCodeableConcept" : {
"text" : "Supportive"
},
"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" : "93044-6",
"display" : "Level of Evidence"
}
]
},
"valueCodeableConcept" : {
"text" : "AMP/ASCO/CAP guidelines - Level A"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "associated-cancer"
}
]
},
"valueCodeableConcept" : {
"text" : "melanoma"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5",
"resource" : {
"resourceType" : "DiagnosticReport",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel', given as 'Master HL7 genetic variant reporting panel'})</span></p><p><b>subject</b>: <a href=\"urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href=\"urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>specimen</b>: <a href=\"urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d\">urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d</a></p><p><b>result</b>: </p><ul><li><a href=\"urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d\">BRAF V600E mutation observed</a></li><li><a href=\"urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524\">melanoma implicated</a></li></ul></div>"
},
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9",
"display" : "Master HL7 genetic variant reporting panel"
}
],
"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" : "BRAF V600E mutation observed"
},
{
"reference" : "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524",
"display" : "melanoma implicated"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
}
]
}
IG © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
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