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" : "HLAB1502-pgx-example",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "http://example.org/fhir/DiagnosticReport/pgx-report",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "pgx-report",
"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>id</b>: pgx-report</p><p><b>meta</b>: </p><p><b>basedOn</b>: ServiceRequest/pgx-request</p><p><b>status</b>: final</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel)</span></p><p><b>subject</b>: Patient/patient</p><p><b>effective</b>: Jan 1, 2016, 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>performer</b>: Organization/lab</p><p><b>result</b>: </p><ul><li>genetics impact for medication metabolism accessment</li><li>Observation/genotype-pgx-example</li></ul></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction",
"valueReference" : {
"reference" : "Task/med-usage-impact-task-pgx-example"
}
}
],
"basedOn" : [
{
"reference" : "ServiceRequest/pgx-request"
}
],
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"result" : [
{
"reference" : "Observation/medication-high-risk",
"display" : "genetics impact for high risk allele"
},
{
"reference" : "Observation/genotype-pgx-example"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
},
{
"fullUrl" : "http://example.org/fhir/Patient/patient",
"resource" : {
"resourceType" : "Patient",
"id" : "patient",
"text" : {
"status" : "additional",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>"
}
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "http://example.org/fhir/Specimen/specimen",
"resource" : {
"resourceType" : "Specimen",
"id" : "specimen",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"subject" : {
"reference" : "Patient/patient"
}
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "http://example.org/fhir/Organization/lab",
"resource" : {
"resourceType" : "Organization",
"id" : "lab",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"name" : "Some lab"
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "http://example.org/fhir/ServiceRequest/pgx-request",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "pgx-request",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: pgx-request</p><p><b>meta</b>: </p><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel)</span></p><p><b>subject</b>: <a href=\"Patient/patient\">Patient/patient</a></p><p><b>reasonCode</b>: Worried about family planning <span style=\"background: LightGoldenRodYellow\">(Details )</span></p></div>"
},
"status" : "active",
"intent" : "original-order",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"reasonCode" : [
{
"text" : "Worried about family planning"
}
]
},
"request" : {
"method" : "POST",
"url" : "ServiceRequest"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/medication-high-risk",
"resource" : {
"resourceType" : "Observation",
"id" : "medication-high-risk",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-high-risk"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: medication-high-risk</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 variation's effect on high-risk allele <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '83009-1' = 'Genetic variation's effect on high-risk allele', given as 'Genetic variation's effect on high-risk allele'})</span></p><p><b>value</b>: High risk <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA19541-4' = 'High risk', given as 'High risk'})</span></p><p><b>derivedFrom</b>: <a href=\"Observation/genotype-pgx-example\">Observation/genotype-pgx-example</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'})</span></p><p><b>value</b>: Carbamazepine <span style=\"background: LightGoldenRodYellow\">(Details : {RxNorm code '2002' = 'Carbamazepine', given as 'Carbamazepine'})</span></p></blockquote><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>: Very strong evidence pathogenic <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA30200-2' = 'Very strong evidence pathogenic', given as 'Very strong evidence pathogenic'})</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" : "83009-1",
"display" : "Genetic variation's effect on high-risk allele"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA19541-4",
"display" : "High risk"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/genotype-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "2002",
"display" : "Carbamazepine"
}
]
}
},
{
"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"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/genotype-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "genotype-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: genotype-pgx-example</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>: genotype display name <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '84413-4' = 'Genotype display name', given as 'genotype display name'})</span></p><p><b>effective</b>: Jan 1, 2018, 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>value</b>: HLA-B*15:02 <span style=\"background: LightGoldenRodYellow\">(Details : {https://www.pharmvar.org/ code 'HLA-B*15:02' = 'HLA-B*15:02', given as 'HLA-B*15:02'})</span></p><p><b>specimen</b>: Specimen/specimen</p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></td><td>HLA-B <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org code 'HGNC:4932' = 'HGNC:4932', given as 'HLA-B'})</span></td></tr></table></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84413-4",
"display" : "genotype display name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"code" : "14909",
"display" : "HLA-B*15:02"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "HGNC:4932",
"display" : "HLA-B"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Task/med-usage-impact-task-pgx-example",
"resource" : {
"resourceType" : "Task",
"id" : "med-usage-impact-task-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: med-usage-impact-task-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: Any Increase does Recommendation Text from the provider <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA26421-0' = 'Consider alternative medication', given as 'Consider alternative medication'})</span></p><p><b>description</b>: Patients positive for this allele\nshould not be treated with CBZ, unless the benefits clearly\noutweigh the risk. Therapy should be discontinued immediately if\nsymptoms of SJS or TEN develop. Alternative medication should be\nused as first line therapy. Consideration in the choice for\nalternative medications should be given to potential\ncross-reactivity with structurally similar aromatic\nantiepileptic drugs such as oxcarbazepine, phenytoin,\nfosphenytoin and lamotrigine, which can also moderately increase\nrisk for SJS/TEN in association with HLA-B*15:02 positivity.</p><p><b>focus</b>: MedicationStatement/current-med-example</p><p><b>for</b>: Patient/patient</p><p><b>reasonReference</b>: Observation/medication-high-risk</p></div>"
},
"status" : "requested",
"intent" : "proposal",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26421-0",
"display" : "Consider alternative medication"
}
],
"text" : "Patients positive for this allele should not be treated with CBZ, unless the benefits clearly outweigh the risk"
},
"description" : "Patients positive for this allele should not be treated with CBZ, unless the benefits clearly outweigh the risk. Therapy should be discontinued immediately if symptoms of SJS or TEN develop. Alternative medication should be used as first line therapy. Consideration in the choice for alternative medications should be given to potential cross-reactivity with structurally similar aromatic antiepileptic drugs such as oxcarbazepine, phenytoin, fosphenytoin and lamotrigine, which can also moderately increase risk for SJS/TEN in association with HLA-B*15:02 positivity.",
"focus" : {
"reference" : "MedicationStatement/current-med-example"
},
"for" : {
"reference" : "Patient/patient"
},
"reasonReference" : {
"reference" : "Observation/medication-high-risk"
}
},
"request" : {
"method" : "POST",
"url" : "Task"
}
},
{
"fullUrl" : "http://example.org/fhir/MedicationStatement/current-med-example",
"resource" : {
"resourceType" : "MedicationStatement",
"id" : "current-med-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medicationstatement"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: current-med-example</p><p><b>meta</b>: </p><p><b>status</b>: unknown</p><p><b>medication</b>: Carbamazepine <span style=\"background: LightGoldenRodYellow\">(Details : {RxNorm code '2002' = 'Carbamazepine', given as 'Carbamazepine'})</span></p><p><b>subject</b>: Patient/patient</p></div>"
},
"status" : "unknown",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "2002",
"display" : "Carbamazepine"
}
]
},
"subject" : {
"reference" : "Patient/patient"
}
},
"request" : {
"method" : "POST",
"url" : "MedicationStatement"
}
}
]
}
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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