Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions
{
"resourceType" : "Bundle",
"id" : "bundle-pgxexample",
"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/genomic-report"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_pgx-report\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport pgx-report</b></p><a name=\"pgx-report\"> </a><a name=\"hcpgx-report\"> </a><a name=\"pgx-report-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>Anonymous Patient (no stated gender), DoB Unknown</td></tr><tr><td>When For</td><td>2016</td></tr><tr><td>Reported</td><td>2018-03-06 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href=\"Organization-ExampleLab.html\">Organization Some lab</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></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action",
"valueReference" : {
"reference" : "Task/med-usage-impact-task-pgx-example"
}
}
],
"basedOn" : [
{
"reference" : "ServiceRequest/pgx-request"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"result" : [
{
"reference" : "Observation/med-impact-pgx-example",
"display" : "genetics impact for medication metabolism accessment"
},
{
"reference" : "Observation/genotype-pgx-example"
},
{
"reference" : "Observation/haplotype-1-pgx-example"
},
{
"reference" : "Observation/haplotype-2-pgx-example"
},
{
"reference" : "Observation/variant-1-pgx-example"
},
{
"reference" : "Observation/variant-2-pgx-example"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
},
{
"fullUrl" : "http://example.org/fhir/Patient/ExamplePatient",
"resource" : {
"resourceType" : "Patient",
"id" : "ExamplePatient",
"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/ExampleSpecimen",
"resource" : {
"resourceType" : "Specimen",
"id" : "ExampleSpecimen",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Specimen_ExampleSpecimen\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen ExampleSpecimen</b></p><a name=\"ExampleSpecimen\"> </a><a name=\"hcExampleSpecimen\"> </a><a name=\"ExampleSpecimen-en-US\"> </a><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>"
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
}
},
"request" : {
"method" : "POST",
"url" : "Specimen"
}
},
{
"fullUrl" : "http://example.org/fhir/Organization/ExampleLab",
"resource" : {
"resourceType" : "Organization",
"id" : "ExampleLab",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_ExampleLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ExampleLab</b></p><a name=\"ExampleLab\"> </a><a name=\"hcExampleLab\"> </a><a name=\"ExampleLab-en-US\"> </a><p><b>name</b>: Some lab</p></div>"
},
"name" : "Some lab"
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "http://example.org/fhir/ServiceRequest/pgx-request",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "pgx-request",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_pgx-request\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest pgx-request</b></p><a name=\"pgx-request\"> </a><a name=\"hcpgx-request\"> </a><a name=\"pgx-request-en-US\"> </a><p><b>status</b>: Active</p><p><b>intent</b>: Original Order</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonCode</b>: <span title=\"Codes:\">Worried about family planning</span></p></div>"
},
"status" : "active",
"intent" : "original-order",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"reasonCode" : [
{
"text" : "Worried about family planning"
}
]
},
"request" : {
"method" : "POST",
"url" : "ServiceRequest"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/med-impact-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "med-impact-pgx-example",
"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_med-impact-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation med-impact-pgx-example</b></p><a name=\"med-impact-pgx-example\"> </a><a name=\"hcmed-impact-pgx-example\"> </a><a name=\"med-impact-pgx-example-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=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example\">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 LA25390-8}\">Rapid metabolizer</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:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</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" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/genotype-pgx-example"
}
],
"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" : "LA25390-8",
"display" : "Rapid metabolizer"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "103",
"display" : "mercaptopurine"
}
]
}
}
]
},
"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\"><a name=\"Observation_genotype-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation genotype-pgx-example</b></p><a name=\"genotype-pgx-example\"> </a><a name=\"hcgenotype-pgx-example\"> </a><a name=\"genotype-pgx-example-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 84413-4}\">genotype display name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example\">Bundle: type = transaction</a></li><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example\">Bundle: type = transaction</a></li></ul><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://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></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" : "84413-4",
"display" : "genotype display name"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "\"CYP2C9",
"display" : "CYP2C9 *4/*35B"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "Observation/haplotype-1-pgx-example"
},
{
"reference" : "Observation/haplotype-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype-1-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype-1-pgx-example",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_haplotype-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-1-pgx-example</b></p><a name=\"haplotype-1-pgx-example\"> </a><a name=\"hchaplotype-1-pgx-example\"> </a><a name=\"haplotype-1-pgx-example-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 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example\">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://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></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" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "\"CYP2C9",
"display" : "CYP2C9 *35B"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "Observation/variant-1-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype-2-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype-2-pgx-example",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_haplotype-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-2-pgx-example</b></p><a name=\"haplotype-2-pgx-example\"> </a><a name=\"hchaplotype-2-pgx-example\"> </a><a name=\"haplotype-2-pgx-example-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 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *4</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example\">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://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></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" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "\"CYP2C9",
"display" : "CYP2C9 *4"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "Observation/variant-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/variant-1-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "variant-1-pgx-example",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_variant-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-1-pgx-example</b></p><a name=\"variant-1-pgx-example\"> </a><a name=\"hcvariant-1-pgx-example\"> </a><a name=\"variant-1-pgx-example-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=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-1-pgx-example\">Bundle: type = transaction</a></p><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:2623}\">CYP2C9</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/projects/SNP rs12345}\">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227976-55227977</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" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "MolecularSequence/sequence-1-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/projects/SNP",
"code" : "rs12345"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69547-8",
"display" : "Ref nucleotide"
}
]
},
"valueString" : "T"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0",
"display" : "Alt allele"
}
]
},
"valueString" : "G"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81254-5"
}
]
},
"valueRange" : {
"low" : {
"value" : 55227976
},
"high" : {
"value" : 55227977
}
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/variant-2-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "variant-2-pgx-example",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_variant-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-2-pgx-example</b></p><a name=\"variant-2-pgx-example\"> </a><a name=\"hcvariant-2-pgx-example\"> </a><a name=\"variant-2-pgx-example-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=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-2-pgx-example\">Bundle: type = transaction</a></p><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:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_007726.3}\">NG_007726.3</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/projects/SNP rs233455}\">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227978-55227979</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" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "MolecularSequence/sequence-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48013-7",
"display" : "Genomic reference sequence ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NG_007726.3"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/projects/SNP",
"code" : "rs233455"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69547-8",
"display" : "Ref nucleotide"
}
]
},
"valueString" : "T"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0",
"display" : "Alt allele"
}
]
},
"valueString" : "G"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81254-5"
}
]
},
"valueRange" : {
"low" : {
"value" : 55227978
},
"high" : {
"value" : 55227979
}
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example",
"resource" : {
"resourceType" : "MolecularSequence",
"id" : "sequence-1-pgx-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-1-pgx-example</b></p><a name=\"sequence-1-pgx-example\"> </a><a name=\"hcsequence-1-pgx-example\"> </a><a name=\"sequence-1-pgx-example-en-US\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
},
"type" : "dna",
"coordinateSystem" : 0,
"referenceSeq" : {
"orientation" : "sense",
"referenceSeqId" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NG-007726.3"
}
]
},
"windowStart" : 55227970,
"windowEnd" : 55227980
}
},
"request" : {
"method" : "POST",
"url" : "MolecularSequence"
}
},
{
"fullUrl" : "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example",
"resource" : {
"resourceType" : "MolecularSequence",
"id" : "sequence-2-pgx-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-2-pgx-example</b></p><a name=\"sequence-2-pgx-example\"> </a><a name=\"hcsequence-2-pgx-example\"> </a><a name=\"sequence-2-pgx-example-en-US\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
},
"type" : "dna",
"coordinateSystem" : 0,
"referenceSeq" : {
"orientation" : "sense",
"referenceSeqId" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NG-007726.3"
}
]
},
"windowStart" : 55227970,
"windowEnd" : 55227980
}
},
"request" : {
"method" : "POST",
"url" : "MolecularSequence"
}
},
{
"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/medication-recommendation"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Task_med-usage-impact-task-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Task med-usage-impact-task-pgx-example</b></p><a name=\"med-usage-impact-task-pgx-example\"> </a><a name=\"hcmed-usage-impact-task-pgx-example\"> </a><a name=\"med-usage-impact-task-pgx-example-en-US\"> </a><p><b>status</b>: Requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LA26423-6}\">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"Bundle-bundle-pgxexample.html#MedicationStatement_current-med-example\">Bundle: type = transaction</a></p><p><b>for</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonReference</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example\">Bundle: type = transaction</a></p></div>"
},
"status" : "requested",
"intent" : "proposal",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26423-6",
"display" : "Increase dose"
}
],
"text" : "Any Increase does Recommendation Text from the provider"
},
"description" : "Any Increase does Recommendation Text from the provider",
"focus" : {
"reference" : "MedicationStatement/current-med-example"
},
"for" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"reasonReference" : {
"reference" : "Observation/med-impact-pgx-example"
}
},
"request" : {
"method" : "POST",
"url" : "Task"
}
},
{
"fullUrl" : "http://example.org/fhir/MedicationStatement/current-med-example",
"resource" : {
"resourceType" : "MedicationStatement",
"id" : "current-med-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MedicationStatement_current-med-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MedicationStatement current-med-example</b></p><a name=\"current-med-example\"> </a><a name=\"hccurrent-med-example\"> </a><a name=\"current-med-example-en-US\"> </a><p><b>status</b>: Unknown</p><p><b>medication</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>"
},
"status" : "unknown",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "103",
"display" : "mercaptopurine"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
}
},
"request" : {
"method" : "POST",
"url" : "MedicationStatement"
}
}
]
}
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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