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" : "diagnosticreport-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/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>: <a href=\"ServiceRequest/pgx-request\">ServiceRequest/pgx-request</a></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>: <a href=\"Patient/patient\">Patient/patient</a></p><p><b>effective</b>: Jan 1, 2016 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>performer</b>: <a href=\"Organization/lab\">Organization/lab</a></p><p><b>result</b>: </p><ul><li><a href=\"Observation/med-impact-pgx-example\">genetics impact for medication metabolism accessment</a></li><li><a href=\"Observation/genotype-pgx-example\">Observation/genotype-pgx-example</a></li><li><a href=\"Observation/haplotype-1-pgx-example\">Observation/haplotype-1-pgx-example</a></li><li><a href=\"Observation/haplotype-2-pgx-example\">Observation/haplotype-2-pgx-example</a></li><li><a href=\"Observation/variant-1-pgx-example\">Observation/variant-1-pgx-example</a></li><li><a href=\"Observation/variant-2-pgx-example\">Observation/variant-2-pgx-example</a></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/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/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\">TODO</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/med-impact-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "med-impact-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-metabolism"
]
},
"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-impact-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>: Genetic variation's effect on drug metabolism <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '53040-2' = 'Genetic variation's effect on drug metabolism', given as 'Genetic variation's effect on drug metabolism'})</span></p><p><b>subject</b>: <a href=\"Patient/patient\">Patient/patient</a></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>performer</b>: <a href=\"Organization/lab\">Organization/lab</a></p><p><b>value</b>: Rapid metabolizer <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA25390-8' = 'Rapid metabolizer', given as 'Rapid metabolizer'})</span></p><p><b>derivedFrom</b>: <a href=\"Observation/genotype-pgx-example\">Observation/genotype-pgx-example</a></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>Medication assessed <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'})</span></td><td>mercaptopurine <span style=\"background: LightGoldenRodYellow\">(Details : {RxNorm code '103' = 'mercaptopurine', given as 'mercaptopurine'})</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" : "53040-2",
"display" : "Genetic variation's effect on drug metabolism"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA25390-8",
"display" : "Rapid metabolizer"
}
]
},
"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" : "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\"><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 12:00:00 AM</p><p><b>value</b>: CYP2C9 *4/*35B <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.pharmvar.org code 'CYP2C9 *4/*35B' = 'CYP2C9 *4/*35B', given as 'CYP2C9 *4/*35B'})</span></p><p><b>specimen</b>: <a href=\"Specimen/specimen\">Specimen/specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Observation/haplotype-1-pgx-example\">Observation/haplotype-1-pgx-example</a></li><li><a href=\"Observation/haplotype-2-pgx-example\">Observation/haplotype-2-pgx-example</a></li></ul><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>CYP2C9 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</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.pharmvar.org",
"code" : "CYP2C9 *4/*35B",
"display" : "CYP2C9 *4/*35B"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"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/geneId",
"code" : "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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: haplotype-1-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>: Haplotype Name <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: CYP2C9 *35B <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.pharmvar.org code 'CYP2C9 *35B' = 'CYP2C9 *35B', given as 'CYP2C9 *35B'})</span></p><p><b>specimen</b>: <a href=\"Specimen/specimen\">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href=\"Observation/variant-1-pgx-example\">Observation/variant-1-pgx-example</a></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>CYP2C9 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</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" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *35B",
"display" : "CYP2C9 *35B"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"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/geneId",
"code" : "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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: haplotype-2-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>: Haplotype Name <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: CYP2C9 *4 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.pharmvar.org code 'CYP2C9 *4' = 'CYP2C9 *4', given as 'CYP2C9 *4'})</span></p><p><b>specimen</b>: <a href=\"Specimen/specimen\">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href=\"Observation/variant-2-pgx-example\">Observation/variant-2-pgx-example</a></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>CYP2C9 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</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" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *4",
"display" : "CYP2C9 *4"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"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/geneId",
"code" : "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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: variant-1-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>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>specimen</b>: <a href=\"Specimen/specimen\">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href=\"MolecularSequence/sequence-1-pgx-example\">MolecularSequence/sequence-1-pgx-example</a></p><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>: CYP2C9 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: dbSNP ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})</span></p><p><b>value</b>: rs12345 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/SNP code 'rs12345' = 'rs12345)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Ref nucleotide'})</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Alt allele'})</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start and end <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'exact-start-end' = 'Variant exact start and end', given as 'Variant exact start and 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"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"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/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81255-2",
"display" : "dbSNP ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "exact-start-end",
"display" : "Variant exact start and end"
}
]
},
"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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: variant-2-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>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>specimen</b>: <a href=\"Specimen/specimen\">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href=\"MolecularSequence/sequence-2-pgx-example\">MolecularSequence/sequence-2-pgx-example</a></p><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>: CYP2C9 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48013-7' = 'Genomic reference sequence [ID]', given as 'Genomic reference sequence ID'})</span></p><p><b>value</b>: NG_007726.3 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: dbSNP ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})</span></p><p><b>value</b>: rs233455 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/SNP code 'rs233455' = 'rs233455)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Ref nucleotide'})</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Alt allele'})</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start and end <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'exact-start-end' = 'Variant exact start and end', given as 'Variant exact start and 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"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"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/geneId",
"code" : "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/nuccore",
"code" : "NG_007726.3"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81255-2",
"display" : "dbSNP ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "exact-start-end",
"display" : "Variant exact start and end"
}
]
},
"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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: sequence-1-pgx-example</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code '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/nuccore",
"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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: sequence-2-pgx-example</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code '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/nuccore",
"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/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 'LA26423-6' = 'Increase dose', given as 'Increase dose'})</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"MedicationStatement/current-med-example\">MedicationStatement/current-med-example</a></p><p><b>for</b>: <a href=\"Patient/patient\">Patient/patient</a></p><p><b>reasonReference</b>: <a href=\"Observation/med-impact-pgx-example\">Observation/med-impact-pgx-example</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/patient"
},
"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",
"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>: mercaptopurine <span style=\"background: LightGoldenRodYellow\">(Details : {RxNorm code '103' = 'mercaptopurine', given as 'mercaptopurine'})</span></p><p><b>subject</b>: <a href=\"Patient/patient\">Patient/patient</a></p></div>"
},
"status" : "unknown",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "103",
"display" : "mercaptopurine"
}
]
},
"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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