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-cgexample",
"type" : "collection",
"entry" : [
{
"fullUrl" : "http://example.org/fhir/DiagnosticReport/report",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "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\">TODO</div>"
},
"basedOn" : [
{
"reference" : "DiagnosticRequest/request"
}
],
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"result" : [
{
"reference" : "Observation/overall-interp"
},
{
"reference" : "Observation/discrete-variant"
},
{
"reference" : "Observation/dis-path"
},
{
"reference" : "Observation/complex-variant"
},
{
"reference" : "Observation/complex-dis-path"
},
{
"reference" : "Observation/pharmPanel"
}
],
"presentedForm" : [
{
"contentType" : "text/plain",
"data" : "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"
}
]
}
},
{
"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>"
}
}
},
{
"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"
}
}
},
{
"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"
}
},
{
"fullUrl" : "http://example.org/fhir/DiagnosticRequest/request",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "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"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/overall-interp",
"resource" : {
"resourceType" : "Observation",
"id" : "overall-interp",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51968-6"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6576-8",
"display" : "Positive"
},
{
"system" : "http://snomed.info/sct",
"code" : "10828004",
"display" : "Positive"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
}
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/discrete-variant",
"resource" : {
"resourceType" : "Observation",
"id" : "discrete-variant",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/clinvar",
"version" : "???",
"code" : "30880",
"display" : "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)"
},
{
"system" : "http://example.org/cigar",
"code" : "tbd"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/hgnc",
"code" : "21497",
"display" : "ACAD9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_014049.4"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48013-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NG_017064.1"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81290-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.g",
"version" : "15.11",
"code" : "NC_000003.11:g.128625063C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81255-2"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/dbsnp",
"version" : "137",
"code" : "rs368949613"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.c",
"version" : "15.11",
"code" : "c.1249C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.p",
"version" : "15.11",
"code" : "p.Arg417Cys"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48019-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6690-7",
"display" : "Substitution"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48006-1"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6698-0",
"display" : "Missense"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69547-8"
}
]
},
"valueString" : "C"
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "exact-start-end"
}
]
},
"valueRange" : {
"low" : {
"value" : 31731
},
"high" : {
"value" : 31731
}
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0"
}
]
},
"valueString" : "T"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48001-2"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/Chrom-Loc",
"code" : "3q21"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48002-0"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53034-5"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6706-1",
"display" : "Heterozygous"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81258-6"
}
]
},
"valueQuantity" : {
"value" : 47,
"system" : "http://unitsofmeasure.org",
"code" : "%"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "82121-5"
}
]
},
"valueQuantity" : {
"value" : 208,
"system" : "http://unitsofmeasure.org",
"code" : "1"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "82155-3"
}
]
},
"valueQuantity" : {
"value" : 1,
"system" : "http://unitsofmeasure.org",
"code" : "1"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81299-0"
}
]
},
"valueQuantity" : {
"value" : 0.48
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81300-6"
}
]
},
"valueQuantity" : {
"value" : 1396929,
"system" : "http://unitsofmeasure.org",
"code" : "1"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81301-4"
}
]
},
"valueRange" : {
"low" : {
"value" : 13200589
},
"high" : {
"value" : 15592000
}
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81302-2"
}
]
},
"valueRange" : {
"low" : {
"value" : 14184616
},
"high" : {
"value" : 15581544
}
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/dis-path",
"resource" : {
"resourceType" : "Observation",
"id" : "dis-path",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/discrete-variant"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/MedGen-Dis",
"code" : "C1970173",
"display" : "Acyl-CoA dehydrogenase family, member 9, deficiency of"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-variant",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-variant",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"hasMember" : [
{
"reference" : "Observation/complex-component-D"
},
{
"reference" : "Observation/complex-component-E"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81263-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26218-0",
"display" : "Haplotype"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-dis-path",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-dis-path",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/complex-variant"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "293498008",
"display" : "Debrisoquine adverse reaction (disorder)"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-component-D",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-component-D",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/clinvar",
"version" : "???",
"code" : "31934",
"display" : "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/RefSeq-T",
"code" : "NM_000106.5"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.c",
"version" : "15.11",
"code" : "c.886C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.p",
"version" : "15.11",
"code" : "p.Arg296Cys"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48019-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6690-7",
"display" : "Substitution"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48006-1"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6698-0",
"display" : "Missense"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-component-E",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-component-E",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/clinvar",
"version" : "???",
"code" : "38486",
"display" : "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/RefSeq-T",
"code" : "NM_000106.5"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/HGVS.c",
"version" : "15.11",
"code" : "c.1457G>C"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/pharmPanel",
"resource" : {
"resourceType" : "Observation",
"id" : "pharmPanel",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/grouper"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction",
"valueReference" : {
"reference" : "Task/usage"
}
}
],
"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" : "grouper"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"hasMember" : [
{
"reference" : "Observation/haplotype"
},
{
"reference" : "Observation/genotype"
},
{
"reference" : "Observation/metab"
},
{
"reference" : "Observation/efficacy"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84414-2"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/???",
"code" : "*2"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "Observation/discrete-variant"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/genotype",
"resource" : {
"resourceType" : "Observation",
"id" : "genotype",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84413-4"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *2/*5",
"display" : "CYP2C9 *2/*5"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "Observation/haplotype"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/hgnc",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://example.org/hgnc",
"code" : "23663",
"display" : "VKORC1"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/metab",
"resource" : {
"resourceType" : "Observation",
"id" : "metab",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-metabolism"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53040-2"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA25390-8",
"display" : "Rapid metabolizer"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/genotype"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "11289",
"display" : "Warfarin"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/efficacy",
"resource" : {
"resourceType" : "Observation",
"id" : "efficacy",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-efficacy"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51961-1"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6676-6",
"display" : "Resistant"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/genotype"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "11289",
"display" : "Warfarin"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/highrisk",
"resource" : {
"resourceType" : "Observation",
"id" : "highrisk",
"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\">TODO</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "83009-1"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA19542-2",
"display" : "Low risk"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/genotype"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "11289",
"display" : "Warfarin"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Task/usage",
"resource" : {
"resourceType" : "Task",
"id" : "usage",
"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\">TODO</div>"
},
"contained" : [
{
"resourceType" : "MedicationStatement",
"id" : "med",
"status" : "unknown",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "11289",
"display" : "Warfarin"
}
]
},
"subject" : {
"reference" : "Patient/patient"
}
}
],
"status" : "requested",
"intent" : "proposal",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26423-6",
"display" : "Increase dose"
}
],
"text" : "May need higher dosage than usual."
},
"focus" : {
"reference" : "#med"
},
"for" : {
"reference" : "Patient/patient"
},
"requester" : {
"reference" : "Organization/lab"
},
"reasonReference" : {
"reference" : "Observation/metab"
}
}
}
]
}
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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