Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
{
"resourceType" : "Bundle",
"id" : "bundle-cgexample-withGrouping",
"type" : "collection",
"entry" : [
{
"fullUrl" : "http://example.org/fhir/DiagnosticReport/report-withGrouping",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "report-withGrouping",
"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_report-withGrouping\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport report-withGrouping</b></p><a name=\"report-withGrouping\"> </a><a name=\"hcreport-withGrouping\"> </a><a name=\"report-withGrouping-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>2016-09-06 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><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table><p><b>Coded Conclusions:</b></p><ul><li><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></li><li><span title=\"Codes:{http://snomed.info/sct 10828004}\">Positive</span></li></ul></div>"
},
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/ExampleServiceRequest"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4",
"display" : "Genetic analysis report"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"result" : [
{
"reference" : "Observation/discrete-variant-1a"
},
{
"reference" : "Observation/dis-path-1a"
},
{
"reference" : "Observation/complex-variant-1a"
},
{
"reference" : "Observation/complex-dis-path-1a"
},
{
"reference" : "Observation/pharmPanel-1a"
},
{
"reference" : "Observation/haplotype-1a"
},
{
"reference" : "Observation/genotype-1a"
},
{
"reference" : "Observation/metab-1a"
},
{
"reference" : "Observation/efficacy-1a"
}
],
"conclusionCode" : [
{
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6576-8",
"display" : "Positive"
}
]
},
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "10828004",
"display" : "Positive"
}
]
}
],
"presentedForm" : [
{
"contentType" : "text/plain",
"data" : "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"
}
]
}
},
{
"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>"
}
}
},
{
"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"
}
}
},
{
"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"
}
},
{
"fullUrl" : "http://example.org/fhir/ServiceRequest/ExampleServiceRequest",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "ExampleServiceRequest",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_ExampleServiceRequest\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest ExampleServiceRequest</b></p><a name=\"ExampleServiceRequest\"> </a><a name=\"hcExampleServiceRequest\"> </a><a name=\"ExampleServiceRequest-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",
"display" : "Genetic analysis report"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"reasonCode" : [
{
"text" : "Worried about family planning"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/discrete-variant-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "discrete-variant-1a",
"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_discrete-variant-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation discrete-variant-1a</b></p><a name=\"discrete-variant-1a\"> </a><a name=\"hcdiscrete-variant-1a\"> </a><a name=\"discrete-variant-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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><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/clinvar 30880}\">NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)</span></p></blockquote><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:21497}\">ACAD9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_014049.4}\">NM_014049.4</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_017064.1}\">NG_017064.1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000003.11:g.128625063C>T}\">NC_000003.11:g.128625063C>T</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 rs368949613}\">rs368949613</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_014049.4:c.1249C>T}\">NM_014049.4:c.1249C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_054768.2:p.Arg417Cys}\">NP_054768.2:p.Arg417Cys</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6690-7}\">Substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: C</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>: 31731-31731</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic alt allele [ID]</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 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">3q21</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 47 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code% = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 208 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82155-3}\">Genomic structural variant copy number</span></p><p><b>value</b>: 1 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81301-4}\">Structural variant outer start and end</span></p><p><b>value</b>: 13200589-15592000</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81302-2}\">Structural variant inner start and end</span></p><p><b>value</b>: 14184616-15581544</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" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"code" : "30880",
"display" : "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC: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" : [
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"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NG_017064.1"
}
]
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},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81290-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
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"system" : "http://varnomen.hgvs.org",
"code" : "NC_000003.11:g.128625063C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9"
}
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://www.ncbi.nlm.nih.gov/projects/SNP",
"code" : "rs368949613"
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{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://varnomen.hgvs.org",
"code" : "NM_014049.4:c.1249C>T"
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}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NP_054768.2: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" : "69547-8"
}
]
},
"valueString" : "C"
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{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81254-5"
}
]
},
"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" : {
"text" : "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" : "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-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "dis-path-1a",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_dis-path-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation dis-path-1a</b></p><a name=\"dis-path-1a\"> </a><a name=\"hcdis-path-1a\"> </a><a name=\"dis-path-1a-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 diagnostic-implication}\">Diagnostic 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>: 2016</p><p><b>issued</b>: 2016-09-06 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-cgexample-withGrouping.html#Observation_discrete-variant-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6668-3}\">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81259-4}\">Associated phenotype</span></p><p><b>value</b>: <span title=\"Codes:{http://purl.obolibrary.org/obo/mondo.owl MONDO:0012624}\">acyl-CoA dehydrogenase 9 deficiency</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" : "diagnostic-implication"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/discrete-variant-1a"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://purl.obolibrary.org/obo/mondo.owl",
"code" : "MONDO:0012624",
"display" : "acyl-CoA dehydrogenase 9 deficiency"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-variant-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-variant-1a",
"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_complex-variant-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-variant-1a</b></p><a name=\"complex-variant-1a\"> </a><a name=\"hccomplex-variant-1a\"> </a><a name=\"complex-variant-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_complex-component-D-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_complex-component-E-1a\">Bundle: type = collection</a></li></ul></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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"hasMember" : [
{
"reference" : "Observation/complex-component-D-1a"
},
{
"reference" : "Observation/complex-component-E-1a"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-dis-path-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-dis-path-1a",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_complex-dis-path-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-dis-path-1a</b></p><a name=\"complex-dis-path-1a\"> </a><a name=\"hccomplex-dis-path-1a\"> </a><a name=\"complex-dis-path-1a-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 diagnostic-implication}\">Diagnostic 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>: 2016</p><p><b>issued</b>: 2016-09-06 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-cgexample-withGrouping.html#Observation_complex-variant-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6668-3}\">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81259-4}\">Associated phenotype</span></p><p><b>value</b>: <span title=\"Codes:{http://snomed.info/sct 293498008}\">Debrisoquine adverse reaction (disorder)</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" : "diagnostic-implication"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/complex-variant-1a"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
}
},
{
"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-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-component-D-1a",
"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_complex-component-D-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-component-D-1a</b></p><a name=\"complex-component-D-1a\"> </a><a name=\"hccomplex-component-D-1a\"> </a><a name=\"complex-component-D-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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><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/clinvar 31934}\">NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000106.5}\">NM_000106.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_000106.5:c.886C>T}\">NM_000106.5:c.886C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_000097.3:p.Arg296Cys}\">NP_000097.3:p.Arg296Cys</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6690-7}\">Substitution</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://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"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://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_000106.5"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_000106.5:c.886C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NP_000097.3:p.Arg296Cys"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48019-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6690-7",
"display" : "Substitution"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/complex-component-E-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "complex-component-E-1a",
"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_complex-component-E-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation complex-component-E-1a</b></p><a name=\"complex-component-E-1a\"> </a><a name=\"hccomplex-component-E-1a\"> </a><a name=\"complex-component-E-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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><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/clinvar 38486}\">NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000106.5}\">NM_000106.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_000106.5:c.1457G>C}\">NM_000106.5:c.1457G>C</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://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"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://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_000106.5"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_000106.5:c.1457G>C"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/pharmPanel-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "pharmPanel-1a",
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_pharmPanel-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation pharmPanel-1a</b></p><a name=\"pharmPanel-1a\"> </a><a name=\"hcpharmPanel-1a\"> </a><a name=\"pharmPanel-1a-en-US\"> </a><p><b>Recommended Action</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Task_usage-1a\">Bundle: type = collection</a></p><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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl C43359}\">Group</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: 2016-09-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_haplotype-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_metab-1a\">Bundle: type = collection</a></li><li><a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_efficacy-1a\">Bundle: type = collection</a></li></ul></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action",
"valueReference" : {
"reference" : "Task/usage-1a"
}
}
],
"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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "C43359",
"display" : "Group"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"hasMember" : [
{
"reference" : "Observation/haplotype-1a"
},
{
"reference" : "Observation/genotype-1a"
},
{
"reference" : "Observation/metab-1a"
},
{
"reference" : "Observation/efficacy-1a"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype-1a",
"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-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-1a</b></p><a name=\"haplotype-1a\"> </a><a name=\"hchaplotype-1a\"> </a><a name=\"haplotype-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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.ebi.ac.uk/ipd/imgt/hla *2}\">*2</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_discrete-variant-1a\">Bundle: type = collection</a></p></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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
"code" : "*2"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "Observation/discrete-variant-1a"
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/genotype-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "genotype-1a",
"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-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation genotype-1a</b></p><a name=\"genotype-1a\"> </a><a name=\"hcgenotype-1a\"> </a><a name=\"genotype-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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*2*5"}\">CYP2C9 *2/*5</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_haplotype-1a\">Bundle: type = collection</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 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:23663}\">VKORC1</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://loinc.org",
"code" : "84413-4"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9*2*5\"",
"display" : "CYP2C9 *2/*5"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/ExampleSpecimen"
},
"derivedFrom" : [
{
"reference" : "Observation/haplotype-1a"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:23663",
"display" : "VKORC1"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/metab-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "metab-1a",
"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_metab-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation metab-1a</b></p><a name=\"metab-1a\"> </a><a name=\"hcmetab-1a\"> </a><a name=\"metab-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</span></p></blockquote><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></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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/genotype-1a"
}
],
"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"
}
]
}
},
{
"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"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/efficacy-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "efficacy-1a",
"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_efficacy-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation efficacy-1a</b></p><a name=\"efficacy-1a\"> </a><a name=\"hcefficacy-1a\"> </a><a name=\"efficacy-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</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 LA6676-6}\">Resistant</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/genotype-1a"
}
],
"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" : "LA6676-6",
"display" : "Resistant"
}
]
}
},
{
"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-1a",
"resource" : {
"resourceType" : "Observation",
"id" : "highrisk-1a",
"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_highrisk-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation highrisk-1a</b></p><a name=\"highrisk-1a\"> </a><a name=\"hchighrisk-1a\"> </a><a name=\"highrisk-1a-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>: 2016</p><p><b>issued</b>: 2016-09-06 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-cgexample-withGrouping.html#Observation_genotype-1a\">Bundle: type = collection</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 LA19542-2}\">Low risk</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 11289}\">Warfarin</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"
}
]
},
"subject" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
🔗 "reference" : "Organization/ExampleLab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/genotype-1a"
}
],
"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" : "LA19542-2",
"display" : "Low risk"
}
]
}
},
{
"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-1a",
"resource" : {
"resourceType" : "Task",
"id" : "usage-1a",
"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_usage-1a\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Task usage-1a</b></p><a name=\"usage-1a\"> </a><a name=\"hcusage-1a\"> </a><a name=\"usage-1a-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}\">May need higher dosage than usual.</span></p><p><b>focus</b>: <a href=\"MedicationStatement-MedicationStatementWarfarin.html\">MedicationStatement: status = unknown; medication[x] = Warfarin</a></p><p><b>for</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>requester</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>reasonReference</b>: <a href=\"Bundle-bundle-cgexample-withGrouping.html#Observation_metab-1a\">Bundle: type = collection</a></p></div>"
},
"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" : "MedicationStatement/MedicationStatementWarfarin"
},
"for" : {
🔗 "reference" : "Patient/ExamplePatient"
},
"requester" : {
🔗 "reference" : "Organization/ExampleLab"
},
"reasonReference" : {
"reference" : "Observation/metab-1a"
}
}
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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