Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "Bundle",
"id" : "bundle-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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"report\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomics-report.html\">Genomics Report</a></p></div><p><b>basedOn</b>: <a href=\"#ServiceRequest_ExampleServiceRequest\">See above (ServiceRequest/ExampleServiceRequest)</a></p><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_overall-interp\">See above (Observation/overall-interp)</a></li><li><a href=\"#Observation_discrete-variant\">See above (Observation/discrete-variant)</a></li><li><a href=\"#Observation_dis-path\">See above (Observation/dis-path)</a></li><li><a href=\"#Observation_complex-variant\">See above (Observation/complex-variant)</a></li><li><a href=\"#Observation_complex-dis-path\">See above (Observation/complex-dis-path)</a></li><li><a href=\"#Observation_haplotype\">See above (Observation/haplotype)</a></li><li><a href=\"#Observation_genotype\">See above (Observation/genotype)</a></li><li><a href=\"#Observation_metab\">See above (Observation/metab)</a></li><li><a href=\"#Observation_efficacy\">See above (Observation/efficacy)</a></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" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/ExampleLab"
}
],
"result" : [
{
"reference" : "Observation/overall-interp"
},
{
"reference" : "Observation/discrete-variant"
},
{
"reference" : "Observation/dis-path"
},
{
"reference" : "Observation/complex-variant"
},
{
"reference" : "Observation/complex-dis-path"
},
{
"reference" : "Observation/haplotype"
},
{
"reference" : "Observation/genotype"
},
{
"reference" : "Observation/metab"
},
{
"reference" : "Observation/efficacy"
}
],
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"ExampleSpecimen\" </p></div><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"ExampleLab\" </p></div><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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"ExampleServiceRequest\" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>reasonCode</b>: Worried about family planning <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></div>"
},
"status" : "active",
"intent" : "original-order",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/ExamplePatient"
},
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"overall-interp\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-overall-interpretation.html\">Overall Interpretation</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Discrete variation analysis overall interpretation <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51968-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Positive <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6576-8; <a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#10828004)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p></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/ExamplePatient"
},
"effectiveDateTime" : "2016",
"issued" : "2016-09-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/ExampleLab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6576-8",
"display" : "Positive"
},
{
"system" : "http://snomed.info/sct",
"code" : "10828004",
"display" : "Positive"
}
]
},
"specimen" : {
"reference" : "Specimen/ExampleSpecimen"
}
}
},
{
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"discrete-variant\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar[???]#30880)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: ACAD9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#21497)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_014049.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_014049.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NG_017064.1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NG_017064.1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000003.11:g.128625063C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NC_000003.11:g.128625063C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs368949613 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Genetic Sequence polymorphism database[137]#rs368949613)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.1249C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.1249C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: p.Arg417Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#p.Arg417Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: Substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6698-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 31731-31731</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic alt allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48001-2)</span></p><p><b>value</b>: 3q21 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Germline <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6683-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: Heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</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>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 208 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic structural variant copy number <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82155-3)</span></p><p><b>value</b>: 1 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant reported arrCGH [Ratio] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81299-0)</span></p><p><b>value</b>: 0.48</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant [Length] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81300-6)</span></p><p><b>value</b>: 1396929 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant outer start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81301-4)</span></p><p><b>value</b>: 13200589-15592000</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant inner start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81302-2)</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"
}
]
}
],
"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",
"version" : "???",
"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/geneId",
"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://varnomen.hgvs.org",
"code" : "NC_000003.11:g.128625063C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/projects/SNP",
"version" : "137",
"code" : "rs368949613"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"version" : "15.11",
"code" : "c.1249C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"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://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" : "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/diagnostic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"dis-path\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_discrete-variant\">See above (Observation/discrete-variant)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: Acyl-CoA dehydrogenase family, member 9, deficiency of <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (medgen#C1970173)</span></p></blockquote></div>"
},
"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-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"
}
],
"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://www.ncbi.nlm.nih.gov/medgen",
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"complex-variant\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"#Observation_complex-component-D\">See above (Observation/complex-component-D)</a></li><li><a href=\"#Observation_complex-component-E\">See above (Observation/complex-component-E)</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>Complex variant type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81263-6)</span></td><td>Haplotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26218-0)</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" : "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"
},
{
"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/diagnostic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"complex-dis-path\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_complex-variant\">See above (Observation/complex-variant)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: Debrisoquine adverse reaction (disorder) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#293498008)</span></p></blockquote></div>"
},
"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-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"
}
],
"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",
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"complex-component-D\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar#31934)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000106.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000106.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.886C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.886C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: p.Arg296Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#p.Arg296Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: Substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6698-0)</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "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",
"version" : "15.11",
"code" : "c.886C>T"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"complex-component-E\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar[???]#38486)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000106.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000106.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.1457G>C <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.1457G>C)</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "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",
"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://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",
"version" : "15.11",
"code" : "c.1457G>C"
}
]
}
}
]
}
},
{
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"haplotype\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-haplotype.html\">Haplotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Haplotype name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84414-2)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: *2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (hla#*2)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_discrete-variant\">See above (Observation/discrete-variant)</a></p></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/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"
}
]
}
},
{
"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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"genotype\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genotype.html\">Genotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genotype display name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84413-4)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *2/*5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *2/*5)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_haplotype\">See above (Observation/haplotype)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: VKORC1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#23663)</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "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"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"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/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"metab\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Rapid metabolizer <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA25390-8)</span></p></blockquote></div>"
},
"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-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"
}
],
"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" : "predicted-therapeutic-implication"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA25390-8",
"display" : "Rapid metabolizer"
}
]
}
}
]
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/efficacy",
"resource" : {
"resourceType" : "Observation",
"id" : "efficacy",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"efficacy\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Resistant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6676-6)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</span></p></blockquote></div>"
},
"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-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"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "predicted-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",
"resource" : {
"resourceType" : "Observation",
"id" : "highrisk",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"highrisk\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Low risk <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA19542-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</span></p></blockquote></div>"
},
"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-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"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "predicted-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",
"resource" : {
"resourceType" : "Task",
"id" : "usage",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"usage\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-medication-recommendation.html\">Medication Recommendation</a></p></div><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: May need higher dosage than usual. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26423-6 \"Increase dose\")</span></p><p><b>focus</b>: <a href=\"MedicationStatement-MedicationStatementWarfarin.html\">MedicationStatement/MedicationStatementWarfarin</a></p><p><b>for</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>requester</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_metab\">See above (Observation/metab)</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"
}
}
}
]
}
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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