Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
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
<Bundle xmlns="http://hl7.org/fhir">
<id value="bundle-cgexample-withGrouping"/>
<type value="collection"/>
<entry>
<fullUrl
value="http://example.org/fhir/DiagnosticReport/report-withGrouping"/>
<resource>
<DiagnosticReport>
<id value="report-withGrouping"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<basedOn>🔗
<reference value="ServiceRequest/ExampleServiceRequest"/>
</basedOn>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51969-4"/>
<display value="Genetic analysis report"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<result>
<reference value="Observation/discrete-variant-1a"/>
</result>
<result>
<reference value="Observation/dis-path-1a"/>
</result>
<result>
<reference value="Observation/complex-variant-1a"/>
</result>
<result>
<reference value="Observation/complex-dis-path-1a"/>
</result>
<result>
<reference value="Observation/pharmPanel-1a"/>
</result>
<result>
<reference value="Observation/haplotype-1a"/>
</result>
<result>
<reference value="Observation/genotype-1a"/>
</result>
<result>
<reference value="Observation/metab-1a"/>
</result>
<result>
<reference value="Observation/efficacy-1a"/>
</result>
<conclusionCode>
<coding>
<system value="http://loinc.org"/>
<code value="LA6576-8"/>
<display value="Positive"/>
</coding>
</conclusionCode>
<conclusionCode>
<coding>
<system value="http://snomed.info/sct"/>
<code value="10828004"/>
<display value="Positive"/>
</coding>
</conclusionCode>
<presentedForm>
<contentType value="text/plain"/>
<data value="UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"/>
</presentedForm>
</DiagnosticReport>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Patient/ExamplePatient"/>
<resource>
<Patient>
<id value="ExamplePatient"/>
<text>
<status value="additional"/>
<div xmlns="http://www.w3.org/1999/xhtml">This would contain patient identifiers, demographics, etc.</div>
</text>
</Patient>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Specimen/ExampleSpecimen"/>
<resource>
<Specimen>
<id value="ExampleSpecimen"/>
<text>
<status value="generated"/>
<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>
</text>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
</Specimen>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Organization/ExampleLab"/>
<resource>
<Organization>
<id value="ExampleLab"/>
<text>
<status value="generated"/>
<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>
</text>
<name value="Some lab"/>
</Organization>
</resource>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/ServiceRequest/ExampleServiceRequest"/>
<resource>
<ServiceRequest>
<id value="ExampleServiceRequest"/>
<text>
<status value="generated"/>
<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>
</text>
<status value="active"/>
<intent value="original-order"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51969-4"/>
<display value="Genetic analysis report"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<reasonCode>
<text value="Worried about family planning"/>
</reasonCode>
</ServiceRequest>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/discrete-variant-1a"/>
<resource>
<Observation>
<id value="discrete-variant-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
<code value="30880"/>
<display value="NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:21497"/>
<display value="ACAD9"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_014049.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NG_017064.1"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81290-9"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NC_000003.11:g.128625063C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
<code value="rs368949613"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_014049.4:c.1249C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NP_054768.2:p.Arg417Cys"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6690-7"/>
<display value="Substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
</coding>
</code>
<valueString value="C"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
</coding>
</code>
<valueRange>
<low>
<value value="31731"/>
</low>
<high>
<value value="31731"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
</coding>
</code>
<valueString value="T"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48001-2"/>
</coding>
</code>
<valueCodeableConcept>
<text value="3q21"/>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6706-1"/>
<display value="Heterozygous"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
</coding>
</code>
<valueQuantity>
<value value="47"/>
<system value="http://unitsofmeasure.org"/>
<code value="%"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
</coding>
</code>
<valueQuantity>
<value value="208"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82155-3"/>
</coding>
</code>
<valueQuantity>
<value value="1"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81301-4"/>
</coding>
</code>
<valueRange>
<low>
<value value="13200589"/>
</low>
<high>
<value value="15592000"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81302-2"/>
</coding>
</code>
<valueRange>
<low>
<value value="14184616"/>
</low>
<high>
<value value="15581544"/>
</high>
</valueRange>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/dis-path-1a"/>
<resource>
<Observation>
<id value="dis-path-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="diagnostic-implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/discrete-variant-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://purl.obolibrary.org/obo/mondo.owl"/>
<code value="MONDO:0012624"/>
<display value="acyl-CoA dehydrogenase 9 deficiency"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-variant-1a"/>
<resource>
<Observation>
<id value="complex-variant-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<hasMember>
<reference value="Observation/complex-component-D-1a"/>
</hasMember>
<hasMember>
<reference value="Observation/complex-component-E-1a"/>
</hasMember>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-dis-path-1a"/>
<resource>
<Observation>
<id value="complex-dis-path-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="diagnostic-implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/complex-variant-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://snomed.info/sct"/>
<code value="293498008"/>
<display value="Debrisoquine adverse reaction (disorder)"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/complex-component-D-1a"/>
<resource>
<Observation>
<id value="complex-component-D-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
<code value="31934"/>
<display value="NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_000106.5"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_000106.5:c.886C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NP_000097.3:p.Arg296Cys"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6690-7"/>
<display value="Substitution"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/complex-component-E-1a"/>
<resource>
<Observation>
<id value="complex-component-E-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
<code value="38486"/>
<display
value="NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_000106.5"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_000106.5:c.1457G>C"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/pharmPanel-1a"/>
<resource>
<Observation>
<id value="pharmPanel-1a"/>
<text>
<status value="extensions"/>
<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>
</text>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
<valueReference>
<reference value="Task/usage-1a"/>
</valueReference>
</extension>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="C43359"/>
<display value="Group"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<hasMember>
<reference value="Observation/haplotype-1a"/>
</hasMember>
<hasMember>
<reference value="Observation/genotype-1a"/>
</hasMember>
<hasMember>
<reference value="Observation/metab-1a"/>
</hasMember>
<hasMember>
<reference value="Observation/efficacy-1a"/>
</hasMember>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/haplotype-1a"/>
<resource>
<Observation>
<id value="haplotype-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84414-2"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.ebi.ac.uk/ipd/imgt/hla"/>
<code value="*2"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<derivedFrom>
<reference value="Observation/discrete-variant-1a"/>
</derivedFrom>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/genotype-1a"/>
<resource>
<Observation>
<id value="genotype-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84413-4"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value="CYP2C9*2*5""/>
<display value="CYP2C9 *2/*5"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<derivedFrom>
<reference value="Observation/haplotype-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:23663"/>
<display value="VKORC1"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/metab-1a"/>
<resource>
<Observation>
<id value="metab-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA25390-8"/>
<display value="Rapid metabolizer"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/efficacy-1a"/>
<resource>
<Observation>
<id value="efficacy-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6676-6"/>
<display value="Resistant"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/highrisk-1a"/>
<resource>
<Observation>
<id value="highrisk-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype-1a"/>
</derivedFrom>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA19542-2"/>
<display value="Low risk"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Task/usage-1a"/>
<resource>
<Task>
<id value="usage-1a"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"/>
</meta>
<text>
<status value="generated"/>
<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>
</text>
<status value="requested"/>
<intent value="proposal"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="LA26423-6"/>
<display value="Increase dose"/>
</coding>
<text value="May need higher dosage than usual."/>
</code>
<focus>🔗
<reference value="MedicationStatement/MedicationStatementWarfarin"/>
</focus>
<for>🔗
<reference value="Patient/ExamplePatient"/>
</for>
<requester>🔗
<reference value="Organization/ExampleLab"/>
</requester>
<reasonReference>
<reference value="Observation/metab-1a"/>
</reasonReference>
</Task>
</resource>
</entry>
</Bundle>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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