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-pgxexample"/>
<type value="transaction"/>
<entry>
<fullUrl value="http://example.org/fhir/DiagnosticReport/pgx-report"/>
<resource>
<DiagnosticReport>
<id value="pgx-report"/>
<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_pgx-report"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport pgx-report</b></p><a name="pgx-report"> </a><a name="hcpgx-report"> </a><a name="pgx-report-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>2018-03-06 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></table></div>
</text>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
<valueReference>
<reference value="Task/med-usage-impact-task-pgx-example"/>
</valueReference>
</extension>
<basedOn>
<reference value="ServiceRequest/pgx-request"/>
</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"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<result>
<reference value="Observation/med-impact-pgx-example"/>
<display
value="genetics impact for medication metabolism accessment"/>
</result>
<result>
<reference value="Observation/genotype-pgx-example"/>
</result>
<result>
<reference value="Observation/haplotype-1-pgx-example"/>
</result>
<result>
<reference value="Observation/haplotype-2-pgx-example"/>
</result>
<result>
<reference value="Observation/variant-1-pgx-example"/>
</result>
<result>
<reference value="Observation/variant-2-pgx-example"/>
</result>
</DiagnosticReport>
</resource>
<request>
<method value="POST"/>
<url value="DiagnosticReport"/>
</request>
</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>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</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>
<request>
<method value="POST"/>
<url value="Specimen"/>
</request>
</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>
<request>
<method value="POST"/>
<url value="Organization"/>
</request>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/ServiceRequest/pgx-request"/>
<resource>
<ServiceRequest>
<id value="pgx-request"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="ServiceRequest_pgx-request"> </a><p class="res-header-id"><b>Generated Narrative: ServiceRequest pgx-request</b></p><a name="pgx-request"> </a><a name="hcpgx-request"> </a><a name="pgx-request-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"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<reasonCode>
<text value="Worried about family planning"/>
</reasonCode>
</ServiceRequest>
</resource>
<request>
<method value="POST"/>
<url value="ServiceRequest"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/med-impact-pgx-example"/>
<resource>
<Observation>
<id value="med-impact-pgx-example"/>
<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_med-impact-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation med-impact-pgx-example</b></p><a name="med-impact-pgx-example"> </a><a name="hcmed-impact-pgx-example"> </a><a name="med-impact-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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-pgxexample.html#Observation_genotype-pgx-example">Bundle: type = transaction</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 LA25390-8}">Rapid metabolizer</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51963-7}">Medication assessed</span></p><p><b>value</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}">mercaptopurine</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"/>
<display value="Therapeutic Implication"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype-pgx-example"/>
</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="LA25390-8"/>
<display value="Rapid metabolizer"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
<display value="Medication assessed"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="103"/>
<display value="mercaptopurine"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/genotype-pgx-example"/>
<resource>
<Observation>
<id value="genotype-pgx-example"/>
<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-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation genotype-pgx-example</b></p><a name="genotype-pgx-example"> </a><a name="hcgenotype-pgx-example"> </a><a name="genotype-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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}">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example">Bundle: type = transaction</a></li><li><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example">Bundle: type = transaction</a></li></ul><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></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"/>
<display value="genotype display name"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value=""CYP2C9"/>
<display value="CYP2C9 *4/*35B"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<derivedFrom>
<reference value="Observation/haplotype-1-pgx-example"/>
</derivedFrom>
<derivedFrom>
<reference value="Observation/haplotype-2-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/haplotype-1-pgx-example"/>
<resource>
<Observation>
<id value="haplotype-1-pgx-example"/>
<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-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation haplotype-1-pgx-example</b></p><a name="haplotype-1-pgx-example"> </a><a name="hchaplotype-1-pgx-example"> </a><a name="haplotype-1-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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}">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></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"/>
<display value="Haplotype Name"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value=""CYP2C9"/>
<display value="CYP2C9 *35B"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<derivedFrom>
<reference value="Observation/variant-1-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/haplotype-2-pgx-example"/>
<resource>
<Observation>
<id value="haplotype-2-pgx-example"/>
<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-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation haplotype-2-pgx-example</b></p><a name="haplotype-2-pgx-example"> </a><a name="hchaplotype-2-pgx-example"> </a><a name="haplotype-2-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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}">CYP2C9 *4</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></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"/>
<display value="Haplotype Name"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value=""CYP2C9"/>
<display value="CYP2C9 *4"/>
</coding>
</valueCodeableConcept>
<specimen>🔗
<reference value="Specimen/ExampleSpecimen"/>
</specimen>
<derivedFrom>
<reference value="Observation/variant-2-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/variant-1-pgx-example"/>
<resource>
<Observation>
<id value="variant-1-pgx-example"/>
<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_variant-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation variant-1-pgx-example</b></p><a name="variant-1-pgx-example"> </a><a name="hcvariant-1-pgx-example"> </a><a name="variant-1-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#MolecularSequence_sequence-1-pgx-example">Bundle: type = transaction</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 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs12345}">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</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 69551-0}">Alt allele</span></p><p><b>value</b>: G</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>: 55227976-55227977</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="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<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>
<derivedFrom>
<reference value="MolecularSequence/sequence-1-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied ID"/>
</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="81252-9"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
<code value="rs12345"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Ref nucleotide"/>
</coding>
</code>
<valueString value="T"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Alt allele"/>
</coding>
</code>
<valueString value="G"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
</coding>
</code>
<valueRange>
<low>
<value value="55227976"/>
</low>
<high>
<value value="55227977"/>
</high>
</valueRange>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Observation/variant-2-pgx-example"/>
<resource>
<Observation>
<id value="variant-2-pgx-example"/>
<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_variant-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation variant-2-pgx-example</b></p><a name="variant-2-pgx-example"> </a><a name="hcvariant-2-pgx-example"> </a><a name="variant-2-pgx-example-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>: 2018</p><p><b>issued</b>: 2018-03-06 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>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#MolecularSequence_sequence-2-pgx-example">Bundle: type = transaction</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 48013-7}">Genomic reference sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_007726.3}">NG_007726.3</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 rs233455}">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</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 69551-0}">Alt allele</span></p><p><b>value</b>: G</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>: 55227978-55227979</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="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<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>
<derivedFrom>
<reference value="MolecularSequence/sequence-2-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied ID"/>
</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="48013-7"/>
<display value="Genomic reference sequence ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NG_007726.3"/>
</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="rs233455"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Ref nucleotide"/>
</coding>
</code>
<valueString value="T"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Alt allele"/>
</coding>
</code>
<valueString value="G"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
</coding>
</code>
<valueRange>
<low>
<value value="55227978"/>
</low>
<high>
<value value="55227979"/>
</high>
</valueRange>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/MolecularSequence/sequence-1-pgx-example"/>
<resource>
<MolecularSequence>
<id value="sequence-1-pgx-example"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="MolecularSequence_sequence-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: MolecularSequence sequence-1-pgx-example</b></p><a name="sequence-1-pgx-example"> </a><a name="hcsequence-1-pgx-example"> </a><a name="sequence-1-pgx-example-en-US"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style="display: none">*</td><td>Sense orientation of referenceSeq</td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>
</text>
<type value="dna"/>
<coordinateSystem value="0"/>
<referenceSeq>
<orientation value="sense"/>
<referenceSeqId>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NG-007726.3"/>
</coding>
</referenceSeqId>
<windowStart value="55227970"/>
<windowEnd value="55227980"/>
</referenceSeq>
</MolecularSequence>
</resource>
<request>
<method value="POST"/>
<url value="MolecularSequence"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/MolecularSequence/sequence-2-pgx-example"/>
<resource>
<MolecularSequence>
<id value="sequence-2-pgx-example"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="MolecularSequence_sequence-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: MolecularSequence sequence-2-pgx-example</b></p><a name="sequence-2-pgx-example"> </a><a name="hcsequence-2-pgx-example"> </a><a name="sequence-2-pgx-example-en-US"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style="display: none">*</td><td>Sense orientation of referenceSeq</td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>
</text>
<type value="dna"/>
<coordinateSystem value="0"/>
<referenceSeq>
<orientation value="sense"/>
<referenceSeqId>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NG-007726.3"/>
</coding>
</referenceSeqId>
<windowStart value="55227970"/>
<windowEnd value="55227980"/>
</referenceSeq>
</MolecularSequence>
</resource>
<request>
<method value="POST"/>
<url value="MolecularSequence"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/Task/med-usage-impact-task-pgx-example"/>
<resource>
<Task>
<id value="med-usage-impact-task-pgx-example"/>
<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_med-usage-impact-task-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Task med-usage-impact-task-pgx-example</b></p><a name="med-usage-impact-task-pgx-example"> </a><a name="hcmed-usage-impact-task-pgx-example"> </a><a name="med-usage-impact-task-pgx-example-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}">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href="Bundle-bundle-pgxexample.html#MedicationStatement_current-med-example">Bundle: type = transaction</a></p><p><b>for</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonReference</b>: <a href="Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example">Bundle: type = transaction</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="Any Increase does Recommendation Text from the provider"/>
</code>
<description
value="Any Increase does Recommendation Text from the provider"/>
<focus>
<reference value="MedicationStatement/current-med-example"/>
</focus>
<for>🔗
<reference value="Patient/ExamplePatient"/>
</for>
<reasonReference>
<reference value="Observation/med-impact-pgx-example"/>
</reasonReference>
</Task>
</resource>
<request>
<method value="POST"/>
<url value="Task"/>
</request>
</entry>
<entry>
<fullUrl
value="http://example.org/fhir/MedicationStatement/current-med-example"/>
<resource>
<MedicationStatement>
<id value="current-med-example"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="MedicationStatement_current-med-example"> </a><p class="res-header-id"><b>Generated Narrative: MedicationStatement current-med-example</b></p><a name="current-med-example"> </a><a name="hccurrent-med-example"> </a><a name="current-med-example-en-US"> </a><p><b>status</b>: Unknown</p><p><b>medication</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}">mercaptopurine</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>
</text>
<status value="unknown"/>
<medicationCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="103"/>
<display value="mercaptopurine"/>
</coding>
</medicationCodeableConcept>
<subject>🔗
<reference value="Patient/ExamplePatient"/>
</subject>
</MedicationStatement>
</resource>
<request>
<method value="POST"/>
<url value="MedicationStatement"/>
</request>
</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
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change