Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions 
<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/genomics-report"/>
</meta>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "pgx-report" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomics-report.html">Genomics Report</a></p></div><p><b>Recommended Action</b>: <a href="#Task_med-usage-impact-task-pgx-example">See above (Task/med-usage-impact-task-pgx-example)</a></p><p><b>basedOn</b>: <a href="#ServiceRequest_pgx-request">See above (ServiceRequest/pgx-request)</a></p><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href="#Organization_ExampleLab">See above (Organization/ExampleLab)</a></p><p><b>result</b>: </p><ul><li><a href="#Observation_med-impact-pgx-example">See above (Observation/med-impact-pgx-example: genetics impact for medication metabolism accessment)</a></li><li><a href="#Observation_genotype-pgx-example">See above (Observation/genotype-pgx-example)</a></li><li><a href="#Observation_haplotype-1-pgx-example">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href="#Observation_haplotype-2-pgx-example">See above (Observation/haplotype-2-pgx-example)</a></li><li><a href="#Observation_variant-1-pgx-example">See above (Observation/variant-1-pgx-example)</a></li><li><a href="#Observation_variant-2-pgx-example">See above (Observation/variant-2-pgx-example)</a></li></ul></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"/>
<display value="Genetics"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81247-9"/>
</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "ExampleSpecimen" </p></div><p><b>subject</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</a></p></div>
</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "ExampleLab" </p></div><p><b>name</b>: Some lab</p></div>
</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "pgx-request" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</a></p><p><b>reasonCode</b>: Worried about family planning <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> ()</span></p></div>
</text>
<status value="active"/>
<intent value="original-order"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81247-9"/>
</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "med-impact-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-therapeutic-implication.html">Therapeutic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Therapeutic Implication <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href="#Organization_ExampleLab">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href="#Observation_genotype-pgx-example">See above (Observation/genotype-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Rapid metabolizer <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA25390-8)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#51963-7)</span></p><p><b>value</b>: mercaptopurine <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html">RxNorm</a>#103)</span></p></blockquote></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</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="predicted-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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genotype-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genotype.html">Genotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: genotype display name <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#84413-4)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *4/*35B <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (www.pharmvar.org#CYP2C9 *4/*35B)</span></p><p><b>specimen</b>: <a href="#Specimen_ExampleSpecimen">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: </p><ul><li><a href="#Observation_haplotype-1-pgx-example">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href="#Observation_haplotype-2-pgx-example">See above (Observation/haplotype-2-pgx-example)</a></li></ul><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#2623)</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>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84413-4"/>
<display value="genotype display name"/>
</coding>
</code>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value="CYP2C9 *4/*35B"/>
<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/geneId"/>
<code value="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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "haplotype-1-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-haplotype.html">Haplotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Haplotype Name <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#84414-2)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *35B <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (www.pharmvar.org#CYP2C9 *35B)</span></p><p><b>specimen</b>: <a href="#Specimen_ExampleSpecimen">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href="#Observation_variant-1-pgx-example">See above (Observation/variant-1-pgx-example)</a></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#2623)</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>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84414-2"/>
<display value="Haplotype Name"/>
</coding>
</code>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value="CYP2C9 *35B"/>
<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/geneId"/>
<code value="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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "haplotype-2-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-haplotype.html">Haplotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Haplotype Name <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#84414-2)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *4 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (www.pharmvar.org#CYP2C9 *4)</span></p><p><b>specimen</b>: <a href="#Specimen_ExampleSpecimen">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href="#Observation_variant-2-pgx-example">See above (Observation/variant-2-pgx-example)</a></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#2623)</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>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84414-2"/>
<display value="Haplotype Name"/>
</coding>
</code>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value="CYP2C9 *4"/>
<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/geneId"/>
<code value="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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "variant-1-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href="#Specimen_ExampleSpecimen">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href="#MolecularSequence_sequence-1-pgx-example">See above (MolecularSequence/sequence-1-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C9 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#2623)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs12345 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-dbSNP.html">Genetic Sequence polymorphism database</a>#rs12345)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 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>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<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/geneId"/>
<code value="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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "variant-2-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href="#Specimen_ExampleSpecimen">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href="#MolecularSequence_sequence-2-pgx-example">See above (MolecularSequence/sequence-2-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C9 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#2623)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48013-7)</span></p><p><b>value</b>: NG_007726.3 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NG_007726.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs233455 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-dbSNP.html">Genetic Sequence polymorphism database</a>#rs233455)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 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>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<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/geneId"/>
<code value="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/nuccore"/>
<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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "sequence-1-pgx-example" </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#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/nuccore"/>
<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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "sequence-2-pgx-example" </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#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/nuccore"/>
<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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "med-usage-impact-task-pgx-example" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-medication-recommendation.html">Medication Recommendation</a></p></div><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: Any Increase does Recommendation Text from the provider <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26423-6 "Increase dose")</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href="#MedicationStatement_current-med-example">See above (MedicationStatement/current-med-example)</a></p><p><b>for</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</a></p><p><b>reasonReference</b>: <a href="#Observation_med-impact-pgx-example">See above (Observation/med-impact-pgx-example)</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "current-med-example" </p></div><p><b>status</b>: unknown</p><p><b>medication</b>: mercaptopurine <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html">RxNorm</a>#103)</span></p><p><b>subject</b>: <a href="#Patient_ExamplePatient">See above (Patient/ExamplePatient)</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 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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