Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
<Bundle xmlns="http://hl7.org/fhir">
<!-- Note: Profiles are declared on most resources to support automatic validation. However, in production, instances might not have profile declarations present - or at least not profiles defined in this implementation guide -->
<id value="diagnosticreport-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><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>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 81247-9}">Master HL7 genetic variant reporting panel</span></p><p><b>subject</b>: <a href="#Patient_patient">See above (Patient/patient)</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_lab">See above (Organization/lab)</a></p><p><b>result</b>: </p><ul><li><a href="#Observation_med-impact-pgx-example">genetics impact for medication metabolism accessment. Generated Summary: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>; <span title="Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes therapeutic-implication}">Therapeutic Implication</span>; effective: 2018; issued: Mar 6, 2018 5:00:00 AM</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/RecommendedAction">
<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/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</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/patient"/>
<resource>
<Patient>
<id value="patient"/>
<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/specimen"/>
<resource>
<Specimen>
<id value="specimen"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<subject>
<reference value="Patient/patient"/>
</subject>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Organization/lab"/>
<resource>
<Organization>
<id value="lab"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</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"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</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/patient"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes therapeutic-implication}">Therapeutic Implication</span></p><p><b>subject</b>: <a href="#Patient_patient">See above (Patient/patient)</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_lab">See above (Organization/lab)</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>: <span title="Codes: {http://loinc.org 53040-2}">Genetic variation's effect on drug metabolism</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>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="therapeutic-implication"/>
<display value="Therapeutic Implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2018"/>
<issued value="2018-03-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype-pgx-example"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53040-2"/>
<display value="Genetic variation's effect on drug metabolism"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 84413-4}">genotype display name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title="Codes: {http://www.pharmvar.org CYP2C9 *4/*35B}">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href="#Specimen_specimen">See above (Specimen/specimen)</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><span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes: {http://www.genenames.org/geneId 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>
<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/specimen"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 84414-2}">Haplotype Name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title="Codes: {http://www.pharmvar.org CYP2C9 *35B}">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href="#Specimen_specimen">See above (Specimen/specimen)</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><span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes: {http://www.genenames.org/geneId 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>
<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/specimen"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 84414-2}">Haplotype Name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title="Codes: {http://www.pharmvar.org CYP2C9 *4}">CYP2C9 *4</span></p><p><b>specimen</b>: <a href="#Specimen_specimen">See above (Specimen/specimen)</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><span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes: {http://www.genenames.org/geneId 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>
<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/specimen"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title="Codes: {http://loinc.org LA9633-4}">Present</span></p><p><b>specimen</b>: <a href="#Specimen_specimen">See above (Specimen/specimen)</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>: <span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></p><p><b>value</b>: <span title="Codes: {http://www.genenames.org/geneId 2623}">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 81255-2}">dbSNP ID</span></p><p><b>value</b>: <span title="Codes: {http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes exact-start-end}">Variant exact start and 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>
<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/specimen"/>
</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>
<!-- Error message: This element does not match any known slice for the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype -Chi -->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81255-2"/>
<display value="dbSNP ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="exact-start-end"/>
<display value="Variant exact start and end"/>
</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><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title="Codes: {http://loinc.org LA9633-4}">Present</span></p><p><b>specimen</b>: <a href="#Specimen_specimen">See above (Specimen/specimen)</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>: <span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></p><p><b>value</b>: <span title="Codes: {http://www.genenames.org/geneId 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/nuccore 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 81255-2}">dbSNP ID</span></p><p><b>value</b>: <span title="Codes: {http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes exact-start-end}">Variant exact start and 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>
<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/specimen"/>
</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>
<!-- Error message: This element does not match any known slice for the profile http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype -Chi -->
<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="81255-2"/>
<display value="dbSNP ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="exact-start-end"/>
<display value="Variant exact start and end"/>
</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><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><span title="Codes: {http://www.ncbi.nlm.nih.gov/nuccore 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/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><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><span title="Codes: {http://www.ncbi.nlm.nih.gov/nuccore 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/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/task-med-chg"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><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="#MedicationStatement_current-med-example">See above (MedicationStatement/current-med-example)</a></p><p><b>for</b>: <a href="#Patient_patient">See above (Patient/patient)</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/patient"/>
</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><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_patient">See above (Patient/patient)</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/patient"/>
</subject>
</MedicationStatement>
</resource>
<request>
<method value="POST"/>
<url value="MedicationStatement"/>
</request>
</entry>
</Bundle>
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
Links: Table of Contents |
QA Report
| Version History |
Search |
|
Propose a change