Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: pgx-report</p><p><b>meta</b>: </p><p><b>basedOn</b>: <a href="ServiceRequest/pgx-request">ServiceRequest/pgx-request</a></p><p><b>status</b>: final</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel)</span></p><p><b>subject</b>: <a href="Patient/patient">Patient/patient</a></p><p><b>effective</b>: Jan 1, 2016 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>performer</b>: <a href="Organization/lab">Organization/lab</a></p><p><b>result</b>: </p><ul><li><a href="Observation/med-impact-pgx-example">genetics impact for medication metabolism accessment</a></li><li><a href="Observation/genotype-pgx-example">Observation/genotype-pgx-example</a></li><li><a href="Observation/haplotype-1-pgx-example">Observation/haplotype-1-pgx-example</a></li><li><a href="Observation/haplotype-2-pgx-example">Observation/haplotype-2-pgx-example</a></li><li><a href="Observation/variant-1-pgx-example">Observation/variant-1-pgx-example</a></li><li><a href="Observation/variant-2-pgx-example">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/medication-metabolism"/> </meta> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: med-impact-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variation's effect on drug metabolism <span style="background: LightGoldenRodYellow">(Details : {LOINC code '53040-2' = 'Genetic variation's effect on drug metabolism', given as 'Genetic variation's effect on drug metabolism'})</span></p><p><b>subject</b>: <a href="Patient/patient">Patient/patient</a></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>performer</b>: <a href="Organization/lab">Organization/lab</a></p><p><b>value</b>: Rapid metabolizer <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA25390-8' = 'Rapid metabolizer', given as 'Rapid metabolizer'})</span></p><p><b>derivedFrom</b>: <a href="Observation/genotype-pgx-example">Observation/genotype-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>Medication assessed <span style="background: LightGoldenRodYellow">(Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'})</span></td><td>mercaptopurine <span style="background: LightGoldenRodYellow">(Details : {RxNorm code '103' = 'mercaptopurine', given as 'mercaptopurine'})</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="53040-2"/> <display value="Genetic variation's effect on drug metabolism"/> </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> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA25390-8"/> <display value="Rapid metabolizer"/> </coding> </valueCodeableConcept> <derivedFrom> <reference value="Observation/genotype-pgx-example"/> </derivedFrom> <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 with Details</b></p><p><b>id</b>: genotype-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: genotype display name <span style="background: LightGoldenRodYellow">(Details : {LOINC code '84413-4' = 'Genotype display name', given as 'genotype display name'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: CYP2C9 *4/*35B <span style="background: LightGoldenRodYellow">(Details : {http://www.pharmvar.org code 'CYP2C9 *4/*35B' = 'CYP2C9 *4/*35B', given as 'CYP2C9 *4/*35B'})</span></p><p><b>specimen</b>: <a href="Specimen/specimen">Specimen/specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href="Observation/haplotype-1-pgx-example">Observation/haplotype-1-pgx-example</a></li><li><a href="Observation/haplotype-2-pgx-example">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">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as '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 with Details</b></p><p><b>id</b>: haplotype-1-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Haplotype Name <span style="background: LightGoldenRodYellow">(Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: CYP2C9 *35B <span style="background: LightGoldenRodYellow">(Details : {http://www.pharmvar.org code 'CYP2C9 *35B' = 'CYP2C9 *35B', given as 'CYP2C9 *35B'})</span></p><p><b>specimen</b>: <a href="Specimen/specimen">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href="Observation/variant-1-pgx-example">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">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as '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 with Details</b></p><p><b>id</b>: haplotype-2-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Haplotype Name <span style="background: LightGoldenRodYellow">(Details : {LOINC code '84414-2' = 'Haplotype name', given as 'Haplotype Name'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: CYP2C9 *4 <span style="background: LightGoldenRodYellow">(Details : {http://www.pharmvar.org code 'CYP2C9 *4' = 'CYP2C9 *4', given as 'CYP2C9 *4'})</span></p><p><b>specimen</b>: <a href="Specimen/specimen">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href="Observation/variant-2-pgx-example">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">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></td><td>CYP2C9 <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as '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 with Details</b></p><p><b>id</b>: variant-1-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>specimen</b>: <a href="Specimen/specimen">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href="MolecularSequence/sequence-1-pgx-example">MolecularSequence/sequence-1-pgx-example</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: CYP2C9 <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: dbSNP ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})</span></p><p><b>value</b>: rs12345 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/SNP code 'rs12345' = 'rs12345)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Ref nucleotide'})</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">(Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Alt allele'})</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start and end <span style="background: LightGoldenRodYellow">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'exact-start-end' = 'Variant exact start and end', given as '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/tbd-codes"/> <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 with Details</b></p><p><b>id</b>: variant-2-pgx-example</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>effective</b>: Jan 1, 2018 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018 12:00:00 AM</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>specimen</b>: <a href="Specimen/specimen">Specimen/specimen</a></p><p><b>derivedFrom</b>: <a href="MolecularSequence/sequence-2-pgx-example">MolecularSequence/sequence-2-pgx-example</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: CYP2C9 <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code '2623' = '2623', given as 'CYP2C9'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48013-7' = 'Genomic reference sequence [ID]', given as 'Genomic reference sequence ID'})</span></p><p><b>value</b>: NG_007726.3 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NG_007726.3' = 'NG_007726.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: dbSNP ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81255-2' = 'dbSNP [ID]', given as 'dbSNP ID'})</span></p><p><b>value</b>: rs233455 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/SNP code 'rs233455' = 'rs233455)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69547-8' = 'Genomic ref allele [ID]', given as 'Ref nucleotide'})</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">(Details : {LOINC code '69551-0' = 'Genomic alt allele [ID]', given as 'Alt allele'})</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start and end <span style="background: LightGoldenRodYellow">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'exact-start-end' = 'Variant exact start and end', given as '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/tbd-codes"/> <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 with Details</b></p><p><b>id</b>: sequence-1-pgx-example</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>NG-007726.3 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code '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 with Details</b></p><p><b>id</b>: sequence-2-pgx-example</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>NG-007726.3 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/nuccore code '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 with Details</b></p><p><b>id</b>: med-usage-impact-task-pgx-example</p><p><b>meta</b>: </p><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">(Details : {LOINC code 'LA26423-6' = 'Increase dose', given as '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">MedicationStatement/current-med-example</a></p><p><b>for</b>: <a href="Patient/patient">Patient/patient</a></p><p><b>reasonReference</b>: <a href="Observation/med-impact-pgx-example">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"/> <meta> <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medicationstatement"/> </meta> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: current-med-example</p><p><b>meta</b>: </p><p><b>status</b>: unknown</p><p><b>medication</b>: mercaptopurine <span style="background: LightGoldenRodYellow">(Details : {RxNorm code '103' = 'mercaptopurine', given as 'mercaptopurine'})</span></p><p><b>subject</b>: <a href="Patient/patient">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 © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
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