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 http://build.fhir.org/ig/HL7/genomics-reporting/diagnosticreport-pgxexample.xml.html --> <id value="HLAB1502-pgx-example"/> <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>: ServiceRequest/pgx-request</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>: Patient/patient</p><p><b>effective</b>: Jan 1, 2016, 12:00:00 AM</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>performer</b>: Organization/lab</p><p><b>result</b>: </p><ul><li>genetics impact for medication metabolism accessment</li><li>Observation/genotype-pgx-example</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/medication-high-risk"/> <display value="genetics impact for high risk allele"/> </result> <result> <reference value="Observation/genotype-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"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: pgx-request</p><p><b>meta</b>: </p><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">(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>reasonCode</b>: Worried about family planning <span style="background: LightGoldenRodYellow">(Details )</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/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/medication-high-risk"/> <resource> <Observation> <id value="medication-high-risk"/> <meta> <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-high-risk"/> </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>: medication-high-risk</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 high-risk allele <span style="background: LightGoldenRodYellow">(Details : {LOINC code '83009-1' = 'Genetic variation's effect on high-risk allele', given as 'Genetic variation's effect on high-risk allele'})</span></p><p><b>value</b>: High risk <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA19541-4' = 'High risk', given as 'High risk'})</span></p><p><b>derivedFrom</b>: <a href="Observation/genotype-pgx-example">Observation/genotype-pgx-example</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed <span style="background: LightGoldenRodYellow">(Details : {LOINC code '51963-7' = 'Medication assessed [ID]', given as 'Medication assessed'})</span></p><p><b>value</b>: Carbamazepine <span style="background: LightGoldenRodYellow">(Details : {RxNorm code '2002' = 'Carbamazepine', given as 'Carbamazepine'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Level of evidence <span style="background: LightGoldenRodYellow">(Details : {LOINC code '93044-6' = 'Level of evidence', given as 'Level of evidence'})</span></p><p><b>value</b>: Very strong evidence pathogenic <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA30200-2' = 'Very strong evidence pathogenic', given as 'Very strong evidence pathogenic'})</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://loinc.org"/> <code value="83009-1"/> <display value="Genetic variation's effect on high-risk allele"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA19541-4"/> <display value="High risk"/> </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="2002"/> <display value="Carbamazepine"/> </coding> </valueCodeableConcept> </component> <!-- <component> <code> <coding> <system value="http://loinc.org"/> <code value="81259-4"/> <display value="Prob assoc phenotype"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://monarchinitiative.org/disease"/> <code value="MONDO:0018229"/> <display value="Stevens-Johnson syndrome"/> </coding> </valueCodeableConcept> </component> --> <component> <code> <coding> <system value="http://loinc.org"/> <code value="93044-6"/> <display value="Level of evidence"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA30200-2"/> <display value="Very strong evidence pathogenic"/> </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, 5:00:00 AM</p><p><b>value</b>: HLA-B*15:02 <span style="background: LightGoldenRodYellow">(Details : {https://www.pharmvar.org/ code 'HLA-B*15:02' = 'HLA-B*15:02', given as 'HLA-B*15:02'})</span></p><p><b>specimen</b>: Specimen/specimen</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>HLA-B <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org code 'HGNC:4932' = 'HGNC:4932', given as 'HLA-B'})</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.ncbi.nlm.nih.gov/clinvar"/> <code value="14909"/> <display value="HLA-B*15:02"/> </coding> </valueCodeableConcept> <specimen> <reference value="Specimen/specimen"/> </specimen> <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="HGNC:4932"/> <display value="HLA-B"/> </coding> </valueCodeableConcept> </component> </Observation> </resource> <request> <method value="POST"/> <url value="Observation"/> </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 'LA26421-0' = 'Consider alternative medication', given as 'Consider alternative medication'})</span></p><p><b>description</b>: Patients positive for this allele should not be treated with CBZ, unless the benefits clearly outweigh the risk. Therapy should be discontinued immediately if symptoms of SJS or TEN develop. Alternative medication should be used as first line therapy. Consideration in the choice for alternative medications should be given to potential cross-reactivity with structurally similar aromatic antiepileptic drugs such as oxcarbazepine, phenytoin, fosphenytoin and lamotrigine, which can also moderately increase risk for SJS/TEN in association with HLA-B*15:02 positivity.</p><p><b>focus</b>: MedicationStatement/current-med-example</p><p><b>for</b>: Patient/patient</p><p><b>reasonReference</b>: Observation/medication-high-risk</p></div> </text> <status value="requested"/> <intent value="proposal"/> <code> <coding> <system value="http://loinc.org"/> <code value="LA26421-0"/> <display value="Consider alternative medication"/> </coding> <text value="Patients positive for this allele should not be treated with CBZ, unless the benefits clearly outweigh the risk"/> </code> <description value="Patients positive for this allele should not be treated with CBZ, unless the benefits clearly outweigh the risk. Therapy should be discontinued immediately if symptoms of SJS or TEN develop. Alternative medication should be used as first line therapy. Consideration in the choice for alternative medications should be given to potential cross-reactivity with structurally similar aromatic antiepileptic drugs such as oxcarbazepine, phenytoin, fosphenytoin and lamotrigine, which can also moderately increase risk for SJS/TEN in association with HLA-B*15:02 positivity."/> <focus> <reference value="MedicationStatement/current-med-example"/> </focus> <for> <reference value="Patient/patient"/> </for> <reasonReference> <reference value="Observation/medication-high-risk"/> </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>: Carbamazepine <span style="background: LightGoldenRodYellow">(Details : {RxNorm code '2002' = 'Carbamazepine', given as 'Carbamazepine'})</span></p><p><b>subject</b>: Patient/patient</p></div> </text> <status value="unknown"/> <medicationCodeableConcept> <coding> <system value="http://www.nlm.nih.gov/research/umls/rxnorm"/> <code value="2002"/> <display value="Carbamazepine"/> </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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