Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) 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-oncology-report-example"/>
<type value="transaction"/>
<entry>
<fullUrl value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
<resource>
<Organization>
<id value="Inline-Instance-for-oncology-report-example-1"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_Inline-Instance-for-oncology-report-example-1"> </a><p class="res-header-id"><b>Generated Narrative: Organization Inline-Instance-for-oncology-report-example-1</b></p><a name="Inline-Instance-for-oncology-report-example-1"> </a><a name="hcInline-Instance-for-oncology-report-example-1"> </a><a name="Inline-Instance-for-oncology-report-example-1-en-US"> </a><p><b>identifier</b>: <code>http://molit.eu/fhir/genomics/NamingSystem/organization</code>/CEGAT</p><p><b>name</b>: CEGAT</p></div>
</text>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/organization"/>
<value value="CEGAT"/>
</identifier>
<name value="CEGAT"/>
</Organization>
</resource>
<request>
<method value="POST"/>
<url value="Organization"/>
<ifNoneExist
value="identifier=http://molit.eu/fhir/genomics/NamingSystem/organization|CEGAT"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
<resource>
<Patient>
<id value="Inline-Instance-for-oncology-report-example-2"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_Inline-Instance-for-oncology-report-example-2"> </a><p class="res-header-id"><b>Generated Narrative: Patient Inline-Instance-for-oncology-report-example-2</b></p><a name="Inline-Instance-for-oncology-report-example-2"> </a><a name="hcInline-Instance-for-oncology-report-example-2"> </a><a name="Inline-Instance-for-oncology-report-example-2-en-US"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">Anonymous Patient (no stated gender), DoB Unknown ( http://molit.eu/fhir/genomics/NamingSystem/cegat/patID#11111)</p><hr/></div>
</text>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/patID"/>
<value value="11111"/>
</identifier>
</Patient>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
<ifNoneExist
value="identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/patID|11111"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516"/>
<resource>
<Specimen>
<id value="Inline-Instance-for-oncology-report-example-3"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_Inline-Instance-for-oncology-report-example-3"> </a><p class="res-header-id"><b>Generated Narrative: Specimen Inline-Instance-for-oncology-report-example-3</b></p><a name="Inline-Instance-for-oncology-report-example-3"> </a><a name="hcInline-Instance-for-oncology-report-example-3"> </a><a name="Inline-Instance-for-oncology-report-example-3-en-US"> </a><p><b>identifier</b>: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><p><b>type</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0487 TUMOR}">Tumor</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><h3>Collections</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Method</b></td><td><b>BodySite</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:">Biopsy</span></td><td><span title="Codes:{http://hl7.org/fhir/sid/icd-10-cm C16.0}">Malignant neoplasm of cardia</span></td></tr></table></div>
</text>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
<value value="UNKNOWN"/>
</identifier>
<type>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0487"/>
<code value="TUMOR"/>
<display value="Tumor"/>
</coding>
</type>
<subject>
<reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
</subject>
<collection>
<method>
<text value="Biopsy"/>
</method>
<bodySite>
<coding>
<system value="http://hl7.org/fhir/sid/icd-10-cm"/>
<code value="C16.0"/>
</coding>
</bodySite>
</collection>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Specimen"/>
<ifNoneExist
value="identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID|UNKNOWN"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-report-example-4"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-4"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-4</b></p><a name="Inline-Instance-for-oncology-report-example-4"> </a><a name="hcInline-Instance-for-oncology-report-example-4"> </a><a name="Inline-Instance-for-oncology-report-example-4-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:8975}">PIK3CA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_006218.4:c.3140A>G}">NM_006218.4:c.3140A>G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_006209.2:p.His1047Arg}">NP_006209.2:p.His1047Arg</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_006218.3}">NM_006218.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2188 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 64 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
</subject>
<effectiveDateTime value="2023-03-05"/>
<performer>
<reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</method>
<specimen>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
<value value="UNKNOWN"/>
</identifier>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:8975"/>
<display value="PIK3CA"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_006218.4:c.3140A>G"/>
<display value="NM_006218.4:c.3140A>G"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
<display value="DNA change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.sequenceontology.org"/>
<code value="SO:1000002"/>
<display value="substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
<display value="Amino acid change (pHGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NP_006209.2:p.His1047Arg"/>
<display value="NP_006209.2:p.His1047Arg"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript reference sequence [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_006218.3"/>
<display value="NM_006218.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
</coding>
</code>
<valueString value="A"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
</coding>
</code>
<valueQuantity>
<value value="0.2188"/>
<unit
value="relative frequency of a particular allele in the specimen"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
<display value="Allelic read depth"/>
</coding>
</code>
<valueQuantity>
<value value="64"/>
<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-report-example-5"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-5"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-5</b></p><a name="Inline-Instance-for-oncology-report-example-5"> </a><a name="hcInline-Instance-for-oncology-report-example-5"> </a><a name="Inline-Instance-for-oncology-report-example-5-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:7989}">NRAS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_002524.4:c.34G>T}">NM_002524.4:c.34G>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_002524.4}">NM_002524.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1793 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 145 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
</subject>
<effectiveDateTime value="2023-03-05"/>
<performer>
<reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</method>
<specimen>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
<value value="UNKNOWN"/>
</identifier>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:7989"/>
<display value="NRAS"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_002524.4:c.34G>T"/>
<display value="NM_002524.4:c.34G>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
<display value="DNA change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.sequenceontology.org"/>
<code value="SO:1000002"/>
<display value="substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript reference sequence [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_002524.4"/>
<display value="NM_002524.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
</coding>
</code>
<valueString value="C"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
</coding>
</code>
<valueQuantity>
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<unit
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<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<component>
<code>
<coding>
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<code value="82121-5"/>
<display value="Allelic read depth"/>
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<valueQuantity>
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<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<request>
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<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-report-example-6"/>
<meta>
<profile
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</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-6"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-6</b></p><a name="Inline-Instance-for-oncology-report-example-6"> </a><a name="hcInline-Instance-for-oncology-report-example-6"> </a><a name="Inline-Instance-for-oncology-report-example-6-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:16712}">FBXW7</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_001349798.2:c.1394G>A}">NM_001349798.2:c.1394G>A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_001336727.1:p.Arg465His}">NP_001336727.1:p.Arg465His</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_001349798.2}">NM_001349798.2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1053 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 57 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
</text>
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<category>
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<code>
<coding>
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<display value="Genetic variant assessment"/>
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<subject>
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<effectiveDateTime value="2023-03-05"/>
<performer>
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<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
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<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</method>
<specimen>
<identifier>
<system
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<value value="UNKNOWN"/>
</identifier>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
</valueCodeableConcept>
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<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"/>
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<display value="FBXW7"/>
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<component>
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<component>
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<display value="Genomic ref allele [ID]"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
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<valueQuantity>
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<unit
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<code value="1"/>
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<request>
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</entry>
<entry>
<fullUrl value="urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-report-example-7"/>
<meta>
<profile
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</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-7"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-7</b></p><a name="Inline-Instance-for-oncology-report-example-7"> </a><a name="hcInline-Instance-for-oncology-report-example-7"> </a><a name="Inline-Instance-for-oncology-report-example-7-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:7133}">KMT2D</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003482.3:c.7900_7901delCA}">NM_003482.3:c.7900_7901delCA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0000159}">deletion</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003482.3}">NM_003482.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: CTG</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.188 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 117 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<status value="final"/>
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<code>
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<specimen>
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<coding>
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<code value="48002-0"/>
<display value="Genomic source class"/>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
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</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
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<code value="HGNC:7133"/>
<display value="KMT2D"/>
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<display value="Human reference sequence assembly version"/>
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<display value="Sample VAF"/>
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<unit
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<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<request>
<method value="POST"/>
<url value="Observation"/>
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<entry>
<fullUrl value="urn:uuid:58828523-8893-45fc-973b-16290366c5e5"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-report-example-8"/>
<meta>
<profile
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</meta>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-9"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-9</b></p><a name="Inline-Instance-for-oncology-report-example-9"> </a><a name="hcInline-Instance-for-oncology-report-example-9"> </a><a name="Inline-Instance-for-oncology-report-example-9-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:6126}">IRS2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003749.2:c.3960C>T}">NM_003749.2:c.3960C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003749.2}">NM_003749.2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1343 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 134 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<meta>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-11"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-11</b></p><a name="Inline-Instance-for-oncology-report-example-11"> </a><a name="hcInline-Instance-for-oncology-report-example-11"> </a><a name="Inline-Instance-for-oncology-report-example-11-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:9949}">RECQL4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_004260.4:c.2086C>T}">NM_004260.4:c.2086C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_004251.4:p.Arg696Cys}">NP_004251.4:p.Arg696Cys</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004260.4}">NM_004260.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2568 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 148 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-12"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-12</b></p><a name="Inline-Instance-for-oncology-report-example-12"> </a><a name="hcInline-Instance-for-oncology-report-example-12"> </a><a name="Inline-Instance-for-oncology-report-example-12-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:10483}">RYR1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_000540.3:c.4964G>A}">NM_000540.3:c.4964G>A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_000531.2:p.Arg1655Leu}">NP_000531.2:p.Arg1655Leu</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000540.2}">NM_000540.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2151 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 93 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-14"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-14</b></p><a name="Inline-Instance-for-oncology-report-example-14"> </a><a name="hcInline-Instance-for-oncology-report-example-14"> </a><a name="Inline-Instance-for-oncology-report-example-14-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:11086}">SLIT2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_004787.3:c.1290C>A}">NM_004787.3:c.1290C>A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004787.3}">NM_004787.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2642 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 53 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-15"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-15</b></p><a name="Inline-Instance-for-oncology-report-example-15"> </a><a name="hcInline-Instance-for-oncology-report-example-15"> </a><a name="Inline-Instance-for-oncology-report-example-15-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:11100}">SMARCA4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003072.5:c.2372C>T}">NM_003072.5:c.2372C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_003063.2:p.Ala791Val}">NP_003063.2:p.Ala791Val</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003072.5}">NM_003072.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1938 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 160 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</method>
<specimen>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
<value value="UNKNOWN"/>
</identifier>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:11100"/>
<display value="SMARCA4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_003072.5:c.2372C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
<display value="DNA change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.sequenceontology.org"/>
<code value="SO:1000002"/>
<display value="substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
<display value="Amino acid change (pHGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NP_003063.2:p.Ala791Val"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript reference sequence [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_003072.5"/>
<display value="NM_003072.5"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
</coding>
</code>
<valueString value="C"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
</coding>
</code>
<valueQuantity>
<value value="0.1938"/>
<unit
value="relative frequency of a particular allele in the specimen"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
<display value="Allelic read depth"/>
</coding>
</code>
<valueQuantity>
<value value="160"/>
<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa"/>
<resource>
<DiagnosticReport>
<id value="Inline-Instance-for-oncology-report-example-16"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="DiagnosticReport_Inline-Instance-for-oncology-report-example-16"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-report-example-16</b></p><a name="Inline-Instance-for-oncology-report-example-16"> </a><a name="hcInline-Instance-for-oncology-report-example-16"> </a><a name="Inline-Instance-for-oncology-report-example-16-en-US"> </a><h2><span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>Subject</td><td>Not done yet</td></tr><tr><td>Reported</td><td>2019-09-15 11:35:05-0400</td></tr><tr><td>Performer</td><td> <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></td></tr><tr><td>Identifier</td><td> <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/reportID</code>/42867</td></tr></table><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>
</text>
<identifier>
<system
value="http://molit.eu/fhir/genomics/NamingSystem/cegat/reportID"/>
<value value="42867"/>
</identifier>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51969-4"/>
<display value="Genetic analysis report"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
</subject>
<issued value="2019-09-15T11:35:05.722-04:00"/>
<performer>
<reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
</performer>
<specimen>
<reference value="urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516"/>
</specimen>
<result>
<reference value="urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae"/>
</result>
<result>
<reference value="urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00"/>
</result>
<result>
<reference value="urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5"/>
</result>
<result>
<reference value="urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358"/>
</result>
<result>
<reference value="urn:uuid:58828523-8893-45fc-973b-16290366c5e5"/>
</result>
<result>
<reference value="urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2"/>
</result>
<result>
<reference value="urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1"/>
</result>
<result>
<reference value="urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf"/>
</result>
<result>
<reference value="urn:uuid:c3587931-242f-4129-93f9-be24500c8f29"/>
</result>
<result>
<reference value="urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6"/>
</result>
<result>
<reference value="urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2"/>
</result>
<result>
<reference value="urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca"/>
</result>
</DiagnosticReport>
</resource>
<request>
<method value="POST"/>
<url value="DiagnosticReport"/>
</request>
</entry>
</Bundle>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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