Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
<Observation xmlns="http://hl7.org/fhir">
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<!-- query4: Observation?component-code-value-concept=http://loinc.org|48006-1$http://varnomen.hgvs.org|p.(Ala412Val) -->
<id value="SNVexample"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>code</b>: <span title="Codes: {http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 48018-6}">Gene studied ID</span></p><p><b>value</b>: <span title="Codes: {http://www.genenames.org/geneId HGNC:644}">AR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 48001-2}">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title="Codes: ">chrX</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 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 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes: {http://varnomen.hgvs.org p.(Ala412Val)}">p.(Ala412Val)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 48006-1}">Amino acid change type</span></p><p><b>value</b>: <span title="Codes: {http://loinc.org LA6698-0}">Missense</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_000044.3}">NM_000044.3</span></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>: 0.44 decimal</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>: 120 reads per base pair</p></blockquote></div>
</text>
<status value="final"/>
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<code value="laboratory"/>
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<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
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</code>
<!--
<subject>
<reference value="Patient/12345" />
</subject>
<performer>
<reference value="Organization/CeGaT"/>
</performer>
-->
<valueCodeableConcept>
<coding>
<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 value="http://slk-kliniken.de/fhir/namingSystem/tissueID"/>
<value value="16-123456-23"/>
</identifier>
</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:644"/>
<display value="AR"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48001-2"/>
<display value="Cytogenetic (chromosome) location"/>
</coding>
</code>
<valueCodeableConcept>
<text value="chrX"/>
</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="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<!-- fine -->
<display value="Somatic"/>
</coding>
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</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="p.(Ala412Val)"/>
<display value="p.(Ala412Val)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48006-1"/>
<display value="Amino acid change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6698-0"/>
<display value="Missense"/>
</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_000044.3"/>
<display value="NM_000044.3"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
</coding>
</code>
<valueQuantity>
<value value="0.44"/>
<unit value="decimal"/>
<system value="http://unitsofmeasure.org"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
<display value="Allelic read depth"/>
</coding>
</code>
<valueQuantity>
<value value="120"/>
<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="{reads}/{base}"/>
</valueQuantity>
</component>
</Observation>
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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