Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
<Procedure xmlns="http://hl7.org/fhir">
<id value="lungMass-analysis2"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"/>
</meta>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Procedure lungMass-analysis2</b></p><a name="lungMass-analysis2"> </a><a name="hclungMass-analysis2"> </a><a name="lungMass-analysis2-en-US"> </a><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs deletion-duplication-analysis}">Deletion/duplication analysis</span></p><p><b>Genomic Study Analysis Source Class</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001019}">CNV</span></p><p><b>Genomic Study Analysis Genome Build</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-genomicSpecimen.html">Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href="Patient-genomicPatient.html">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <a href="DocumentReference-WES-FullSequencedRegion-GRCh38.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>called: <a href="DocumentReference-CNVAnalysis-called.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11120; status = current; docStatus = preliminary; description = CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}">VCF</span></li><li>file: <a href="DocumentReference-genomicVCFfile-cnv.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11121; status = current; docStatus = preliminary; description = genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><p><b>instantiatesUri</b>: <a href="https://pubmed.ncbi.nlm.nih.gov/33927380/">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Patient-genomicPatient.html">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>performed</b>: 2019-03-01 01:01:10-0600</p><h3>Performers</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Function</b></td><td><b>Actor</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}">Performer</span></td><td><a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></td></tr></table><p><b>note</b>: For technical reasons, PIK3CB was deemed uncallable using this method.</p></div>
</text>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type">
<valueCodeableConcept>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs"/>
<code value="deletion-duplication-analysis"/>
<display value="Deletion/duplication analysis"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class">
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type">
<valueCodeableConcept>
<coding>
<system value="http://www.sequenceontology.org"/>
<code value="SO:0001019"/>
<display value="CNV"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build">
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26806-2"/>
<display value="GRCh38"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen">
<valueReference>🔗
<reference value="Specimen/genomicSpecimen"/>
</valueReference>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus">
<valueReference>🔗
<reference value="Patient/genomicPatient"/>
</valueReference>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions">
<extension url="studied">
<valueReference>🔗
<reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
</valueReference>
</extension>
<extension url="called">
<valueReference>🔗
<reference value="DocumentReference/CNVAnalysis-called"/>
</valueReference>
</extension>
</extension>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output">
<extension url="type">
<valueCodeableConcept>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</valueCodeableConcept>
</extension>
<extension url="file">
<valueReference>🔗
<reference value="DocumentReference/genomicVCFfile-cnv"/>
</valueReference>
</extension>
</extension>
<instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
<status value="completed"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<subject>🔗
<reference value="Patient/genomicPatient"/>
</subject>
<performedDateTime value="2019-03-01T01:01:10-06:00"/>
<performer>
<function>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
<code value="PRF"/>
<display value="Performer"/>
</coding>
</function>
<actor>🔗
<reference value="Practitioner/practitioner02"/>
</actor>
</performer>
<note>
<text
value="For technical reasons, PIK3CB was deemed uncallable using this method."/>
</note>
</Procedure>
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
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change