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 in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
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<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Procedure lungMass-analysis1</b></p><a name="lungMass-analysis1"> </a><a name="hclungMass-analysis1"> </a><a name="lungMass-analysis1-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 sequence-analysis-of-the-entire-coding-region}">Sequence analysis of the entire coding region</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:0001483}">SNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:0002007}">MNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000032}">delins</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 Device</b></p><ul><li>device: <a href="Device-triodenovo-software.html">Device: identifier = http://www.somesystemabc.net/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></li></ul></blockquote><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>uncalled: <a href="DocumentReference-UncallableRegions.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted</a></li><li>called: <a href="DocumentReference-SimpleVariantAnalysis-called.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_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-simple.html">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: 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>
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<extension
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<valueReference>🔗
<reference value="Specimen/genomicSpecimen"/>
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<extension
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<valueReference>🔗
<reference value="Patient/genomicPatient"/>
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<extension
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<extension url="device">
<valueReference>🔗
<reference value="Device/triodenovo-software"/>
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<extension url="studied">
<valueReference>🔗
<reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
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<valueReference>🔗
<reference value="DocumentReference/genomicVCFfile-simple"/>
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<instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
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<actor>🔗
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<note>
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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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