Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
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
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"div" : "<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\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (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\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (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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IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-24
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