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
{
"resourceType" : "Procedure",
"id" : "lungMass-analysis1",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
]
},
"text" : {
"status" : "extensions",
"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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
"code" : "sequence-analysis-of-the-entire-coding-region",
"display" : "Sequence analysis of the entire coding region"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6684-0",
"display" : "Somatic"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001483",
"display" : "SNV"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0002007",
"display" : "MNV"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:1000032",
"display" : "delins"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
"valueReference" : {
🔗 "reference" : "Specimen/genomicSpecimen"
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
"valueReference" : {
🔗 "reference" : "Patient/genomicPatient"
}
},
{
"extension" : [
{
"url" : "device",
"valueReference" : {
🔗 "reference" : "Device/triodenovo-software"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
},
{
"extension" : [
{
"url" : "studied",
"valueReference" : {
🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
},
{
"url" : "uncalled",
"valueReference" : {
🔗 "reference" : "DocumentReference/UncallableRegions"
}
},
{
"url" : "called",
"valueReference" : {
🔗 "reference" : "DocumentReference/SimpleVariantAnalysis-called"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
},
{
"extension" : [
{
"url" : "type",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
"code" : "vcf",
"display" : "VCF"
}
]
}
},
{
"url" : "file",
"valueReference" : {
🔗 "reference" : "DocumentReference/genomicVCFfile-simple"
}
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
}
],
"instantiatesUri" : [
"https://pubmed.ncbi.nlm.nih.gov/33927380/"
],
"status" : "completed",
"category" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
"subject" : {
🔗 "reference" : "Patient/genomicPatient"
},
"performedDateTime" : "2019-03-01T01:01:10-06:00",
"performer" : [
{
"function" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
},
"actor" : {
🔗 "reference" : "Practitioner/practitioner02"
}
}
],
"note" : [
{
"text" : "For technical reasons, PIK3CB was deemed uncallable using this method."
}
]
}
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