Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot 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
| Page standards status: Informative |
{
"resourceType" : "GenomicStudy",
"id" : "lungMass",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy lungMass</b></p><a name=\"lungMass\"> </a><a name=\"hclungMass\"> </a><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:\">Solid tumor whole exome sequencing panel</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>startDate</b>: 2019-03-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-genomicServiceRequest.html\">ServiceRequest Molecular genetic test (procedure)</a></p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://snomed.info/sct 309529002}\">Lung mass (finding)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable.</p>\n</div></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>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><p><b>specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://example.org/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>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote><p><b>regionsStudied</b>: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/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></p><p><b>regionsCalled</b>: <a href=\"DocumentReference-SimpleVariantAnalysis-called.html\">DocumentReference: identifier = http://example.org/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></p><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicVCFfile-simple.html\">DocumentReference: identifier = http://example.org/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></td><td><span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-triodenovo-software.html\">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-methodtype deletion-duplication-analysis}\">Deletion/duplication analysis</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">CNV</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>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><p><b>specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://example.org/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>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote><p><b>regionsStudied</b>: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/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></p><p><b>regionsCalled</b>: <a href=\"DocumentReference-CNVAnalysis-called.html\">DocumentReference: identifier = http://example.org/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></p><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicVCFfile-cnv.html\">DocumentReference: identifier = http://example.org/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></td><td><span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table></blockquote></div>"
},
"status" : "available",
"type" : [
{
"text" : "Solid tumor whole exome sequencing panel"
}
],
"subject" : {
🔗 "reference" : "Patient/genomicPatient"
},
"startDate" : "2019-03-01",
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/genomicServiceRequest"
}
],
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"reason" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "309529002",
"display" : "Lung mass (finding)"
}
]
}
}
],
"note" : [
{
"text" : "For technical reasons, PIK3CB was deemed uncallable."
}
],
"analysis" : [
{
"methodType" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-methodtype",
"code" : "sequence-analysis-of-the-entire-coding-region",
"display" : "Sequence analysis of the entire coding region"
}
]
}
],
"changeType" : [
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001483",
"display" : "SNV"
}
]
},
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0002007",
"display" : "MNV"
}
]
},
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:1000032",
"display" : "delins"
}
]
}
],
"genomeBuild" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
},
"instantiatesUri" : "https://pubmed.ncbi.nlm.nih.gov/33927380/",
"focus" : [
{
🔗 "reference" : "Patient/genomicPatient"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/genomicSpecimen"
}
],
"date" : "2019-03-01T01:01:10-06:00",
"note" : [
{
"text" : "For technical reasons, PIK3CB was deemed uncallable using this method."
}
],
"regionsStudied" : [
{
🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
],
"regionsCalled" : [
{
🔗 "reference" : "DocumentReference/SimpleVariantAnalysis-called"
}
],
"output" : [
{
"file" : {
🔗 "reference" : "DocumentReference/genomicVCFfile-simple"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
{
"actor" : {
🔗 "reference" : "Practitioner/practitioner02"
},
"role" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
}
}
],
"device" : [
{
"device" : {
🔗 "reference" : "Device/triodenovo-software"
}
}
]
},
{
"methodType" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-methodtype",
"code" : "deletion-duplication-analysis",
"display" : "Deletion/duplication analysis"
}
]
}
],
"changeType" : [
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001019",
"display" : "CNV"
}
]
}
],
"genomeBuild" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
},
"instantiatesUri" : "https://pubmed.ncbi.nlm.nih.gov/33927380/",
"focus" : [
{
🔗 "reference" : "Patient/genomicPatient"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/genomicSpecimen"
}
],
"date" : "2019-03-01T01:01:10-06:00",
"note" : [
{
"text" : "For technical reasons, PIK3CB was deemed uncallable using this method."
}
],
"regionsStudied" : [
{
🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
],
"regionsCalled" : [
{
🔗 "reference" : "DocumentReference/CNVAnalysis-called"
}
],
"output" : [
{
"file" : {
🔗 "reference" : "DocumentReference/genomicVCFfile-cnv"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
{
"actor" : {
🔗 "reference" : "Practitioner/practitioner02"
},
"role" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
}
}
]
}
]
}
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-ballot based on FHIR 6.0.0-ballot3. Generated 2025-10-16
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