Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
| Page standards status: Informative |
{
"resourceType" : "GenomicStudy",
"resourceDefinition" : "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
"id" : "example-lungMass",
"language" : "en",
"text" : // from Resource: id, meta, implicitRules, and language
// from DomainResource: text, contained, extension, and modifierExtension
{
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy example-lungMass</b></p><a name=\"example-lungMass\"> </a><a name=\"hcexample-lungMass\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Language: en</p></div><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:1111-1111-1111-1112\u00a0(use:\u00a0temp,\u00a0)</p><p><b>status</b>: Registered</p><p><b>type</b>: <span title=\"Codes:{http://snomed.info/sct 443968007}\">Sequencing of entire coding region of gene (procedure)</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>encounter</b>: <a href=\"Encounter-genomicEncounter.html\">Encounter: status = in-progress; class = inpatient encounter</a></p><p><b>startDate</b>: 2019-03-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-genomicServiceRequest2.html\">ServiceRequest Carrier detection, molecular genetics (procedure)</a></p><p><b>referrer</b>: <a href=\"Practitioner-practitioner01.html\">Practitioner John Doel </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, PIK3CA was deemed uncallable.</p>\n</div></blockquote><p><b>description</b>: </p><div><p>Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.</p>\n</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1112\u00a0(use:\u00a0official,\u00a0)</p><p><b>methodType</b>: <span title=\"Codes:{http://snomed.info/sct 117040002}\">Nucleic acid sequencing (procedure)</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>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>title</b>: Simple variant analysis</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, PIK3CA was deemed uncallable using this method.</p>\n</div></blockquote><h3>Metrics</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>ReadDepth</b></td><td><b>SequencingCoverage</b></td><td><b>Description</b></td></tr><tr><td style=\"display: none\">*</td><td>120 x<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></td><td>98 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code% = '%')</span></td><td>120x average read depth with 98% coverage of target regions.</td></tr></table><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}\">Studied</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><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.</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype called}\">Called</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><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.</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype uncalled}\">Uncalled</span></p><h3>Locus</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://www.genenames.org HGNC:8975}\">PIK3CA</span></td></tr></table></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/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><td><b>Function</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1115\u00a0(use:\u00a0official,\u00a0)</p><p><b>methodType</b>: <span title=\"Codes:{http://snomed.info/sct 117040002}\">Nucleic acid sequencing (procedure)</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>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>title</b>: CNV analysis</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><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}\">Studied</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><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.</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype called}\">Called</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Reference</b></td></tr><tr><td style=\"display: none\">*</td><td><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.</a></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype uncalled}\">Uncalled</span></p><h3>Locus</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://www.genenames.org HGNC:8975}\">PIK3CA</span></td></tr></table><p><b>description</b>: PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay.</p></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/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>"
},
"identifier" : [
// from DomainResource: text, contained, extension, and modifierExtension
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicstudies",
"value" : "urn:uuid:1111-1111-1111-1112"
}
],
"status" : "registered",
"type" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "443968007",
"display" : "Sequencing of entire coding region of gene (procedure)"
}
]
}
],
"subject" : {
🔗 "reference" : "Patient/genomicPatient"
},
"encounter" : {
🔗 "reference" : "Encounter/genomicEncounter"
},
"startDate" : "2019-03-01",
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/genomicServiceRequest2"
}
],
"referrer" : {
🔗 "reference" : "Practitioner/practitioner01"
},
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"reason" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "309529002",
"display" : "Lung mass (finding)"
}
]
}
}
],
"note" : [
{
"text" : "For technical reasons, PIK3CA was deemed uncallable."
}
],
"description" : "Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.",
"analysis" : [
// 0..1 Description of the genomic study
{
"identifier" : [
{
"use" : "official",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1112"
}
],
"methodType" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "117040002",
"display" : "Nucleic acid sequencing (procedure)"
}
]
}
],
"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"
}
]
},
"genomicSourceClass" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6684-0",
"display" : "Somatic"
}
]
},
"title" : "Simple variant analysis",
"specimen" : [
// 0..1 Name of the analysis event (human friendly)
{
🔗 "reference" : "Specimen/genomicSpecimen"
}
],
"date" : "2019-03-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "For technical reasons, PIK3CA was deemed uncallable using this method."
}
],
"metrics" : {
"readDepth" : {
"value" : 120,
"unit" : "x",
"system" : "http://unitsofmeasure.org",
"code" : "1"
},
"sequencingCoverage" : {
"value" : 98,
"unit" : "%",
"system" : "http://unitsofmeasure.org",
"code" : "%"
},
"description" : "120x average read depth with 98% coverage of target regions."
},
"genomicRegion" : [
// genomicRegion: studied scope = full exome BED file
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "studied",
"display" : "Studied"
}
]
},
"locus" : [
{
"reference" : {
🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
}
]
},
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "called",
"display" : "Called"
}
]
},
"locus" : [
{
"reference" : {
🔗 "reference" : "DocumentReference/SimpleVariantAnalysis-called"
}
}
]
},
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "uncalled",
"display" : "Uncalled"
}
]
},
"locus" : [
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:8975",
"display" : "PIK3CA"
}
]
}
}
]
}
],
"output" : [
// genomicRegion: called = variant-callable regions expressed as a BED file
// genomicRegion: uncalled = PIK3CA could not be called; no variant call is implied
{
"type" : // 0..* outputs for the analysis event
// <file>
<reference value="DocumentReference/genomicVCFfile_simple"/>
</file>
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
{
"actor" : // 0..* Performer for the analysis event
{
🔗 "reference" : "Practitioner/practitioner02"
},
"role" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
}
}
],
"device" : [
{
"device" : // 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters
{
🔗 "reference" : "Device/NGS-device"
},
"function" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
}
}
]
},
{
"identifier" : [
{
"use" : "official",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1115"
}
],
"methodType" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "117040002",
"display" : "Nucleic acid sequencing (procedure)"
}
]
}
],
"changeType" : [
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001019",
"display" : "CNV"
}
]
}
],
"genomeBuild" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
},
"genomicSourceClass" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6684-0",
"display" : "Somatic"
}
]
},
"title" : "CNV analysis",
"specimen" : [
// 0..1 Name of the analysis event (human friendly)
{
🔗 "reference" : "Specimen/genomicSpecimen"
}
],
"date" : "2019-03-01T01:01:10-06:00",
"genomicRegion" : [
// 0..1 The date of the analysis event
// genomicRegion: studied scope = full exome BED file
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "studied",
"display" : "Studied"
}
]
},
"locus" : [
{
"reference" : {
🔗 "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
}
}
]
},
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "called",
"display" : "Called"
}
]
},
"locus" : [
{
"reference" : {
🔗 "reference" : "DocumentReference/CNVAnalysis-called"
}
}
]
},
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "uncalled",
"display" : "Uncalled"
}
]
},
"locus" : [
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:8975",
"display" : "PIK3CA"
}
]
}
}
],
"description" : "PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay."
}
],
"output" : [
// genomicRegion: called = CNV-callable regions expressed as a BED file
// genomicRegion: uncalled = PIK3CA could not be called with this CNV method
{
"type" : // 0..* Inputs for the analysis event
// <file>
<reference value="DocumentReference/genomicVCFfile_cnv"/>
</file>
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
{
"actor" : // 0..* Performer for the analysis event
{
🔗 "reference" : "Practitioner/practitioner02"
},
"role" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
}
}
]
}
]
}
IG © 2026+ HL7 International / Clinical Genomics.
Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3.
Generated
2026-03-24
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change