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-trio2",
"language" : "en",
"text" : // from Resource: id, meta, implicitRules, and language
{
"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-trio2</b></p><a name=\"example-trio2\"> </a><a name=\"hcexample-trio2\"> </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:1111-1111-1111-1113\u00a0(use:\u00a0temp,\u00a0)</p><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type trio}\">Trio analysis</span></p><p><b>subject</b>: <a href=\"Patient-proband.html\">Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><p><b>encounter</b>: <a href=\"Encounter-denovoEncounter.html\">Encounter: status = in-progress; class = inpatient encounter</a></p><p><b>startDate</b>: 2022-05-01</p><p><b>basedOn</b>: </p><ul><li><a href=\"ServiceRequest-genomicSRProband.html\">ServiceRequest Carrier detection, molecular genetics (procedure)</a></li><li><a href=\"ServiceRequest-genomicSRMother.html\">ServiceRequest Carrier detection, molecular genetics (procedure)</a></li><li><a href=\"ServiceRequest-genomicSRFather.html\">ServiceRequest Carrier detection, molecular genetics (procedure)</a></li></ul><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 67799006}\">Cystic fibrosis, prenatal detection (procedure)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>This de novo mutation is urgent and important for establishing the treatment plan.</p>\n</div></blockquote><p><b>description</b>: </p><div><p>De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.</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:\u00a0temp,\u00a0)</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Maternal Sequence Variation Detection Using Next Generation Sequencing</p><p><b>focus</b>: <a href=\"Patient-mother.html\">Jane Mother Doe (official) Female, DoB: 2000-01-01 ( Medical record number: 11112\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-specimenMother.html\">Specimen: identifier = http://example.org/identifiers/specimens#6; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2022-07-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a mother of a proband.</p>\n</div></blockquote><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-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1113\u00a0(use:\u00a0temp,\u00a0)</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Paternal Sequence Variation Detection Using Next Generation Sequencing</p><p><b>focus</b>: <a href=\"Patient-father.html\">John Father Doe (official) Male, DoB: 2000-01-01 ( Medical record number: 11113\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-specimenFather.html\">Specimen: identifier = http://example.org/identifiers/specimens#7; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2022-07-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a father of a proband.</p>\n</div></blockquote><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-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1114\u00a0(use:\u00a0temp,\u00a0)</p><p><b>title</b>: De Novo Mutation Detection and Interpretation</p><p><b>focus</b>: </p><ul><li><a href=\"Patient-denovoChild.html\">Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></li><li><a href=\"RelatedPerson-relatedPersonDenovoFather.html\">RelatedPerson John Father Doe (official)</a></li><li><a href=\"RelatedPerson-relatedPersonDenovoMother.html\">RelatedPerson Jane Mother Doe (official)</a></li></ul><p><b>date</b>: 2022-07-01 03:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.</p>\n</div></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFileProband.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFileMother.html\">DocumentReference: identifier = http://example.org/identifiers/files#11119; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFileFather.html\">DocumentReference: identifier = http://example.org/identifiers/files#111110; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat bam}\">BAM</span></p></blockquote><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-genomicFileGroupAsSubject.html\">DocumentReference: identifier = http://example.org/identifiers/files#11115; status = current; docStatus = preliminary; description = Combined VCF file of a Proband and Parents that may be used as input or output of a genomic analysis pipeline.</a></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></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-Triodenovo-SW.html\">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></td></tr></table></blockquote></div>"
},
"identifier" : [
// from DomainResource: text, contained, extension, and modifierExtension
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicstudies",
"value" : "urn:uuid:1111-1111-1111-1113"
}
],
"status" : "available",
"type" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type",
"code" : "trio",
"display" : "Trio analysis"
}
]
}
],
"subject" : {
🔗 "reference" : "Patient/proband"
},
"encounter" : {
🔗 "reference" : "Encounter/denovoEncounter"
},
"startDate" : "2022-05-01",
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/genomicSRProband"
},
{
🔗 "reference" : "ServiceRequest/genomicSRMother"
},
{
🔗 "reference" : "ServiceRequest/genomicSRFather"
}
],
"referrer" : {
🔗 "reference" : "Practitioner/practitioner01"
},
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"reason" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "67799006",
"display" : "Cystic fibrosis, prenatal detection (procedure)"
}
]
}
}
],
"note" : [
{
"text" : "This de novo mutation is urgent and important for establishing the treatment plan."
}
],
"description" : "De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.",
"analysis" : [
{
"identifier" : [
// 0..* Genomic Analysis Event of mother
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1112"
}
],
"genomicSourceClass" : // <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>
{
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
}
]
},
"title" : "Maternal Sequence Variation Detection Using Next Generation Sequencing",
"focus" : [
// 0..1 Name of the analysis event (human friendly)
{
🔗 "reference" : "Patient/mother"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/specimenMother"
}
],
"date" : "2022-07-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of a mother of a proband."
}
],
"performer" : [
// <input>
<file>
<reference value="DocumentReference/genomicFile2"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
{
"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" : [
// <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>
{
"device" : // 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters
{
🔗 "reference" : "Device/NGS-device"
}
}
]
},
{
"identifier" : [
// 0..* Genomic Analysis Event of father
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1113"
}
],
"genomicSourceClass" : // <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>
{
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
}
]
},
"title" : "Paternal Sequence Variation Detection Using Next Generation Sequencing",
"focus" : [
{
🔗 "reference" : "Patient/father"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/specimenFather"
}
],
"date" : "2022-07-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of a father of a proband."
}
],
"performer" : [
// <input>
<file>
<reference value="DocumentReference/genomicFile3"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
{
"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" : [
// <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>
{
"device" : // 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters
{
🔗 "reference" : "Device/NGS-device"
}
}
]
},
{
"identifier" : [
// 0..* De Novo Mutation Analysis
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1114"
}
],
"title" : "De Novo Mutation Detection and Interpretation",
"focus" : [
// <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>
{
🔗 "reference" : "Patient/denovoChild"
},
{
🔗 "reference" : "RelatedPerson/relatedPersonDenovoFather"
},
{
🔗 "reference" : "RelatedPerson/relatedPersonDenovoMother"
}
],
"date" : "2022-07-01T03:01:10-06:00",
"note" : [
// 0..1<specimen> Reference(Specimen) The specimen used in the analysis event </specimen>
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."
}
],
"input" : [
// <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>
{
"file" : // 0..* Inputs for the analysis event, a combined vcf file
{
🔗 "reference" : "DocumentReference/genomicFileProband"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
},
{
"file" : // 0..* Inputs for the analysis event, a combined vcf file
{
🔗 "reference" : "DocumentReference/genomicFileMother"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
},
{
"file" : // 0..* Inputs for the analysis event, a combined vcf file
{
🔗 "reference" : "DocumentReference/genomicFileFather"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "bam",
"display" : "BAM"
}
]
}
}
],
"output" : [
// <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>
// <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>
{
"file" : // 0..* Outputs for the analysis event
{
🔗 "reference" : "DocumentReference/genomicFileGroupAsSubject"
},
"type" : {
"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" : [
// <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>
{
"device" : // 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters
{
🔗 "reference" : "Device/Triodenovo-SW"
}
}
]
}
]
}
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
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