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",
"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</b></p><a name=\"example\"> </a><a name=\"hcexample\"> </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:1111-1111-1111-1111\u00a0(use:\u00a0temp,\u00a0)</p><p><b>status</b>: Unknown</p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type fam-var-segr}\">Familial variant segregation</span></p><p><b>subject</b>: <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></p><p><b>encounter</b>: <a href=\"Encounter-denovoEncounter.html\">Encounter: status = in-progress; class = inpatient encounter</a></p><p><b>startDate</b>: 2021-01-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-genomicServiceRequest.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 267431006}\">Disorder of lipid metabolism (disorder)</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.</p>\n</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1111\u00a0(use:\u00a0temp,\u00a0)</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Proband Sequence Variation Detection Using Next Generation Sequencing</p><p><b>specimen</b>: <a href=\"Specimen-denovo-1.html\">Specimen: identifier = http://example.org/identifiers/specimens#1; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a proband.</p>\n</div></blockquote><h3>Inputs</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-genomicFile1.html\">DocumentReference: identifier = http://example.org/identifiers/files#11111; 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></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:1111-1111-1111-1112\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-denovoMother.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-denovo-2.html\">Specimen: identifier = http://example.org/identifiers/specimens#2; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 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>Inputs</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-genomicFile2.html\">DocumentReference: identifier = http://example.org/identifiers/files#11112; 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></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-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-denovoFather.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-denovo-3.html\">Specimen: identifier = http://example.org/identifiers/specimens#3; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 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>Inputs</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-genomicFile3.html\">DocumentReference: identifier = http://example.org/identifiers/files#11113; 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></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-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>date</b>: 2021-01-01 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-genomicFile1.html\">DocumentReference: identifier = http://example.org/identifiers/files#11111; 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 vcf}\">VCF</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFile2.html\">DocumentReference: identifier = http://example.org/identifiers/files#11112; 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 vcf}\">VCF</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFile3.html\">DocumentReference: identifier = http://example.org/identifiers/files#11113; 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 vcf}\">VCF</span></p></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-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:1111-1111-1111-1111"
}
],
"status" : "unknown",
"type" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type",
"code" : "fam-var-segr",
"display" : "Familial variant segregation"
}
]
}
],
"subject" : {
🔗 "reference" : "Patient/denovoChild"
},
"encounter" : {
🔗 "reference" : "Encounter/denovoEncounter"
},
"startDate" : "2021-01-01",
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/genomicServiceRequest"
}
],
"referrer" : {
🔗 "reference" : "Practitioner/practitioner01"
},
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"reason" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "267431006",
"display" : "Disorder of lipid metabolism (disorder)"
}
]
}
}
],
"note" : [
{
"text" : "This de novo mutation is urgent and important for establishing the treatment plan."
}
],
"description" : "De novo mutation study of the patient.",
"analysis" : [
{
"identifier" : [
// 0..* Genomic Analysis Event of proband
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:1111-1111-1111-1111"
}
],
"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" : "Proband Sequence Variation Detection Using Next Generation Sequencing",
"specimen" : [
{
🔗 "reference" : "Specimen/denovo-1"
}
],
"date" : "2021-01-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of a proband."
}
],
"input" : [
// <protocolPerformed>0..1 Reference(Procedure|Task) The protocol that was performed for the analysis event</protocolPerformed>
// <genomicRegion> 0..* Grouped genomic region sets by type (studied/called/uncalled)
Each repetition: <type> required code, <locus> 0..* CodeableReference(DocumentReference), <description> 0..1 string
</genomicRegion>
// <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 of Child
{
🔗 "reference" : "DocumentReference/genomicFile1"
},
"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" : [
{
"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" : [
// 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/denovoMother"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/denovo-2"
}
],
"date" : "2021-01-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of a mother of a proband."
}
],
"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 of Mother
{
🔗 "reference" : "DocumentReference/genomicFile2"
},
"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/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/denovoFather"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/denovo-3"
}
],
"date" : "2021-01-01T01:01:10-06:00",
"note" : [
// 0..1 The date of the analysis event
{
"text" : "This is a next generation sequencing analysis of a father of a proband."
}
],
"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
{
🔗 "reference" : "DocumentReference/genomicFile3"
},
"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/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",
"date" : "2021-01-01T03:01:10-06:00",
"note" : [
// <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>
// <specimen> 0..1 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 of Child
{
🔗 "reference" : "DocumentReference/genomicFile1"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
},
{
"file" : // 0..* Inputs for the analysis event of Mother
{
🔗 "reference" : "DocumentReference/genomicFile2"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
},
{
"file" : // 0..* Inputs for the analysis event of Father
{
🔗 "reference" : "DocumentReference/genomicFile3"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
// <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]>
{
"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
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change