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 |
<GenomicStudy xmlns="http://hl7.org/fhir">
<!-- from Resource: id, meta, implicitRules, and language -->
<id value="example"/>
<language value="en"/>
<text>
<status value="generated"/>
<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 (use: temp, )</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 (use: temp, period: 2021-01-01 --> (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>
</div></blockquote><p><b>description</b>: </p><div><p>De novo mutation study of the patient.</p>
</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1111 (use: temp, )</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>
</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 (use: temp, )</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 (use: temp, period: 2021-01-01 --> (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>
</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 (use: temp, )</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 (use: temp, period: 2021-01-01 --> (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>
</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 (use: temp, )</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>
</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>
</text>
<!-- from DomainResource: text, contained, extension, and modifierExtension -->
<identifier>
<use value="temp"/>
<system value="http://example.org/identifiers/genomicstudies"/>
<value value="urn:uuid:1111-1111-1111-1111"/>
</identifier>
<status value="unknown"/>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type"/>
<code value="fam-var-segr"/>
<display value="Familial variant segregation"/>
</coding>
</type>
<subject>🔗
<reference value="Patient/denovoChild"/>
</subject>
<encounter>🔗
<reference value="Encounter/denovoEncounter"/>
</encounter>
<startDate value="2021-01-01"/>
<basedOn>🔗
<reference value="ServiceRequest/genomicServiceRequest"/>
</basedOn>
<referrer>🔗
<reference value="Practitioner/practitioner01"/>
</referrer>
<interpreter>🔗
<reference value="Practitioner/practitioner02"/>
</interpreter>
<reason>
<concept>
<coding>
<system value="http://snomed.info/sct"/>
<code value="267431006"/>
<display value="Disorder of lipid metabolism (disorder)"/>
</coding>
</concept>
</reason>
<note>
<text
value="This de novo mutation is urgent and important for establishing the treatment plan."/>
</note>
<description value="De novo mutation study of the patient."/>
<analysis>
<!-- 0..* Genomic Analysis Event of proband -->
<identifier>
<use value="temp"/>
<system value="http://example.org/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1111"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<genomicSourceClass>
<coding>
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</coding>
</genomicSourceClass>
<title
value="Proband Sequence Variation Detection Using Next Generation Sequencing"/>
<specimen>🔗
<reference value="Specimen/denovo-1"/>
</specimen>
<date value="2021-01-01T01:01:10-06:00"/>
<!-- 0..1 The date of the analysis event -->
<note>
<text
value="This is a next generation sequencing analysis of a proband."/>
</note>
<!-- <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]> -->
<input>
<!-- 0..* Inputs for the analysis event of Child -->
<file>🔗
<reference value="DocumentReference/genomicFile1"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<performer>
<!-- 0..* Performer for the analysis event -->
<actor>🔗
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
<code value="PRF"/>
<display value="Performer"/>
</coding>
</role>
</performer>
<device>
<!-- 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters -->
<device>🔗
<reference value="Device/NGS-device"/>
</device>
<function>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</function>
</device>
</analysis>
<analysis>
<!-- 0..* Genomic Analysis Event of mother -->
<identifier>
<use value="temp"/>
<system value="http://example.org/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1112"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<genomicSourceClass>
<coding>
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</coding>
</genomicSourceClass>
<title
value="Maternal Sequence Variation Detection Using Next Generation Sequencing"/>
<!-- 0..1 Name of the analysis event (human friendly) -->
<focus>🔗
<reference value="Patient/denovoMother"/>
</focus>
<specimen>🔗
<reference value="Specimen/denovo-2"/>
</specimen>
<date value="2021-01-01T01:01:10-06:00"/>
<!-- 0..1 The date of the analysis event -->
<note>
<text
value="This is a next generation sequencing analysis of a mother of a proband."/>
</note>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
<input>
<!-- 0..* Inputs for the analysis event of Mother -->
<file>🔗
<reference value="DocumentReference/genomicFile2"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<performer>
<!-- 0..* Performer for the analysis event -->
<actor>🔗
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
<code value="PRF"/>
<display value="Performer"/>
</coding>
</role>
</performer>
<!-- <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 -->
<device>🔗
<reference value="Device/NGS-device"/>
</device>
</device>
</analysis>
<analysis>
<!-- 0..* Genomic Analysis Event of father -->
<identifier>
<use value="temp"/>
<system value="http://example.org/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1113"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<genomicSourceClass>
<coding>
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</coding>
</genomicSourceClass>
<title
value="Paternal Sequence Variation Detection Using Next Generation Sequencing"/>
<focus>🔗
<reference value="Patient/denovoFather"/>
</focus>
<specimen>🔗
<reference value="Specimen/denovo-3"/>
</specimen>
<date value="2021-01-01T01:01:10-06:00"/>
<!-- 0..1 The date of the analysis event -->
<note>
<text
value="This is a next generation sequencing analysis of a father of a proband."/>
</note>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
<input>
<!-- 0..* Inputs for the analysis event -->
<file>🔗
<reference value="DocumentReference/genomicFile3"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<performer>
<!-- 0..* Performer for the analysis event -->
<actor>🔗
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
<code value="PRF"/>
<display value="Performer"/>
</coding>
</role>
</performer>
<!-- <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 -->
<device>🔗
<reference value="Device/NGS-device"/>
</device>
</device>
</analysis>
<analysis>
<!-- 0..* De Novo Mutation Analysis -->
<identifier>
<use value="temp"/>
<system value="http://example.org/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1114"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<title value="De Novo Mutation Detection and Interpretation"/>
<!-- <specimen> 0..1 Reference(Specimen) The specimen used in the analysis event</specimen> -->
<date value="2021-01-01T03:01:10-06:00"/>
<!-- 0..1 The date of the analysis event -->
<note>
<text
value="This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."/>
</note>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
<input>
<!-- 0..* Inputs for the analysis event of Child -->
<file>🔗
<reference value="DocumentReference/genomicFile1"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
<input>
<!-- 0..* Inputs for the analysis event of Mother -->
<file>🔗
<reference value="DocumentReference/genomicFile2"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
<input>
<!-- 0..* Inputs for the analysis event of Father -->
<file>🔗
<reference value="DocumentReference/genomicFile3"/>
</file>
<type>
<coding>
<system
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
</input>
<performer>
<!-- 0..* Performer for the analysis event -->
<actor>🔗
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
<code value="PRF"/>
<display value="Performer"/>
</coding>
</role>
</performer>
<!-- <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 -->
<device>🔗
<reference value="Device/Triodenovo-SW"/>
</device>
</device>
</analysis>
</GenomicStudy>
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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