type: exampleresource: GenomicStudyexample: genomicstudy-example
GenomicStudy Example: genomicstudy-example
Example XML
<GenomicStudy xmlns="http://hl7.org/fhir">
<!-- from Resource: id, meta, implicitRules, and language -->
<id value="example"/>
<!-- from DomainResource: text, contained, extension, and modifierExtension -->
<identifier>
<use value="temp"/>
<system value="http://www.somesystemabc.net/identifiers/genomicstudies"/>
<value value="urn:uuid:1111-1111-1111-1111"/>
</identifier>
<status value="unknown"/>
<type>
<coding>
<system value="http://hl7.org/fhir/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://www.somesystemabc.net/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1111"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
<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> -->
<!-- <regionsCalled>0..1 Reference(DocumentReference) Genomic regions actually called in the analysis event (BED file)</regionsCalled> -->
<input> <!-- 0..* Inputs for the analysis event of Child-->
<file>
<reference value="DocumentReference/genomicFile1"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<performer> <!-- 0..* Performer for the analysis event -->
<actor>
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/>
<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>
<display value="Next Generation Sequencing"/>
</coding>
</function>
</device>
</analysis>
<analysis> <!-- 0..* Genomic Analysis Event of mother -->
<identifier>
<use value="temp"/>
<system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1112"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
<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>
<input> <!-- 0..* Inputs for the analysis event of Mother-->
<file>
<reference value="DocumentReference/genomicFile2"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<performer> <!-- 0..* Performer for the analysis event -->
<actor>
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/>
<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>0..1 CodeableConcept Specific function for the device used for the analysis</function> -->
</device>
</analysis>
<analysis> <!-- 0..* Genomic Analysis Event of father -->
<identifier>
<use value="temp"/>
<system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1113"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
<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>
<input> <!-- 0..* Inputs for the analysis event -->
<file>
<reference value="DocumentReference/genomicFile3"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<performer> <!-- 0..* Performer for the analysis event -->
<actor>
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/>
<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>0..1 CodeableConcept Specific function for the device used for the analysis</function> -->
</device>
</analysis>
<analysis> <!-- 0..* De Novo Mutation Analysis -->
<identifier>
<use value="temp"/>
<system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/>
<value value="urn:uuid:1111-1111-1111-1114"/>
</identifier>
<!-- <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical> -->
<instantiatesUri value="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/"/>
<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>
<input> <!-- 0..* Inputs for the analysis event of Child-->
<file>
<reference value="DocumentReference/genomicFile1"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<input> <!-- 0..* Inputs for the analysis event of Mother-->
<file>
<reference value="DocumentReference/genomicFile2"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<input> <!-- 0..* Inputs for the analysis event of Father -->
<file>
<reference value="DocumentReference/genomicFile3"/>
</file>
<type>
<coding>
<code value="vcf"/>
<display value="VCF"/>
</coding>
</type>
<!-- <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]> -->
</input>
<performer> <!-- 0..* Performer for the analysis event -->
<actor>
<reference value="Practitioner/practitioner02"/>
</actor>
<role>
<coding>
<system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/>
<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/Triodenovo-SW"/>
</device>
<!-- <function>0..1 CodeableConcept Specific function for the device used for the analysis</function> -->
</device>
</analysis>
</GenomicStudy>