GenomicStudy - Trio study - De novo mutation 1 (id = "example")

<?xml version="1.0" encoding="UTF-8"?>

<GenomicStudy xmlns="http://hl7.org/fhir">
    <!--   from Resource: id, meta, implicitRules, and language   -->
    <id value="example"/> 
    <!--   from DomainResource: text, contained, extension, and modifierExtension   -->
    <text> 
        <status value="additional"/> 
        <div xmlns="http://www.w3.org/1999/xhtml">This is a genomic study that involves a de novo mutation analysis of a proband, mother,
       and father. The analysis involves the use use of NGS device and a specilized analysis
       platform.</div> 
    </text> 
    <identifier> 
        <use value="temp"/> 
        <system value="http://www.somesystemabc.net/identifiers/genomicstudies"/> 
        <value value="urn:uuid:1111-1111-1111-1111"/> 
    </identifier> 
    <status> 
        <coding> 
            <system value="http://hl7.org/fhir/genomicstudy-status"/> 
            <code value="unknown"/> 
            <display value="Unknown"/> 
        </coding> 
    </status> 
    <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"/> 
        <subject> 
            <reference value="Patient/denovoChild"/> 
        </subject> 
        <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)   -->
        <subject> 
            <reference value="Patient/denovoMother"/> 
        </subject> 
        <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"/> 
        <subject> 
            <reference value="Patient/denovoFather"/> 
        </subject> 
        <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"/> 
        <subject> 
            <reference value="Patient/denovoChild"/> 
        </subject> 
        <!--   <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>