GenomicStudy - Trio study - De novo mutation 2 (id = "example-trio2")

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

<GenomicStudy xmlns="http://hl7.org/fhir">
      <!--   from Resource: id, meta, implicitRules, and language   -->
    <id value="example-trio2"/> 
      <!--   from DomainResource: text, contained, extension, and modifierExtension   -->
    <text> 
        <status value="additional"/> 
        <div xmlns="http://www.w3.org/1999/xhtml">Prenatal Trio Whole Exome Sequencing testing to identify causal mutations of inherited
       diseases. Test order was for trio testing with three specimens i.e., proband, mother,
       father included. A comparator analysis-based trio report was to be generated for
       the proband; both parents had consented to receive reports on secondary findings.</div> 
    </text> 
    <identifier> 
        <use value="temp"/> 
        <system value="http://www.somesystemabc.net/identifiers/genomicstudies"/> 
        <value value="urn:uuid:1111-1111-1111-1113"/> 
    </identifier> 
    <status> 
        <coding> 
            <system value="http://hl7.org/fhir/genomicstudy-status"/> 
            <code value="available"/> 
            <display value="Available"/> 
        </coding> 
    </status> 
    <type> 
        <coding> 
            <code value="trio"/> 
            <display value="Trio-analysis"/> 
        </coding> 
    </type> 
    <subject> 
        <reference value="Patient/proband"/> 
    </subject> 
    <encounter> 
        <reference value="Encounter/denovoEncounter"/> 
    </encounter> 
    <startDate value="2022-05-01"/> 
    <basedOn> 
        <reference value="ServiceRequest/genomicSRProband"/> 
    </basedOn> 
        <basedOn> 
        <reference value="ServiceRequest/genomicSRMother"/> 
    </basedOn> 
    <basedOn> 
        <reference value="ServiceRequest/genomicSRFather"/> 
    </basedOn> 
    <referrer> 
        <reference value="Practitioner/practitioner01"/> 
    </referrer> 
    <interpreter> 
        <reference value="Practitioner/practitioner02"/> 
    </interpreter> 
    <reason> 
        <concept> 
            <coding> 
                <system value="http://snomed.info/sct"/> 
                <code value="67799006"/> 
                <display value="Cystic fibrosis, prenatal detection (procedure) |"/> 
            </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. 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>     <!--   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/mother"/> 
        </subject> 
        <specimen> 
            <reference value="Specimen/specimenMother"/> 
        </specimen> 
        <date value="2022-07-01T01:01:10-06:00"/>   <!--   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>
            <file>
                <reference value="DocumentReference/genomicFile2"/>
            </file>
            <type>
                <coding>
                    <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/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/father"/> 
        </subject> 
        <specimen> 
            <reference value="Specimen/specimenFather"/> 
        </specimen> 
        <date value="2022-07-01T01:01:10-06:00"/>   <!--   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>
            <file>
                <reference value="DocumentReference/genomicFile3"/>
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            <type>
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                    <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/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/proband"/> 
        </subject> 
          <!--   0..1<specimen> Reference(Specimen) The specimen used in the analysis event </specimen>
      -->
        <date value="2022-07-01T03:01:10-06:00"/>   <!--   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, a combined vcf file  -->
            <file> 
                <reference value="DocumentReference/genomicFileProband"/> 
            </file> 
            <type> 
                <coding> 
                    <system value="http://hl7.org/fhir/genomicstudy-dataformat"/> 
                    <code value="bam"/> 
                    <display value="BAM"/> 
                 </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, a combined vcf file  -->
            <file> 
                <reference value="DocumentReference/genomicFileMother"/> 
            </file> 
            <type> 
                <coding> 
                    <system value="http://hl7.org/fhir/genomicstudy-dataformat"/> 
                    <code value="bam"/> 
                    <display value="BAM"/> 
                 </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, a combined vcf file  -->
            <file> 
                <reference value="DocumentReference/genomicFileFather"/> 
            </file> 
            <type> 
                <coding> 
                    <system value="http://hl7.org/fhir/genomicstudy-dataformat"/> 
                    <code value="bam"/> 
                    <display value="BAM"/> 
                 </coding> 
            </type> 
              <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or
       other GenomicStudy that generated this input file</generatedBy[x]>   -->
        </input> 
        <output>     <!--   0..* Outputs for the analysis event   -->
            <file> 
                <reference value="DocumentReference/genomicFileGroupAsSubject"/> 
            </file> 
            <type> 
                <coding> 
                    <system value="http://hl7.org/fhir/genomicstudy-dataformat"/> 
                    <code value="vcf"/> 
                    <display value="VCF"/> 
                </coding> 
            </type> 
        </output> 
        <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>