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   -->
  <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>   -->
    <!--   <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> 
          <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> 
        <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> 
    <!--   <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> 
          <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> 
    <!--   <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://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> 
    <!--   <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> 
          <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> 
    <!--   <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://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> 
    <!--   <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> 
          <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> 
          <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> 
          <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> 
    <!--   <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>