Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: genomicstudyanalysis-trio2 - XML Representation

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<Procedure xmlns="http://hl7.org/fhir">
  <id value="genomicstudyanalysis-trio2"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Procedure genomicstudyanalysis-trio2</b></p><a name="genomicstudyanalysis-trio2"> </a><a name="hcgenomicstudyanalysis-trio2"> </a><a name="genomicstudyanalysis-trio2-en-US"> </a><p><b>instantiatesUri</b>: <a href="https://pubmed.ncbi.nlm.nih.gov/33927380/">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Patient-denovoChild.html">Child Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 1234-11111 (use: temp, ))</a></p><p><b>performed</b>: 2023-10-01</p></div>
  </text>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26806-2"/>
        <display value="GRCh38"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus">
    <valueReference>🔗 
      <reference value="Patient/denovoFather"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus">
    <valueReference>🔗 
      <reference value="Patient/denovoMother"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title">
    <valueString
                 value="Parental Sequence Variation Detection Using Next Generation Sequencing"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed">
    <valueReference>🔗 
      <reference value="Procedure/SequencingProcedure"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input">
    <extension url="file">
      <valueReference>🔗 
        <reference value="DocumentReference/genomicFileProbandBAM"/>
      </valueReference>
    </extension>
    <extension url="type">
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
          <code value="bam"/>
          <display value="BAM"/>
        </coding>
      </valueCodeableConcept>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input">
    <extension url="file">
      <valueReference>🔗 
        <reference value="DocumentReference/genomicFileMotherBAM"/>
      </valueReference>
    </extension>
    <extension url="type">
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
          <code value="bam"/>
          <display value="BAM"/>
        </coding>
      </valueCodeableConcept>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input">
    <extension url="file">
      <valueReference>🔗 
        <reference value="DocumentReference/genomicFileFatherBAM"/>
      </valueReference>
    </extension>
    <extension url="type">
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
          <code value="bam"/>
          <display value="BAM"/>
        </coding>
      </valueCodeableConcept>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output">
    <extension url="file">
      <valueReference>🔗 
        <reference value="DocumentReference/genomicFileProbandVCF"/>
      </valueReference>
    </extension>
    <extension url="type">
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
          <code value="vcf"/>
          <display value="VCF"/>
        </coding>
      </valueCodeableConcept>
    </extension>
  </extension>
  <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
  <status value="completed"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <subject>🔗 
    <reference value="Patient/denovoChild"/>
  </subject>
  <performedDateTime value="2023-10-01"/>
</Procedure>