Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

Page standards status: Informative

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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="extensions"/>
        <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><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomic-study-analysis.html">Genomic Study Analysis</a></p></div><p><b>Genomic Study Analysis Genome Build</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>Genomic Study Analysis Focus</b>: <a href="Patient-denovoFather.html">Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Focus</b>: <a href="Patient-denovoMother.html">Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Title</b>: Parental Sequence Variation Detection Using Next Generation Sequencing</p><p><b>Genomic Study Analysis Protocol Performed</b>: <a href="Procedure-SequencingProcedure.html">Procedure Sequencing of entire coding region of gene (procedure)</a></p><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href="DocumentReference-genomicFileProbandBAM.html">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href="DocumentReference-genomicFileMotherBAM.html">DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href="DocumentReference-genomicFileFatherBAM.html">DocumentReference: identifier = http://example.org/identifiers/files#11132; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>file: <a href="DocumentReference-genomicFileProbandVCF.html">DocumentReference: identifier = http://example.org/identifiers/files#11150; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}">VCF</span></li></ul></blockquote><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>