MII Implementierungsleitfaden Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 - Germany

MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht - Downloaded Version 2027.0.0-ballot.1 See the Directory of published versions

: WES Sequencing Analysis

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<Procedure xmlns="http://hl7.org/fhir">
  <id value="mii-exa-molgen-genomic-study-analysis-wes-sequencing"/>
  <meta>
    <profile
             value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study-analysis"/>
    <profile
             value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1"/>
  </meta>
  <language value="de"/>
  <text>
    <status value="extensions"/>
    <div xml:lang="de" lang="de"><hr/><p><b>German</b></p><hr/><p class="res-header-id"><b>Generated Narrative: Procedure mii-exa-molgen-genomic-study-analysis-wes-sequencing</b></p><a name="de-mii-exa-molgen-genomic-study-analysis-wes-sequencing"> </a><a name="de-hcmii-exa-molgen-genomic-study-analysis-wes-sequencing"> </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">Profiles: <a href="StructureDefinition-mii-pr-molgen-genomic-study-analysis.html">MII PR MolGen Genomic Study Analysis</a>, <a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&amp;canonical=https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1">https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1</a></p></div><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-mii-exa-molgen-specimen-dna-library.html">Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#LIB-2024-001; type = Saliva specimen</a></p><blockquote><p><b>Genomic Study Analysis Device</b></p><ul><li>device: <a href="Device-mii-exa-molgen-device-illumina-novaseq.html">Device: identifier = https://www.medizininformatik-initiative.de/fhir/sid/lab-devices#NOVASEQ-6000-SN12345; status = active; manufacturer = Illumina Inc.; serialNumber = SN12345; modelNumber = NovaSeq 6000; type = Medical laboratory analyzer</a></li></ul></blockquote><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><blockquote><p><b>Genomic Study Analysis Metrics</b></p><ul><li>read-depth: 120 reads<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></li><li>sequencing-coverage: 98.5 percent<span style="background: LightGoldenRodYellow"> (Details: UCUM  code% = '%')</span></li><li>metrics-description: High-quality sequencing run with mean coverage of 120X. 98.5% of target regions achieved &gt;20X coverage. Q30 bases: 92%. Contamination estimate: &lt;1%. Sample identity confirmed by SNP fingerprinting.</li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>description: Whole Exome - Agilent SureSelect Human All Exon V7</li></ul></blockquote><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-mii-exa-molgen-patient.html">Maja Julia Van-der-Dussen (official) Female, DoB: 1968-09-19 ( Krankenaktennummer (use: usual, ))</a></p></div>
  </text>
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             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen">
    <valueReference>🔗 
      <reference value="Specimen/mii-exa-molgen-specimen-dna-library"/>
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  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device">
    <extension url="device">
      <valueReference>🔗 
        <reference value="Device/mii-exa-molgen-device-illumina-novaseq"/>
      </valueReference>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26398-0"/>
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    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics">
    <extension url="read-depth">
      <valueQuantity>
        <value value="120"/>
        <unit value="reads"/>
        <system value="http://unitsofmeasure.org"/>
        <code value="1"/>
      </valueQuantity>
    </extension>
    <extension url="sequencing-coverage">
      <valueQuantity>
        <value value="98.5"/>
        <unit value="percent"/>
        <system value="http://unitsofmeasure.org"/>
        <code value="%"/>
      </valueQuantity>
    </extension>
    <extension url="metrics-description">
      <valueString
                   value="High-quality sequencing run with mean coverage of 120X. 98.5% of target regions achieved &gt;20X coverage. Q30 bases: 92%. Contamination estimate: &lt;1%. Sample identity confirmed by SNP fingerprinting."/>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions">
    <extension url="description">
      <valueString
                   value="Whole Exome - Agilent SureSelect Human All Exon V7"/>
    </extension>
  </extension>
  <status value="completed"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <subject>🔗 
    <reference value="Patient/mii-exa-molgen-patient"/>
  </subject>
</Procedure>