Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

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: Genomic Study Region Type

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-regiontype"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
  </meta>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem genomicstudy-regiontype</b></p><a name="genomicstudy-regiontype"> </a><a name="hcgenomicstudy-regiontype"> </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="http://hl7.org/fhir/R5/shareablecodesystem.html">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype</code> defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style="white-space:nowrap">studied<a name="genomicstudy-regiontype-studied"> </a></td><td>Studied</td><td>Genomic regions targeted by the analysis. This represents the full intended scope of the analysis (e.g., a gene panel, exome, or genome). May be expressed as a coded list of gene symbols or a reference to a BED file.</td></tr><tr><td style="white-space:nowrap">called<a name="genomicstudy-regiontype-called"> </a></td><td>Called</td><td>The subset of studied genomic regions where there was sufficient coverage and data quality to produce variant calls. Regions not represented here were either uncalled or not studied.</td></tr><tr><td style="white-space:nowrap">uncalled<a name="genomicstudy-regiontype-uncalled"> </a></td><td>Uncalled</td><td>Genomic regions that were within the scope of the analysis (i.e., studied) but for which no variant calls were produced. This does not imply that a pathogenic variant was present or missed; it indicates that data quality was insufficient to make calls in these regions. Common reasons include low sequencing coverage, poor mapping quality, or technical limitations of the assay. Use the genomicRegion.description element to document the specific reason.</td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="draft"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"/>
  <version value="0.1.0-ci-build"/>
  <name value="GenomicStudyRegionType"/>
  <title value="Genomic Study Region Type"/>
  <status value="draft"/>
  <experimental value="true"/>
  <date value="2026-03-24T14:41:48+00:00"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="clingenomics@lists.hl7.org"/>
    </telecom>
  </contact>
  <description
               value="The type or status of a set of genomic regions within a GenomicStudy analysis, indicating the relationship of those regions to the analysis outcome."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <valueSet
            value="http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-regiontype"/>
  <content value="complete"/>
  <concept>
    <code value="studied"/>
    <display value="Studied"/>
    <definition
                value="Genomic regions targeted by the analysis. This represents the full intended scope of the analysis (e.g., a gene panel, exome, or genome). May be expressed as a coded list of gene symbols or a reference to a BED file."/>
  </concept>
  <concept>
    <code value="called"/>
    <display value="Called"/>
    <definition
                value="The subset of studied genomic regions where there was sufficient coverage and data quality to produce variant calls. Regions not represented here were either uncalled or not studied."/>
  </concept>
  <concept>
    <code value="uncalled"/>
    <display value="Uncalled"/>
    <definition
                value="Genomic regions that were within the scope of the analysis (i.e., studied) but for which no variant calls were produced. This does not imply that a pathogenic variant was present or missed; it indicates that data quality was insufficient to make calls in these regions. Common reasons include low sequencing coverage, poor mapping quality, or technical limitations of the assay. Use the genomicRegion.description element to document the specific reason."/>
  </concept>
</CodeSystem>