{
  "resourceType" : "CodeSystem",
  "id" : "genomicstudy-regiontype",
  "meta" : {
    "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablecodesystem"]
  },
  "language" : "en",
  "text" : {
    "status" : "generated",
    "div" : "<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>"
  },
  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "cg"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
    "valueCode" : "draft"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 1
  }],
  "url" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
  "version" : "0.1.0-ci-build",
  "name" : "GenomicStudyRegionType",
  "title" : "Genomic Study Region Type",
  "status" : "draft",
  "experimental" : true,
  "date" : "2026-03-24T14:41:48+00:00",
  "publisher" : "HL7 International / Clinical Genomics",
  "contact" : [{
    "name" : "HL7 International / Clinical Genomics",
    "telecom" : [{
      "system" : "url",
      "value" : "http://www.hl7.org/Special/committees/clingenomics"
    },
    {
      "system" : "email",
      "value" : "clingenomics@lists.hl7.org"
    }]
  }],
  "description" : "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" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
      "code" : "001",
      "display" : "World"
    }]
  }],
  "caseSensitive" : true,
  "valueSet" : "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-regiontype",
  "content" : "complete",
  "concept" : [{
    "code" : "studied",
    "display" : "Studied",
    "definition" : "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."
  },
  {
    "code" : "called",
    "display" : "Called",
    "definition" : "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."
  },
  {
    "code" : "uncalled",
    "display" : "Uncalled",
    "definition" : "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."
  }]
}