{
  "description": "Determine if structural variants are present that overlap range(s).",
  "_filename": "OperationDefinition-find-subject-structural-intersecting-variants.json",
  "package_name": "hl7.fhir.uv.genomics-reporting",
  "date": "2024-12-12T20:43:36+00:00",
  "system": false,
  "publisher": "HL7 International / Clinical Genomics",
  "instance": false,
  "jurisdiction": [ {
    "coding": [ {
      "code": "001",
      "system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
      "display": "World"
    } ]
  } ],
  "name": "FindSubjectStructuralIntersectingVariants",
  "type": "true",
  "experimental": null,
  "resourceType": "OperationDefinition",
  "title": "Find Subject Structural Intersecting Variants",
  "package_version": "3.0.0",
  "extension": [ {
    "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode": "cg"
  } ],
  "status": "active",
  "id": "03a1ba69-8e70-47a8-8965-98887c6970c9",
  "kind": "operation",
  "url": "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-structural-intersecting-variants",
  "code": "match",
  "version": "3.0.0",
  "contact": [ {
    "name": "HL7 International / Clinical Genomics",
    "telecom": [ {
      "value": "http://www.hl7.org/Special/committees/clingenomics",
      "system": "url"
    }, {
      "value": "cg@lists.HL7.org",
      "system": "email"
    } ]
  } ],
  "parameter": [ {
    "max": "1",
    "min": 1,
    "use": "in",
    "name": "subject",
    "type": "string",
    "searchType": "reference",
    "documentation": "The subject of interest."
  }, {
    "max": "*",
    "min": 1,
    "use": "in",
    "name": "ranges",
    "type": "string",
    "searchType": "special",
    "documentation": "List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820')."
  }, {
    "max": "*",
    "min": 0,
    "use": "in",
    "name": "testIdentifiers",
    "type": "string",
    "searchType": "token",
    "documentation": "Supply a list of test identifiers. Only results originating from one of these tests will be returned."
  }, {
    "max": "1",
    "min": 0,
    "use": "in",
    "name": "testDateRange",
    "type": "Period",
    "documentation": "Supply a date range. Only results generated during this range will be returned."
  }, {
    "max": "*",
    "min": 0,
    "use": "in",
    "name": "specimenIdentifiers",
    "type": "string",
    "searchType": "token",
    "documentation": "Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned."
  }, {
    "max": "1",
    "min": 0,
    "use": "in",
    "name": "genomicSourceClass",
    "type": "string",
    "searchType": "token",
    "documentation": "Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class."
  }, {
    "max": "1",
    "min": 0,
    "use": "in",
    "name": "includeVariants",
    "type": "boolean",
    "documentation": "Include variants in response if set to true. Default=false."
  }, {
    "max": "*",
    "min": 1,
    "use": "out",
    "name": "variants",
    "part": [ {
      "max": "1",
      "min": 1,
      "use": "out",
      "name": "rangeItem",
      "type": "string",
      "documentation": "range from rangeList"
    }, {
      "max": "1",
      "min": 1,
      "use": "out",
      "name": "presence",
      "type": "boolean",
      "documentation": "True if as least one variant is identified that intersects the range"
    }, {
      "max": "*",
      "min": 0,
      "use": "out",
      "name": "variant",
      "type": "Observation",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/operationdefinition-profile",
        "valueUri": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
      } ],
      "documentation": "If includeVariants=true then include variants that intersect the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:coding-change-type; component:genomic-ref-seq; component:coordinate-system (valued with '0-based interval counting'); components outer-start-end and/or inner-start-end."
    } ],
    "documentation": "(one for each range in rangeList)"
  } ]
}