Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

: Find Subject Variants - JSON Representation

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{
  "resourceType" : "OperationDefinition",
  "id" : "find-subject-variants",
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>FindSubjectVariants</h2><p>OPERATION: FindSubjectVariants</p><p>The official URL for this operation definition is: </p><pre>http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants</pre><p>Parameters</p><table class=\"grid\"><tr><td><b>Use</b></td><td><b>Name</b></td><td><b>Cardinality</b></td><td><b>Type</b></td><td><b>Binding</b></td><td><b>Documentation</b></td></tr><tr><td>IN</td><td>subject</td><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#reference\">reference</a>)</td><td/><td><div><p>The subject of interest.</p>\n</div></td></tr><tr><td>IN</td><td>region</td><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#Range\">Range</a></td><td/><td><div><p>Region of interest is specified as a 0-based integer interval range. Variants that overlap the range are returned.</p>\n</div></td></tr><tr><td>IN</td><td>genomicRefSeq</td><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#token\">token</a>)</td><td/><td><div><p>Genomic reference sequence is a valid NCBI chromosome-level ('NC_') build 37 or build 38 identifier, or a valid mitochondrion identifier (NC_012920.1, NC_001807.4)</p>\n</div></td></tr><tr><td>OUT</td><td>regionStudied</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied] Must include 1..* component:ranges-examined; 1..1 component:coordinate-system (valued with '0-based interval counting'); 1..1 component:genomic-ref-seq.</p>\n</div></td></tr><tr><td>OUT</td><td>variant</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] Must include valueCodeableConcept; component:genomic-source-class; component:genomic-ref-seq; component:allelic-state; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end.</p>\n</div></td></tr><tr><td>OUT</td><td>sequencePhaseRelationship</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship] Must include valueCodeableConcept; 2..2 derivedFrom:variant.</p>\n</div></td></tr></table></div>"
  },
  "url" : "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants",
  "version" : "2.0.0",
  "name" : "FindSubjectVariants",
  "title" : "Find Subject Variants",
  "status" : "active",
  "kind" : "operation",
  "date" : "2022-05-09T16:59:16+00:00",
  "publisher" : "HL7 Clinical Genomics Working Group",
  "contact" : [
    {
      "name" : "HL7 Clinical Genomics Working Group",
      "telecom" : [
        {
          "system" : "url",
          "value" : "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system" : "email",
          "value" : "cg@lists.HL7.org"
        }
      ]
    }
  ],
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "code" : "match",
  "system" : false,
  "type" : true,
  "instance" : false,
  "parameter" : [
    {
      "name" : "subject",
      "use" : "in",
      "min" : 1,
      "max" : "1",
      "documentation" : "The subject of interest.",
      "type" : "string",
      "searchType" : "reference"
    },
    {
      "name" : "region",
      "use" : "in",
      "min" : 1,
      "max" : "1",
      "documentation" : "Region of interest is specified as a 0-based integer interval range. Variants that overlap the range are returned.",
      "type" : "Range"
    },
    {
      "name" : "genomicRefSeq",
      "use" : "in",
      "min" : 1,
      "max" : "1",
      "documentation" : "Genomic reference sequence is a valid NCBI chromosome-level ('NC_') build 37 or build 38 identifier, or a valid mitochondrion identifier (NC_012920.1, NC_001807.4)",
      "type" : "string",
      "searchType" : "token"
    },
    {
      "name" : "regionStudied",
      "use" : "out",
      "min" : 0,
      "max" : "*",
      "documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied] Must include 1..* component:ranges-examined; 1..1 component:coordinate-system (valued with '0-based interval counting'); 1..1 component:genomic-ref-seq.",
      "type" : "canonical",
      "targetProfile" : [
        "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied"
      ]
    },
    {
      "name" : "variant",
      "use" : "out",
      "min" : 0,
      "max" : "*",
      "documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] Must include valueCodeableConcept; component:genomic-source-class; component:genomic-ref-seq; component:allelic-state; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end.",
      "type" : "canonical",
      "targetProfile" : [
        "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
      ]
    },
    {
      "name" : "sequencePhaseRelationship",
      "use" : "out",
      "min" : 0,
      "max" : "*",
      "documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship] Must include valueCodeableConcept; 2..2 derivedFrom:variant.",
      "type" : "canonical",
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        "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
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  ]
}