Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Find Population Specific Variants - XML Representation

Active as of 2023-12-18

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<OperationDefinition xmlns="http://hl7.org/fhir">
  <id value="find-population-specific-variants"/>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p>Parameters</p><table class="grid"><tr><td><b>Use</b></td><td><b>Name</b></td><td><b>Scope</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>variants</td><td/><td>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#string">string</a>)</td><td/><td><div><p>List of variants being sought. Must be in HGVS or SPDI format.</p>
</div></td></tr><tr><td>IN</td><td>genomicSourceClass</td><td/><td>0..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>Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.</p>
</div></td></tr><tr><td>IN</td><td>includePatientList</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#boolean">boolean</a></td><td/><td><div><p>Include list of matching patients if set to true. Default=false.</p>
</div></td></tr><tr><td>OUT</td><td>variants</td><td/><td>1..*</td><td></td><td/><td/></tr><tr><td>OUT</td><td>variants.variantItem</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td/><td><div><p>variant from variantList</p>
</div></td></tr><tr><td>OUT</td><td>variants.numerator</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#Quantity">Quantity</a></td><td/><td><div><p>Count of patients having this variant</p>
</div></td></tr><tr><td>OUT</td><td>variants.denominator</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#Quantity">Quantity</a></td><td/><td><div><p>Count of patients in the cohort searched</p>
</div></td></tr><tr><td>OUT</td><td>variants.subject</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td/><td><div><p>Patient ID. Include if includePatientList=true</p>
</div></td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-population-specific-variants"/>
  <version value="3.0.0-ballot"/>
  <name value="FindPopulationSpecificVariants"/>
  <title value="Find Population Specific Variants"/>
  <status value="active"/>
  <kind value="operation"/>
  <date value="2023-12-18T22:45:59+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="cg@lists.HL7.org"/>
    </telecom>
  </contact>
  <description
               value="Retrieve count or list of patients having specified variants."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <code value="match"/>
  <system value="false"/>
  <type value="true"/>
  <instance value="false"/>
  <parameter>
    <name value="variants"/>
    <use value="in"/>
    <min value="1"/>
    <max value="*"/>
    <documentation
                   value="List of variants being sought. Must be in HGVS or SPDI format."/>
    <type value="string"/>
    <searchType value="string"/>
  </parameter>
  <parameter>
    <name value="genomicSourceClass"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class."/>
    <type value="string"/>
    <searchType value="token"/>
  </parameter>
  <parameter>
    <name value="includePatientList"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Include list of matching patients if set to true. Default=false."/>
    <type value="boolean"/>
  </parameter>
  <parameter>
    <name value="variants"/>
    <use value="out"/>
    <min value="1"/>
    <max value="*"/>
    <part>
      <name value="variantItem"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation value="variant from variantList"/>
      <type value="string"/>
    </part>
    <part>
      <name value="numerator"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation value="Count of patients having this variant"/>
      <type value="Quantity"/>
    </part>
    <part>
      <name value="denominator"/>
      <use value="out"/>
      <min value="0"/>
      <max value="1"/>
      <documentation value="Count of patients in the cohort searched"/>
      <type value="Quantity"/>
    </part>
    <part>
      <name value="subject"/>
      <use value="out"/>
      <min value="0"/>
      <max value="*"/>
      <documentation value="Patient ID. Include if includePatientList=true"/>
      <type value="string"/>
    </part>
  </parameter>
</OperationDefinition>