Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: FindSubjectVariantsOutput - XML Representation

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<Parameters xmlns="http://hl7.org/fhir">
  <id value="FindSubjectVariantsOutput"/>
  <parameter>
    <name value="variants"/>
    <part>
      <name value="rangeItem"/>
      <valueString value="NC_000017.11:39688093-39728660"/>
    </part>
    <part>
      <name value="presence"/>
      <valueBoolean value="false"/>
    </part>
  </parameter>
  <parameter>
    <name value="variants"/>
    <part>
      <name value="rangeItem"/>
      <valueString value="NC_000007.14:140713327-140924929"/>
    </part>
    <part>
      <name value="presence"/>
      <valueBoolean value="true"/>
    </part>
    <part>
      <name value="variant"/>
      <resource>
        <Observation>
          <id value="dv-5a7f781e83514"/>
          <meta>
            <profile
                     value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
          </meta>
          <text>
            <status value="generated"/>
            <div xmlns="http://www.w3.org/1999/xhtml">Variant</div>
          </text>
          <status value="final"/>
          <category>
            <coding>
              <system
                      value="http://terminology.hl7.org/CodeSystem/observation-category"/>
              <code value="laboratory"/>
            </coding>
          </category>
          <category>
            <coding>
              <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
              <code value="GE"/>
            </coding>
          </category>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69548-6"/>
              <display value="Genetic variant assessment"/>
            </coding>
          </code>
          <subject>🔗 
            <reference value="Patient/HG00403"/>
          </subject>
          <effectiveDateTime value="2023-07-01"/>
          <performer>🔗 
            <reference value="Organization/ExampleOrg"/>
          </performer>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA9633-4"/>
              <display value="Present"/>
            </coding>
          </valueCodeableConcept>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="48002-0"/>
                <display value="Genomic source class [Type]"/>
              </coding>
            </code>
            <valueCodeableConcept>
              <coding>
                <system value="http://loinc.org"/>
                <code value="LA6684-0"/>
                <display value="Somatic"/>
              </coding>
            </valueCodeableConcept>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="48013-7"/>
                <display value="Genomic reference sequence ID"/>
              </coding>
            </code>
            <valueCodeableConcept>
              <coding>
                <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
                <code value="NC_000007.14"/>
              </coding>
            </valueCodeableConcept>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="81258-6"/>
                <display value="Sample VAF"/>
              </coding>
            </code>
            <valueQuantity>
              <value value="0.1793"/>
              <unit
                    value="relative frequency of a particular allele in the specimen"/>
              <system value="http://unitsofmeasure.org"/>
              <code value="1"/>
            </valueQuantity>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="69547-8"/>
                <display value="Genomic Ref allele [ID]"/>
              </coding>
            </code>
            <valueString value="A"/>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="69551-0"/>
                <display value="Genomic Alt allele [ID]"/>
              </coding>
            </code>
            <valueString value="T"/>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="92822-6"/>
                <display value="Genomic coord system"/>
              </coding>
            </code>
            <valueCodeableConcept>
              <coding>
                <system value="http://loinc.org"/>
                <code value="LA30100-4"/>
                <display value="0-based interval counting"/>
              </coding>
            </valueCodeableConcept>
          </component>
          <component>
            <code>
              <coding>
                <system value="http://loinc.org"/>
                <code value="81254-5"/>
              </coding>
              <text value="Genomic allele start-end"/>
            </code>
            <valueRange>
              <low>
                <value value="140753335"/>
              </low>
            </valueRange>
          </component>
        </Observation>
      </resource>
    </part>
  </parameter>
</Parameters>