This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example - Inherited Disease Pathogenicity - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="obs-idh-ex"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
  </meta>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><p><b>Related Artifact</b>: </p><p><b style="color: maroon">Exception generating Narrative: type org.hl7.fhir.r5.model.RelatedArtifact not handled - should not be here</b></p></div>
  </text>
<!--       <reference value="https://www.ncbi.nlm.nih.gov/pubmed/23974870,21520337,21228398,25087612,18951463,20880762,20460946,7539342,23891399,12955726"/>
 -->
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact">
    <valueRelatedArtifact>
      <type value="citation"/>
      <url
           value="https://www.ncbi.nlm.nih.gov/clinvar/variation/53685/#clinical-assertions"/>
    </valueRelatedArtifact>
  </extension>
  <status value="final"/>
  <category>
    <coding>
      <system value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <code>
  <!-- HL7 CG consider changing display name -->
    <coding>
      <system
              value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
      <code value="diagnostic-implication"/>
      <display value="Diagnostic Implication"/>
    </coding>
  </code>
<!--  REMOVE INVALID REFS
  <subject>
	<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
    <display value="TestPat"/>
  </subject>
  <issued value="2019-01-07T17:41:18+05:30"/>
  <encounter>
    <reference value="Encounter/example"/>
  </encounter>

 -->
  <derivedFrom>
    <reference value="Observation/SNVexample"/>
  </derivedFrom>
  <component>
    <code>
    <!-- HL7 CG consider changing display name -->
      <coding>
        <system value="http://loinc.org"/>
        <code value="53037-8"/>
        <display value="Genetic variation clinical significance [Imp]"/>
      </coding>
    </code>
    <valueCodeableConcept>
    <!--  should apply to all assoicated phenotype entries -->
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6668-3"/>
        <display value="Pathogenic"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81259-4"/>
        <display value="Associated phenotype"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/medgen"/>
        <code value="C0010674"/>
        <display value="Cystic fibrosis"/>
      </coding>
      <coding>
        <system value="http://www.orpha.net"/>
        <code value="ORPHA:586"/>
      </coding>
      <coding>
        <system value="http://www.omim.org"/>
        <code value="219700"/>
      </coding>
      <text value="Cystic fibrosis"/>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
        <code value="condition-inheritance"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/ConditionInheritanceMode"/>
        <code value="HP:0000007"/>
        <display value="Autosomal recessive inheritance"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>