This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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

Example - Inherited Disease Pathogenicity - XML Representation

(back to narrative)

Raw xml

<Observation xmlns="http://hl7.org/fhir">
  <id value="obs-idh-ex"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: obs-idh-ex</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style="background: LightGoldenRodYellow">(Details : {LOINC code '53037-8' = 'Genetic variation clinical significance [Imp]', given as 'Genetic variation clinical significance [Imp]'})</span></p><p><b>value</b>: Pathogenic <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA6668-3' = 'Pathogenic', given as 'Pathogenic'})</span></p><p><b>derivedFrom</b>: <a href="obs-idh-ex.html">Generated Summary: id: SNVexample; <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>; <span title="Codes: {http://loinc.org 69548-6}">Genetic variant assessment</span>; <span title="Codes: {http://loinc.org LA9633-4}">Present</span>; <span title="Codes: {http://loinc.org LA26398-0}">Sequencing</span></a></p><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Cystic fibrosis <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0010674' = 'C0010674', given as 'Cystic fibrosis'}; {http://www.orpha.net code 'ORPHA:586' = 'ORPHA:586; {http://www.omim.org code '219700' = '219700)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Congenital bilateral absence of the vas deferens <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0403814' = 'C0403814; {http://www.orpha.net code 'ORPHA:48' = 'ORPHA:48; {http://www.omim.org code '277180' = '277180; {http://www.omim.org code '300985' = '300985)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: mode-of-inheritance <span style="background: LightGoldenRodYellow">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'mode-of-inheritance' = 'mode-of-inheritance', given as 'mode-of-inheritance'})</span></p><p><b>value</b>: Autosomal recessive <span style="background: LightGoldenRodYellow">(Details : {http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns code 'Autosomal recessive' = 'Autosomal recessive', given as 'Autosomal recessive'})</span></p></blockquote></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/RelatedArtifact">
    <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://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>
<!--  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>
      <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://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="C0403814"/>
      </coding>
      <coding>
        <system value="http://www.orpha.net"/>
        <code value="ORPHA:48"/>
      </coding>
      <coding>
        <system value="http://www.omim.org"/>
        <code value="277180"/>
      </coding>
      <coding>
        <system value="http://www.omim.org"/>
        <code value="300985"/>
      </coding>
      <text value="Congenital bilateral absence of the vas deferens"/>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
        <code value="mode-of-inheritance"/>
      <!--  it is important that this be true for each of the Assoicated Phenotypes. If not, use multiple idh profile instances -->
        <display value="mode-of-inheritance"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system
                value="http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns"/>
        <code value="Autosomal recessive"/>
        <display value="Autosomal recessive"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>