Observation-example-genetics-1.xml

Genetics Observation of Somatic Variant in Lung Cancer (id = "ob-genetics-1")

<Observation xmlns="http://hl7.org/fhir">
  <id value="ob-genetics-1"/>
  <text><status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: ob-genetics-1</p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis master panel <span>(Details : {LOINC code '55233-1' = 'Genetic analysis master panel - Blood or Tissue by
           Molecular genetics method', given as 'Genetic analysis master panel'})</span></p><p><b>subject</b>: <a>Molecular Lab Patient ID: HOSP-23456</a></p><p><b>issued</b>: 11/03/2013 10:28:00 AM</p><p><b>performer</b>: <a>Molecular Diagnostic Laboratory</a></p><p><b>value</b>: Positive <span>(Details : {SNOMED CT code '10828004' = '10828004', given as 'Positive'})</span></p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic disease assessed <span>(Details : {LOINC code '51967-8' = 'Genetic disease assessed [Identifier] in Blood or
             Tissue by Molecular genetics method', given as 'Genetic disease assessed'})</span></p><p><b>value</b>: Lung cancer <span>(Details : {SNOMED CT code '363358000' = '??', given as 'Malignant tumor of lung (disorder)'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genetic disease sequence variation interpretation <span>(Details : {LOINC code '53037-8' = 'Genetic disease sequence variation interpretation
             [interpretation] in Blood or Tissue by Molecular genetics method', given as 'Genetic disease
             sequence variation interpretation'})</span></p><p><b>value</b>: Pathogenic <span>(Details : {[not stated] code 'LA6669-1' = '??', given as 'Pathogenic'})</span></p></blockquote></div></text><extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
      <valueReference>
          <reference value="Sequence/example"/>
      </valueReference>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSource">
      <valueCodeableConcept>
          <coding>
              <system value="http://hl7.org/fhir/LOINC-48002-0-answerlist"/>
              <code value="LA6684-0"/>
              <display value="somatic"/>
          </coding>
      </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS">
      <extension url="genomeBuild">
          <valueCodeableConcept>
              <text value="GRCh 38"/>
          </valueCodeableConcept>
      </extension>
      <extension url="name">
          <valueCodeableConcept>
              <text value="NG_007726.3:g.146252T&gt;G"/>
          </valueCodeableConcept>
      </extension>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
      <valueCodeableConcept>
          <coding>
              <system value="http://www.genenames.org"/>
              <code value="3236"/>
              <display value="EGFR"/>
          </coding>
      </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion">
      <valueCodeableConcept>
          <text value="Exon 21"/>
      </valueCodeableConcept>
  </extension>
  <status value="final"/>
  <code>
      <coding>
          <system value="http://loinc.org"/>
          <code value="55233-1"/>
          <display value="Genetic analysis master panel"/>
      </coding>
  </code>
  <subject>
      <reference value="Patient/genetics-example1-somatic"/>
      <display value="Molecular Lab Patient ID: HOSP-23456"/>
  </subject>
  <issued value="2013-03-11T10:28:00+01:00"/>
  <performer>
      <reference value="Practitioner/genetics-example1-somatic"/>
      <display value="Molecular Diagnostic Laboratory"/>
  </performer>
  <valueCodeableConcept>
      <coding>
          <system value="http://snomed.info/sct"/>
          <code value="10828004"/>
          <display value="Positive"/>
      </coding>
  </valueCodeableConcept>
  <specimen>
      <reference value="Specimen/genetics-example1-somatic"/>
      <display value="Molecular Specimen ID: MLD45-Z4-1234"/>
  </specimen>
  <component>
      <code>
          <coding>
              <system value="http://loinc.org"/>
              <code value="51967-8"/>
              <display value="Genetic disease assessed"/>
          </coding>
      </code>
      <valueCodeableConcept>
          <coding>
              <system value="http://snomed.info/sct"/>
              <code value="363358000"/>
              <display value="Malignant tumor of lung (disorder)"/>
          </coding>
          <text value="Lung cancer"/>
      </valueCodeableConcept>
  </component>
  <component>
      <code>
          <coding>
              <system value="http://loinc.org"/>
              <code value="53037-8"/>
              <display value="Genetic disease sequence variation interpretation"/>
          </coding>
      </code>
      <valueCodeableConcept>
          <coding>
              <code value="LA6669-1"/>
              <display value="Pathogenic"/>
          </coding>
      </valueCodeableConcept>
  </component>
</Observation>