Obs-genetics-example1-somatic.xml

Genetics Observation of Somatic Variant in Lung Cancer (id = "genetics-example1-somatic")

Raw XML

<Observation xmlns="http://hl7.org/fhir">
  <id value="genetics-example1-somatic"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><!-- Snipped for brevity --></div>
  </text>
  <contained>
    <Condition>
      <id value="c1"/>
      <patient>
        <reference value="Patient/p1"/>
      </patient>
      <code>
        <coding>
          <system value="http://snomed.info/sct"/>
          <code value="254626006"/>
        </coding>
        <text value="Adenocarcinoma of lung "/>
      </code>
      <category>
        <coding>
          <system value="http://hl7.org/fhir/condition-category"/>
          <code value="finding"/>
          <display value="Finding"/>
        </coding>
      </category>
      <clinicalStatus value="working"/>
    </Condition>
  </contained>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomeBuild">
    <valueString value="GRCh 37"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsChromosome">
    <valueString value="7"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicReferenceSequenceId">
    <valueCode value="NC_000007.13"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicStart">
    <valueInteger value="55259515"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicStop">
    <valueInteger value="55259515"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsReferenceAllele">
    <valueString value="T"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsObservedAllele">
    <valueString value="G"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGeneId">
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org"/>
        <code value="3236"/>
        <display value="EGFR"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsTranscriptReferenceSequenseId">
    <valueCode value="ENSESTT00000085772.1"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariation">
    <valueString value="c.2573T&gt;G"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsVariationId">
    <valueCode value="COSM12979G"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsDNARegionName">
    <valueString value="Exon 21"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariationType">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6690-7"/>
        <display value="Substitution"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsProteinReferenceSequenceId">
    <valueCode value="ENSESTP00000085772.1"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsAminoAcidChange">
    <valueString value="p.Leu858Arg"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsAlleleName">
    <valueString value="p.L858R"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6684-0"/>
        <display value="Somatic"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsSpecies">
    <valueString value="Human"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsCIGAR">
    <valueString value="GATTTTGGGCtGGCCAAACTG"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsAssessedCondition">
    <valueReference>
      <reference value="#c1"/>
    </valueReference>
  </extension>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="21665-5"/>
      <display value="EGFR gene mutation analysis"/>
    </coding>
  </code>
  <comments value="The EGFR p.L858R mutation has been associated with response to anti-EGFR therapy"/>
  <status value="final"/>
  <subject>
    <reference value="Patient/genetics-example1-somatic"/>
    <display value="Molecular Lab Patient ID: HOSP-23456"/>
  </subject>
  <specimen>
    <reference value="Specimen/genetics-example1-somatic"/>
    <display value="Molecular Specimen ID: MLD45-Z4-1234"/>
  </specimen>
  <performer>
    <reference value="Practitioner/genetics-example1-somatic"/>
    <display value="Molecular Diagnostic Laboratory"/>
  </performer>
</Observation>