Obs-genetics-example2-germline.xml

Genetics Observation of Germline BRCA1 Variant (id = "genetics-example2-germline")

<Observation xmlns="http://hl7.org/fhir">
  <id value="genetics-example2-germline"/>
  <text><status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: genetics-example2-germline</p><p><b>status</b>: final</p><p><b>code</b>: BRCA1 gene mutation analysis <span>(Details : {LOINC code '21636-6' = 'BRCA1 gene mutations found [Identifier] in Blood or
           Tissue by Molecular genetics method Nominal', given as 'BRCA1 gene mutation analysis'})</span></p><p><b>subject</b>: <a>Molecular Lab Patient ID: HOSP-23456</a></p><p><b>performer</b>: <a>Molecular Diagnostic Laboratory</a></p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p></div></text><extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomeBuild">
    <valueString value="GRCh 37"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsChromosome">
      <valueCodeableConcept>
          <coding>
              <system value="http://www.ncbi.nlm.nih.gov/gene"/>
              <code value="NC_000017"/>
          </coding>
          <text value="Homo sapiens chromosome 17"/>
      </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicStart">
    <valueInteger value="41258504"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicStop">
    <valueInteger value="41258505"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsReferenceAllele">
    <valueString value="A"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsObservedAllele">
    <valueString value="C"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGene">
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org"/>
        <code value="1100"/>
        <display value="BRCA1"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariation">
    <valueString value="c.181T&gt;G"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsVariationId">
      <valueCodeableConcept>
          <coding>
              <system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
              <code value="17661"/>
              <display value="c.181T&gt;G"/>
          </coding>
      </valueCodeableConcept>
  </extension>

  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsDNARegionName">
    <valueString value="Exon 4"/>
  </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/geneticsAminoAcidChange">
    <valueString value="p.Cys61Gly"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6683-2"/>
        <display value="Germline"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsSpecies">
    <valueCodeableConcept>
        <coding>
            <system value="http://snomed.info/sct"/>
            <code value="337915000"/> 
        </coding>
        <text value="Homo sapiens"/>
    </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/geneticsCIGAR">
    <valueString value="1M"/>
  </extension>
  <status value="final"/>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="21636-6"/>
      <display value="BRCA1 gene mutation analysis"/>
    </coding>
  </code>
  <subject>
    <reference value="Patient/genetics-example2-germline"/>
    <display value="Molecular Lab Patient ID: HOSP-23456"/>
  </subject>
  <performer>
    <reference value="Practitioner/genetics-example2-germline"/>
    <display value="Molecular Diagnostic Laboratory"/>
  </performer>
  <specimen>
    <reference value="Specimen/genetics-example2-germline"/>
    <display value="Molecular Specimen ID: MLD45-Z4-1234"/>
  </specimen>
</Observation>