Observation-example-genetics-6-2.xml

Genetics Observation for BRCA1 c.181T>A (id = "ob-genetics-6-2")

<Observation xmlns="http://hl7.org/fhir">
  <id value="ob-genetics-6-2"/>
  <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-6-2</p><p><b>contained</b>: </p><p><b>status</b>: final</p><p><b>code</b>: BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method
         Nominal <span>(Details : {https://loinc.org/ code '21636-6' = '??', given as 'BRCA1 gene mutations found
           [Identifier] in Blood or Tissue by Molecular genetics method Nominal'})</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></div></text><contained>
      <Sequence>
          <id value="g-2"/>
          <type value="DNA"/>
          <variationID>
              <coding>
                  <system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
                  <code value="28897672"/>
              </coding>
          </variationID>
          <referenceSeq>
              <coding>
                  <system value="http://www.ncbi.nlm.nih.gov/nuccore/"/>
                  <code value="NM_007298.3"/>
              </coding>
          </referenceSeq>
          <coordinate>
              <chromosome>
                  <coding>
                      <code value="17"/>
                  </coding>
              </chromosome>
              <start value="43106487"/>
              <end value="43106488"/>
              <genomeBuild>
                  <text value="GRCh38.p2"/>
              </genomeBuild>
          </coordinate>
          <observedAllele value="A"/>
          <referenceAllele value="T"/>
      </Sequence>
  </contained>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
      <valueReference>
          <reference value="#g-2"/>
      </valueReference>
  </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="c.181T&gt;A"/>
          </valueCodeableConcept>
      </extension>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
      <valueCodeableConcept>
          <coding>
              <system value="http://www.genenames.org"/>
              <code value="672"/>
              <display value="BRCA1"/>
          </coding>
      </valueCodeableConcept>
  </extension>
  
  <status value="final"/>
  <code>
      <coding>
          <system value="https://loinc.org/"/>
          <code value="21636-6"/>
          <display value="BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method
       Nominal"/>
      </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>

</Observation>