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Diagnosticreport-genetics-example-1.xml

Raw XML (canonical form)
An example of a genetics test report (id = "dg1")
<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="dg1"/>
  <text><status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: dg1</p><p><b>contained</b>: , , , , </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory test <span>(Details : {SNOMED CT code '15220000' = '15220000', given as 'Laboratory test'}; {http://hl7.org/fhi
          r/v2/0074 code 'LAB' = 'Laboratory)</span></p><p><b>code</b>: ABCB4 gene mutation analysis <span>(Details : {LOINC code '49874-1' = 'ABCB4 gene mutation analysis in Blood or Tissue by
           Molecular genetics method Narrative', given as 'ABCB4 gene mutation analysis'})</span></p><p><b>subject</b>: <a>Molecular Lab Patient ID: HOSP-23456</a></p><p><b>effective</b>: 04/03/2014 8:30:00 AM</p><p><b>issued</b>: 16/05/2014 10:28:00 AM</p><p><b>performer</b>: <a>Molecular Diagnostic Laboratory</a></p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p><p><b>result</b>: </p><ul><li>Genetic analysis master panel for ABCB4 -variant1. Generated Summary: id: od-1; Extensions:
           todo, Extensions: todo, Extensions: todo, Extensions: todo; status: final; ABCB4 gene
           mutation analysis <span>(Details : {LOINC code '49874-1' = 'ABCB4 gene mutation analysis in Blood or Tissue by
             Molecular genetics method Narrative', given as 'ABCB4 gene mutation analysis'})</span>; positive <span>(Details : {http://hl7.org/fhir/v2/0078 code 'POS' = 'Positive)</span></li><li>Genetic analysis master panel for ABCB4 -variant2. Generated Summary: id: od-2; Extensions:
           todo, Extensions: todo, Extensions: todo, Extensions: todo; status: final; ABCB4 gene
           mutation analysis <span>(Details : {LOINC code '49874-1' = 'ABCB4 gene mutation analysis in Blood or Tissue by
             Molecular genetics method Narrative', given as 'ABCB4 gene mutation analysis'})</span>; positive <span>(Details : {http://hl7.org/fhir/v2/0078 code 'POS' = 'Positive)</span></li><li>Genetic analysis master panel for ABCB4 -variant3. Generated Summary: id: od-3; Extensions:
           todo, Extensions: todo, Extensions: todo, Extensions: todo; status: final; ABCB4 gene
           mutation analysis <span>(Details : {LOINC code '49874-1' = 'ABCB4 gene mutation analysis in Blood or Tissue by
             Molecular genetics method Narrative', given as 'ABCB4 gene mutation analysis'})</span>; positive <span>(Details : {http://hl7.org/fhir/v2/0078 code 'POS' = 'Positive)</span></li><li>Genetic analysis master panel for ABCB4 -variant4. Generated Summary: id: od-4; Extensions:
           todo, Extensions: todo, Extensions: todo, Extensions: todo; status: final; ABCB4 gene
           mutation analysis <span>(Details : {LOINC code '49874-1' = 'ABCB4 gene mutation analysis in Blood or Tissue by
             Molecular genetics method Narrative', given as 'ABCB4 gene mutation analysis'})</span>; positive <span>(Details : {http://hl7.org/fhir/v2/0078 code 'POS' = 'Positive)</span></li></ul></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>
          <verificationStatus value="provisional"/>
      </Condition>
  </contained>
  <contained>
      <Observation>
          <id value="od-1"/>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
              <valueReference>
                  <reference value="Sequence/seq2-1"/>
              </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.2708T&gt;C"/>
                  </valueCodeableConcept>
              </extension>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
              <valueCodeableConcept>
                  <coding>
                      <system value="http://www.genenames.org"/>
                      <code value="5244"/>
                      <display value="ABCB4"/>
                  </coding>
              </valueCodeableConcept>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion">
              <valueCodeableConcept>
                  <text value="Exon 23"/>
              </valueCodeableConcept>
          </extension>
          <status value="final"/>
          <code>
              <coding>
                  <system value="http://loinc.org"/>
                  <code value="49874-1"/>
                  <display value="ABCB4 gene mutation analysis"/>
              </coding>
          </code>
          <interpretation>
              <coding>
                  <system value="http://hl7.org/fhir/v2/0078"/>
                  <code value="POS"/>
              </coding>
              <text value="positive"/>
          </interpretation>
          <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="LA6682-4"/>
                      <display value="Unknown significance"/>
                  </coding>
              </valueCodeableConcept>
          </component>
      </Observation>
  </contained>
  <contained>
      <Observation>
          <id value="od-2"/>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
              <valueReference>
                  <reference value="Sequence/seq2-2"/>
              </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;G"/>
                  </valueCodeableConcept>
              </extension>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
              <valueCodeableConcept>
                  <coding>
                      <system value="http://www.genenames.org"/>
                      <code value="5244"/>
                      <display value="ABCB4"/>
                  </coding>
              </valueCodeableConcept>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion">
              <valueCodeableConcept>
                  <text value="Exon 6"/>
              </valueCodeableConcept>
          </extension>
          <status value="final"/>
          <code>
              <coding>
                  <system value="http://loinc.org"/>
                  <code value="49874-1"/>
                  <display value="ABCB4 gene mutation analysis"/>
              </coding>
          </code>
          <interpretation>
              <coding>
                  <system value="http://hl7.org/fhir/v2/0078"/>
                  <code value="POS"/>
              </coding>
              <text value="positive"/>
          </interpretation>
          <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="LA6675-8"/>
                      <display value="Benign"/>
                  </coding>
              </valueCodeableConcept>
          </component>
      </Observation>
  </contained>
  <contained>
      <Observation>
          <id value="od-3"/>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
              <valueReference>
                  <reference value="Sequence/seq2-3"/>
              </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.2211+16C&gt;T"/>
                  </valueCodeableConcept>
              </extension>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
              <valueCodeableConcept>
                  <coding>
                      <system value="http://www.genenames.org"/>
                      <code value="5244"/>
                      <display value="ABCB4"/>
                  </coding>
              </valueCodeableConcept>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion">
              <valueCodeableConcept>
                  <text value="intron 16"/>
              </valueCodeableConcept>
          </extension>
          <status value="final"/>
          <code>
              <coding>
                  <system value="http://loinc.org"/>
                  <code value="49874-1"/>
                  <display value="ABCB4 gene mutation analysis"/>
              </coding>
          </code>
          <interpretation>
              <coding>
                  <system value="http://hl7.org/fhir/v2/0078"/>
                  <code value="POS"/>
              </coding>
              <text value="positive"/>
          </interpretation>
          <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="LA6675-8"/>
                      <display value="Benign"/>
                  </coding>
              </valueCodeableConcept>
          </component>
      </Observation>
  </contained>
  <contained>
      <Observation>
          <id value="od-4"/>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence">
              <valueReference>
                  <reference value="Sequence/seq2-4"/>
              </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.3487-16T&gt;C"/>
                  </valueCodeableConcept>
              </extension>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene">
              <valueCodeableConcept>
                  <coding>
                      <system value="http://www.genenames.org"/>
                      <code value="5244"/>
                      <display value="ABCB4"/>
                  </coding>
              </valueCodeableConcept>
          </extension>
          <extension url="http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion">
              <valueCodeableConcept>
                  <text value="intron 26"/>
              </valueCodeableConcept>
          </extension>
          <status value="final"/>
          <code>
              <coding>
                  <system value="http://loinc.org"/>
                  <code value="49874-1"/>
                  <display value="ABCB4 gene mutation analysis"/>
              </coding>
          </code>
          <interpretation>
              <coding>
                  <system value="http://hl7.org/fhir/v2/0078"/>
                  <code value="POS"/>
              </coding>
              <text value="positive"/>
          </interpretation>
          <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="LA6675-8"/>
                      <display value="Benign"/>
                  </coding>
              </valueCodeableConcept>
          </component>
      </Observation>
  </contained>
  
  <extension url="http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsAssessedCondition">
      <valueReference>
          <reference value="#c1"/>
      </valueReference>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsAnalysis">
      <extension url="type">
          <valueCodeableConcept>
              <coding>
                  <system value="http://loinc.org"/>
                  <code value="51968-6"/>
                  <display value="Genetic Disease Analysis Overall Interpretation"/>
              </coding>
          </valueCodeableConcept>
      </extension>
      <extension url="interpretation">
          <valueCodeableConcept>
              <coding>
                  <code value="LA9663-1 "/>
                  <display value="Inconclusive"/>
              </coding>
          </valueCodeableConcept>
      </extension>
  </extension>
  
  <status value="final"/>
  <category>
    <coding>
      <system value="http://snomed.info/sct"/>
      <code value="15220000"/>
      <display value="Laboratory test"/>
    </coding>
    <coding>
      <system value="http://hl7.org/fhir/v2/0074"/>
      <code value="LAB"/>
    </coding>
  </category>
  <code>
      <coding>
          <system value="http://loinc.org"/>
          <code value="49874-1"/>
          <display value="ABCB4 gene mutation analysis"/>
      </coding>
  </code>
  <subject>
      <reference value="Patient/genetics-example2"/>
      <display value="Molecular Lab Patient ID: HOSP-23456"/>
  </subject>
  <effectiveDateTime value="2014-03-04T08:30:00+11:00"/>
  <issued value="2014-05-16T10:28:00+01:00"/>
  <performer>
      <reference value="Practitioner/genetics-example2"/>
      <display value="Molecular Diagnostic Laboratory"/>
  </performer>
  <specimen>
      <reference value="Specimen/genetics-example2"/>
      <display value="Molecular Specimen ID: MLD45-Z4-1234"/>
  </specimen>
  <result>
    <reference value="#od-1"/>
    <display value="Genetic analysis master panel for ABCB4 -variant1"/>
  </result>
  <result>
      <reference value="#od-2"/>
      <display value="Genetic analysis master panel for ABCB4 -variant2"/>
  </result>
  <result>
      <reference value="#od-3"/>
      <display value="Genetic analysis master panel for ABCB4 -variant3"/>
  </result>
  <result>
      <reference value="#od-4"/>
      <display value="Genetic analysis master panel for ABCB4 -variant4"/>
  </result>

</DiagnosticReport>
Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.