Observation-consensus-sequence-block-example-1.xml

Example of HLA genotyping results - consensus sequence block 1 (id = "consensus-sequence-block-example-1")

<Observation xmlns="http://hl7.org/fhir">
  <id value="consensus-sequence-block-example-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>: consensus-sequence-block-example-1</p><p><b>contained</b>: , </p><p><b>status</b>: final</p><p><b>code</b>: HLA-A [Type] <span>(Details : {LOINC code '13298-5' = 'HLA-A [Type])</span></p></div></text><contained>
      <Sequence>
          <id value="variant-1"/>
          <type value="DNA"/>
          <coordinate>
              <start value="29945809"/>
              <end value="29942810"/>
          </coordinate>
          <observedAllele value="AT"/>
          <referenceAllele value="C"/>
      </Sequence>
  </contained>
  <contained>
      <Sequence>
          <id value="variant-2"/>
          <type value="DNA"/>
          <coordinate>
              <start value="29942940"/>
              <end value="29942942"/>
          </coordinate>
          <observedAllele value="G"/>
          <referenceAllele value="CT"/>
      </Sequence>
  </contained>

  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockReferenceSeq">
      <valueCodeableConcept>
          <coding>
              <system value="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/"/>
              <code value="ref1"/>
          </coding>
      </valueCodeableConcept>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockStart">
      <valueInteger value="29942412"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockEnd">
      <valueInteger value="29942852"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockPhaseSet">
      <valueInteger value="1"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockExpectedCopyNumber">
      <valueInteger value="1"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockContinuity">
      <valueBoolean value="true"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockVariant">
      <valueReference>
          <reference value="#variant-1"/>
      </valueReference>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockVariant">
      <valueReference>
          <reference value="#variant-2"/>
      </valueReference>
  </extension>
  
  <status value="final"/>
  <code>
      <coding>
          <system value="http://loinc.org"/>
          <code value="13298-5"/>
      </coding>
  </code>
</Observation>