This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example - CYP2C19 report from 1000 Genomes - XML Representation

(back to narrative)

Raw xml

<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="report-CYP2C19"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: report-CYP2C19</p><p><b>meta</b>: </p><p><b>contained</b>: , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , </p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis report <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel)</span></p><p><b>result</b>: </p><ul><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li></ul></div>
  </text>
  <contained>
    <Observation>
      <id value="rs-5c7e9e1ca6214"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="53041-0"/>
          <display value="DNA Region of interest panel"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48018-6"/>
            <display value="Gene studied ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.genenames.org/geneId"/>
            <code value="HGNC:2621"/>
            <display value="CYP2C19"/>
          </coding>
        </valueCodeableConcept>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca62b5"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="A"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Alt allele"/>
          </coding>
        </code>
        <valueString value="G"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="96448129"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca6342"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="C"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Alt allele"/>
          </coding>
        </code>
        <valueString value="G"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="96448380"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca63bf"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="A"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Alt allele"/>
          </coding>
        </code>
        <valueString value="C"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="96448994"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca643a"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="G"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Alt allele"/>
          </coding>
        </code>
        <valueString value="A"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="96454156"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca64b5"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6705-3"/>
            <display value="homozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="G"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Alt allele"/>
          </coding>
        </code>
        <valueString value="A"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="96454241"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca6531"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
        </coding>
      </valueCodeableConcept>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000010.10"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Ref nucleotide"/>
          </coding>
        </code>
        <valueString value="C"/>
      </component>
      <component>
        <code>
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