Genomics Reporting Implementation Guide (STU1)

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 - subset of CYP2C19 report from 1000 Genomes showing phase - XML Representation

(back to narrative)

Raw xml 


<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="sequence-phase-relation-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>: sequence-phase-relation-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></ul></div>
  </text>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca8252"/>
      <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="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="96527334"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="dv-5c7e9e1ca82e4"/>
      <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="96527722"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="sid-5c7e9e1ca8a29"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"/>
      </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="82120-7"/>
          <display value="Allelic phase"/>
        </coding>
      </code>
      <issued value="2019-03-05T16:04:44+00:00"/>
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/seq-phase-relationship"/>
          <code value="Cis"/>
          <display value="Cis"/>
        </coding>
      </valueCodeableConcept>
      <derivedFrom>
        <reference value="#dv-5c7e9e1ca8252"/>
      </derivedFrom>
      <derivedFrom>
        <reference value="#dv-5c7e9e1ca82e4"/>
      </derivedFrom>
    </Observation>
  </contained>
  <status value="final"/>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="81247-9"/>
    </coding>
    <text value="Genetic analysis report"/>
  </code>
  <result>
    <reference value="#dv-5c7e9e1ca8252"/>
  </result>
  <result>
    <reference value="#dv-5c7e9e1ca82e4"/>
  </result>
  <result>
    <reference value="#sid-5c7e9e1ca8a29"/>
  </result>
</DiagnosticReport>