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 - Complex Variant (unpacked) - XML Representation

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Raw xml 


<Bundle xmlns="http://hl7.org/fhir">
  <id value="complexVariant-nonHGVS"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
    <resource>
      <Observation>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.769G&gt;A <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.769G&gt;A'})</span></td></tr></table></div>
        </text>
        <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>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
      <!-- HGVS which was unpacked -->
      <!-- component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
						HGVS which was unpaceked
              <system value="http://varnomen.hgvs.org"/>
              <display value="NM_022787.3:c.769G&gt;A"/>
            </coding>
          </valueCodeableConcept>
        </component -->
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript ref sequence ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_022787.3"/>
              <display value="NM_022787.3"/>
            </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="769"/>
            </low>
            <high>
              <value value="769"/>
            </high>
          </valueRange>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
            </coding>
          </code>
          <valueString value="G"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Genomic alt allele [ID]"/>
            </coding>
          </code>
          <valueString value="A"/>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
    <resource>
      <Observation>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.53A&gt;G <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.53A&gt;G'})</span></td></tr></table></div>
        </text>
        <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>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
      <!-- HGVS which was unpaceked -->
      <!-- component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
			HGVS which was unpaceked
			<system value="http://varnomen.hgvs.org"/>
              <display value="NM_022787.3:c.53A&gt;G"/>
            </coding>
          </valueCodeableConcept>
        </component -->
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript ref sequence ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_022787.3"/>
              <display value="NM_022787.3"/>
            </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="53"/>
            </low>
            <high>
              <value value="53"/>
            </high>
          </valueRange>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
            </coding>
          </code>
          <valueString value="A"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Genomic alt allele [ID]"/>
            </coding>
          </code>
          <valueString value="G"/>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a"/>
    <resource>
      <Observation>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>hasMember</b>: </p><ul><li>NM_022787.3:c.53A&gt;G</li><li/></ul><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Complex Variant Type <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81263-6' = 'Complex variant type', given as 'Complex Variant Type'})</span></td><td>Compound heterozygous <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA26217-2' = 'Compound heterozygous', given as 'Compound heterozygous'})</span></td></tr></table></div>
        </text>
        <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>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <hasMember>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
          <display value="unpacked representation of NM_022787.3:c.53A&gt;G"/>
        </hasMember>
        <hasMember>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
          <display value="unpacked representation of NM_022787.3:c.769G&gt;A"/>
        </hasMember>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81263-6"/>
              <display value="Complex Variant Type"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA26217-2"/>
              <display value="Compound heterozygous"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
</Bundle>