Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: bundle-compound-heterozygote - XML Representation

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<Bundle xmlns="http://hl7.org/fhir">
  <id value="bundle-compound-heterozygote"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-compound-heterozygote-1"/>
        <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"><a name="Observation_Inline-Instance-for-compound-heterozygote-1"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-1</b></p><a name="Inline-Instance-for-compound-heterozygote-1"> </a><a name="hcInline-Instance-for-compound-heterozygote-1"> </a><a name="Inline-Instance-for-compound-heterozygote-1-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_022787.3:c.769G&gt;A}">NM_022787.3:c.769G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6706-1}">Heterozygous</span></p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
        </subject>
        <effectiveDateTime value="2019-03-05"/>
        <issued value="2019-03-05T16:04:44+00:00"/>
        <performer>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
        </performer>
        <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="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_022787.3:c.769G&gt;A"/>
              <display value="NM_022787.3:c.769G&gt;A"/>
            </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>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-compound-heterozygote-2"/>
        <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"><a name="Observation_Inline-Instance-for-compound-heterozygote-2"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-2</b></p><a name="Inline-Instance-for-compound-heterozygote-2"> </a><a name="hcInline-Instance-for-compound-heterozygote-2"> </a><a name="Inline-Instance-for-compound-heterozygote-2-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_022787.3:c.53A&gt;G}">NM_022787.3:c.53A&gt;G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6706-1}">Heterozygous</span></p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
        </subject>
        <effectiveDateTime value="2019-03-05"/>
        <issued value="2019-03-05T16:04:44+00:00"/>
        <performer>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
        </performer>
        <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="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_022787.3:c.53A&gt;G"/>
              <display value="NM_022787.3:c.53A&gt;G"/>
            </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>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-compound-heterozygote-3"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-compound-heterozygote-3"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-3</b></p><a name="Inline-Instance-for-compound-heterozygote-3"> </a><a name="hcInline-Instance-for-compound-heterozygote-3"> </a><a name="Inline-Instance-for-compound-heterozygote-3-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 84413-4}">Genotype display name</span></p><p><b>subject</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/clinvar RCV000664188.1}">NM_022787.3(NMNAT1):c.[53A&gt;G];[769G&gt;A] AND Cone-rod dystrophy</span></p><p><b>hasMember</b>: </p><ul><li><a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12e">NM_022787.3:c.53A&gt;G</a></li><li><a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d">NM_022787.3:c.769G&gt;A</a></li></ul></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="84413-4"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
        </subject>
        <effectiveDateTime value="2019-03-05"/>
        <issued value="2019-03-05T16:04:44+00:00"/>
        <performer>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
            <code value="RCV000664188.1"/>
            <display
                     value="NM_022787.3(NMNAT1):c.[53A&gt;G];[769G&gt;A] AND Cone-rod dystrophy"/>
          </coding>
        </valueCodeableConcept>
        <hasMember>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
          <display value="NM_022787.3:c.53A&gt;G"/>
        </hasMember>
        <hasMember>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
          <display value="NM_022787.3:c.769G&gt;A"/>
        </hasMember>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"/>
    <resource>
      <Organization>
        <id value="performingLab"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_performingLab"> </a><p class="res-header-id"><b>Generated Narrative: Organization performingLab</b></p><a name="performingLab"> </a><a name="hcperformingLab"> </a><a name="performingLab-en-US"> </a><p><b>name</b>: aTypingLab Inc</p><p><b>alias</b>: aTL</p><p><b>telecom</b>: ph: 1-800-555-1234(Work)</p><p><b>address</b>: 123 Main St, Sometown, ND 99999(work)</p></div>
        </text>
        <name value="aTypingLab Inc"/>
        <alias value="aTL"/>
        <telecom>
          <system value="phone"/>
          <value value="1-800-555-1234"/>
          <use value="work"/>
          <rank value="1"/>
        </telecom>
        <address>
          <use value="work"/>
          <type value="both"/>
          <text value="123 Main St, Sometown, ND 99999"/>
          <line value="123 Main St"/>
          <city value="Sometown"/>
          <state value="ND"/>
          <postalCode value="99999"/>
          <country value="USA"/>
        </address>
      </Organization>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Organization"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"/>
    <resource>
      <Patient>
        <id value="patient"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_patient"> </a><p class="res-header-id"><b>Generated Narrative: Patient patient</b></p><a name="patient"> </a><a name="hcpatient"> </a><a name="patient-en-US"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">John Storm(official) Male, DoB: 1986-12-31</p><hr/></div>
        </text>
        <name>
          <use value="official"/>
          <text value="John Storm"/>
          <family value="Storm"/>
          <given value="John"/>
        </name>
        <name>
          <use value="nickname"/>
          <text value="Johnny Storm"/>
          <family value="Storm"/>
          <given value="Johnny"/>
        </name>
        <name>
          <use value="nickname"/>
          <text value="The Human Torch"/>
        </name>
        <gender value="male"/>
        <birthDate value="1986-12-31"/>
      </Patient>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Patient"/>
    </request>
  </entry>
</Bundle>