Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

: bundle-sequence-phase-relation-CYP2C19 - XML Representation

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<Bundle xmlns="http://hl7.org/fhir">
  <id value="bundle-sequence-phase-relation-CYP2C19"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60"/>
    <resource>
      <Observation>
        <id value="dv-5c7e9e1ca8252"/>
        <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_dv-5c7e9e1ca8252"> </a><p class="res-header-id"><b>Generated Narrative: Observation dv-5c7e9e1ca8252</b></p><a name="dv-5c7e9e1ca8252"> </a><a name="hcdv-5c7e9e1ca8252"> </a><a name="dv-5c7e9e1ca8252-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 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48013-7}">Genomic reference sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}">NC_000010.10</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><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Alt allele</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92822-6}">Genomic coord system</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30102-0}">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Genomic allele start-end</span></p><p><b>value</b>: 96527334-?</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="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/refseq"/>
              <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://loinc.org"/>
              <code value="81254-5"/>
            </coding>
          </code>
          <valueRange>
            <low>
              <value value="96527334"/>
            </low>
          </valueRange>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"/>
    <resource>
      <Observation>
        <id value="dv-5c7e9e1ca82e4"/>
        <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_dv-5c7e9e1ca82e4"> </a><p class="res-header-id"><b>Generated Narrative: Observation dv-5c7e9e1ca82e4</b></p><a name="dv-5c7e9e1ca82e4"> </a><a name="hcdv-5c7e9e1ca82e4"> </a><a name="dv-5c7e9e1ca82e4-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 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48013-7}">Genomic reference sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}">NC_000010.10</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><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92822-6}">Genomic coord system</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30102-0}">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Genomic allele start-end</span></p><p><b>value</b>: 96527722-?</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="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/refseq"/>
              <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://loinc.org"/>
              <code value="81254-5"/>
            </coding>
          </code>
          <valueRange>
            <low>
              <value value="96527722"/>
            </low>
          </valueRange>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02"/>
    <resource>
      <Observation>
        <id value="sid-5c7e9e1ca8a29"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_sid-5c7e9e1ca8a29"> </a><p class="res-header-id"><b>Generated Narrative: Observation sid-5c7e9e1ca8a29</b></p><a name="sid-5c7e9e1ca8a29"> </a><a name="hcsid-5c7e9e1ca8a29"> </a><a name="sid-5c7e9e1ca8a29-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 82120-7}">Allelic phase</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://terminology.hl7.org/CodeSystem/sequence-phase-relationship-cs Cis}">Cis</span></p><p><b>derivedFrom</b>: </p><ul><li><a href="Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfe60">Bundle: type = transaction</a></li><li><a href="Bundle-bundle-CYP2C19.html#urn-uuid-20ac0aeb-6bd4-4e92-a891-d44a807bfe01">Bundle: type = transaction</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="82120-7"/>
            <display value="Allelic phase"/>
          </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"/>
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        <valueCodeableConcept>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/sequence-phase-relationship-cs"/>
            <code value="Cis"/>
            <display value="Cis"/>
          </coding>
        </valueCodeableConcept>
        <derivedFrom>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60"/>
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        <derivedFrom>
          <reference value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"/>
        </derivedFrom>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
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  </entry>
  <entry>
    <fullUrl value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe03"/>
    <resource>
      <DiagnosticReport>
        <id value="sequence-phase-relation-CYP2C19"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="DiagnosticReport_sequence-phase-relation-CYP2C19"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport sequence-phase-relation-CYP2C19</b></p><a name="sequence-phase-relation-CYP2C19"> </a><a name="hcsequence-phase-relation-CYP2C19"> </a><a name="sequence-phase-relation-CYP2C19-en-US"> </a><h2><span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"/><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>
        </text>
        <status value="final"/>
        <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="51969-4"/>
          </coding>
        </code>
        <result>
          <reference value="urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60"/>
        </result>
        <result>
          <reference value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01"/>
        </result>
        <result>
          <reference value="urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02"/>
        </result>
      </DiagnosticReport>
    </resource>
    <request>
      <method value="POST"/>
      <url value="DiagnosticReport"/>
    </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>