Genomics Reporting Implementation Guide
3.0.0 - release 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 3.0.0 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-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>
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      <Observation>
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        <meta>
          <profile
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        <text>
          <status value="generated"/>
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      <Observation>
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        <meta>
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                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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        <text>
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          <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>
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            <coding>
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              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
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            <coding>
              <system value="http://loinc.org"/>
              <code value="LA14029-5"/>
              <display value="GRCh37"/>
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              <system value="http://loinc.org"/>
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              <display value="Genomic reference sequence ID"/>
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          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="53034-5"/>
              <display value="Allelic state"/>
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            <coding>
              <system value="http://loinc.org"/>
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              <display value="heterozygous"/>
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          <code>
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              <system value="http://loinc.org"/>
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              <display value="Ref nucleotide"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Alt allele"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="92822-6"/>
              <display value="Genomic coord system"/>
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  <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>
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        <id value="sequence-phase-relation-CYP2C19"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
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        <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>
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            <code value="51969-4"/>
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        <result>
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    <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>
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        <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"/>
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      <url value="Organization"/>
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      <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"/>
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</Bundle>