Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 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

: Concept mapping for DNA Change Type - XML Representation

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<ConceptMap xmlns="http://hl7.org/fhir">
  <id value="dna-change-type-map"/>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><h2>DNAChangeType (http://hl7.org/fhir/uv/genomics-reporting/ConceptMap/dna-change-type-map)</h2><p>Mapping from http://loinc.org to http://www.sequenceontology.org</p><p>DRAFT. Published on Apr 13, 2021 7:13:37 PM by HL7 International Clinical Genomics Work Group (<a href="http://www.hl7.org/Special/committees/clingenomics">http://www.hl7.org/Special/com...</a>). This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.</p><div><p>LOINC and SequenceOntology mappings for dna change type</p>
</div><br/><table class="grid"><tr><td><b>Source Code</b></td><td><b>Relationship</b></td><td><b>Destination Code</b></td></tr><tr><td>LA9658-1 (Wild type)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:0002073</td></tr><tr><td>LA6692-3 (Deletion)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:0000159</td></tr><tr><td>LA6686-5 (Duplication)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:1000035</td></tr><tr><td>LA6687-3 (Insertion)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:0000667</td></tr><tr><td>LA6688-1 (Insertion/Deletion)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:1000032</td></tr><tr><td>LA6689-9 (Inversion)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:1000036</td></tr><tr><td>LA6690-7 (Substitution)</td><td><a href="http://hl7.org/fhir/R4/codesystem-concept-map-equivalence.html#equivalent">is equivalent to</a></td><td>SO:1000002</td></tr></table></div>
  </text>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/ConceptMap/dna-change-type-map"/>
  <version value="1.1.0"/>
  <name value="DNAChangeType"/>
  <status value="draft"/>
  <date value="2021-04-13T19:13:37+00:00"/>
  <publisher value="HL7 International Clinical Genomics Work Group"/>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
  </contact>
  <description value="LOINC and SequenceOntology mappings for dna change type"/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
    </coding>
  </jurisdiction>
  <copyright
             value="This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc."/>
  <sourceCanonical value="http://loinc.org"/>
  <targetCanonical value="http://www.sequenceontology.org"/>
  <group>
    <source value="http://loinc.org"/>
    <target value="http://www.sequenceontology.org"/>
    <element>
      <code value="LA9658-1"/>
      <display value="Wild type"/>
      <target>
        <code value="SO:0002073"/>
        <display value="no_sequence_alteration"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6692-3"/>
      <display value="Deletion"/>
      <target>
        <code value="SO:0000159"/>
        <display value="deletion"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6686-5"/>
      <display value="Duplication"/>
      <target>
        <code value="SO:1000035"/>
        <display value="duplication"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6687-3"/>
      <display value="Insertion"/>
      <target>
        <code value="SO:0000667"/>
        <display value="insertion"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6688-1"/>
      <display value="Insertion/Deletion"/>
      <target>
        <code value="SO:1000032"/>
        <display value="delins"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6689-9"/>
      <display value="Inversion"/>
      <target>
        <code value="SO:1000036"/>
        <display value="inversion"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
    <element>
      <code value="LA6690-7"/>
      <display value="Substitution"/>
      <target>
        <code value="SO:1000002"/>
        <display value="substitution"/>
        <equivalence value="equivalent"/>
      </target>
    </element>
  </group>
</ConceptMap>