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

TBD Code System - XML Representation

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Raw xml 


<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="tbd-codes"/>
  <meta>
    <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><h2>tbd-codes</h2><div><p>These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.</p>
</div><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style="white-space:nowrap">grouper<a name="tbd-codes-grouper"> </a></td><td>grouper</td><td>A means to bundle several observations such as one would find in a genetics test panel.</td></tr><tr><td style="white-space:nowrap">mode-of-inheritance<a name="tbd-codes-mode-of-inheritance"> </a></td><td>mode-of-inheritance</td><td>This is actually LOINC code 79742-3. And the IG will be updated</td></tr><tr><td style="white-space:nowrap">effect-transporter-function<a name="tbd-codes-effect-transporter-function"> </a></td><td>effect-transporter-function</td><td>Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.</td></tr><tr><td style="white-space:nowrap">somatic-diagnostic<a name="tbd-codes-somatic-diagnostic"> </a></td><td>somatic-diagnostic</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer. Example values are: Pathognomonic, Supportive, Argues Against, Rules Out.</td></tr><tr><td style="white-space:nowrap">somatic-prognostic<a name="tbd-codes-somatic-prognostic"> </a></td><td>Somatic Prognostic Implication</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.</td></tr><tr><td style="white-space:nowrap">somatic-prognostic-medication<a name="tbd-codes-somatic-prognostic-medication"> </a></td><td>somatic-prognostic-medication</td><td>The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication).</td></tr><tr><td style="white-space:nowrap">somatic-prognostic-treatment<a name="tbd-codes-somatic-prognostic-treatment"> </a></td><td>somatic-prognostic-treatment</td><td>The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc.</td></tr><tr><td style="white-space:nowrap">somatic-predictive<a name="tbd-codes-somatic-predictive"> </a></td><td>Somatic variant predicted effect on Cancer medication</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts an impact on medication efficay or prediction of an adverse event caused by a medication. Example values are: Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response.</td></tr><tr><td style="white-space:nowrap">somatic-predictive-medication<a name="tbd-codes-somatic-predictive-medication"> </a></td><td>somatic-predictive-medication</td><td>The medication or medication class whose implication on the cancer is being predicted.</td></tr><tr><td style="white-space:nowrap">associated-cancer<a name="tbd-codes-associated-cancer"> </a></td><td>associated-cancer</td><td>Associated Cancer</td></tr><tr><td style="white-space:nowrap">region-coverage<a name="tbd-codes-region-coverage"> </a></td><td>region-coverage</td><td>Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.</td></tr><tr><td style="white-space:nowrap">functional-annotation<a name="tbd-codes-functional-annotation"> </a></td><td>functional-annotation</td><td>Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.</td></tr><tr><td style="white-space:nowrap">exact-start-end<a name="tbd-codes-exact-start-end"> </a></td><td>Variant exact start and end</td><td>The genomic coordinates of the exact genomic range in which the variant resides.</td></tr><tr><td style="white-space:nowrap">inner-start-end<a name="tbd-codes-inner-start-end"> </a></td><td>Variant inner start and end</td><td>The genomic coordinates of the inner genomic range in which the variant might reside.</td></tr><tr><td style="white-space:nowrap">outer-start-end<a name="tbd-codes-outer-start-end"> </a></td><td>Variant outer start and end</td><td>The genomic coordinates of the outer genomic range in which the variant might reside.</td></tr><tr><td style="white-space:nowrap">variant-inheritance<a name="tbd-codes-variant-inheritance"> </a></td><td>Variant inheritance</td><td>A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762</td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
  <version value="1.0.0"/>
  <name value="ToBeDeterminedCodes"/>
  <title value="tbd-codes"/>
  <status value="draft"/>
  <experimental value="false"/>
  <date value="2019-08-21T00:00:00-04:00"/>
  <publisher value="HL7 (Clinical Genomics)"/>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="http://hl7.org/fhir"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="fhir@lists.hl7.org"/>
    </telecom>
  </contact>
  <description
               value="These codes are currently &#39;TBD-LOINC&#39; codes. The CG WG is requesting formal LOINC codes."/>
  <caseSensitive value="true"/>
  <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes"/>
  <content value="complete"/>
  <concept>
    <code value="grouper"/>
    <display value="grouper"/>
    <definition
                value="A means to bundle several observations such as one would find in a genetics test panel."/>
  </concept>
  <concept>
    <code value="mode-of-inheritance"/>
    <display value="mode-of-inheritance"/>
    <definition
                value="This is actually LOINC code 79742-3. And the IG will be updated"/>
  </concept>
  <concept>
    <code value="effect-transporter-function"/>
    <display value="effect-transporter-function"/>
    <definition
                value="Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug&#39;s performance."/>
  </concept>
  <concept>
    <code value="somatic-diagnostic"/>
    <display value="somatic-diagnostic"/>
    <definition
                value="Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer. Example values are: Pathognomonic, Supportive, Argues Against, Rules Out."/>
  </concept>
  <concept>
    <code value="somatic-prognostic"/>
    <display value="Somatic Prognostic Implication"/>
    <definition
                value="Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions."/>
  </concept>
  <concept>
    <code value="somatic-prognostic-medication"/>
    <display value="somatic-prognostic-medication"/>
    <definition
                value="The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication)."/>
  </concept>
  <concept>
    <code value="somatic-prognostic-treatment"/>
    <display value="somatic-prognostic-treatment"/>
    <definition
                value="The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc."/>
  </concept>
  <concept>
    <code value="somatic-predictive"/>
    <display value="Somatic variant predicted effect on Cancer medication"/>
    <definition
                value="Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts an impact on medication efficay or prediction of an adverse event caused by a medication. Example values are: Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response."/>
  </concept>
  <concept>
    <code value="somatic-predictive-medication"/>
    <display value="somatic-predictive-medication"/>
    <definition
                value="The medication or medication class whose implication on the cancer is being predicted."/>
  </concept>
  <concept>
    <code value="associated-cancer"/>
    <display value="associated-cancer"/>
    <definition value="Associated Cancer"/>
  </concept>
  <concept>
    <code value="region-coverage"/>
    <display value="region-coverage"/>
    <definition
                value="Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence."/>
  </concept>
  <concept>
    <code value="functional-annotation"/>
    <display value="functional-annotation"/>
    <definition
                value="Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537."/>
  </concept>
  <concept>
    <code value="exact-start-end"/>
    <display value="Variant exact start and end"/>
    <definition
                value="The genomic coordinates of the exact genomic range in which the variant resides."/>
  </concept>
  <concept>
    <code value="inner-start-end"/>
    <display value="Variant inner start and end"/>
    <definition
                value="The genomic coordinates of the inner genomic range in which the variant might reside."/>
  </concept>
  <concept>
    <code value="outer-start-end"/>
    <display value="Variant outer start and end"/>
    <definition
                value="The genomic coordinates of the outer genomic range in which the variant might reside."/>
  </concept>
  <concept>
    <code value="variant-inheritance"/>
    <display value="Variant inheritance"/>
    <definition
                value="A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762"/>
  </concept>
</CodeSystem>