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Example CodeSystem/genomicstudy-type (XML)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: Informative

Raw XML (canonical form + also see XML Format Specification)

Definition for Code SystemGenomicStudyType

<?xml version="1.0" encoding="UTF-8"?>

<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-type"/> 
  <meta> 
    <lastUpdated value="2024-05-14T16:17:27.012-05:00"/> 
    <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/> 
  </meta> 
  <text> 
    <status value="generated"/> 
    <div xmlns="http://www.w3.org/1999/xhtml">
      <p> This case-sensitive code system 
        <code> http://hl7.org/fhir/genomicstudy-type</code>  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">alt-splc
            <a name="genomicstudy-type-alt-splc"> </a> 
          </td> 
          <td> Alternative splicing detection</td> 
          <td> Identification of multiple different processed mRNA transcripts from the same DNA
             template</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">chromatin
            <a name="genomicstudy-type-chromatin"> </a> 
          </td> 
          <td> Chromatin conformation</td> 
          <td> Analysis of the spacial organization of chromatin within a cell</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">cnv
            <a name="genomicstudy-type-cnv"> </a> 
          </td> 
          <td> CNV detection</td> 
          <td> Detection of a change in the number of copies of a defined region of genomic DNA
             sequence resulting in structural variation when compared to the reference sequence</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">epi-alt-hist
            <a name="genomicstudy-type-epi-alt-hist"> </a> 
          </td> 
          <td> Epigenetic Alterations - histone modifications</td> 
          <td> Detection of biochemical modifications covalently bound to the N-terminal tail
             of a histone protein. These modifications may alter chromatin compaction and gene
             expression</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">epi-alt-dna
            <a name="genomicstudy-type-epi-alt-dna"> </a> 
          </td> 
          <td> Epigenetic Alterations -DNA methylation</td> 
          <td> Detection of the presence of an additional methyl group on a DNA nucleobase, which
             may alter gene transcription</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">fam-var-segr
            <a name="genomicstudy-type-fam-var-segr"> </a> 
          </td> 
          <td> Familial variant segregation</td> 
          <td> Determining if a variant identified in an individual is present in other family
             members</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">func-var
            <a name="genomicstudy-type-func-var"> </a> 
          </td> 
          <td> Functional variation detection</td> 
          <td> Detection of sequence variants which may alter gene expression or gene product
             function when compared to the reference sequence</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">gene-expression
            <a name="genomicstudy-type-gene-expression"> </a> 
          </td> 
          <td> Gene expression profiling</td> 
          <td> Measurement and characterization of activity from all gene products</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">post-trans-mod
            <a name="genomicstudy-type-post-trans-mod"> </a> 
          </td> 
          <td> Post-translational Modification Identification</td> 
          <td> Detection of biochemical modifications covalently bound to the amino acid monomers
             of a processed protein</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">snp
            <a name="genomicstudy-type-snp"> </a> 
          </td> 
          <td> SNP Detection</td> 
          <td> Determination of which nucleotide is base present at a known variable location
             of the genomic sequence</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">str
            <a name="genomicstudy-type-str"> </a> 
          </td> 
          <td> STR count</td> 
          <td> Quantification of the number of sequential microsatellite units in a repetitive
             sequence region</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">struc-var
            <a name="genomicstudy-type-struc-var"> </a> 
          </td> 
          <td> Structural variation detection</td> 
          <td> Detection of deletions, insertions, or rearrangements of DNA segments compared
             to the reference sequence</td> 
        </tr> 
      </table> 
    </div> 
  </text> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/> 
  </extension> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="trial-use"/> 
  </extension> 
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/> 
  </extension> 
  <url value="http://hl7.org/fhir/genomicstudy-type"/> 
  <identifier> 
    <system value="urn:ietf:rfc:3986"/> 
    <value value="urn:oid:2.16.840.1.113883.4.642.4.1975"/> 
  </identifier> 
  <version value="6.0.0-cibuild"/> 
  <name value="GenomicStudyType"/> 
  <title value="Genomic Study Type"/> 
  <status value="active"/> 
  <experimental value="true"/> 
  <date value="2022-08-17T16:19:24-05:00"/> 
  <publisher value="HL7 (FHIR Project)"/> 
  <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="The type relevant to GenomicStudy."/> 
  <jurisdiction> 
    <coding> 
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/> 
      <code value="001"/> 
      <display value="World"/> 
    </coding> 
  </jurisdiction> 
  <caseSensitive value="true"/> 
  <valueSet value="http://hl7.org/fhir/ValueSet/genomicstudy-type"/> 
  <content value="complete"/> 
  <concept> 
    <code value="alt-splc"/> 
    <display value="Alternative splicing detection"/> 
    <definition value="Identification of multiple different processed mRNA transcripts from the same DNA
     template"/> 
  </concept> 
  <concept> 
    <code value="chromatin"/> 
    <display value="Chromatin conformation"/> 
    <definition value="Analysis of the spacial organization of chromatin within a cell"/> 
  </concept> 
  <concept> 
    <code value="cnv"/> 
    <display value="CNV detection"/> 
    <definition value="Detection of a change in the number of copies of a defined region of genomic DNA
     sequence resulting in structural variation when compared to the reference sequence"/> 
  </concept> 
  <concept> 
    <code value="epi-alt-hist"/> 
    <display value="Epigenetic Alterations - histone modifications"/> 
    <definition value="Detection of biochemical modifications covalently bound to the N-terminal tail
     of a histone protein. These modifications may alter chromatin compaction and gene
     expression"/> 
  </concept> 
  <concept> 
    <code value="epi-alt-dna"/> 
    <display value="Epigenetic Alterations -DNA methylation"/> 
    <definition value="Detection of the presence of an additional methyl group on a DNA nucleobase, which
     may alter gene transcription"/> 
  </concept> 
  <concept> 
    <code value="fam-var-segr"/> 
    <display value="Familial variant segregation"/> 
    <definition value="Determining if a variant identified in an individual is present in other family
     members"/> 
  </concept> 
  <concept> 
    <code value="func-var"/> 
    <display value="Functional variation detection"/> 
    <definition value="Detection of sequence variants which may alter gene expression or gene product
     function when compared to the reference sequence"/> 
  </concept> 
  <concept> 
    <code value="gene-expression"/> 
    <display value="Gene expression profiling"/> 
    <definition value="Measurement and characterization of activity from all gene products"/> 
  </concept> 
  <concept> 
    <code value="post-trans-mod"/> 
    <display value="Post-translational Modification Identification"/> 
    <definition value="Detection of biochemical modifications covalently bound to the amino acid monomers
     of a processed protein"/> 
  </concept> 
  <concept> 
    <code value="snp"/> 
    <display value="SNP Detection"/> 
    <definition value="Determination of which nucleotide is base present at a known variable location
     of the genomic sequence"/> 
  </concept> 
  <concept> 
    <code value="str"/> 
    <display value="STR count"/> 
    <definition value="Quantification of the number of sequential microsatellite units in a repetitive
     sequence region"/> 
  </concept> 
  <concept> 
    <code value="struc-var"/> 
    <display value="Structural variation detection"/> 
    <definition value="Detection of deletions, insertions, or rearrangements of DNA segments compared
     to the reference sequence"/> 
  </concept> 
</CodeSystem> 

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.