Definition for Code SystemGenomicStudyType

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

<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-type"/> 
  <meta> 
    <lastUpdated value="2022-09-06T19:58:29.429-05:00"/> 
    <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/> 
  </meta> 
  <text> 
    <status value="generated"/> 
    <div xmlns="http://www.w3.org/1999/xhtml">
      <p> This 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="0"/> 
  </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="5.0.0-ballot"/> 
  <name value="GenomicStudyType"/> 
  <title value="GenomicStudyType"/> 
  <status value="draft"/> 
  <experimental value="false"/> 
  <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."/> 
  <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>