Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

: Genomic Study Type

Page standards status: Draft Maturity Level: 1

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-type"/>
  <meta>
    <lastUpdated value="2022-08-17T16:18:24.148-05:00"/>
    <profile
             value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
  </meta>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem genomicstudy-type</b></p><a name="genomicstudy-type"> </a><a name="hcgenomicstudy-type"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Last updated: 2022-08-17 16:18:24-0500</p><p style="margin-bottom: 0px">Profile: <a href="http://hl7.org/fhir/R5/shareablecodesystem.html">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/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><tr><td style="white-space:nowrap">trio<a name="genomicstudy-type-trio"> </a></td><td>Trio analysis</td><td>Analysis involving a child and both parents to identify inherited and de novo variants</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="draft"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/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="0.1.0-ci-build"/>
  <name value="GenomicStudyType"/>
  <title value="Genomic Study Type"/>
  <status value="draft"/>
  <experimental value="true"/>
  <date value="2022-08-17T16:19:24-05:00"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="clingenomics@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/uv/cg-incubator/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>
  <concept>
    <code value="trio"/>
    <display value="Trio analysis"/>
    <definition
                value="Analysis involving a child and both parents to identify inherited and de novo variants"/>
  </concept>
</CodeSystem>