Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
| Active as of 2024-04-09 |
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="genomic-study-type-cs"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs</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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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="genomic-study-type-cs-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>
<url
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs"/>
<version value="3.0.1-SNAPSHOT"/>
<name value="GenomicStudyTypeCS"/>
<title value="Genomic Study Type CodeSystem"/>
<status value="active"/>
<experimental value="true"/>
<date value="2024-04-09T13:57:55+00:00"/>
<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="cg@lists.HL7.org"/>
</telecom>
</contact>
<description value="Backport of http://hl7.org/fhir/genomicstudy-type"/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<caseSensitive value="true"/>
<content value="complete"/>
<count value="12"/>
<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>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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