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Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative |
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Definition for Code SystemGenomicStudyType
<?xml version="1.0" encoding="UTF-8"?> <CodeSystem xmlns="http://hl7.org/fhir"> <id value="genomicstudy-type"/> <meta> <lastUpdated value="2024-11-27T14:21:04.917-05:00"/> <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/> </meta> <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> <a name="genomicstudy-type-en-US"> </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: 2022-08-17T16:18:24.148-05:00</p> <p style="margin-bottom: 0px">Profile: <a href="shareablecodesystem.html">Shareable CodeSystem</a> </p> </div> <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-ballot2"/> <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.
FHIR ®© HL7.org 2011+. FHIR R6 hl7.fhir.core#6.0.0-ballot2 generated on Wed, Nov 27, 2024 19:48+0000.
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