Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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 2024-12-12 |
{
"resourceType" : "CodeSystem",
"id" : "genomic-study-type-cs",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem genomic-study-type-cs</b></p><a name=\"genomic-study-type-cs\"> </a><a name=\"hcgenomic-study-type-cs\"> </a><a name=\"genomic-study-type-cs-en-US\"> </a><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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs",
"version" : "3.0.0",
"name" : "GenomicStudyTypeCS",
"title" : "Genomic Study Type CodeSystem",
"status" : "active",
"experimental" : true,
"date" : "2024-12-12T20:13:16+00:00",
"publisher" : "HL7 International / Clinical Genomics",
"contact" : [
{
"name" : "HL7 International / Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "cg@lists.HL7.org"
}
]
}
],
"description" : "Backport of http://hl7.org/fhir/genomicstudy-type",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"caseSensitive" : true,
"content" : "complete",
"count" : 12,
"concept" : [
{
"code" : "alt-splc",
"display" : "Alternative splicing detection",
"definition" : "Identification of multiple different processed mRNA transcripts from the same DNA template"
},
{
"code" : "chromatin",
"display" : "Chromatin conformation",
"definition" : "Analysis of the spacial organization of chromatin within a cell"
},
{
"code" : "cnv",
"display" : "CNV detection",
"definition" : "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"
},
{
"code" : "epi-alt-hist",
"display" : "Epigenetic Alterations - histone modifications",
"definition" : "Detection of biochemical modifications covalently bound to the N-terminal tail of a histone protein. These modifications may alter chromatin compaction and gene expression"
},
{
"code" : "epi-alt-dna",
"display" : "Epigenetic Alterations -DNA methylation",
"definition" : "Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription"
},
{
"code" : "fam-var-segr",
"display" : "Familial variant segregation",
"definition" : "Determining if a variant identified in an individual is present in other family members"
},
{
"code" : "func-var",
"display" : "Functional variation detection",
"definition" : "Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence"
},
{
"code" : "gene-expression",
"display" : "Gene expression profiling",
"definition" : "Measurement and characterization of activity from all gene products"
},
{
"code" : "post-trans-mod",
"display" : "Post-translational Modification Identification",
"definition" : "Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein"
},
{
"code" : "snp",
"display" : "SNP Detection",
"definition" : "Determination of which nucleotide is base present at a known variable location of the genomic sequence"
},
{
"code" : "str",
"display" : "STR count",
"definition" : "Quantification of the number of sequential microsatellite units in a repetitive sequence region"
},
{
"code" : "struc-var",
"display" : "Structural variation detection",
"definition" : "Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence"
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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