{ "resourceType": "CodeSystem", "id": "genomicstudy-type", "meta": { "lastUpdated": "2023-03-25T23:21:02.749-05:00", "profile": [ "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ] }, "text": { "status": "generated", "div": "

This code system http://hl7.org/fhir/genomicstudy-type defines the following codes:

CodeDisplayDefinition
alt-splc Alternative splicing detectionIdentification of multiple different processed mRNA transcripts from the same DNA template
chromatin Chromatin conformationAnalysis of the spacial organization of chromatin within a cell
cnv CNV detectionDetection 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
epi-alt-hist Epigenetic Alterations - histone modificationsDetection of biochemical modifications covalently bound to the N-terminal tail of a histone protein. These modifications may alter chromatin compaction and gene expression
epi-alt-dna Epigenetic Alterations -DNA methylationDetection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription
fam-var-segr Familial variant segregationDetermining if a variant identified in an individual is present in other family members
func-var Functional variation detectionDetection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence
gene-expression Gene expression profilingMeasurement and characterization of activity from all gene products
post-trans-mod Post-translational Modification IdentificationDetection of biochemical modifications covalently bound to the amino acid monomers of a processed protein
snp SNP DetectionDetermination of which nucleotide is base present at a known variable location of the genomic sequence
str STR countQuantification of the number of sequential microsatellite units in a repetitive sequence region
struc-var Structural variation detectionDetection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence
" }, "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg", "valueCode": "cg" }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status", "valueCode": "trial-use" }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm", "valueInteger": 1 } ], "url": "http://hl7.org/fhir/genomicstudy-type", "identifier": [ { "system": "urn:ietf:rfc:3986", "value": "urn:oid:2.16.840.1.113883.4.642.4.1975" } ], "version": "5.0.0", "name": "GenomicStudyType", "title": "Genomic Study Type", "status": "active", "experimental": true, "date": "2022-08-17T16:19:24-05:00", "publisher": "HL7 (FHIR Project)", "contact": [ { "telecom": [ { "system": "url", "value": "http://hl7.org/fhir" }, { "system": "email", "value": "fhir@lists.hl7.org" } ] } ], "description": "The type relevant to GenomicStudy.", "jurisdiction": [ { "coding": [ { "system": "http://unstats.un.org/unsd/methods/m49/m49.htm", "code": "001", "display": "World" } ] } ], "caseSensitive": true, "valueSet": "http://hl7.org/fhir/ValueSet/genomicstudy-type", "content": "complete", "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" } ] }