Genomic Study Type

active

ContentcompleteURL

http://hl7.org/fhir/genomicstudy-type

Version

5.0.0

Date2022-08-17T16:19:24-05:00PublisherHL7 (FHIR Project)Description

The type relevant to GenomicStudy.

Concepts

Select a concept to view details

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

Code	Display	Definition
alt-splc	Alternative splicing detection	Identification of multiple different processed mRNA transcripts from the same DNA template
chromatin	Chromatin conformation	Analysis of the spacial organization of chromatin within a cell
cnv	CNV detection	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
epi-alt-hist	Epigenetic Alterations - histone modifications	Detection 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 methylation	Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription
fam-var-segr	Familial variant segregation	Determining if a variant identified in an individual is present in other family members
func-var	Functional variation detection	Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence
gene-expression	Gene expression profiling	Measurement and characterization of activity from all gene products
post-trans-mod	Post-translational Modification Identification	Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein
snp	SNP Detection	Determination of which nucleotide is base present at a known variable location of the genomic sequence
str	STR count	Quantification of the number of sequential microsatellite units in a repetitive sequence region
struc-var	Structural variation detection	Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence

{
  "description" : "The type relevant to GenomicStudy.",
  "date" : "2022-08-17T16:19:24-05:00",
  "meta" : {
    "lastUpdated" : "2023-03-25T23:21:02.749-05:00",
    "profile" : [ "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ]
  },
  "publisher" : "HL7 (FHIR Project)",
  "jurisdiction" : [ {
    "coding" : [ {
      "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
      "code" : "001",
      "display" : "World"
    } ]
  } ],
  "content" : "complete",
  "property" : null,
  "name" : "GenomicStudyType",
  "experimental" : true,
  "resourceType" : "CodeSystem",
  "title" : "Genomic Study Type",
  "extension" : [ {
    "valueCode" : "cg",
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"
  }, {
    "valueCode" : "trial-use",
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"
  }, {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 1
  }, {
    "extension" : [ {
      "valueString" : "concept",
      "url" : "path"
    }, {
      "url" : "count",
      "valueInteger" : 12
    } ],
    "url" : "http://health-samurai.io/extensions/excised-data"
  }, {
    "url" : "http://health-samurai.io/extensions/source",
    "valueCode" : "db"
  } ],
  "status" : "active",
  "id" : "genomicstudy-type",
  "valueSet" : "http://hl7.org/fhir/ValueSet/genomicstudy-type",
  "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"
  } ],
  "caseSensitive" : true,
  "version" : "5.0.0",
  "contact" : [ {
    "telecom" : [ {
      "system" : "url",
      "value" : "http://hl7.org/fhir"
    }, {
      "system" : "email",
      "value" : "fhir@lists.hl7.org"
    } ]
  } ],
  "text" : {
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <p>This code system \n              <code>http://hl7.org/fhir/genomicstudy-type</code> defines the following codes:\n            </p>\n            <table class=\"codes\">\n              <tr>\n                <td style=\"white-space:nowrap\">\n                  <b>Code</b>\n                </td>\n                <td>\n                  <b>Display</b>\n                </td>\n                <td>\n                  <b>Definition</b>\n                </td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">alt-splc\n                  <a name=\"genomicstudy-type-alt-splc\"> </a>\n                </td>\n                <td>Alternative splicing detection</td>\n                <td>Identification of multiple different processed mRNA transcripts from the same DNA template</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">chromatin\n                  <a name=\"genomicstudy-type-chromatin\"> </a>\n                </td>\n                <td>Chromatin conformation</td>\n                <td>Analysis of the spacial organization of chromatin within a cell</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">cnv\n                  <a name=\"genomicstudy-type-cnv\"> </a>\n                </td>\n                <td>CNV detection</td>\n                <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>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">epi-alt-hist\n                  <a name=\"genomicstudy-type-epi-alt-hist\"> </a>\n                </td>\n                <td>Epigenetic Alterations - histone modifications</td>\n                <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>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">epi-alt-dna\n                  <a name=\"genomicstudy-type-epi-alt-dna\"> </a>\n                </td>\n                <td>Epigenetic Alterations -DNA methylation</td>\n                <td>Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">fam-var-segr\n                  <a name=\"genomicstudy-type-fam-var-segr\"> </a>\n                </td>\n                <td>Familial variant segregation</td>\n                <td>Determining if a variant identified in an individual is present in other family members</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">func-var\n                  <a name=\"genomicstudy-type-func-var\"> </a>\n                </td>\n                <td>Functional variation detection</td>\n                <td>Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">gene-expression\n                  <a name=\"genomicstudy-type-gene-expression\"> </a>\n                </td>\n                <td>Gene expression profiling</td>\n                <td>Measurement and characterization of activity from all gene products</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">post-trans-mod\n                  <a name=\"genomicstudy-type-post-trans-mod\"> </a>\n                </td>\n                <td>Post-translational Modification Identification</td>\n                <td>Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">snp\n                  <a name=\"genomicstudy-type-snp\"> </a>\n                </td>\n                <td>SNP Detection</td>\n                <td>Determination of which nucleotide is base present at a known variable location of the genomic sequence</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">str\n                  <a name=\"genomicstudy-type-str\"> </a>\n                </td>\n                <td>STR count</td>\n                <td>Quantification of the number of sequential microsatellite units in a repetitive sequence region</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">struc-var\n                  <a name=\"genomicstudy-type-struc-var\"> </a>\n                </td>\n                <td>Structural variation detection</td>\n                <td>Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence</td>\n              </tr>\n            </table>\n          </div>",
    "status" : "generated"
  }
}