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Example CodeSystem/genomicstudy-type (JSON)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: Informative

Raw JSON (canonical form + also see JSON Format Specification)

Definition for Code SystemGenomicStudyType

{
  "resourceType" : "CodeSystem",
  "id" : "genomicstudy-type",
  "meta" : {
    "lastUpdated" : "2024-05-14T16:17:27.012-05:00",
    "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablecodesystem"]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><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>"
  },
  "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" : "6.0.0-cibuild",
  "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"
  }]
}

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.