Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

: Genomic Study Type CodeSystem - JSON Representation

Active as of 2024-04-09

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{
  "resourceType" : "CodeSystem",
  "id" : "genomic-study-type-cs",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><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" : "3.0.1-SNAPSHOT",
  "name" : "GenomicStudyTypeCS",
  "title" : "Genomic Study Type CodeSystem",
  "status" : "active",
  "experimental" : true,
  "date" : "2024-04-09T13:57:55+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"
    }
  ]
}