{
  "description": "These codes are currently 'TBD' codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated.",
  "_filename": "CodeSystem-tbd-codes-cs.json",
  "package_name": "hl7.fhir.uv.genomics",
  "date": "2022-05-09T16:53:07+00:00",
  "publisher": "HL7 Clinical Genomics Working Group",
  "jurisdiction": [ {
    "coding": [ {
      "code": "001",
      "system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
      "display": "World"
    } ]
  } ],
  "content": "complete",
  "name": "TbdCodesCS",
  "type": null,
  "experimental": null,
  "resourceType": "CodeSystem",
  "title": "To Be Determined Codes",
  "package_version": "reporting-2.0.0",
  "status": "active",
  "id": "4312ba96-9afc-4af2-a1ee-d64b607e039c",
  "kind": null,
  "count": 13,
  "url": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
  "concept": [ {
    "code": "predicted-therapeutic-implication",
    "display": "Predicted Therapeutic Implication",
    "definition": "A predicted ramification based on the presence of associated molecular finding(s). Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies."
  }, {
    "code": "prognostic-implication",
    "display": "Prognostic Implication",
    "definition": "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions."
  }, {
    "code": "associated-therapy",
    "display": "Associated Therapy",
    "definition": "The non-medication therapy (procedure) associated with this implication."
  }, {
    "code": "region-coverage",
    "display": "Region Coverage",
    "definition": "Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence."
  }, {
    "code": "molecular-consequence",
    "display": "Molecular Consequence",
    "definition": "Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence."
  }, {
    "code": "variant-inheritance",
    "display": "Variant Inheritance",
    "definition": "A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762."
  }, {
    "code": "diagnostic-implication",
    "display": "Diagnostic Implication",
    "definition": "An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition."
  }, {
    "code": "therapeutic-implication",
    "display": "Therapeutic Implication",
    "definition": "An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy."
  }, {
    "code": "uncallable-regions",
    "display": "Uncallable Regions",
    "definition": "Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system."
  }, {
    "code": "functional-effect",
    "display": "Functional Effect",
    "definition": "The effect of a variant on downstream biological products or pathways (from Sequence Ontology)."
  }, {
    "code": "conclusion-string",
    "display": "Conclusion Text",
    "definition": "Clinical conclusion (interpretation) of the observation."
  }, {
    "code": "condition-inheritance",
    "display": "Condition Inheritance",
    "definition": "The transmission pattern of the condition/phenotype in a pedigree."
  }, {
    "code": "variant-confidence-status",
    "display": "Variant Confidence Status",
    "definition": "The confidence of a true positive variant call."
  } ],
  "caseSensitive": true,
  "version": "2.0.0",
  "contact": [ {
    "name": "HL7 Clinical Genomics Working Group",
    "telecom": [ {
      "value": "http://www.hl7.org/Special/committees/clingenomics",
      "system": "url"
    }, {
      "value": "cg@lists.HL7.org",
      "system": "email"
    } ]
  } ]
}