{
  "description": "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.",
  "_filename": "CodeSystem-tbd-codes.json",
  "package_name": "hl7.fhir.uv.genomics-reporting",
  "date": "2019-08-21T00:00:00-04:00",
  "meta": {
    "profile": [ "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ]
  },
  "publisher": "HL7 (Clinical Genomics)",
  "content": "complete",
  "name": "ToBeDeterminedCodes",
  "type": null,
  "experimental": "false",
  "resourceType": "CodeSystem",
  "title": "tbd-codes",
  "package_version": "1.0.0",
  "extension": [ {
    "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode": "cg"
  } ],
  "status": "draft",
  "id": "3339b688-0ff6-4b88-bb40-108d662e7822",
  "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes",
  "kind": null,
  "url": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
  "concept": [ {
    "code": "grouper",
    "display": "grouper",
    "definition": "A means to bundle several observations such as one would find in a genetics test panel."
  }, {
    "code": "mode-of-inheritance",
    "display": "mode-of-inheritance",
    "definition": "This is actually LOINC code 79742-3. And the IG will be updated"
  }, {
    "code": "effect-transporter-function",
    "display": "effect-transporter-function",
    "definition": "Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance."
  }, {
    "code": "somatic-diagnostic",
    "display": "somatic-diagnostic",
    "definition": "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer. Example values are: Pathognomonic, Supportive, Argues Against, Rules Out."
  }, {
    "code": "somatic-prognostic",
    "display": "Somatic 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": "somatic-prognostic-medication",
    "display": "somatic-prognostic-medication",
    "definition": "The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication)."
  }, {
    "code": "somatic-prognostic-treatment",
    "display": "somatic-prognostic-treatment",
    "definition": "The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc."
  }, {
    "code": "somatic-predictive",
    "display": "Somatic variant predicted effect on Cancer medication",
    "definition": "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts an impact on medication efficay or prediction of an adverse event caused by a medication. Example values are: Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response."
  }, {
    "code": "somatic-predictive-medication",
    "display": "somatic-predictive-medication",
    "definition": "The medication or medication class whose implication on the cancer is being predicted."
  }, {
    "code": "associated-cancer",
    "display": "associated-cancer",
    "definition": "Associated Cancer"
  }, {
    "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": "functional-annotation",
    "display": "functional-annotation",
    "definition": "Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537."
  }, {
    "code": "exact-start-end",
    "display": "Variant exact start and end",
    "definition": "The genomic coordinates of the exact genomic range in which the variant resides."
  }, {
    "code": "inner-start-end",
    "display": "Variant inner start and end",
    "definition": "The genomic coordinates of the inner genomic range in which the variant might reside."
  }, {
    "code": "outer-start-end",
    "display": "Variant outer start and end",
    "definition": "The genomic coordinates of the outer genomic range in which the variant might reside."
  }, {
    "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"
  } ],
  "caseSensitive": true,
  "version": "1.0.0",
  "contact": [ {
    "telecom": [ {
      "value": "http://hl7.org/fhir",
      "system": "url"
    }, {
      "value": "fhir@lists.hl7.org",
      "system": "email"
    } ]
  } ]
}