Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "CodeSystem",
"id" : "tbd-codes",
"meta" : {
"profile" : [
"http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>tbd-codes</h2><div><p>These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.</p>\n</div><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes 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\">grouper<a name=\"tbd-codes-grouper\"> </a></td><td>grouper</td><td>A means to bundle several observations such as one would find in a genetics test panel.</td></tr><tr><td style=\"white-space:nowrap\">mode-of-inheritance<a name=\"tbd-codes-mode-of-inheritance\"> </a></td><td>mode-of-inheritance</td><td>This is actually LOINC code 79742-3. And the IG will be updated</td></tr><tr><td style=\"white-space:nowrap\">effect-transporter-function<a name=\"tbd-codes-effect-transporter-function\"> </a></td><td>effect-transporter-function</td><td>Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.</td></tr><tr><td style=\"white-space:nowrap\">somatic-diagnostic<a name=\"tbd-codes-somatic-diagnostic\"> </a></td><td>somatic-diagnostic</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">somatic-prognostic<a name=\"tbd-codes-somatic-prognostic\"> </a></td><td>Somatic Prognostic Implication</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">somatic-prognostic-medication<a name=\"tbd-codes-somatic-prognostic-medication\"> </a></td><td>somatic-prognostic-medication</td><td>The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication).</td></tr><tr><td style=\"white-space:nowrap\">somatic-prognostic-treatment<a name=\"tbd-codes-somatic-prognostic-treatment\"> </a></td><td>somatic-prognostic-treatment</td><td>The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc.</td></tr><tr><td style=\"white-space:nowrap\">somatic-predictive<a name=\"tbd-codes-somatic-predictive\"> </a></td><td>Somatic variant predicted effect on Cancer medication</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">somatic-predictive-medication<a name=\"tbd-codes-somatic-predictive-medication\"> </a></td><td>somatic-predictive-medication</td><td>The medication or medication class whose implication on the cancer is being predicted.</td></tr><tr><td style=\"white-space:nowrap\">associated-cancer<a name=\"tbd-codes-associated-cancer\"> </a></td><td>associated-cancer</td><td>Associated Cancer</td></tr><tr><td style=\"white-space:nowrap\">region-coverage<a name=\"tbd-codes-region-coverage\"> </a></td><td>region-coverage</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">functional-annotation<a name=\"tbd-codes-functional-annotation\"> </a></td><td>functional-annotation</td><td>Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.</td></tr><tr><td style=\"white-space:nowrap\">exact-start-end<a name=\"tbd-codes-exact-start-end\"> </a></td><td>Variant exact start and end</td><td>The genomic coordinates of the exact genomic range in which the variant resides.</td></tr><tr><td style=\"white-space:nowrap\">inner-start-end<a name=\"tbd-codes-inner-start-end\"> </a></td><td>Variant inner start and end</td><td>The genomic coordinates of the inner genomic range in which the variant might reside.</td></tr><tr><td style=\"white-space:nowrap\">outer-start-end<a name=\"tbd-codes-outer-start-end\"> </a></td><td>Variant outer start and end</td><td>The genomic coordinates of the outer genomic range in which the variant might reside.</td></tr><tr><td style=\"white-space:nowrap\">variant-inheritance<a name=\"tbd-codes-variant-inheritance\"> </a></td><td>Variant inheritance</td><td>A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762</td></tr></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"version" : "1.0.0",
"name" : "ToBeDeterminedCodes",
"title" : "tbd-codes",
"status" : "draft",
"experimental" : false,
"date" : "2019-08-21T00:00:00-04:00",
"publisher" : "HL7 (Clinical Genomics)",
"contact" : [
{
"telecom" : [
{
"system" : "url",
"value" : "http://hl7.org/fhir"
},
{
"system" : "email",
"value" : "fhir@lists.hl7.org"
}
]
}
],
"description" : "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.",
"caseSensitive" : true,
"valueSet" : "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes",
"content" : "complete",
"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"
}
]
}
IG © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
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