Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 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" : "TbdCodes",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes 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=\"TbdCodes-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\">effect-transporter-function<a name=\"TbdCodes-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\">effect-medication-efficacy<a name=\"TbdCodes-effect-medication-efficacy\"> </a></td><td>Medication Efficacy</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-medication-metabolism<a name=\"TbdCodes-effect-medication-metabolism\"> </a></td><td>Medication Metabolism</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-medication-transporter<a name=\"TbdCodes-effect-medication-transporter\"> </a></td><td>Medication Transporter Function</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-high-risk-allele<a name=\"TbdCodes-effect-high-risk-allele\"> </a></td><td>High Risk Allele</td><td/></tr><tr><td style=\"white-space:nowrap\">prognostic-implication<a name=\"TbdCodes-prognostic-implication\"> </a></td><td>Prognostic Implication component</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\">associated-cancer<a name=\"TbdCodes-associated-cancer\"> </a></td><td>associated-cancer</td><td/></tr><tr><td style=\"white-space:nowrap\">associated-therapy<a name=\"TbdCodes-associated-therapy\"> </a></td><td>Genomically linked therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style=\"white-space:nowrap\">region-coverage<a name=\"TbdCodes-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\">molecular-consequence<a name=\"TbdCodes-molecular-consequence\"> </a></td><td>Molecular Consequence</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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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><tr><td style=\"white-space:nowrap\">diagnostic-implication<a name=\"TbdCodes-diagnostic-implication\"> </a></td><td>Diagnostic Implication</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">therapeutic-implication<a name=\"TbdCodes-therapeutic-implication\"> </a></td><td>Therapeutic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.</td></tr><tr><td style=\"white-space:nowrap\">uncallable-regions<a name=\"TbdCodes-uncallable-regions\"> </a></td><td>Uncallable Regions</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">functional-effect<a name=\"TbdCodes-functional-effect\"> </a></td><td>Functional Effect</td><td>The effect of a variant on downstream biological products or pathways (from Sequence Ontology).</td></tr><tr><td style=\"white-space:nowrap\">conclusion-string<a name=\"TbdCodes-conclusion-string\"> </a></td><td>Conclusion text</td><td>Clinical conclusion (interpretation) of the observation.</td></tr><tr><td style=\"white-space:nowrap\">condition-inheritance<a name=\"TbdCodes-condition-inheritance\"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr></table></div>"
},
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
"version" : "1.1.0",
"name" : "TbdCodes",
"title" : "ToBeDeterminedCodes ('TbdCodes')",
"status" : "active",
"date" : "2021-04-13T19:13:37+00:00",
"publisher" : "HL7 International Clinical Genomics Work Group",
"contact" : [
{
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
}
]
}
],
"description" : "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001"
}
]
}
],
"content" : "complete",
"count" : 21,
"concept" : [
{
"code" : "grouper",
"display" : "grouper",
"definition" : "A means to bundle several observations such as one would find in a genetics test panel."
},
{
"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" : "effect-medication-efficacy",
"display" : "Medication Efficacy"
},
{
"code" : "effect-medication-metabolism",
"display" : "Medication Metabolism"
},
{
"code" : "effect-medication-transporter",
"display" : "Medication Transporter Function"
},
{
"code" : "effect-high-risk-allele",
"display" : "High Risk Allele"
},
{
"code" : "prognostic-implication",
"display" : "Prognostic Implication component",
"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-cancer",
"display" : "associated-cancer"
},
{
"code" : "associated-therapy",
"display" : "Genomically linked 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."
},
{
"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."
},
{
"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."
}
]
}
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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