Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "CodeSystem",
"id" : "tbd-codes-cs",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs 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\">predicted-therapeutic-implication<a name=\"tbd-codes-cs-predicted-therapeutic-implication\"> </a></td><td>Predicted Therapeutic Implication</td><td>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.</td></tr><tr><td style=\"white-space:nowrap\">prognostic-implication<a name=\"tbd-codes-cs-prognostic-implication\"> </a></td><td>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\">associated-therapy<a name=\"tbd-codes-cs-associated-therapy\"> </a></td><td>Associated Therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style=\"white-space:nowrap\">region-coverage<a name=\"tbd-codes-cs-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=\"tbd-codes-cs-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. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style=\"white-space:nowrap\">variant-inheritance<a name=\"tbd-codes-cs-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=\"tbd-codes-cs-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=\"tbd-codes-cs-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=\"tbd-codes-cs-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=\"tbd-codes-cs-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=\"tbd-codes-cs-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=\"tbd-codes-cs-condition-inheritance\"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr><tr><td style=\"white-space:nowrap\">variant-confidence-status<a name=\"tbd-codes-cs-variant-confidence-status\"> </a></td><td>Variant Confidence Status</td><td>The confidence of a true positive variant call.</td></tr></table></div>"
},
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"version" : "2.0.0",
"name" : "TbdCodesCS",
"title" : "To Be Determined Codes",
"status" : "active",
"date" : "2022-05-09T16:53:07+00:00",
"publisher" : "HL7 Clinical Genomics Working Group",
"contact" : [
{
"name" : "HL7 Clinical Genomics Working Group",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "cg@lists.HL7.org"
}
]
}
],
"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.",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"caseSensitive" : true,
"content" : "complete",
"count" : 13,
"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."
}
]
}
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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