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

Value Set /ValueSet/tbd-codes

Summary

Defining URL:http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes
Version:1.0.0
Name:ToBeDeterminedCodes
Definition:

This value set includes all TBD Codes

Publisher:HL7 (Clinical Genomics)
Source Resource:XML / JSON / Turtle

This value set is not used

Content Logical Definition

tbd-codes

This value set includes all TBD Codes

This value set includes codes from the following code systems:

 

Expansion

This value set contains 16 concepts

Expansion based on http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes version 1.0.0

All codes from system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes

CodeDisplayDefinition
groupergrouperA means to bundle several observations such as one would find in a genetics test panel.
mode-of-inheritancemode-of-inheritanceThis is actually LOINC code 79742-3. And the IG will be updated
effect-transporter-functioneffect-transporter-functionPredicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.
somatic-diagnosticsomatic-diagnosticFinding 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.
somatic-prognosticSomatic Prognostic ImplicationFinding 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.
somatic-prognostic-medicationsomatic-prognostic-medicationThe medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication).
somatic-prognostic-treatmentsomatic-prognostic-treatmentThe non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc.
somatic-predictiveSomatic variant predicted effect on Cancer medicationFinding 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.
somatic-predictive-medicationsomatic-predictive-medicationThe medication or medication class whose implication on the cancer is being predicted.
associated-cancerassociated-cancerAssociated Cancer
region-coverageregion-coverageGiven 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.
functional-annotationfunctional-annotationAnnotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.
exact-start-endVariant exact start and endThe genomic coordinates of the exact genomic range in which the variant resides.
inner-start-endVariant inner start and endThe genomic coordinates of the inner genomic range in which the variant might reside.
outer-start-endVariant outer start and endThe genomic coordinates of the outer genomic range in which the variant might reside.
variant-inheritanceVariant inheritanceA quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762

Explanation of the columns that may appear on this page:

Level A few code lists that FHIR defines are hierarchical - each code is assigned a level. In this scheme, some codes are under other codes, and imply that the code they are under also applies
Source The source of the definition of the code (when the value set draws in codes defined elsewhere)
Code The code (used as the code in the resource instance)
Display The display (used in the display element of a Coding). If there is no display, implementers should not simply display the code, but map the concept into their application
Definition An explanation of the meaning of the concept
Comments Additional notes about how to use the code