NCPI FHIR Implementation Guide
0.2.0 - ci-build

NCPI FHIR Implementation Guide - Local Development build (v0.2.0). See the Directory of published versions

ValueSet: tbd-codes

Official URL: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes Version: 0.2.0
Active as of 2019-08-21 Computable Name: ToBeDeterminedCodes

This value set includes all TBD Codes

References

This value set is not used here; it may be used elsewhere (e.g. specifications and/or implementations that use this content)

Logical Definition (CLD)

 

Expansion

This value set contains 18 concepts

Expansion based on codesystem ToBeDeterminedCodes ('TbdCodes') v0.2.0 (CodeSystem)

CodeSystemDisplayDefinition
  grouperhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesgrouper

A means to bundle several observations such as one would find in a genetics test panel.

  mode-of-inheritancehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesmode-of-inheritance

This is actually LOINC code 79742-3. And the IG will be updated

  effect-transporter-functionhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codeseffect-transporter-function

Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.

  effect-medication-efficacyhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesMedication Efficacy
  effect-medication-metabolismhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesMedication Metabolism
  effect-medication-transporterhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesMedication Transporter Function
  effect-high-risk-allelehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesHigh Risk Allele
  prognostic-implicationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesPrognostic Implication component

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.

  associated-cancerhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesassociated-cancer
  associated-therapyhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesGenomically linked therapy

The non-medication therapy (procedure) associated with this implication.

  region-coveragehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesregion-coverage

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.

  functional-annotationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesfunctional-annotation

Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.

  exact-start-endhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesVariant exact start and end

The genomic coordinates of the exact genomic range in which the variant resides.

  inner-start-endhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesVariant inner start and end

The genomic coordinates of the inner genomic range in which the variant might reside.

  outer-start-endhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesVariant outer start and end

The genomic coordinates of the outer genomic range in which the variant might reside.

  variant-inheritancehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesVariant inheritance

A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.

  diagnostic-implicationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesDiagnostic Implication

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.

  therapeutic-implicationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codesTherapeutic Implication

An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.


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
System 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