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

TBD Code System

Format(s):

Narrative view

tbd-codes

These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.

This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes defines the following codes:

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