minimal Common Oncology Data Elements (mCODE) Implementation Guide
1.16.0 - STU Release 2 (Ballot Version)

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v1.16.0: 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

Terminology

This implementation guide draws on a number of formal terminologies (code systems). Several guiding principles were applied in selecting terminologies for mCODE:

  1. Fit for purpose
  2. Conformance with US Core and FHIR
  3. Commonly used in real world practice

The following table presents the external code systems (and naming conventions) adopted in mCODE, and their primary purpose:

Code System Application FHIR IG Publishing support? HL7 Canonical
AJCC Cancer staging codes No Missing
CPT Procedure codes No http://www.ama-assn.org/go/cpt
HGNC Gene identification No http://www.genenames.org
HGVS Sequence variant nomenclature Yes http://varnomen.hgvs.org
HTA Various HL7 V2 and FHIR-specific codes Yes http://terminology.hl7.org
ICD-O-3 Cancer morphology and topology codes No http://terminology.hl7.org/CodeSystem/icd-o-3
ICD-10-CM Diagnosis codes Yes http://hl7.org/fhir/sid/icd-10-cm
ICD-10-PCS Procedure codes No http://www.cms.gov/Medicare/Coding/ICD10
LOINC Observation and laboratory codes, answer codes Yes http://loinc.org
NCBI GTR Genetic test codes No Missing
NCBI ClinVar Genetic variations No Missing
RxNorm Medication codes Yes http://www.nlm.nih.gov/research/umls/rxnorm
Sequence Ontology DNA change types No Missing
SNOMED CT Disorders, body structures, findings, qualifiers Yes http://snomed.info/sct
UCUM Units of measure Yes http://unitsofmeasure.org
UMLS Staging systems, radiotherapy No http://terminology.hl7.org/CodeSystem/umls

Key:

  • AJCC - American Joint Committee on Cancer
  • CPT - Current Procedural Terminology (American Medical Association)
  • HGNC - Human Genome Organisation (HUGO) Gene Nomenclature Committee
  • HGVS - Human Genome Variation Society
  • HTA - HL7 Terminology Authority
  • ICD - International Classification of Diseases (World Health Organization)
    • ICD-O-3 - Oncology, 3rd revision
    • ICD-10-CM - Clinical Modification, 10th revision
    • ICD-10-PCS - Procedure Coding System, 10th revision
  • LOINC - Logical Observation Identifiers Names and Codes
  • NCBI - National Center for Biotechnology Information (National Institutes of Health) (US)
    • NCBI GTR - Genetic Testing Registry
    • NCBI ClinVar - Not an acronym
  • RxNorm - From National Library of Medicine (US)
  • SNOMED CT - Systematized Nomenclature of Medicine Clinical Terms
  • UCUM - Unified Code for Units of Measure
  • UMLS - Unified Medical Language System Metathesaurus

Local Code Systems

New code systems were created when no existing code systems were deemed fit for purpose. The following code systems were created (none of which have IG publishing support):

Code System Application
Radiotherapy Code System Radiotherapy modalities, techniques, and body sites
Elixhauser Code System Codes for comorbidity categories
Catch Codes Codes for positive identification of FHIR instances
Resource Identifier Codes Codes describing resource types

These systems are described below:

Radiotherapy Code System

Not all required concepts exist in established sources such as SNOMED CT and UMLS. A local code system was created for the missing codes, at the same time requests were made to SNOMED CT for new terms to fill these gaps.

Elixhauser Code System

For the purposes of mCODE, comorbidities are classified using the Elixhauser system. This is a somewhat arbitrary choice, and other systems such as Charlson could have been selected, and profiles and value sets would have to change accordingly.

There is no established code system that represents the 30+ Elixhauser comorbidity categories. For example, there are no SNOMED CT concepts for Elixhauser categories such as “Liver disease, mild”, “Renal failure, moderate”, or “Thyroid disorders other than hypothyroidism”. In some cases there are SNOMED CT disorder codes that superficially correspond to Elixhauser categories, such as congestive heart failure (SCTID: 42343007). However, the SNOMED codes subsumed under that code do not necessarily correspond to the disorders included in the Elixhauser CHF category. This is a subtle difference, and perhaps not clinically meaningful. However, there is no obvious or automatic equivalence between the set of disorders in each Elixhauser comorbidity category and the set of disorders subsumed in a SNOMED CT hierarchy. If Charlson or another comorbidity index were used, the same issue would arise. Feedback is welcomed.

More discussion is found here.

Catch Codes

The “catch code” code system was established to represent “Other, specify: _______” as often offered as the last in a list of choices. In addition, this approach prevents certain FHIR validation problems that would result from use of extensible bindings. A detailed explanation is found here.

Resource Identifier Codes

Certain resources, particularly in the radiotherapy area, are missing appropriate LOINC codes. Local codes have been defined to fill this gap, at least temporarily.

Links: