Adding ORPHAcodes as a new non-standard vocabulary with mapping to SNOMED, ICD10 and ICD10GM

[m-zoch]

ORPHAcodes

Background

Rare diseases include approximately 5,000 to 8,000 distinct conditions. Their prevalence is less than 1 in 2,000 individuals in the European Union and less than 1 in 1,250 in the United States. Globally, 6 to 8% of the population, or up to 446 million people, are affected by rare diseases.
In the context of rare diseases is also a lack of reliable data and proper documentation. Only 355 out of the 8,000 rare diseases can be accurately coded in the ICD-10 system, highlighting the need for alternative systems to improve data utilization and patient care. The Orphanet classification offers a distinct identifier for each rare disease: ORPHAcodes.

Usage of ORPHAcodes

OrphaCodes are used in the routine documentation of rare diseases in several European countries, including Germany, France, Malta, Romania, Czech Republic and Spain.
The ETL process FHIR-to-OMOP based on the core data set of the German Medical Informatics Initiative has already been adapted for the storage of ORPHAcodes.

ORPHAcodes as new non-standard vocabulary

To promote international research on rare diseases, ORPHAcodes should be included in OMOP in the future. Existing mappings were harmonized, compared and expanded as a basis.

1. Orphadata provides freely available content from the Orphanet database. We used the Orphanet Nomenclature Pack for Coding of January 2024, which includes the mapping of ORPHAcodes to ICD10.
2. The German Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneitmittel und Medizinprodukte; BfArM) provides alphabetical lists of ICD10GM derived identifiers / synonyms. We used the 2024 version, which includes the mapping of ORPHAcodes to Alpha-ID and ICD10GM.
3. We also used the SNOMED mappings for ICD10 and ICD10GM from ATHENA.

The combined mappings offer insights into overlaps and potential gaps, with a specific emphasis on OrphaCodes not mapped to ICD-10 or SNOMED CT. Identified gaps are manually verified using Usagi, although medical validation of these mappings is still pending.
The mappings are also available on Zenodo:

• Manual mapping with Usagi, which includes OrphaCodes and SNOMED CT: 10.5281/zenodo.10817772
• Requisite tables for the process path “Adding a new vocabulary as non-standard with mappings (full or partial) to a standard vocabulary”: 10.5281/zenodo.10818023

Related Work

• ORPHAcodes use for the coding of rare diseases: comparison of the accuracy and cross country comparability
• Adaption of the OMOP CDM for Rare Diseases
• OHDSI Forum

[TinyRickC137]

Thank you for this impressive work! I wrote you an email with details regarding this contribution.