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6. Good practice guidelines on Orphanet Nomenclature
Particular use-cases are brought up regularly by medical coders across Member States through our National Helpdesks and are discussed in a dedicated forum with all the Hubs and the Scientific team. This collaborative methodology that brings together insights from the field via Orphanet national Nomenclature Hubs and the Orphanet Scientific results in a set of Good practice ORPHAcoding guidelines, which aim to promote coherent, accurate, and comparable ORPHAcoding practices across countries, which are essential to ensuring data quality and cross-border consistency.
N.B. to make these guidelines more robust, relevant, and applicable in real-world settings, we are adding to the methodology a final validation by experts in the medical coding field, to strengthen the credibility and practical value of these recommendations, helping to further ensure they are both scientifically sound and operationally feasible. A Good Practice Guidelines on Orphanet Nomenclature Committee has been set up and will provide this last validation step of the above mentioned guidelines (if not already validated by an external committee)
Keep in mind: ORPHAcodes are A RARE DISEASE IDENTIFICATION NUMBER THAT IS UNIQUE, and ORPHACODE (disorder level) DESCRIBE DIAGNOSES NOT PATIENTS . Standardised use allows to perform reliable statistical analysis and to generate data on RD.
We recommend to code the diagnosis of a patient with the most precise code available at the level “disorder” or “subtype of disorder”.Of note, whichever granularity you decide to choose between the two levels, the “disorder” level is the one recommended as the aggregation level for statistical purposes and data sharing across Europe in the Standard procedure and guide for the coding with ORPHAcodes document delivered by the RD-CODE project.
On the other hand, we strongly advise against using the “group of disorders” level for coding confirmed diagnosis. This practice can be tolerated for coding non confirmed diagnosis if a diagnosis assertion option is available in the coding system. However, we suggest that the group code is replaced by a disorder code when investigations are concluded.
Orphanet classification can be visualised in:
Orphanet website Orphanet website classification. & via the tools mentioned (see FAQ Orphanet Tools for coders)
N.B. An additional classification exists: “Orphanet classification of rare disorder without a determined diagnosis”. This hierarchy does not represent a medical domain and is used to class one single disorder ORPHA: 616874 Rare disorder without a determined diagnosis after full investigation. (see FAQ How to code undiagnosed rare diseases patients using ORPHA:616874?)
It is not recommended to use an ORPHAcode for a patient who does not match with the full description of the diagnosis, if this is the case you must search for the most appropriate ORPHAcode and if none of the available ORPHAcode, in your system or on orpha.net, fits: please contact the Helpdesk (see FAQ How to submit a ORPHAcode Creation demand or a ORPHAcode modification Demand))
N.B. An additional classification exists: “Orphanet classification of rare disorder without a determined diagnosis”. This hierarchy does not represent a medical domain and is used to class one single disorder ORPHA: 616874 Rare disorder without a determined diagnosis after full investigation. (see FAQ How to code undiagnosed rare diseases patients using ORPHA:616874?)
ORPHAcodes (disorder level) describe diagnosis, therefore the only reason to use 2 or several ORPHAcodes is if patients are effectively affected by two or more independent diseases. In this case it is correct to code them with 2 or more ORPHAcodes, if your system allows it. This is coherent as all the ORPHAcodes used will describe different diagnosis co-existing and observed in the same patient at the same time.
For a clinical manifestation of a main diagnosis: use the patient’s main diagnosis ORPHAcode AND additional descriptive field if available (genetic, phenotypic trait). ORPHAcodes describe diagnosis, not patients; they are not meant to be used as phenotypic descriptors. ORPHAcodes can be complemented with other terminologies, and it is very important that a coding system includes the use of other descriptors (such as phenotypic signs using the Human phenotypic ontology for example, genetic information, etc), even within a specific descriptive text field.
If patients are affected by a single disease and coders are using additional ORPHAcodes as phenotypic descriptors, this use is strongly discouraged. This incorrect usage misrepresents/overrepresents certain diseases, compromising data reliability
Example: a patient with Classical-like Ehlers-Danlos syndrome type 1 ORPHA:230839 also presents with mitral valve prolapse (MVP) Cardiac abnormalities such as MVP are reported to be common features of the Ehlers Danlos syndrome
Coding with MVP would imply a « partial » diagnosis relative to one medical specialty. However, clinicians might need to indicate the specific type of cardiac defect for appropriate surgical management and statistical analysis
** Solution ** : Use the patient’s main diagnosis ORPHAcode AND additional descriptive field if available (genetic, phenotypic trait)
*in this case ICD-10 code as the standard can be used to complement the main diagnosis
If an ORPHAcode in the Orphanet nomenclature of RD is classified as "moved to" are we allowed to still use this ORPHAcode ?
If an entity has been deprecated it means there was an evolution of scientific knowledge (based on recent literature) and Orphanet assessed that the current representation is no longer accurate and a disease initially recognized independently is now described as part of another disease. Thus, the corresponding ORPHAcode has been inactivated and a relationship 'moved to' is applied toward the target entity. The deprecated code should not be used anymore and the target ORPHAcode is the one recommended to use.
N.B. In some systems it is not possible to replace assigned ORPHAcodes that have been inactivated in later years, in this case we strongly recommend to quality control your data and replace all inactivated ORPHAcodes once starting working on your data for analysis purposes.
This FAQ is being revised
In the frame of the RD-CODE project, undiagnosed patients have been defined as patients for whom no clinically known disorder could be confirmed by a RD expert center after all reasonable efforts to obtain a diagnosis according to the state of the art and diagnostic capabilities available. 3 recommendations have been assessed RD-CODE guidelines for coding undiagnosed patients: Whenever possible, capture the diagnostic assertion for all RD cases. Use the options “Suspected rare disease”, “Confirmed rare disease” and “Undetermined diagnosis”. ** Use the new code: ORPHA:616874, 'Rare disorder without a determined diagnosis after full investigation', alone or in addition to the diagnostic assertion. Provide a phenotype and a genotype description of undiagnosed patients, especially in registries. ** In registries, each undiagnosed patient should be described by its phenotype, using HPO. When available, the genotype should be associated to help future diagnosis, using HGVS. Additional phenotypic descriptors could be used (i.e. ICD, SNOMED, Orphanet categories, etc) as well as genetics descriptors (using a system generally recommended to describe genetic or genomic anomalies). Note: ORPHAcodes should never be used as phenotypic descriptors. Hence as mentionned 'Orphanet categories' or Group of Disorders should be mentioned as a complementary information only if RD experts can restrain the diagnosis orientation to a single system or medical specialty (e.g. not in a multisystemic syndrome context)