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Rare diseases / Orphan diseases

Dear all,
Does anyone know of any sites having rare disease (orphan disease) data represented in OMOP? This can either be clinical data or registry data, and may or may not involve information regarding newborn genetic screening, about “controls” (i.e., non-cases), and may focus on specific types of rare diseases, or be broadly defined. Happy to hear what already exists and what interest there is in this topic.

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Hi- I wanted to revive this topic/question. Are there any OMOP sites that have Rare Diseases mapped to standard concepts? We’ve been looking at Orphanet and see that they have mappings to ICD10 and ICD11.

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Hello, @PriyaDesai

ICD10 codes are currently mapped to standard concepts and available in Athena, so you can take any condition you want. ICD11 is not incorporated yet.

Unfortunately, I can’t contribute to the original question on the topic.

Hi @PriyaDesai and @ronaldcornet ,
there is actually an interesting initiative by Dresden University Germany, led by @Michele_Zoch .
We just recently had a discussion with the good people from orphadata and are considering ways how we can make the orphadata codes available as a source vocabulary together with its mappings to SNOMED.
If we can collect more use cases internationally we could better justify the need for this as a new Athena vocabulary. Please share yours with us and if having the orphanet codes in Athena would help you!
Thanks ~ mik

Hello @PriyaDesai and @ronaldcornet,

like Mik already mentioned we are in contact with Orphadata. They provide mappings of OrphaCodes to ICD-10-WHO, ICD-11 and also to SNOMED. A new version will be released in October 2022.
The mapping to SNOMED is a great basis to transfer OrphaCodes into ATHENA and to enable mappings to standard concepts.
Our team in Dresden is currently working on an evaluation of the mapping (provided by OrphaData) compared to other mappings (for example provided by the German Federal Institute for Drugs and Medical Devices). We then reflect the results back to the OHDSI community and esp. to the Vocabulary Work Group.

Regarding the use cases: We need the mapping to consider rare disease in OMOP in general. (Unfortunately, rare diseases cannot be adequately coded with ICD-10 (see Aymé2015). In addition, mapping to international terminologies is important in order to expand the cohort of the few medical cases through international collaboration.) Specifically, we want to map, for example, pediatric patients with Kawasaki disease and Multisystem Inflammatory Syndrome in Children and Adults (PIMS), which emerged during the COVID 19 pandemic.

Thank you @Michele_Zoch !
one question that I have… An Orphadata vocabulary would be a classic “source” vocabulary helping in your ETL process. That obviously would require that your data source actually provides those codes in relevant numbers. Can you tell us about that?
Thanks - mik

So far, there are individual efforts, especially by centers for rare diseases, which already document with OrphaCodes. In Germany, coding using OrphaCode (and the German Alpha-ID-SE) is expected to become mandatory in 2023. Therefore, the codes will then also be available in the source data.

In addition, a minimum data set for rare diseases is used in the European Union through projects such as EUCERD Joint Action, EPIRARE, and RD-Connect (see Set of Common Data Elements). This also focus on coding with OrphaCodes. This means that there are also many centers for rare diseases and other clinics that have these codes in the source data.

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