Orphanet Annotations in VarSeq

         March 18, 2021

Orphanet is a public database available in VarSeq that aims to improve the current understanding and treatment options for patients affected by rare diseases. This resource was established in France in 1997 and has gradually grown to cover a consortium of over 40 countries in Europe. The primary goal of this database is to provide a universal nomenclature to classify rare diseases while promoting interoperability and access to relevant services and information for all parties.

As mentioned above, the term orphan disease refers to a rare disease but the history behind the term is rather interesting. Rare disease means that the disease occurs in a very small percentage of the population. In Europe, this frequency is 1 person in 2,000 people, and in the United States, it is 1 person in 200,000 people (1). Due to the scarcity of affected patients, the prescription drug industry deemed that the profit for creating drugs for these rare groups would be abysmal. Due to the lack of adoption by these industries, these types of rare diseases were referred to as orphan diseases. Fortunately, the Orphan Drug Act (ODA) incentivized drug and biological manufacturers to focus on orphan diseases, which paved the way to create, to date, around 250 orphan drugs. This was a momentous step, as prior to the ODA, there were fewer than 10 such products (2).

As an annotation source, Orphanet has over 4,000 features and multiple fields to derive variant information. As shown in Figure 1, the nomenclature used in Orphanet is aligned with other databases, such as OMIM and Entrez, which is valuable for cross-referencing different resources. Orphanet also provides clinical descriptions of rare diseases based on abnormalities referenced in the Human Phenotype Ontology and provides evidence of pathognomonic signs. Pathognomonic signs indicate that a particular disease is present beyond any doubt, which can provide strong evidence that the variant in question is clinically relevant. Lastly, phenotypic abnormalities are presented by order of frequency in the patient population. This is broken down into very frequent, frequent, occasional, and rare.

Figure 1: Features available in Orphanet.

To date there are thousands of rare diseases that may have actionable treatment options and having resources, such as Orphanet, will help expand the current knowledge of variant analysis in your workflow. This database is a public resource and if you would like to implement Orphanet into your existing workflow, you can do so by going to Add>Variant Annotation and selecting Orphanet Gene Associations.

If you have any questions about this blog post, database, or those pertaining to implementing our software, please contact us at support@goldenhelix.com. You can also leave a comment below and we will be happy to respond. Feel free to also check out some of our other blogs that contain important, useful news and updates for the next-gen sequencing community.

Works Cited:

  1. https://rarediseases.info.nih.gov/diseases/pages/31/faqs-about-rare-diseases
  2. https://www.fda.gov/drugs/information-consumers-and-patients-drugs/orphan-products-hope-people-rare-diseases

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