PRBB Computational Genomics Seminar
by Alberto Corvo & Carles Hernandez Ferrer, Bioinformatics Unit, CRG
Although next-generation sequencing (NGS) has drastically improved diagnosis for patients with rare diseases (RDs), access to knowledge of effective treatments is still sparse and often unclear. The large number of RDs (>7,000 estimated) and their genetic heterogeneity make the identification of existing treatments difficult for clinicians. Herein we report Treatabolome DB, a database of RD-specific treatments mapped at gene and variant level to allow easy identification of published therapies. Materials and methods: A relational database was developed to collect variant-to-treatment mappings from systematic literature reviews (SLRs) produced by disease experts. To date, 8 SLRs have been completed on congenital myasthenic syndromes, laminopathies, muscular channelopathies, mitochondrial disorders (Leigh syndromes), hereditary peripheral neuropathies, genetic forms of Parkinson ´s disease, and metabolic myopathies; additional participation from RD experts is welcomed. Results: A data model based on the use of public ontologies and international recommendations was defined by the Treatabolome working group to enable system interoperability. The Treatabolome DB schema is based on data submission and allows discoverability of information from the SLRs. Treatabolome DB will be publicly accessible through programmatic interfaces and a web portal supporting queries of terms including diagnostic (ORDO, OMIM, and HPO), gene, variant, and treatment (ChEBI, UMLS or MeSH). Conclusion: Treatabolome DB enables identification of existing treatments for RD patients at the time of diagnosis. Future developments include its connection with genomic analysis tools such as the RD-Connect GPAP.
Host: Garrido Enamorado, Romina