Identifying Phenotypes for Earlier Diagnosis of Rare Diseases

Rare diseases, while individually rare, cumulatively affect a large population, and patients often undergo long and arduous diagnostic odysseys. Toward the goal of supporting earlier diagnosis of rare diseases, we developed generalizable methods of extracting rare diseases and phenotypes from structured electronic health records and clinical notes. We analyzed the distributions of the age of onset of phenotypes per disease to identify disease-phenotype associations, producing a dataset with over 500 thousand associations covering 2300 rare diseases. Disease-phenotype associations are characterized by disease prevalence and mean age of onset of the phenotype to aid phenotype selection according to the priorities of the clinical decision support task.