POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study

Abstract

AbstractObjectiveFor the UK Biobank, standardized phenotype codes are associated with patients who have been hospitalized but are missing for many patients who have been treated exclusively in an outpatient setting. We describe a method for phenotype recognition that imputes phenotype codes for all UK Biobank participants.Materials and MethodsPOPDx (Population-based Objective Phenotyping by Deep Extrapolation) is a bilinear machine learning framework for simultaneously estimating the probabilities of 1538 phenotype codes. We extracted phenotypic and health-related information of 392 246 individuals from the UK Biobank for POPDx development and evaluation. A total of 12 803 ICD-10 diagnosis codes of the patients were converted to 1538 phecodes as gold standard labels. The POPDx framework was evaluated and compared to other available methods on automated multiphenotype recognition.ResultsPOPDx can predict phenotypes that are rare or even unobserved in training. We demonstrate substantial improvement of automated multiphenotype recognition across 22 disease categories, and its application in identifying key epidemiological features associated with each phenotype.ConclusionsPOPDx helps provide well-defined cohorts for downstream studies. It is a general-purpose method that can be applied to other biobanks with diverse but incomplete data.