Deep learning is rarely used in population genomics because of the computational burden and challenges in interpreting neural networks. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In this framework, interpretable and memory-efficient neural network architectures are constructed by embedding biological knowledge from public databases, resulting in neural networks that contain only biological plausible connections. We applied the framework to seventeen phenotypes from a case-control study, a population-based study and the UK Biobank. Interpreting the networks revealed well-replicated genes such as HERC2 and OCA2 for hair and eye color and novel genes such as ZNF773 and PCNT for schizophrenia. Additionally, the framework obtained an AUC of 0.74 in the held-out test set and identified ubiquitin mediated proteolysis, endocrine system and viral infectious diseases as most predictive biological pathways for schizophrenia. GenNet is a freely available, end-to-end deep learning framework that allows researchers to develop and use interpretable neural networks to obtain novel insights into the genetic architecture of complex traits and diseases.

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