Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning

Genomewide association studies (GWAS) have identified a large number of loci associated with neuropsychiatric traits, however, understanding the molecular mechanisms underlying these loci remains difficult. To help prioritize causal variants and interpret their functions, computational methods have been developed to predict regulatory effects of non-coding variants. An emerging approach to variant annotation is deep learning models that predict regulatory functions from DNA sequences alone. While such models have been trained on large publicly available dataset such as ENCODE, neuropsychiatric trait-related cell types are under-represented in these datasets, thus there is an urgent need of better tools and resources to annotate variant functions in such cellular contexts. To fill this gap, we collected a large collection of neurodevelopment-related cell/tissue types, and trained deep Convolutional Neural Networks (ResNet) using such data. Furthermore, our model, called MetaChrom, borrows information from public epigenomic consortium to improve the accuracy via transfer learning. We show that MetaChrom is substantially better in predicting experimentally determined chromatin accessibility variants than popular variant annotation tools such as CADD and delta-SVM. By combining GWAS data with MetaChrom predictions, we prioritized 31 SNPs for Schizophrenia, suggesting potential risk genes and the biological contexts where they act. In summary, MetaChrom provides functional annotations of any DNA variants in the neuro-development context and the general method of MetaChrom can also be extended to other disease-related cell or tissue types.