iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes

BACKGROUND: A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal genomes of individual patients and to facilitate the development of personalized treatment or therapeutic approaches. METHODS: Leveraging deep neural network on the TensorFlow framework, we developed a computational tool, integrated Mental-disorder GEnome Score (iMEGES), for analyzing whole genome/exome sequencing data on personal genomes. iMEGES takes as input genetic mutations and phenotypic information from a patient with mental disorders, and outputs the rank of whole genome susceptibility variants and the prioritized disease-specific genes for mental disorders by integrating contributions from coding and non-coding variants, structural variants (SVs), known brain expression quantitative trait loci (eQTLs), and epigenetic information from PsychENCODE. RESULTS: iMEGES was evaluated on multiple datasets of mental disorders, and it achieved improved performance than competing approaches when large training dataset is available. CONCLUSION: iMEGES can be used in population studies to help the prioritization of novel genes or variants that might be associated with the susceptibility to mental disorders, and also on individual patients to help the identification of genes or variants related to mental diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2469-7) contains supplementary material, which is available to authorized users.