Neighborhood embedding and re-ranking of disease genes with ADAGIO

Abstract

We present ADAGIO, a new method for network-based disease gene prioritization that balances network interconnection structure with an embedding measure of network similarity. We show ADAGIO performs better than previous methods for recovering known disease genes in a recent benchmark set encompassing disease-associated genes for 22 polygenic diseases. We find ADAGIO discovers some interesting new disease gene candidates in both Alzheimer's and Parkinson's diseases. Code, ranked lists of disease genes, and supplementary figures and tables appear at https://github.com/merterden98/ADAGIO.