A network-guided protocol to discover susceptibility genes in genome-wide association studies using stability selection

Abstract

Summary: We present a network-based protocol to discover susceptibility genes in case-control genome-wide association studies (GWASs). In short, this protocol looks for biomarkers that are informative of disease status and interconnected in an underlying biological network. This boosts discovery and interpretability. Moreover, the protocol tackles the instability of network methods, producing a stable set of genes most likely to replicate in external cohorts. To apply the procedure to a provided GWAS dataset, install the required software and execute our command-line tool.For complete details on the use and execution of this protocol, please refer to Climente-González et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Genetics
• Genomics