From Genetic Association to Therapeutic Target: A Pipeline for Pleiotropic Gene Prioritization

Abstract

As our understanding of human health grows, we often see that similar biological dysfunction underlies the co-occurrence of various complex diseases. It remains difficult to determine if there are common genetic mechanisms contributing to clinically distinct conditions or if expression of both conditions relates to other shared risk factors. For example, in some situations, genetic variation may increase risk for one condition, and expression of this condition then increases risk for another disease. Identifying potentially pleiotropic genes is crucial for advancing the development of more effective treatment options, especially in instances where current therapies are insufficient. Genome-wide association studies (GWAS) provide cross-trait associations but do not provide the full functionality of how dysfunction in genes being tagged by GWAS hits are contributing to two or more distinct phenotypes. Fortunately, as other types of available data continue to grow exponentially (e.g., RNA-seq, mass spectrometry, mouse knock-out phenotype associations), these can be leveraged to help process GWAS results into meaningful information. The aim of this protocol is to provide clear instructions for using various databases and available software tools to identify key pleiotropic genes contributing to two distinct phenotypes of interest. The protocol uses information from various publicly available databases, including GWAS Catalog, Functional Mapping and Annotation (FUMA), Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT), International Mouse Phenotype Consortium (IMPC), STRINGdb, Pharos, and Cytoscape for network visualization. This pipeline, with code written in R and RStudio software, helps the user identify and generate hypotheses about shared genetic mechanisms contributing to their selected phenotypes of interest as well as prioritize genes of interest to functionally follow up in model systems that are more likely to be clinically relevant. © 2025 Wiley Periodicals LLC.

Basic Protocol: Pleiotropic gene prioritization pipeline for studies in model systems