EQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals

Theodore G Drivas,Anastasia Lucas,Marylyn D Ritchie

doi:10.1186/s13040-021-00267-6

Theodore G Drivas, Anastasia Lucas + Show 1 more

Open Access

https://doi.org/10.1186/s13040-021-00267-6

Copy DOI

Abstract

BackgroundGenomic studies increasingly integrate expression quantitative trait loci (eQTL) information into their analysis pipelines, but few tools exist for the visualization of colocalization between eQTL and GWAS results. Those tools that do exist are limited in their analysis options, and do not integrate eQTL and GWAS information into a single figure panel, making the visualization of colocalization difficult.ResultsTo address this issue, we developed the intuitive and user-friendly R package eQTpLot. eQTpLot takes as input standard GWAS and cis-eQTL summary statistics, and optional pairwise LD information, to generate a series of plots visualizing colocalization, correlation, and enrichment between eQTL and GWAS signals for a given gene-trait pair. With eQTpLot, investigators can easily generate a series of customizable plots clearly illustrating, for a given gene-trait pair: 1) colocalization between GWAS and eQTL signals, 2) correlation between GWAS and eQTL p-values, 3) enrichment of eQTLs among trait-significant variants, 4) the LD landscape of the locus in question, and 5) the relationship between the direction of effect of eQTL signals and the direction of effect of colocalizing GWAS peaks. These clear and comprehensive plots provide a unique view of eQTL-GWAS colocalization, allowing for a more complete understanding of the interaction between gene expression and trait associations.ConclusionseQTpLot provides a unique, user-friendly, and intuitive means of visualizing eQTL and GWAS signal colocalization, incorporating novel features not found in other eQTL visualization software. We believe eQTpLot will prove a useful tool for investigators seeking a convenient and customizable visualization of eQTL and GWAS data colocalization.Availability and implementationthe eQTpLot R package and tutorial are available at https://github.com/RitchieLab/eQTpLot

Highlights

Genomic studies increasingly integrate expression quantitative trait loci information into their analysis pipelines, but few tools exist for the visualization of colocalization between eQTL and genome wide association studies (GWAS) results
In its simplest implementation, eQTplot takes as input two data frames, one of GWAS summary data and the other of eQTL summary data, with the user specifying the name of the gene to be analyzed, the GWAS trait to be analyzed (useful if the GWAS data contains information on multiple associations, as one might obtain from a Phenomewide Association Study (PheWAS)), and the tissue type to use for the eQTL analysis
If the argument congruence is set to TRUE, all variants are divided into two groups: congruous, or those with the same direction of effect on gene expression and the GWAS trait, and incongruous, or those with opposite directions of effect on gene expression and the GWAS trait

Summary

Introduction

Genomic studies increasingly integrate expression quantitative trait loci (eQTL) information into their analysis pipelines, but few tools exist for the visualization of colocalization between eQTL and GWAS results. EQTpLot generates a series of plots intuitively illustrating the colocalization of GWAS and eQTL signals in chromosomal space, and the enrichment of and correlation between the candidate gene eQTLs and trait-significant variants.

Results

Conclusion