ukbFGSEA: an R Package for Applying Fast Preranked Gene Set Enrichment Analysis to UK Biobank Exome Data

TL;DR

This paper introduces ukbFGSEA, an R package that applies fast preranked gene set enrichment analysis to UK Biobank exome data, enabling efficient identification of gene set associations with various phenotypes.

Contribution

The paper presents a novel R package, ukbFGSEA, specifically designed for applying FGSEA to UK Biobank exome data, filling a gap in gene set enrichment analysis methods for this dataset.

Findings

Successfully identified known gene-phenotype associations.

Revealed potential new links between gene sets and neurodevelopmental disorders.

Validated the method's effectiveness on autism and developmental disorder gene sets.

Abstract

The Genebass dataset, released by Karczewski et al. (2022), provides a comprehensive resource elucidating associations between genes and 4,529 phenotypes based on nearly 400,000 exomes from the UK Biobank. This extensive dataset enables the evaluation of gene set enrichment across a wide range of phenotypes, facilitating the inference of associations between specified gene sets and phenotypic traits. Despite its potential, no established method for applying gene set enrichment analysis (GSEA) to Genebass data exists. To address this gap, we propose utilizing fast pre-ranked gene set enrichment analysis (FGSEA) as a novel approach to determine whether a specified set of genes is significantly enriched in phenotypes within the UK Biobank. We developed an R package, ukbFGSEA, to implement this analysis, completed with a hands-on tutorial. Our approach has been validated by analyzing gene sets associated with autism spectrum disorder, developmental disorder, and neurodevelopmental disorders, demonstrating its capability to reveal established and novel associations.