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eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

By Nurlan Kerimov, James D. Hayhurst, Jonathan R Manning, Peter Walter, Liis Kolberg, Kateryna Peikova, Marija Samoviča, Tony Burdett, Simon Jupp, Helen Parkinson, Irene Papatheodorou, Daniel R. Zerbino, Kaur Alasoo

Posted 29 Jan 2020
bioRxiv DOI: 10.1101/2020.01.29.924266

An increasing number of gene expression quantitative trait locus (QTL) studies have made summary statistics publicly available, which can be used to gain insight into human complex traits by downstream analyses such as fine-mapping and colocalisation. However, differences between these datasets in their variants tested, allele codings, and in the transcriptional features quantified are a barrier to their widespread use. Here, we present the eQTL Catalogue, a resource which contains quality controlled, uniformly re-computed QTLs from 19 eQTL publications. In addition to gene expression QTLs, we have also identified QTLs at the level of exon expression, transcript usage, and promoter, splice junction and 3ʹ end usage. Our summary statistics can be downloaded by FTP or accessed via a REST API and are also accessible via the Open Targets Genetics Portal. We demonstrate how the eQTL Catalogue and GWAS Catalog APIs can be used to perform colocalisation analysis between GWAS and QTL results without downloading and reformatting summary statistics. New datasets will continuously be added to the eQTL Catalogue, enabling systematic interpretation of human GWAS associations across a large number of cell types and tissues. The eQTL Catalogue is available at https://www.ebi.ac.uk/eqtl/.

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