A compendium of uniformly processed human gene expression and splicing quantitative trait loci

By N. Kerimov, J. Hayhurst, Kateryna Peikova, J. Manning, P. Walter, Liis Kolberg, Marija Samoviča, M. P. Sakthivel, I. Kuzmin, S. Trevanion and 7 more. Nature Genetics, 2021

318 citations recorded by the source corpus.

Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues. The eQTL Catalogue provides uniform processing of 21 eQTL studies, allowing the identification of highly reproducible eQTLs affecting whole gene and transcript expression levels.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9c00c71d0f9e159c65d74f6299dae8630235f7ae

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets (2023, unknown): “To determine whether the trans -pQTL sentinel variants are likely to be causal cis -eQTL variants in the eQTL Catalogue and GTEx data, we used the fine-mapped eQTL credible sets available at the eQTL Catalogue (https://www.ebi.ac.uk/eqtl/ Data_access).”
Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “In addition, databases of expression quantitative trait loci in human populations can be used to validate distal candidate CREs 134–136 .”
Ensembl 2022 (2021, methodology): “The regulatory build annotation complements other approaches, such as the SCREEN Catalogue, based on open chromatin regions from ENCODE, or emerging approaches using deep learning (22–24).”