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

View ORCID ProfileNurlan Kerimov, View ORCID ProfileJames D. Hayhurst, View ORCID ProfileJonathan R. Manning, View ORCID ProfilePeter Walter, View ORCID ProfileLiis Kolberg, Kateryna Peikova, Marija Samoviča, View ORCID ProfileTony Burdett, View ORCID ProfileSimon Jupp, View ORCID ProfileHelen Parkinson, View ORCID ProfileIrene Papatheodorou, View ORCID ProfileDaniel R. Zerbino, View ORCID ProfileKaur Alasoo
doi: https://doi.org/10.1101/2020.01.29.924266
Nurlan Kerimov
Institute of Computer Science, University of Tartu, Tartu, 51009, EstoniaOpen Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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James D. Hayhurst
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Jonathan R. Manning
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Peter Walter
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Liis Kolberg
Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
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Kateryna Peikova
Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
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Marija Samoviča
Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
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Tony Burdett
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Simon Jupp
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Helen Parkinson
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Irene Papatheodorou
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Daniel R. Zerbino
Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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  • For correspondence: zerbino@ebi.ac.uk kaur.alasoo@ut.ee
Kaur Alasoo
Institute of Computer Science, University of Tartu, Tartu, 51009, EstoniaOpen Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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  • For correspondence: zerbino@ebi.ac.uk kaur.alasoo@ut.ee
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Abstract

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/.

Footnotes

  • ↵* These authors jointly supervised this work.

  • https://www.ebi.ac.uk/eqtl/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 29, 2020.
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eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
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
bioRxiv 2020.01.29.924266; doi: https://doi.org/10.1101/2020.01.29.924266
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eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
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
bioRxiv 2020.01.29.924266; doi: https://doi.org/10.1101/2020.01.29.924266

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