eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs
-
Published:2023-09-18
Issue:9
Volume:19
Page:e1010932
-
ISSN:1553-7404
-
Container-title:PLOS Genetics
-
language:en
-
Short-container-title:PLoS Genet
Author:
Kerimov NurlanORCID,
Tambets Ralf,
Hayhurst James D.,
Rahu IdaORCID,
Kolberg PeepORCID,
Raudvere UkuORCID,
Kuzmin Ivan,
Chowdhary Anshika,
Vija AndreasORCID,
Teras Hans J.,
Kanai MasahiroORCID,
Ulirsch Jacob,
Ryten Mina,
Hardy John,
Guelfi Sebastian,
Trabzuni DaniahORCID,
Kim-Hellmuth SarahORCID,
Rayner William,
Finucane Hilary,
Peterson Hedi,
Mosaku Abayomi,
Parkinson Helen,
Alasoo KaurORCID
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
Funder
Open Targets
European Molecular Biology Laboratory
Horizon 2020
Eesti Teadusagentuur
Estonian Centre of Excellence in ICT Research
European Regional Development Fund
Emmy Noether Programme
Deutsche Forschungsgemeinschaft
Publisher
Public Library of Science (PLoS)
Subject
Cancer Research,Genetics (clinical),Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献