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eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.
PLoS Genet. 19:e1010932 (2023)
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.
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Publikationstyp
Artikel: Journalartikel
Dokumenttyp
Wissenschaftlicher Artikel
Schlagwörter
Genetic-variation; Functional Variation; Expression; Quantification; Annotation; Conversion; Thousands; Alignment; Reveals
ISSN (print) / ISBN
1553-7390
e-ISSN
1553-7404
Zeitschrift
PLoS Genetics
Quellenangaben
Band: 19,
Heft: 9,
Artikelnummer: e1010932
Verlag
Public Library of Science (PLoS)
Verlagsort
1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa
Nichtpatentliteratur
Publikationen
Begutachtungsstatus
Peer reviewed
Institut(e)
Institute of Translational Genomics (ITG)
Förderungen
The RNA-seq quantification and QTL analyses were performed at the High Performance Computing Center, University of Tartu. We thank O.E. Oopkaup, S. Kuusemets and the rest of the team of the High Performance Computing Center for their professional and time