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. 2023 Jan 6;51(D1):D986-D993.
doi: 10.1093/nar/gkac1017.

GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies

Tim Beck  1   2 , Thomas Rowlands  1 , Tom Shorter  1 , Anthony J Brookes  1   2
Affiliations

GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies

Tim Beck et al. Nucleic Acids Res. .

Abstract

The GWAS Central resource gathers and curates extensive summary-level genome-wide association study (GWAS) data and puts a range of user-friendly but powerful website tools for the comparison and visualisation of GWAS data at the fingertips of researchers. Through our continued efforts to harmonise and import data received from GWAS authors and consortia, and data sets actively collected from public sources, the database now contains over 72.5 million P-values for over 5000 studies testing over 7.4 million unique genetic markers investigating over 1700 unique phenotypes. Here, we describe an update to integrate this extensive data collection with mouse disease model data to support insights into the functional impact of human genetic variation. GWAS Central has expanded to include mouse gene-phenotype associations observed during mouse gene knockout screens. To allow similar cross-species phenotypes to be compared, terms from mammalian and human phenotype ontologies have been mapped. New interactive interfaces to find, correlate and view human and mouse genotype-phenotype associations are included in the website toolkit. Additionally, the integrated browser for interrogating multiple association data sets has been updated and a GA4GH Beacon API endpoint has been added for discovering variants tested in GWAS. The GWAS Central resource is accessible at https://www.gwascentral.org/.

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Figures

Figure 1.
Figure 1.
Studies and experiments added to the GWAS Central database since 2011. There was a large increase in the number of experiments in 2021, with 2022 being comparable (* includes studies up to July 2022).
Figure 2.
Figure 2.
GWAS Central region browser example. Markers from eight data sets investigating corneal morphology phenotypes are compared in a 50 kb region on chromosome 16. Three data sets have significant associations with SNP rs35193497. Hovering over rs35193497 in the 1000 Genomes track displays the allelic expression in super populations. Tracks can be displayed or hidden as required (some tracks have been hidden). Super population abbreviations: AFR – African, AMR – American, EAS – East Asian, EUR – European, SAS – South Asian.
Figure 3.
Figure 3.
Interfaces for exploring integrated GWAS and mouse gene data. (A) The results from the text search displays term mappings and the number of GWAS studies and mouse gene knockouts matching the query term(s). (B) The ontology hierarchy comparison interface displays which terms are associated with human and mouse data sets. A search using one ontology will retrieve records annotated to the mapped term. In this example, a MeSH GWAS search for ‘eye’ phenotypes also retrieves mouse genes annotated to ‘abnormal eye morphology’. (C) The ontology mapping graphic presents the source of the term mapping. (D) The heatmap alongside each chromosome indicates the number of mouse genes (first column) and GWAS markers (second column) per 3 Mb bin having a P-value that passes a tunable significance threshold. (E) A dynamic region-level browser, where scale and position may be tailored to one's preferences, presents optional tracks for individual GWAS marker associations and IMPC mouse genes.
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