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

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/.

A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

“…4b and downloaded from [ https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733 ]. GWAS 89 was used to generate data from Supplementary Fig. 19 .…”

Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes

“…This will enable a broad range of applications—from PheRS to identify patients likely to benefit from genetic testing to PheWAS to explore molecular mechanisms of disease at a population-scale in the EHR. 13 , 21 Our map helps build a foundation for bridging genome biology and medicine by enabling connection to existing large disease biology networks linking genes, phenotypes, cross-species diseases, and model organisms (eg, Monarch Initiative 22 , 23 ) and it broadens the scope of tools or resources that use the language of HPO (eg, Phenomizer, 24 Exomiser, 25 SimulConsult, 26 Matchmaker Exchange, 27 PhenoTips, 28 GeneNetwork Assisted Diagnostic Optimization [GADO], 29 and GWAS Central 30 ). 31 …”

Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease

“…No known effect on gross phenotype or evidence of association with disease has yet been reported among the population-enriched variants identified with the 20 genes listed in Table 6 . However, a newly released resource, GWAS Central ( 457 ), was accessed to provide phenotype associations with a subset of variants in Table 6 . Further, disease disparities related to the parent gene and/or other variants of the gene were identified and/or the predicted impact of a population-enriched variant on the coded change in protein function were evaluated and listed in Table 6 .…”