Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

By M. Ghoussaini, Edward Mountjoy, M. Carmona, Gareth Peat, Ellen M. Schmidt, Andrew Hercules, Luca Fumis, Alfredo Miranda, D. Carvalho-Silva, A. Buniello and 25 more. Nucleic Acids Res., 2020

535 citations recorded by the source corpus.

Abstract Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes. This enables systematic identification and prioritisation of likely causal variants and genes across all published trait-associated loci. In this paper, we describe the public resources we aggregate, the technology and analyses we use, and the functionality that the portal offers. Open Targets Genetics can be searched by variant, gene or study/phenotype. It offers tools that enable users to prioritise causal variants and genes at disease-associated loci and access systematic cross-disease and disease-molecular trait colocalization analysis across 92 cell types and tissues including the eQTL Catalogue. Data visualizations such as Manhattan-like plots, regional plots, credible sets overlap between studies and PheWAS plots enable users to explore GWAS signals in depth. The integrated data is made available through the web portal, for bulk download and via a GraphQL API, and the software is open source. Applications of this integrated data include identification of novel targets for drug discovery and drug repurposing.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3fca54afe8baac2bd5439919163b74e470822eb1

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Citations in the corpus

• The next-generation Open Targets Platform: reimagined, redesigned, rebuilt (2022, methodology): “For common variation, the Platform uniquely relies on the closely developed post-GWAS analysis available in Open Targets Genetics (https: //genetics.opentargets.org/) (16).”
• Open Targets Platform: supporting systematic drug–target identification and prioritisation (2020, unknown): “The Open Targets Genetics Portal addresses this problem by interpreting manually curated associations from the GWAS catalog, as well as independent signals from GWAS with publicly available summary statistics, most importantly the UK Biobank GWAS data (7,24,25).”
• The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource (2022, background): “( B ) The landing page for a published study additionally provides the final journal citation [4], more detailed study and sample information [5], ontology annotations [6] and curated top associations [7].”