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Open Targets

Resource Location

/labs/SysMedBio/Q/Resources/Genomics/OpenTargets

/Volumes/lab/SysMedBio/Resources/Genomics/OpenTargets

Q:\SysMedBio\Resources\Genomics\OpenTargets

Open Targets is a public-private partnership that aims to systematically identify and prioritize drug targets using genetic and genomic evidence.

Scientific Context

A major challenge in drug discovery is establishing the causal connection between disease-associated variants (primarily identified via Genome-Wide Association Studies, or GWAS) and target genes.

Within this ecosystem, Open Targets Genetics focuses on resolving these connections. The Open Targets VEP Plugin (OpenTargets.pm) allows researchers running Ensembl's Variant Effect Predictor (VEP) to annotate genetic variants with disease- and target-centric information directly: - Locus-to-Gene (L2G) Scores: Rather than relying purely on variant-to-gene distance or simple variant pathogenicity, Open Targets utilizes an L2G machine-learning model. This model integrates credible sets of fine-mapped variants with functional genomic features (such as chromatin interactions and colocalised QTLs) to predict the causal gene at a disease-associated locus. - QTL Associations: Variant annotations include tissue-specific expression (eQTL), splicing (sQTL), and protein (pQTL) associations. - Disease/Trait Context: Variants are directly linked to trait-associated findings, facilitating translational bioinformatics and target validation.

Main Publication

  • Title: Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics
  • Authors: Maya Ghoussaini, Edward Mountjoy, Miguel Carmona, Gail Peat, Emily M Schmidt, Alfredo Hercules, Laura Fumis, Andrea Miranda, David Carvalho-Silva, Anja Buniello, Tony Burdett, Joann Hayhurst, Jane Baker, Jorge Ferrer, Asier Gonzalez-Uriarte, Ellen M McDonagh, Sandra Ouelle, Janet Pinero, Maria J Martin, Justin P Croft, Helen Parkinson, Andrew P Morris, Jeffrey C Barrett, Ian Dunham
  • Journal: Nucleic Acids Research (2021, Volume 49, Issue D1, Pages D1311–D1320)
  • DOI: 10.1093/nar/gkaa840

Available Files

The Open Targets resource folder contains the processed target-association dataset:

  • OTGenetics.tsv.gz: Compressed tab-separated values file containing variant annotation data from Open Targets Genetics tailored for the Ensembl VEP plugin.
  • OTGenetics.tsv.gz.tbi: Tabix index file corresponding to OTGenetics.tsv.gz, enabling fast random access by genomic coordinate.