Open Targets: Integrating genetics and genomics for disease biology and translational medicine

Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. The consortium was founded in 2014 by GSK, EMBL-EBI and the Wellcome Sanger Institute, and later welcomed three new partners, Biogen, Takeda, and Celgene. Underpinning this partnership is the Open Targets Platform, an open source, user-friendly web interface to investigate causal links between genes, pathways and diseases. These links are computed, scored and ranked using biological evidence integrated from many public data sources, including the NHGRI-EBI GWAS Catalog, Genomics England, PheWAS, ClinVar, Expression Atlas, UniProt, and ChEMBL to name a few.

In addition to data integration, Open Targets also generates new data using human cellular models (e.g. organoids, iPSCs) and genome editing (CRISPR/Cas9) to identify drug targets in oncology, immunology and neurodegenerative diseases. This will be publicly available in the public domain and integrated into the Open Targets Platform.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

• This course is suitable for all users who have an interest in biomedical research and therapeutics. A special emphasis will be given on drug discovery and target validation. It will also be useful to those who seek for practical examples on how large-scale genomic experiments and computational techniques are integrated and visualised in a web platform.
• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here

• Some prior knowledge of basic genetics and molecular biology in addition to familiarity with some existing reference sources (e.g. Ensembl, UniProt) is desirable to make the best use of this course.
• No programmatic skills required.

Number of sessions: 1

Bioinformatics, Data retrieval, Data visualisation, Database search, Genotype and phenotype, Pharmacogenomics

After this course you should be able to:

• Find diseases, phenotypes and traits associated with human genes
• Find genes associated with diseases, phenotypes and traits
• Get information on protein, genetic variation, gene expression, gene ontology, drugs, pathways (and more) for a gene
• Retrieve a list of publications supporting target and disease association
• To query the Open Targets REST server with simple HTTPS calls

During this course you will learn about:

• The Open Targets partnership and its goals
• The Open Targets Platform and the integration of the genomic datasets and drug information
• How to visualise and interpret gene-disease associations using the Open Targets Platform
• How to browse gene, protein, genetic variants (and much more) in the context of human diseases
• Alternatives ways of accessing this data e.g. REST-API

Presentations, demonstrations and practicals

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

0.5

A number of times per year

• EMBL-EBI: Protein Sequence Databases with UniProt
• COSMIC: Integrating and interpreting the world’s knowledge of somatic mutations in cancer
• EMBL-EBI: Bioinformatics resources for exploring disease related data
• Using the Ensembl Genome Browser (ONLINE LIVE TRAINING)