CRUK: Mining gene-disease associations and drug target validation with Open Targets

New

Open Targets was founded by three global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics: GSK, EMBL-EBI, the Wellcome Trust Sanger Institute, and recently joined by Biogen, the world’s oldest independent biotechnology company.

We develop two major areas of work, which are further subdivided into projects. The major areas are the Core Bioinformatics and Computational Pipelines, which created and developed the Target Validation Platform, and Experimental projects, which combine large-scale genomics with statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases. The Target Validation Platform integrates comprehensive datasets from a myriad of renowned public databases, such as UniProt, ChEMBL, Ensembl, NHGRI-EBI GWAS, EuropePMC, COSMIC, amongst others, and will incorporate the newly generated data by our Experimental projects in Oncology, Immunity, Inflammation and other areas for free and open access.

The purpose of this half-day workshop is to acquaint participants with the Open Targets consortium. We will highlight the experimental projects in the Consortium but focus on the Target Validation Platform to introduce the tools for visualisation and interpretation of gene-disease associations and target validation. By the end of this half-day workshop, users will be able to carry out effective searches of data, and use the web application to visualise genes, variants, ontology, pathways (and more) in the context of human disease and therapeutics.

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.

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 to 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 drug target
• Retrieve a list of publications supporting target and disease association
• Get disease and phenotype evidence based on animal models

During this course you will learn about:

• The Open Targets project and its goals
• The Target Validation Platform and the integration of the different datasets available
• How to visualise and interpret gene - disease associations according to the different datasets
• How to browse gene, protein, genetic variants and expression data in the context of human diseases

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 days

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)