Major European project to create knowledge base of gene-disease relationships

A Euro 12m project funded by the European Commission will provide improved access to information connecting genes with diseases such as diabetes, obesity, heart disease and cancer.

The initiative, called Genotype-To-Phenotype Databases: A Holistic Solution (GEN2PHEN), will be led by Professor Anthony Brookes at the Department of Genetics, University of Leicester (UK), and executed by 19 leading research institutions, including 17 in European, one in India and one in South Africa. The project is funded with €12m awarded by the European Commission following a competitive call targeting this area of research in the recently initiated 7th Framework Programme for research and technological development.

The GEN2PHEN project aims to harness the web to capture and unify genetic information that fundamentally impacts on a person's health and disease processes. It plans to orchestrate internationally the electronic gathering and use of data that show how genotypes contribute to inter-individual differences in disease, drug response, and other characteristics (phenotypes). These relationships - usually in the form of genotype-phenotype information stored in scattered databases - are deemed to become essential for future prognosis, diagnosis and treatment of diseases.

GEN2PHEN will build a set of database components, tools and technologies that will help all research results pertaining to genome variation and disease to be properly integrated and immediately available for holistic analysis via the internet. The project will deploy a major internet portal, called the GEN2PHEN Knowledge Centre, which will prominently profile the solutions generated by the project and set these in the context of powerful search capabilities for genotype-phenotype data and the very latest expertise on genotype-phenotype databases.

"Technologies for the exploration of genetic variation in disorders such as diabetes, heart disease, obesity and autoimmune states have been devised only in the last few years," said lead scientist Professor Anthony Brookes, at the University of Leicester.

"An unprecedented torrent of exciting, valuable, and important research observations is therefore now arriving, and yet there is no universal internet-ready system able to receive all these data, to store and combine them, and to make them available for researchers and doctors alike to evaluate and exploit."

Specific project activities will include:

• Analysis of the genotype-phenotype field, to specify current needs and practices
• Development of key standards for the genotype-phenotype field
• Analysis of ethical aspects that need to be addressed regarding the managed data
• Creation of generic database components, services and integration infrastructures for the genotype-phenotype domain
• Creation of data search and presentation solutions for genotype-phenotype knowledge
• Facilitation of the transfer of data into research and diagnostic genotype-phenotype databases
• Building a major genotype-phenotype internet portal (a "knowledge domain")
• Deployment of genotype-phenotype solutions to the community
• Innovative ways to address system durability and long-term financing
• Repeated system utility and validation pilots

GEN2PHEN participants

The full list of participating institutions is:
University of Leicester, UK
EMBL-European Bioinformatics Institute, UK
Fundació IMIM, Spain
Leiden University Medical Center, Netherlands
Institut National de la Santé et de la Recherche Médicale, France
Karolinska Institute, Sweden
Foundation for Research and Technology ¢€ Hellas, Greece
Centre National de Génotypage, France
Erasmus University Medical Center, Netherlands
Institute for Molecular Medicine Finland, University of Helsinki, Finland
University of Aveiro ¢€ IEETA, Portugal
University of Western Cape, South Africa
Institute of Genomics and Integrative Biology, India
Swiss Institute of Bioinformatics, Switzerland
University of Manchester, UK
BioBase GmbH, Germany
deCODE genetics ehf, Iceland
PhenoSystems SA, Belgium
Biocomputing Platforms Ltd Oy, Finland