Genotype to Phenotype Databases: a Holistic Approach (GEN2PHEN) is a European project aiming to develop a knowledge web portal integrating information from the genotype to the phenotype in a unifying portal: The Knowledge Centre].
Summary and Objectives.
The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. The project will establish the technological building-blocks needed for the evolution of today’s diverse G2P databases into a future seamless G2P biomedical knowledge environment, by the projects end. This will consist of a European-centred but globally networked hierarchy of bioinformatics GRID-linked databases, tools and standards, all tied into the Ensembl genome browser. The project has the following specific objectives:
The GEN2PHEN Consortium members have been selected from a talented pool of European research groups and companies that are interested in the G2P database challenge. Additionally, a few non-EU participants have been included to bring extra capabilities to the initiative. The final constellation is characterised by broad and proven competence, a network of established working relationships, and high-level roles/connections within other significant projects in this domain...
Background and Concept.
By providing a complete Homo sapiens ‘parts list’ (the gene sequences) and a powerful ‘toolkit’ (technologies), the Human Genome Project has revolutionised mankind’s ability to explore how genes cause disease and other phenotypes. Studies in this domain are proceeding at a rapid and ever-increasing pace, generating unprecedented amounts of raw and processed data. It is now imperative that the scientific community finds ways to effectively manage and exploit this flood of information for knowledge creation and practical benefit to society. This fundamental goal lies at the heart of the “Genotype-To-Phenotype Databases: A Holistic Solution (GEN2PHEN)” project.
Previous genetics studies have shown that inter-individual genome variation plays a major role in differential normal development and disease processes. However, the details of how these relationships work are far from clear, even in the case of most Mendelian disorders where single genetic alterations are fully penetrant (essentially causative, rather than risk modifying). Background genetic effects (modifier genes), epistasis, somatic variation, and environmental factors all complicate the situation. This is particularly the case in complex, multi-factorial disorders (e.g., cancer, heart disease, diabetes, dementia) that will affect most of us at some stage in our lifetime. Strategies do, however, now exist to study the genetics of these disorders, and such investigations are a major focus of research throughout Europe and beyond. A common thread in these studies is the need to create ever-larger datasets and integrate these more effectively.
Notes and references.
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