About the I-DCC consortium
Partner 1. The Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/)
The Sanger Institute is a state of the art research facility, originally established to sequence the human and model organism genomes. It has significant sequencing capacity, performing over 100,000 sequence reactions every day. The Institute has invested heavily in automation which serve it’s sequencing pipeline as well as other activities. The Institute has invested heavily in IT infrastructure and bioinformatics which enable it to handle the upfront and down stream analysis of data associated with high throughput projects and deliver this data at no cost to the global scientific community. The automation for sequencing is being adapted to other projects, such as high-throughput gene trapping and gene targeting programs and this data can be observed in Ensembl.
The Sanger Institute has a wide range of research activities many of which involve genetic analysis in a variety of model systems, such as S. Pombe, C.elegans, zebrafish, mouse and human. Of particular relevance to this project are our investments in mouse genetics which include the recruitment of 6 groups using the mouse as a model organism and the construction of a 25,000 cage mouse facility. The Sanger Institute has established a very successful ES mutagenesis program under the leadership of Bill Skarnes and displays clone resources for mouse knockouts on the Ensembl mouse genome browser.
Principle investigator: Dr. William Skarnes (www.sanger.ac.uk/Teams/Team87/)
Dr. Bill Skarnes is a Wellcome Trust Senior Investigator and head of the ES Mutagenesis team (Team 87) at the Sanger Institute. Dr. Skarnes is the project leader for the Sanger component of the EUCOMM and KOMP high-throughput knock-out programs. Previous to this project, he established the Sanger Institute Gene Trap Resource (SIGTR; www.sanger.ac.uk/genetrap ), an extension of BayGenomics gene trapping program initiated by Dr. Skarnes in 2000 while an assistant professor at UC Berkeley. Dr Skarnes is one of the early pioneers of gene trapping technology and a founding member of the International Gene Trap Consortium (www.genetrap.org/) and a member of the International Mouse Knockout Consortium (IKMC) Steering Committee.
Partner 2. IDG – Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Developmental Genetics (http://www.helmholtz-muenchen.de/)
The Institute of Developmental Genetics, National Research Centre for Environment and Health in Munich/ Neuherberg, is member of the Helmholtz Program ‘Comparative Genome Research for Human Health’. The IDG is part of the National Genome Research Network (NGFN) as headquarter of the German Gene Trap Consortium (GGTC) and the RNAi platform (SMP RNAi) and as partner in the NeuroNet. Furthermore, it is member of the German Mouse Clinic (GMC), of the International Gene Trap Consortium (IGTC), co-coordinator of EUCOMM (European Conditional Mouse Mutagenesis Program) and a member of the International Mouse Knockout Consortium (IKMC) Steering Committee. The institute has at its disposal all the infrastructure and latest equipment necessary to fulfil its tasks in the present project. The Institute has increasingly invested in IT infrastructure and bioinformatics which enable it to handle the analysis of data associated with high throughput projects and delivers this data to the global scientific community. Furthermore, the institute closely cooperates with the IDG – Computing Centre, which provides further state-of-the-art IT equipment and capacities.
Principle investigator: Prof. Wolfgang Wurst (www.gsf.de/idg/groups/neurogenetics/start.html)
Prof. Dr. Wolgang Wurst is Director of the Institute of Developmental Genetics, National Research Centre for Environment and Health (IDG) in Munich/Neuherberg, Professor at the Technical University of Munich and Head of the Research Group ‘Molecular Neurogenetics’ at the Max-Planck-Institute of Psychiatry in Munich. He is coordinator of the German Gene Trap Consortium (GGTC), co-coordinator of EUCOMM, founding member of the International Gene Trap Consortium (IGTC) as well as coordinator of the RNAi platform inside the National Genome Research Network (NGFN; funded by the German Federal Ministry of Education and Research (BMBF)). His main scientific interests concern the application of functional genomic approaches to model diseases, in particular for the identification of molecular networks underlying neurodegenerative, neurodevelopmental and psychiatric diseases.
Partner 3. Fondazione Telethon (www.telethon.it)
Telethon Italy is an Italian charity whose mission is to advance biomedical research towards the diagnosis, cure and prevention of muscular dystrophies and other human genetic diseases. It was founded in 1990 by a patient’s association, the Italian Union for Muscular Dystrophy (UILDM). The initiative was inspired
by- but it is not affiliated with- other Telethon marathons promoted in the USA and France. Telethon Italy focuses on scientific research and does not offer healthcare, material assistance to patients and families or advocacy. It is the second biggest biomedical charity in Italy. As part of its mission, Telethon is also involvedin informing patients’ associations and in raising awareness on the scientific and social issues related to genetics and hereditary diseases.
Since 1991, Telethon Italy has invested 254 million Euros in research and funded 2,080 research projectson more than 400 human genetic diseases, which range from basic research to clinical trials. The research portfolio includes intramural research (performed in three institutes) and extramural research through grants to universities, public and not-for-profit research institutes in Italy.
Principle investigator: Prof. Andrea Ballabio (www.tigem.it/researchers/ballabio/andrea-ballabio.html)
Prof. Andrea Ballabio is director of the Telethon Institute of Genetics and Medicine (TIGEM) and Professor of Medical Genetics of the Federico II University in Naples, Italy. He holds an M.D degree and is board-certified in Pediatrics. He was formerly Associate Professor of Molecular and Human Genetics and Co-Director of the Human Genome Center at Baylor College of Medicine in Houston, TX, USA. He is an EMBO member and former President of the European Society of Human Genetics. His main scientific interests are the identification of the molecular basis and pathogenetic mechanisms of genetic diseases as well as the use of functional genomics in medicine. Dr. Ballabio is also the coordinator of the EURExpress project (www.eurexpress.org).
Partner 4. The European Molecular Biology Laboratory (www.embl.org)
The European Molecular Biology Laboratory is Europe's flagship laboratory for basic research in molecular biology and funded by public research monies from 20 member states and the one associate member. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory operates from five sites: the main Laboratory in Heidelberg, and Outstations in Hinxton [the European Bioinformatics Institute], Grenoble, Hamburg, and Monterotondo near Rome.
The cornerstones of EMBL's mission are: to perform basic research in molecular biology, to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states, to develop new instruments and methods in the life sciences, and technology transfer.
EMBL runs an international PhD Programme with a student body of about 170. The Laboratory also sponsors an active Science and Society programme and welcomes visitors from the press and public.
Principle investigator: Dr. Ewan Birney (www.ebi.ac.uk/~birney/)
Dr Ewan Birney is head of Genome Annotation at the EBI, and leads the EBI half of the Ensembl and Reactome projects. He also runs his own independent research group at the EBI. In total there are 21 scientists at a variety of levels in his group. He is a Senior Scientist of EMBL.
Partner 5: BSRC Fleming – Fleming Biomedical Sciences Research Centre (http://www.fleming.gr/)
The Institute for Immunology at the ‘Alexander Fleming’ Biomedical Sciences Research Centre has been awarded twice in recent years the status of ‘Excellence’ by an international review committee set by the Greek Government to review its progress and future prospects and currently coordinates a European network of excellence (MUGEN) on animal modelling of human immunological diseases. The Institute of Immunology has established the largest operative SPF animal house in Greece (>15,000 mice), runs a microarray unit (headed by the PI), a FACS/FACS sorting facility, a complete mouse histopathology unit and a transgenic and knockout facility.
Vassilis Aidinis' research group (est. 2003) concentrates on molecular, genetic and computational dissection of pathogenetic mechanisms of chronic inflammatory diseases such as rheumatoid arthritis, pulmonary fibrosis and multiple sclerosis. In this context lab expertise include animal modelling, expression profiling with DNA microarrays and related computational tools. Moreover, the lab has recently constructed a number of databases on mutant mouse resources and participates in a number of international efforts towards the interoperability and sustainability of mouse databases, towards the systems biology of the mouse.
Principle investigator: Dr. Vassilis Aidinis (www.fleming.gr/en/investigators/Aidinis/index.html)
Dr. Vassilis Aidinis is a molecular biologist by training, has a sound expertise in animal modelling and expression profiling, has trained numerous students and has participated in several European scientific networks. His team has created MMdb, a database of mutant mice, and Tgdb, a database of Cre-drivers mice and participates in CASIMIR, an EC coordination action on database interoperability and sustainability. Michalis Zouberakis is the lead programmer and Christina Chandras the chief curator of both databases. The Fleming team will coordinate interactions and interoperability of I-DCC ES cells database with the other major European and international mouse databases.
Partner 6: The Jackson Laboratory (http://www.jax.org/)
The Jackson Laboratory (TJL or JAX; www.jax.org), a non-profit institution located in Bar Harbor, Maine, USA, is a world-renowned centre for mammalian genetics. Its main missions are to discover the genetic basis for preventing, treating, and curing human diseases by developing and studying mouse models; and to provide mouse genetic resources, data, and training to the scientific community worldwide. There are 35 research groups all of which are fully dependent on grant funding. A major research area is bioinformatics. TJL hosts several large community databases that are directed by the leader and co-investigators of WP1 (Drs. Ringwald, Bult, Kadin, and Eppig) and that are directly relevant to this project:
The Mouse Genome Informatics database (MGI; www.informatics.jax.org) is the major community resource for mouse data providing integrated access to data on the genetics, genomics, and biology of the laboratory mouse. MGI is a consortium effort of several projects, including the Mouse Genome Database (MGD) project, the Gene Expression Database (GXD) project, the Mouse Tumour Biology (MTB) database project, and the Gene Ontology (GO) project portion at MGI (www.informatics.jax.org/mgihome/projects/aboutmgi.shtml).
Principle investigator: Dr. Martin Ringwald (www.jax.org/staff/martin_ringwald.html)
Dr Martin Ringwald is a molecular biologist and mouse developmental biologist with long-standing experience in bioinformatics. His research during the last 14 years focused on the development of databases that help to understand the complex molecular mechanism of mammalian development. He is the Principal Investigator of the Gene Expression Database (GXD) project and of the KOMP-DCC project. As part of this work, he has established close interactions with the EUCOMM and NorCOMM projects. He is also a member of the International Knockout Mouse Consortium (IKMC) Steering Committee.
Partner 7: MICB - Manitoba Institute of Cell Biology, University of Manitoba (Homepage)
The Mammalian Functional Genomics Centre is located at the Manitoba Institute of Cell Biology (MICB; http://www.EScells.ca). MICB is a joint research institute of CancerCare Manitoba and the University of Manitoba. The Centre is world renowned for its high throughput ES cell mutagenesis capacity and its associated Genetic Modelling Centre is one of the most comprehensive transgenic centres in Canada.
Directed by Dr. Geoff Hicks, the institute is a founding member of the International Gene Trap Consortium (IGTC), the Federation of International Mutant Mouse Resources (FIMRe) and is the lead institution for the North American Conditional Mouse Mutagenesis Project (NorCOMM), a founding member of the International Mouse Knockout Consortium (IKMC). The institute has all the informatics infrastructure required to meet the goals described in the present project, notably a dedicated bioinformatics team, infrastructure for high throughput data handling capacity, and a strong track record of providing resource access to the scientific community at large. The Institute has increasingly invested in IT infrastructure and bioinformatics which enable it to handle the analysis of data associated with high throughput projects and delivers this data to the global scientific community. In addition, the institute has already established strong collaborative interactions with the Wellcome Trust Sanger Centre, the IDG, and the KOMP Data Coordination Centre.
Principle investigator: Dr. Geoff Hicks (http://www.umanitoba.ca/faculties/medicine/units/physiology/contacts/hicks.html)
Dr. Geoff Hicks is the Director of the MICB Mammalian Functional Genomics Centre; Senior Investigator of the Manitoba Institute of Cell Biology; Associate Professor of Biochemistry & Medical Genetics, Faculty of Medicine, University of Manitoba; and hold the Canada Research Chair in Functional Genomics. Notably to this proposal, Dr Hicks is the Lead Principal Investigator of the Genome Canada funded NorCOMM project, founding member of the IGTC, and Scientific Member of the International Mouse Knockout Consortium (IKMC). His main research interests focus on the development of mouse models of human disease with a special emphasis on cancer. He is the Scientific Director of the University of Manitoba’s Genetic Modeling Centre and the designated Director of the Canadian Mouse Consortium.
