Commissariat á l'Energie Atomique, Evry, France
The Centre National de Génotypage (CNG) was created in 1999 with the objective to establish national and international collaborations with the scientific community for the identification of the genetic basis of disease. The CNG is organised around a series of integrated platforms that implement a wide-range of technologies and methods for identification of biomarkers of disease and other phenotype traits. A biological banking facility manages a working archive of more than 600.000 biological samples, and annually undertakes preparation and quality control of more than 50.000 biological samples for analysis. Genomic analysis platforms include high-throughput genotyping, sequencing and proteomics with rigorous quality control procedures, and laboratories for functional analysis and bioinformatics. The CNG develops and applies MS-based proteomics analysis. The overall operation is supported centralised quality control, computerised sample tracking (LIMS), technology development, bioinformatics and statistical analysis. With this operation, the CNG has in the last ten years contributed to more than 300 collaborative projects resulting in over 400 publications. The CNG participates in many EU- funded projects, and co-ordinates the EU FP7 large-scale projects READNA (on new-generation sequencing) and CAGEKID (renal cancer genomics).
Our activities focus on sensing the physical world and transforming raw data into predictive insights. Sensor based technologies are distinctly interdisciplinary. They cover not only new transducers (diamond, imaging devices, particle detectors) and their front-end electronics, but also a wide range of computing topics in the fields of applied mathematics (signal and data analysis, spectrum analysis, statistics, Bayesian methods, data mining, image and multidimensional objects processing) and physics (particle-matter interactions simulation and experimentation). Our integrated systems can be found in security, defense, nuclear, health care, environment and various manufacturing industries.
The « Institut de Recherche sur les lois fondamentales l'Univers » (IRFU) is one of the institutes of « Direction des Sciences de la Matière » (DSM) of the « Commissariat à l'Energie Atomique » (CEA). The approximately 250 IRFU researchers stemming from three disciplinary fields, astrophysics, nuclear physics and particle physics, approach in a complementary way the big questions on the fundamental laws of the universe:
- What are the elementary mater constituents of the universe?
- What is the energetic content of the universe?
- How has the universe been structured from the Big-Bang to the planets?
- How do the nuclear matter constituents organize themselves?
These fundamental questions are investigated through the involvement of IRFU in large international experiments at LHC (ATLAS, CMS, ALICE), at GANIL or in large space experiments (HERSCHEL, PLANCK, JWST, EUCLID).
Whatever the scale of the observed phenomena is, small or large, the exploration of the universe is still related to the production and detection of radiations. Therefore, IRFU is organized around a strong technical support staff of 400 engineers and technicians which participate to the conception and development of large cryogenic magnets, particle accelerators, complex detection systems or space craft lunched experiments.
The simulation and the data analysis are crucial components for the scientific return over investment into experiments. IRFU has therefore invested into the grid research and development EGEE European program since more than 10 years. It is one of the founders of the GRIF project which is one of the large Tier2 centres of the LHC grid. Actually GRIF-IRFU is hosting around 2200 cores and 1PetaByte of storage. The Irfu node is open to a large number of HEP (High Energy Physics) communities as well as bio-informatics, thermonuclear fusion, nuclear physics and astro-particle communities. The Grid resource is completed by an interactive cluster running final analysis tasks on grid subsample data stored on a GPFS SAN system.
IRFU is also strongly involved in large scale massively parallel simulation in astrophysics and in sophisticated image treatment for which IRFU obtained this last year two starting grants and one advanced ERC grant. IRFU is therefore hosting an HPC cluster used for post-treatment of large simulations run at national and international HPC simulation resources as well as for the development and testing of such software. This equipment is completed by a cluster devoted to data final treatment of spacecraft mission like HERSHELL and PLANK. The data are stored on dedicated a GPFS SAN system.
Both for space mission image treatment and for QCD simulations, IRFU has started since three years to use GPU technologies to speed up the HPC simulation whenever possible. A small cluster of four times three CPU+GPU is used for our participation into the PETAQCD R&D program. Another CPU+GPU is devoted to development of image treatments in frame of the COAST project.
Within CEA, the Laboratory for Electronics & Information Technology (CEA-Leti) works with companies in order to increase their competitiveness through technological innovation and transfers. CEA-Leti is focused on micro and nanotechnologies and their applications, from wireless devices and systems, to biology and healthcare or photonics. The CEA-Leti is a key player of the MINATEC and NanoBio campuses. With 1,400 employees, CEA-Leti trains more than 190 Ph.D. students and hosts 200 assignees from partner companies. Strongly committed to the creation of value for the industry, CEA-Leti puts a strong emphasis on intellectual property and owns more than 1,700 patent families.
Within CEA-Leti, the Department Technologies for Biology and Health (DTBS) regroups 200 researchers and engineers. It focuses on the development for micro-nanotechnologies for applications in the fields of diagnostics, health care, life science and environment. At the frontier between micro nanotechnonologies and biology, R&D activities aim at developing highly parallel and miniaturized devices as well as highly integrated portable systems, such as wearable biosensors. The DTBS's key competencies are micro machining, microfluidics, surface chemistry, integrated optical detection, electronics, signal processing and information analysis but more so in there integration in a final system, comprising a sensor, its front end hardware, embedded data processing and RF link. The DTBS has several industrial collaborations, in particular a joint research team with BioMérieux in the diagnostic field. The Leti has already accumulated significant instrumentation know-how through several micro-biochip and biosensors industrial projects. Facilities includes a clean room for biological microsystem development, a clean room specifically dedicated to Biochip packaging, a biological and chemical laboratory as well as specific equipment in biosensor design, manufacturing and characterization.
Mark Lathrop is the scientific director of the Centre National de Génotypage (CNG) and the Fondation Jean Dausset - Centre d'Etude du Polymorphism Humain (CEPH), major laboratories providing infrastructure for large-scale studies in biomedical and other life-sciences fields. Dr. Lathrop has coordinated several large-scale public and public/private consortia tackling projects in human genetics and medical genomics. He is responsible for large-scale programmes in cancer genomics in France and Europe conducted as part of the International Cancer Genome Consortium. Other areas in which he plays in international initiatives include asthma genetics (e.g. EU FP6 Gabriel consortium), Alzheimer's disease (IGAP) and cardiovascular disease (e.g. EU FP6 Procardis).
Profiles of staff members
Key people at the CNG are Dr. Mark Lathrop (Head of the Institute), Dr. Jörg Hager (Head of Genetics and Functional Genomics Discovery), Dr. Diana Zelenika (Programme Manager), Dr. Jörg Tost (Group Leader Epigenetics group), Dr. Susanne Schwonbeck (Proteomics), Dr. Marie-Therese Bihoreau (Head of Genomic Platforms) and Mario Foglio (Head of Bioinformatics). The CNG has approximately 100 staff with a distribution of females to males of 60:40 overall and 50:50 on the level of scientists.
Nora Benhabiles holds a Ph. D. in Molecular Biophysics from Paris 6 University (Paris, France) and an Executive MBA from IESE (Barcelona, Spain). She worked on in silico protein folding (ab initio, threading, homology), force field optimization/molecular dynamic studies, in silico DNA desolvation, bioinformatics platform development, omics analysis, data integration, biomarker discovery (cancer, metabolic syndrome associated diseases) and modelling with systems biology approaches. Among former positions in Europe, she was head of the bioinformatics and IT department in a biotech developing drugs for cardiovascular related diseases (France), Visiting Professor of Biomedicine in the Katholieke Universiteit of Leuven (Belgium) and worked on the launch of a startup project related to blood biomarkers and diagnostics (France & Spain). She is in a FP7-Health evaluation committee in systems biology in the European commission (2011, 2012) and vice president of Emergence committee in the French National Research Agency ANR (president health sub-section, 2012).
Since 2011, she is managing the business development for the health activities in the Department Sensor Signal and Information (DCSI) of the List institute in CEA Saclay (France).
Laurent DISDIER is graduated from the engineering school INPG (Institut National Polytechnique de Grenoble) and hold a Ph. D. in Photonic science from Paris 11 University (Paris, France). He is employed by Commissariat à L'Énergie Atomique in France where he is leading a division (150-personnes) that works for system and technology dedicated to measurements. The activities cover not only new transducers (diamond, imaging devices, and particle detectors) and their front-end electronics, but also a wide range of computing topics in the fields of applied mathematics (signal and data analysis, spectrum analysis, statistics, Bayesian methods, data mining, image and multidimensional objects processing). In the past, he worked in field of Inertial Confinement Fusion (ICF), specializing in the areas of fusion-plasma diagnostics. In particular, He had a key role in the neutron-imaging diagnostic, which is designed to show the spatial distribution of the thermonuclear burn. In a joint effort collaboration between CEA and the 3 US-national laboratories (LLE, LNLL and LANL), he install a development platform and test some innovative concept on the diagnostic components.
Dr. Raymond Campagnolo received his Engineer degree in 1976 from Ecole Nationale Supérieure d'Electronique et Radio Electricité de Grenoble (France) and his PhD. degree of Doctor from the Institut National Polytechnique de Grenoble (France). In 1982, he received the George Von HEVESY Prize for Nuclear Medicine for its contribution to the Time Of Flight Information to POSITRON TOMOGRAPHIC IMAGING. He was lab manager of the Electronic & Biology Laboratory at CEA-LETI, focusing on the development of dedicated instrumentation for fluorescent measurements in the field of DNA biochip and Lab-On-Chip using detection technologies for micro-capillaries. He was associated manager of the joint team between CEA-LETI and the French company bioMérieux (World leader of microbiology bacterial identification and antimicrobial susceptibility testing system). Since 2006, he is Scientific Program Manager in the field of Implantable Medical Devices at CEA-LETI in the Microtechnologies for Biology and Healtcare Department (DTBS). He is currently involved in R&D in the area of electrochemical detection in micro-fluidic sensors and electrical interaction of microsystems with tissues for In vitro and In vivo applications (implantable and wearable sensors)
Recent publications relevant to the project
1. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, von Mutius E, Farrall M, Lathrop M, Cookson WOCM. A GABRIEL consortium large-scale genome-wide association study of asthma. New Eng J Med 363:1211-1221, 2010.
2. Reeves GK, Travis RC, Green J, Bull D, Tipper SJ, Baker K, Beral V, Peto R, Bell J, Zelenika D, Lathrop M, Risk of breast cancer and its subtypes in relation to individual and multiple genetic susceptibility loci. JAMA 304:426-34, 2010.
3. Travis RC, Gillian K. Reeves GK, Green J, Bull D, Tipper SJ, Baker K, Beral V, Peto R, Bell J, Zelenika D, Lathrop M, Systematic investigation of gene-environment interactions among 7610 women with breast cancer in the Million Women Study. Lancet 375:2143-51, 2010
4. Cookson W, Liang L, Abecasis G, Moffatt M and Lathrop M, Mapping complex disease traits with global gene expression. Nat Rev Genet, 10: p. 184-94. 2009.
5. Lambert JC, Heath S, Even G, Campion D, Sleegers K, Hiltunen M, Combarros O, Zelenika D, Bullido MJ, Tavernier B, Letenneur L, Bettens K, Berr C, Pasquier F, Fievet N, Barberger Gateau P, Engelborghs S, De Deyn P, Mateo I, Franck A, Helisalmi S, Porcellini E, Hanon O, de Pancorbo MM, Lendon C, Dufouil C, Jaillard C, Leveillard T, Alvarez V, Bosco P, Mancuso M, Panza F, Nacmias B, Bossu P, Piccardi P, Annoni G, Seripa D, Galimberti D, Hannequin D, Licastro F, Soininen H, Ritchie K, Blanche H, Dartigues JF, Tzourio C, Gut I, Van Broeckhoven C, Alperovitch A, Lathrop M and Amouyel P, Genome- wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat Genet, 41: p. 1094-9. 2009.