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  • High Throughput Platform - Sequencing
    machines of last generation the laboratory runs 1 Hiseq 4000 and 3 HiSeq on 2500 besides the X Five system dedicated to whole genome sequencing Seven technicians assure the production 24h 7 days per week Our sequencing projects are focused on whole genome sequencing targeted re sequencing gene regulation and epigenetic sequencing RNASeq Stranded RNASeq ChIPSeq MeDIP BiSeq small RNA With our in house developed LIMS Laboratory Information Management System the tracking of high number of samples is guaranteed The software allows an automated workflow and includes the quality control from sample preparation to generated sequence analyses Reagent tracking with the LIMS Laboratory PRE PCR Laboratory POST PCR The sequencing platform is separated in dedicated PRE and POST PCR areas For the main applications the sample preparation is automated 2 Sciclone NGSx and 1 Bravo Workstation In the Post PCR laboratory the samples are hybridised onto the Flowcell glass support for sequencing reaction using the cluster station cBot cBot cluster stations Clusterisation step for FC 2500 The cBot cluster station needs four hours for the preparation of a Flowcell Fully automation allows overnight runs and consequently an increase of productivity Flowcell loading Data image acquisition The HiSeq can run two

    Original URL path: http://www.cng.fr/en/organisation/laboratories/haut_debit/sequencing/index.html (2016-01-29)
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  • High Throughput Platform
    Publications Marie Thérèse Bihoreau obtained a Ph D in Endocrinology and Development at the University Pierre and Marie Curie Paris VI After a post doc at McGill University in Montreal Canada and at INSERM U299 for developing a blood substitute she worked several years at the Wellcome Trust Centre for Human Genetics in Oxford United Kingdom In charge of the development of genetic resources for the rat genome RH map

    Original URL path: http://www.cng.fr/en/organisation/laboratories/haut_debit/bihoreau_cv_en.html (2016-01-29)
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  • CNG - PROGRAMMES
    Organisation FONDATION JEAN DAUSSET CENTRE D ETUDE DU POLYMORPHISME HUMAIN FONDATION RUE JULIETTE DODU PARIS 10 FRANCE Web site https www cng fr cagekid Project description The International Cancer Genome Consortium ICGC has the goal of obtaining a comprehensive description of genomic transcriptomic and epigenomic changes in 50 different tumour types and or subtypes with the aim of elucidating the genomic changes present in the many forms of cancers that contribute to the burden of disease throughout the world We present a proposal for a European contribution to this effort through application of state of the art approaches to the genomics of the most common form of renal cell cancer RCC RCC is of particular importance within Europe where the highest global incidence rates are observed Disease incidence has increased over the last two decades and it is now the 8th most common cancer in the EU CAGEKID brings clinical and epidemiological resources that are unique worldwide together with the necessary genetics and genomics expertise required for this effort In the first phase of the study we will provide a full genomic characterisation of 100 matched pairs of DNA extracted from the tumour and constitutional samples DNA will be completely sequenced and the data brought together with those from whole genome transcript and methylation analyses Follow up studies of potential targets will be made in further samples The results acquired will be relied to targeted protein analyses The primary data will be made available to the scientific community and the programme will contribute to establishing norms for the manipulation and storage of biological samples CAGEKID will provide the first systematic analysis of this tumour site providing new insights into disease aetiology with application for diagnosis and treatment It addresses a major need to identify new biological markers for renal cell

    Original URL path: http://www.cng.fr/en/projects/fp7_cagekid.html (2016-01-29)
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  • CNG - PROGRAMMES
    inadequate and we do not have sufficient tools to predict disease progression or response to current or future therapies Our consortium Airway Disease PRedicting Outcomes through Patient Specific Computational Modelling AirPROM brings together the existing clinical consortia EvA FP7 U BIOPRED IMI and BTS Severe Asthma and expertise in physiology radiology image analysis bioengineering data harmonization data security and ethics computational modelling and systems biology We shall develop an integrated multi scale model building upon existing models This airway model will be comprised of an integrated micro scale and macro scale airway model informed and validated by omic data and ex vivo models at the genome transcriptome cell tissue scale and by CT and functional MRI imaging coupled to detailed physiology at the tissue organ scale utilising Europe s largest airway disease cohort Validation will be undertaken cross sectionally following interventions and after longitudinal follow up to incorporate both spatial and temporal dimensions AirPROM has a comprehensive data management platform and a well developed ethico legal framework Critically AirPROM has an extensive exploitation plan involving at its inception and throughout its evolution those that will develop and use the technologies emerging from this project AirPROM therefore will bridge the critical gaps in our clinical management of airways disease by providing validated models to predict disease progression and response to treatment and the platform to translate these patient specific tools so as to pave the way to improved personalised management of airways disease Participants THE UNIVERSITY OF NOTTINGHAM NOTTINGHAM UNITED KINGDOM HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH NEUHERBERG DEUTSCHLAND COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES PARIS 15 FRANCE KAROLINSKA INSTITUTET STOCKHOLM SVERIGE ACADEMISCH MEDISCH CENTRUM BIJ DE UNIVERSITEIT VAN AMSTERDAM AMSTERDAM NEDERLAND THE UNIVERSITY OF WARWICK COVENTRY UNITED KINGDOM UNIVERSITE DE LA MEDITERRANEE D

    Original URL path: http://www.cng.fr/en/projects/fp7_airprom.html (2016-01-29)
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  • CNG - PROGRAMMES
    OF EXETER Northcote House The Queen s Drive EXETER UNITED KINGDOM Web site http www ceed3 org Project description CEED3 Collaborative European Effort to Develop Diabetes Diagnostics has as its central objective the development of diagnostic tools to differentiate specific subgroups of diabetic patients to allow individualization of patient care CEED3 will achieve this by integrating basic science findings from animal models cell studies and large scale genetic studies with clinical observations and testing of patients phenotype The development of diabetes diagnostic tools will involve a clearly defined process of discovery of potential novel genetic and non genetic biomarkers validation within test and population based data samples development of a clinical application and then dissemination of this application The areas of focus for the diabetes diagnostics will be three areas where there is potential for considerable improvement in care and reduction in the burden of diabetes the identification of patients with specific subgroups of monogenic diabetes the identification of non diabetic and diabetic subjects with initial pancreatic beta cell dysfunction at high risk of rapidly deteriorating glycaemia and the detection of diabetic patients at increased risk of vascular complications For each of these patient groups the identification of the subgroups

    Original URL path: http://www.cng.fr/en/projects/fp7_ceed3.html (2016-01-29)
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  • CNG - PROGRAMMES
    The mission of CHeartED is to identify genetic and environmental pathways that can be modified with the goal of reducing preventable CVM incidence Epidemiological studies have shown that the stress of maternal hypo or hyperglycemia increases the incidence of CVM We plan a genetic association study in individuals with and without CVM born to diabetic mothers to test whether genetic variants are associated with CVM A similar study without prior risk hypothesis addresses tetralogy of Fallot a CVM which requires surgery in early life These studies will reveal common genetic variants associated with CVM and thus add to existing knowledge on the aetiology of CVM Moreover the identification of genetic factors that differ in the context of maternal diabetes will disclose any associations in genetic pathways influenced by environmental factors RNA expression studies in the mouse to identify new genes and pathways involved in outflow tract malformations and maternal diabetes associated with CVM will complement the human studies Finally we will develop a 3D atlas of gene expression patterns and cardiac morphology at key developmental stages that will serve as a morphological framework Central to our proposal is the development of a bioinformatics tool complemented by an open access Wiki based database The bioinformatics tool will combine the sequence data and expression data generated by the human and mouse studies with morphology and literature to prioritize genes and generate hypotheses The Wiki which will contain existing and new genetic and environmental knowledge on heart development will be an aid for many groups working on cardiovascular development and a novel means of disseminating our findings In a major effort to tackle the underlying biological and genetic questions our project has formulated four work themes bringing together existing and novel knowledge on the environment and its interaction with genetic factors in causing

    Original URL path: http://www.cng.fr/en/projects/fp7_chearted.html (2016-01-29)
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  • CNG - PROGRAMMES
    INFRAQTL MADO Other Programmes France Japan Programme Franco croatian coop PHENOGENE EFRAIM Mechanisms of early protective exposures on allergy development Coordinator Contact Person VON MUTIUS Erika Professor Tel 49 8951602709 Fax 49 8951604452 Email Contact Organisation LUDWIG MAXIMILIANS UNIVERSITAET MUENCHEN Geschwister Scholl Platz 1 MUENCHEN GERMANY Web site http www efraim online com Project description Allergy has developed into a major health concern in Europe Allergic diseases can currently be managed effectively but not cured The onset of allergies stars early in life and there is increasing evidence that exogenous factors affecting the incidence of these illnesses exert their effect early in life in part even prenatally The highly interdisciplinary EFRAIM project will prospectively investigate the main protective factors in early life influencing the development of allergies in birth cohorts conducted in allergy protective environments in five European countries These birth cohorts have been enrolling over 1 000 children and have collected detailed information on the onset of allergic illnesses objective measures of allergies and a vast amount of information about a number of environmental exposures Large biobanks with a variety of biological samples have been established In the EFRAIM project particular attention will be given to the potential role

    Original URL path: http://www.cng.fr/en/projects/fp7_efraim.html (2016-01-29)
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  • CNG - PROGRAMMES
    The objective of this project is the integration of world class high throughput sequencing and genotyping facilities that will provide sequencing and genotyping technologies and data analysis methodologies to the scientific community The European Sequencing and Genotyping Infrastructure ESGI will enable external users to generate data rapidly and to acquire knowledge efficiently By providing access to the ESGI facilities in order to benefit from the sequencing and genotyping technologies there will be an outreach and sustainable impact for the scientific community in the area of biological and medical research to generate new knowledge The ESGI will optimise European research programs and foster transnational collaborations In general the ESGI will defragment and thereby strengthen the European research capacities in genetics and genomics and improve the knowledge transfer from large genomics centres among themselves and to external expert groups or scientists who are focusing on specific research questions Our aim is to apply and improve new high throughput nucleic acids analysis technologies for a broad range of genetic and systems biology studies using well phenotyped samples for example those derived from standardised European biobanks and animal facilities In particular massively parallel sequencing technologies are essential components of modern biomedical research and are

    Original URL path: http://www.cng.fr/en/projects/fp7_esgi.html (2016-01-29)
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