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Sequencing and Genotyping platforms of the CEA Institute of Genomics

The F.Jacob Institute of Biology of the CEA (French Commission for Atomic Energy and Alternative Energies) brings together two national research centres, the Genoscope (French National Sequencing Centre) and the CNRGH (French National Research Centre for Human Genomics).

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Expertise
Genoscope focuses on the study of biodiversity, in particular de novo sequencing of large whole genomes, complex metagenomes and more generally collections of DNA that require a large-scale sequencing approach.

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The CNRGH, in contrast, focuses on human genetics, including large-scale genotyping, resequencing, transcriptomics and epigenomics, for the identification and analysis of variants associated with major diseases or with rare diseases..

Equipment
Genoscope
- Sequencers : 1 NovaSeq Illumina, 2 HiSeq 4000 Illumina, 2 HiSeq 2500 Illumina, 2 MiSeq Illumina, 6 MinION Oxford Nanopore Technologies, 1 PromethION Oxford Nanopore Technologies
- Optical mapping : 1 Irys Bionano Genomics, 1 Saphyr Bionano Genomics
- Robotics : 3 Biomek FXP Beckman Coulter, 2 Freedom Evo Tecan, 1 Liquid Handling Station Brand
- DNA Fragmentation : 1 E220 Covaris, 1 Megaruptor Diagenode

CNRGH
- Sequencing : 1 NovaSeq Illumina, 5 Hiseq X Illumina, 1 HiSeq 4000 Illumina, 3 HiSeq 2500 Illumina, 1 NextSeq5000, 2 MiSeq Illumina, 8 MinION Oxford Nanopore Technologies, 1 Promethion Oxford Nanopore Technologies, 1 Proton Ion Torrent, 1 PGM Ion Torrent
1 Chromium 10X Genomics
- Robotics : 4 Bravo-Working Station Agilent, 7 Freeddom Evo Tecan, 3 Janus Perkin Elmer,1 Zephyr Perkin Elmer, 3 Sciclone NGSx Perkin Elmer, 1 Epimotion Qiagen
- DNA Fragmentation : 1 E220 Covaris, 1 LE220 Covaris
- Genotyping : 3 iScan Illumina
- Automated DNA extraction : 1 Autopure LS Qiagen

Computer tools
80 computing servers, including one with 1 TB of RAM, NAS storage 1 PB (Netapp+Isilon), robotic backup and archiving to LTO4 and LTO5 storage cartridges.

To undertake its projects, the Institute of Genomics relies on major resources and expertise in bioinformatics and bioanalysis (LIS and LABIS, MicroScope platform), which are an integral part of the Institute’s platforms and capacity, are which are also made available to the scientific community.

Main achievements
Genoscope played a key role in the Human Genome Project (Chromsome 14). Genoscope has also been involved in the sequencing of plants (algae, vine, banana, thalecress, rice, cocoa), animals (tetraodon, anopheline) and fungi (truffle, rapeseed fungal pathogen, Leptosphaeria maculans), and has sequenced more than 50 prokaryotic genomes. In addition, Genoscope has provided services to more than 650 projects submitted by the national scientific community. Genoscope’s research projects focus on environmental microbial genomics : marine protists (TARA Oceans project) and bacterial flora in the human gastrointestinal tract and bacterial flora in water treatment processes.
The CNRGH participates in large European research programmes for technological development and also for disease studies. CNRGH has been involved in large national programmes such as the “Alzheimer programme”, funded by the Alzheimer Foundation and backed by INSERM (National Institute for Health and Medical Research). The CNRGH teams have undertaken more than 200 research projects for around 300 French laboratories and for more than 60 laboratories internationally. Globally, the activities of CNRGH have resulted in more than 500 publications since its creation.

Certification / Quality Assurance
Laboratory Information Management System (LIMS) dedicated to the different platforms of the facility, and automated primary analysis pipelines with integrated QC systems.

Platform Managment
Arnaud Lemainque (Genoscope)
Anne Boland (CNRGH)

CEA / DRF / Institut de Biologie F.Jacob (Genoscope & CNRGH)
2 rue Gaston Crémieux
CP5706
91057 Evry cedex (France)

Contacts
alemainque@genoscope.cns.fr
boland@cng.fr

For further information :
www.genoscope.cns.fr (Genoscope)
www.cng.fr (Centre National de Recherche en Génomique Humaine)

last update : 2018


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