The Genomics platform (PF1) is dedicated to the development and use high throughput technologies for genomic studies. It is involved in projects centered on model microorganisms, pathogens mainly, bacterial, fungi and yeasts species. PF1 has the IBiSA label (IBiSA: Infrastrutures en Biologie Santé et Agronomie created in may 2007).

In mid 2008, the Pasteur Genopole acquired a next generation sequencing machine (Illumina Genome Analyzer) which allows the production of millions of short reads (from 36 to 100 bases) in a single run. This equipment was shared with the Transcriptome and Epigenome Platform (PF2). High throughput sequencing (HTS) is replacing the Sanger sequencing approach for applications such as resequencing of whole genomes allowing to identify single nucleotide polymorphism (SNP) and indels. In 2009, the HTS approach has become a central component of the activity of the platform. During the last two years, PF1 has been involved in more 15 HTS projects focused on microorganism studies. PF1 performs the first level analysis (reports quality control of the run) but also mapping of the sequences on the reference genome, detection of SNPs and de novo assembly.

Due to the continuing growing demand, the GAIIx has been replaced by an Illumina HiSeq2000 in September 2010. This HTS technology requires an adapted information technology infrastructure, both for data management and for data analysis. PF1 benefits of the support of the local computer team (Systems and Network Group) of Institut Pasteur for the network and carries on a collaboration with the “Biological Software and Databases” Group for installation and testing the data analysis software required by this technology.

Since July 2008, High Throughput Synthesis of Long Oligonucleotides Platform has been attached to PF1. Synthesize oligodeoxynucleotides modified in the 5' and/or 3' end by different fluorophores, quenchers (molecular beacons), by amino-alkyl groups or by modified bases through out the sequence is maintained.

Short RNA and siRNA sequences can be made too.

Since 2009, PF1 carried on its close collaboration with the CIP in an European project, EMbaRC having in charge a research workpackage (JRA2-Exploring new approaches in species identification) in this project. EMbaRC is an EU project funded under the Seventh Framework Programme Research Infrastructures (INFRA-2008-1.1.2.9: Biological Resources Centres (BRCs)) for microorganisms.

PF1 aims at grouping state-of-the-art equipment and corresponding technical and methodological processes to fufill the needs of the research teams of Institut Pasteur and its International Network in the field of sequencing projects.

Keywords: second generation sequencing, genomics

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