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Production Platforms in Human Genomics (L2PGH)
Responsible : Céline BesseE-mail: besse[at]cng.fr
In April 2004, the CNRGH was one of the first sites to set up single-nucleotide polymorphism (SNP) analyses on a totally automated Illumina platform. The 'Beadlab' consists of a distinct PRE-PCR laboratory and POST-PCR laboratory with independent ventilation and air-conditioning systems. The Beadlab is currently equipped with 6 Tecan automated pipetting systems and 3 iScan systems +.
Scanner slide reading
Four technicians work in the 2 laboratories under the supervision of the platform manager. The stages of the 'Infinium Assay' protocol are totally tracked by a laboratory-information management system (LIMS) from the DNA plate through the automated stages to reading on the scanners. The data generated are verified by the quality control team contributing to the generation of very high quality phenotypes. The slide processing time is 3 days, including the hybridization stage which is conducted overnight. Several batches of 96 DNA samples are processed concomitantly each day.
The current throughput is 1200 DNA samples per week, equivalent to the production of over 2,000,000,000 genotypes per week.
The whole-genome analysis technology 'Infinium Assay' is based on hybridization of the DNA with magnetic beads placed on a slide and on the elongation of a single specific base complementary to the allele under study. At the CNG, we use 'high-density' slides (~250 K to 5 M markers): Human Core, OmniExpress, Omni 2.5 and Omni 5.0. The preselected SNP throughout the whole genome are used for association studies and studies of copy number variability.
CEA is a French government-funded technological research organisation in four main areas: low-carbon energies, defense and security, information technologies and health technologies. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world.