In response to user needs, CIGENE has acquired a high-throughput genotyping platform from Affymetrix. At our facility we have two state-of-the-art four color Affymetrix GeneChip Scanners 3000 (7G-Plus; each with 48-position autoloaders), three FS450 Fluidics Stations, two GCOS and one GTGS workstations, dedicated pre- and post-PCR laboratories, and the full suite of software and hardware (coupled to our existing robotics and LIMS systems) required for most Affymetrix GeneChip applications.
Affymetrix product lines support both DNA analysis (whole genome, targeted genotyping, and sequence analysis) and expression analysis (quantitation, regulation); a detailed list of Affymetrix application areas is available at www.affymetrix.com. However as a FUGE core facility CIGENEs primary responsibility is for SNP genotyping; whole genome mapping, and targeted genotyping.
At CIGENE we have experience running human GeneChip Mapping Arrays (available with 100K, 250K, and 500K SNPs). With the largest of these well-validated, high-coverage arrays it is possible to process 96 samples per day and generate 48 million genotypes, in a process requiring no more than 500ng DNA per sample. This is a very competitive technology for conducting large-scale linkage and association studies, and analyzing copy number variation. Affymetrix expect to release a 1000K SNP array in the first quarter of 2007.CIGENE is presently the only facility in Europe to possess four-color GCS3000 7G-Plus scanners which places us in a unique position to offer users Targeted Genotyping employing the Molecule Inversion Probe (MIP) technology. After identifying SNPs of interest in whole genome association or linkage studies, researchers can design customized SNP assay panel to genotype 3, 5, 10 or 20K SNPs in a single sample. The utility of this approach is that it is performed on a focused selection of investigator defined, rather than supplier defined, SNPs thereby facilitating candidate gene analysis and fine mapping. CIGENE has good experience running 25K Bovine Targeted Genotyping and is indeed the only customer worldwide to have access to this, the largest Targeted Genotyping panel released by Affymetrix.