This particular gene chip (BeadChip) is produced by the San Diego-based company Illumina, which develops and manufactures platforms for the analysis of genetic variation and biological function for the rapidly growing sequencing, genotyping and gene expression markets.
A BeadChip is a ~30 x100 mm silica slide containing twenty-four arrays, each allowing for genotyping of a single biological sample. Each array contains a very large number of microscopic microwells etched into the surface of the slide. The microwells (<3 micrometer in diameter, 3 micrometer deep) are uniformly spaced across the silica surface, i.e., each array contains more than 0.5 million about microwells. The microwells are filled with tiny silica beads (one type per well) held to the wells by non-covalent forces. Each bead is covered with hundreds of thousands of copies of a known short nucleotide sequence (50 nucleotides long). In addition, each bead also contains an address sequence that allows for decoding, once beads have been randomly distributed across the chip wells. The design allows for 3,000 to 90,000 bead types, each of which represents one single nucleotide polymorphism (SNP) to be analysed.
The assay is based on genomic DNA that is extracted from blood samples. The DNA is amplified, fragmented, precipitated and resuspended before being loaded onto the BeadChip for hybridization with the short nucleotide sequences on the beads. After hybridization, the chip is washed to remove unhybridized or non-specifically bound DNA. Then fluorescently labeled nucleotides are added to extend the hybridized DNA that thus act as primers. Finally, the chip is coated for protection against photo bleaching. Following coating, the chip must be scanned immediately. If necessary, the chip can be stored for up to 72 hours in a dark vacuum with minimal signal loss.
It was our senior curator Bente Vinge Pedersen who suggested we could use one of the chips left over from the ‘Genomic Enlightenment’ art installation earlier in the spring:[biomed]ypr22zGPH-o[/biomed]
(see also the video from the installation work here; more about the ‘Genomic Enlightenment’ installation in a later post).
And here’s a larger image of the piece: