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The Illumina approach for gene expression arrays is as follows: an oligonucleotide targeting a single gene transcript is synthesized and conjugated to a micrometer diameter silica bead. In addition an oligonucleotide with a unique sequence (molecular barcode) is also conjugated to the same bead. Millions of beads for thousands of gene targets are synthesized in parallel and then mixed together in equal proportion. Separately, glass slides with silica coating are manufactured and etched with an array of millions of small holes to fit the beads. Beads are spread onto the slides, enter the holes and are held by van der waals forces. The beads are positioned randomly, and each gene is targeted by multiple beads. In gene expression experiments, a fluorescently labeled RNA transcript is then hybridized to the array and signal read by an array scanner. To find the bead to gene correspondence, a clever decoding strategy is used. All beads have a unique barcode, but there are subsequences that are shared between each. One oligonucleotide conjugated to a green dye, and another conjugated to a red dye are hybridized to the array and signal is read. Roughly half of the beads will have signal with green the other half with red. The array is subjected to denaturing conditions to remove the annealed oligonucleotides and the process is repeated with a different pair of green and red strands.
Again, half of the beads will have green or red signal, but the signal may not the same as the previous iteration. For example, a bead may have four signal sequences: red-green, green-red, red-red or green-green. This process divides all beads into four groups. Using successive hybridization cycles, millions of beads can be individually decoded to identify which gene transcript they target. The same method applies for decoding beads in genotyping or methylation assays. The three major applications of the BeadArray platform are for genotyping, gene transcription quantification, and cytosine methylation. As of March 2012, more than 4,000 genotyping samples have been processed with an average call rate of >0.99%. Human genotyping studies are most often performed using the Infinium HD using OmniExpress (750k SNPs) or Omni2.5-8 arrays (2.4M SNPs).
These chips are also capable of copy number variant estimation (CNV). Custom content chips for Genome Wide Association Studies (GWAS) are also available; please contact us with details of your project. See details on all genotyping and CNV arrays from Illumina Learn more about Formalin Fixed, paraffin embedded samples that can be used for genotyping studies using a specialized kit from Illumina [PDF]
Gene expression analysis chips are available for Human, Mouse and Rat; all chips contain all known genes and many regulatory RNAs. As of March 2012, microRNA chips and custom gene expression services have been discontinued by Illumina. Find out more about the composition of gene expression chips Genome-wide methylation scanning in human samples (including stem cells and tumor cells) can be accomplished with the Human Methylation 450K array. This array covers CpG islands, sites known to be methylated in promoters, DNase hypersensitive sites and miRNA promoter regions. Learn more For more information, see details on Illumina’s site or HiScan_iScan-datasheet [PDF].