Chemistry for Sequencing
Illumina’s sequencing by synthesis (SBS) technology is the most successful and widely-adopted next-generation sequencing platform worldwide. TruSeq technology supports massively parallel sequencing using a proprietary reversible terminator-based method that enables detection of single bases as they are incorporated into growing DNA strands. A fluorescently-labeled terminator is imaged as each dNTP is added and then cleaved to allow incorporation of the next base. Since all four reversible terminator-bound dNTPs are present during each sequencing cycle, natural competition minimizes incorporation bias. The end result is true base-by-base sequencing that enables the industry’s most accurate data for a broad range of applications. See a video of Illumina sequencing technology in action.

Applications for Sequencing
SBS technology supports both single read and paired-end libraries. It is the only platform that offers a short-insert paired-end capability for high-resolution genome sequencing as well as long-insert paired-end reads using the same robust chemistry for efficient sequence assembly, de novo sequencing, large-scale structural variation detection, and more. The combination of short inserts and longer reads increase the ability to fully characterize any genome. A wide array of available sample preparation methods serve to enable diverse applications, including: whole-genome and candidate region resequencing, transcriptome analysis, small RNA discovery, methylation profiling, and genome-wide protein-nucleic acid interaction analysis.

Illumina’s BeadArray Technology is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in one of Illumina’s assays. BeadArray technology is utilized in Illumina's iScan System for a broad range of DNA and RNA analysis applications. The original Infinium II Assay was great, but Infinium HD is remarkable. Most samples have an average call rate of 99.9% off the shelf, which makes downstream curation of data a whole lot easier. For those who aren’t curating their data, there's much less downstream work because there is less likelihood of false positives and negatives due to the higher sample call rates. In addition to data quality, the ability to run four samples per chip clearly gets to the answers a lot faster.

BeadArray technology is deployed on either of two multi-sample array formats for DNA or RNA-analysis applications. With multi-sample BeadChip formats, uniform pits are etched into the surface of each substrate to a depth of approximately 3 microns prior to assembly. Beads are then randomly assembled and held in these microwells by Van der Waals forces and hydrostatic interactions with the walls of the well.

The Universal BeadChip format is used in Illumina's GoldenGate Genotyping and Focused Arrays applications. The BeadChip format is used in Illumina's Infinium Genotyping, DASL Gene Expression, and Focused Arrays applications.