Illumina officially entered the next-gen sequencing market with their acquisition of Solexa in late 2006. Despite not being the first to market, this platform has become the dominant next-gen sequencing technology. The workflow involves the use of bridge amplification to clonally amplify the fragments that are then sequenced using sequencing-by-synthesis (SBS) chemistry.
Illumina has a broad portfolio of instruments that covers wide range of needs, from the large HiSeq X Ten, a $10M system capable of sequencing >18,000 genomes per year, to the desktop-sized MiSeq that can complete smaller runs in under a day.
HiSeq X Ten
The HiSeq X Ten, launched in March 2014, is a specialized version of the HiSeq 2500 system that has specifically been created to bring down the price of human whole genome sequencing to under $1,000. It is their highest output system, generating 1.8 Tb of sequence per instrument run. It achieves this output through a number of improvements, including patterned flow cells with new clustering chemistry (which allows for higher cluster density), improved optics and improved SBS chemistry.
The only official application for the HiSeq X Ten is that of human whole genome sequencing. It has been tuned to serve this high throughput market and, at least for nothing, other applications (e.g., exome, RNA-Seq, etc) are not allowed. As the system is sold in a minimum of 10 units (at a price of $1M per unit), owners of the HiSeq X Ten will be able to generate over 18,000 human whole genomes per year.
The HiSeq 2500, an upgrade of the original HiSeq 2000, has two separate operating modes, both using the standard SBS chemistry. The ‘high throughput mode’ will be able to generate up to 1Tb per 6 day run (with v4 chemistry set to launch in early 2014). For those willing to pay a premium for faster results, there is also a ‘rapid mode’ that is capable of generating 180Gb in 40 hours. It uses modified single-channel flow cells, on-board amplification and ‘fast’ chemistry to achieve the faster run times.
Launched in January 2014, the NextSeq 500 is Illumina’s mid-range instrument capable of generating up to 120Gb and 400M reads per run, while maintaining the footprint of a desktop sized system. Its reasonably high output, large number of reads and flexibility of operating with both ‘high’ and ‘mid’ output flow cells make it a good choice for all of the major NGS applications.
While the NextSeq 500 is based on the same SBS chemistry as all of the other Illumina systems, it has been modified to use a 2-dye sequencing chemistry where ‘C’ is red-only, T is green-only, A is a mix of red and green, and G is ‘dark’ (no red or green). This two color system needs only half the number of images (allowing for faster cycle times) and less demanding optics (allowing for a less expensive platform).
The MiSeq, which launched in the fall of 2011, is Illumina’s desktop or “personal sequencing system”. It is a smaller, faster and lower output sequencer, aimed primarily at the emerging sequencing-based diagnostics market. It is a self-contained system with on-board cluster generation, simplified reagent handling, and tight integration with BaseSpace, Illumina’s cloud-based data analysis platform. In November 2013 Illumina launched an FDA-cleared version of the instrument, called the MiSeqDx.
Illumina Specifications Table
|HiSeq X Ten*||Hi Seq 2500||NextSeq 500||MiSeq|
|HT v4||HT v3||Rapid||High||Mid|
|Total output||1.8 Tb||1 Tb||600 Gb||180 Gb||129 Gb||39 Gb||15 Gb|
|Run time||3 days||6 days||11 days||40 hrs||29 hrs||26 hrs||~65 hrs|
|Output/day||600 Gb||167 Gb||55 Gb||~110 gb||~100 Gb||~36 Gb||~5.5 Gb|
|Read length||2 X 150||2 X 125||2 X 100||2 X 150||2 X 150||2 X 150||2 X 300|
|# of single reads||6B||4B||3B||600M||400M||130M||25M|
Illumina Applications Table
|HiSeq X Ten||Hi Seq 2500||NextSeq 500||MiSeq|
|Human Whole Genome|
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