Your Independent Sequencing Guide
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Sequencing Platforms > Illumina
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 2000, capable of generating 55 Gb of data per day over a period of 11 days, to the desktop-sized MiSeq that can complete smaller runs in under a day.
Currently most of their development seems to be focused on the new MiSeq platform, although some of the latest features are migrating to the HiSeq systems. In addition to these commercially released platforms, Illumina has hinted that they are working on ‘single molecule sequencing’ technology for future platforms.
The HiSeq 2000, Illumina’s flagship sequencer, is a workhorse of the genomics industry and capable of sequencing six human genomes over an 11 day period. While the official specification is an industry leading 600 Gb per run, internal runs at Illumina have exceeded 1 Tb, so there is still room for output improvements for customers in the future. It is also capable of generating 3 billion single reads (or 6 billion paired end reads), making it an ideal system for applications which require high counting depth. The system is capable of running two flow cells independently, with the optics for capturing sequencing data from both the top and bottom surfaces of each flow cell.
The HiSeq 1000 is a slightly less expensive system with about half the output of the HiSeq 2000, as it is capable of running only a single flow cell. However, it can be upgraded to match the capabilities of the HiSeq 2000.
The HiSeq 2500, set to be launched mid-2012, is an upgrade of the original HiSeq 2000. While retaining all of the same specifications when run in ‘high output’ mode, it comes with a new ‘fast output’ mode capable of generating ~120 Gb (enough for a whole human genome) in about 24 hours. It uses modified single-channel flow cells and ‘fast’ chemistry to achieve the faster run times. These fast runs come at the expense of lower total output (120 vs. 600 Gb) and probably a higher cost per Gb (although final pricing has yet to be announced). The HiSeq 1500 operates on a single flow cell instead of two, so it has half the output. Both the HiSeq 2000 and HiSeq 1000 can be upgraded with the ‘fast run’ capability for $50k. Note that when run in ‘fast mode’ the 2500/1500 systems perform bridge amplification without the need of a cBot (but ‘high output’ mode runs still require a separate cBot).
Genome Analyzer IIx
The GAIIx is Illumina’s sequencer with the longest tenure and is the latest (and probably final) iteration of the original “Solexa 1G” sequencer. While many have been traded in for HiSeqs, they are still popular as they are cheaper and capable of generating sizeable outputs and a good amount of high quality reads for counting applications. However, chemistry and instrument improvements are no longer being developed for this platform, so it is unlikely to see improved performance in the future.
The HiScanSQ is Illumina’s answer to the transition from microarrays to sequencing. This machine consists of two components – the HiScan Reader for scanning microarrays and the SQ Module for sequencing. As the SQ Module shares the same single flow cell mechanics of the HiSeq 1000, output improvements to that system tend to make their way to the SQ. However, as the SQ Module is only capable of scanning a single surface of the flowcell, it has half the output of the HiSeq 1000.
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. Despite having the lowest output in Illumina’s stable of sequencers, it appears to be the one getting the most attention, so it will likely see substantial improvements over the next couple of years.
* HiSeq 2500 and 1500 available mid-2012
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