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Illumina's Low-Cost MiSeq Promises to Speed up Next-Gen Sequencing


By Julia Karow

This article, originally published Jan. 11, has been updated with additional information from Illumina's presentation at the JP Morgan Healthcare Conference and from the company's website.

Illumina last week announced a new low-cost sequencing platform called MiSeq, which promises to go from purified DNA to analyzed data in as few as eight hours, and to generate more than a gigabase of sequence in slightly more than a day of total experimental time.

The instrument has a list price of under $125,000 and runs Illumina's existing TruSeq sequencing-by-synthesis chemistry. The company plans to start shipping MiSeq to customers in the third quarter, and in larger quantities in the fourth quarter, according to CEO Jay Flatley. Orders will be taken starting in April.

Flatley told In Sequence last week that MiSeq is the result of a development program that Illumina formed after acquiring Avantome two years ago (IS 7/29/2008). "We learned a lot from the Avantome technology, we built upon it, and that's what resulted in the launch of MiSeq," he said, adding that Illumina "essentially used that [Avantome] team to continue to evolve our platform."

MiSeq will perform both single and paired-end sequencing with read lengths of up to 2 x 150 base pairs, which might increase over time. It generates more than 3.4 million single reads, or more than 6.8 million paired-end reads per run. Speedy runs are enabled by a "brand-new fluidics system" and architecture, he said, as well as through improvements in the sequencing chemistry that lead to faster cycle times.

Using 35-base reads, it is possible to go from purified DNA to more than 120 megabases of analyzed data in as few as eight hours, and the maximum output per run is about 1.5 gigabases.

The eight-hour workflow starts with a 1.5-hour library prep, enabled by the Nextera technology, which Illumina acquired with Epicentre Biotechnologies last week (see other article, this issue). Cluster generation and sequencing takes about 4.5 hours, and data analysis and "demultiplexing" about two hours, Flatley said.

The system has a footprint of approximately two square feet as well as a simple user interface and workflow, according to the company. Unlike other Illumina sequencers, the instrument auto-positions the flow cell.

miseq.jpgThe $125,000 list price includes an integrated cluster station and paired-end module as well as data analysis hardware for on-board alignment of the reads. Unlike other low-cost next-gen sequencing platforms that use emulsion PCR — like Life Tech's Ion Torrent Personal Genome Machine or Roche's 454 GS Junior — MiSeq requires no additional amplification equipment, which adds to the cost of those systems.

A run on MiSeq will cost between $400 and $750, depending on the application, and reagents will come in one-time use cartridges. The instrument takes one sample per run, though several barcoded samples can be combined.

Flatley said it is too early to discuss the system's anticipated data accuracy at launch, but that it will be "as good as or better than" that of the other Illumina sequencing platforms.

Prior to launch, Illumina will make sure the instrument is robust, and build up the infrastructure and supply chain for the reagents. "One of the critical factors on a product like this is to make sure we have the reagent manufacturing ramped up, because this is done in a cartridge," Flatley said. "We have to have all of that designed in a way that's highly repeatable and of high quality."

Illumina expects that MiSeq will be used in the clinic and plans eventually to apply for 510(k) approval from the FDA, though it has not set a timeline for that yet. "We think it's ideally suited, from an output and a turnaround time and a design perspective, to be used in clinical applications, and we think that's a very large emerging market," Flatley said.

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The company aims to sell MiSeq to individual researchers, hoping that it will replace Sanger sequencing for a number of applications. Applications supported include amplicon sequencing, clone checking, small genome sequencing, ChIP-seq, and RNA-seq.

For sequencing tens to hundreds of amplicons in parallel on MiSeq, Illumina will offer a new protocol that Flatley said will be about 10-fold cheaper than current capillary electrophoresis sequencing technology and "will be ideal for diagnostic applications in the future."

Besides Sanger sequencing, MiSeq will most likely compete with Ion Torrent's $49,500 PGM and 454's $100,000 GS Junior, both next-gen sequencers with short run times.

But Flatley said MiSeq has a number of competitive advantages. For a start, its output of between 120 megabases and more than a gigabase per run is higher than that of the PGM — currently about 10 megabases per run, to be increased to 100 megabases this spring (IS 1/11/2011) — and the GS Junior, which generates about 35 megabases per run.

In terms of read length, with 400-base pair reads, the GS Junior beats MiSeq, and the PGM generates reads between 100 and 200 base pairs. But MiSeq offers paired-end sequencing, Flatley pointed out, which at least the Ion Torrent platform does not, and MiSeq has no trouble sequencing through long homopolymeric stretches, a potential issue with both the Ion Torrent and the 454 platforms.

Also, users of other Illumina sequencing platforms can rapidly develop new applications on MiSeq, which uses the same sequencing chemistry, and port them over to their high-throughput Illumina sequencer. MiSeq also allows users to take advantage of existing application protocols and publications for the other Illumina platforms.

Flatley said he foresees future performance improvements for MiSeq "along all of the dimensions that we have improved in the past," including faster cycle times that translate into shorter runs, longer reads, and denser clusters that result in higher throughput.

Have topics you'd like to see covered in In Sequence? Email the editor at jkarow [at] genomeweb [.] com.