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Intelligent Bio-Systems, Dover, Azco Partner to Launch Max-Seq Low-Cost Short-Read Sequencer


By Julia Karow

This article has been updated to correct the spelling of Jingyue Ju's name.

Intelligent Bio-Systems, Danaher Motion's Dover, and Azco BioTech have joined forces to launch the Max-Seq Genome Sequencer, a short-read DNA sequencing platform that promises high throughput at low cost.

The instrument, launched in April, uses a sequencing-by-synthesis chemistry from IBS and components of Dover's Polonator and costs less than an Illumina Genome Analyzer. It is distributed and serviced by Azco.

For several years, IBS had been independently developing a platform for its four-color reversible terminator sequencing chemistry, which it exclusively licensed from inventor Jingyue Ju and Columbia University in 2006. Originally, the system was called the PinPoint but has now been rebranded as the Max-Seq.

According to Steve Gordon, IBS' president and CEO, after talking to Danaher about helping it to manufacture the platform, IBS decided to use some components — mostly stages and optics — that are also part of the Polonator. However, "much of the [Max-Seq] system is different, including the software, fluidics, and instrument body," he told In Sequence, adding that the new platform should not be characterized as a Polonator.

IBS is also developing a low-cost sequencing platform for the clinical market, called PinPoint Mini, which it plans to launch next year (IS 3/29/2011). So far, Azco is not collaborating with IBS on distributing that instrument, Gordon said.

According to J Adams, Azco's president, Azco serves as IBS and Dover's global sales, service, and distribution partner for the Max-Seq and its reagents and plans to develop upstream sample-preparation reagents and kits in collaboration with the two firms. Besides selling the platform, Azco also offers customer training, instrument maintenance and repair, and user support. Changes on the hardware side, compared to the Polonator, include the fluidics system, optimized flow cells, a faster 5-megapixel camera, and better heating and cooling systems for the stage.

Adams said the list price for the Max-Seq differs between countries but that in the US it is about 10 percent below the list price of the Illumina GA.

Azco had been selling the Polonator, a sequencer originally developed by George Church's lab at Harvard Medical School in collaboration with Dover, since 2009 under a value-added reseller agreement. That system uses a sequencing-by-ligation chemistry and produces 2x13-base gapped paired-end reads.

The company no longer sells the Polonator but offers existing customers an "upgrade path" to the Max-Seq. Dover will still offer the Polonator platform for purchase directly, according to Adams. A Dover representative did not respond to a request for comment prior to deadline.

Max-Seq is essentially "an evolution" of the Polonator that "has taken all the good features of the Polonator and optimized it for SBS chemistry" from IBS, according to Jeremy Edwards, an early customer of the Polonator and a co-developer of its protocols. In addition, the software "is now very easy to run with a nice user interface," said Edwards, an associate professor of molecular genetics and microbiology at the University of New Mexico Health Sciences Center.

The three partners, who Edwards said he helped bring together, complement each other because Dover "can build very good instruments," IBS "has very nice chemistry" and Azco "provides sales and customer support," he said.

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Edwards has been running the IBS chemistry for about a year on the Polonator now and has been "very happy" with it because it is "very robust" and provides longer reads than the old SBL chemistry. He said he hopes to obtain a Max-Seq system in the near future, which he expects "should be much easier to use than the Polonator."

Some potential customers are cautious about the new platform. Vladimir Benes, head of the genomics core facility at the European Molecular Biology Laboratory in Heidelberg, said that a list price 10 percent below the GAIIx "is still too high to make Max-Seq with its present specifications a serious competitor to other platforms." He also said he was concerned that the description of rolling circle, or rolony, library construction on Azco's website appears to contain unattributed material from Complete Genomics.

According to marketing material for the instrument, the Max-Seq currently generates between 2.6 gigabases and 66 gigabases of high-quality sequence data from unpaired reads that are between 35 and 55 base pairs long. Azco currently offers kits for both 35-base and 55-base reads and plans to launch kits for longer reads "in the future."

In addition, it still offers SBL reagent kits originally designed for the Polonator, which can be used on a "specially SBL-configured Max-Seq instrument." The company noted, however, that it plans to phase out these SBL kits.

Max-Seq uses two reusable eight-lane flow cells, with each lane producing up to 100 million reads. While generating 35-base reads for a single lane takes less than a day, 55-base reads on two full flow cells take about 2.5 days. Paired-end reads require "additional time."

The read quality is "consistent with that expected for sequencing by synthesis," according to the instrument brochure. Eighty-six percent of reads up to 35 base pairs in length and 82 percent of reads up to 55 base pairs in length have a quality score of at least Q30.

Potential customers can review datasets from Escherichia coli and from a human genome to evaluate the data quality, Adams said

Azco offers two types of library preparation and amplification kits, each for either fragment or paired-end libraries: bead-based library construction followed by emulsion PCR, and DNA nanoball library construction that involves rolling circle amplification.

The company also provides both types of library preparation as a service, offered by Edwards' laboratory at the University of New Mexico. In addition, the lab, through Azco, will provide sequencing services on Max-Seq.

The consumables cost per run for Max-Seq ranges between $1,200 and $2,500, depending on the type of library construction, according to the brochure.

For comparison, the Illumina GAIIx produces between 10 gigabases of data from 35-base reads in two days and 95 gigabases of data from 2x150-base paired-end reads in 14 days, according to Illumina's website. At 2x50 base pairs, more than 85 percent of bases have a quality value higher than Q30.

According to Edwards, of the commercially available next-gen sequencing systems, the Max-Seq's current read length and throughput — which he said are based on bead-based library construction — are most similar to the Illumina GA.

However, in the future, with rolony library construction, which allows for higher read densities, the throughput could increase further, he said, reaching that of the HiSeq, which currently generates up to 600 gigabases per run. "I suspect the Max-Seq will be a nice alternative to the HiSeq," Edwards said.

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