Danaher Motion – Dover, a branch of a US technology conglomerate that has been developing a low-cost open-source next-generation sequencer with George Church’s group at Harvard Medical School, is scheduled to ship the first commercial version of the tool later this week to the Church lab, In Sequence has learned.
In addition, the Broad Institute said it will order at least one of the instruments in order to evaluate the technology, according to the company.
Danaher has already received other orders and order commitments for the instrument, including an order from the Max Planck Institute of Molecular Genetics in Berlin, and plans to showcase the instrument in a hotel suite at the Advances in Genome Biology and Technology meeting on Marco Island this week.
The company said it will market the instrument, called the Polonator G.007, with reagent kits, flow cells, user support, and protocols and software developed by the Church lab.
Previously, reagents and flow cells were supposed to come from third-party vendors, and Danaher was only going to take care of hardware problems. Also, Danaher had originally planned to ship the first systems by the end of last year (see In Sequence 12/4/2007), but “everything takes longer than you think it’s going to,” Kevin McCarthy, chief technology officer at Danaher Motion – Dover, told In Sequence this week.
The system currently supports paired-end sequencing with read lengths of two times 13 bases. Performance metrics such as accuracy and throughput will be available within a month, according to the Church lab.
According to marketing literature, the Danaher-Church team has “identified the upfront and recurring cost of second-generation sequencing as key factors inhibiting the rate of adoption, and have assiduously sought to drive these as low as possible.”
The instrument’s list price, $150,000, is indeed lower than those of other available next-generation sequencers, which list for between $430,000 and almost $600,000 (see In Sequence 1/1/2008).
The Polonator, which consists of a number of modular subsystems, comes with two computers — one dedicated to image acquisition and instrument control, the other to image processing and base calling — as well as with three terabytes of local storage and a gigabit Ethernet interface.
“Our user community will shortly judge how well we will deliver on our remaining goals of recurring cost reduction, throughput, accuracy, and reliability,” the brochure reads.
Prices for reagent kits were not available as of early this week, but McCarthy said that he expects to have pricing information during the conference this week. Because of production scaling, reagent prices will decrease if demand rises, he added.
Danaher will sell four reagent kits for paired-end tag library construction, emulsion PCR, bead capping and enrichment, and polony sequencing. These kits will include a “very low cost” PCR polymerase, according to the brochure, as well as oligonucleotides with license-free fluors.
In addition to reagent kits, Danaher will sell flow cells for the system, each with 18 individual wells.
Software to run the instrument, consisting of a program that handles image acquisition and instrument control and another one that processes images and generates base calls in real time, comes from the Church lab and is expected to be available under an open-source license in early March.
Danaher will support the hardware and reagents, and has partnered with the Church lab to support the protocols and software as well. This will include training on how to use the instrument, according to McCarthy, who said that different optional support plans are available.
Researchers in the Church lab are still determining the performance of the instrument, including its throughput and accuracy, and “expect those figures within the next month,” Greg Porreca, a developer in the Church group, told In Sequence by e-mail.
“Our user community will shortly judge how well we will deliver on our remaining goals of recurring cost reduction, throughput, accuracy, and reliability.”
According to the brochure, the system, which will run two flow cells in parallel, similar to Applied Biosystems’ SOLiD sequencer, will be able to generate approximately 10 gigabases of high-quality data per 3.5-day run. It currently supports a paired-end tag polony sequencing-by-ligation protocol developed by the Church lab that generates paired tags, each 13 bases in length.
For comparison, Illumina specifies more than 2.6 gigabases of high-quality data per 6-day run with two 35-base paired reads for its Genome Analyzer, and Applied Biosystems says its SOLiD sequencer generates 2 to 4 gigabases of high-quality data per 10-day run with two 25-base paired reads (see In Sequence 1/1/2008).
According to McCarthy, library construction and sample preparation, which involves emulsion PCR, take approximately a week, similar to ABI’s SOLiD system. Illumina has said sample prep for its Genome Analyzer takes less than a day. Starting in April, a combined vortexer and thermocycler to facilitate the ePCR protocol will be available for sale, according to McCarthy.
But potential users have yet to see data generated on the system. The Church lab plans to make one of its most current datasets, comprising 10 terabytes of image data, available to researchers for evaluation, according to Porreca.
“We'll provide images, processed data, base calls, and the full open-source software pipeline necessary to reproduce the results from the images,” he told In Sequence.
Initially, the system will only come with protocols for paired-end sequencing, but McCarthy hopes that users will develop protocols for other applications, such as RNA analysis, DNA-methylation analysis, and ChIP sequencing. Researchers outside the Church lab are already working on improving the read length to two times 18 bases, he said.
While some users have already committed to the new system, others say they are paying close attention.
The Max Planck Institute for Molecular Genetics in Berlin, which already owns an Illumina Genome Analyzer, put in an order for the Polonator late last year. “We believe that more flexibility and a broader community for development is needed to get things faster done and costs faster down,” said Richard Reinhardt, head of the institute’s automation and service unit, in an e-mail message. The instrument will not be part of the institute’s sequencing production pipeline, he said. “It’s truly a developmental system.”
Bill Farmerie, who heads a core facility at the University of Florida, Gainesville, agreed that “the platform will attract the innovators.” Though he would like to be able to “tinker with this machine” himself, his service facility has no R&D budget that would allow him to do so. “Our users want results, not us testing new ideas on their samples,” he said. However, the fact that Danaher will sell consumables and provide technical support “makes the system more appealing to most customers” than before.
Service providers are taking note, too. “Currently, we are watching the development and performance of this machine very closely,” Marcus Benz, chief operating officer at GATC Biotech in Germany, told In Sequence by e-mail. GATC already owns next-generation sequencers from 454/Roche, Illumina, and Applied Biosystems. The company will pay special attention to the workflow prior to loading the instrument, to the data accuracy, and to the availability of technical support in Europe. “Definitely we are [intrigued] by the fact that it is an open system,” he said.
The company is taking orders for the system now, which it estimates it can fill within 8 to 10 weeks. More information about the system is available at this website.