Agilent Technologies last week said it plans to launch later this month its SureSelect Target Enrichment System, which is designed to enable scientists to sequence genomic areas of interest with second-generation sequencing instruments.
According to Agilent, researchers can use the platform to capture a subset of exons or other genome targets and wash away the rest of the genome prior to sequencing. The company views the product as a replacement for what it calls “labor-intensive” methods for targeted re-sequencing, such as PCR.
The kit, which will be available beginning Feb. 26, is currently available for the Illumina Genome Analyzer system, and Agilent said it is now optimizing it for the SOLiD System from Applied Biosystems, now a subsidiary of Life Technologies.
Agilent also said it plans later this year to introduce an array-based genome-partitioning method for smaller-scale experiments.
Agilent made its debut in the target-enrichment market on the heels of Roche NimbleGen, which markets its array-based Sequence Capture service; Raindance Technologies, which last week launched an in-solution sequence-enrichment product called RainStorm; and Febit, which provides a sequence-capture service called HybSelect.
Fred Ernani, Agilent’s product manager of emerging genomics applications, told BioArray News this week that the company believes the demand for the system will be “substantial,” and that Agilent already has the resources to serve this particular market need.
“The sequencing community has been expressing a need for this type of tool since the advent of next-generation sequencing,” Ernani said. “Agilent already possessed a high level of expertise in custom oligo synthesis, so we saw this as a logical entry into the next-gen sequencing workflow.
“Target enrichment is a very powerful and enabling technology as it lets researchers perform experiments that were previously unfeasible economically,” he added. “Therefore, our products will enable researchers to more efficiently uncover, for example, the genetic variations associated with disease states.”
According to Agilent, its target-enrichment kit contains a customer-specified mixture of up to 55,000 biotinylated RNA probes delivered in a single tube. Users can design their own custom SureSelect mixtures using Agilent’s eArray online design tool, which contains many genomes and allows users to upload their own sequences.
‘A Good Deal’
Agilent licensed the technology on which the target-enrichment method is based from the Broad Institute last year, and began laying plans for market entry last summer (see BAN 7/8/2008).
Chad Nusbaum, co-director of the Genome Sequencing and Analysis program at the Broad, helped to develop the method. Nusbaum told BioArray News this week that, of the target-enrichment methods currently available, the Agilent method has the advantage that it will come in a kit and “should be easy to use, as it is just a series of liquid-handling and incubation steps,” with no special hardware needed.
“Since the oligos that the kit is made from are a fixed cost, the process becomes less expensive as the number of samples increases,” Nusbaum said. “It's inexpensive for larger sample sets, more expensive for small ones,” he said.
In addition, the Agilent method, “at least in our hands, captures smaller fragments in the 150-250 base range, so for exon sequencing there is a lot less wasted sequence,” he added.
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Among the competitors Agilent will face in the target-enrichment market is Roche NimbleGen, whose sequence-capture method enables customers to produce targeted, sequencing-ready samples using NimbleGen arrays. Samples are first hybridized to the arrays, which are designed to capture sequences for specific regions of the genome. The captured sequences are then released and ready for amplification and sequencing, according to the Swiss company.
Over the past year, Roche has inked a number of deals that use its sequence-capture arrays with its 454 GS FLX Titanium second-generation sequencer. Most recently, French agricultural biotechnology firm Biogemma adopted the sequence-capture approach for use in a research collaboration aimed at developing new technologies for its crop-breeding programs (see BAN 1/3/2009).
Nusbaum said that the reason companies like Agilent and NimbleGen have come up with products for target enrichment or sequence capture is because customers have been demanding front-end sample preparation tools and because it is likely such tools will be in use for several years, at least.
“No matter how cheap sequencing a whole genome gets, it will still be cheaper to sequence a subset,” Nusbaum said. “Exons are only 1.5 percent of the human genome, but right now most of the experiments people want to do are to target a hundred or a thousand genes, which would probably be 0.01 percent or 0.1 percent of the genome, respectively. As long as the prep is cheaper than the sequencing, this remains a good deal.”
Nusbaum estimated that researchers using second-gen sequencing tools will be using target-enrichment methods for “at least” three to five years. “Given how rapidly things are advancing, this is a long time for any technology to stay current,” he said.
Elaine Mardis, co-director of the Genome Sequencing Center at Washington University in St. Louis, told BioArray News this week that she, too, believes there is a place for target enrichment in the market.
“While I personally think it's much more straightforward to just sequence the entire genome, and the costs are falling rapidly, there probably is a place for targeted capture,” said Mardis, who sits on the scientific advisory board of Pacific Biosciences, a Menlo Park, Calif.-based sequencing startup.
“In general, I quite favor solution-phase capture [applications] over solid-phase, mainly because I like to think about how efforts will scale to high-throughput, and I think that's quite difficult logistically for solid-phase, whereas solution-phase can readily be adapted to laboratory automation in the 96-well format,” she said.
Mardis said that her lab has had success using an internally developed solution-phase approach that uses biotin-labeled PCR products derived from long oligos to form the "bait" in the application. She said that she hopes to publish a protocol on the application soon.
“I think it is great that these enrichment technologies are coming to fruition and we are adopting them now, [but] it is too early for me to pick favorites,” said John McPherson, director of cancer genomics at the Ontario Institute for Cancer Research. “All of the platforms will have a different bias and where one is better or a combination is best remains to be seen.”
McPherson told BioArray News this week that as “sequencing costs go down, it is tempting to think that sequencing the genome will be better,” but that the real choice confronting second-gen sequencing users is more complex.
“The important balancing factors are: ‘Do you know what regions you want to focus on and are willing to accept that you might miss new things?’; and ‘How much is the enrichment costing you?’” McPherson said.
“With regard to the former, for many applications [these enrichment platforms] may be acceptable. With regards to the latter, it may cost too much to us the enrichment platforms effectively on a large scale but the market price points have yet to be set as the competition is just heating up,” he said.
Agilent also said it plans later this year to “introduce an array-based genome partitioning method for smaller-scale experiments” that will “provide researchers a complete range of products for target enrichment.”
Ernani said that the “on-array product is designed for smaller projects,” which he defined as “those requiring the ability to iterate design for up to 10 samples.” Ernani said that the product will be based on the Agilent 244K microarray platform, but will be of a different design type than Agilent’s existing microarrays.
“Like the in-solution SureSelect Target Enrichment System, the on-array product will also have an eArray on-line design portal to support it,” he said.
Chris Grimley, Agilent’s senior marketing director for genomics, last week provided an update on the launch of the company’s new, 1-million-feature microarray platform. The company launched a new scanner last June, followed by upgraded software in September, to support the impending, higher-density array launch (see BAN 6/10/2008, BAN 9/23/2008).
Grimley said that 1-million-feature microarrays are now in limited release for comparative genomic hybridization, and that a full-scale release should occur next quarter. He noted that CGH is Agilent’s “highest-growth microarray application.”