Febit last week announced a partnership with the Translational Genomics Research Institute in Phoenix to evaluate the use of its Geniom array platform in capturing DNA for second-generation sequencers.
TGen will be Febit’s first US pilot user for HybSelect, a method the Heidelberg, Germany-based company said allows selective DNA capture and elution in order to pre-select sequences for second-gen sequencing runs.
It is the second time in as many years that Febit has looked to pair its array technology with second-generation sequencers. Last year, the firm joined with Prognosys Biosciences to offer a microbial genome-to-array service.
Febit’s decision to expand into the nascent market for selective DNA capture also coincides with similar moves from rivals Roche NimbleGen and Agilent Technologies.
Febit President Cord Stähler said in a statement that the TGen study will provide “important data” that will help the company prepare to launch HybSelect early next year. Stähler told BioArray News this week that the HybSelect application relies on Geniom’s biochip design capabilities to synthesize the oligos that will be used in the method.
More specifically, defined oligonucleotides can be synthesized within the eight channels of a Geniom biochip and then used as capture probes for the targeted genomic DNA loci within a sample. Fragmented genomic DNA is then hybridized to the biochip, washed, and eluted. After elution, the selected DNA can be used for sequencing on all currently available second-generation sequencers, Stähler said.
He called the deal with TGen the beginning of HybSelect’s “route to commercialization,” and said that the company has other initial projects that will soon expand into a HybSelect early-access program. “We will broaden our expertise, involve further high-profile partners to validate and optimize the technology, and expand our network,” said Stähler.
He added that automated instruments would be made available to centers offering second-gen sequencing upon the completion of early-access projects.
Febit is moving into the array-based, DNA sequence-capture market at a time when both NimbleGen and Agilent have made comparable gestures to second-gen sequencing users. Last month, for instance, Roche inked deals with two UK research centers to use NimbleGen’s sequence-capture methodology together with 454’s Genome Sequencer FLX instrument in cytogenetics and leukemia-related projects (see BAN 7/22/2008).
Agilent, meantime, is preparing to make a method called genome partitioning available this fall. Co-developed with the Broad Institute, genome partitioning is an extension of Agilent’s oligo library synthesis offering, where oligos are synthesized using the firm’s inkjet microarray fabrication capabilities, cleaved from the arrays, and made available in liquid phase to customers.
Unlike NimbleGen and Febit’s approach, genome partitioning is based on hybridization to biotinylated baits. Chad Nusbaum, co-director of the Genome Sequencing and Analysis program at the Broad, told BioArray News last month that “these methods scale nicely because they are purely liquid handling steps, and can be done in microtiter plate format by robots, so they can realize the economies of scale” (see BAN 7/22/2008).
Stähler said that Febit’s advantage in the budding sequence-capture market is both its “unique, holistic approach to microarrays” plus its “robust microfluidic system,” both of which result in “less hands-on time and improved performance” based on automation.
“We have established a first protocol that automates most of the complex sequence-capture process using our new Geniom RT Analyzer instrument,” Stähler said. “It is beneficial for this purpose that microfluidic biochips prevent evaporation, enable active-motion hybridization and allow very efficient washing and elution processes.”
According to Matt Huentelman, an associate investigator in the neurogenomics division at TGen, the institute’s decision to evaluate HybSelect was based on his lab’s previous experience with the Geniom instrument plus the desire to complement second-gen sequencing projects with array-based sequence capture.
“I do think that it is hard to deny that as a field we are heading toward an age where everyone in our studies will have their genome sequenced simply by default.”
“We, and frankly a lot of others in the sequencing field, are excited about the possibilities of genomic enrichment on microarrays and the HybSelect approach is one such option,” Huentelman told BioArray News this week. “There are a few unique characteristics of the Febit Geniom system, especially when you consider the speed at which you can generate a fully custom array, and I feel it will be extremely constructive to examine the pros and cons.”
Huentelman said that TGen will evaluate HybSelect by generating the arrays using the Geniom and assessing their ability to achieve successful enrichment of particular genomic regions of interest. Success, according to Huentelman, will be gauged through “measurements of specificity, sensitivity, and ease of use, among other things.”
The final analyzed data in the evaluation will be the output from several second-gen sequencing platforms. Huentelman said that TGen will most likely use HybSelect together with Illumina’s Genome Analyzer platform and Applied Biosystems’ SOLiD sequencer.
Stähler said that Febit expects to “learn a lot about potential differences between the use of HybSelect with different sequencers, and if there will be a need for adoption of protocols to gain the best results” based on TGen’s evaluation. “Our previous research on HybSelect showed that in principal it can be used with every kind of sequencer,” he noted. “It is just a method for pre-selection.”
One issue surrounding sequence capture is whether it is just a short-term fix for scientists who wish to avoid the costs and data-analysis issues associated with sequencing an entire sample, or whether it will prove efficient enough to remain in use, even as the cost of sequencing declines and data-analysis issues are solved.
For example, Roderick Jensen, director of the Virginia Bioinformatics Institute and a 454 and Affymetrix customer, told BioArray News last month that the popularity of integrating array-based sample-prep methods with second-gen sequencing is likely to increase in coming months, but that the probable decline in sequencing costs will make such pairings less necessary, therefore diminishing the financial benefit for array companies.
“As you can imagine, there are lots of companies in the wings trying to do this with an abstract target of $1,000 per human genome, so this is a freight train coming really fast,” he said. Sequence capture is a “stop-gap measure that is going to be very valuable in the short run, but as sequencing gets cheaper and cheaper, you can just go ahead and sequence the whole thing; you don’t have to capture." (see BAN 7/22/2008)
“It is an important discussion,” Huentelman said this week. “When sequencing gets so cheap, why not just sequence the entire genome across everyone in your cohort even if you are only interested in a few key areas of the genome?
“I personally think there will be a place for enrichment or sequence capture at least in the near future,” he said. “This is under the assumption that sequence capture becomes a fairly routine and cost effective lab practice.”
Huentelman cautioned that it was tough to predict the future when it comes to genomics research tools. He said it is likely that the second-gen sequencing field will see improved throughput, decreased costs, and easier data analysis that eventually could make enrichment unnecessary.
“I do think that it is hard to deny that as a field we are heading toward an age where everyone in our studies will have their genome sequenced simply by default because it will be so affordable. The harder question to answer is, ‘Just how long do we have to wait?’” he said. “During this ‘waiting period’ I think it is worthwhile to explore the feasibility and usefulness of sequence capture.”
HybSelect is the most recent of Febit’s efforts to cash in on the second-gen sequencing market. Last September, the company announced a partnership with La Jolla, Calif.-based Prognosys Biosciences that enables microbial genome researchers to have their organism of interest sequenced by Prognosys on the Genome Analyzer, and then more affordable custom arrays fabricated by Febit’s US office near Boston for further research (see BAN 9/25/2007).
“This service is starting to take shape,” Stähler said this week. He said that Febit also plans to extend the service to include a HybSelect module that would cover the “whole process chain from genomic DNA to HybSelect and all the way through ... sequencing to the final sequencing reads.
“That way customers are free to concentrate on biology, while we take care of the technology necessary to achieve the results needed,” he said. Stähler added that Febit will soon provide additional information about the pairing of HybSelect with its genome-to-array service.