The market for so-called target enrichment or sequence-capture applications has prompted companies such as Roche NimbleGen, Agilent Technologies, and RainDance Technologies to commercialize products to researchers performing studies on second-generation sequencers.
Now Febit is also looking to elbow its way into a market competitors have described as offering "substantial commercial potential." After six months of making its HybSelect method available via an early-access program, the Heidelberg, Germany-based vendor plans to debut the offering in March, according to a company official.
Chief Scientific Officer Peer Stähler told BioArray News last week that the firm will debut the product at Cambridge Healthtech Institute's Next-Generation Sequencing conference in San Diego next month. The firm will support the roll-out with an online product demonstration, as well as via its direct sales organizations in Europe and North America.
"I think that [second-generation sequencing] itself is performing very well, and the combination of sequencing with this extraction technology turns our offering into a brute-force, disruptive tool," Stähler said. "HybSelect together with [second-gen sequencing] will fill a gap that microarrays cannot fill."
Febit inked early-access agreements last August for HybSelect with the Phoenix-based Translational Genomics Research Institute and with San Diego-based Prognosys Biosciences, a long-term customer (see BAN 8/19/2009).
The HybSelect method makes use of Febit's Geniom instrument and will be made available both as a service and as a standalone application for Geniom owners. 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, according to Febit.
"Microfluidic arrays are made for processing," Stähler said of HybSelect. "We combine protocol, bioinformatics, and a very easy-to-use instrument and you can quickly create a lot of good data with it."
He described the launch of HybSelect as a "key project" for the company. He also touted the firm's eventual sequencer "agnosticism," which distinguishes it from rival Roche NimbleGen, which works closely with fellow Roche company 454 Life Sciences in marketing its method, though NimbleGen's arrays can be used with other sequencing platforms. HybSelect will initially be available for use with Illumina's Genome Analyzer instrument, and will later be optimized to work with Applied Biosystems' SOLiD system, as well as 454 Life Sciences' FLX sequencer.
"We never lost sight that this was one of the key applications we have had in mind for our system," Stähler said. "This kind of application is easy to perform if you have microfluidics and more difficult to do on a flat glass slide," he said. "This will also be extremely cheap compared to other classical technologies. It will take a while to become high-throughput, but we will get there."
Stähler said he anticipates that the majority of HybSelect's first adopters will be existing Geniom RT Analyzer customers. "A lot of people already own a next-gen instrument, and this is the perfect combination for them, but there is also interest from companies that do not want to run a center at all," he said.
Describing Febit's decision to first make HybSelect compatible with Illumina's GA platform, Stähler said "we have concentrated on [the] Illumina instrument because it gives you sequence reads you need for SNP discovery and mutation discovery. The platforms from Illumina and ABI are rather similar, so ABI is next on our list.
"This spring we will adapt [ABI's SOLiD] protocol together with three early-access partners," he added, without disclosing them. "We are sure that, with a little work and some validation, it will be available soon."
In this regard, HybSelect mirrors Agilent's SureSelect Target Enrichment System, scheduled to launch next week, which is currently available for use on the Genome Analyzer and will be optimized for use on the SOLiD at a later date (see BAN 2/10/2009).
[ pagebreak ]
Fred Ernani, Agilent's product manager of emerging genomics applications, told BioArray News last week that the company believes the demand for his firm's 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."
Roche NimbleGen has expressed similar expectations for its sequence-capture array offering. Spokesperson Kary Staples told BioArray News last month that the firm plans to expand its sequence-capture portfolio later this year to include "products that streamline the path to next-generation sequencing of captured samples and make genomic capture more user friendly with higher-throughput capabilities" (see BAN 1/6/2009).
Biomarker Discovery Center
Separately last week, Febit announced it will participate in the establishment of the Biomarker Discovery Center Heidelberg, a project recently awarded funding from the Excellence Cluster Initiative of the German Federal Ministry of Education and Research.
The project, set to begin this month, is being funded as part of a €40 million ($51.6 million) grant to develop a biotech excellence cluster in the region of Rhine Neckar in southwestern Germany that can create drugs, diagnostics, and technologies in cellular and molecular biology.
As part of its contribution, Febit said it will offer both array and second-generation sequencing-based analysis to help develop and validate novel biomarkers. The company will also work with the German Cancer Research Center (DKFZ) on studies to identify markers for various cancer types, and to develop these markers into standardized diagnostic assays.
Stähler said last week that Febit at first will work with Prognosys on sequencing-related projects, but hopes to purchase one or several sequencers for use in the project next year.
The "key milestone" will be to increase the throughput of HybSelect within the context of the new center's research goals. "An Illumina [Genome Analyzer] instrument is able to analyze seven samples in five working days. The technology is incredible, but it is not high-throughput yet," said Stähler. "We want to establish a pipeline that can handle hundreds of thousands of samples and we will do this in close cooperation with our partners, mainly DKFZ."
According to Stähler, DKFZ will test several cancer types as part of the project, starting with pancreatic and breast cancers. The partners also plan to use Febit's microRNA Geniom biochips in the studies.