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Array Firms Debut New Products to Cash in on 'Lucrative' Sequence-Capture Market

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By Justin Petrone

Agilent Technologies and Febit this week separately announced expansions to their sequence-capture product lines, while Roche NimbleGen discussed plans to grow its seq-cap portfolio by year end.

Clients of these firms use sequence capture, an application also known as target enrichment and targeted resequencing, to select specific target sequences for deep sequencing on second-generation tools sold by Illumina, Life Technologies' Applied Biosystems, and Roche 454 Life Sciences.

SureSelect

Agilent launched its SureSelect target enrichment system in February. The company initially offered customers an in-solution customer-specified mixture of up to 55,000 biotinylated RNA probes delivered in a single tube. Now Agilent is offering on-array resequencing, a product it pledged to make available earlier this year (see BAN 2/10/2009).

Agilent said its SureSelect DNA capture arrays are designed for smaller-scale studies and complement the target-enrichment system, which was designed for medium- to large-scale sequencing studies in automated workflows.

Fred Ernani, Agilent's emerging genomics applications product manager, told BioArray News in an e-mail this week that he believes "small studies that require a fair bit of design iteration can benefit from the array-based approach" versus the in-solution system.

"When a researcher would like to target 10 samples or more, when they would like the flexibility of automation or when their sample input requirements are very low, then they should probably use the in-solution approach," Ernani advised.

Agilent's capture arrays were developed together with Gregory Hannon's lab at Cold Spring Harbor Laboratory. The probes on the chip were designed through Agilent's web-based eArray design tool and manufactured by Agilent. Ernani said that the company launched its in-solution product before its on-chip resequencing because that was the "sequence in which the technology became ready for commercialization."

In April, Agilent signed a co-marketing deal to sell its target-enrichment system together with Illumina's Genome Analyzer II sequencer. Ernani said that the agreement with Illumina is "meeting [Agilent's] expectations" and said that, overall, the company is "very pleased" with the adoption of its products.

HybSelect

Febit, another competitor in the sequence capture market, this week launched a catalog cancer biochip for targeted resequencing. The new chip features 115 genes reported to be associated with common types of cancer by the Wellcome Trust Sanger Institute.

Febit initially launched its offering, called HybSelect, in February. The Heidelberg, Germany-based firm can synthesize oligonucleotides within the eight channels of one of its Geniom biochip and then use the oligos as capture probes for the targeted genomic DNA loci within a sample. The fragmented genomic DNA is then hybridized to the biochip, washed, and eluted, after which the selected DNA can be used for sequencing (see BAN 2/17/2009).

Chief Scientific Officer Peer Stähler told BioArray News this week that the new chip was developed within the "context of enabling a higher-throughput pipeline for NGS" than currently exists.

In sequencing for "pharma or clinically relevant studies, you need to cover hundreds or even thousands of samples," Stähler said. "The current setups in the field are low or medium throughput. Our focus is to sequence a particular set of genes to enable multiplexing so that you soon will be able to cover those genes in a study without prohibitive cost in 1,000 samples."

Febit's HybSelect cancer biochip was designed in partnership with Eckart Meese, director of the department of human molecular genetics at Saarland University in Germany. Meese is one of a number of researchers working with Febit in the Biomarker Discovery Center, established in February as part of a research cluster funded through the German Federal Ministry for Education and Research.

Stähler said that the center is currently working on about 20 oncology projects and five inflammatory disease-related projects that are using its technology together with ABI and Illumina sequencers.

"This is a very lucrative market," Stähler said of the interest in HybSelect. "We have more inquiries for service projects than we can address," he said. "The market is very active."

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While oncology is the "most active" market for the technology, Stähler said that the firm is also seeing interest from researchers working in the areas of neurodegenerative diseases, monogenic human diseases, and agbio.

According to Stähler, the adoption of HybSelect has been "faster" than the adoption of large-scale microarray studies. "Sequence capture is transitioning from being a technology method to being applied to biology — much like arrays [were] in the mid-1990s," he said. "Back then researchers would publish papers that just described a spotting method. Since the end of the 90s, though, you concentrate purely on biology. If the adoption rate stays the same, we will translate into that in the next few years."

While Agilent has decided to offer both in-solution and on-array targeted resequencing, Stähler said that Febit has decided not to work on developing an in-solution kit for the time being.

"Our biochips are fully automated and very straightforward while oligo solutions are more complex for the customer," he said. "In terms of simplicity and robustness, there is nothing better than arrays. My guess is the field in the future will use more arrays than solution."

Sequence Capture

Roche NimbleGen is also planning to expand its sequence-capture portfolio. The company originally launched its sequence-capture application in April 2008.

According to the firm, the application begins with the fragmentation of genomic DNA sample by sonication or nebulization. The sample is then hybridized to a NimbleGen sequence capture array, unbound fragments are washed away, the target-enriched pool is amplified, and the sample is considered ready for sequencing.

Roche NimbleGen CEO Gerd Maass told BioArray News last week that the company now has an in-solution kit in development that should launch by the end of this year (see related Q&A, this issue).

"We have a very exciting product in development to do sequence capture in liquid phase to provide either a solid-phase or liquid-phase sequence capture product to the market depending on the researcher’s requirements," Maass said. "We expect to launch it in the fourth quarter of this year."