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Roche to Phase out Chip-Based Sequence Capture; Peptide Arrays 'Close' to Commercialization

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When Roche stops making NimbleGen DNA microarrays at the end of this year, its sequence capture chips will also no longer be available. At the same time, the company will continue to use the NimbleGen brand with its in-solution target enrichment products, and is close to launching a new, high-density peptide array platform, according to a company official.

Thomas Schinecker, head of Roche's Sequencing Solutions business, told BioArray News this week that the firm will no longer offer array-based sequence capture to clients after Dec. 31.

"We plan to phase that out by the end of the year and we are currently switching customers to our in-solution sequence capture," Schinecker said. Array-based sequence capture is "clearly a market that will not exist very soon in our view," he added.

Roche NimbleGen was among the first companies to offer array-based sequence capture when the target enrichment market first emerged five years ago, and for a time the firm competed against similar on-array offerings from Agilent Technologies and Febit, to name a few. However, in-solution offerings have since become the most widely used sequence capture approach, and those researchers who do use an on-array approach do so because they want to revise their experiments multiple times, and are typically using them in small-scale studies (BAN 10/25/2011).

An Agilent spokesperson this week said that the company will continue to offer array-based sequence capture as it still sees demands for the product.

When Roche earlier this year announced the reorganization of its NimbleGen and 454 Life Sciences businesses into a new business unit called Sequencing Solutions, it laid off the majority of NimbleGen's staffers, pledging to discontinue production of most arrays by year end in order to focus exclusively on the sequence capture market (BAN 6/12/2012).

Schinecker, who had been president of 454, became head of the new business unit, which consists of teams based in Madison, Wis., and Brantford, Conn., which had been Roche NimbleGen and 454's headquarters, respectively. The company will maintain the NimbleGen brand, Schinecker said, because "we feel that we have a very loyal and very strong customer base out there for our sequence capture products and it is a very strong brand in that segment."

According to Schinecker, Roche does have customers who use its on-array sequence capture products, but "most of those customers are now switching to products that are in solution." He said that there are "huge benefits to working with sequence capture in solution," among them being that it has an "easier, higher-throughput workflow."

Schinecker noted that Roche is still relying on its NimbleGen array resources to generate the oligo pools that are at the heart of its sequence capture offering. But instead of using its light-directed chemical synthesis approach to pattern high-density microarrays, the probes are generated off of the array and offered to customers in tubes. Paired with Caliper Life Sciences' automated SciClone NGS Workstation, customers can process up to 288 samples per week.

The company also continues to innovate on the sequence capture front. This week it launched a number of new products, including disease-specific target enrichment panels for clinical research applications. The firm's SeqCap EZ Comprehensive Cancer Design covers 578 genes implicated in a wide range of common and rare cancers, and its SeqCap EZ Neurology Panel Design covers 256 genes associated with 87 neurological disorders, including Parkinson’s and Alzheimer’s disease, epilepsy, and autism. Schinecker said that Roche is planning more disease-focused SeqCap EZ panels, but declined to further elaborate.

Peptide Chips on the Horizon

While Roche is committed to phasing out DNA arrays by the end of the year, it has set its sights on a different microarray arena — the market for peptide arrays.

Roche last month confirmed that it was offering custom high-density peptide arrays to early-access customers, including scientists at Sweden's SciLifeLab (BAN 9/18/2012).

Schinecker this week portrayed the product as nearing commercialization, saying it is "very close in terms of being a final product," but declined to further discuss timing for its launch.

Once it enters the peptide array market, Roche is likely to face more competitors than it did in the DNA array market. Companies that sell peptide arrays include Berlin-based JPT Peptide Technologies, seen by some as the market leader; Köln, Germany-based Intavis; Heidelberg, Germany-based PepPerPrint; Gardner, Mass.-based New England Peptide; Lelystad, the Netherlands-based Pepscan; and Copenhagen, Denmark-based Shafer-N.

The density of Roche's chips may provide it with an advantage, however. JPT offers arrays of 165,000 peptides, while Pepscan offers arrays of 96 peptides in a 96-well format. Roche said its chips will contain 2.1 million peptides.

According to Schinecker, Roche sees its peptide arrays as a "very highly innovative product" that is "going to address a lot of unmet needs out there from customers." He added that the firm "will continue that development" and reiterated that the company is already providing customers with early access to the peptide arrays.

As for other sequencing solutions projects in development, Schinecker acknowledged the existence of other "early-stage products" but declined to comment on them at this time.

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