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Big Array Vendors Promise New Chips, Acquisitions, and Diagnostics in 2009

2009 is likely to be a busy year for array manufacturers as firms with different resources and strengths seek to make good on previous promises to launch new chips and platforms, acquire complementary companies and technologies, and push new array-based tests out into the molecular diagnostics market.
Array companies with larger shares of the gene-expression and genotyping markets in particular, such as Affymetrix, Illumina, Agilent Technologies, and Roche NimbleGen, have pledged to launch new products this year, and some have talked of potential acquisitions, consolidating manufacturing infrastructure, and laying the foundation for a move into diagnostics.
For instance, Affymetrix this year plans to debut a number of new products.
In October 2008 the firm launched the GeneTitan System, a fully automated instrument that offers array processing from hybridization to data analysis, as well as a new chip format called “peg array” that enables customers to run assays on strips of 24, 48, or 96 arrays on microtiter plates (see BAN 9/30/2008). 
Affy’s first GeneTitan products were for whole-genome expression profiling using its HT 3' IVT Express Assay, which the company claims benefits from a streamlined protocol and the ability to work with less sample material. Around this time Affy launched peg array versions of its human, rat, and mouse expression cartridges.
During its third-quarter earnings call in October, Santa Clara, Calif.-based Affy affirmed its plans to launch peg array strips for genotyping on the GeneTitan by the middle of this year. The content on the new genotyping peg arrays, though, will not be based on existing Affymetrix products, but will instead be drawn from an internal screen of 1,300 individuals performed by Affy.
During the firm’s Q3 call, CEO Kevin King said that Affy hopes sales of the GeneTitan will help revive the company’s sagging sales to pharmaceutical customers. King said that the system is targeted towards downstream research and is the “only complete platform to automate customer workflow from target preparation through array processing data analysis.
“These new products provide pharma with higher levels of performance than current offerings,” he said at the time. “Specifically, these products offer lower cost for sample, they require fewer [full-time employees], and they deliver highly consistent sample-to-sample data reproducibility.
“We expect the adoption of these technologies will take time. And in the near term, the growth in the drug development in clinical trial segment will not offset the decline in the research segments of pharma,” he added.
While Affy prepares its new genotyping arrays for launch, it also is integrating USB, True Materials, and Panomics, the three companies it spent a combined $173 million to acquire during the course of 2008. Last month, Chief Financial Officer John Batty hinted that Affy, which had $315 million in cash and equivalents as of Sept. 30, could acquire more companies this year to support its goal of providing a broad scope of genomic research tools (see BAN 12/9/2008).
“At this point, I would say that we have the large building blocks that we need to execute on our plan,” Batty said at the time. “However, given the fact that we have access to liquidity right now, we likely will be opportunistic over the next year.
In particular, Batty said that Affy may look to buy smaller private companies that could benefit from combining with a larger, well-funded parent. “It is pretty clear that access to capital has become very difficult for many private companies,” Batty said. Being acquired by a company “such as Affymetrix, which has global brand equity and sales and distribution channels, would be a very compelling” option for such companies, he said.  
Affy is also looking forward to the possible US Food and Drug Administration clearance of a number of tests based on its platform. Several partners under its “Powered by Affymetrix” program, such as Almac Diagnostics, Skyline Ventures, and Ipsogen, have announced plans to seek 510(k) clearance this year (see BAN 12/2/2008).
Affy rival Illumina is at work laying the foundation for an expansion into the market for molecular diagnostics, according to company officials.
In November 2008, the company said that it hopes to have an assay cleared by the US Food and Drug Administration in 2009 and to open a Clinical Laboratory Improvement Act-compliant laboratory by the middle of the year (see BAN 11/18/2008).
Though Illumina’s first assay, which the company plans to submit to US regulators this quarter, will run on its digital microbead-based BeadXpress reader, the San Diego company said its CLIA lab will offer both sequencing and array-based services.

“At this point, I would say that we have the large building blocks that we need to execute on our plan.”

Speaking about Illumina’s diagnostic plans during the firm’s Analyst Day on Nov. 6, Greg Heath, senior vice president and general manager of diagnostics, said “oncology is the sweet spot of growth in molecular diagnostics,” and discussed ongoing research programs in ovarian and gastric cancer.
CEO Jay Flatley also told BioArray News in November that the array-based services the company hopes to offer through the lab could include processing samples for its consumer genomics partners 23andMe and Decode Genetics. Flatley said that while the direct-to-consumer genetic services offered by its partners are currently a “rich and famous” market, Illumina sees DTC as a future revenue driver.
“We believe that there will be consolidation of the consumer and personal diagnostic markets,” Flatley said at the time. “At the end of the day, diagnostics and consumer markets become indistinguishable; they will become one single market.”
In addition to diagnostics and DTC, Illumina has recently discussed the market opportunity for agricultural biotechnology tools and could launch more arrays to serve agbio customers this year. Carsten Rosenow, Illumina’s senior marketing manager of DNA-analysis products, told BioArray News in October 2008 that the company has seen an increase in interest from the agbio community. The firm so far has made available SNP arrays for bovine, equine, and canine studies (see BAN 10/28/2008).
“I think it became clear once we were approached by a few of the ag consortia, and particularly the bovine consortia, that there was a big interest in the ag community to do disease studies similar to the ones we do with humans, but also trait studies within animals and use that information to better understand these traits,” said Rosenow.
Rosenow said at that time that Illumina will add two new content-themed arrays to its ag menu, though he declined to discuss for what research segments those arrays would be targeted. Rosenow added that Illumina has been hiring more specialists to work with its agbio customers. He declined to elaborate.
Agilent Technologies
In 2008, Agilent began preparing to roll out a higher-density generation of its microarray platform. The company has pledged to launch the 1-million-feature arrays, a jump in content from its current 244,000-feature chips, sometime this quarter.
In June 2008, Agilent released a new version of its DNA Microarray Scanner that allows users to scan array images at up to 2-micron resolution. The scanner is designed to deliver data from Agilent’s current generation of 65-micron feature arrays, as well as output from the 30-micron features of the impending million-feature arrays, and works with a pre-existing 48-slide carousel (see BAN 6/10/2008).
Agilent followed the scanner launch with a bioinformatics upgrade. In September, the company launched GeneSpring GX 10.0, the next generation of its gene-expression bioinformatics platform. Agilent said at the time that GeneSpring GX 10 offers tools for systems-level data interpretation and pathway analysis and was designed with systems biologists in mind. According to Agilent, the new product can enable users to analyze data from gene-expression, microRNA-expression, alternative-splicing, and RT-PCR experiments (see BAN 9/23/2008).
Last month Chris Grimley, senior marketing director of genomics at Agilent, told BioArray News that Agilent will “continue to develop its gene-expression portfolio,” including a new protocol for obtaining “high quality results” from formalin-fixed, paraffin-embedded samples, due out this quarter.
Roche NimbleGen
Madison, Wis.-based Roche NimbleGen spent 2008 upgrading its arrays for a number of different applications to make use of its new HD2 platform, which provides 2.1 million probes per array. NimbleGen’s previous generation of arrays contained 385,000 probes per chip.
In November 2008, the company, which was acquired by Roche in 2007 for $272.5 million, launched HD2 arrays and services for chromatin immunoprecipitation studies. That set of arrays includes the Human Deluxe Promoter array, which allows researchers to interrogate all known and alternative-start site promoters at 10-kilobase promoter coverage, as well as all annotated CpG islands, and microRNA promoters on a slide. NimbleGen launched whole-genome tiling sets for human, mouse, rat, and other species at the same time (see BAN 11/18/2008).
The following month, the company launched its Human CGH 12x135K Whole-Genome Tiling version 2.0 arrays for the analysis of DNA copy number variation, as well as NimbleScan version 2.5, software that includes an experimental metrics report and enhanced analysis features for the arrays (see BAN 12/2/2008).
This week, NimbleGen spokesperson Kary Staples told BioArray News that the firm plans to expand its epigenetic array portfolios by introducing 2.1M DNA Methylation Whole-Genome Tiling and the Deluxe Promoter arrays in addition to the currently available ChIP-chip 2.1M arrays this year.
The company also plans to launch a human exome product for sequence capture on the HD2 platform this month. “This product takes the discovery of human genomic variation to an unprecedented level by targeting essentially all human protein-coding exons,” Staples said.
Later in 2009, the NimbleGen sequence capture portfolio will include “products that streamline the path to next-generation sequencing of captured samples and make genomic capture more user friendly with higher-throughput capabilities,” Staples said. “These improvements will lower cost per sample and increase sample throughput, thereby greatly facilitating re-sequencing studies,” he said.
According to Staples, NimbleGen also plans to enter the instrument market this year. He said that NimbleGen plans to launch its MS 200 Microarray Scanner in early 2009, and the higher-resolution MS 250 Microarray Scanner later in the year. 
“The MS 200 Microarray Scanner is optimized to scan NimbleGen standard density 385,000 and high-density 2.1-million feature arrays in the industry standard 1 x 3 inch format,” Staples said. Instrument features will include an autoloader, an integrated barcode reader, ozone-control, and on-demand calibration combine with adjustable 2 or 5 micron pixel resolution. 
The NimbleGen MS 250 Microarray Scanner will accompany the launch of “ultra-high-density NimbleGen arrays undergoing field testing in the second half of 2009,” Staples said. “The MS 250 Microarray Scanner will have workflow enhancements to enable automated data analysis and application-specific intelligent data handling,” he said.  “All scanners will include a workstation pre-loaded with software necessary for data collection, visualization, and analysis,” he added.

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