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Illumina Ready to Roll Its Bead Arrays Into the Gene Expression Marketplace

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San Diego-based Illumina is preparing to make its entry into the high-stakes gene-expression profiling market by rolling out its bead-based technology platforms for application in high-throughput RNA analysis.

The introduction of this new line of products — set for official launch next week at the UBS-Warburg conference in New York — is a big milestone forthe five-year-old company, Todd Dickinson, Illumina’s gene-expression product manager, told BioArray News. “It’s a new field and a different application area for us. We have been systematic in developing our products and now, we are starting to branch out and commercialize. This is the beginning of a long series of products that we will roll out.”

Illumina, thus far, has concentrated on large-scale genotyping, a market opportunity estimated at $200 million to $300 million annually. This new product line represents a diversification for its platform, a new market, and a chance to create new revenue streams as it attempts to become cash-flow positive in 2004.

The company had $4.8 million in revenues for its second quarter ending in June, compared to $1.9 million for the year-ago quarter, a rise that reflected the installation of one of its flagship BeadLab SNP genotyping platforms. The company, which had cash and equivalents of $58 million on hand at the end of the quarter, operated at a net loss of $8.6 million for the quarter, compared to $16.4 million for the year-ago period.

Illumina’s entry into the estimated $800 million gene-expression analysis arena follows a developmental period of a year and a half, and comes at a time when the 10-year-old microarray industry faces regulatory pressure from the FDA to show that the technology is rigorous and accurate enough to begin to begin to make the move from the laboratory bench to the clinic.

But regulatory pressure is the least of the challenges facing Illumina, which enters the market at a decided disadvantage in terms of market share, in comparison to Affymetrix, which provides the most widely accepted gene-expression analysis platform outside the self-spotting market, and to Applied Biosystems, which is preparing to launch its own gene-expression platform by the end of the year, as well as to Agilent and Amersham.

Dickinson said the company is not seeking to go head-to-head with Affymetrix but is focusing instead on researchers with focused lists of genes of interest for analysis.

“There is a shift of researchers who want to increase sample throughput for targeted sets of genes,” he said. “We think the Illumina technology is well suited for those who want to zoom in.”

The Platforms

Illumina’s core technology consists of color-coded 3-micron microspheres that randomly self-assemble into microwells at the ends of fiber-optic bundles, which are themselves assembled into so-called “arrays of arrays.” The company divides its gene-expression array products into two platforms — the Sentrix Array Matrix, in which the collections of microspheres are arrayed onto a microtiter plate-sized substrate, and the Sentrix BeadChip array, in which the bundles containing microspheres are arrayed on a glass-slide-sized chip.

An Array of Arrays

Perhaps the best way to describe the platform the company is offering is that each feature of the array — on a microtiter plate, or on a glass-slide format chip — is itself a microarray that can process its own sample.

The Array Matrix, designed for highest throughput, includes fiber-optic bundles of nearly 50,000 individual fiber strands, each containing a bead. These bundles are arrayed into 96 clusters, spaced 6 microns apart.

The company’s new BeadChip format, introduced in June, is based on a 1-inch by 3-inch glass slide format, on a novel substrate, containing eight separate array clusters spaced 20 microns apart, each which can process a single sample. The BeadChip is scannable on the Axon 4000B laser scanner.

The Array Matrix platform targets the needs of larger organizations such as pharmaceutical companies, while the BeadChip product targets smaller users such as academic and core facilities who already have an array scanner.

BeadArray technology starts with the preparation of libraries of 3-micron beads, with each bead having a 23-mer oligo “address” attached to it, to which is then attached a 50-mer sequence-specific oligo probe.

The beads are scattered across etched substrates in random fashion during the array production process, with each array bundle containing about 50,000 of the beads. The company said that each designed probe is represented on average 30 times on each bundle. The company designs two probe sequences for each gene.

After the arrays are assembled, the company analyzes the arrays, a process it calls “decoding,” to determine which oligos are present at each matrix coordinate for every array. That information is archived and delivered on a CD-ROM for researchers.

The company will begin shipping bead chips and matrix arrays within weeks. Illumina will offer sampler sets, six-packs of BeadChip arrays, in a startup package that includes a hybridization chamber, software, and a user manual.

The product launch follows two pilot studies conducted with the National Institute of Environmental Health Sciences.

—MOK