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Illumina Leverages BeadArray to Take On Affy, ABI in Gene-Expression Space

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Illumina has just tripled its market.

This week, the SNP-genotyping company rolled out its bead-based technology platform for use in high-throughput RNA analysis, and took the plunge into the roiling gene expression-profiling market.

“It’s a new field and a different application area for us,” Todd Dickinson, Illumina’s gene-expression product manager, told BioArray News, SNPtech Reporter’s sister publication. “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’s entry into the gene expression-analysis market, estimated to be worth between $500 million and $800 million, follows a year and a half of development, and comes at a time when the microarray industry faces regulatory pressure from the FDA and the pharmaceutical industry to show that the technology is accurate enough to move from the bench to the bedside.

But regulatory pressure aside, Illumina has entered the space in a decidedly subordinate market-share position compared to Affymetrix, whose gene expression-analysis platform is the most widely accepted outside the self-spotting market; Sequenom, whose MassArray-based genotyping platform has been shown to have a gene-expression application; and Applied Biosystems, which is expected to launch its own gene-expression platform by the end of the year.

“There is a shift of researchers who want to increase sample throughput for targeted sets of genes,” said Dickinson, who explained that the BeadArray gene-expression application is intended for researchers with focused lists of genes to analyze. “We think the Illumina technology is well suited for those who want to zoom in.”

The Platform

Illumina’s core technology comprises 3-micron microspheres that 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 high-throughput Sentrix Array Matrix, in which the collections of microspheres are arrayed onto a microtiter plate-sized substrate, and the mid-throughput Sentrix BeadChip array, in which the bundles containing microspheres are arrayed on a glass-slide sized chip.

The Array Matrix 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 platform will be marketed to pharmaceutical companies and large research centers performing screening experiments.

The BeadChip format, meantime, is based on a 1-inch by 3-inch glass slide sitting on a novel substrate and containing 50,000 beads on eight array clusters spaced 20 microns apart, and processes a single sample. The BeadChip is scannable on the Axon 4000B laser scanner, Illumina said. The BeadChip product targets smaller users such as academic and core facilities, and biotech firms that already have an array scanner. The BeadChip will be sold in part by Illumina’s oligo sales team.

“Over time, we believe that the home-grown spotted arrays are ultimately going to disappear, and that this will appeal to that moderate end of the market,” Jay Flatley, Illumina president and CEO, said of the BeadChip.

Illumina said it will price the Array Matrix at less than $100, including the sample prep, on a per-array basis — or one per bundle on the Array Matrix. By comparison, it costs around $120 to do sample prep for gene expression. Illumina has so far sold the Array Matrix to the National Institute of Environmental Health Sciences, which originally performed two studies using the technology as a beta customer.

The BeadChip, meantime, will cost around $640 per chip with eight samples — or $80 per sample without the sample prep, Flatley said in an e-mail message. There are no customers for the BeadChip yet.

Hoping to give the BeadChip a running start, Illumina has begun offering at a “substantial discount” sampler sets of arrays that contain human, murine, and Arabidopsis genes. These are sold with a startup package comprising a hybridization chamber, software, and a user manual. It will also offer a human toxicology set of 623 genes for toxicology applications, Illumina said.

The Strategy

The market for these platforms — “studying a focused set of genes over very large numbers of samples” — is underserved and emerging, Flatley told SNPtech Reporter. “Our belief is that as customers that have worked with whole genome technologies before, they are beginning increasingly to know more and more about the genes they care about, and now want to do more of a parametric analysis across large numbers of samples.

“The idea here is to enter a new application [gene expression-analysis], to do it using the same infrastructure that we’ve developed for genotyping, to allow customers … to do both genotyping and expression on focused genes on the same platform, and then ultimately to … launch whole-genome capabilities that can run on the same platform,” Flatley said. He said Illumina has not yet set a timeline to develop the whole-genome platform.

The BeadChip, which Illumina unveiled in June as a technology platform, is also expandable. The product, represents the first offering based on that technology, can be manufactured in a 16-sample high-density version that can be used with the BeadArray reader, said Flatley “It’s very easy to modify the number of beads per section times the number of samples,” he said.

Flatley said that one reason behind the gene-expression launch, and certainly the low-density BeadChip product, is Illumina’s desire to change the way potential customers perceive the company — namely, as a high-end vendor that sells multi-million-dollar systems. “Clearly that’s not going to be the case,” Flatley said. Indeed, Illumina CFO Tim Kish said recently thzat within a year and a half the company will introduce a medium-throughput version of its flagship BeadLab platform. Illumina will contine selling the high-throughput version.

Though Flatley conceded that Affy and ABI will be competitors — he dismissed Sequenom’s MassArray-based gene-expression technology as little more than a published protocol — he stressed that these products are mostly whole-genome offerings. “So in some sense we’ve segmented the market,” he said. “Of course, the trade-off is that researchers will be able to look at fewer genes.”

Some academics expressed confidence that Illumina’s BeadArray platform can be used effectively to analyze gene expression, and that there is room in the market for another segment.

“For a lot of researchers, I think the Affymetrix chips that look at 30,000 or so genes are the way to go, particularly if you don’t have a list of candidates that you want to focus in on,” said Alan Scott, who runs the core genotyping facility at Johns Hopkins’ Institute of Genetic Medicine. “Where the Illumina system will be more useful is that, once you have a set of [gene] candidates ... you can customize your own set and do 1,200 or so genes, or whatever your system will allow.”

To be sure, single-gene assays exist that cater to this smaller market — ABI’s TaqMan, for example, enables researchers to use RT-PCR to analyze gene expression one gene at a time. “The niche that Illumina fills will be to look at 1,200 to 1,500, or whatever their beads will support. But it will be in that ballpark.”

Scott, whose lab uses Illumina’s BeadLab for SNP-genotyping, told SNPtech Repoter that “the real plus for the Illumina system is that you can look at a 96-well plate worth of samples at the same time, whereas to do 96 Affy chips is an incredible amount of work. For the TaqMan, you can do one assay at a time, but 384 separate samples.”

— KL

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