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BioArray News Coming Change: Illumina's Six Genomes, Affy's New Markets


Change is afoot in the microarray industry. In January, Illumina entered the race for ultra-high-density microarrays when it began beta testing two BeadChip products that allow researchers to interrogate six separate samples against six whole-human-genome probes on one slide.

Separately, at a time when the research market for microarrays may be reaching saturation, Affymetrix CEO Stephen Fodor spoke in January at a financial conference about developing “consumer-type markets” for his company’s technology.

Don’t expect an Affymetrix GeneChip to be available for your family any time soon, but products with the company’s helix-and-pixel logo may soon be found in a wide variety of labs. The company is considering marketing its platform for applications such as human identification and human family studies; animal applications such as testing of feedstuffs and animal breeding; and applications in microbiology, homeland security, and plant breeding, Fodor told the conference, adding that applications would be considered “as these markets mature.”

“Our goal is to provide the entire information content of the human genome, in different snapshots on these chips, into different marketplaces.”

Illumina’s Response

Meanwhile, Illumina has jumped into the running for the most dense microarray, joining the ranks of Agilent, which in October began touting its chip containing the entire human genome, and Affymetrix, which has since begun selling customized versions of a whole-genome microarray chip. San Diego-based Illumina has begun beta testing two slides in its BeadChip product line that are targeted for commercial launch in the middle of the year. The company declined to provide pricing information.

One BeadChip product is set up to analyze six discrete whole-human-genome samples on one 1” by 3” chip; the second product is set up to analyze eight samples in parallel against the approximately 22,000 genes represented in the RefSeq database, also on one chip. The eight-sample chip is designed for researchers who aren’t interested in any more content than the genes available from the RefSeq database, says Bill Craumer, Illumina’s director of marketing communications.

On the six-sample chip, the beads are arrayed into 12 lines, each containing thousands of wells, which are designed to interrogate approximately 48,000 transcripts from the estimated 30,000 genes in the human genome.

Unlike conventional microarray hybridization, Illumina’s BeadArray technology is built around beads that self-assemble into microwells etched into an array substrate. To form an array, a pool of the coated beads is flooded onto the array surface where they are drawn into the wells, one per well. A subsequent decoding process enables the company to determine which bead type or sensor occupies each microwell, which results in a map that is used in downstream analysis and operates as a quality-control metric for each bead in each array.

The new products require Illumina’s proprietary hybridization reagents, sample preparation, and labeling protocols, and, because of their format, are only readable on the company’s Bead- Array Reader. The company provides software for analysis and the ability to export data to other commercial expression programs.

“This is an exciting time for Illumina,” Jay Flatley, the company’s chief executive officer and president, told attendees at the JPMorgan Healthcare conference in San Francisco in January when the chips were announced. “Illumina’s goal is to have industry-leading pricing on the chips,” he said. “We will set a new standard in quality, performance, cost, and customer satisfaction.”

A version of this article appeared in the January 21, 2004, edition of BioArray News.


Mo Krochmal is editor of BioArray News, a weekly newsletter from GenomeWeb at www. He can be reached at mok @genomeweb. com.


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