Skip to main content
Premium Trial:

Request an Annual Quote

Affymetrix, Agilent, Illumina, and ABI Set 2004 Milestones for Microarrays


Affymetrix is considering “consumer-type markets” for its technology as well as other emerging markets, chairman and chief executive officer Stephen Fodor said last week in a webcast presentation at a financial conference in San Francisco.

Affymetrix, the microarray industry leader and the manufacturer of a proprietary platform, and Agilent Technologies, regarded as the No. 2 player in the pre-printed array market, joined Illumina and Applied Biosystems in making beginning-of-the-year pitches to the financiers in attendance at the 22nd annual JPMorgan Healthcare conference.

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 other places beside the lab. 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; as well as microbiological applications, homeland security, and plant breeding, said Fodor, adding that applications would be considered “as these markets mature.”

This potential expansion of the company’s target markets is a continuance of a corporate strategy that Susan Siegel, Affymetrix’s president, discussed in October (see BAN 10/1/03). It also comes at a time when the research market for microarrays may be reaching saturation, leaving the industry searching for new applications to fuel growth.

Affymetrix’s revenues play a large part in estimated measurements of the micrarray market as the comp-any is the leader in a market where homebrew technology represents the majority of the installed base.

Affymetrix’s presentation was not without glitches. The company filed a form 8-K with the US Securities and Exchange Commission on Jan. 15 to disclose that a slide that was inadvertently included on the webcast replay of Fodor’s presen-tation was not originally provided at the live presentation made on Monday. The slide, the company said, graphically displayed Fiscal Year 2003 product and product-related revenue guidance. As a result of the webcast disclosure, Affymetrix reaffirmed its previous guidance of approximately $280 million in product-related revenue for 2003. The company will report its Q4 and FY 2003 earnings on Jan. 28.

Affymetrix, said Fodor, is aiming to “push this technology” into emerging markets.

He said that the U133 whole human array is the company’s flagship product in expression, the market that represents the largest economic opportunity for Affymetrix. The company launched the U133 Plus 2.0, a whole-human-genome, single microarray, in October and Affymetrix says the chip is now publicly available.

Affymetrix this year will introduce a commercial version of an automated, high-throughput array platform that Fodor said includes its chips on 96 small “pegs” that are made to dip into 96-well microtiter plates.

The technology, Fodor said, will allow the company to break into high-volume markets such as compound profiling, molecular toxicol-ogy, and clinical trials.

The company currently manufactures its highest profile products at an 11-micron format. Fodor said that at a 5-micron format, such an “array of arrays” can hold 120 million data points.

While gene expression is the company’s core skill, it is also developing products for DNA analysis. For that market, Fodor said that the company last quarter began working with collaborators on a tool that it hopes will be able to simultaneously examine 100,000 markers across the human genome.

“Affymetrix is beginning to mature into an industry leader,” Fodor said. “Our goal is to provide the entire information content of the human genome, in different snapshots on these chips, into different marketplaces.”

The company, he said, has created a manufacturing infrastructure that today is only operating at 40 percent of its capacity. “We have huge leverage here,” said Fodor.

Agilent Technologies

Darlene Solomon, who was named senior vice president and director of Agilent Laboratories in October, said that her organization, Agilent’s central research organization, “will power Agilent’s future through breakthrough technologies.”

While a relative newcomer to the industry, Agilent, which uses inkjets to manufacture an “open” platform chip that can be read and measured on most current microarray technology, reached milestones of 100,000 microarrays manufactured in a year, and now lists 400 customers and an installed base of 200 scanners, Solomon said.

“This is a very exciting year for Agilent as we have seen really continued and increased migration to the Agilent microarray platform,” Solomon said. “Array volume this year reached a level 100,000 per year, and we have doubled our customer base.”

She said the company perceives the homebrew market as “starting to see the benefits of moving to commercial arrays.”

Agilent’s advantage, she said, is in the open platform, its ink-jet technology, and the 60-mer format that it uses, which, she said, “is by a factor of five to 8 more sensitive than traditional 25-mer array performance.”

She highlighted the company’s new 8-pack format array, a 1x3 slide that can be divided into eight discrete sections, as exemplary of the company’s drive to reduce microarray experiments’ cost and to enable clinical and diagnostic applications.

In the labs, she said, Agilent is working to create new protocols for sample preparation with lower initial sample volumes that, along with the 8-pack chip, will lower, by a factor of six, experiment costs.

“Next-generation molecular diagnostics are on the horizon,” said Solomon, pointing to Agilent’s collaboration with Netherlands Cancer Institute spinoff Agendia, a company that is in the process of using the Agilent microarray platform as part of a process of validating a series of 70 genes that may act as a predictor of survival in breast cancer.


Jay Flatley, president and chief executive officer of San Diego-based Illumina, took the podium after his company had announced two new products for its gene-expression platform (see page 1).

Gene expression is an arena that Illumina sees as its “biggest market opportunity,” Flatley said. Thus, he said, the company is moving to attack that opportunity with products and pricing.

“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.”

Applied Biosystems

Foster City, Calif.-based Applied Biosystems, the leader in the DNA sequencing market, entered the gene-expression analysis market in July (see BAN 07-30-03) with the announcement of a new platform, the Expression Array system, which the company has said should be launched sometime this month (see BAN 12/17/2003).

Mike Hunkapiller, president of Applied Biosystems and senior vice president of parent company, Applera, made a presentation that focused on the systems biology trend while including several slides of the Applied Biosystems promised gene expression system and the company’s rationale for developing it.

“The precision and the accuracy [with current gene-expression microarray platforms] is not very good,” he said.”There are a lot of genes that you can’t see because of the limitations of the technology.”

The opportunity, he said, is for an instrument that looks at “all the human genome with high enough sensitivity, or high enough accuracy, to be able to pick out all of the genes in a survey experiment that can guide you down to a more detailed analysis.”


The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.