Skip to main content
Premium Trial:

Request an Annual Quote

Affymetrix Makes a Custom Entry Into High-Density Microarray Competition


[This article includes a correction inserted after publication. The new Affymetrix scanner does not cost $200,000, as the article originally stated. The company does not provide a list price for the scanner. As a rule of thumb, labs can expect to pay from $200,000 to $250,000, to install a single instance of the Affymetrix platform.]

The 800-pound gorilla of microarrays has flexed its muscle.

Affymetrix weighed in on the density race sweeping through the microarray industry last week, saying it is now ready to manufacture its GeneChip-brand microarrays at an 11-micron format — a move from its current 18-micron format that will allow the industry leader to more densely pack gene probes into its products.

The new format chips will initially sell as custom microarrays, using content of customers’ choosing. Catalog arrays, with content of Affymetrix’s choosing, will follow at an undetermined time.

“Anything on two chips can now fit onto one,” Elizabeth Kerr, Affymetrix senior director of gene expression, told BioArray News. “And, there are genomes out there that are getting to the point where you can put on one chip [entire genomes of] wheat, pig, chicken, cow.”

This announcement comes at a time when the microarray industry is locked in a race to mass-produce and sell a single microarray chip capable of holding different collections of what is accepted today as the content of the human genome — a technological milestone measuring the pace of innovation in the young industry.

Affymetrix currently offers a two-chip set containing its choice of human genome content, as do competitors Agilent Technologies and Amersham Biosciences. Newcomer Applied Biosystems has promised to present its own whole-human-genome single microarray and instrumentation platform by the end of the year. Additionally, a Taiwan-based competitor, Phalanx Group, also plans to check in with its own mass-produced whole-human-genome, single microarray by the end of the year.

And while Affymetrix now has its own entry, it can not yet claim the checkered flag that goes to the first company that produces — and sells — off-the-shelf whole human genome arrays.

“We are getting comfortable with the new platform and we are testing and developing catalog products,” Kerr said. “To create catalog products takes a little longer.”

She didn’t provide a time frame for the introduction of the new catalog products.

Some Savings

GeneChip microarray buyers may not see per-chip savings with this move, but will certainly achieve savings in reagents and labor costs — if they have coughed up the approximately $200,000-$250,000 to install one set of the company's instrumentation that includes the company’s new PC-sized GeneChip 3000 scanner, introduced in March — the company’s first instrumentation replacement in six years. The company doesn't provide a list price for the new scanner, but competitor Agilent Technologies sells a microarray scanner for $120,000, list.

“Scanners were one of the hurdles to shrinking feature size,” Greg Schiffman, the company’s CFO told a financial conference last week. “We had to have a new scanner in order to read [the smaller format].”

At the center of the Affymetrix announcement comes the inkling of a platform war — photolithography vs. ink-jet — that is flaring up as competition intensifies in an industry that is roughly valued at $800 million in 2003.

Affymetrix mirrors semiconductor giant Intel in its marketing processes, even to the point where it boasts an Affymetrix Inside product label — a straight grab from the Intel Inside tag — on products it sells for licensees such as the pharmaceutical giant Roche. The company points to the precepts of Moore’s Law as its guiding light for manufacturing and production.

Affymetrix is the microarray standard-bearer for the photolithography manufacturing process, a method that borrows from well-developed semiconductor manufacturing techniques, using masks and light, much like old-fashioned darkroom development, in order to lay down ordered patterns of oligonucleotides onto 5x5 inch quartz glass substrates that are then sliced and inserted into a plastic cassette to be sold for use in the company’s proprietary system.

The company manufactures its catalog microarrays in a 50,000-square-foot factory in an industrial park on the outskirts of Sacramento, and in early 2003 celebrated the manufacture of its 1 millionth array.

This format jump represents the biggest leap Affymetrix has taken in miniaturizing its microarrays.

The company has been manufacturing its catalog arrays at an 18-micron format since it introduced the HU-133 microarray set in January 2002. The previous formats for its catalog chips were at 20, 24, 50, and 100 [1994] microns, respectively.

“This is huge; it’s a milestone for the company and a big jump,” said Kerr. “This was a wholesale change in the manufacturing processes in place to improve the quality and the ability to do 11-micron [manufacturing].”


The new chips will each contain 1.3 million probes and 61,000 genes, compared to 500,000 probes and 23,000 genes on each array in the HU-133 chip set.

The company reports an installed base of some 860 GeneChip systems globally. So far, the company reported in August, some 100 of the new 3000 model scanners have been sold, presumably based on the attributes of the instrument, and the promise of a bolt-on automation system, which the company had originally targeted for release in August.

Been There, Done That

In recorded comments made at the Thomas Weisel Partners Healthcare Conference in Boston ast week, Schiffman took the opportunity to emphasize company’s ostensible lead on the competition.

“The competition is pushing, at the high end, 30,000 genes per slide,” he said. “We were doing that five years ago. Every year, there are new competitors. To see a company like ABI express interest in this market is exciting. The potential of the market is exciting.”


The Scan

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.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.