They can’t be first. But Agilent Technologies, Incyte, and Corning all know they may be able to capture a share of the high-density microarray market by providing products researchers view as better than Affymetrix GeneChips, and each company is trying to figure out the magic formula for doing so.
Incyte’s secret weapon is its extensive database of full-length gene clones and ESTs. “One of our huge advantages is our content,” said Chris Hopkins, senior scientist for Incyte’s microarray program. “Incyte has 5,000 reads of our own that no one else has. Affymetrix is having to put down [on its chips] what is publicly available.”
Agilent, meanwhile, has up its sleeve a proprietary inkjet deposition method that allows it to print a greater number of cDNA spots — 13,600 — on a single slide than any other competitor and to use tiny picoliter amounts of cDNA.
“The advantage with the inkjet technology is that it’s a non-contact process,” said Paul Diehl, product manager for Agilent’s catalog arrays. “Most arrays being made have pins that actually touch the array, and surface tension can create artifacts in the array. With inkjet, the head is moving just above the surface of the array and there is no surface tension effect.”
Corning has also sought to improve upon array printing by combining technologies from diverse areas of its business, including catalytic converters, Pyrex glass, and fiber optic cable, in a single device that prints 10,000 spots of cDNA on a slide.
The company uses the same type of ultra-flat glass for its slides that it uses to produce computer display glass, because of its low background fluorescence, according to Thomas Hinman, the division vice president and general manager of Corning Microarray Technology Life Sciences. Corning has licensed content for the arrays from Incyte and Invitrogen.
While Corning recently said it would release its human array by the end of the summer, pushing off an initial June launch date set at the beginning of the year, Incyte and Agilent have both recently launched commercial high-density arrays.
Incyte offers a series of five human LifeArrays, with 10,000 data points on each. “Our strategy is to put down as many genes as possible,” said Hopkins. Each spot represents a single gene: Incyte decided not to put duplicates on the chip because it has high confidence in its methods and has been able to detect gene expression changes as low as 1.7 fold, with 95 percent confidence, Hopkins said.
In its internal validation studies, the company has found the arrays to differ by a 12 percent coefficient of variation. Next month, Incyte is adding two more arrays to the series, Hopkins said. Incyte also offers a Human Drug Target array, a Mouse UniGene 1 array, several rat arrays, as well as Arabadopsis, C. albicans, and S. aureus arrays.
On May 16, Agilent literally took a page from Incyte’s book, and introduced its human cDNA microarray kit, which includes cDNA from Incyte’s Human UniGene 1 and Human Drug Target clone sets. Agilent has labeled duplicate probes with two different dyes in order to provide cross-references that help researchers compare results. The company has said its new product would be the first in a number of microarrays it will launch this year. “Agilent is looking to mass produce arrays for the larger market,” said Diehl.
Corning also eventually hopes to offer a full spectrum of arrays with content from human and other organisms’ genes. A $10 million partnership with MIT’s Whitehead Institute provides Corning with insights on the field and opportunities to field test its arrays in a central research setting.
It remains to be seen whether these companies can actually produce a market-viable alternative to Affymetrix’s GeneChip, which has been validated on the market for several years. But one advantage these chips have over GeneChips, and a selling point that all three companies are emphasizing, is that researchers who already have readers and scanners don’t have to invest in any other equipment. Unlike Affymetrix chips, which require Affy equipment, these other products can all be read using standard chip readers and scanners. And the market is always looking for a product that is not only better, but also helps to keep costs low.