Call them the microarray boutiques. A number of smaller companies are foregoing the genome-on-a-chip idea in favor of low-density arrays with selected sets of genes involved in specific metabolic pathways.
The two leading companies in this arena, OriGene and SuperArray, are located along Maryland’s 270 Technology Corridor, just a stone’s throw from the National Institutes of Health and genomics giants Celera and Human Genome Sciences.
OriGene, which was founded in 1996, had until recently focused on supplying RNA, cDNA, and transgenic animals to labs. But last year, the Rockville-based company decided to develop a group of “SmartSet” arrays, collections of several hundred pathway-specific cDNA PCR fragments printed on Schleicher & Schuell nitrocellulose-coated glass slides.
The sets include groups of transcription regulators; genes involved in a tyrosine phosphorylation signaling pathway; signal transduction pathway genes for GPCRs; ion and biomolecule transport genes; a group of proteinases; a cytokine and chemokine group; and a cell adhesion cluster.
With these arrays, “you don’t have to sort through the jungle to find the gem,” said Gillian Jay, the company’s manager of marketing strategy. “Whatever you find is your target gene.”
Georgetown University researcher Li Shen applied a similar principle when she co-founded SuperArray in 1998. Working with high-density arrays on studies of the protein kinase C process, Shen found the arrays to be ineffective as well as prohibitively expensive for most researchers, and she wanted to design a product for other researchers that would better suit their needs.
“Ninety-five percent of labs that exist today don’t do a lot of gene discovery work,” said Shen. “They do analysis of specific pathway function. We provide the specific tools analyzing their specific genes.”
While pathway arrays are just one avenue of revenue for OriGene, they are the sole focus for SuperArray, which has offices in Bethesda, and Frederick, Md. The company offers over 50 different nylon membrane-based arrays for different pathways, some with as few as 20 genes on an array. SuperArray has consulted researchers from around the world to help design its arrays for their use, Shen said.
Both OriGene and SuperArray emphasize that their arrays are affordable, as they require no additional lab equipment to read. While OriGene’s arrays sell for between $325 and $525 for a two-slide set, SuperArrays cost $249 for a kit of two arrays.
OriGene has designed its arrays with radioactive probes so the arrays can be read easily with x-ray film, while SuperArray has decided to offer both radioactive and non-radioactive sets that can be read with a simple phosphoimager.
SuperArray uses a proprietary probe-specific chemiluminescent labeling technique that eliminates the 3’ bias present with most arrays, as well as the problem of the RNA structure annealing to the template or binding to itself, said SuperArray R&D director and array designer Sean Yu.
In July, SuperArray is preparing to launch its second-generation GEArray 2.0. sets. The first four arrays, which are to be available next month, will cover human and mouse cell cycle and apoptosis genes, respectively. The next two second-generation arrays, to be launched in August, will be human and mouse cytokine arrays.
The array kits are priced at under $90 per array and include a new feature called tetraspot, a square of four spots per probe that can more easily distinguish spurious results from true results, as contaminants will show up as blobs rather than four square dots. Yu is working on software to assist in chip reading and analysis.
By 2003, SuperArray would like to have arrays in nearly all areas of genetic and genomic research, said Shen.
Meanwhile, larger companies like Clontech have offerings in the field as well, and even giant Affymetrix, which has so far only offered p53 and CYP450 arrays, has indicated it is interested in getting further into the low-density diagnostics arena.
These Maryland startups see this movement as a sign that they’re riding a trend.
“For four or five years big pharma has been using Affymetrix, but we believe the time of 20 thousand genes on a chip is slowly coming to an end,” said Jay.