The gene array sector has turned over a new leaf.
Last week, Affymetrix hitched its plow to Monsanto in a deal that includes licensing of its arraying technology and a joint project to develop a custom Arabidopsis chip. Affymetrix told BioArray News it also plans to offer made-to-order Arabidopsis arrays to all its customers this month, and to begin shipping in May.
This week, Lynx Therapeutics announced it was moving further into the ag-bio field with its bead-based assays by signing a five-year extension of its agreement with Adventis Crop Science to perform genomics discovery and develop an agricultural assay.
Meanwhile, Agilent Technologies said it will release its Arabidopsis genome array, developed in collaboration with Paradigm Genetics, some time this summer, after initial testing is completed.
This crop of new partnerships and product releases reflects the growing market for microarrays in the plant genomics/agricultural biotechnology sector. At the 10th annual Plant and Animal Genome Conference in San Diego this January, microarray companies reported a flood of interest in their technologies — a trend that plant molecular biologists say is continuing.
“Microarrays are becoming more user-friendly, affordable, and reproducible,” said Detlef Weigel, of the Salk Institute Plant Biology Laboratory and the Max Plank Institute for Developmental Biology. “It’s increasingly becoming standard to perform microarray analysis for new mutants.”
Affymetrix has seen “a lot of interest” in its custom array program from the plant science community, both academics and “agricultural biotech companies interested in the genomics of crop plants,” said company spokeswoman Anne Bowdidge.
Monsanto Jumps on the Affy Wagon with Custom Arabidopsis Array
Unlike the typical tiered silver EasyAccess subscriptions Affymetrix has with most big pharma companies, which include a subscription price and discounts on catalog arrays, the company’s agreement with Monsanto involves only custom arrays.
This deal came about as a result of persistent legwork by Affymetrix sales reps, according to Bowdidge. “Our sales group has been working with individuals at Monsanto for quite some time to demonstrate the advantages of the GeneChip technology over other methods,” said Bowdidge. “We were quite pleased when they finally signed on as a GeneChip customer.”
Monsanto said that it chose to go with Affymetrix as the supplier of its Arabidopsis arrays because it “felt that their platform was better suited” to Arabidopsis arrays. “We don’t want to say that we feel that Affymetrix would always be the best, but for the nature of this one chip, the ability to get [the Arabidopsis genome] all on one microarray made the Affymetrix platform” best in this case, said Mark Buckingham, a Monsanto spokesman.
Arabidopsis: Ag Bio’s Laboratory Mouse
The Arabidopsis custom array that Affymetrix is developing for Monsanto as part of the agreement falls under the rubric of its plan to update its Arabidopsis array in collaboration with The Institute for Genomic Research.
The new arrays will represent over 22,500 transcripts arrived at through TIGR’s sequencing and annotation efforts, and are being produced with input from “leading researchers in the Arabidopsis community,” Bowdidge said.
The company plans to release the new array as a catalog product later in the year.
This interest in Arabidopsis commercial arrays by Affymetrix and others partly stems from the fact that its genome has been sequenced, said David Galbraith, a professor of Plant Sciences at the University of Arizona.
Not only does the completed genome make Arabidopsis a more useful model organism for researchers interested in gene regulation, he said. “The fact that the whole Arabidopsis genome is sequenced makes it possible to design [presynthesized] oligonucleotide arrays or use the Affymetrix approach.”
Still, many academic researchers, like Galbraith, are going to spot their own Arabidopsis arrays until the price of commercial arrays comes down a bit more. “The problem is that the budgets are rather limited in the plant area,” Galbraith said. Now Galbraith’s lab can spot a batch of up to a “couple of thousand” 10,000-spot arrays for about $10,000, meaning that each array would cost about $5, not including the cost of the technician or postdoc. Even with these ‘labor’ costs included, the price would be tens rather than hundreds or thousands of dollars per chip.
Galbraith’s lab is also making the PCR product maize arrays for the academic community. He says the next new plant array will likely be rice, as this organism’s genome was just published in Science.
Lynx in the Barnyard
When it comes to functional genomics of crops, however, at least one ag-bio giant has shown that it is willing to leave the chip behind.
Aventis CropScience’s deal with Lynx, which extends a 1999 collaboration, involves co-developing and commercializing a plant genomics assay based on Lynx’s bead-based technologies.
Lynx’s foundation technology, MegaClone, uses microbeads to sort millions of DNA molecules according to sequence. Each different molecule binds to a microbead, with each bead able to hold up to 100,000 identical molecules. Fluorescent tags on each bead indicate how much of a particular DNA molecule is on the bead.
Terms of the collaboration, which extends by five years a deal the firms inked in March 1999 that gave the Frankfurt, Germany ag-bio firm access to Lynx’s genomics-discovery services, will give the companies joint ownership of the assay technology.
Lynx will manufacture and sell the services or products and will pay related royalties to Aventis CropScience. Lynx will be paid for “performing genomics-discovery services” for Aventis CropScience during the deal’s development and commercialization stage.