SANTA CLARA, Calif. — It’s been a year since Agilent Technologies paid $246 million in stock to acquire Stratagene, and the firm has increasingly found ways to make the buy count for its array customers, especially by bulking up its reagent-manufacturing process, according to a company official.
Yvonne Linney, Agilent’s general manager of genomics, said that by the end of this year all of the firm’s labeling kits will be manufactured by Stratagene. Moreover, the firm is looking to pair Stratagene’s portfolio of RT-PCR kits with its arrays for data validation, and also plans to leverage Stratagene’s manufacturing capabilities in Agilent’s budding oligo library synthesis business.
“We are working with Stratagene to look at ways to offer benefits to our array customers,” said Linney, who spoke with BioArray News during a site visit to Agilent’s headquarters here this week. For instance, she said, “Stratagene is now making all of our labeling kits for us.”
In some ways, the acquisition mirror’s Affymetrix’s plans for reagent maker USB, which it bought earlier this year: Affymetrix said it intends to use USB’s portfolio to more directly provide reagent kits to its customers (see BAN 2/12/2008).
The first new Stratagene-manufactured array reagent kit to hit the market was Agilent’s miRNA Complete Labeling and Hyb Kit, which launched late last month. The kit is used with Agilent’s miRNA Microarray System and replaces an older kit that required customers to purchase additional reagents from several companies, including Invitrogen, USB, and Takara Bio.
“Before, customers could only buy pieces of their labeling kits from us,” said Linney. “Now, it is nice to be in full control.”
In addition, Agilent has replaced its older labeling kits for gene-expression experiments with a kit manufactured by Stratagene. This month, the new Quick Amp Labeling Kit replaced the Low RNA Input Linear Amplification Kit PLUS, which required customers to buy additional components from Qiagen, Invitrogen, and PerkinElmer, among others.
“We are switching our customers over to the new QuickAmp kit, which is manufactured by Stratagene, and [we] are in the process of validating the Stratagene-manufactured DNA-labeling kit,” said Linney. “Our goal is to ensure that the kits work as well [as], if not better than, the ones we supplied previously that were made by third parties. Once we do that, we’ll be done.”
According to Linney, the DNA-labeling kit, designed to be used with Agilent’s comparative genomic hybridization arrays, will be available sometime later this year, though the company still has an agreement to offer Kreatech Biotechnology’s Universal Linkage System kit as an alternative for direct labeling of DNA, especially for applications that label formalin-fixed, paraffin-embedded samples, she said.
RT-PCR and Oligo Library Synthesis
In addition to using Stratagene’s resources as a reagents manufacturer to capture more of its customers’ business, Agilent plans to use Stratagene technologies, such as its RT-PCR capabilities, to complement its array line in other ways.
“RT-PCR is used very often in validation, and we are looking to validate all of our probes with their RT-PCR kits to make sure they all match and there is good concordance,” Linney said. “We are going through that exercise with our miRNA arrays, for instance.”
Another application area in which Stratagene will play a role is oligo library synthesis. Linney said that Agilent uses its microarray-fabrication capabilities to offer users the ability to design and acquire ready-to-use, custom mixtures of biotinylated, long RNA probes in a single tube.
“Before, customers could only buy pieces of their labeling kits from us. Now, it is nice to be in full control.”
In collaboration with the Broad Institute, Agilent has also developed a method called genome partitioning that makes use of oligo library synthesis to study specific parts of the genome using second-generation sequencers.
Linney said that the oligo library-synthesis process requires users to design a library of probes using Agilent’s eArray tool. The library is then manufactured by Agilent and moves on to Stratagene’s reagent-manufacturing site in Texas, where is goes through a process of in vitro transcription and biotinylation to become a cRNA biotinylated library.
“We will use the arrays to make the libraries and ship [them] out to Stratagene’s [manufacturing facility] where they will develop the kits, customize the libraries, and ship it out to our customers,” she said. “That process should go live by November with validated protocols.”
Linney said that Agilent is currently putting an automated process together to provide custom target resequencing oligo pools. The company is also considering adding catalog library products, depending on market needs.
“Basically catalog products would be specific exons or genes of mass interest [that] would be a common design, so [they] would not require the eArray component and could be manufactured in more of a batch process,” Linney said. She added that the firm views oligo library synthesis as a “big opportunity.”
The Business Plan
Nick Roelofs, vice president of Agilent’s Life Sciences Solutions Unit, told BioArray News this week that the genome-partitioning method co-developed with the Broad was specifically designed to work with Illumina’s Genome Analyzer. Now the company is looking to work with other second-generation sequencer vendors to develop protocols to work with their systems.
“That would require knowledge of the platforms if not cooperation from the vendors, but it creates a whole new field of possibilities for arrays,” he said. “The way I see it, you could screen first with an array and then move to sequencing, or partition with an array, which would increase the horsepower of sequencing downstream and so you have what could be complementary techniques.”
In April, Roche NimbleGen, a competitor of Agilent’s, launched a front-end sample preparation technology on its arrays called sequence capture.The process uses NimbleGen’s arrays for the targeted hybridization and elution of pre-selected genome regions.
“I see as much advantage in complementing the surveying power of arrays with sequencing power as I do in the disadvantage of arrays to be replaced by sequencing in some application areas,” Roelofs added.
Roelofs said that Stratagene’s ability to bolster Agilent’s array business was apparent at the time it decided to buy the company exactly one year ago (see BAN 6/12/2007). “Our growth tenet has been to grow the business organically, either through R&D or by adding technology that augments our existing business,” Roelofs said at the time.
Prior to the acquisition, Agilent saw that “Stratagene could manufacture reagents kits better than we could because they were primarily a reagents company,” he said. “They also had the ability to create better labeling kits, purification kits, and had array quality control strengths. So, this was very much part of our business plan.”