This article was originally published on Dec. 6.
By Ben Butkus
Labcyte and Roche today announced an agreement to enable high-throughput qPCR-based gene expression studies from cell lysates using Labcyte's automated liquid handling platform with Roche's LightCycler qPCR platforms.
According to Roche, the agreement has the potential to reduce the cost and time associated with primary compound screening in cells, and as such is expected to help the company sell more of its LightCycler 480 and 1536 instruments into the pharmaceutical arena.
Meantime, the agreement marks Labcyte's first major foray into the qPCR space and is expected to open up additional doors in this segment for the company's acoustic energy-based Echo liquid handling platform, a company official said.
Details of the agreement call for Roche to couple its RealTime ready cell lysis kits, which enable gene expression directly from cell lysates, with Labcyte's Echo liquid handler and recently released tissue culture microplates.
In addition, the companies said that customers will be able to fully automate the process using the Access workstation from Labcyte, which integrates the Echo liquid handler with either the LightCycler 480 or 1536 instrument.
In a statement, Matthias Hinzpeter, project leader for qPCR and nucleic acid purification systems at Roche, noted that the integrated platform "reduces data costs associated with gene expression profiling, allowing efficient incorporation of qPCR into the early stages of drug discovery."
The companies did not quantify this potential cost reduction. However, in an e-mail to PCR Insider, a Roche spokesperson added that for the LightCycler 1536 the reaction volume can be reduced to 500 nanoliters, "which is at least a factor of 10 in reagent savings compared to a 384-well system."
The spokesperson further noted that the workflow constituted a "paradigm shift" in primary compound screening workflows where a primary compound is directly tested against genes of interest. "The primary compound is added to cells, cell are then lysed with the RealTime ready Cell Lysis Kit, and then the lysate is directly subjected to qPCR, omitting any nucleic acid isolation," the spokesperson said.
Labcyte's Echo liquid handler uses acoustic energy to transfer liquids. According to the company's website, sound waves eject precisely sized droplets from a source liquid into a microplate, microscope slide, or other surface. The platform uses no tips, pin tools, or nozzles, so there is no contact between the instrument and the liquid.
The company has sold the platform to customers for a wide array of applications, including compound management, pharmaceutical screening, protein- and nucleic acid-based assays, and cell-based assays.
According to Brad Nelson, senior director of product marketing at Labcyte, various customers have been using the Echo for PCR work, but the deal with Roche is one of the first major agreements the company has made to specifically address the high-throughput qPCR market.
"The first major placement for [the Echo in PCR] was probably within the last year, and most of the users right now are doing kind of general qPCR setup — to dispense cDNA, mastermix, probes," Nelson said.
"It's still relatively new, though, and … it's taken some time for the market to pick it up," he added. "This is the first one-step, directly-from-cell-lysate workflow that we're announcing with Roche."
Nelson said that the company has made some subtle changes to the Echo platform over the past two years or so that made it more amenable to the high-throughput qPCR workflow. First, the platform now features drop-by-drop volume interrogation and adjustment on the fly, whereas in the past the platform worked by consulting built-in data tables to determine optimal dispensing conditions for specific applications.
"Then, it did take working with someone like Roche and some other partners to vet it out; to make sure all the components were working and … there were no big surprises or cross-contamination at 1,536-well densities. We did that in house a while ago, but nobody really cares if you do it in house."
Nelson said that Labcyte and Roche have already beta-tested the combined workflow with a pair of undisclosed customers — one in the pharmaceutical industry and one at a large genome center. "One of them is currently using a two-step process to create cDNA, and they are now working with Roche to investigate switching to the one-step process. And another site has been using [Life Technologies Applied Biosystems] products and is looking to switch everything over to Roche."
Nelson predicted that in light of the Labcyte-Roche partnership, this latter scenario may become more commonplace. "I think this is beneficial [for Roche] in trying to get the [LightCycler] going in the pharma space. We have very good coverage in pharma, but [Applied Biosystems] has better coverage in pharma than Roche does, so I think it was good for Roche."
For Labcyte, the deal may also open up new doors in the qPCR market. Nelson noted that the agreement is not exclusive, and that the company is eyeing similar pacts with other PCR players.
And the Echo may even be able to penetrate another rapidly burgeoning subset of the PCR market — digital PCR, which requires the kind of precise droplet generation and reagent dispensing that the instrument can provide.
"Digital PCR is definitely feasible with the Echo, in a couple of different ways," Nelson said. "You can actually do digital PCR in a couple of 1,536-well microplates. It doesn't need to be on individual droplets."
Nelson added that most digital PCR methods "essentially do serial dilutions in the beginning, diluting down to find the correct concentration to be working at. The Echo has the ability … to basically take two different stock concentrations, and from those two source wells directly make a serial dilution. We're looking into ways of whether or not you actually need 10,000 data points to get a good digital PCR read — maybe we can cut that down to only 2,000 by basically fine tuning earlier on in the dilution, so basically the first 8,000 data points that you get aren't really statistically necessary. So yes, we are working on that now, although we don't have any applications notes on it yet."
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