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GenCell's Automated CLiC System Generates 768 Libraries per Day; First Shipments this Summer

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GenCell Biosystems of Ireland has developed a fully automated library preparation instrument, called the CLiC LP, that can process up to 768 samples per day.

The system, which has a list price of $300,000, uses a proprietary droplet reaction technology developed by GenCell called "Composite Liquid Cell" (CLC) technology. Including consumables and labor, the platform has three to five times lower running costs than other library prep methods, according to the company.

"It's a true sample in–library out solution," CEO Kieran Curran told In Sequence.

Initially, the CLiC will be able to make targeted sequencing libraries with Ion Torrent's AmpliSeq, followed by protocols for Illumina's Nextera technology. However, in principle, it will be compatible with any commercially available library preparation protocol.

GenCell showcased the CLiC for the first time at the Advances in Genome Biology and Technology conference in Marco Island, Fla., last month.

Curran, who has a PhD in engineering and a background in microfluidic technology, founded the Limerick-based company in 2011. In the meantime, it has grown to about 45 full-time employees and last year opened a small US facility in Madison, Wis.

GenCell has been mostly privately funded. In 2012, the firm raised €2.7 million ($3.7 million) from private investors as well as Enterprise Ireland, which provides funding from the Irish government. While the company does not disclose how much cash it has raised in total, Curran said it is cash-flow positive and is not seeking any additional funding this year.

For the last three years, GenCell has been developing microfluidic technology for large agricultural biotechnology organizations, and the CLiC – the company's first commercial product for general sale – resulted from one of these agreements.

The company also plans to apply its technology in other areas, such as clinical diagnostics and genotyping, and is looking for partners for those. "We are a company focused on a number of technologies and applications – NGS is just one of them," Curran said.

Last month, for example, GenCell signed a two-year partnership with the Fiocruz Public Health Foundation, which is linked to the Brazilian Ministry of Health, and the Institute of Molecular Biology of Paraná in Brazil to jointly develop a new pathogen diagnostic screening platform. The project, which is funded with $12 million from the partners, will make use of GenCell's CLC technology.

The CLC technology, which was co-invented by Curran and is protected by US Patent No. 8,465,707, lies at the heart of the CLiC system. Reactions take place within an aqueous droplet that sits within a larger oil droplet, which in turn rests in a carrier oil. Encapsulating reaction droplets in oil "mimics a natural cell structure," according to the company, and allows researchers to add reagents along the way and purify the reaction products at the end.

The technology provides "a nice microenvironment to conduct the reaction without evaporation, giving you optical access, the flexibility to … do multiple steps such as adding more master mix, and all while it's thermally incubating the process," Curran explained.

Library preparation on the CLiC, which looks a bit like a liquid handling station, typically starts with 1 to 10 nanograms of input DNA in as little as 300 nanoliters. However, unlike a liquid handling system, it requires no plastic consumables such as pipette tips because it uses non-contact microfluidic technology for sample dispensing.

Sample DNA and barcodes are placed into the system in standard microtiter plates, from which they are automatically transferred into a thermally controlled chip with an array of "CLC nodes." The droplet reactors are generated on chip and other reagents, such as PCR master mix or ligase, are added. All DNA amplification and library prep steps, such as PCR, tagmentation, ligation, and incubation, take place on the thermal chip.

Finally, magnetic beads are added to the reactions, the sample is sucked from the thermal chip into long, thin tubes, and the DNA is washed and eluted, either individually or as a pool.

Set-up of the instrument takes about 20 minutes, and a typical run, which can be monitored remotely, is completed in five to six hours. Each run generates a minimum of 24 and up to 768 sequencing libraries.

The instrument comes in two versions, one that can generate up to 384 libraries per run and has a list price of $300,000, and another that creates up to 768 libraries per run and costs $330,000.

By reducing manual labor, reagent volumes, and plastic consumables waste, the cost of library preparation goes down three- to five-fold per sample, according to GenCell. "That's potentially very disruptive," Curran said, noting that library prep can be one of the most expensive aspects of next-gen sequencing, "dwarfing even the actual sequencing operation itself."

At launch, the CLiC will support library prep for targeted sequencing applications, "but we are working really hard to roll out exome and RNA-seq in short order," Curran said.

It will initially run with Ion Torrent's AmpliSeq chemistry but GenCell plans to add protocols for Illumina's Nextera technology later this year. In addition, customers can automate their own protocols on the platform.

GenCell is initially targeting the instrument at sequencing facilities at research institutions, as well as biotechnology and pharmaceutical companies. The company is currently taking orders for the CLiC and plans to ship the first units to customers this summer. Prototype systems have already been in operation at several agricultural biotechnology companies over the past two years, Curran said.

The company is not the only that has turned its attention to automated sequencing library preparation. Illumina, for example, recently announced the NeoPrep, a $50,000 system based on Advanced Liquid Logic's electrowetting technology, that will be launched this summer and will support library preparation for Illumina sequencers, handling up to 16 samples per run at launch.

Also, researchers have been using liquid handling systems from a number of providers for a while to help automate library preparation, for example PerkinElmer's SciClone NGS Workstation, which handles between 8 and 96 samples per run and supports a variety of protocols.

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