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At AGBT, Illumina Provides Details, Initial Data on NeoPrep

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MARCO ISLAND, Fla. (GenomeWeb) – At this week's Advances in Genome Biology and Technology meeting in Marco Island, Fla., Illumina presented additional details and initial data of its NeoPrep system, an instrument it launched this week that performs library prep, quantification, and normalization.

NeoPrep is currently compatible with Illumina's TruSeq Nano kit, both for a short-insert library of 350 base pairs and a long-insert library of 550 base pairs, as well as TruSeq Stranded mRNA. In the second quarter, the system will also support the TruSeq PCR Free kit, followed by a "steady stream of protocols" beginning in the second half of the year and including targeted resequencing panels, Kirk Malloy, senior vice president and general manager of life sciences at Illumina, told GenomeWeb.

The system has a list price of $49,000, but Illumina is currently offering it at an introductory price of $39,000.

NeoPrep combines electrowetting technology that Illumina acquired when it purchased Advanced Liquid Logic in 2013 with microfluidics. It consists of a printed circuit board with a plastic chamber to contain liquid. On the bottom of the circuit board are small squares of electrodes and voltage changes serve to move the liquids through the system.

It is "literally moving a droplet of fluid by changing voltage across the surface of a board," Malloy explained. The instrument is not like a traditional liquid handling system, he added. "There is no movement of plates or changing of tips … and no pumps or hoses," Malloy said.

Stephan Schuster, a professor at Nanyang Technological University in Singapore, told GenomeWeb at AGBT that he is beta testing the NeoPrep instrument. While he said it is too early to comment on the data of the instrument, he thinks that using microfluidics technology for library prep is the way to go. And, although he said the box itself was not too expensive, "relative to manual [library prep methods], I had hoped the cost would be lower."

Illumina said that with its TruSeq Nano kit, reagent costs would run around $30 per sample, and with the TruSeq Stranded mRNA kit, reagent costs would run around $55 per sample.

Alejandro Gutierrez, senior manager of product marketing at Illumina, said during a presentation here that the "fully loaded cost per sample" using NeoPrep would be around $75 per sample, which includes the cost of amortization of the instrument, compared to around $80 per sample for manual library prep, assuming 1,000 samples are run per year.

Gutierrez also presented some initial data from the NeoPrep system, comparing library prep to manual techniques. Looking at the mRNA stranded prep and a sequencing run on the NextSeq, he showed that concordance between the two libraries was 0.97. Pushing inputs down to 10ng and even 2ng, compared to 100ng for the manual prep, concordance remained high at 0.97. However, when input got down to 2ng, there were some drawbacks, including a lower yield and increased numbers of duplicates, he said.

Similar results were seen when comparing NeoPrep on the TruSeq Nano kit for whole human genome sequencing and manual library prep. Starting input for NeoPrep with a 550bp insert was 75ng, and for the manual version starting input was 200ng of DNA. The two techniques had very similar coverage of genes and exons. Reducing NeoPrep's input to 10ng of DNA still resulted in good alignment, but coverage dropped to 25 percent of the bases being covered at 90x as opposed to 90 percent of the bases covered at 90x.

Also during the Illumina presentation here at AGBT, Mitu Chaudhary, senior product manager of application automation at the firm, explained the electrowetting effect that drives the system. Essentially, drops of liquid on a hydrophobic surface are moved around via applied voltage. When voltage is applied to a hydrophobic surface it causes the droplet to spread, which allows the instrument to "precisely control movement of droplets inside the library card," Chaudhary said. Voltage changes are used to "move, mix, merge, and split droplets."

In addition, the microfluidics technology enables between four to five times less starting material. For the TruSeq Nano kit, Illumina recommends using between 25ng and 75ng of input DNA for whole-genome sequencing, although internally, it has tested inputs as low as 10ng. For TruSeq mRNA, it recommends starting material of 25ng, but has tested inputs down to 2ng. 

Total hands-on time for NeoPrep is about 30 minutes, as opposed to several hours with standard library prep protocols, and NeoPrep's total run time is around 7.5 hours for the TruSeq Nano protocol and 10.5 hours for the TruSeq Stranded mRNA protocol, compared to over a day and a half using manual techniques. Sixteen libraries can be generated in each run, and up to 7,000 libraries can be created annually — if a run is started both in the morning and again in the evening.

NeoPrep is geared both toward customers experienced with and new to NGS. For experienced customers, NeoPrep will save time, Malloy said. But the real opportunity is for customers that are new to NGS and want reproducibility. "That's where the market is headed," Malloy said. "Investigators have a sample and a question and they want an answer."

Malloy added that the company would consider bringing NeoPrep through US Food and Drug Administration regulatory clearance. "We are in the process of putting together our regulatory road map," he said. "If we see a demand for this in clinical workflows, it's possible we'd include it, but that will be driven by the platform strategy and test menus we think are the most likely to be adopted."

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