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Life Tech Streamlines Sample Prep for Ion Torrent; Moves Away from Traditional Emulsion PCR

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By Julia Karow

This article, originally published April 13, has been updated to clarify the underlying technology for the Ion OneTouch System.

Life Technologies said last week that it is improving sample preparation for its Ion Torrent Personal Genome Machine sequencer, shortening both the overall time and the amount of manual labor involved in template preparation.

Available immediately is a new emulsion PCR kit called Ion Xpress that cuts the time of the existing protocols in half, to about five hours, and reduces the hands-one time to about 90 minutes.

In addition, in late June the company will start shipping a $5,000 automated sample-prep device for the PGM, called the Ion OneTouch System, that will use an improved version of emulsion PCR, though it will still rely on bead-based clonal amplification. That system will be broadly available in the third quarter.

With the new template prep products, Life Tech is addressing a chief complaint about its "post-light" sequencing technology — that sample prep takes several times longer than the system's two-hour sequencing runs and involves a lot of manual labor.

"We got feedback from day one that the template prep was quite complicated and, for many people, quite difficult," said Maneesh Jain, Ion Torrent's vice president of marketing and business development. "We took that feedback seriously and are going to launch a product that will hopefully address this."

The new products do not address library preparation, which precedes template amplification. That process is "no different than any other for next-gen sequencing," according to an Ion Torrent spokesperson.

For the Ion Xpress kit, which has already been in the hands of several early-access users, Life Tech improved several aspects of the existing protocols, especially regarding the emulsion breaking step. "We spent a lot of effort on using different solutions and buffers for breaking [the emulsion]," Jain explained. Other improvements were made to the amplification and enrichment steps.

The entire protocol takes about five hours, including a few minutes of mixing the sequencing library with reagents to make the emulsion, three hours of PCR amplification, one hour of emulsion breaking, half an hour of bead enrichment, and 20 minutes of mixing reagents to load on the sequencer. The total hands-on time is about 90 minutes.

Like the old protocol, which took about 10 hours in total, the Ion Xpress kit requires the Ultra-Turrax Tube Drive from IKA to make the emulsion and a thermal cycler for the amplification step. Users can process up to six samples in parallel with the new kit. Jain said the company expects all Ion Torrent customers to switch to the Xpress kit.

The upcoming OneTouch System, meantime, reduces the template prep to about three hours, with about five minutes of hands-on time. It uses a process that is "quite different from traditional emulsion PCR," though Life Tech declined to provide details at this time.

This will bring the time for amplifying a template and sequencing it on the Ion Torrent PGM close to that for Illumina's MiSeq sequencer, which that firm plans to launch in the third quarter. Illumina has said that cluster amplification and sequencing on the MiSeq will take about 4.5 hours (IS 1/18/2011).

According to Jain, the Ion OneTouch still clonally amplifies DNA on the same Ion Sphere microbeads used today, but instead of generating microreactors in an emulsion, they are created on a filter plate on the instrument after users load the library and amplification master mix. This is followed by an "in-line process" to amplify the DNA and recover the beads. After adding sequencing reagents, the sample can then be loaded onto the PGM.

Jain said the OneTouch System has been in product development for about three months, and the company developed its underlying technology internally. He said that while the company had "some ideas" for improving the sample prep for some time, it only started focusing on the issue after the launch of the PGM in December.

The Ion OneTouch will support the Ion 314, 316, and 318 chips, which range in data output from 10 megabases to 1 gigabase per run. The company expects "probably the vast majority" of Ion Torrent customers to adopt the device, according to Jain.

Jain said that both the Ion Xpress kit and the reagent kit for the Ion OneTouch System are expected to be "comparable" in price to the existing template prep kit, which currently costs about $250.


Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com.

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