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Illumina, Life Tech Launch Front-End, Software Updates for Short-Read Sequencers

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Julia Karow

This article, originally published Oct. 22, has been updated with comments from users.

In an effort to further improve their competing short-read sequencing systems, including their user-friendliness and throughput, both Illumina and Life Technologies launched updates to their systems last week.

The updates are part of a roadmap that both companies outlined for their respective systems earlier this year — including improvements in software, hardware, reagents, and processes — that they said will increase their throughput to approximately 100 gigabases per run by year end (see In Sequence 2/10/2009).

While Illumina introduced a new DNA cluster generation module that further automates front-end sample preparation for the Genome Analyzer IIx, Life Tech launched new software for the Applied Biosystems SOLiD 3 to increase its throughput and facilitate data analysis.

cBot Targets Small Labs

Illumina's new module, called cBot, streamlines the clonal DNA amplification process and will replace the company's current cluster station starting November. Beta-testers for the cBot include both genome centers and "a few very small labs," Suresh Pisharody, senior marketing manager for sequencing platforms at Illumina, told In Sequence.

According to Pisharody, the new amplification station is intended to make the Illumina GA attractive even to small labs interested in next-gen sequencing. "More and more customers purchasing these instruments are going to be the smaller labs," he said, "so we wanted to build an instrument and a workflow that any and every lab can use to do big projects."

He said that the cBot has been in the works for a little over a year and is intended to address "unmet needs" of customers.

For example, although the current cluster station only needs about half an hour of hands-on time, and a total processing time of about five hours, "it requires the customer to go back and forth to the instrument, to change multiple manifolds, to change reagents," he said, adding that there are about 14 "touch points" with the instrument during that time.

With cBot, users only have to interact with the instrument once for about 10 minutes to load a pre-packaged 96-well plate of reagents, put in a single flow cell manifold, and program the run. The entire process has also been shortened, to four hours.

Compared to the existing cluster station, the new instrument also adds a touch-screen monitor and a barcode reader, and it allows users to monitor runs remotely via the web or phone. The company also claims that the cBot can be installed by customers themselves and does not require training by the company.

The cBot costs up to $10,000 more than the existing cluster station, which has a list price of $45,000, but Pisharody said that the company has "very strong incentives in place" to move current customers over from the cluster station, though he declined to elaborate.

In marketing material, Illumina stresses the user-friendliness of its cluster amplification approach, both in terms of manual labor and total time required, compared to emulsion PCR, the amplification process used by both the Applied Biosystems SOLiD and the 454 GS FLX systems. "It's been a very strong differentiator," Pisharody said, adding that the cBot "really widens the gap between our workflow and the competing ePCR-based workflows."

The overall reduction in process time with the cBot would be "very welcome," according to James Hadfield, head of the genomics core facility at the Cambridge Research Institute in the UK, and the reduction in hands-on time would be "a real help."

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Hadfield, who runs three Illumina GAs in his lab, said he does not have the cBot yet and did not even know it was coming, but he thinks that "most users will want to replace cluster stations with cBots to save time and improve reproducibility."

Dan Turner, head of sequencing development at the Wellcome Trust Sanger Institute, also said he would be interested in acquiring a cBot, which would allow him to use different reagents in different lanes of a flow cell, "which will make my R&D experiments much less expensive."

New Software for 'SOLiD 3 Plus'

Life Technologies introduced new instrument and analysis software for its SOLiD 3 system this week, which increases the instrument's throughput, reduces the cost of sequencing, and turns it into "SOLiD 3 Plus."

According to Rosy Lee, director of the SOLiD product line at Life Tech, the software has been optimized to identify more beads, deposited at higher density on the slides, than before, leading to a doubling in mappable data output from 30 to more than 60 gigabases per run. "Customers use the same protocols as they always do, deposit the appropriate number of beads, and the software will find them," she said. As a result, the cost per gigabase of data decreases by about 50 percent, according to a company statement.

Data file sizes are also about 40 percent smaller now, so the total "data footprint" per run does not double, she said. "We made sure we streamlined the entire process by which the data is managed and collected, made sure there is no redundancy, made sure we use all of the processing power on the instrument as efficiently as possible."

Upgrading to SOLiD Plus will cost existing SOLiD users $5,000 and includes a visit by a service engineer to install the software, and Life Tech plans to upgrade its customers as soon as possible, according to Lee.

In addition, the company has introduced a new data analysis software package, called BioScope, which includes several applications and "creates a framework for customers to do their data analysis on a computer off the instrument," Lee said. At present, she added, users have to create their own pipeline by installing the tools they need individually.

Currently, seven different applications run under BioScope, including ABI's mapping software. Later versions will include more applications and allow customers to plug in their own tools, "whether it's something they have written themselves or something they have gotten from a third party," she said.

BioScope allows researchers to export SOLiD data into a standard format, the standard sequence alignment map or SAM format, allowing them to combine data from multiple sequencing platforms for analysis, according to a company statement.

While SOLiD 3 Plus increases the system's throughput, it does not yet address its sample-prep front end, which the company said this week it will automate early next year (see other article in this issue).

According to Donna Muzny, director of operations at the Human Genome Sequencing Center at Baylor College of Medicine, which has had access to several components of SOLiD 3 Plus, the ability to process higher-density slides "has basically doubled throughput on the instrument without incurring additional reagent costs." She said that data output from 50-base fragment runs has gone up to between 26 and 30 gigabases, and data from 50-base mate-pair runs to between 46 and 50 gigabases.

Muzny also mentioned that the new version of the aligner that comes with BioScope — called "mapreads" — is multi-threaded and uses "a novel seed-and-extend algorithm" that is designed to improve mapping yield. "Our testing with an early-access version shows dramatically improved performance and significantly improved alignments that allow for small indels and variable alignment length," she told In Sequence.

Bill Farmerie, a SOLiD user at the University of Florida, Gainesville, said that he plans to order the SOLiD Plus update, and looks forward to the improved throughput and lower data generation cost. The BioScope software, he added, "has been needed for some time." He said he liked the on-instrument mapper better than the prior version, "but not being able to run it off instrument has been a pain. This solves the problem, I hope."

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