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Roche Rolls Out Genome Sequencer FLX; Cost Per Base Down But Cost Per Run Up

Roche Applied Science has sold several of its new Genome Sequencer FLX systems and is in the process of upgrading existing GS 20 customers, In Sequence has learned.
This week, Roche and 454 Life Sciences officially launched the new instrument, which boasts longer read lengths, improved single-read accuracy, and higher throughput than the GS20.
The GS FLX promises to bring the cost of sequencing down on a per-base basis, though the cost per run will go up due to the higher output of the system. The price for reagents per run has increased less than twofold, but each run on the GS FLX produces three to five times as much DNA sequence as the GS 20, Tim Harkins, Roche’s marketing manager for genome sequencing, told In Sequence last week. As a result, the cost per base has dropped by as much as 2.5-fold.
Every GS 20 customer is entitled to an upgrade to the GS FLX as part of the original purchase agreement, “similar to a software upgrade plan,” Harkins said. The cost for the upgrade varies depending on the agreement, but Roche would not disclose further details.
Demand for the upgrade is high, and “we are just trying to schedule everyone to get everyone upgraded as fast as we physically can do it,” Harkins said.
Roche has not disclosed the total number of GS systems it has installed, but based on revenues reported by 454’s parent company, CuraGen, in 2005 and 2006, the number is likely to be on the order of 50 to 60. In Sequence is aware of customers in the US, several European countries, Korea, and Singapore.
The upgrade, including a test run, takes about two to three days, during which the entire instrument except for the camera is replaced. While the new machine looks very similar to the GS 20 on the outside, Harkins said, it has changed significantly under the hood.
“One of the big changes has been the microfluidics,” he said, which have been improved to speed reaction cycles. Instead of 42 cycles in a 5-hour-run like the GS 20, the new instrument runs 100 cycles in a 7.5-hour-run.
Due to the increased number of cycles, the average read length has gone up from 100 bases on the GS 20 to between 200 and 300 bases on the FLX, depending on the application and organism. The instrument’s throughput has increased from 20 megabases in 5 hours to 100 megabases in 7.5 hours.
In addition, the software for running the instrument and analyzing the data has been upgraded, Harkins said, and reagents now come pre-assembled on a tray.
Single-read accuracy on the GS FLX is now 99.5 percent over 200 bases, up from 99 percent over 100 bases on the GS 20, owing to “enhancements to the reagents, the mechanical aspects of the instrument, and software upgrades,” Harkins said.

“For a genome center focused on whole-genome sequencing, per-base cost reduction is welcome. However, for our other applications, when long read length is not essential, we still would like to keep the per-run cost low.”

Importantly, “the price per base will be considerably lower,” Harkins said, though he acknowledged that the cost per run will be higher than with the GS 20 due to the increased output of the system, which requires additional reagents.
Several existing GS 20 users told In Sequence they appreciate these changes. However, in terms of sequencing expenses, cost per base is not always what matters. “For a genome center focused on whole-genome sequencing, per-base cost reduction is welcome,” Feng Chen of the US Department of Energy’s Joint Genome Institute told In Sequence by e-mail. “However, for our other applications, when long read length is not essential, we still would like to keep the per-run cost low,” he added.
New GS FLX customers pay approximately the same price for the instrument as existing customers paid for the GS 20, which retailed on the order of $400,000 to $500,000 last year. Roche is still deciding whether it will continue to sell the GS 20.  
Prior to the first commercial shipments of the GS FLX late last year, Roche and 454 validated the instrument’s performance at the sites of three early access customers — “major sequencing centers” that had all been existing GS 20 customers, according to Harkins. “This way, we could deliver instruments immediately to the market, recognizing sales, …and have high confidence that the instrument would perform to [our] established specifications.”
New customers for the GS FLX include the Virginia Bioinformatics Institute (see “Transcript” this week), GATC Biotech, and the Göttingen Genomics Laboratory.

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