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Benchtop sequencers ship off

Life Technologies began shipments of its new benchtop sequencing instrument on Thursday, but the sequencing race is still on. Illumina and Oxford Nanopore have also promised new machines by the end of the year, each capable of sequencing a human genome in less than a day.

Greg Lucier, CEO of Life Technologies, says well over a hundred new machines have been ordered. The latest machine, the Ion Proton, costs $150,000 and performs sequencing runs using $1,000 disposable chips. In about 4 hours, each chip can sequence 60-80 million filtered DNA fragments, with lengths of up to 200 bases, enough to provide several-fold coverage on a human exome. A second-generation chip capable of sequencing a full human genome is scheduled to be released next year.

“If it works as advertised, it’s a big deal,” says Michael Snyder, director of the Stanford Center for Genetics and Personalized Medicine. Current instruments are too expensive to buy and maintain, so cheaper alternatives will allow more sequencing. Still, he doubts, any single technology will be sufficient. “All DNA sequencing technologies have lots of errors,” he says. “I think it will become commonplace to sequence genomes with two different methods in order to obtain highly accurate genome sequences.”

The machines from the three companies read DNA bases in different ways. Illumina reads different colors of light depending on whether A,C,T, or G is incorporated. Life Technologies’ Ion Proton detects tiny changes in pH as different bases are added, and Oxford Nanopore detects disruption in an electrical current as a single DNA molecule slides through a nano-sized hole. Though Nanopore promises to be quickest and cheapest, it has higher error rates than Illumina or Ion Torrent machines. Also, Nanopore has not yet publicly released its instruments or data, so researchers are still unsure how the technology will perform.

The light-based methods currently dominate, with Illumina machines producing most of the world’s sequencing data. At a conference with stock analysts earlier this week, Illumina CEO Jay Flatley fielded more questions about potential cuts in federal science funding (70% of its market is academic) than about competitors.

However, Life’s Lucier is quick to point out that the benchtop sequencer his company launched last year, the PGM Torrent, has outsold Illumina’s benchtop sequencer, MiSeq. (The coverage and accuracy of these machines, as well as Pacific Biosciences’s platform, were recently compared in BMC Genomics. Nick Loman has posted an analysis of the latest and upcoming products.)

Life Technologies’ Lucier expects to see the machines in labs that do not focus on sequencing, with increasing use in clinical settings. But competition in the clinical setting is set to be fierce. Both Life and Illumina have released products for use with clinical samples, and plan to file for FDA approval of their instruments next year.


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