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New Semiconductor Technology Accelerates Whole Genome Sequencing at Reduced Cost

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Clinical and anatomic pathology laboratories may soon find next-generation DNA sequencing reliable and affordable

Swift advances in whole human genome sequencing may bring clinical applications to pathology on a much faster timeline than expected.

One impressive example of the fast pace of technology improvements is the Ion Torrent, which is a semiconductor-based DNA sequencer now capable of sequencing 100 million base pairs. That is ten times the sequencer’s capacity when it was launched just last December!

It was August of last year when Life Technologies (NASDAQ: LIFE) in Carlsbad, California, paid $375 million to acquire Ion Torrent Systems, a start-up with operations in Guilford, Connecticut, and South San Francisco. If Ion Torrent achieves certain technical milestones through 2012, it will earn another $350 million.

Months later, in December, 2010, Life Technologies began selling the Ion Personal Genome Machine (PGM) in North America, Europe and Asia Pacific, at a price of $49,500. “This really is different than all the machines we’ve had before,” said Jonathan Rothberg, Ion Torrent’s founder and CEO, according to an article at NatureNews.

Here is how the Ion Torrent “Personal Genome Machine” was displayed at the Advancements in Genome Biology and Technology (AGBT) conference which took place in Marco Island, Florida, earlier this year. The photo shows the small footprint for this instrument, which will sell for a price of $49,500. That price makes it feasible for certain clinical laboratories to acquire the system and use it to create laboratory-developed tests. (Photo by Applied Biosystems)

Most clinical laboratory managers and pathologists recognize that, at a price point of $49,500, Ion Torrent’s Personal Genome Machine becomes affordable for any number of academic pathology departments and larger medical laboratories. It is the type of tool that can allow these laboratories to develop home brew diagnostic assays that require a great deal of gene sequencing “horsepower.”

Semiconductor Eliminates Need for Expensive Lasers and Cameras

Currently, most sequencing technologies use fluorescent tags and cameras and can take as long as a week to process DNA samples. The bench-top PGM uses semiconductor technology to read the individual chemical units of DNA, according to Xconomy. The Ion Torrent detects DNA sequences electronically on a disposable $99 chip (down from the initial $250 cost), and takes a couple of hours. “This isn’t optics—it’s just a computer,” added Rothberg.

“The technology makes the system cheap and scalable,” Rothberg stated in the Nature article. He added that the technology will not compete with established platforms such as Illumina’s (NASDAQ: ILMN), HiSeq, which costs about $700,000 and can read 250 billion bases in a single run. He believes the Ion Torrent sequencer will likely be most suitable for microbiology labs and clinical researchers, working with moderately-sized samples, according to the article.

Developers Are Competing For $10 Million Archon Genomics X-Prize

Developers of high-throughput, high content sequencers have their eyes on the Archon Genomics X-Prize. According to the official website, the prize challenges scientists and engineers to create better, cheaper and faster ways to sequence genomes. Specifically, the website states that the $10 million prize will be awarded to the first team that builds a device and uses it to:

  • sequence 100 human genomes
  • within 10 days or less
  • with an accuracy of no more than one error in every 100,000 bases sequenced
  • with sequences accurately covering at least 98% of the genome
  • at a recurring cost of no more than $10,000 per genome.

According to the Xconomy article, Life Technologies’ new sequencer will be watched closely by the major competitors in the field, such as Illumina, Roche Molecular, Pacific Biosciences (NASDAQ: PACB), and Complete Genomics (NASDAQ: GNOM).

Rothberg told a reporter for Technology Review that a third-generation chip capable of sequencing a billion bases will be available next year. He also declared that the Ion Torrent technology is getting better faster than competitors’ technology. Rothberg also predicted that, by 2013, the company will have developed a chip capable of sequencing an entire human genome.

Forward-looking pathologists believe that new rapid whole genome sequencing technology will be game-changing for clinical laboratories and pathology groups. As Jeffrey Saffitz, M.D., Ph.D., and Chairman of the Department of Pathology at Beth Israel Deaconess Medical Center (BIDMC) in Boston, Massachusetts, told The Dark Report in October, 2010, “We envision a future in which every community hospital clinical laboratory will… do this type of testing and analysis.”

The disruptive potential of new, small-scale rapid gene sequencing technology for clinical laboratories and anatomic pathology groups is a certainty. The leap from bench to bedside threatens to be swift for the unprepared. The potential to expand the value that the pathology profession contributes to clinical care is immense. The diagnostic and prognostic value of interpretations of genome sequence data promise to be significant.

Already, some academic pathology laboratories are developing training programs to prepare young pathologists on how to use these whole genome sequencing technologies to advance patient care. Given how rapidly this technology is improving, it may take only a few years before most medical laboratories and pathology groups will offer diagnostic tests that incorporate these gene sequencing technologies.

—Pamela Scherer McLeod

 

Related Information:

A Semiconductor DNA Sequencer

Life Technologies Debuts Ion Torrent Machine, Next Big Bet on Fast, Cheap Sequencing

DNA sequencing for the masses: The launch of a new technology marks a move towards small-scale sequencing in every lab

For information about the Archon Genomics X-Prize

Ion Torrent Racing to Change Healthcare, VentiRx to Close SD Office, RF Surgical Raises $12M, and More San Diego Life Sciences News

Whole Genome Sequencing: Is It Ready for Prime Time?

“Primary-Care Pathology”

Rapid Genome Sequencing Predicted by Mid-2009

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