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Big, Blue Horse Enters Sequencing Race

Now, this is interesting.

Writing in the New York Times, John Markoff reports that  “one of the oldest names in computing is joining the race to sequence the genome for $1,000. On Tuesday, I.B.M. plans to give technical details of its effort to reach and surpass that goal, ultimately bringing the cost to as low as $100, making a personal genome cheaper than a ticket to a Broadway play.”

The field in the “race,” according to the Times, now includes at least 17 startup and existing companies pursuing a range of third-generation technologies. (See this earlier post for a more on these players plus an animated run-through of sequencing methods.)

The original Human Genome Project successfully sequenced the first genome in 2001 at a cost of roughly $1 billion. But in recent years the cost of sequencing has been falling exponentially — sequencing the human genome now costs $5,000 to $50,000, depending on whom you believe. Markoff quotes Harvard’s George Church saying that that none of the efforts so far had been completely successful, and no research group had yet sequenced the entire genome of a single individual. (I’m looking to learn more about exactly what he means by that.)

Simulation of the “DNA transistor” reading DNA pulled through an atomic-size hole.

IBM’s entering into the fray at this point serves to highlight just how much genomics and computing have converged in the past half-decade. “More and more of biology is becoming an information science, which is very much a business for I.B.M.,” the Times story quotes Ajay Royyuru, senior manager for I.B.M.’s computational biology center at its Thomas J. Watson Laboratory in Yorktown Heights, New York.

The I.B.M. approach is based on what the company describes as a “DNA transistor,” which it hopes will be able to read individual nucleotides in a single strand of DNA as it is pulled through an atomic-size hole known as a nanopore. The goal, says I.B.M., is to sequence an individual genome of up to three billion nucleotide bases “in several hours” — a speed that I.B.M. and others see as key to delivering on the promise of genome-informed personalized medicine. Unrelated to the IBM announcement in particular, today the Genomics Law Report offers a typically thoughtful perspective on the legal, ethical, and emotional implications of such whole-genome knowledge becoming commonly available — and whether we’ll be ready for it.

ADDED 10.8.09: Daniel MacArthur at the blog Genetic Future offers some perspective on IBM’s announcement: “[T]his announcement represents more of an expression of interest in the field rather than anything close to a mature technology; IBM will not be rolling out a machine to sequence your genome at any stage in the near future. Rather, the press release seems to have been triggered by yesterday’s announcement that IBM had been awarded a $557,000 grant from the National Human Genome Research Institute to help develop the sequencing technology.” MacArthur also explains that the concept of nanopore technology, which the IBM platform would use, has already been the subject of intense research by other companies, notably Oxford Nanopore.

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