IBM to commercialise genome reading

IBM has partnered with Roche, a manufacturer of medical devices, to build a low-cost device that can read human genomes, the company announced Thursday.

Although the technology may still be a decade or more away from commercialization, once finished it should give every doctor a low-cost and speedy way of examining a patient's genomic makeup, said Ajay Royyuru, senior manager of computational biology at IBM Research.

"The cost of genome sequencing has come down, and the speed has begun to improve, but there are still problems with speed, scale, throughput, as well as cost," Royyuru said.

The project will use IBM's "DNA Transistor." These transistors contain nanopores, or very tiny pores, through each of which a strand of deoxyribonucleic acid (DNA) can be run. The nanopore identifies each base of the DNA by using an electric field.

Because the nanopore is made in part from silicon, it should be able to be mass-produced by the same lithography techniques used to make microprocessors, thus keeping the production cost down, Royyuru said.

While other researchers have also explored the use of nanopores, such designs cannot accurately read the DNA, because the DNA travels too quickly through the pore.

"It's like sucking on spaghetti. Once DNA starts moving through the nanopore, it goes really fast. We've seen 48,000 units of DNA go through in 10 or 20 milliseconds. At that speed you have very little chance of reading that correctly," Royyuru said.

To slow the speed of the DNA, IBM has crafted onto the nanopore an electrical control to ratchet the flow to the desired speed. "We can electrically control the DNA's movement through the pore. We can advance it unit by unit," he said.

Although the DNA sequencing technologies have been around since the early 1970s, the entire human genome was not decoded in its entirety until 2001, due to the automaton needed to decode the large numbers of base pairs that need to be read. Each person's DNA contains about 3 billion base pairs of nucleotides.

While DNA sequencing technology has improved since then, it still costs a few hundred thousand dollars to read an entire human genome, Royyuru said. Once ready, this device should be able to do the job for anywhere from US$100 to $1,000 per read, Royyuru estimated.

Royyuru declined to offer a time when the machine would be commercially available, citing the many steps needed to bring any radically new technology to production. He estimated it would take about five to 10 years to finish the research alone.

Roche's sequencing subsidiary, 454 Life Sciences, will ultimately market the resulting products that come from this collaboration. IBM will bring to the partnership its expertise in building electronics and data management, while Roche will apply its knowledge in medical diagnostics and genome sequencing, Royyuru said.

Reading an individual's genetic code could have multiple medical benefits, Royyuru explained. Most notably it will permit doctors to "personalize the provisioning of medical care," he said. For instance, many medications will work on some, but not all, people. Having a person's DNA in hand will help a doctor prescribe the appropriate medicine. Also, reading the genome can reveal susceptibility to certain diseases.

Perhaps another early use could be in determining how long individuals may live. On Thursday, Boston University researchers announced that they have found what appears to be genetic signatures of longevity.

Joab Jackson covers enterpise software and general technology breaking news for The IDG News Service. Follow Joab on Twitter at @Joab_Jackson. Joab's e-mail address is Joab_Jackson@idg.com