Monday, October 5, 2009

IBM Research jumps into genetic sequencing

It took 13 years for researchers to catalog all the information in a human genome the first time. Now IBM believes it can do better--somewhat perversely by equipping a newer genetic sequencing method with brakes.

Big Blue is among those who believe electronics technology can be applied to the task of sequencing a person's genes, thereby bringing genetic testing into the computing era and lowering its cost to something like $100 to $1,000.

IBM is working on prototype DNA-processing electronics that slurps strands of DNA through an extremely small hole called a nanopore, measuring the electrical properties of the chemicals as they go by to determine the genetic information. That technique is used beyond IBM, but what Big Blue researchers have been working on is a way to slow down, an essential step toward improving its precision, said Gustavo Stolovitzky/a>, manager of the IBM Functional Genomics and Systems Biology Group.

IBM Chief Executive Sam Palmisano is scheduled to unveil the project and what the company calls its "DNA transistor" Tuesday in a talk, "IT Innovation in Healthcare," at the Cleveland Clinic, IBM said.

The ultimate goal for such research is affordable genetic sequencing. "It would allow DNA sequences to be more or less routine," Stolovitzky said, forecasting that the technology will arrive in five or ten years.

OK, but why should you care?

"It would enable the possibility of going to the doctor with some infection, and the doctor gets the sequence pretty much on spot of the bacteria affecting the patient or the virus is in the blood," Stolovitzky said.

Or another possibility: knowing patients' specific genotypes could mean doctors would know if they had a negative reaction to some drug. That could mean some drugs useful that today are banned could become useful to a subset of the population.

IBM isn't the only one working on this technology. In addition to various academic efforts, start-up 23andMe offers some genetic analysis today.

The genes of animals and plants are encoded in DNA with just four molecular-scale substances--adenine, thymine, guanine, and cytosine. Their particular order governs not only their the formation of humans and other organisms but also the day-to-day biochemistry that keeps us alive.

IBM's sequencing technique to transcribe this biochemical data has been under way for three years, and it's easier said than done. The company is in the process of creating a new prototype device updated to reflect what IBM learned from an earlier one that didn't work as hoped.

"Translocation control we should have in a year's time more or less," Stolovitzky said, referring to the ability to ease the DNA through the nanopore one pair at a time.

The distance scales alone make the work difficult. Each DNA base is about 5 or 6 angstroms away from its neighbor--about half a billionth of a meter. By comparison, a human hair is colossal, about a ten-thousandth of a meter in diameter. And the DNA strands slip through a nanopore that's 2 to 3 billionths of a meter wide.

One problem with the nanopore approach is that it's hard to distinguish the four substances, called bases, as they slip through the hole. The four bases have overlapping electrical properties, so the more time spent measuring each, the better the accuracy.

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