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Merck is using a new technique that it believes could turn genetic information into new drugs, a key bottleneck for the pharmaceutical industry as it struggles to invent new medicines.

The techniques, described in the current version of the journal Nature, are an example of a technique biologists have been touting for years: treating all 25,000 genes as a complicated network. Each gene is seen not as a single switch, but as part of a vast and complex circuit board. Scientists call this "systems biology."

"There's a heck of a lot that's going on between the change in DNA and the onset of the disease," says Eric Schadt, the Merck (nyse: MRK - news - people ) researcher who masterminded the work. "This is telling us the disease is a lot more complex than we imagined." He says his new technique, which could identify changes in this genetic circuit board that would stop obesity without causing harm, is "a path forward for how to leverage the amazing rate of discovery in genomics."

Schadt's technique combines two research approaches. The first, known as a genome-wide association study, samples DNA at thousands of places to find "spelling" differences that are more common among those who have a particular disease than among those who don't. Genome-wide association studies have linked some two-dozen spelling mistakes to diseases including heart disease, diabetes and macular degeneration.

The second approach, called gene expression, looks at which genes are being used in a particular cell. This is akin to being able to see which bits of software a computer is using at a particular time. Schadt has developed computational methods to examine how genetic spelling mistakes are linked to changes in gene expression, and then at how both are connected to obesity.

He tried the technique out first in mice, then, with the help of Iceland's DeCode Genetics, in people. The result is a circuit diagram of more than 1,000 genes that interact to determine whether or not a mouse or person becomes obese.

Francis Collins, director of the National Human Genome Research Institute, said the paper combined two different ways of looking at genes in "a marvelously integrated way," leading to "stunning and unexpected" observations about the biology of obesity.

"We've heard a lot of talk for several years about the promise of systems biology--but now that promise is really coming through," says Collins.

The Merck work could identify "pressure points" in the gene network that could be tuned using drugs, says
Dietrich Stephan, a researcher at the Translational Genomics Research Institute (TGen) in Phoenix. "These are really very important papers," says Stephan. "What he's done is really flesh out the biology of that DNA variation."

The new technique isn't a final solution to the problem of how to figure out which genetic defects actually cause disease, says Leroy Hood head of the Institute for Systems Biology. Leonid Kruglyan of Princeton University led a 2003 team that used the same basic ideas to understand genes in yeast. "It's nice to see this beginning to bear fruit in human studies," he says.

George Church of Harvard University says his project to sequence the DNA of thousands of people--called the Personal Genome Project--is collecting data from tissue samples to do similar kinds of work. Researchers at the Institute for Systems Biology have been taking a similar approach to understanding ailments like mad cow disease that are caused by malformed proteins called prions.

If Schadt's approach becomes popular among drug firms, it could be a boon to Illumina (nasdaq: ILMN - news - people ) and Affymetrix (nasdaq: AFFX - news - people ), the biotechnology companies which make the DNA chips used both for finding genetic misspellings and for examining which genes are accessed in different tissues.

The research comes out of Merck's May 2001 purchase of Rosetta InPharmatics, a tiny Seattle biotech. While Rosetta Chief Executive Stephen Friend became the boss of Merck's anti-cancer effort, researchers like Schadt continued to push forward with Rosetta's original mission: figuring out how to use genetic data to invent drugs.

Schadt, who switched from pure math to genetics during the genomics boom of the 1990s, and who previously worked at Roche (other-otc: RHHBY.PK - news - people ), published a paper using similar techniques to understand the genes of corn plants in 2003. Another paper, published in 2005, was hailed by Science as one of several examples indicating the systems biology approach was starting to yield results.

Schadt says that he believes the techniques he applied against obesity could also be used to understand other diseases, but cautions that it could be years before they lead to the invention of new drugs.

But the research could help drug giants like Merck or Pfizer (nyse: PFE - news - people )--which are facing an industry-wide dry spell when it comes to inventing new medicines--- to test medicines faster by identifying chemicals whose blood levels should change if a drug for a disease like obesity is actually going to work. That could make clinical trials go more quickly.

"This is going to take time," Schadt cautions. "Drug discovery is not a one-year process."