When the stimulus bill passed last year--allocating $20 billion to help doctors and hospitals adopt electronic medical records (EMRs)--many scientists were excited about the possibilities for medical research. EMRs provide vast amounts of medical information that can be combed automatically and used to ask questions that are too expensive or perhaps unethical to study in traditional clinical trials, such as whether newer, more expensive treatments are more effective than older ones.

"There is a lot of federal funding right now supporting the development of the infrastructure to do that kind of work, as well as to look at comparative effectiveness research using databases," says Richard Tannen, a physician at the University of Pennsylvania, in Philadelphia. "But it's a complex and difficult problem, in some ways more difficult than people appreciate."

While the idea of using electronic medical records for research has been around for more than a decade, it's only recently started to take off. Scientists and physicians are now scouring the growing number of electronic medical records and genomic databases to figure out how to use this vast medical resource to answer a number of questions in medicine, such as why patients can respond so variably to treatment, and how genetics or other factors might contribute to this.

It has been necessary to invent new analysis methods to glean useful data from often disparate databases, and to make sure that the results produced aren't biased. Studies based on data from EMRs are subject to the same concerns as observational studies, in which scientists look for links between an individual's natural behavior and their health. It was observational study that suggested that hormone replacement in postmenopausal women reduced risk of heart attack, while subsequent clinical trials found that the treatment increased risk of heart disease and stroke.

Dan Roden, a clinical pharmacologist at Vanderbilt University, in Nashville, TN, is beginning to address some of those challenges in a pilot project linking EMRs to genomics databases. While he ultimately wants to use EMRs to better understand why different patients can react so differently to the same drug, the project is starting with the most basic questions. "We wanted to ask what genetic information would you want to access to take care of someone, what are the informatics challenges, and what are the ethical challenges in storing people's information?" says Roden.