Just two years ago, scientists published the sequence of the first cancer genome, detailing the constellation of genetic mutations that likely enabled tumor cells to grow out of control. Now a handful of scientists and physicians are starting to use data from this "whole genome analysis" to help them choose the best drugs for their patients. Over the weekend at the Personal Genomes conference in Cold Spring Harbor, New York, three researchers presented cases highlighting how the approach can work on rare tumors and other unusual cases.

"It's time to use whole genome sequencing as a diagnostic tool to understand atypical cancer cases," said Richard Wilson, a geneticist at Washington University School of Medicine who led one of the studies.

Scientists have long known that cancer results when healthy cells acquire a combination of genetic mutations that let them grow out of control. Previous research has identified genetic variations that increase the risk that an individual will develop certain kinds of cancer, as well as specific mutations within the cancer cells themselves that render them sensitive to certain drugs.

With the advent of cheap sequencing, researchers can now scour tumors with unprecedented depth. They can compare almost all of the three billion letters of DNA in a patient's healthy cells and cancer cells and look for differences. Using this approach, researchers have sequenced hundreds of cancer genomes in the last year.

In one of the first cases to apply the technology to clinical practice, scientists from the BC Cancer Center in Vancouver twice sequenced the genome of cancer cells in a patient with a very rare type of tumor--an adenocarcinoma of the tongue. They sequenced the DNA after the cancer had spread, and then again after it developed resistance to a drug.

Because the cancer is so rare, there were no standard courses of treatment for oncologists to choose from. So Steven Jones and collaborators used the genetic variations that they had identified, along with their knowledge of the molecular pathways that have been implicated in cancer, to create a model for what might be driving cancer in that patient. They narrowed in on a defect in a specific molecular pathway linked to cancer cell growth. The patient's physician then chose to treat him with a drug that inhibits that pathway, and the patient's tumor stopped growing for eight months. "A rare tumor is never going to have clinical trials," says Jones. "With diseases with no options, any level of information is appreciated."

Unfortunately, as often happens with molecularly targeted drugs, the cancer eventually grew resistant to the treatment and started growing again. So researchers sequenced the new tumor tissue to determine what kind of genetic changes gave the cancer its new power. They found that the pathway implicated in the previous analysis had become even more active, and that a second pathway, also linked to cancer, had been altered as well. The research was published last month in Genome Biology.

The second set of findings came too late to help the patient. But Jones envisions how to move forward should a similar case come along. In a technique that is gaining traction in clinical cancer research, scientists implant tumor cells biopsied from a patient into a mouse, which then grows a tumor similar to the patient's. Jones's team could then hypothesize which drugs would work best using the model created from the genome analysis, and test those drugs on the mouse before trying them in the patient.