Large-scale research projects have begun to give scientists knowledge about the entire collection of genetic mutations in different cancers, but so far very little of that knowledge is applied to patients. A startup called Foundation Medicine is hoping to change that, bringing comprehensive analysis of cancer genomes to the clinic. The company, based in Cambridge, MA, has several leading cancer and genomics researchers from the Boston area behind it. It was formed in 2009 and raised its first $25 million in financing this April, led by Boston-based venture capital firm Third Rock Ventures.

Many cancer researchers believe that therapies could be more effective if they target genetic aberrations in a patient's cancer. In recent years, there have been a handful of successes in targeting cancer treatments in this way: for example, the drug Herceptin can be effective in breast cancer patients with a specific mutation in the HER2 gene. But so far, this kind of targeted cancer treatment has been limited to a select few genetic mutations in specific cancers, even though most cancers derive from several genetic mutations in combination. Foundation Medicine wants to create a test that gives a comprehensive view of the genetic aberrations in a cancer sample.

Foundation Medicine's CEO, Alexis Borisy, believes that the time is right to start thinking beyond single mutations. Drugs that target specific genetic mutations in cancer are now "starting to come fast and furious," he says. But other mutations can indicate that a drug will not work, eliminating wasted time with ineffective treatments. And scientists have begun to uncover that mutations known to be important in one kind of cancer can also occur in another: a drug developed for lung cancer could, in rare cases, help a patient with melanoma. Borisy believes that this discovery in particular illustrates that all cancer patients should receive a comprehensive test for known genetic mutations. "Our belief is that knowing that information can have a profound effect on treatment," he says.

The company plans to develop a laboratory test for physicians that would analyze a patient's cancer sample for genetic aberrations that could influence clinical decision-making. As a start, the test would focus on 100 genes that have been shown scientifically to play a role in cancer treatment and progression. Eventually, the company would like to include any additional genomic information that may be actionable clinically. And over the long term, the hope is to expand to analyzing not only genes but the chemical makeup of cancer samples as well. The testing would take place at a central laboratory, and the plan is to offer an interpretation of the data and how it could influence a patient's treatment. Borisy says the test would cost in the low thousands--in line with other clinical cancer tests.