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Startup to Offer Patients a Genetic Profile of their Cancer

Foundation Medicine will provide a personalized picture of a patient’s disease.

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.

Borisy says that the company is focusing on bringing together four areas of expertise: genomic sequencing and analysis, cancer biology, clinical oncology, and information science. The first challenge is to translate genomics research tools into a clinically useful and reliable test. The company will then need to verify the utility and cost effectiveness of such a test in a real-world clinical setting. Another challenge will be to provide clinicians with straightforward information about how to interpret the results and act on them.

Foundation Medicine’s founding scientific advisors are Eric Lander, head of the Broad Institute, a genomics research center in Cambridge, MA and three leading figures in cancer genomics at the Broad and Harvard Medical School: Todd Golub, Matthew Meyerson, and Levi Garraway. Myerson says that the company’s approach will harness the power of advanced genomic sequencing to give clinicians accurate information about a patient’s cancer. “A relatively comprehensive picture of the cancer genome is probably the best way to get a good understanding of what is the right diagnostic and the right treatment for the patient,” he says.

Myerson also believes it makes sense to act now, even though the ability to target decision-making to specific genetic alterations is still in its infancy. Borisy points out that in a few years the federally funded Cancer Genome Atlas Project will have sequenced tens of thousands of cancer genomes, several thousand for each type of cancer. The company is banking on the fact that these efforts will yield usable information that can to be translated to clinical practice.

“The idea is fabulous,” says Gerold Bepler, CEO of the Karmanos Cancer Institute, in Detroit. “I think that in the future this will really revolutionize the way we treat patients.” The question, he says, is whether this concept is truly actionable right now. For example, one of the technical hurdles that stands in the way of bringing cancer genomics to patient care is the way cancer samples are made. Most research studies involve fresh frozen samples that are much easier to glean information from; clinical samples are typically chemically fixed and embedded in paraffin, which can alter the chemical state of the cells. These samples may also have a relatively low level of cancer cells to work from. So getting accurate information from real-world clinical samples will be a significant challenge, particularly if the company wants to expand its analysis to the chemistry of cancers.

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