Foundation Medicine Raises $25M to Get to the Bottom of Cancer Genomes

Xconomy Boston — 

The trick to beating cancer could be a single test that shows all known genetic traits in each person’s tumor, and that also matches those results to the best treatments. Boston-based Foundation Medicine reports today that it has raised the first part of a planned $25 million round of Series A venture funding to make comprehensive genomic analyses of tumors a standard tool in the fight against cancer.

A crack team of cancer, genetics, and industry veterans from the Boston area has assembled around the startup. Boston-based Third Rock Ventures, founded by former executives of the cancer drugmaker Millennium Pharmaceuticals, has incubated the company and led the first-round financing. Alexis Borisy, an entrepreneur-in-residence at Third Rock and the former CEO of Cambridge-based CombinatoRx (NASDAQ:CRXX), is the startup’s founding chief executive (something we were the first to report back in February). And Eric Lander, a pioneer of genomics research and an advisor to President Barack Obama on science and technology policy, is headlining the group of scientists and physicians who are advising the startup.

Foundation Medicine, which was formed in 2009, has come into being as high-speed DNA sequencing and a slew of academic studies help to uncover new genetic mutations that, say, protect tumors from certain therapies, or help cancer cells grow out of control. Drug companies are developing cancer drugs for patients who have specific genes that make them likely to respond well to the treatments, building on Roche-Genentech’s success in marketing the breast cancer drug trastuzumab (Herceptin) for women with the HER2 gene. Also, a growing number of startups are focusing on providing new genetic tests that help guide physicians in treating cancer patients.

Foundation Medicine is taking its own approach to personalizing cancer treatments. While many previous firms have focused on developing tests to detect specific genes linked to likely outcomes of cancer treatments, Foundation Medicine is planning to use high-throughput DNA sequencing technologies to expose the plethora of genes and genetic variants in cancer genomes, according to Borisy. Borisy and Third Rock are betting that the future of cancer treatment will involve a single analysis of cancer DNA in guiding treatments, rather than multiple tests that screen for individual genes or groups of genes.

Today DNA sequencing is done primarily in research settings, with extremely limited clinical use. Borisy, however, says that it’s time to put this technology to work for people with cancer. “If many patients would benefit from this deep understanding, then there needs to be a way to take this from being a research tool to something that would be useful and meaningful and work in the routine practice of clinical oncology,” he says. “That has been the driving motivation and inspiration behind Foundation, and it’s quite clear that this is the way the world is going.”

The company’s exact strategy is evolving, according to Borisy, yet some details are clear. The firm plans to set up a central lab in the … Next Page »

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One response to “Foundation Medicine Raises $25M to Get to the Bottom of Cancer Genomes”

  1. gpawelski says:

    Most cancer patients won’t benefit from molecular profiling.

    Molecular profiling examines a single process within the cell or relatively small number of processes. All the gene mutation or amplification studies can tell is whether or not the cells are potentially susceptible to a mechanism of attack. The aim is to tell if there is a theoretical predisposition to drug response. It doesn’t tell you the effectiveness of one drug (or combination) or any other drug which may target this in the individual. There are differences.

    There are many mechanisms/pathways to altered cellular function. I believe functional tumor cell profiling would be more beneficial. It measures what happens at the end, rather than the status of the individual mechanisms/pathways. It assesses the activity of a drug (or combinations) upon combined effect of all cellular processes, using combined metabolic and morphologic endpoints, at the cell population level, measuring the interaction of the entire genome.

    Cancer is a complex disease and needs to be attacked on many fronts.

    What is needed is to measure the net effect of all processes within the cancer, acting with and against each other in real time, and test living (fresh) cells actually exposed to drugs and drug combinations of interest. The key to understanding the genome is understanding how cells work. How is the cell being killed regardless of the mechanism.

    Cancer cells often have many mutations in many different pathways, so even if one route is shut down by a targeted treatment, the cancer cell may be able to use other routes. Targeting one pathway may not be as effective as targeting multiple pathways in a cancer cell.

    Functional tumor cell profiling tests additional drug concentrations for the “targeted” agents, some of which have very steep dose response relationships (unexpected toxicities such as the recently described microangiopathic hemolytic anemia that can occur from the Sutent/Avastin combination). Should patients knowingly take the unknown risks of combination therapy that is known to work well in vitro against their tumor?

    Another challenge is to identify for which patients the targeted treatment will be effective. Tumors can become resistant to a targeted treatment, or the drug no longer works, even if it has previously been effective in shrinking a tumor. Drugs are combined with existing ones to target the tumor more effectively. Most cancers cannot be effectively treated with targeted drugs alone.