Just 18 months after its launch, cancer diagnostic startup Foundation Medicine has already developed a clinical diagnostic test, forged partnerships with several pharmaceutical companies, and discovered a number of novel mutations that may point toward new drug treatments for cancer.

The company is at the forefront of a growing trend in cancer: choosing drugs based on the genetic profile of a patient’s tumor cells. The plunging cost of gene sequencing means scientists can read the entire genome of an individual’s cancer, leading to the rapid discovery of more and more cancer-linked mutations. Foundation Medicine is putting those findings—and cheap sequencing technology—to work to detect these mutations in newly diagnosed cancers.

The startup was formed last year by a handful of cancer and genomics experts in Boston, including genomics pioneer Eric Lander, with funding from Boston-based venture capital group Third Rock Ventures. They have since raised $33.5 million from several investors, including Google Ventures.

While most cancer diagnostics focus on individual genes or specific mutations, Foundation Medicine developed a diagnostic test to read the entire sequence of hundreds of cancer-linked genes. The company has yet to finalize the price of the test, but says it will be similar to the cost of testing five or six individual molecular markers. 

Foundation Medicine has so far processed several thousand tumor samples provided by academic medical centers, pharmaceutical companies, and clinical oncologists. The analysis detects whether the individual has mutations tied to existing drugs—both drugs that are approved for the patient’s specific cancer, and those that are approved for other conditions. The test, which takes about two weeks, will also highlight whether a patient has mutations that make him a candidate for experimental drugs in clinical trials. While the test is currently available to some oncologists, the company doesn’t plan an international launch until later next year.

The number of genes analyzed in the test will grow as the number of cancer-linked genes expands. The company will release an updated version of the test once or twice a year, says Michael Pellini, the company’s chief executive officer. “That’s why our work with pharma and academic medical centers is so important, because we get great insight into new therapeutics coming down the pike,” he says. “If a new therapy targeting a specific molecular profile is getting ready for human testing, we want to make sure we are adding that gene to our test.”

A number of pharmaceutical companies are using the test in clinical trials of new drugs. For example, if a study of a specific new drug failed to show a benefit in the patient population overall but did appear to work in a subset of patients, researchers can use Foundation Medicine’s test to determine if there is a particular genetic alteration that predicts who is most likely to respond.

Companies are also using the technology to direct patients into specific studies of drugs designed to target different mutations; it can often be difficult to enroll enough patients in such studies. Furthermore, if researchers collect multiple tumor samples from the same patient over time, they can use the test to understand how the tumor evolves and try to predict why one person’s tumor might recur more quickly than another’s.

Pellini says at least two pharmaceutical companies are considering using the technology in all cancer clinical trials going forward. “Pharma’s willingness to accept this type of molecular approach has been my single greatest surprise since joining Foundation Medicine,” he says. Historically, the pharmaceutical industry has been reluctant to test drugs in only a subset of patients, because this limits the number of people who might buy the drug.

“There has been a transformation among many pharmaceutical companies to where they understand that targeted therapeutics is the new paradigm,” says Pellini. Targeting clinical trials to only the patients who are most likely to respond to a drug makes it faster and cheaper to show that a drug works. “As everyone works to turn cancer into a chronic disease, as an industry, we will have the ability to treat patients for years rather than months—pharma has caught on to those concepts,” he says.

Because Foundation Medicine’s test is based on sequencing genes, rather than detecting known mutations, it can also find novel genetic changes. “As a by-product, a lot of novel discovery is coming out of these efforts,” says Pellini. “We are identifying novel gene fusions, translocations, and mutations, many of which have clinical significance.”

For example, researchers at Foundation Medicine identified a genetic translocation—where a segment of DNA is flipped around—in cancer tissue from a patient with non-small-cell lung cancer. Subsequent studies found that this mutation, which lies in a part of the genome that is being targeted by pharmaceutical companies, is present in about 5 percent of small-cell lung cancers. Pellini says the company is still working on how to deal with such new discoveries. “We are not a therapeutic company, and our primary interest tends to be on the diagnostic side,” he says. “But we recognize that some findings may have strong therapeutic implications.”