An Omniseq scientist working in a lab at the company's facility in Western NY.

Omniseq: Customizing Cancer Care

March 28, 2019

Fighting cancer is one of the most frustrating challenges of modern science. Cancer cells offer untold varieties of genetic mutations. No one treatment works for all, and even effective regimens may fall short once the cancer evolves.

It’s a deadly cat-and-mouse game that kills more than 600,000 people a year in the U.S. alone, according to the National Cancer Institute.

Consider the 66-year-old great-grandmother whose uterine cancer responded to hormone treatment. A few years later, it spread to her lungs. But this new iteration was different. Doctors examining her tumor in the lab determined that even the latest targeted therapies, geared to specific genetic profiles, offered nothing that might work against the recurrence. The earlier hormone treatment regimen, which had been so effective, proved useless.

Luckily, a new cancer diagnostic laboratory spun out of the vibrant Roswell Park Comprehensive Cancer Center in upstate New York offered hope. OmniSeq (pronounced omni-seek), which was founded in 2015, and has received significant funding from the Center, applied its innovative profiling methods to cancer tumor samples sent to its labs in Buffalo. The company’s Immune Report Card revealed that the personal specifics of her immune system indicated that pembrolizumab, a newly approved drug, could help her body’s immune system kill off the mutant cells. The advice from OmniSeq proved correct. The pembrolizumab treatment destroyed the cancer.

Omniseq: Customizing Cancer Care

Learn more about how one New York State company is changing cancer treatment.

This story is one of the inspiring examples of the potential for immuno-oncology, a field of cancer research and treatment with great promise. Rather than bombarding cancer cells with radiation or chemicals, immuno-oncology seeks various methods — from drugs to genetic engineering — to rewire either the body’s immune system or the cancer cells themselves. The immune system then pounces on rebellious cells within the patient’s body just as if they were an invading infection.

The key is matching the right treatment to the right patient. Most treatments work only on specific subgroups of patients, and even then on only specific subgroups of cancers. Making the match requires analyzing the patient’s tumor and immune system in detail, and finding FDA-approved or experimental treatments that have a chance of winning the battle on one specific field. Taking too long to decide a treatment path, even a few months, could prove fatal.

OmniSeq CEO Mark Gardner, who left a 12-year position at biotech giant Thermo Fisher Scientific outside of San Diego to run the Buffalo start-up, understands how critical his work is. “Given how precious time is for patients with late-stage cancer, our core mission is to focus on who is likely to respond to one or more of the approved drugs,” he says. “If they don’t, those tests will lead us to what clinical trials might be appropriate to try.”

Gardner was drawn to the shores of Lake Erie by the researchers, clinicians, and entrepreneurs in and around Roswell Park. The Center, which receives state funds, promotes health and well-being through a variety of programs, ranging from advanced cancer research to free breast cancer screenings to call-in lines for smokers who are trying to quit. It’s a community that Gardner says is big and talented enough to break new ground, but small enough that its cancer fighters are supportive rather than suspicious of one another.

“If I ask for a meeting with anyone in Buffalo, I never get turned down,” he says. “And while we’re a for-profit company, we collaborate on grant proposals for others because we want to encourage and support the community. That doesn’t happen everywhere.”

When pursuing a cancer cure with OmniSeq, the patient’s physician first submits tissue samples, often through the company’s nationwide arrangement with testing giant LabCorp. OmniSeq offers several tests: basic genomic and immune profiles, evaluation of both immunotherapy and targeted therapy options, and a specific test that identifies patients who might benefit from pembrolizumab, sold as KEYTRUDA, for use against many types of tumors, from cervical and gastric cancer to melanoma and classical Hodgkin lymphoma — and of course, the great-grandmother’s lung tumor mentioned earlier.

Their assays test for variants in all the known genes for which there are FDA-approved drugs, or for which there are clinical trials of experimental drugs with clinical evidence of benefit, Gardner says. They also test for up-and-coming variants in early-stage clinical trials. In addition, he says, “We use a much gentler method of extracting the DNA and RNA that we test than our competitors. This enables us to report results much more frequently on very small amounts of tumor tissue.” Traditional tests, by contrast, sometimes require the patient to schedule another biopsy to provide more sample tissue.

Besides improved tissue collection and test methods, OmniSeq has built a proprietary database in which they can match test results to treatments observed to work for patients with similar profiles, and identify those which are geographically closer to home. The result: Instead of what could be months of analysis and searching, the company can return a report to physicians within a month. With cancer, months are often in short supply.

Gardner repeatedly stresses that advances in testing aren’t a cure-all. Not every patient matches a treatment or trial. Treatment plans may still involve grueling chemotherapy, and the success rates of different treatments and trials vary widely, from likely to long shots. About 15 percent of the cancer patients OmniSeq tested had a gene mutation in their submitted tissue sample for which there was an FDA-targeted therapy.

Yet for cancer patients and those who treat them, having more options sooner to help even a fraction of patients is nonetheless a life-saving improvement. That’s why Roswell Park, the nation’s oldest cancer hospital, provided Series A funding for OmniSeq. It has also allowed the accomplished pathologist Carl Morrison to set up a for-profit business across the street from his role at Roswell, where he’s still Executive Director.

“Roswell is a big hospital,” Gardner says. “But it wasn’t big enough to support all the IT and infrastructure needed to do an excellent job. Morrison and others reasoned that selling to other hospitals as a for-profit company was the best way to continue what they had started at Roswell Park’s Center for Personalized Medicine.”

In 2017, LabCorp supplied a Series B investment and began to offer OmniSeq’s reports as part of its nationwide medical testing services. To date, most of the patients whose tumors OmniSeq evaluates and reports on are in western New York, but LabCorp’s reach is broadening that to the entire U.S. — and possibly beyond.

Breakthroughs in treatment-matching don’t only save the lives of the patients, they help advance the development of new drugs and other therapies. They bring qualified patients with niche genetic profiles and rare cancers into clinical trials that are perennially short on participants. This has the potential to more quickly identify winning treatments and speed the path to market for future treatments.

That potential upside for big pharma is huge. This past summer, Swiss giant Roche acquired a similar start-up, Foundation Medicine, for $5.3 billion. The unicorn-level valuation was based not on the potential to charge for tests, but the promise of much better patient-matching to populate clinical trials, bring more treatments to market, and eventually find more customers for them.

Medicine is taking the same route that tech giants do: Encourage innovative start-ups like OmniSeq, and then license or flat-out buy the successes. Yes, it’s a more profitable approach to healthcare research, but for patients whose days are numbered, it’s also a faster route to defusing cancer’s ticking bomb.

Visit: esd.ny.gov/life-sciences 
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This story was produced by the WIRED Brand Lab for Empire State Development