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Strata Oncology Aims to Match Patients With Pharma-Sponsored Precision Medicine Trials

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NEW YORK (GenomeWeb) – Strata Oncology plans to help pharmaceutical companies recruit patients for their targeted cancer drug trials more quickly by providing medical centers with free tumor sequencing and access to those trials for their advanced cancer patients.

Backed by $12 million from a recent Series A financing and a strategic partnership with Thermo Fisher Scientific, the startup, based in Ann Arbor, Michigan, plans to sequence the tumors of 100,000 cancer patients over the next three years or so, starting at the end of this year or early next year, and to match them to pharma-sponsored clinical trials of targeted cancer agents.

Dan Rhodes, Strata's CEO, told GenomeWeb that the idea for the company emerged when he was working at Thermo Fisher Scientific, where he was part of a team that helped to implement the Oncomine assay, a targeted sequencing panel that runs on the Ion Torrent PGM , for the National Cancer Institute's Molecular Analysis for Therapy Choice (MATCH) trial.

Originally, Rhodes was the co-founder and CEO of Compendia Bioscience, a cancer genomics and informatics firm that built the Oncomine database of cancer mutations. Life Technologies, which became part of Thermo Fisher Scientific two years ago, acquired Compendia in 2012. Peter Wyngaard, the former CTO of Compendia, has joined Rhodes at Strata.

The MATCH trial, which opened last summer and is led by Keith Flaherty at the Massachusetts General Hospital Cancer Center and Harvard Medical School, studies how well patients stratified for treatment through genomic testing of their tumor respond to phase 2 targeted cancer drugs. Patients are screened using Thermo Fisher Scientific's Oncomine Comprehensive Panel, which analyzes about 150 cancer-related genes and sequences both DNA and RNA. Last year, researchers at the University of Michigan Medical School, led by Scott Tomlins, and at Thermo Fisher Scientific published their validation of the assay.

While working on the MATCH trial, Rhodes said, he and his colleagues realized that quite a number of trials for targeted cancer drugs require genetic markers for enrollment but that many advanced cancer patients never have their tumors sequenced because health insurance doesn't pay for it, for lack of demonstrated clinical utility.

"Because of that, most patients never know if they're eligible for precision medicine trials, and then the pharma trials can take years to enroll," delaying the approval of drugs that could benefit patients with specific mutations, Rhodes explained. "It's sort of a Catch-22."

As a result, Rhodes, Flaherty, and Tomlins founded Strata Oncology last year to offer cancer patients a screening trial that is similar in nature to NCI MATCH but proceeds on a much larger scale, focusing on pharma-sponsored rather than NCI-sponsored trials.

MATCH already proved that a clinical study can be conducted at a national scale across hundreds of investigators, Rhodes said, and "we want to take that sort of model and scale it up."

Instead of recruiting 3,000 to 5,000 patients like MATCH, Strata hopes to enroll 100,000 patients over the next few years to its Strata Trial, providing sequencing free of charge to advanced cancer patients treated at one of its partner institutions. These patients would then be matched to a portfolio of clinical trials from pharmaceutical firms. "We believe that if we can do that, we can turn what is multiple years of enrollment into months," Rhodes said.

"What we've recognized is that to complete these clinical trials that often target very small sub-populations of patients … and power them for drug approval, you really need to screen tens of thousands of patients, and it's beyond the scale of any single institution," he said. And while Strata's trial may be less attractive for large academic cancer centers, which have built their own sequencing capabilities and run their own trials, those centers treat the minority of cancer patients in the US, he said.

Eventually, the pharma companies will pay Strata, based on the value the company provides to them in the form of accelerated clinical trials and drug approvals. "We're not planning to generate revenues per test. Our revenues come via our pharma partnerships," he said, which is a different business model than, for example, that of Foundation Medicine, which gains part of its revenue from testing fees. "We recognized that the real sweet spot for clinical sequencing today is in clinical trials," Rhodes said.

"Ultimately, if we're successful, perhaps sequencing will be more likely to be reimbursed, and all of the sequencing providers would benefit from that, including, for example, Thermo Fisher's customers and Foundation Medicine and the like," he said.

Earlier this year, Thermo Fisher Scientific became a strategic partner of Strata, providing it with Ion S5 XL sequencing instruments, AmpliSeq reagents, and Oncomine assays, though the terms of the partnership remain undisclosed. 

Together with a $12M Series A financing round that Strata announced last month, the company, which has a staff of about 15 and plans to grow to about 25 by year's end, is now building a CLIA-certified high-throughput sequencing laboratory in Ann Arbor. Arboretum Ventures and Baird Capital jointly led the financing, and additional funding came from Strata's existing investor Michigan eLab.

The sequencing lab will have sufficient capacity to run hundreds of samples per day and up to 50,000 samples per year and will be exclusively equipped with Ion Torrent sequencing instrumentation. It will run both the Oncomine Comprehensive Assay, which analyzes almost 150 genes, and the Oncomine Focus Assay, which targets about 50 genes. To enable such high throughput, Strata had to develop new workflows and protocols for automated DNA isolation from formalin-fixed paraffin-embedded tissue blocks, Rhodes said. On the back end, the company combines Thermo Fisher Scientific's existing software for variant calling with its own reporting and medical review tools.

Strata is in the process of building a portfolio of clinical trials from pharmaceutical firms that it will offer to clinical sites participating in the Strata Trial. For that, it is looking for drugs that have shown a response in genetically defined patients and for which a dose for phase 2 studies has been determined. "The concept has been proven, the dose is identified, and now these studies really just need to be powered," Rhodes said. On the patient side, "these are the medicines that the patients really should have access to," he added.

At the moment, most studies use tissue-based genetic alterations for enrollment that are either small mutations, copy number variants, or gene fusions. But as studies start looking at liquid biopsy markers as inclusion criteria, "we will absolutely move into that direction as well," Rhodes said.

Also, the company plans to include immune-oncology trials in the future, some of which will likely use gene-expression-based biomarkers, which will become part of the RNA sequencing component of Strata's test, he said.

Offering access to clinical trials, in addition to genetic testing, is an important part of Strata's business model. "What we realized was, sequencing alone is not enough," Rhodes said. Even if a patient matches to a trial based on their test results, for example, that trial might not be available to their physician or at their institution, he said, and advanced cancer patients are often reluctant to travel far distances.

Also, at the moment, advanced cancer patients usually only have their tumors sequenced after they fail standard therapy. "We're trying to change the dynamic to say, as part of the Strata trial, we will screen the patient's tumor as soon as advanced disease is diagnosed, so we know the mutation status," Rhodes said. "You can put the patient on standard therapy, but the moment the patient progresses, you already know what trial they are eligible for, and that trial will be available to you locally."

Rhodes said Strata is currently in discussion with a number of pharmaceutical companies and anticipates announcing its first couple of partners soon. "We think there are about a dozen trials that we would like to have in the portfolio," he said, but it will likely take a number of months to assemble them. "Our goal is that when we launch the sequencing capability to our partner sites later this year, we'll have our initial set of therapeutic protocols but we will continue to build that out over the first half of next year."

Likewise, Strata is in talks with large academic medical centers, private hospitals, and oncology practice networks that will participate in the Strata Trial. Specifically, the company is looking for institutions that have experience with running clinical trials, have large patient volumes, and are interested in improving their precision medicine offering for their cancer patients.

As the Strata Trial gets going next year, Rhodes said, the company will be able to estimate how large of a clinical network it needs to build to reach capacity for its sequencing lab, but the hope is that the Strata Trial will be available at 50 to 100 sites around the US.

"By participating in the trial, institutions gain access to no-cost tumor sequencing for their entire advanced solid tumor cancer population," Rhodes said, which is attractive to oncologists because they do not need to worry about insurance coverage of the test for patients or whether their institution can shoulder the costs.

"We believe that's going to really dramatically increase participation in sequencing and in precision oncology trials," he said. "But this is a new model, and we've got to see just how much we can increase participation, so that just becomes a standard at an institution."

"For us, our measure of success will be how quickly we can get to scale and have tens of thousands of patients sequenced every year, and how quickly we can get these patients on to appropriate precision medicine studies and get these drugs approved more quickly," Rhodes said.

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