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Toma Biosciences Launches with ddPCR-based Copy Number Test to Guide Tailored Cancer Therapy


NEW YORK (GenomeWeb) — Bay Area startup Toma Biosciences emerged from stealth mode this month with a new cancer assay designed to provide physicians with information to help them personalize and optimize treatments for cancer patients.

The company's test, called Amplinome, specifically uses Bio-Rad's Droplet Digital PCR platform to detect copy number alterations, also called amplifications, in 12 different genes that are known to be important in cancer and have been linked to specific, existing US Food and Drug Administration-approved therapies.

Armed with nearly $6 million from a recent private financing, Toma is now looking to drum up customers for Amplinome, which it offers out of the company's Foster City, Calif.-based CLIA-certified laboratory. In addition, the company plans to launch a variety of other products in coming months that focus on copy number variation or use Droplet Digital PCR, President and CEO Mike Lucero told PCR Insider in a recent interview.

Toma has been around for several months and obtained CLIA licensure in January but was under the radar until it launched a new website this month, Lucero said. In addition, the company will have a presence at the American Society of Clinical Oncology meeting next week in Chicago.

The company's co-founders and scientific/medical advisors are all affiliated with the Department of Medicine at the Stanford University School of Medicine: Hanlee Ji, an assistant professor of oncology; Lincoln Nadauld, an adjunct professor of oncology; James Ford, an associate professor of oncology and genetics; and Calvin Kuo, a professor of hemaotology. Nadauld is also a medical oncologist and director of cancer genomics at Salt Lake City, Utah-based non-profit health system Intermountain Healthcare.

Amplinome, Toma's first test, uses digital PCR to interrogate formalin-fixed, paraffin-embedded solid tumor samples for the presence of amplifications in 12 different genes: AURKA, BRAF, CDK4, CDK6, EGFR, FGFR1, HER2, HER3, JAK2, MET, SRC, and VEGFA, according to the company's website.

As the company further explains, copy number alterations are a common structural feature of the genome, underlying both population-level genetic heterogeneity and somatic mosaicism within individuals and tissue. Gene amplifications are also known to underlie the pathogenesis of some cancers, and a number of FDA-approved drugs currently exist to target those genetic alterations — for example, Herceptin, which interferes with the HER2 receptor.

In order to identify the 12 genes comprising its panel, Toma scoured The Cancer Genome Atlas, "which has thousands of profiled samples … and includes the amplifications, and also RNA-seq data," Lucero said. "We searched across that for genes that are commonly amplified in cancer, and then we looked for the overlap where those genes also have drugs associated with them."

"If you search TCGA, you'll find about a 30 percent hit rate [where] the atlas would predict [that] one of the 12 genes would be amplified and we'd be able to make a recommendation," Lucero added. "Our service has actually been available for about five months now, and we've seen that it's better than that — more like 50 percent of the samples that come through our door actually have an amplification that we can detect and make a recommendation to an oncologist."

A crucial aspect of the Amplinome assay is the use of Bio-Rad's QX100 or QX200 Droplet Digital PCR system. Toma's selection of this platform is perhaps not surprising considering that Lucero was previously vice president of sales and marketing at QuantaLife, the company that developed the Droplet Digital PCR technology and was acquired by Bio-Rad in 2011 for approximately $162 million.

"Digital PCR really enables copy number detection more than anything else that has existed," Lucero said. "Arrays really pointed to the existence of copy number alterations — that there were a lot more of them out there than people were expecting — but digital PCR really has great quantitative resolution." Lucero also noted that because solid tumors are typically mixed populations of cells, other technologies have difficulty detecting amplifications whereas digital PCR does not.

Furthermore, digital PCR has "great workflow characteristics, so it is inexpensive to put out a test like this … for 12 genes, and charge customers a price that isn't ridiculous," Lucero said. Currently, Amplinome has a list price of about $1,900, he added.

Finally, the fact that digital PCR enables direct analysis from FFPE tissue samples gives it an advantage over other technologies such as sequencing, which requires relatively large amounts of sample to be effective.

Derrick Haslem, director of medical oncology at the Southwest Regional Cancer Clinic at Intermountain Healthcare, is an early adopter of Amplinome, having used the test for a few months in order to better personalize cancer treatments for his patients.

"Certainly everyone right now is noticing this paradigm shift in oncology, focusing less on the anatomic location of cancers and more on the genomics behind it," Haslem told PCR Insider. "Because of this paradigm shift, we're looking at ways to personalize cancer care and move away from traditional standard chemotherapies, which are toxic and cause all kinds of problems and, quite frankly, often don't work very well."

Haslem noted that his clinic is currently using Amplinome as a way to help better tailor palliative care to cancer patients. "We are really obligated to treat people with standard treatments up front, but these are patients with metastatic disease or incurable cancer, and particularly solid tumors," Haslem said. "The goal is to buy quality time. But once these people have failed these first-line treatments … then we start scratching our heads a little bit. We can do more standard chemo, second- or third-line treatments, but with each round you're introducing more complications or side effects, and much less possibility of response."

The confluence of technologies that are able to test for the genetic underpinnings of cancer progression and the development of new drugs that target these mutations has "opened up this whole new world of potential treatment options," Haslem said.

Now if a patient fails first-line treatment, Haslem said, his clinic suggests the possibility of an Amplinome test to see if targeted drugs exist that could potentially block specific mutations and slow cancer progression.

"Most of these drugs are orally administered … and they're not without their side effects," Haslem said. "But in that situation we're trying to ride that response as long as possible and turn this into a chronic disease, where they might never be cured but can live pretty normal lives."

Haslem conceded that it doesn't matter as much to physicians what methodology is used to provide genetic testing. "The end user wants fast, accurate results," he said. "The way Toma does it, it does come faster, and it is a very clear result — almost like a binary system: it's there or it's not. There is not a lot of interpretation there for me. As an end-user oncologist who's trying to explain it to a patient, just to say … it's there or it's not is a really powerful tool."

Both Haslem and Lucero said that the turnaround time for an Amplinome test is typically less than two weeks.

Neither Toma nor the early adopters of its test have yet published or presented data on Amplinome, but Haslem said that his cancer center recently received approval to conduct a retrospective study that will compare Amplinome results with historical controls in the clinic's database.

"That will be kind of our first step toward that, and we'll use these data to justify doing a prospective study, as well," Haslem said. "The important thing about this is that it's relatively new, so every patient is really an n of one. We hope to continue to store this data and track these outcomes so we can make informed decisions, such as deciding that all these patients who had [a particular] amplification and didn't respond to this drug, so we won't continue administering it. But if they did have a good response, maybe we push that up the line."

As for Toma, it will present some preliminary data from Amplinome at ASCO next week, Lucero said, and the company is already mulling the possibility of expanding the panel of genes comprising the test. Furthermore, "we do have a robust pipeline and you'll see other products from us," Lucero said. "I guarantee they will feature copy number variation, but I don't want to talk about it yet."

Further, Toma is currently seeking CAP accreditation for its Foster City lab, and the company just raised almost $6 million in new funding from private investors led by Paladin Capital Group, Prolog Ventures, and Vital Venture Capital. Lucero said that the firm also has some prominent angel investors, as well as an unnamed academic institution investor.