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GeneKey Sees Breadth of Cancer Genome Advisory Service as Differentiator in Rapidly Growing Market

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By Molika Ashford

GeneKey, a spinoff from online cancer-guidance software firm CollabRx, is looking to differentiate itself in the rapidly growing personalized oncology market by offering a comprehensive service that uses a range of genomic approaches to recommend treatment options that physicians might otherwise overlook.

The company, which spun out of CollabRx last year, is currently looking to ramp up its customer base after evaluating the service in around 20 cancer patients since its start.

However, recognizing that the high price tag for the service — around $30,000 — has limited its market to date, company officials are also exploring options for developing a simpler version that would be accessible to a larger patient base.

GeneKey's president Raphael Lehrer told PGx Reporter this week that the firm hopes to attract more patients for its full-service analysis and support program, even as it considers ways to create a cheaper process that it could market to a wider population some time in the future.

The GeneKey service is based on gene expression and copy number analysis across the whole genome of a patient's tumor and normal tissue. This data, which can also include genome sequencing if necessary, is coupled with a systems biology-based triangulation of the most promising drug candidates for each patient; deep, in-person consultation with a patient's physician; and ongoing support for therapeutic decision making, according to the company.

"We had started off fairly slowly to gain confidence on a number of fronts and [now], while I wouldn't say we've got it completely, [my] confidence [has grown] that this is something that can be helpful to patients," Lehrer said.

Now, he added, "we are hoping to begin to do this more broadly."

The company faces competition from a number of genomically informed personalized oncology services, such as Foundation Medicine, which is developing a sequencing panel intended to guide therapy. A growing number of academic research centers are pursuing similar strategies, including the University of Michigan, Fox Chase Cancer Center, Baylor College of Medicine, the University of Washington, and others.

Many of these offerings are available at a tenth of the cost of GeneKey's service, but the company is hoping to distinguish itself in its breadth and personal touch.

Another differentiator, Lehrer said, is its agnosticism in regard to actionable pathways and thus potential treatments. While many personalized oncology offerings limit their guidance to cancer drugs that are already on the market or in clinical trials, GeneKey scans a broader swath of the pharmacopeia to identify compounds not traditionally considered for oncology indications. The firm cites thalidomide, rapamycin, and metformin as examples of non-cancer therapies that have recently been found to have anticancer potential.

Nevertheless, without data to show that the company's service actually affects patient outcomes, it remains unclear whether GeneKey's broader service actually offers better odds against cancer.

A Face-to-Face Approach

GeneKey's procedure, Lehrer explained, is similar to that previously offered by CollabRx under the name CollabRx One.

"We work with individual patients and their physicians generating full-genome data across a number of platforms, and use that data to triangulate and understand what the driving mechanisms are behind the cancer," he said. "Then we focus on which ones represent actionable therapies and work with the physician to talk about the implications for the patient."

Lehrer explained that GeneKey split off from CollabRx because the company had come to the point where it was essentially two different businesses. "One of them was a web-based business, and the other, [GeneKey], is essentially a life science business for individual patients and physicians," he said.

CollabRx has since developed a web-based application called the Targeted Therapy Finder that patients can use to search for possible drugs and clinical trials associated with their cancer's molecular profile (PGx Reporter 4/27/2011).

Initially, the CollabRx One service was integrated with CollabRx's web-based projects, but as GeneKey, the focus seems to have become more face-to-face.

"Typically we have a face-to-face meeting with doctor and patient to go through why we think these are the best, strongest cases that we have, [and] if they decided they want to integrate this into therapy, [how best to] help them do so," said Lehrer. "Depending on the doctor and the patient's desire for it, it can [really] become an adjunct" to the medical team, he said.

Lehrer took care to stress that GeneKey does not recommend treatments, nor is it a patient-directed service, but rather a physician consultation, and so would not likely fall under the umbrella of direct-to-consumer testing services that have come under increasing scrutiny by the US Food and Drug Administration.

He explained the service's role as a form of "support" to physicians, who ultimately make decisions and recommendations to their patients about treatment.

When CollabRx initially launched its service in 2009, it planned to look at 15,000 genes and determine which cancer drugs and investigational compounds patients would likely respond to based on their genetic characteristics. GeneKey initially contracted with Expression Analysis and the University of Southern California's Core Laboratories for data generation (PGx Reporter 03/11/2009).

Lehrer said Expression Analysis is still GeneKey's primary vendor for expression/CNV analysis, but the company is evaluating alternative labs. For cases where sequencing is required, the company has so far used ABI's SOLiD platform, but he noted that GeneKey will likely use Illumina for an upcoming case.

"From a technology perspective, we are fairly agnostic. We are looking to use technology that provides the best data and we outsource our data generation precisely so we're not tied to any specific technology and can really evolve as we go," Lehrer said. As sequencing costs continue to plummet, it's likely that the company will move away from array-based gene expression analysis toward RNA-seq and whole-genome sequencing, he said.

Lehrer also stressed that the potential therapies that can be identified through the GeneKey's "triangulation" are not limited to known cancer-associated pathways.

"What we're doing for every patient is looking across all of known canonized biology, basically. So we are open not just to cancer pathways or pathways already known for cancer, but also things that are [potentially] not yet known."

"We're pulling from the entire pharmacopoeia as well as clinical trials," he said.

Lehrer acknowledged that the $30,000 price tag for the service has so far limited the number and types of customers who seek it out.

"I think that we are seeing out there a lot of demand for this, but … our patients tend to fit a certain class … looking for, if you will, no stone unturned and the best that is out there."

He said that the company has some ideas about how it might distill knowledge gained in performing its full service into a narrower procedure that is affordable and accessible to a wider audience.

Lehrer envisions the service evolving into a two-part process — "first focusing on areas that we essentially have experience with seeing before, [but in a] relatively simple process which could have broader interest. Then the big guns come after that."

Essentially, the company would start with a more limited analysis for most customers, while patients who either need or desire a deeper look would follow up with the comprehensive service.

However, he said, these adaptations would not take place any time soon. "I'd say right now, as long as we are finding novel things, things that we didn't expect in terms of our approach, we would be doing a disservice to grow too quickly."

Other Services

GeneKey stresses the agnosticism of its method for linking genomic information and potential cancer treatments as a hallmark of the service. But it is not alone in taking this approach.

Personalized medicine software company Intervention Insights recently raised $7.2 million to support commercial growth of its molecular drug-matching service, OncInsights, which it also touts as highly agnostic (PGx Reporter 7/27/2011).

OncInsights is also an expression analysis-based service that measures "more than 20,000 genes and 54,000 molecular data points" to create what it calls a "full molecular pathway map" of the patient’s disease. Using bioinformatics technology developed over the last decade at the Van Andel Research Institute, the service then matches drugs to the genes and pathways identified. As of July, the service cost $3,950, according to Intervention Insight's CEO Jerry Callahan.

Lehrer said that to his knowledge, GeneKey casts a wider net in its genomic analysis, and also offers greater support to physicians than OncInsights.

"I think we push it a bit farther to make sure the physician has a specific understanding of why we are pointing to certain [therapies] for a specific patient," he said.

He also said that coupling expression analysis with copy number variation, and in some cases whole-genome sequencing, strengthens the raw data in GeneKey's service. "What is important from our perspective is the ability, on a patient-by-patient basis, to assess statistically whether or not we are seeing something that is [above background] from a quantitative perspective."

While Intervention Insights has published some validation data in abstract form on its program, neither company has yet published any peer-reviewed studies on whether its services actually lead to better outcomes for patients than standard treatment.

Lehrer said the company has been tracking outcomes for its 20 or so patients as a form of "small-v" validation, and has had initial discussions with potential research partners about a controlled clinical study.

"We are definitely exploring that with a number of investigators and are in the early stages of seeking grants to do such a thing," he said.


Have topics you'd like to see covered in Pharmacogenomics Reporter? Contact the editor at mashford [at] genomeweb [.] com.

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