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BU Spinout AllegroDx to Launch Array-Based Lung Cancer Test This Year

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By Justin Petrone

Allegro Diagnostics later this year plans to begin marketing a microarray-based test for early-stage lung cancer, according to CEO Dan Rippy.

Rippy told BioArray News that the Boston-based molecular diagnostics firm intends to offer the test, called BronchoGen, as a service through its Clinical Laboratory Improvement Acts-compliant lab by the end of 2010. The four-year-old firm is also mulling submitting the test, which is manufactured by Affymetrix, to the US Food and Drug Administration for clearance.

"From a CLIA perspective, we anticipate being able to offer BronchoGen in 2010," Rippy said. "It's not entirely clear if we will get it cleared through FDA as a kit; we may offer it as an FDA-cleared service through the lab instead," he said. "Either way, we would hope to be able to submit BronchoGen to the FDA by year end 2010 or thereabouts."

Allegro was founded in 2006 by BU investigators Avrum Spira and Jerome Brody. BronchoGen, its flagship test, is an 80-gene biomarker assay that can detect and rule out the presence of lung cancer using histologically normal large-airway epithelial cells obtained at bronchoscopy from smokers suspected to have the disease. Allegro's founders have published several times on the development of the assay. BioArray News interviewed Spira about a related project in 2008 (see BAN 12/16/2008).

Rippy said that, once available, the test should serve as a complementary method to bronchoscopy, a century-old procedure in which a clinician examines the airways of a patient using a scope to identify or rule out the presence of cancer in patients.

"Bronchoscopy is not a very accurate method," Rippy said. "You are limited physically by how far into the lungs the scope can go because of the size of the scope itself," he said. "By getting a simple brushing at the base of of the bronchus and looking at the gene expression pattern, we can make a call on lung cancer."

Still, the test is not being positioned as a replacement for bronchoscopy. Instead, the company envisions patients being given a bronchoscopy as part of standard care, and then using BronchoGen in cases where cancer can neither be identified nor ruled out.

"One of the compelling aspects of the opportunity is that we are developing a test that will piggyback on a well-understood procedure," Rippy said. "We are not eliminating a procedure, because asking clinicians to do a brushing is something clinicians do today. As we think of doctors as being pressured for time, an elegant aspect of what we will offer is that it does not require more time in the procedure," he added.

Because Allegro is not trying to change the behavior of clinicians, Rippy said he believes that BronchoGen will face relatively few challenges in being adopted, even though microarray technology continues to be a new and unfamiliar technology for the community of clinicians the firm intends to serve.

"Anything that can save time will be viewed by clinicians very favorably," Rippy said. "We believe this is a good offering for clinicians. This will help them become more accurate and timely. That is a benefit for their work practice."

According to Rippy, BronchoGen will play in a "billion dollar US market opportunity," and could also be a similarly sized opportunity outside the US. "We believe it would applicable for anyone undergoing bronchoscopy to rule out lung cancer," Rippy said.

He said that Allegro plans to charge "north of $2,000" for the test, which he described as "high value," as it could be used to make a diagnosis before clinicians move to more expensive methods of cancer identification, such as a positron emission tomography scan, which can cost between $3,000 and $6,000.

"As a modality, our test is less expensive that many other things that come afterward," said Rippy. "You are better off than if you do more invasive procedures that carry higher risks for the patients."

Still, there are a number of other assays in development for early-stage lung cancer detection, including some based on arrays, though some of the indications differ. Almac Diagnostics, for instance, has developed a lung cancer Disease Specific Array, also manufactured by Affymetrix, and has previously discussed plans to develop an assay that predicts which patients will likely go on to have disease-free survival after surgery and which are at risk for relapse for early non-small cell lung cancer, the most common form of lung cancer (see BAN 8/19/2008).

Vancouver, BC-based Med BioGene is planning a similar route to market for its LungExpress Dx test (see story, this issue). LungExpress Dx is a 15-gene-expression-based assay that classifies patients into high- and low-risk prognostic groups based upon the molecular profile of a particular patient’s tumor. Originally developed on the Affy platform, Med BioGene has opted to transfer the assay to a RT-PCR-based assay (see BAN 3/24/2009).

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While all of these tests are different, they do have one thing in common: the use of Affy's platform. "We have found the Affy platform to be an excellent discovery platform," Rippy said. "All of our discovery work has been done on Affy and it’s a platform we know and understand."

Allegro will continue to use the chips, rather than migrate the assay to a RT-PCR-based assay like Med Biogene has done, due to the larger number of probe sets, Rippy said.

"One of the other reasons for using the Affy platform is that it is known and has been cleared by the FDA," Rippy added. "The FDA knows the platform well. We believe that will be advantageous for us when we go to file with them."

BronchoGen Trials

To achieve its goal of selling BronchoGen later this year, Allegro is currently testing the assay in multi-site trials. In October, Allegro received a $2.8 million SBIR grant from the National Cancer Institute to study samples collected from 800 patients at sites in the US, Canada, and Ireland.

The trials are being performed both to achieve CLIA certification for its Boston lab and to collect data that will later be used in a potential submission to the FDA. "We received a preliminary exemption from the FDA in October," Rippy said. "What that allows for us is to commence a clinical trial and enroll patients and obtain patient samples at sites we specified at that time," he said. "We have the FDA's consent to do the trial to gather data."

Allegro's $2.8 million grant plus funds remaining from a $4 million financing round in 2008 are being used to support the trial. Rippy said that Allegro expects to have enrollment for the trial completed by mid-year. The data collected during the trial could also be used to support the development of future products.

"We have a series of products that will be aimed at lung cancer applications," Rippy said. "We are gaining data on those products in the same trial we are doing currently. Those products will have different applications, but will be aimed at suspect lung cancer populations."

Rippy declined to discuss the specific purposes of the products. He said one test "has a similar market opportunity size" to BronchoGen, and another test in development, geared towards screening high-risk patients, has a "larger opportunity, probably in the neighborhood of $6 billion to $8 billion, worldwide."

As it scales up to develop these tests, Allegro is growing its headcount. Rippy declined to discuss how large the firm is, but said it is "expanding selectively in areas pertaining to science and bioinformatics." Allegro has also "been efficient in outsourcing a number of functions up to this point," he said. "We will do that until we are basically at the point to offer a product commercially. At that point, we envision larger expansion," he added.

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