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Akonni's $3M Grant Latest in String of NIH Awards for PCR Array-Based Infectious Disease Dxs

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By Ben Butkus

Akonni Biosystems said this week that it has received an approximately $3 million Challenge Grant from the National Institutes of Health to further develop a test for multi-drug-resistant and extensively drug-resistant tuberculosis on its TruDrop gel-drop PCR microarray biochip technology.

This is the third NIH grant Akonni has received in the past year to develop diagnostic tests around its various technologies. The company has also recently won funding to develop a "sample-to-answer" point-of-care test for multi-drug-resistant TB using its TruTip sample prep technology; and a test for influenza and drug-resistant strains of the virus using TruDrop and the TruDiagnosis array reader.

In addition, a company official told PCR Insider this week that Akonni is working with Johns Hopkins University to conduct pre-clinical testing on a methicillin-resistant Staphylococcus aureus test using the TruDrop PCR array in order to prepare a 510(k) filing with the US Food and Drug Administration.

The overarching theme of Akonni's technology development is addressing "the emergence of drug resistance and the need to interrogate a broader range of markers," Kevin Banks, vice president of sales and marketing, told PCR Insider this week. Akonni's technology, which combines the power of real-time PCR interrogation with microarray analysis, may be well-positioned to address such problems.

"We're really focusing on diseases where you're beginning to see a rapid emergence of drug resistance," Banks said. "For TB, it's changing all the time, and more and more markers are needed to get an accurate diagnosis. And PCR is kind of running out of bandwidth to interrogate those markers. Our technology comes in somewhere in between PCR and sequencing, when you need to interrogate a broader range of markers."

The TruDrop technology was primarily developed at Argonne National Laboratory, from whom Akonni has licensed pertinent IP surrounding the platform. TruDrop is a low-density microarray of immobilized three-dimensional 100-by-20-micron drops containing all probes and chemistry necessary for a PCR reaction. The reaction volumes are arrayed on a valveless biochip that can be placed into the TruDiagnosis imaging device.

Meantime, the company also is developing TruTip, which uses a patented nucleic acid-binding matrix inserted in a pipette tip to extract and purify inhibitor-free DNA or RNA for downstream PCR applications in as few as four minutes, according to Akonni. For higher-throughput applications, such as preparing samples for analysis on the TruDiagnosis biochips, TruTip can be paired with Eppendorf’s automated epMotion 5070 liquid handling system. Akonni and Eppendorf inked a co-marketing agreement around the technologies in April (PCR Insider, 4/29/10).

Akonni's latest grant, made possible under the American Recovery and Reinvestment Act, will allow it to develop a prototype MDR-TB PCR TruArray by expanding test coverage, completing manufacturing scale-up for future kits, and performing pre-clinical verification experiments, according to the grant's abstract.

In order to do this, Akonni will partner with the New York State Department of Health's Wadsworth Center Laboratory of Clinical Mycobacteriology in Albany, NY, which will cultivate MDR and XDR-TB isolates and provide pre-clinical verification on amended sputum samples, Akonni said.

In addition, Akonni said it will subsequently conduct pre-clinical testing of its platform at several international reference centers in regions of the world where TB is most prevalent, such as at the Medical Research Council of South Africa.

Akonni said that its TB assay aims to identify genetic markers associated with susceptibility to the antibiotic drugs rifampin and isoniazid by screening for the most common mutations in the rpoB, katG, and inhA genes. The test will also differentiate between M. tuberculosis and M. avium, the company said.

The Challenge Grant is the second NIH grant Akonni has received this year to develop TB testing capabilities. In July, the company was awarded a two-year, $435,000 Phase I Small Business Innovation Research grant from the NIH's National Institute of Biomedical Imaging and Bioengineering (PCR Insider, 7/29/10).

Under that grant, Akonni is working with researchers from Mexico's Laboratorios Medicos Especializados to evaluate TruTip's ability to purify Mycobaterium tuberculosis samples. The NIBIB grant is also allowing Akonni to verify TB assays run on TruArray, expand the multiplexing capacity of its TB arrays, develop a lysis method, and translate the assay to a prototype TruDiagnosis device.

The company also said at the time that Phase II of the grant will help further expand the genotyping capacity of the assays and translate the point-of-care device to the Laboratorios Medicos Especializados clinic in Juarez.

Banks told PCR Insider this week that although both grants involve TB testing, they are different in that the Challenge Grant focuses on extending only the TruArray component to extensively drug-resistant TB while the NIBIB grant is focused on developing a fully integrated POC test for multi-drug-resistant TB.

As such, Akonni will likely first develop the TruArray XDR test system with manual sample prep up front; and then eventually transfer that test to the full automated, sample-on-answer platform being developed under the NIBIB grant, Banks said.

One of the hallmarks of Akonni's system is that its array-based gel-drop format allows it to have a small footprint and low price point, which would be a boon for the technology's use in developing countries and low-resource settings where TB is most prevalent.

Banks said that Akonni is driving for a POC test in the $20 to $40 range, and a high-throughput test, such as would be administered in a central testing laboratory, for around $15. In July, an Akonni official told PCR Insider that the company envisions selling an instrument platform for around $5,000.

For comparison, Cepheid's CE Marked PCR-based molecular diagnostic test for TB and drug-resistant TB, the performance of which was recently lauded in a New England Journal of Medicine paper, costs a little over $60 and runs on an instrument that normally costs $30,000 (PCR Insider, 9/2/2010). Cepheid has said that it believes it can eventually offer "compassionate" pricing of under $10,000 for its system.

And although Cepheid's system has a leg up on Akonni's technology and most other TB molecular tests on the market, Banks believes that Akonni's system may eventually be competitive. "Because our array is multiplex-enabled, we can find more content than platforms from companies like Cepheid or other real-time based platforms," Banks said.

Akonni also has an ongoing NIH grant to develop its technology to detect influenzas A and B and their antigenic subtypes, including antiviral-resistant types (PCR Insider, 12/3/2009); and is currently conducting pre-clinical studies with academic collaborators to prepare for a 510(k) filing with the US Food and Drug Administration for its most advanced technology, a PCR array-based test for MRSA.

Banks said that Akonni is in the second year of its influenza test-development grant and that the project is "coming along," though he declined to provide additional details on its progress. However, he did highlight the fact that Akonni's PCR array-based test would be able to probe multiple Tamiflu drug-resistance markers, which will be "a competitive advantage" for the company.

As for the MRSA test, PCR Insider previously reported in July that Akonni was gathering pre-clinical data to prepare a 510(k) filing with the FDA. This week, Banks disclosed for the first time that Akonni was working with clinicians at Johns Hopkins on this project, and said that Akonni has had discussions with the FDA about the approval process but has not yet initiated the filing process.

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