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IRS Awards Array Firms $16M to Develop Next-Generation Tests

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By Justin Petrone

Companies developing array- or biochip-based molecular diagnostics received a shot in the arm earlier this month when the Internal Revenue Service announced the recipients of grants under the Qualifying Therapeutic Discovery Project program.

Created by the US Patient Protection and Affordable Care Act of 2010, the program oversaw the allocation of $1 billion in tax credits and grants for the 2009 and 2010 tax years with a $5 million limit per each eligible applicant. While most of the QTDP awards went to therapeutic development, some nearly $16 million was awarded to advance diagnostics that run on microarrays or biochips, as well as the development of new technology platforms.

An analysis of the new grants conducted by BioArray News identified 46 awardees who, based on knowledge of the firms or the project titles, appear to be developing tests that use microarray or biochip technology. While a few companies received more than $1 million in grants, the bulk of awardees received grants of $244,479. A complete list of array-related, QTDP-funded projects can be found below.

Somalogic received the largest amount of array-related QTDP funding. The Boulder, Colo.-based proteomics firm netted nearly $1.9 million to support the development of blood tests for the early detection of mesothelioma, non-small cell lung cancer, ovarian cancer, pancreatic cancer, and chronic kidney disease. Somalogic also received grants to develop therapeutics for cancer and neurodegenerative diseases.

Company officials discussed Somalogic's diagnostic programs in lung cancer, chronic kidney disease, and pancreatic cancer with BioArray News in June. The company aims to bring a US Food and Drug Administration-cleared protein panel to the clinical market in 2010 (BAN 6/15/2010). The company's technology platform can quantify the presence of proteins in blood by using Somamers, chemically modified nucleic acid aptamers made via a process called systematic ligand evolution by exponential enrichment. Somalogic's assay converts target protein concentration to a specific Somamer concentration, which is then quantified with DNA technologies, including microarrays.

Pasadena, Calif.-based GenMark Diagnostics, formerly known as Clinical Micro Sensors, received the second largest amount of QTDP money in the array sector. The company netted more than $1.6 million to develop tests to detect cystic fibrosis, thrombophilia risk, warfarin sensitivity, Plavix sensitivity, KRAS mutations, and respiratory pathogens. GenMark's benchtop eSensor XT-8 System relies on the firm's electrochemical detection technology to detect nucleic acids on a microarray. The company has already received FDA 510(k) clearance for several assays, including its cystic fibrosis genotyping test, thrombophilia risk test, and warfarin sensitivity test.

During the firm's second-quarter earnings call in August, CEO John Faiz Kayyem said that GenMark is developing a respiratory viral panel that it expects will detect 21 different upper respiratory viruses; and a genotyping test for cytochrome P450 2C19, which is intended to assess drug metabolism in patients and could be used to assess population frequency of different genotypes thought to be associated with poor Plavix response (BAN 8/10/2010).

Northbrook, Ill.-based Nanosphere gained $977,917 to develop tests for the early detection of cancer, infectious diseases, immune system disorders, and cardiac and vascular diseases — the third largest amount of funding awarded to any company. The company makes and sells its benchtop Verigene System, which relies on the firm's gold nanoparticle technology to detect nucleic acid and protein targets of interest.

Nanosphere's array-based assays are conducted on its Verigene Test Cartridges. The company sells a number of cleared in vitro diagnostics for use on the system related to coagulation, thrombophilia, and cystic fibrosis. In August, Nanosphere acquired part of Eppendorf's IP estate related to that firm's Silverquant detection technology (BAN 8/24/2010).

As BioArray News reported earlier this month, Quanterix was awarded $733,437 in grants under the QTDP program. The Cambridge, Mass.-based firm said it will use the funds to develop its AccuPSA prostate cancer test, which runs on its single-molecule array, or SiMoA, platform. The company said it will also use the money to develop tests for Alzheimer's disease and Crohn's disease (BAN 11/2/2010).

In a statement announcing the award, Quanterix touted its AccuPSA test as being more than 1,000 times more sensitive than the most sensitive commercial prostate specific antigen assays, and said the assay is designed to determine which prostate cancer patients will remain cancer-free after surgery and to detect early signs of disease recurrence.

Quanterix's technology platform includes arrays of femtoliter-sized reaction vessels, each vessel sized to confine a single molecule of interest. The arrays are formed by etching tens to hundreds of thousands of separate reaction vessels into the end of an optical fiber bundle. According to the firm, each vessel can be used to trap single molecules, and the optical fiber bundle carries light into and out of each vessel, allowing each well to function as an independent assay for a single molecule.

High Throughput Genomics received the fifth largest amount of QTDP grants. The Tucson, Ariz.-based firm was awarded $703,908 to support both assay and platform development projects. On the molecular diagnostics side, HTG will use the new funds to develop tests for melanoma screening, pathogen detection, diffuse large B-cell lymphoma cell of origin identification, and radiation monitoring.

In terms of platform development, HTG received funds to further develop its quantitative nuclease protection assay, or qNPA, platform. The qNPA assay relies on the treatment of samples with the firm's internally developed lysis buffer, which eliminates the need for RNA extraction.

HTG received QTDP funding specifically to invest in its line of qNPA microRNA arrays and array plates, as well as its qBead gene expression assay, which it codeveloped and launched with Luminex earlier this year (BAN 5/25/2010). The qBead Assay places HTG's qNPA chemistry on the Luminex xMAP technology multiplexing platform.

Other array companies that received QTDP grants include Irvine, Calif.-based CombiMatrix, which received $488,950 to develop its microRNA-based comprehensive cancer array; and Frederick, Md.-based Akonni Biosystems, which received the same amount to develop a PCR and microarray-based point-of-care test for respiratory infections.

The following is a state-by-state listing of companies awarded grants to develop array and biochip-based tests and platforms. A list of all QTDP awards can be found at "http://www.irs.gov/businesses/small/article/0,,id=228690,00.html".

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Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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