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FDA, DNAVision, CombiMatrix, US Army, Geneservice, Gene Logic


FDA Seeks Microarray Datasets for Quality Control Project

The US Food and Drug Administration is soliciting gene expression datasets from microarray experiments as part of its MicroArray Quality Control project.

In a notice of solicitation dated April 13 and included in the Federal Register last week, FDA said that it is seeking datasets "as well as proposals to analyze these datasets in order to evaluate the impact of different analysis protocols on the selection of genes and their associated signatures for biomarker pattern development."

The FDA's National Center for Toxicological Research is collecting the datasets and proposals for participation in the project. The evaluation process is open to the public, FDA said.

"The popular notion is that there can be no consensus on how to analyze gene expression data from DNA chips," Federico Goodsaid, a senior staff scientist at FDA's Center for Drug Evaluation and Research who is involved in the project, told BioArray News last week about the solicitation.

"We want to survey the way in which the analyses are done," Goodsaid said. "It's a great way to challenge the findings of the MAQC project," he added.

The MAQC project involves six FDA centers, several microarray vendors, government agencies, and academic labs that are working to develop baseline practices for the analysis of hybridization data. The project is preparing nearly a dozen manuscripts on its findings for submission for a special issue of Nature Biotechnology, which is due out in September (see BAN 3/28/2006).

DNAVision Becomes First European Lab to Offer Services on Eppendorf DualChip Arrays

DNAVision has become a service provider for Eppendorf's DualChip microarrays, DNAVision said earlier this month.

The deal makes DNAVision the first European lab to provide services for low- to medium-density microarray testing, and "completes very well our actual gene expression offer using high density microarray and real time PCR," Jean-François Laes, microarray unit manager at DNAVision, said in a statement.

Financial terms of the deal were not disclosed.

The DualChip platform is one of the platforms used in the US Food and Drug Administration's MicroArray Quality Control project.

CombiMatrix Reports Slight Uptick in Q1 Revenue …

CombiMatrix last week said that first-quarter revenue inched up 2 percent as R&D spending and net losses more than doubled.

Total receipts for the three months ended March 31 increased to $1.2 million from $1.1 million in the year-ago period.

Year over year, revenue from government contracts fell to $264,000 from $731,000 while receipts from product sales surged to $924,000 from $278,000, CMBX said.

CombiMatrix said that the decrease in government contracts was due to the completion of its $5.9 million biological threat detection contract with the Department of Defense in December 2005. A new $2.1 million contract to support development of its biological and chemical detector system was executed in February, "resulting in lower contract costs in the first quarter of 2006 than in the comparable 2005 period," the company said in a statement.

"Our product and service revenue is increasing nicely, and this trend should continue as our products continue to gain acceptance with our customers," CombiMatrix President Amit Kumar said. "Additionally, the launch of products from our diagnostics division, earlier than originally planned, will augment our revenue growth.

"Our defense contracting revenue for the quarter was modest due to an unforeseen delay in initiation of our new government contract," Kumar said. "We expect this revenue to increase in the following quarters."

R&D spending in the period increased to $2.4 million from $1.1 million year over year. This increase was due "primarily" to developments ongoing at the CombiMatrix Molecular Diagnostics division.

The company said net losses increased to $7.7 million from $3 million in the year-ago period. The current quarter's loss included non-cash stock compensation, patent amortization and depreciation charges totaling $1.2 million versus $427,000 in the comparable 2005 period.

… and Snags $1.9M Contract with US Army to Develop Miniaturized Array Reader

Acacia Research said this week that its CombiMatrix group has been awarded $1.9 million from the US Army Research Office to develop a miniaturized microarray reader for biodefense applications.

The award brings the company's total biodefense funding to around $14 million, including a $5.9 million Department of Defense contract that the company completed at the end of 2005, a $2.4 million award from the DoD in January, and two additional contracts worth $2.1 million and $2.16 million (see BAN 3/10/2004, BAN 1/17/2006).

CombiMatrix said that $6 million of this funding will support its R&D activities in 2006 and 2007, and that it has "grant applications and requests into the government for more than $25 million" for 2007 and beyond.

The objective of the latest contract is to develop a self-contained and disposable device for rapidly detecting a variety of microorganisms. The instrument will be capable of rapid "multiplexed PCR amplification, [electrochemical detection]-based microarray detection, and data-interpretation capabilities," the company said.

Robin Liu, the principal investigator on the contract, said in a statement that the company is developing "a compact, toaster-size [microarray] reader that costs $20,000."

Applications for the system include the detection of anthrax, plague, and infectious diseases such as influenza, SARS, and HIV. Following completed development, CombiMatrix said it expects to seek FDA approval for the system and arrays.

Geneservice Receives ISO Certification

The International Standards Organization has awarded Geneservice's facilities its ISO 9001:2000 certification for functional genomic products and the conduct of contract research for academic and commercial customers, the company said last week.

Geneservice is based in Cambridge, UK. The company offers a microsatellite and microarray-based genotyping service. Geneservice also offers gene expression services on the Affymetrix and Applied Biosystems platforms.

Gene Logic's Q1 Revenues Fall 35 Percent; Net Losses More than Double

Gene Logic last week reported a 35-percent drop in first-quarter revenues amid widened net losses.

For the quarter ended March 31, Gene Logic's total revenue fell to $12.8 million from $19.7 million in the first quarter of 2005. Revenues fell across all three of the firm's operating divisions: Genomics Division revenue declined to $8.7 million from 13.2 million in the prior-year period; Preclinical revenue fell to $4 million from $6.4 million in the prior-year period; and Drug Repositioning revenue dropped to $20,000 from $67,000 in the same period of 2005.

Gene Logic said in a statement that the Genomics Division has been "transitioning" over the past five quarters from a model based on database subscriptions and a few large customers to one with multiple sources of revenue — including revenues "from perpetual licenses and microarray data generation and analysis services" — and a broader customer base. The company added that the division's results are likely to be "variable," however, "when certain opportunities fail to materialize or are deferred."

The results for the Genomics Division in the first quarter reflect "lower sales due to the non-signing of a previously anticipated perpetual license and the deferral of several opportunities until later in the year," the company said.

Gene Logic's net losses ballooned to $11.8 million, nearly three times the company's net loss of $4.1 million in the first quarter of 2005. The company attributed the widening losses to the revenue shortfall in the Genomics Division.

R&D spending increased to $2.4 million from $1.5 million in the first quarter of 2005.

Gene Logic had $28.4 million in cash and cash equivalents as of March 31, and $63.9 million in cash, cash equivalents, and marketable securities available for sale.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.