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Almac Diagnostics, Biogen-Idec, Affymetrix, University of Utah, Vanderbilt University, LineaGen, Nanogen, Applera, Celera, Applied Biosystems, Gentel Biosciences, PriTest, Lumera, Plexera Bioscience, Fluidigm, AME Bioscience, Stanford University School of

Almac Dx Shows Off New FFPE Service Through Biogen-Idec Deal
Almac Diagnostics will help Biogen-Idec extract genetic information from formalin-fixed paraffin-embedded tissue, Almac said last week.
Craigavon, UK-based Almac announced that Biogen-Idec would use the process to analyze SNPs in a phase II study of a drug for treating gastrointestinal stromal tumors. The firm’s analysis capabilities enable researchers to use FFPE samples in qPCR and microarray SNP-genotyping and gene-expression studies, the company said.
Julie Ranuio-Kelley, senior associate scientist at Cambridge, Mass.-based Biogen-Idec, said in a statement that Almac’s technology would allow the firm to “uncover biomarkers that will help us discover additional drug candidates and identify specific patient populations that will benefit from a particular treatment.”
According to CEO Paul Harkin, the work with Biogen-Idec is among the first to make use of Almac’s capability to profile SNPs in FFPA samples. Previously the company had only offered gene expression analysis services for companies working with FFPE samples.
“Here at Almac we have been working with FFPE for a number of years now and [FFPE sample analysis] is the cornerstone of our business,” Harkin told BioArray News this week. “All of our initial experience was with RNA for gene expression; we can now extend this service for DNA as well.”
Almac’s new service is based on “modified and perfected techniques for the extraction of DNA from FFPE that is actually usable for SNP genotyping,” according to Harkin. For the study with Biogen-Idec, Almac will take a “targeted approach” offering both quantitative PCR analysis as well as genome-wide profiling on Affymetrix’s SNP 6.0 array. Pricing for the service was not discussed.
Beyond Biogen-Idec, Harkin said that Almac is also offering the new service to several partners, who he declined to name. Almac’s business is divided between drug discovery and development projects, such as the one with Biogen-Idec, as well as the sale of disease-specific arrays and the development of diagnostic assays on the Affy platform.
For example, Almac is working with Cancer Research UK to develop a prognostic that will guide clinicians in treating early stage breast cancer (see BAN 8/7/2007). The company is also engaged in discussions with the US Food and Drug Administration in relation to a colorectal cancer recurrence prognostic (see BAN 5/29/2007).
Harkin declined to comment on whether or not the gastrointestinal stromal tumor work with Biogen-Idec could result in a disease specific array or diagnostic program within Almac.

Affymetrix Expecting 2008 Restructuring Charges of $15.4M
Affymetrix expects to realize $15.4 million in restructuring charges for fiscal-year 2008 as part of its efforts to relocate the majority of its probe array manufacturing from West Sacramento, Calif., to Singapore, the company disclosed this week in a filing with the US Securities and Exchange Commission.
Affy initially revealed its plans for the relocation in an SEC filing on Feb. 29. At the time, it said it expected to incur non-cash charges of around $12 million to $15 million related to the abandonment of certain manufacturing assets and approximately $500,000 related to employee severance in the first quarter of 2008.
According to the 10-Q filing today, the firm said of the $15.4 million in charges it now expects to incur, roughly $2.9 million will relate to employee severance and $12.5 million will relate to the abandonment of the manufacturing assets. Affy also said that depending on the rate at which it transfers operations to Singapore, it may incur additional expenses.
For the first quarter of 2008, Affy recognized approximately $1.4 million of charges related to employee severance and $12.5 million related to the manufacturing assets. The firm recently reported that its Q1 revenues were flat with the comparable period a year ago, excluding a $90 million settlement payment recognized during the quarter.
In a separate SEC filing this week, Affy disclosed that investment advisor Fidelity Management & Research now owns 5,050,490 shares of the firm’s common stock, which represents a nearly 7.3 percent stake in Affy. Of that total amount, the Fidelity Growth Company Fund owns 4,403,190 shares, representing a stake of 6.34 percent in Affy as of April 30.

LineaGen's MS, Autism Diagnostics Project Using Affy Arrays
Researchers at the University of Utah and Vanderbilt University are using Affymetrix’s genotyping arrays along with LineaGen’s biomarker diagnostics technology to hunt for genetic markers that could be used in the treatment and diagnosis of multiple sclerosis and autism, Affymetrix and LineaGen jointly announced this week.
In a project funded and managed by Salt Lake City-based LineaGen, the scientists are using Affy’s Genome-Wide Human SNP Array 6.0 to analyze data from the Utah Population Database to compare genetic information with “decades’ worth of longitudinal clinical data,” the firms said.
The researchers expect the study will lead to enhanced understanding of these two diseases, more effective use of existing treatments, and the development of molecular diagnostics and therapies.
The Affy arrays will be run at the Vanderbilt Microarray Shared Resource at Vanderbilt University Medical Center.
“We have a valuable and unique genetic population resource at the University of Utah and now we can cost-effectively conduct larger-scale studies to determine the genetic associations of common diseases like MS and autism," Mark Leppert, co-chair of the University of Utah’s department of human genetics, said in a statement.
Financial terms of the agreement were not released.

Nanogen Posts 10.3-Percent Rise in Q1 Revenue; Loss Rises on Charges
Nanogen reported this week that its first-quarter revenues rose 10.3 percent but its net loss nearly doubled on a charge related to the extinguishment of debt.
The San Diego-based molecular diagnostics firm brought in total revenues of $10.7 million for the three-month period ended March 31, compared to revenues of $9.7 million in the first quarter of 2007. Its product sales increased 32.8 percent to $8.1 million from $6.1 million year over year, while license fees and royalty income increased to $1.8 million from $1.2 million. Its contracts and grant revenue dropped to $852,000 from $2.3 million.
Nanogen’s net loss for the quarter was $23 million, or $.31 per share, compared to a net loss of $11.9 million, or $.17 per share, for the first quarter of 2007. The most recent quarter’s results include a $2.9 million charge for a “warrant valuation adjustment” and a $10.2 million charge related to the extinguishment of certain debt.
The firm’s R&D costs declined 26.2 percent to $4.2 million from $6.5 million, while its SG&A expenses fell 5.6 percent to $8.7 million from $8.9 million.
"Our Q1 results clearly demonstrate that the restructuring plan, initiated in the fourth quarter, has substantially improved our financial performance,“ Nanogen Chairman and CEO Howard Birndorf said in a statement. “Consistent with our prior guidance, we have achieved meaningful cost reductions while at the same time have experienced a 36 percent increase in product revenue from the prior quarter."
Nanogen said in September that it would sell its microarray business in an effort to focus on building its RT-PCR and point-of-care testing businesses and more rapidly achieve profitability. The firm began shutting down the microarray business in November.
Nanogen said that it expects its 2008 revenues to increase around 25 percent over its 2007 revenues of $38.2 million.

Celera, ABI to Split on July 1
Applera said last week that its two groups, Celera and Applied Biosystems, would be formally separated on July 1.
The firm said that the board of directors approved the proposed separation, which will be accomplished by the redemption of all outstanding shares of Celera’s stock. Each share of the current Celera tracking stock will be exchanged for one share of the independent Celera Corp.
Last month, Celera filed with the US Securities and Exchange Commission a preliminary prospectus to split off from parent company Applera. Officials from both Celera and ABI have hinted for months that a split of the two companies would be the likely outcome of a review begun in August by investment firm Morgan Stanley, which was hired to explore options for restructuring the groups.
Completion of the split is subject to a number of conditions including "an opinion from counsel to Applera regarding the tax consequences of the separation," as well as the SEC declaring effective Celera's registration statement on or prior to June 15.
Kathy Ordoñez, the current president of Celera, will become CEO of the firm, which will retain its headquarters in Alameda, Calif. Celera will trade on the NASDAQ.
ABI will continue to trade on the New York Stock Exchange.

Gentel Licenses IP from PriTest for Use in Protein Arrays
Gentel Biosciences said last week that it has signed a licensing agreement with diagnostic firm PriTest that expands its intellectual property portfolio in the area of nitrocellulose coatings for protein microarrays.
Under the terms of the exclusive agreement, Gentel has licensed US Patent No. 6,861,251, “Translucent solid matrix assay device for microarray analysis,” which covers arrays with a translucent nitrocellulose surface.
Gentel said in a statement that nitrocellulose surface chemistry offers “unparalleled sensitivity and dynamic range for protein microarray applications.”
The company did not disclose the financial terms of the licensing agreement.

Lumera's Revenues Fall 44 Percent as It Shuts Down Plexera's Operations
Lumera reported last week that its first-quarter revenues fell 44 percent and its net loss rose 124 percent as the company has stopped making investments in its Plexera Bioscience proteomics business.
Lumera said in its earnings report that it had revenues of $484,000 for the three-month period ended March 31, 2008, compared to revenues of $860,000 in the first quarter of 2007.
Bothell, Wash.-based Lumera posted a net loss of $6 million, or $.30 per share, compared to a net loss of $2.7 million, or $.13 per share, in the comparable period of 2007.
Lumera’s R&D spending rose more than 80 percent to $2.3 million, up from $1.3 million, while SG&A costs nearly doubled to $4.1 million from $2.2 million.
The firm finished the quarter with $2.5 million in cash and cash equivalents.
Lumera announced in March that it had discontinued Plexera’s operations and had reached an agreement to merge with GigOptix, a private company that makes integrated circuits for optical systems.
The firm reported a total of $934,000 in restructuring costs related to Plexera over the quarter. Those costs included $534,000 for severance for 29 total positions (23 of which were Plexera layoffs), a $243,000 provision for the impairment of Plexera’s fixed assets, and contract and license termination costs of $157,000.
The company said it is currently “seeking ways to realize the value from Plexera’s assets and intellectual property.”

Fluidigm Inks Nordic Distribution Pact with AME Bioscience
Fluidigm said last week it has signed up AME Bioscience to distribute its BioMark integrated fluidic circuits in Norway, Sweden, Iceland, Finland, and Denmark.
The BioMark system, which has not been cleared or approved by the US Food and Drug Administration for use as a diagnostic, is used in real-time PCR, genotyping, cancer detection, and absolute quantification for research purposes.
Financial terms of the agreement were not released.

Stanford to Study Pathwork Dx's Unknown Tissue Cancer Test
The Stanford University School of Medicine is evaluating a Pathwork Diagnostics tissue-of-origin diagnostic test for tumors that are hard to identify, the company said last week.
The company said the new test uses genomics technology to help doctors determine the origin of a tumor and help them plan treatments. Stanford physicians will evaluate the test for its impact on diagnosis for cancer patients with tumors that have been hard to identify, and they will process the samples at the medical school.
"Our test is available as a service through our CLIA-certified laboratory so that physicians outside of Stanford University can have specimens processed and clinical results provided,” said Deborah Neff, president and CEO of Pathwork Diagnostics. Neff added that the company is “actively working to obtain FDA clearance so that we can offer a diagnostics kit directly to clinical laboratories at major medical centers.”
Stanford also was involved in a four-lab comparison study that used the Pathwork Tissue of Origin Test to perform diagnosis of 60 metastatic and poorly differentiated and undifferentiated tissue samples, the company said.
The test measures the expression of over 1,500 genes to compare a tumor’s gene expression profile to 15 known tissues, and provides a probability-based score for each potential tissue, helping doctors to rule out some tissue types.
The test uses the company’s Pathchip microarray and runs on the Affymetrix GeneChip System.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.