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Affymetrix, Nanogen, Affymetrix, NuGen, EPA, Cogenics, Epigenomics, Illumina

Affy to Help Fund European Cancer Research via New Alliance
Affymetrix this week announced that it has formed the Collaborations in Cancer Research Program, an alliance between Affymetrix and around 30 European cancer researchers.
Researchers from Cancer Research UK, the German Cancer Research Center, and Erasmus University in the Netherlands are among the initial participants in the program.
As part of the alliance, Affymetrix will partially fund selected research projects that demonstrate clinical utility. In addition to helping participants obtain tools and training, Affymetrix will also provide forums where investigators can exchange knowledge and share best practices.
The studies selected for the program will make use of a number of different applications on the Affymetrix platform, including copy number analysis, chromatin immunoprecipitation (ChIP)-on-chip, gene expression, and splicing pattern analysis.
Later this year, Affymetrix said it will expand the Collaborations in Cancer Research Program to selected groups in North America and Japan.

Nanogen Submits CF Assay on NanoChip 400 System for FDA Clearance
Nanogen said this week that it has filed a 510 (k) submission with the US Food and Drug Administration for a cystic fibrosis kit for use on its NanoChip 400 microarray system.
The cystic fibrosis kit is intended to be used for carrier testing in adults of reproductive age, as an aid in newborn screening, and in confirmatory diagnostic testing in newborns and children, Nanogen said.
The genetic assay screens for 23 mutations that account for approximately 90 per cent of cystic fibrosis cases in the US Caucasian population, the company added.

Affymetrix, NuGen to Co-Market FFPE Sampling and GeneChip Combo
Affymetrix this week said it will co-market a NuGen Technologies product that helps Affy GeneChip customers analyze formalin-fixed, paraffin-embedded tissue samples.
Affy said NuGen’s WT-Ovation technology will work with standard Affy three-inch arrays and will allow researchers to analyze gene expression on small and degraded tissue samples.
The company said the technology needs 50 nanograms of RNA and can generate several micrograms of cDNA in six hours.
Affymetrix said the Ovation/GeneChip offering is currently available for sample processing jobs through Expression Analysis, a NuGen and Affymetrix service provider.
The WT-Ovation system will be available for sale this week, Affymetrix said.

EPA Hires Expression Analysis for ToxCast Program
Expression Analysis last week said that the Environmental Protection Agency has hired it to provide gene-expression and genotyping services for the Agency’s ToxCast program.
Under the contract, Expression Analysis will use microarrays from Affymetrix, Illumina, and Applied Biosystems to support the program, which intends to study more than 300 “chemicals of concern” for environmental and human toxicity.
CEO Steve McPhail said recent agreements with tool companies and the expansion of its facilities in Durham, NC, “allowed us to present the EPA with an attractive suite and continuum of genomic services” (see BAN 2/27/2007).
Financial terms of the agreement were not released.

Cogenics, Epigenomics Pen Co-Marketing Pact
Cogenics and Epigenomics have signed a co-marketing agreement for DNA methylation, Cogenics’ parent company Clinical Data said last week.
Under the deal, Cogenics will promote Epigenomics' services for genome-wide DNA methylation analysis, bisulfite sequencing, and PCR, which are performed in Epigenomics’ facilities in Germany.
Also under the deal, the companies will offer regulated DNA methylation analyses in Cogenics’ US labs. Epigenomics will promote these services through its Clinical Solutions segment.
Robert Bondaryk, senior vice president and general manager of Cogenics, said the pact expands the company’s biomarker offerings to include DNA methylation for disease diagnosis, prognosis, and drug response prediction.
Christina Dahlstroem, Clinical Solutions’ senior vice president, said the agreement will be “particularly important” to the company when pharmaceutical customers begin to use these biomarkers in clinical trials.

Illumina to Shutter Connecticut Facility That Builds BeadXpress, Will Consolidate in San Diego
Illumina plans to shutter its manufacturing operations in Wallingford, Conn., and fold some of the assets from the space into its San Diego facilities, the company said last week.
The Wallingford site was originally established in connection with the acquisition of CyVera, and has helped Illumina develop and manufacture the BeadXpress system. The platform debuted last month.
CEO Jay Flatley said that Illumina decided to consolidate the facility after its recent acquisition of Solexa enabled the company to evaluate “all of our operations.” He said that combining the operations “will provide us with efficiencies from both the manufacturing and development perspective.”
It was not immediately clear whether the closure would result in lay-offs.
Flatley said Illumina will concentrate its R&D and manufacturing work in San Diego and in its facility in Little Chesterford, UK.

The company said it will incur roughly $2 million in incremental charges related to the consolidation, and expects that the move will be complete “over the course of 2007."