Affymetrix, Inc. (NASDAQ:AFFX) today announced a co-marketing agreement naming BioDiscovery, Inc. its preferred software provider for Affymetrix OncoScan™ FFPE Express Service data analysis. BioDiscovery, a leader in integrated software for high-throughput microarrays and other technologies, customized its Nexus Copy Number™ solution for Affymetrix to make the most user-friendly, flexible, and compatible tool available for OncoScan FFPE Express microarray data analysis. Cancer researchers using the OncoScan Service and Nexus software can now obtain critical cancer genome measurements from archived formalin-fixed, paraffin-embedded (FFPE) tumor samples and obtain an end-to-end solution for faster data visualization and analysis.

“By simplifying data interpretation with the Nexus Copy Number software, we’re providing a complete solution to our customers,” said Nargol Faravashi, Affymetrix Global Strategic Marketing Manager, DNA Cancer Applications. “Our array technology accommodates challenging FFPE tumor samples as old as 28 years. Now that it’s coupled with a best-in-class software solution for visualizing the cancer genome at fine resolution, researchers have a very powerful method to streamline their data analysis processes and accelerate scientific discoveries.”

Under the co-marketing agreement, customers accessing the OncoScan FFPE Express Service through the Affymetrix® Research Services Laboratory (ARSL) will receive a preliminary Nexus Copy Number data analysis. Additionally, BioDiscovery will provide a one-on-one consultation session to assist each researcher with the downstream analysis of their data to elucidate pathways and identify copy number variations (CNV) and copy-neutral loss of heterozygosity (LOH) events, which are important for understanding characterizations of mutations.

“Pairing Nexus Copy Number software with Affymetrix’ unique service is an ideal solution for a comprehensive workflow—from FFPE samples to final analysis and visualization of CNV and LOH results,” said BioDiscovery CEO Dr. Soheil Shams. “The latest 6.0 version of our Nexus Copy Number solution is well-designed to analyze data generated from the OncoScan FFPE Express Service, especially with the addition of custom tools for cancer sample analysis.”

The OncoScan™ FFPE Express Service, based on Affymetrix’ unique molecular inversion probe (MIP) array technology, was designed in collaboration with leading cancer scientists. It overcomes the challenge of analyzing DNA from FFPE tissues to extract important retrospective clinical data from archived samples and goes beyond the limitations of standard array comparative genomic hybridization (CGH) methods to yield copy number, allelic ratio, and somatic mutation data from minimal amounts of input DNA.

“Many leading cancer researchers are avid users of Nexus Copy Number for its ease of use, robustness, and flexibility to suit each individual’s needs,” added BioDiscovery CEO Dr. Shams. “Now, customers of the OncoScan FFPE Express Service will receive not only high-quality raw data from Affymetrix, but also reliable analysis of experimental results that further streamline and speed their research.”

BioDiscovery’s software is platform-independent and available for Mac OS X, Linux, and Windows operating systems. In a single project, Nexus Copy Number can integrate and process the data from nearly all commercial array platforms, as well as custom arrays. With free access to a web-based repository for querying and storing genomic data from any location across the globe, Nexus Copy Number is a powerful solution for large study groups and consortia. The software is applicable to many types of studies, from focused cytogenetic projects studying chromosome defects to large-scale cancer or genome-wide association studies (GWAS).

About Affymetrix

Affymetrix technology is used by the world's top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government and nonprofit research institutes. More than 2,000 systems have been shipped around the world and more than 23,000 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Santa Clara, Cleveland, Ohio, and Singapore. The company has about 900 employees worldwide and maintains sales and distribution operations across Europe, Asia, and Latin America. For more information about Affymetrix, please visit

About BioDiscovery

BioDiscovery is a leader in the development of advanced microarray bioinformatics software and services that enable its customers to revolutionize drug discovery and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray technology. Contact BioDiscovery at (310) 414-8100 or

NOTE: Affymetrix, the Affymetrix logo, and OncoScan are trademarks or registered trademarks of Affymetrix, Inc.; Nexus Copy Number is a trademark or registered trademark of BioDiscovery, Inc.

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