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Affymetrix and BioDiscovery Announce Software for Analysis of Whole Genome Copy Number Data

Published: Thursday, April 11, 2013
Last Updated: Thursday, April 11, 2013
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Generated from FFPE solid tumor samples for accelerating cancer translational research.

Affymetrix, Inc. and BioDiscovery announce the availability of the Nexus for OncoScan® Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan® FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscovery’s flagship Nexus Copy Number™, is available to customers who are analyzing data generated using this service.

Affymetrix, Inc. and BioDiscovery announce the availability of the Nexus for OncoScan® Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan® FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscovery’s flagship Nexus Copy Number™, is available to customers who are analyzing data generated using this service.

Obtaining high-quality copy number data using limited amounts of DNA from degraded FFPE samples is extremely challenging for cancer researchers. Utilizing Affymetrix’ unique Molecular Inversion Probe (MIP) technology, the OncoScan FFPE assay is capable of analyzing highly degraded DNA in FFPE tumor samples, even from less than 100 ng of starting DNA material, and is currently available as a service through Affymetrix Research Service Laboratory (ARSL) based in Santa Clara, California.

OncoScan FFPE Express 2.0 Service has been successfully used by more than 30 leading cancer research institutes, including M. D. Anderson Cancer Center, University of California San Francisco, and the Huntsman Cancer Institute at the University of Utah.

“Cancer translational researchers have been able to quickly and easily analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data,” said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. “Nexus for OncoScan Software is especially optimized for solid tumor copy number analysis and can generate whole genome copy number calls from raw data in minutes. We are very excited to continue to partner with BioDiscovery to bring this powerful and easy-to-use software to the cancer research community.”

"The OncoScan FFPE assay is an amazing technology for cancer researchers allowing them to unlock DNA information from masses of archived FFPE samples to obtain high quality data," said Soheil Shams, President of BioDiscovery. “Combining the powerful OncoScan FFPE technology with the proven power of Nexus Copy Number gives scientists a unique solution that is sure to accelerate cancer research, impact diagnosis, and ultimately lead to better patient care and treatment. We are very pleased to partner with Affymetrix in offering this powerful solution.”

A next generation OncoScan FFPE product will be available in late 2013 enabling researchers to perform the assay and analysis in their own lab. Delivering results in about 48 hours, this new product will provide whole genome copy number coverage with high resolution in known cancer genes, loss of heterozygozity (LOH) as well as clinically relevant somatic mutation data - all from a single assay. An updated version of Nexus for OncoScan Software will be released in conjunction with the launch.


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