Affymetrix Simplifies Copy Number Data Analysis for Association and Cytogenetic Studies

Business Wire, Dec 17, 2007

New Genotyping Console[TM] 2.0 Offers up to 10 Times the Sensitivity for Detecting Copy Number Changes Than Competing Platforms

SANTA CLARA, Calif. -- Affymetrix Inc. (Nasdaq:AFFX) today announced the availability of its Genotyping Console[TM] 2.0 (GTC 2.0) Software, an easy-to-use analysis tool for determining single nucleotide polymorphism (SNP) genotypes and chromosomal copy number changes in whole-genome association and cytogenetic studies. GTC 2.0 works together with the Genome-Wide Human SNP Array 6.0 to offer researchers up to 10 times the sensitivity for detecting copy number changes than competing platforms.

GTC 2.0 displays and organizes all of the data from the SNP Array 6.0, which features more than 1.8 million markers that accurately measure copy number changes. Users can now uncover small chromosomal gains and losses that they could not have detected with classical karyotyping methods or previous array technologies. Geneticists can now better refine boundaries for common copy number variants and detect small chromosomal regions that cause genetic disease. Additionally, the ability to detect loss of heterozygosity (LOH) in the context of copy number changes enables scientists to identify copy-neutral events like uniparental disomies, genetic abnormalities that are frequent in many congenital diseases.

The new features of GTC 2.0 make it easier for researchers to extract and interpret both inherited and novel copy number changes. Over the past year, an increasing number of association studies have proven that certain common copy number variants are associated with diseases, such as Alzheimer's, HIV susceptibility and Parkinson's, while many cytogenetic abnormalities have been linked to congenital conditions like mental retardation.

"Affymetrix GTC 2.0 is an excellent software platform that is highly intuitive and user-friendly. When combined with the high-density SNP Array 6.0, this software will greatly improve our ability to detect copy number changes across the genome," said Tamim H. Shaikh, Ph.D., assistant professor, Departments of Pediatrics and Genetics at the University of Pennsylvania School of Medicine and The Children's Hospital of Philadelphia. "This information will further enable us to decipher how different types of genetic variation impact disease."

"Over the past year, the genetics community has learned that copy number changes are far more common than previously thought and are directly linked to a number of biomedical consequences," said Steve Lincoln, vice president of informatics at Affymetrix. "Affymetrix customers are now able to uncover and measure more copy number changes as well as SNP genotypes in whole-genome association and cytogenetic studies. GTC 2.0 harnesses the true genetic power of our flagship SNP Array 6.0 product and simplifies the data analysis process through an intuitive interface and seamless integration with industry-leading data analysis software solutions."

GTC 2.0 offers new algorithms for the SNP Array 6.0, as well as new visualization and reporting tools that help streamline genotyping and copy number analysis. Additionally, the export features make it easy to share data with collaborators and downstream application software. New GTC 2.0 features include:

* Robust Copy Number and LOH Algorithms for SNP Array 6.0 - Proven to offer up to 10 times the sensitivity for detecting copy number changes than competing platforms.

* Segment Reporting Tool - Describes every copy number change detected across each sample, including precise start/stop breakpoints and the percent of overlap with known copy number changes.

* Genotyping Console Genome Browser - Offers intuitive graphical interface including one-click navigation between whole-genome karyoview and individual chromosome annotations.

* GeneChip-compatible[TM] Software Enhancements - Integrates seamlessly with industry-leading data analysis packages.

For more information or to download Genotyping Console 2.0, please visit: http://www.affymetrix.com/genechip/GTC2_0.affx

The Affymetrix SNP Array 6.0 is a single microarray that simultaneously measures more than 1.8 million markers for genetic variation. The array enables researchers to perform the most powerful whole-genome association and copy number studies ever by genotyping more markers across more individuals at a lower cost per sample. These higher-powered studies increase the probability of discovering genes associated with adverse drug response or complex diseases. For more information about the SNP Array 6.0, please visit: http://www.affymetrix.com/genechip/snp6.affx.> GTC 2.0 is the latest addition to the complete Affymetrix software suite, which includes Affymetrix([R]) GeneChip([R]) Command Console([R]) (AGCC) and Affymetrix([R]) Expression Console[TM]. The suite provides scientists with integrated laboratory and data analysis workflows to suit their growing and diverging research requirements. AGCC supports modern laboratory best practices with new features for sample and array registration, fluidics and scanning instrument control as well as automated image processing. It also offers enhanced data management options with extensive search capabilities, desktop and web user interfaces and simple customization. In addition to Expression Console and Genotyping Console, AGCC is easily integrated with more than 30 leading GeneChip-compatible[TM] applications from Affymetrix' third-party software partners.