Thursday, June 15, 2006

role of exon arrays in alternate splicing

genomics: May 2006

Research indicates that 60 percent or more of the best characterized genes in the human genome comprise multiple exons, or small blocks of RNA that can be rearranged, or "spliced" together to create different transcripts from the same gene. Each of those transcripts can potentially be translated into a different protein carrying out different functions, which greatly increases the diversity of proteins generated from the genome. The GeneChip exon arrays offer a new and high resolution view to examine these alternatively expressed exons, enabling researchers to conduct experiments that were not possible before. More than a dozen leading academic and industrial research organizations are already using the exon arrays through an early technology access program.

Since each Affymetrix exon array has a capacity of more than six million data points, whole-genome exon expression analysis is possible on a single array. Other platforms with significantly lower data capacity require as many as 50 arrays, which demand more sample, reagent and labor to conduct a comparable experiment.

"Biology occurs at the transcript level and any one of these transcripts could hold the key to a new treatment or diagnostic. Affymetrix exon arrays offer scientists the only solution for accessing genome-wide exon data on a single array," said John E. Blume, Ph.D., vice president of RNA Products at Affymetrix. "We anticipate that access to this data could dramatically accelerate research, publication and, ultimately, bring new tests and therapies to market."

Exon Array Design

The first-generation genome-wide exon arrays from Affymetrix are designed to include all annotated exons. In addition, these new arrays include computationally predicted and empirically identified exon content, enabling researchers to study known splicing events as well as to discover novel splice variants. All of the probes are based on genomic sequence and annotated on the genome, making it easier for researchers to correlate expression and alternative splicing data with genetic variations or mutations related to the disease.

Exon Array Applications

Exon-level analysis can provide important new data in a number of different research areas. For example, the whole-genome, exon-level detail these arrays provide makes them ideal for identifying novel biomarkers. The array's alternative splicing and gene expression information could also be used to help find a precise, predictive signature for drug response or pathological mechanism. As a discovery tool, the exon array's high resolution view of coding sequence gene expression will help researchers validate new gene content, providing in-depth analysis for drug-discovery targets and biological mechanisms. In addition, the exon arrays provide a possible fast-track for linking genetic information such as SNPs to functional effects at the expression level.

Exon Array System

Affymetrix exon arrays are built on the same GeneChip technology that has been the industry standard in microarray research for the past decade. The Affymetrix exon array system launched today includes:

-- GeneChip Human Exon 1.0 ST (Sense Target) Array

-- Optimized and validated reagents that are based on a whole transcript assay

-- The Exon Array Computational Tool (ExACT), which incorporates new algorithms for detection and signal estimation. Together with the existing NetAffx(TM) Analysis Center and the Integrated Genome Browser, these tools provide basic analysis and array design information and annotation.

For more information on the Affymetrix GeneChip exon arrays, please visit the company's website at

About Affymetrix

Affymetrix scientists invented the world's first microarray in 1989 and began selling the first commercial microarray in 1994. Since then, Affymetrix GeneChip(R) technology has become the industry standard in molecular biology research. Affymetrix technology is used by the world's top pharmaceutical, diagnostic and biotechnology companies as well as leading academic, government and not-for-profit research institutes. More than 1,200 systems have been shipped around the world and more than 3,000 peer-reviewed papers have been published using the technology. Affymetrix' patented photolithographic manufacturing process provides the most information capacity available today on an array, enabling researchers to use a whole-genome approach to analyze the relationship between genetics and health. Headquartered in Santa Clara, Calif., Affymetrix has subsidiaries in Europe and Asia in addition to manufacturing facilities in Sacramento, Calif. and Bedford, Mass. The company has about 900 employees worldwide. For more information about Affymetrix, please visit the company's website at

All statements in this press release that are not historical are "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix' "expectations," "beliefs," "hopes," "intentions," "strategies" or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected, including, but not limited to risks of the Company's ability to achieve and sustain higher levels of revenue, higher gross margins, reduced operating expenses, uncertainties relating to technological approaches, manufacturing, product development (including uncertainties relating to commercial and technological success of the GeneChip Human Exon 1.0 ST Arrays discussed in this press release and the timing of the Company's release of mouse and rat exon arrays), personnel retention, uncertainties related to cost and pricing of Affymetrix products, dependence on collaborative partners, uncertainties relating to sole source suppliers, uncertainties relating to FDA and other regulatory approvals, competition, risks relating to intellectual property of others and the uncertainties of patent protection and litigation. These and other risk factors are discussed in Affymetrix' Form 10-K for the year ended December 31, 2004 and other SEC reports, including its Quarterly Reports on Form 10-Q for subsequent quarterly periods. Affymetrix expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in Affymetrix' expectations with regard thereto or any change in events, conditions, or circumstances on which any such statements are based.

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