Affymetrix Scientists and Technology Help Decipher the Encyclopedia of Functional DNA Elements.

ENCODE Project Challenges the Traditional Protein-Coding, Gene-Centric View of the Human Genome 

SANTA CLARA, Calif. -- Affymetrix Inc. (Nasdaq:AFFX) announced today that a team from Affymetrix Laboratories has helped redefine the structure of the human genome as part of the ENCyclopedia Of DNA Elements (ENCODE) project. Organized by the National Human Genome Research Institute (NHGRI), the ENCODE pilot-phase project was a four-year set of studies designed to identify the functional elements present in one percent of the human genome. The results of the project were published in a set of papers in the June 14th issue of Nature and the June issue of Genome Research.

As part of these ENCODE studies, the team of Affymetrix scientists headed by Thomas R. Gingeras, Ph.D., vice president for biological science, used a collection of the company's high-density tiling arrays to yield several striking observations of the structure and organization of the human genome that will have important implications for both basic research and medical studies. The results of these studies are chronicled in four technical and one perspective manuscripts.

"This series of ENCODE studies confirms that the genome is much more intricate and complex than we were previously led to believe," said Gingeras. "The Affymetrix tiling technology enables any researcher to conduct unbiased analyses of genomes to better understand where informational content is located in the DNA sequences."

During the ENCODE project, the team of Affymetrix researchers was able to challenge the protein-coding, gene-centric view of the human genome. Traditionally, the majority of the genomic regions interrogated by the ENCODE project have been considered to be "junk" DNA. The team of Affymetrix researchers determined that approximately 93 percent of the ENCODE regions were transcribed as nuclear primary transcripts. Additionally, 65 percent of the previously unannotated protein-coding genes found within the ENCODE regions were observed to have alternative tissue-specific promoter regions and transcription start sites. These newly discovered promoters and transcription start sites can be located far away from the commonly annotated start sites of these protein-coding genes, causing the cell to skip over other intervening gene sequences between the novel promoter sequence and gene of interest.

Gingeras and his laboratory have been pioneering GeneChip([R]) tiling technology since 2000. These arrays look far beyond the known protein-coding genes to deliver the industry's most detailed and unbiased view of the entire human and mouse genomes, enabling researchers to map transcription factors, as well as sites of DNA and histone modification.

To learn more about how Affymetrix tools are supporting ENCODE-related research and to gain access to interviews and webinars, please visit: www.affymetrix.com/encode.affx

About Affymetrix

Affymetrix GeneChip([R])microarray technology is the industry-standard tool for analyzing complex genetic information. After inventing microarray technology in the late 1980s, Affymetrix scientists have been dedicated to developing innovative products that provide researchers with a more complete view of the genome. These products continue to accelerate genetic research and enable scientists to develop diagnostics and tailor treatments for individual patients by identifying and measuring the genetic information associated with complex diseases.

Today, 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 1,500 systems have been shipped around the world and more than 8,500 peer-reviewed papers have been published using the technology.

Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Sacramento, Calif., and Singapore. The company has about 1,100 employees worldwide and maintains sales and distribution operations across Europe and Asia. For more information about Affymetrix, please visit the company's website at www.affymetrix.com.

Forward-looking Statements 

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 and uncertainties associated with the use of the Affymetrix technology and uncertainties related to the implications of the findings of the ENCODE studies discussed in this press release; risks of the company's ability to achieve and sustain higher levels of revenue, higher gross margins and reduced operating expenses; uncertainties related to technological approaches, manufacturing and product development; personnel retention; uncertainties related to cost and pricing of Affymetrix products; dependence on collaborative partners; uncertainties related to sole-source suppliers; uncertainties related to FDA and other regulatory approvals; competition; risks related 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, 2006, 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.

NOTE: Affymetrix, the Affymetrix logo and GeneChip([R]) are registered trademarks owned or used by Affymetrix Inc.