While the complete human genome sequence is now available, nearly all of it (about 98%) has been considered "junk" and its function not studied because there has been no technology available to examine millions or even billions of bases of DNA. The ENCODE project, as outlined in today's issue of Science, has brought together an impressive collection of international laboratories to evaluate strategies and new technologies to tackle what may be the biggest biological question ever asked.

Affymetrix' ENCODE microarray is playing a key role in helping to answer this important question. The ENCODE array contains millions of DNA probes evenly spaced or "tiled" across 35 million base pairs of DNA that was specifically chosen by the ENCODE project as a representative sampling of the complete genome sequence. In an industry first, these "tiling" arrays provide scientists with the only single tool available for genome-wide analyses of many important biological functions, including: transcription, transcription factor binding sites, sites of chromatin modification, sites of DNA methylation and even chromosomal origins of replication.

"In the process of climbing the steps of whole genome research, the ENCODE array is a wonderful tool," said Katsuhiko Shirahige, Ph.D., Division for Gene Research, Tokyo Institute of Technology. "The design content is extremely easy to use for basic research areas such as human transcription, replication and chromatin structure, to name a few."

In addition to Affymetrix arrays being used in large-scale initiatives like the ENCODE project, Affymetrix has established an Early Access program that gives individual researchers the opportunity to purchase tiling arrays for human chromosomes 21 and 22. Affymetrix has also developed high-resolution tiling arrays for the entire human genome and several model organisms, including Drosophila, Arabidopsis, S. cerevisiae and S. pombe. These arrays have been made available to several research groups through a technology access program or through collaborative projects with Affymetrix. A full range of tiling arrays are expected to be commercially available in the second half of 2005.

A number of early studies using Affymetrix tiling arrays have already resulted in publication:

--In 2002, Affymetrix scientists used Human Chromsome 21 and 22 tiling arrays,and found that there is an order of magnitude more transcription - the conversion of DNA into RNA - than accounted for by current annotations [link to publication].
--In 2003, Japanese researchers used custom S. cerevisiae tiling arrays to discover new parts of the yeast genome that are involved in DNA replication, a fundamental biological process critical to all walks of life [link to publication].
--Also, in 2003, an international research team studying the plant, Arabidopsis thaliana, used custom Arabidopsis whole-genome tiling arrays to discover nearly 6,000 new genes that had never been seen before [link to publication].
--In 2004, Affymetrix scientists again used Human Chromosome 21 and 22 tiling arrays to prove that the millions of newly discovered RNA molecules are turned on and off by the same regulators used by protein coding genes [link to publication].
--Also, in 2004, British and Japanese scientists used custom S. cerevisiae and S. pombe yeast tiling arrays to link DNA replication with transcription, two events that were previously thought to be separate processes [link to publication].

The results from these papers are changing the way that we understand the genome. For the past 50 years, research has focused almost exclusively on protein coding genes. Using tiling arrays, scientists are beginning to understand the genome is far more complex than that.

"Piece by piece, we are beginning to create a high-resolution map of the human transcriptome, providing detailed information well beyond its basic sequence," said Thomas Gingeras, Ph.D., Vice President of Biological Sciences, Affymetrix Laboratories. "The hope is that one day, scientists can more readily understand the biology of health and disease by correlating sequence of DNA from anywhere in the genome to its function."

About Affymetrix:
Affymetrix is a pioneer in creating breakthrough tools that are driving the genomic revolution. By applying the principles of semiconductor technology to the life sciences, Affymetrix develops and commercializes systems that enable scientists to improve quality of life. The Company's customers include pharmaceutical, biotechnology, agrichemical, diagnostics and consumer products companies as well as academic, government and other non-profit research institutes. Affymetrix offers an expanding portfolio of integrated products and services, including its integrated GeneChip brand platform, to address growing markets focused on understanding the relationship between genes and human health. Additional information on Affymetrix can be found at www.affymetrix.com.

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 the success of the ENCODE array discussed in this press release), market acceptance, 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, 2003 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 are registered trademarks owned or used by Affymetrix, Inc.

SOURCE Affymetrix, Inc. 10/22/2004

CONTACT: media, Wes Conard, Associate Director, Public Relations, +1-408-731-5791, or investors, Doug Farrell, Vice President, Investor Relations, +1-408-731-5285, both of Affymetrix Web site: http://www.affymetrix.com