Affymetrix Announces New ChIP-on-Chip Array Product Line; New Whole-Genome Tools Help Scientists Discover DNA-Protein Interactions.

SANTA CLARA, Calif. -- Affymetrix Inc. (Nasdaq:AFFX) announced today the launch of nine tiling array products for five different organisms, further expanding the industry's broadest selection of whole-genome microarrays. Researchers in any laboratory can use the GeneChip(R) tiling arrays to map sites of DNA-protein interaction in chromatin immunoprecipitation (ChIP)-on-chip experiments, discover new RNA transcripts or investigate global epigenomic changes like methylation or acetylation.

Affymetrix tiling arrays deliver an unbiased view of entire genomes, enabling scientists to look beyond the known protein-coding gene sequences and thoroughly study gene structure, function and regulation. Scientists using the tiling arrays have reported unexpected functions for already known genes and new functions for previously unexplored parts of the genome. Several seminal manuscripts have already been published in major scientific journals, including Science, Cell and Genome Research.

"We are extremely pleased with the performance of the GeneChip tiling arrays for mapping transcription factor binding sites by ChIP-on-chip," said Myles Brown, M.D., associate professor of Medicine, Harvard Medical School and participant in Affymetrix' Tiling Array Early Access Program. "These arrays have allowed us to comprehensively explore the non-repetitive regions of the entire human genome. This unbiased approach is already leading us to important new insights into the gene regulatory networks controlled by steroid hormones and their receptors."

For the past six years, Affymetrix scientists have been pioneering tiling microarray technology. Thomas R. Gingeras, Ph.D., vice president of biological science, and his team at Affymetrix Research Laboratories have used the tiling arrays to uncover broad transcriptional activity in large regions of the genome that were once considered "junk" DNA.

"Affymetrix tiling array technology is revealing a very important and unappreciated genetic realm that is challenging fundamental concepts of biology," said Gingeras. "Using these arrays, we have been able to discover novel non-coding RNA transcripts and map the sites of DNA-protein interactions."

Tiling Array System

Affymetrix tiling arrays are built on the same GeneChip technology that has been the industry standard in microarray research for the past decade. The high-density tiling array sets interrogate all of the non-repetitive portions of the various genomes. For example, the human tiling arrays interrogate nearly 90 million data points at regular 35 base pair intervals across the human genome. The complete tiling array systems include an assay kit, analysis software and an integrated browser that enables researchers to compare experimental results to computational results. Affymetrix has also released a tested and qualified assay protocol for chromatin immunoprecipitation experiments.

The following tiling array products are available today:

Whole-genome Human Tiling Arrays

--Human Tiling 2.0R Array Set -- seven array set designed for ChIP-on-chip experiments (A-G arrays also available separately)

--Human Promoter 1.0R Array -- one array comprised of more than 4.6 million probes tiled to interrogate more than 25,500 human promoter regions, enabling researchers to easily identify thousands of regulatory sequences

Whole-genome Mouse Tiling Arrays

--Mouse Tiling 2.0R Array Set -- seven array set for ChIP-on-chip experiments (A-G arrays also available separately)

--Mouse Promoter 1.0R Array -- one array comprised of more than 4.6 million probes tiled to interrogate more than 28,000 mouse promoter regions, enabling researchers to easily identify thousands of regulatory sequences

Whole-genome Tiling Array Supporting Products

--GeneChip WT Double-Stranded DNA Terminal Labeling Kit

--Affymetrix Tiling Analysis Software (TAS)

--Integrated Genome Browser (IGB)

--Affymetrix Chromatin Immunoprecipitation Assay Protocol

The following tiling array products will be available during the second quarter:

Whole-genome Human Tiling Arrays

--ENCODE01 1.0R Array -- one array designed to study the pilot ENCODE regions of DNA, or approximately one percent of the human genome. The ENCODE Project (Encyclopedia of DNA Elements) has been undertaken to identify all of the functional elements of the human genome sequence.

--Chromosome 21/22 1.0R Array Set -- three array set designed to study human chromosomes 21 and 22

Whole-genome Model Organism Tiling Arrays

--Arabidopsis Tiling 1.0R Array

--S. cerevisiae Tiling 1.0R Array

--S. pombe Tiling 1.0FR Array

The latest arrays complement the recently launched Human and Mouse 1.0R Tiling Array Sets, which are 14 array sets for whole-genome transcript mapping. For more information on the complete family of Affymetrix GeneChip tiling arrays, please visit the company's Web site at: http://www.affymetrix.com/products/application/quantitation.affx.

Further Reading

Scientific Publications

--Review of different whole-genome microarray designs and applications to obtain a wide variety of genomic-scale information - Mockler T et al. Applications of DNA Tiling Arrays for Whole-Genome Analysis. Genomics. 2005;85:1-15.

--Scientists at the Dana-Farber Cancer Institute mapped the association of the estrogen receptor with the complete nonrepetitive sequence of human chromosomes 21 and 22 by combining chromatin immunoprecipitation with tiled microarrays -- Carroll J et al. Chromosome-wide Mapping of Estrogen Receptor Binding Reveals Long-range Regulation Requiring the Forkhead Protein Fox A1. Cell. 2005; 122:33-43.

--Affymetrix scientists 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 -- Cawley S et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004;116(4):499-509. PMID: 14980218.

--Scientists at Harvard University mapped histone H3 lysine 4 di- and trimethylation and lysine 9/14 acetylation across the nonrepetitive portions of human chromosomes 21 and 22 and compared patterns of lysine 4 dimethylation for several orthologous human and mouse loci -- Bernstein B et al. Genomic Maps and Comparative Analysis of Histone Modification in Human and Mouse. Cell. 2005;120:169-181.

--Affymetrix scientists used Human Chromosome 21 and 22 tiling arrays to find that there is an order of magnitude more transcription than accounted for by current annotations - Kapranov P et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002;296:916-9.

--The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence - ENCODE Consortium, The ENCODE Project. Science. 2004;306:636-640.

--Scientists at Princeton developed a software tool for to predict single nucleotide polymorphisms using GeneChip S.cerevisiae 1.0R Tiling Array. - Gresham et al. Genome-wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray. Science. 2006; March 9; (Epub ahead of print).

Affymetrix Microarray Bulletin Interviews

--Struhl, Kevin. Interview with Myles Brown. "Thousands of Previously Unknown Transcription Factor Binding Sites Mapped Using Tiling Microarrays." Affymetrix Microarray Bulletin 2005 October 1;1(4):1-5. To view the story: http://www.microarraybulletin.com/community/article.php?p=44

--Liu, Shirley. Interview with David Nix. "New Bioinformatics Algorithm Predicts Forkhead Protein Plays a Role in Breast Cancer Estrogen Response." Affymetrix Microarray Bulletin 2005 October 1;1(4):5-8. To view the story: http://www.microarraybulletin.com/community/article.php?p=45

--Dutta, Anindya. Interview with Michael Botchan. "Highest Resolution Study of Genome Replication Surprises Scientists with Unexpected Timing in S-phase." Affymetrix Microarray Bulletin 2005 October 1;1(4):12-15. To view the story: http://microarraybulletin.com/community/article.php?p=43

--Quackenbush, John. Interview with Paul Bertone. "Developing Tools and Methodologies for Whole-genome Transcript Mapping." Affymetrix Microarray Bulletin 2005 April 1;1(1):18-21. To view the story: http://www.microarraybulletin.com/community/article.php?p=14

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 1,400 systems have been installed around the world and nearly 4,000 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 analyzing the relationship between genetics and health. Affymetrix is headquartered in Santa Clara, Calif., with subsidiaries in Europe and Asia, as well as manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company has about 1,000 employees worldwide. For more information about Affymetrix, please visit the company's Web site 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 (including risks related to the Company's ability to achieve hoped-for manufacturing yields for certain array products, including the ability to identify and resolve manufacturing problems), product development (including uncertainties relating to commercial and technological success of the GeneChip Tiling Arrays discussed in this press release); 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, 2005, 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.