Second Phase to Analyze the Genetic Information of 36,000 Additional Individuals to Better Understand Seven New Common Disorders SANTA CLARA, Calif.–Affymetrix, Inc. (Nasdaq:AFFX – News) today announced that the Wellcome Trust of Great Britain has awarded to Affymetrix the second phase of its Case Control Consortium (WTCCC) project, the world’s largest-ever study of the genetics behind common diseases. The second phase will analyze the genetic information of 60,000 additional individuals, 30,000 of them with the Affymetrix® Genome-Wide Human SNP Array 6.0, plus 6,000 common controls. Over the next year, 14 UK research groups will collaborate with the WTCCC to identify genetic contributions to 14 common diseases and drug responses, including schizophrenia, ulcerative colitis, psychosis, bacteriosis, pre-eclampsia and statin response, as well as an additional genome-wide association study (GWAS) study on learning difficulties. Researchers will use Affymetrix technology to genotype samples for seven of these disorders. This latest WTCCC study builds on the success of the first phase, in which Affymetrix and the Wellcome Trust collaborated to genotype more than 17,000 samples to detect 24 genetic associations across bipolar disorder, coronary artery disease, Crohn’s disease, hypertension, rheumatoid arthritis, type 1 diabetes and type 2 diabetes. More than 10 billion individual genotypes were produced as part of this project. The results of these studies are detailed in a manuscript entitled “Genome-wide Association Study of 14,000 Cases of Seven Common Diseases and 3,000 Shared Controls,” published in the June 7, 2007 issue of Nature. “The first phase of the WTCCC study has been one of the most successful scientific collaborations in disease genetics worldwide,” said Leena Peltonen, M.D., Ph.D., professor, head of human genetics and deputy chair of WTCCC2 at the Wellcome Trust Sanger Institute. “The second phase will substantially increase the genetic knowledge of common diseases and drug response.” Panos Deloukas, Ph.D., head of the Genotyping Centre at the Sanger Institute, added, “The latest genotyping technology offers increased genetic coverage in many ethnic populations, as well as copy number information, which will provide even further benefit to this study.” “Utilizing genotyping chip technology, genome-wide association studies have tremendous power to highlight previously unsuspected pathways that predispose us to common diseases,” said Miles Parkes, Ph.D., consultant gastroenterologist at Addenbrooke’s Hospital and the University of Cambridge. “In Crohn’s disease for example, we now know of over 30 susceptibility genes and loci where previously we knew of just two. We are very hopeful that the next phase of the WTCCC will be even more successful, applying the lessons from the initial study in terms of sample size requirements and analytic methods, together with the technological advantages in the Affymetrix chip design to ultimately facilitate the development of new treatments for our patients, and more effective disease-prevention strategies.” “The first phase of the WTCCC run by Affymetrix and the Wellcome Trust helped uncover significant associations of common diseases,” said Kevin King, president of Affymetrix. “The Wellcome Trust’s sustained commitment to Affymetrix demonstrates the confidence that the scientific community places in our products and services. This project is a great example of how our innovative genotyping products are enabling more powerful, larger-scale studies, which are impacting human life.” Since its launch in 2007 the Affymetrix® SNP Array 6.0 has been used by more than 120 research groups across the world, mostly in whole genome association studies. Increasingly it is also being used in applications such as cytogenetics and personal genomics. The 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: https://www.affymetrix.com/genechip/snp6.affx. The genotyping services for this project are being conducted through a partnership with the Affymetrix Services Lab, which assists customers with strategic high-throughput projects and helps test and validate new technologies. About Affymetrix Affymetrix GeneChip® 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 1,700 systems have been shipped around the world and more than 13,000 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Sacramento, Calif., Cleveland, Ohio 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. About the Wellcome Trust The Wellcome Trust is the largest charity in the UK. It funds innovative biomedical research, in the UK and internationally, spending around £600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust supports public debate about biomedical research and its impact on health and wellbeing. www.wellcome.ac.uk 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 relating to commercial success of the agreement with the Wellcome Trust 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; risks associated with past and future acquisitions; 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, 2007, 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.