AFFX Affymetrix, Inc.

Affymetrix Inc. (NASDAQ:AFFX) announced today that scientists working on the International Genome Structural Variation Consortium�s Copy Number Variation Project have used the 500K Array to help generate the first comprehensive copy number variation (CNV) map of the human genome.�The team discovered hundreds of CNVs that will enable researchers to perform more powerful association studies on diseases such as cancer, Parkinson�s and Alzheimer�s.�The results of this study have been published in the November 23, 2006 issue of Nature1 along with a supporting paper in Genome Research2. The study is the first publication to demonstrate the performance of whole-genome single nucleotide polymorphism (SNP) arrays in detecting CNVs in the general population. The Affymetrix 500K Array genotypes more than 500,000 SNPs and offers the industry�s highest-resolution view of CNVs in the human genome. Researchers in the study discovered that CNVs are much more prevalent than previously thought. CNV regions were found to comprise about 360 megabases, or around 12 percent of the human genome. To read an Affymetrix Microarray Bulletin interview about this study, please visit: http://microarraybulletin.com/community/article.php?p=277. CNVs can consist of deletions, duplications or multi-site variants in DNA segments, ranging from a few kilobases to megabases in length. They are particularly important in genetic research because they can be associated with specific diseases, such as an increased susceptibility to cancer, Parkinson�s and Alzheimer�s, as well as to conditions like HIV-1 infection and glomerulonephritis.�Certain CNVs also appear to influence drug metabolism and increase sensitivity to particular chemical carcinogens, which will also help to decipher the complex ways in which an individual�s genes and the environment impact disease. �Our results suggest that sub-microscopic structural variants along chromosomes are more widespread than previously thought and that researchers should study both SNPs and CNVs when undertaking disease research,� said Stephen Scherer, Ph.D., senior scientist in Genetics & Genome Biology at The Hospital for Sick Children, director of The Center for Applied Genomics and one of the lead researchers in the study. �Our new approach will be useful in understanding the role of copy number alteration in disease pathology. This information should lead to the development of diagnostic tests with sub-microscopic resolution that can detect not only mutations in cancer but other genetic variations associated with common diseases,� said Hiroyuki Aburatani, M.D., Ph.D., professor at the University of Tokyo and one of the lead researchers. �This study illustrates that in addition to generating genotypes for�over 500,000 SNPs, the Affymetrix 500K Array�enables researchers to detect more CNVs than any other available platform. It's important to�note that�the combination of high-density markers and robust analysis methods have allowed us to�identify CNVs and delineate the boundaries at a high resolution, which helps in establishing the link between CNVs and disease pathology,� said Keith Jones, Ph.D., vice president of molecular genetics at Affymetrix and another of the lead researchers. Researchers in the Nature study constructed the CNV map of the human genome by analyzing samples from 270 people of European, Asian or African descent, who were originally included in the International HapMap Project. The DNA from these individuals was scanned using the Affymetrix 500K Array and a BAC array platform developed by the Wellcome Trust Sanger Institute. Using this combination of techniques on these samples, the researchers discovered 1,447 CNV regions containing hundreds of genes, disease loci, functional elements and segmental duplications. The other lead researchers working on the International Genome Structural Variation Consortium�s Copy Number Variation Project were Nigel Carter and Matthew Hurles of the Wellcome Trust Sanger Institute and Charles Lee at the Department of Pathology at Brigham and Women�s Hospital. The raw data from the 500K Arrays are posted online at the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo). The CNV calls have been released at the Database of Genomic Variants (http://projects.tcag.ca/variation) together with all other data. Additional genotyping microarray-based CNV analysis downloads can be found at the website for the Genome Science Division RCAST, The University of Tokyo (http://www2.genome.rcast.u-tokyo.ac.jp/CNV/). New Combined SNP/CNV Array With more than 25 peer-reviewed publications to date, Affymetrix Human Mapping Arrays have pioneered the utilization of whole-genome SNP arrays for copy number analysis.�Later this year, Affymetrix will introduce the SNP 5.0 Array that was developed in collaboration with the Broad Institute of Harvard and the Massachusetts Institute of Technology. The new product will redefine the way association studies are performed by assaying both SNPs and CNVs within the human population on a single array. In addition to featuring the majority of the SNPs from the 500K Array Set, the SNP 5.0 Array will also include 500,000 non-polymorphic tiling probes to assess CNV in association studies. Around 100,000�of�the non-polymorphic tiling probes are specifically targeted at�approximately 2,000 previously identified CNVs, thereby allowing future whole-genome association studies to better�identify and understand the contribution of CNVs�in common diseases. References 1Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G, ... Carter, N.P., Aburatani, H., Lee, C., Jones K.W., Scherer, S.W. and Hurles, M.E. Global variation in copy number in the human genome. Nature. 2006 Nov 23; 444: 444-454. 2Komura, D., Shen, F., Ishikawa, S., Fitch, K.R., Chen, W., Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles, M.E., Lee, C., Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J. and Aburatani, H. 2006. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 2006. Advance online publication doi:10.1101/gr.5629106. About Affymetrix Affymetrix scientists invented the world's first high-density microarray in 1989 and began selling the first commercial microarray in 1994. Since then, Affymetrix GeneChip� 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 more than 7,000 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 manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company maintains important sales and marketing operations in Europe and Asia, and has about 1,100 employees worldwide. For more information about Affymetrix, please visit the company's website 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 and uncertainties associated with the use of the 500K Array to develop the CNV map discussed in this press release; 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; 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/A 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. Affymetrix Inc. (NASDAQ:AFFX) announced today that scientists working on the International Genome Structural Variation Consortium's Copy Number Variation Project have used the 500K Array to help generate the first comprehensive copy number variation (CNV) map of the human genome. The team discovered hundreds of CNVs that will enable researchers to perform more powerful association studies on diseases such as cancer, Parkinson's and Alzheimer's. The results of this study have been published in the November 23, 2006 issue of Nature(1) along with a supporting paper in Genome Research(2). The study is the first publication to demonstrate the performance of whole-genome single nucleotide polymorphism (SNP) arrays in detecting CNVs in the general population. The Affymetrix 500K Array genotypes more than 500,000 SNPs and offers the industry's highest-resolution view of CNVs in the human genome. Researchers in the study discovered that CNVs are much more prevalent than previously thought. CNV regions were found to comprise about 360 megabases, or around 12 percent of the human genome. To read an Affymetrix Microarray Bulletin interview about this study, please visit: http://microarraybulletin.com/community/article.php?p=277. CNVs can consist of deletions, duplications or multi-site variants in DNA segments, ranging from a few kilobases to megabases in length. They are particularly important in genetic research because they can be associated with specific diseases, such as an increased susceptibility to cancer, Parkinson's and Alzheimer's, as well as to conditions like HIV-1 infection and glomerulonephritis. Certain CNVs also appear to influence drug metabolism and increase sensitivity to particular chemical carcinogens, which will also help to decipher the complex ways in which an individual's genes and the environment impact disease. "Our results suggest that sub-microscopic structural variants along chromosomes are more widespread than previously thought and that researchers should study both SNPs and CNVs when undertaking disease research," said Stephen Scherer, Ph.D., senior scientist in Genetics & Genome Biology at The Hospital for Sick Children, director of The Center for Applied Genomics and one of the lead researchers in the study. "Our new approach will be useful in understanding the role of copy number alteration in disease pathology. This information should lead to the development of diagnostic tests with sub-microscopic resolution that can detect not only mutations in cancer but other genetic variations associated with common diseases," said Hiroyuki Aburatani, M.D., Ph.D., professor at the University of Tokyo and one of the lead researchers. "This study illustrates that in addition to generating genotypes for over 500,000 SNPs, the Affymetrix 500K Array enables researchers to detect more CNVs than any other available platform. It's important to note that the combination of high-density markers and robust analysis methods have allowed us to identify CNVs and delineate the boundaries at a high resolution, which helps in establishing the link between CNVs and disease pathology," said Keith Jones, Ph.D., vice president of molecular genetics at Affymetrix and another of the lead researchers. Researchers in the Nature study constructed the CNV map of the human genome by analyzing samples from 270 people of European, Asian or African descent, who were originally included in the International HapMap Project. The DNA from these individuals was scanned using the Affymetrix 500K Array and a BAC array platform developed by the Wellcome Trust Sanger Institute. Using this combination of techniques on these samples, the researchers discovered 1,447 CNV regions containing hundreds of genes, disease loci, functional elements and segmental duplications. The other lead researchers working on the International Genome Structural Variation Consortium's Copy Number Variation Project were Nigel Carter and Matthew Hurles of the Wellcome Trust Sanger Institute and Charles Lee at the Department of Pathology at Brigham and Women's Hospital. The raw data from the 500K Arrays are posted online at the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo). The CNV calls have been released at the Database of Genomic Variants (http://projects.tcag.ca/variation) together with all other data. Additional genotyping microarray-based CNV analysis downloads can be found at the website for the Genome Science Division RCAST, The University of Tokyo (http://www2.genome.rcast.u-tokyo.ac.jp/CNV/). New Combined SNP/CNV Array With more than 25 peer-reviewed publications to date, Affymetrix Human Mapping Arrays have pioneered the utilization of whole-genome SNP arrays for copy number analysis. Later this year, Affymetrix will introduce the SNP 5.0 Array that was developed in collaboration with the Broad Institute of Harvard and the Massachusetts Institute of Technology. The new product will redefine the way association studies are performed by assaying both SNPs and CNVs within the human population on a single array. In addition to featuring the majority of the SNPs from the 500K Array Set, the SNP 5.0 Array will also include 500,000 non-polymorphic tiling probes to assess CNV in association studies. Around 100,000 of the non-polymorphic tiling probes are specifically targeted at approximately 2,000 previously identified CNVs, thereby allowing future whole-genome association studies to better identify and understand the contribution of CNVs in common diseases. References (1) Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G, ... Carter, N.P., Aburatani, H., Lee, C., Jones K.W., Scherer, S.W. and Hurles, M.E. Global variation in copy number in the human genome. Nature. 2006 Nov 23; 444: 444-454. (2) Komura, D., Shen, F., Ishikawa, S., Fitch, K.R., Chen, W., Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles, M.E., Lee, C., Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J. and Aburatani, H. 2006. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 2006. Advance online publication doi:10.1101/gr.5629106. About Affymetrix Affymetrix scientists invented the world's first high-density 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 more than 7,000 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 manufacturing facilities in Sacramento, Calif., and Bedford, Mass. The company maintains important sales and marketing operations in Europe and Asia, and has about 1,100 employees worldwide. For more information about Affymetrix, please visit the company's website 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 and uncertainties associated with the use of the 500K Array to develop the CNV map discussed in this press release; 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; 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/A 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.