New Affymetrix Tiling Arrays Deliver Unbiased View of Entire Genomes; Recent Experiments Using GeneChip® Microarrays Challenge Concept of ''Junk'' DNA

Business Wire, Jan 24, 2006

SANTA CLARA, Calif. -- Affymetrix Inc. (Nasdaq:AFFX) announced today the launch of the GeneChip(R) Human Tiling 1.0R Array Set and Mouse 1.1R Array Set, the only commercially available microarrays for whole-genome transcript mapping. These new arrays look far beyond the known protein-coding genes to deliver the most detailed and unbiased view of the entire human and mouse genomes, enabling researchers to map transcription factors and other protein binding domains. Recent scientific publications using Affymetrix tiling arrays have uncovered broad transcriptional activity in large regions of the genome that were once considered "junk" DNA.

Thomas R. Gingeras, Ph.D., vice president of biological science, and his team at Affymetrix Research Laboratories have been pioneering GeneChip tiling technology since 2000. In a series of seminal manuscripts published in Science, Cell and Genome Research, this team has reported that at least 35 percent of the human genome is transcribed and can be detected as stable, processed RNA transcripts, much more than the two percent of the genome previously assumed to be active.

"During the past six years, the work we have done at Affymetrix has motivated scientists to reconsider how the genome is organized and regulated," said Gingeras. "Now, with the commercial availability of GeneChip tiling arrays, researchers everywhere can generate higher-resolution maps of the entire human or mouse genome. This new information will accelerate biological understanding of human health."

The GeneChip Human and Mouse tiling array sets consist of 14 arrays. The arrays interrogate all of the non-repetitive portions of the human and mouse genomes. Each set of arrays generates almost 90 million data points at regular 35 base pair intervals. In conjunction with standard Affymetrix GeneChip equipment, researchers in any laboratory can use these arrays as discovery tools to gain a better understanding of gene structure, function and regulation.

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. Today's launch includes the following supporting products:

--WT Amplified Double-Stranded cDNA Synthesis Kit

--WT DS DNA Terminal Labeling Kit

--Affymetrix Tiling Array Software

--Integrated Genome Browser

For more information on the Affymetrix GeneChip tiling arrays, please visit the company's Web site at: www.affymetrix.com/products/arrays/specific/human_tiling.affx.> Further Reading

Scientific Publications

--Affymetrix scientists mapped transcription sites of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes at 5-base pair resolution in eight cell lines: Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005; 308 (5725):1149-54.

--Affymetrix scientists mapped transcription sites across approximately 30 percent of the human genome and elucidated the structure of several hundred novel transcripts: Kapranov, P. et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research 2005; 15:987-997.

--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.

--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 led by Dr. Anindya Dutta of the University of Virginia discovered critical information about how the cancer genome replicates and how it might be restored to healthy growth. The team made their findings through the most detailed whole-genome scan of origins of replication ever performed using high-resolution tiling microarrays that measured every 35th base of chromosomes 21 and 22: Jeon, Y. et al. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci USA 2005; 102(18):6419-24.

--An international research team studying Arabidopsis used custom whole-genome GeneChip tiling arrays to discover nearly 6,000 new genes: Yamada, K. et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 2003; 302(5646):842-6.

Affymetrix Microarray Bulletin Interviews

--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