Affymetrix Launches GeneChip Human Exon Array

New Microarray Offers Exon-Level, Genome-Wide Expression Profiling on a Single Array

Affymetrix Inc. today announced the launch of the GeneChip Human Exon 1.0 ST Array, offering whole-genome, exon-level expression profiling on a single array for the first time. Designed to interrogate approximately one million exons, the array helps researchers better understand the roles that alternative splicing and gene expression play in biology. Affymetrix expects to offer GeneChip Mouse and Rat exon arrays toward the end of the year.

Research indicates that 60 percent or more of the best characterized genes in the human genome comprise multiple exons, or small blocks of RNA that can be rearranged, or "spliced" together to create different transcripts from the same gene. Each of those transcripts can potentially be translated into a different protein carrying out different functions, which greatly increases the diversity of proteins generated from the genome. The GeneChip exon arrays offer a new and high resolution view to examine these alternatively expressed exons, enabling researchers to conduct experiments that were not possible before. More than a dozen leading academic and industrial research organizations are already using the exon arrays through an early technology access program.

Since each Affymetrix exon array has a capacity of more than six million data points, whole-genome exon expression analysis is possible on a single array. Other platforms with significantly lower data capacity require as many as 50 arrays, which demand more sample, reagent and labor to conduct a comparable experiment.

"Biology occurs at the transcript level and any one of these transcripts could hold the key to a new treatment or diagnostic. Affymetrix exon arrays offer scientists the only solution for accessing genome-wide exon data on a single array," said John E. Blume, Ph.D., vice president of RNA Products at Affymetrix. "We anticipate that access to this data could dramatically accelerate research, publication and, ultimately, bring new tests and therapies to market."

Exon Array Design
The first-generation genome-wide exon arrays from Affymetrix are designed to include all annotated exons. In addition, these new arrays include computationally predicted and empirically identified exon content, enabling researchers to study known splicing events as well as to discover novel splice variants. All of the probes are based on genomic sequence and annotated on the genome, making it easier for researchers to correlate expression and alternative splicing data with genetic variations or mutations related to the disease.

Exon Array Applications
Exon-level analysis can provide important new data in a number of different research areas. For example, the whole-genome, exon-level detail these arrays provide makes them ideal for identifying novel biomarkers. The array's alternative splicing and gene expression information could also be used to help find a precise, predictive signature for drug response or pathological mechanism. As a discovery tool, the exon array's high resolution view of coding sequence gene expression will help researchers validate new gene content, providing in-depth analysis for drug-discovery targets and biological mechanisms. In addition, the exon arrays provide a possible fast-track for linking genetic information such as SNPs to functional effects at the expression level.

Exon Array System
Affymetrix exon arrays are built on the same GeneChip technology that has been the industry standard in microarray research for the past decade. The Affymetrix exon array system launched today includes:

• GeneChip Human Exon 1.0 ST (Sense Target) Array
  
• Optimized and validated reagents that are based on a whole transcript assay
  
• The Exon Array Computational Tool (ExACT), which incorporates new algorithms for detection and signal estimation. Together with the existing NetAffx(TM) Analysis Center and the Integrated Genome Browser, these tools provide basic analysis and array design information and annotation.

SOURCE: Affymetrix