Illumina, Inc. (NASDAQ:ILMN) today introduced GenomeStudio Software, a primary analysis software program designed to analyze both microarray and sequencing data. For researchers, GenomeStudio Software enables the correlation of biological variation across multiple applications and graphical display of the results. The flexibility of GenomeStudio Software also allows researchers to integrate with third-party software providers for advanced downstream analysis. GenomeStudio Software will be broadly available to researchers in November 2008.

Under an early access program, Illumina offered GenomeStudio Software to customers from both academic research institutes and genome centers around the world. Among them was Stephen Kingsmore’s lab at the National Center for Genetic Research (NCGR), Richard Michelmore’s lab at University of California, Davis, Andy Fire’s Lab at Stanford University, Barbara Wold’s lab at the California Institute of Technology, and James Hadfield’s lab at Cancer Research UK-Cambridge Research Institute.

“The rate at which we can go from sample preparation to visualizing exon-level expression is staggering,” said Greg May, Ph.D., Director of the Genome Center at NCGR. “GenomeStudio Software allows us to see meaningful changes in RNA processing and will allow us to further unravel the complexities of transcriptional regulation in complex conditions such as schizophrenia and sepsis, a blood poisoning disease.”

In addition to algorithms for copy number variation detection, single-nucleotide polymorphism calling, and differential analysis, GenomeStudio Software contains tools for visualizing sequencing data that are fueled by a new and expanded version of Illumina’s Genome Analyzer Analysis Pipeline. A new processing module known as CASAVA (Consensus Assessment of Sequence and Variation) allows users to detect sequence variants from one or more Genome Analyzer sequencing runs. These new features allow users to align reads directly to sequences representing processed RNAs, and identify and quantify genes, exons, and splice junctions. Results are imported directly into GenomeStudio Software for visual and graphical analysis.

“The flexibility of Illumina’s technologies allows scientists to conduct a number of genome-wide research applications. When developing GenomeStudio Software, we focused on overall integration and ease-of-use for genomic researchers,” said Scott Kahn, Chief Information Officer at Illumina. “Researchers need graphical results to interpret data across multiple applications. Careful performance optimization allows us to bring the point-and-click simplicity of a laptop or desktop system to problems that once required teams of informaticians and heavy computational hardware.”

Advanced analysis of data can be completed using a growing number of third-party analysis applications. In 2007 Illumina launched Illumina Connect to ensure that an analysis workflow that includes multiple software applications is streamlined. Illumina Connect is a bioinformatics software partnership program established to advance data integration and analysis. As part of this program, vendors receive example data sets and data formats that can optimize their applications’ analytical abilities to best mine data generated by Illumina’s sequencing and microarray-based applications. Vendors create customized plug-ins to Illumina’s GenomeStudio Software to help expedite the transfer of data between applications. To date, more than 30 commercial and academic partners have joined Illumina Connect. For more information about Illumina Connect, please visit www.illumina.com/illuminaconnect.