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mRNA-Seq Expands Illumina's Gene Expression Product Portfolio

Illumina, Inc. today announced the broad availability of mRNA-Seq, a new product for full-length, complementary DNA (cDNA) sequencing on the Genome Analyzer. In contrast to tiling and exon arrays, researchers can use mRNA-Seq to obtain a more in-depth, comprehensive view of the transcriptome, revealing aspects previously unseen using array-based or expression sequence tag (EST) technologies.

Beta testing for mRNA-Seq was carried out at multiple research facilities, including Andy Fire’s Lab at the Stanford University School of Medicine and James Hadfield’s lab at Cancer Research UK's - Cambridge Research Institute (CRI). “The mRNA-Seq protocols from Illumina have proven to be robust and simple to perform,” said James Hadfield, “We will be using this technology at CRI to increase our understanding of cancer biology. The current technology has provided us with our first detailed look at differential splicing on a genome wide scale.”

mRNA-Seq, powered by Illumina's sequencing technology and the Genome Analyzer, provides the industry’s most robust discovery tool for the profiling of mRNA. mRNA-Seq delivers unbiased and unparalleled information about the transcriptome because it does not require design of probes or primers. Researchers can use this platform to quickly generate a full sequence from any poly-A tailed RNA to discover and profile novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs (coding region single nucleotide polymorphisms) in one experiment.

“The introduction of mRNA-Seq for full-length cDNA sequencing further enhances Illumina's suite of sequencing-based expression profiling products and demonstrates the flexibility of the Genome Analyzer,” said Adam Lowe, Director of Product Marketing for the Life Sciences Business at Illumina. “This technology enables researchers to interrogate the transcriptome at a level of detail that had not been possible prior to the commercial availability of next generation sequencing. Simplicity of the sample preparation and sequencing chemistry, combined with an automated workflow of the Genome Analyzer II makes it easy for just one person to generate a rich RNA sequence database in one month.”

To support the large quantities of data generated using mRNA-Seq, Illumina will launch a primary data analysis software program - GenomeStudio™. This program enables the simultaneous analysis of over 100 million sequence reads, in addition to microarray data, all within the same project workflow paradigm. This software offers researchers a range of tools to analyze their genomics data and visualize results of exon abundance, genes and splice junctions against a reference genome. GenomeStudio offers application programming interfaces (APIs) that enable data integration with third party software providers for more advanced downstream analysis. The company expects to make this software broadly available in November 2008.

Illumina’s sequencing technology is founded on large-scale parallel sequencing of millions of nucleic acid fragments using proprietary reversible terminator-based sequencing chemistry. This approach, with Illumina’s automated workflow and the Genome Analyzer, has been broadly adopted by both single-investigator laboratories and genome centers worldwide. As a result, researchers have leveraged the platform’s extensive range of applications, including whole-genome, targeted and de novo sequencing, analysis of bisulfite converted DNA, transcriptome profiling and characterization of protein-nucleic acid interactions to publish groundbreaking studies at an unprecedented rate. Since its commercial release in early 2007, more than 120 original research studies have been published on the Genome Analyzer in peer-reviewed journals.

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