Applied Biosystems Expands Sequencing-based RNA Analysis Solutions Portfolio
27 Aug 2008

Applied Biosystems Inc. today announced the development of a sequencing-based molecular tool for the genomic analysis of whole transcriptomes, the vast collection of RNAs transcribed from a genome. This technology, which provides detailed characterization of expressed protein-encoding genes, identifies many non-coding RNAs, and includes sample multiplexing capability, is expected to be available for limited release through an early access program that will begin in November 2008. This offering will expand the company’s RNA expression analysis solutions portfolio for use with its SOLiD™ System, the company’s ultra-high-throughput genomic analysis platform.

The SOLiD™ Whole Transcriptome Expression Kit is expected to provide researchers greater insights into biological pathways and molecular mechanisms that regulate cell fate decision, development and disease progression. The kit is designed to provide new views of a cell’s transcriptome, such as expression of non-coding RNAs, identification of alternative splicing events, expressed SNPs (single nucleotide polymorphisms) or mutations, or translocations and fusion transcripts. The application of the kit should advance treatment of complex diseases, such as diabetes, heart disease and cancer, and accelerate time course studies in which analysis of differential RNA expression provides insight into the level and mechanism of action of a particular treatment.

John McPherson, Ph.D., cancer genomics director at the Ontario Institute for Cancer Research (OICR), is cataloging genetic alterations that occur in different types of cancers to better classify tumors and identify the important early events driving the disease. He has been exploring different approaches for identifying how genetic variants in both coding and non-coding RNA transcripts impact cancer formation. OICR will be one of the customer sites evaluating the whole transcriptome kit.

“We recognize the growing importance of understanding how altered expression of genetic variants contributes to the formation of complex diseases such as cancer,” said Dr. McPherson. “Of the various technologies available for detecting expression levels of disease-specific genetic variants where altered expression provides insights into the disease, sequencing-based methods for RNA expression analysis provide the most specific measurement possible, especially for detecting all kinds of alterations that can occur to both coding and non-coding RNA transcripts. I’m very interested in evaluating this new technology from Applied Biosystems for RNA expression analysis applications.”
Like the recently introduced SOLiD Small RNA Expression Kit, the whole transcriptome kit is based on proprietary Ambion® technology and is expected to provide researchers with an innovative workflow that greatly reduces the time, cost, and experimental variability associated with RNA library preparation. Use of either of these kits is expected to reduce the time researchers need to prepare samples for RNA analysis by approximately 50 percent, compared to alternative approaches. Applying multiplexing further simplifies the downstream workflow for RNA analysis. For example, using the multiplexing capability of the kit, up to 10 RNA libraries can be sequenced simultaneously, thereby reducing the cost of analysis per sample. In addition, the technology conserves strandedness of cDNA which allows researchers to discern between overlapping RNAs transcribed from the sense or antisense strand.

The SOLiD System is capable of generating up to 240 million sequence reads, or tags per run, for RNA expression analysis applications. This is the highest demonstrated throughput for a sequencing-based RNA expression analysis application. This throughput is necessary to assure the highest sensitivity and dynamic range for these kinds of applications. Also, the high number of tags enables researchers to multiplex samples in a single sequencing reaction, further reducing the cost of this type of analysis.

Currently, the most widely used method to analyze global patterns of gene expression is the DNA microarray. However, because microarrays are hybridization-based technologies, they are unable to detect RNA transcripts expressed at low levels and they cannot be used to detect RNA transcripts from repeated sequences. Additionally, microarrays offer limited dynamic range to detect subtle changes in expression level of target genes, which is critical in understanding biological response to stimuli or environmental changes. By enabling global, hypothesis-neutral analysis of gene expression profiles, researchers who use this kit will be able to detect all known and novel RNAs present in biological samples, with no bias toward known RNA molecules as with probe-based array technologies.

“Global transcriptome analysis is becoming a crucial area of investigation for researchers who strive to have a more complete understanding of the human genome,” said Shaf Yousaf, president for Applied Biosystems’ molecular and cell biology genomic analysis division. “The whole transcriptome kit will follow on the recent launch of the SOLiD Small RNA Expression kit, providing the company a broad portfolio of tools for analysis of coding and non-coding RNAs on a genomic analysis platform. Based on the positive reception we received for the small RNA kit, we accelerated our efforts to develop a kit for whole transcriptome analysis based on the same Ambion technology.”

To use the SOLiD Whole Transcriptome Expression Kit, researchers first isolate and purify total RNA or mRNA from cell or tissue samples. Since the whole transcriptome kit is not limited to human samples, it can also be used to analyze the transcriptomes of model organisms in agricultural study applications. Ribosomal RNA is removed from these samples, followed by a RNA fragmentation step. Researchers then hybridize and ligate adapters to these RNA fractions, and a reverse transcription reaction results in double stranded cDNA. Since both adapters are ligated in a defined manner, the strandedness of cDNA is conserved in the resulting library. Data analysis tools will also be available to early access participants, and accessible to all researchers on the SOLiD System Software Community website.

By developing genome, epigenome and transcriptome analysis solutions for its genomic analysis platforms, Applied Biosystems continues to advance science, demonstrating its leadership by helping scientists to better understand the biology underlying health and disease.

For more information about the SOLiD RNA expression analysis portfolio, please visit the article webpage.

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