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Applied Biosystems Expands Applications for Gene Expression Discovery with Next-Generation Sequencing Platform

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Only in recent years have scientists begun to understand the role of small, non-protein coding RNA molecules in living cells. Breakthroughs in science and technology have revealed that this newly discovered class of regulatory molecules plays a critical role in cellular processes with applications for understanding both basic biology and complex diseases such as cancer.

Researchers now have a new tool to enable the discovery of microRNAs and other small RNA molecules using the latest genomic analysis technology from Applied Biosystems, an Applera Corporation business.

The company has announced that it has enhanced its solution for performing highly sensitive digital gene expression analysis on its next-generation sequencing platform with its new SOLiD™ RNA Expression Solution.

The offering includes a sample preparation kit to enable high throughput discovery of novel RNA molecules without requiring previous knowledge of sequence information. The solution is expected to improve the ability of researchers to identify small RNA molecules and enable experiments that were previously not possible.

The SOLiD Small RNA Expression Kit provides researchers with an innovative workflow that greatly reduces the time, cost, and experimental variability associated with small RNA library preparation. The kit converts total RNA into a library suitable for input into the SOLiD System workflow for high throughput genomic analysis. The simple protocol reduces the sample preparation workflow to a single day compared to four days with alternative platforms.

As a result, the kit is expected to improve the detection of biologically relevant changes for researchers working with small RNA molecules. It also requires very small sample quantities, enabling studies not possible before using methods requiring more RNA than was available to the researcher. The new sample preparation kit is currently available through an early access program.

Once small RNAs are discovered using the SOLiD system, researchers can use Applied Biosystems’ industry-leading TaqMan® Assays to validate their results or focus on specific microRNAs of interest, providing a complete workflow solution for microRNA analysis. Applied Biosystems also announced today that it has begun an early access program for Custom TaqMan MicroRNA Assays to support customers discovering novel microRNAs.

Victor Ambros, PhD, a professor of molecular medicine at the University of Massachusetts Medical School who helped pioneer the field of small RNA analysis, is one of more than 10 early access customers so far for the SOLiD Small RNA Expression kit. Dr Ambros is using the kit, in combination with the TaqMan microRNA Assays, as part of his investigation into the role microRNAs play in cancer.

“This is really a transformative technology in that it allows scientists to perform experiments we couldn’t contemplate before and in a manner that is much easier than previous methods,” said Dr Ambros. “In my experience the kit requires at least 10-fold less RNA per sample, and requires far fewer steps than techniques I have used in the past. Furthermore, the straightforward and simple protocol opens up the possibility for more scientists to do these types of analyses.”

Fewer than 800 microRNAs have been discovered so far, but advances in technology such as the SOLiD System are expected to reveal many more novel molecules of potential scientific interest. Because the SOLiD System can detect and quantify small RNA molecules without requiring prior knowledge of DNA sequences of the molecules being targeted, it is an effective tool for profiling both known and currently unknown microRNAs and other small RNAs expressed in biological samples.

“The SOLiD System is ideally suited for gene expression analysis because it provides the industry’s highest level of throughput and delivers the sensitivity required to detect genes expressed at very low levels and to detect changes in low abundance molecules,” said Roland Wicki, director of SOLiD gene expression strategy for Applied Biosystems.

“With the new Small RNA Expression Kit, we have expanded the applications for gene expression analysis on the SOLiD System to include these less understood but highly important small RNA molecules.”