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Apr 15, 2010 (Vol. 30, No. 8)

Single-Molecule Gene-Expression Analysis

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    According to NanoString Technologies, its nCounter Analysis System requires no enzymatic manipulation or amplification of the sample and can measure up to 550 gene targets in one reaction from various sample types including unprocessed cell and tissue lysates, purified total RNA, blood samples, and RNA extracted from FFPE samples.

    Several recent publications have demonstrated the capabilities of NanoString Technologies’ nCounter™ Analysis System, including one study in which researchers used the technology to construct a transcriptional network in mouse primary dendritic cells that regulates their response to pathogens. Another report describes a method for high-throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples, in which the system was used for biomarker measurement in low-abundance patient samples.

    A presentation at “AGBT” entitled, “The nCounter™ System: Digital Gene-Expression Analysis Downstream of Next-Generation Sequencing Results,” described the company’s gene-expression assay system that incorporates individual molecule detection technology. Using color-coded molecular barcodes, the system performs direct multiplexed measurements of gene expression at a sensitivity of <1 copy/cell. A fluorescent barcode is attached to a reporter probe specific for the gene of interest. For each unique gene transcript, NanoString prepares two probes: the reporter probe and a capture probe, which aligns and immobilizes the target/reporter probe complex in the nCounter cartridge. A digital analyzer detects the barcodes present on the surface of the cartridge and individually counts the unique transcripts present in a sample.

    The technology requires no enzymatic manipulation or amplification of the sample and can measure up to 550 gene targets in one reaction from various sample types including unprocessed cell and tissue lysates, purified total RNA, blood samples, and RNA extracted from formalin-fixed paraffin-embedded samples. Customers select the genes of interest, and the company provides the appropriate barcoded probe pairs.

    “We see the power of our system in performing follow-up studies to whole genome analysis,” said Philippa Webster, Ph.D., senior principal scientist at NanoString, emphasizing the technology’s ability to analyze “hundreds of genes quickly and inexpensively, relative to next-generation sequencing” in many samples at once on an automated platform. In development are additional probes to expand the available gene set and a microRNA analysis system that will include a panel of probes from 700 to 800 miRNAs.



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