NanoString for Highly Multiplexed Target Gene Analysis

The NanoString nCounter Sprint Profiler — a new addition to NUSeq (as of September 2020) — is a platform for multiplex analysis of up to 800 RNA or DNA targets. For common pathways or bio-functions, NanoString provides a number of ready-to-use, predesigned gene panels, including those for oncology, immunology, and neurobiology. In addition to the catalogued gene panels, NUSeq Core users have the option of designing custom panels based on specific needs. This system is ideal for studies that interrogate genes in a particular pathway or bio-function, or to validate expression pattern of a group of genes after global gene expression profiling with RNA-seq. The system also enables detection of gene fusions using junction probes, analysis of miRNAs, and simultaneous measurement of DNA/RNA/proteins.

The NanoString System achieves digital read-out of up to 800 targets based on the use of target-specific hybridization probe pairs (see the figure below). Each probe pair contains a reporter probe that carries a unique fluorescence barcode, and a capture probe that is biotinylated for immobilization (or capture) of the target-probe complex to a streptavidin-coated slide for scanning and signal collection. Both probes contain sequences that are specific to its designated target. There is no enzymatic step in this process, reducing the chance of introducing bias. Through the unique fluorescence barcoding scheme and single molecule imaging, gene targets are quantified in a single reaction at high sensitivity. Its super sensitivity means limited sample input, such as patient biopsy, is feasible, and single cell profiling at the pathway level is achievable with minimal amplification.