Multiplexed measurements of gene signatures in different analytes using the Nanostring nCounter™ Assay System

BACKGROUND: We assessed NanoString's nCounter™ Analysis System for its ability to quantify gene expression of forty-eight genes in a single reaction with 100 ng of total RNA or an equivalent amount of tissue lysate. In the nCounter™ System, multiplexed gene expression target levels are directly detected, without enzymatic reactions, via two sequence-specific probes. The individual mRNA is captured with one mRNA target sequence-specific capture probe that is used in a post-hybridization affinity purification procedure. The second mRNA target specific-sequence and fluorescent-labeled colored coded probe is then used in the detection with the 3-component complex separated on a surface via an applied electric field followed by imaging. We evaluated reproducibility, accuracy, concordance with quantitative RT-PCR, linearity, dynamic range, and the ability of the system to assay different inputs (matched samples of total RNA from Flash Frozen (FF) and Formalin Fixed Paraffin Embedded Tissues (FFPET), and crude tissue lysates (CTL)). FINDINGS: The nCounter™ Analysis System provided data equivalent to that produced by Taqman(®)-based assays for genes expressed within the ranges of the calibration curves (above ~0.5 mRNA copies per human cell based on an assumption of 10 pg of total RNA per cell). System response was linear over more than two orders of magnitude with typical CVs of ~6% for concentrations above 1 fM (10(5 )molecules per mL). Profiling the industry-standard MAQC data set yielded correlation coefficients of >0.83 for intensity values and >0.99 for measured ratios. Ninety percent of nCounter™ ratio measurements were within 1.27–1.33 fold changes of the Taqman(® )data (0.34–0.41 in log(2 )scale) for FF total RNA samples. CONCLUSION: The nCounter™ Analysis System generated robust data for multi-gene expression signatures across three different sample preparation conditions.