Highly robust digital gene expression profiling of 96 gene targets for IO Lymphocyte and Myeloid activity in 96 Colorectal FFPE samples without any enzyme (RT or amplification) reactions

Abstract

Abstract The NanoString nCounter Analysis platform uses a novel molecular barcoding technology to measure multiplexed gene expression of up to 800 targets. The assay counts fluorescent barcodes hybridized to targets to provide precise digital data. The standard nCounter gene expression assay can be used to process 12 samples per run. We recognize an additional need for a higher sample-throughput assay which would enable researchers to quickly evaluate tens of multiplexed targets in hundreds of samples. Here we present data from a new nCounter assay, nCounter PlexSet Reagents for gene expression, which is performed in a 96-sample format and is capable of digitally profiling up to 96 gene targets per sample. We used two preselected pathway panels for IO Lymphocyte Activity (96 gene targets) and IO Myeloid Activity (79 gene targets), chosen from our 400+ preselected pathway panels list, in order to evaluate the presence of immune signatures in 44 colorectal cancer (CRC) samples. Each CRC sample was ran in duplicates across the two panels in addition to a Reference Sample to calibrate for variability between PlexSet reagents. The results show that the PlexSet reagents for gene expression provides highly reproducible data with an average R2 > 95% between duplicate samples.