Supplemental Figure 5 from Evaluating Robustness and Sensitivity of the NanoString Technologies nCounter Platform to Enable Multiplexed Gene Expression Analysis of Clinical Samples

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posted on 2023-03-30, 23:08 authored by Margaret H. Veldman-Jones, Roz Brant, Claire Rooney, Catherine Geh, Hollie Emery, Chris G. Harbron, Mark Wappett, Alan Sharpe, Michael Dymond, J. Carl Barrett, Elizabeth A. Harrington, Gayle Marshall

Supplemental Figure 5A: Correlation scatter plot of normalised log2 values illustrating stability of a CodeSet after expiry date. A CodeSet consisting of 30 genes including 4 housekeeping genes was tested with a set of 6 identical samples (5 Fresh DLBCL tissues and 1 DLBCL cell line HBL-1) over an extended time-period of 2.5 years; the second test was performed 1.5 years after the CodeSet expiry date. Supplemental Figure 5B: Correlation scatter plot of mean normalised log2 counts of triplicate UHR samples tested with a CodeSet consisting of 463 genes including 18 housekeeping genes subjected to 4 freeze/thaw cycles.

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ARTICLE ABSTRACT

Analysis of clinical trial specimens such as formalin-fixed paraffin-embedded (FFPE) tissue for molecular mechanisms of disease progression or drug response is often challenging and limited to a few markers at a time. This has led to the increasing importance of highly multiplexed assays that enable profiling of many biomarkers within a single assay. Methods for gene expression analysis have undergone major advances in biomedical research, but obtaining a robust dataset from low-quality RNA samples, such as those isolated from FFPE tissue, remains a challenge. Here, we provide a detailed evaluation of the NanoString Technologies nCounter platform, which provides a direct digital readout of up to 800 mRNA targets simultaneously. We tested this system by examining a broad set of human clinical tissues for a range of technical variables, including sensitivity and limit of detection to varying RNA quantity and quality, reagent performance over time, variability between instruments, the impact of the number of fields of view sampled, and differences between probe sequence locations and overlapping genes across CodeSets. This study demonstrates that Nanostring offers several key advantages, including sensitivity, reproducibility, technical robustness, and utility for clinical application. Cancer Res; 75(13); 2587–93. ©2015 AACR.

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Keywords

Cancer Interception Clinical-Stage Research Computational Methods Gene expression profiling

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