title: Evaluating Robustness and Sensitivity of the NanoString Technologies nCounter Platform to Enable Multiplexed Gene Expression Analysis of Clinical Samples.
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.
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom. Margaret.Veldmanjones@astrazeneca.com.
authors.forename: Margaret H
authors.initials: MH
authors.lastname: Veldman-Jones
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Roz
authors.initials: R
authors.lastname: Brant
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Claire
authors.initials: C
authors.lastname: Rooney
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Catherine
authors.initials: C
authors.lastname: Geh
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Hollie
authors.initials: H
authors.lastname: Emery
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Chris G
authors.initials: CG
authors.lastname: Harbron
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Mark
authors.initials: M
authors.lastname: Wappett
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Alan
authors.initials: A
authors.lastname: Sharpe
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Dymond
authors.affiliation: AstraZeneca, Waltham, Massachusetts.
authors.forename: J Carl
authors.initials: JC
authors.lastname: Barrett
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Harrington
authors.affiliation: AstraZeneca Oncology and Discovery Sciences Innovative Medicines, Alderley Park, Macclesfield, United Kingdom.
authors.forename: Gayle
authors.initials: G
authors.lastname: Marshall
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D006801:Humans; D036103:Nanotechnology / Q000379:methods* / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity