Dataset Information

Easy NanoString nCounter data analysis with the NanoTube.

ABSTRACT:

Summary

The NanoTube is an open-source pipeline that simplifies the processing, quality control, normalization and analysis of NanoString nCounter gene expression data. It is implemented in an extensible R library, which performs a variety of gene expression analysis techniques and contains additional functions for integration with other R libraries performing advanced NanoString analysis techniques. Additionally, the NanoTube web application is available as a simple tool for researchers without programming expertise.

Availability and implementation

The NanoTube R package is available on Bioconductor under the GPL-3 license (https://www.bioconductor.org/packages/NanoTube/). The R-Shiny application can be downloaded at https://github.com/calebclass/Shiny-NanoTube, or a simplified version of this application can be run on all major browsers, at https://research.butler.edu/nanotube/.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Class CA

PROVIDER: S-EPMC9805552 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Publications

Easy NanoString nCounter data analysis with the NanoTube.

Class Caleb A CA Lukan Caiden J CJ Bristow Christopher A CA Do Kim-Anh KA

Bioinformatics (Oxford, England) 20230101 1

<h4>Summary</h4>The NanoTube is an open-source pipeline that simplifies the processing, quality control, normalization and analysis of NanoString nCounter gene expression data. It is implemented in an extensible R library, which performs a variety of gene expression analysis techniques and contains additional functions for integration with other R libraries performing advanced NanoString analysis techniques. Additionally, the NanoTube web application is available as a simple tool for researchers ...[more]

PMID: 36440915

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Project description:BackgroundWith the development of new drug combinations and targeted treatments for multiple types of cancer, the ability to stratify categories of patient populations and to develop companion diagnostics has become increasingly important. A panel of 325 RNA biomarkers was selected based on cancer-related biological processes of healthy cells and gene expression changes over time during nonmalignant epithelial cell organization. This "cancer in reverse" approach resulted in a panel of biomarkers relevant for at least 7 cancer types, providing gene expression profiles representing key cellular signaling pathways beyond mutations in "driver genes." Objective. To further investigate this biomarker panel, the objective of the current study is to (1) validate the assay reproducibility for the 325 RNA biomarkers and (2) compare gene expression profiles side by side using two technology platforms.Methods and resultsWe have mapped the 325 RNA transcripts and in a custom NanoString nCounter expression panel to be compared to all potential probe sets in the Affymetrix Human Genome U133 Plus 2.0. The experiments were conducted with 10 unique biological formalin-fixed paraffin-embedded (FFPE) breast tumor samples. Each site extracted RNA from four sections of 10-micron thick FFPE tissue over three different days by two different operators using an optimized standard operating procedure and quality control criteria. Samples were analyzed using mas5 in BioConductor and NanoStringNorm in R. Pearson correlation showed reproducibility between sites for all 60 samples with r = 0.995 for Affymetrix and r = 0.999 for NanoString. Correlation in multiple days and multiple users was for Affymetrix r = (0.962 - 0.999) and for NanoString r = (0.982 - 0.991).ConclusionThe 325 RNA biomarkers showed reproducibility in two technology platforms with moderate to high concordance. Future directions include performing clinical validation studies and generating rationale for patient selection in clinical trials using the technically validated assay.

Dataset Information

Easy NanoString nCounter data analysis with the NanoTube.

Summary

Availability and implementation

Supplementary information

Publications

Easy NanoString nCounter data analysis with the NanoTube.

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