Development of Gene Expression-Based Biomarkers on the nCounter® Platform for Immuno-Oncology Applications

  • Sarah WarrenEmail author
  • Patrick Danaher
  • Afshin Mashadi-Hossein
  • Lynell Skewis
  • Brett Wallden
  • Sean Ferree
  • Alessandra Cesano
Part of the Methods in Molecular Biology book series (MIMB, volume 2055)


Biomarkers based on transcriptional profiling can be useful in the measurement of complex and/or dynamic physiological states where other profiling strategies such as genomic or proteomic characterization are not able to adequately measure the biology. One particular advantage of transcriptional biomarkers is the ease with which they can be measured in the clinical setting using robust platforms such as the NanoString nCounter system. The nCounter platform enables digital quantitation of multiplexed RNA from small amounts of blood, formalin-fixed, paraffin-embedded tumors, or other such biological samples that are readily available from patients, and the chapter uses it as the primary example for diagnostic assay development. However, development of diagnostic assays based on RNA biomarkers on any platform requires careful consideration of all aspects of the final clinical assay a priori, as well as design and execution of the development program in a way that will maximize likelihood of future success. This chapter introduces transcriptional biomarkers and provides an overview of the design and development process that will lead to a locked diagnostic assay that is ready for validation of clinical utility.

Key words

Biomarker development Clinical diagnostics RNA transcription Gene expression NanoString nCounter 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Sarah Warren
    • 1
    Email author
  • Patrick Danaher
    • 1
  • Afshin Mashadi-Hossein
    • 1
  • Lynell Skewis
    • 1
  • Brett Wallden
    • 1
  • Sean Ferree
    • 1
  • Alessandra Cesano
    • 1
    • 2
  1. 1.NanoString Technologies, Inc.SeattleUSA
  2. 2.ESSA PharmaSouth San FranciscoUSA

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