DNA-Based Sequencing Assays

  • Pasquale Pisapia
  • Miriam Cieri
  • Francesco Pepe
  • Umberto Malapelle
  • Giancarlo TronconeEmail author


Modern cytopathologists need to incorporate molecular testing into their clinical practice and be able to translate molecular assays into patient care. The detection of genomic alterations may not only refine uncertain morphological diagnoses but may also provide crucial theranostic information. Gene sequencing remains a core technology for molecular cytopathology. Sanger sequencing has paved the way for the development and the clinical implementation of next-generation sequencing (NGS) assays. In this chapter, the NGS workflow is described, focusing mainly on the technical aspects of NGS analysis, the diverse platforms available, the principles underlying the selection of targeted gene panels, and the issues related to validation of the “wet” procedure and the bioinformatics pipeline.


NGS Molecular cytopathology Personalized medicine Gene panel Validation Cytologic samples Oncogene Sequencing by synthesis Molecular analysis 



v-raf murine sarcoma viral oncogene homolog B


Deoxyribonucleic acid


Epidermal growth factor receptor


In vitro diagnostic


KIT proto-oncogene receptor tyrosine kinase


Kirsten rat sarcoma viral oncogene homolog


Laboratory developed tests


Limit of detection


Next-generation sequencing


Neuroblastoma RAS viral oncogene


Platelet-derived growth factor receptor A


Positive percentage agreement


Positive predictive value


Real-time polymerase chain reaction


Turnaround time


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pasquale Pisapia
    • 1
  • Miriam Cieri
    • 1
  • Francesco Pepe
    • 1
  • Umberto Malapelle
    • 1
  • Giancarlo Troncone
    • 1
    Email author
  1. 1.Department of Public HealthUniversity of Naples “Federico II”NaplesItaly

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