Single-Nucleotide Polymorphism and Mutation Identification by the Nanogen Microelectronic Chip Technology

  • Maurizio Ferrari
  • Laura Cremonesi
  • Pierangelo Bonini
  • Barbara Foglieni
  • Stefania Stenirri
Part of the Methods in Molecular Medicine™ book series (MIMM, volume 114)


The present chapter describes a microarray technology developed by Nanogen Inc., for the identification of DNA variations based on the use of microelectronics.

The NMW 1000 NanoChip™ Molecular Biology Workstation allows the active deposition and concentration of charged biotinylated molecules on designated test sites. The DNA at each pad is then hybridized with specific oligonucleotide probes, complementary to normal or mutant sequences, that labeled with Cy3 or Cy5 dyes, respectively. The array is imaged, and fluorescence signals are scanned, monitored, and quantified by highly developed, digital image-processing procedures. The experimental steps to be performed for the development and execution of a microchip assay are described. Attention is focused on the fundamental aspects of probe design, and guidelines and useful suggestions are given. Protocols for sample preparation, addressing, reporting, and data analysis are also detailed.

Key Words

Microarray microelectronic Nanogen SNPs mutation 



This work was supported by Amplimedical S.p.A. Diagnostic Group, Italy and FIRB grant RBNE01SLRJ (to M. Ferrari).


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Copyright information

© Humana Press Inc. 2005

Authors and Affiliations

  • Maurizio Ferrari
    • 1
    • 2
  • Laura Cremonesi
    • 1
  • Pierangelo Bonini
    • 3
  • Barbara Foglieni
    • 1
  • Stefania Stenirri
    • 1
  1. 1.Unit of Genomics for Diagnosis of Human PathologiesIstituto di Ricovero e Cura a Carattere Scientifico Ospedale San RaffaeleMilanItaly
  2. 2.Diagnostica e Ricerca San Raffaele S.p.AMilanItaly
  3. 3.Diagnostica e Ricerca San Raffaele S.p.A.Università Vita-Salute S. RaffaeleMilanItaly

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