Oligonucleotide array comparative genomic hybridization profiling of neuroblastoma tumours

Paola Scaruffi, Stefano Moretti, Simona Coco, Katia Mazzocco, Raffaella Defferrari, Domenico Albino, Stefano Bonassi, Gian Paolo Tonini

Research output: Contribution to journalArticle

Abstract

Neuroblastoma (NB) is one of the most common paediatric solid tumours and displays a broad variety of genomic alterations. Recently, array comparative genomic hybridization (aCGH) has emerged as a novel technology enabling high-resolution detection of DNA copy number aberrations. We have previously optimized a custom cDNA-array to detect MYCN gain and chromosome 1p36 loss, two molecular markers of tumour aggressiveness in NB. In spite of the power of this technique, the production of cDNA arrays is time-consuming and expensive. In the present study, we report a printed 55-mer oligonucleotide aCGH with the aim of increasing the resolution and the sensitivity of our platform. The oligonucleotide probes, designed and validated for expression profiling, reproducibly assessed amplifications, even when using whole genomes as targets. On the contrary, this microarray platform seems to offer little accuracy in measuring genomic single-copy deletions. Therefore, an oligo library specifically designed for aCGH should improve the performance of oligonucleotide aCGH in accurately mapping unbalanced chromosomal abnormalities.

Original languageEnglish
Pages (from-to)245-252
Number of pages8
JournalCancer Genomics and Proteomics
Volume3
Issue number3-4
Publication statusPublished - May 2006

Keywords

  • CGH
  • Chromosome 1p
  • Microarray
  • MYCN
  • Neuroblastoma

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Cancer Research
  • Biochemistry

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  • Cite this

    Scaruffi, P., Moretti, S., Coco, S., Mazzocco, K., Defferrari, R., Albino, D., Bonassi, S., & Tonini, G. P. (2006). Oligonucleotide array comparative genomic hybridization profiling of neuroblastoma tumours. Cancer Genomics and Proteomics, 3(3-4), 245-252.