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Research Article

Oligonucleotide Array Comparative Genomic Hybridization Profiling of Neuroblastoma Tumours

PAOLA SCARUFFI, STEFANO MORETTI, SIMONA COCO, KATIA MAZZOCCO, RAFFAELLA DEFFERRARI, DOMENICO ALBINO, STEFANO BONASSI and GIAN PAOLO TONINI
Cancer Genomics & Proteomics May 2006, 3 (3-4) 245-252;
PAOLA SCARUFFI
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  • For correspondence: paola.scaruffi@istge.it
STEFANO MORETTI
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SIMONA COCO
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KATIA MAZZOCCO
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RAFFAELLA DEFFERRARI
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DOMENICO ALBINO
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STEFANO BONASSI
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GIAN PAOLO TONINI
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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.

  • Neuroblastoma
  • microarray
  • CGH
  • MYCN
  • chromosome 1p

Footnotes

    • Received April 7, 2006.
    • Accepted April 14, 2006.
  • Copyright© 2006 International Institute of Anticaner Research (Dr. John G. Delinassios), All rights reserved
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Cancer Genomics - Proteomics: 3 (3-4)
Cancer Genomics & Proteomics
Vol. 3, Issue 3-4
May-August 2006
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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
Cancer Genomics & Proteomics May 2006, 3 (3-4) 245-252;

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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
Cancer Genomics & Proteomics May 2006, 3 (3-4) 245-252;
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