Detection of MYCN amplification and chromosome 1p36 loss in neuroblastoma by cDNA microarray comparative genomic hybridization.
BACKGROUND
In the last decade, microarray technology has been extensively used to evaluate gene expression profiles and genome imbalances. We have developed a microarray-based comparative genomic hybridization (CGH) approach to identify MYCN gene amplification and 1p36 chromosome loss, two markers of tumor aggressiveness in neuroblastoma.


OBJECTIVE
The aim was to use microarray CGH technology to detect the two major prognostic markers for neuroblastoma, MYCN amplification and 1p36 chromosome deletion, in neuroblastoma patients and, therefore, confirm the usefulness of this approach in this cancer.


METHODS
DNA was purified from 16 tumors containing at least 90% malignant neuroblasts and collected at the onset of disease. Pooled fluorescent-labeled reference and neuroblastoma tumor genomic DNA was hybridized to epoxide-coated glass slides on laboratory-made complementary DNA microarray. The microarray contained cDNA mapped at the 1p36.33-36.1 chromosomal region and MYCN gene. cDNA from the 2q33-q34 and 12p13 chromosomes was used as a control and Arabidopsis thaliana DNA was spotted to control unspecific hybridization. Fluorescence in situ hybridization analysis was also performed to validate results from the microarray CGH.


RESULTS
Both MYCN amplification and 1p36 chromosome deletion were detected by microarray CGH. The sensitivity and specificity for 1p36 loss detection were 66.7% and 90.0%, respectively. The method had a sensitivity of 66.7% and specificity of 90.9% to detect MYCN amplification.


CONCLUSIONS
Our results demonstrated that the microarray CGH can be efficiently applied to study DNA gain and loss of specific chromosome regions.
Scaruffi
Paola
P
Laboratory of Neuroblastoma, National Cancer Research Institute (IST), Genoa, Italy.
Parodi
Stefano
S
Mazzocco
Katia
K
Defferrari
Raffaella
R
Fontana
Vincenzo
V
Bonassi
Stefano
S
Tonini
Gian Paolo
GP
D002467:Cell Nucleus / Q000737:chemistry; D002872:Chromosome Deletion; D002878:Chromosomes, Human, Pair 1 / Q000737:chemistry / Q000235:genetics*; D005456:Fluorescent Dyes / Q000737:chemistry; D005784:Gene Amplification; D005819:Genetic Markers; D006801:Humans; D007211:Indoles / Q000737:chemistry; D000071447:N-Myc Proto-Oncogene Protein; D009447:Neuroblastoma / Q000175:diagnosis* / Q000235:genetics; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015513:Oncogene Proteins / Q000737:chemistry / Q000235:genetics*; D011379:Prognosis
D005456:Fluorescent Dyes; D005819:Genetic Markers; D007211:Indoles; C459801:MYCN protein, human; D000071447:N-Myc Proto-Oncogene Protein; D009687:Nuclear Proteins; D015513:Oncogene Proteins; C007293:DAPI