BACKGROUDN: Genomic imbalances especially structural chromosomal aberrations are associated with a poor prognosis and a malignancy in neuroblastoma (NB). Microarray Comparative Genomic Hybridization (aCGH) permits the detection of genome-wide copy number alterations with high resolution. However, the use of this technique with DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) tissue specimens usually has quantitative and qualitative limitations.
AIM: The aCGH application for testing DNA samples extracted from FFPE NB tissues by standard protocols not intended especially for FFPE samples.
MATERIALS AND METHODS: DNA was obtained from 2 FFPE NB tissue samples of 2 patients, using representative 6-μm sections of the tumor samples. Specimens were treated with xylene, and then washed with ethanol. DNA was extracted automatically using the QuickGene DNA tissue kit (Kurabo, Osaka, Japan) according to the manufacturer’s protocol. The aCGH profiles were defined by SurePrint G3 CGH ISCA v2 Microarray Kit 8x60K (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. Chromosomal aberrations in selected patients have been previously verified by FISH and MLPA analysis on fresh tissues.
RESULTS: According to aCGH results for first patient, it has been revealed 100% compatibility with FISH and MLPA. It has been detected MYCN amplification, 1p36 deletion and 17q gain for this patient. Although for second patient, a discrepancy between raw aCGH and confirmatory tests has been indicated. However, a holistic view for data from all used techniques was consistent. It has been shown 2p gain, 1p36 deletion, 11q23 deletion, 17q gain and few additionally imbalances.
CONCLUSIONS: Our pilot study has shown that a material recovered from FFPE tissue specimens may be effectively examined by aCGH. It should be emphasized that an extremely important analysis of genomic imbalances in NB patients could be carried out also by aCGH method.