Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

• Published in: Neoplasia (New York, N.Y.) Vol. 5; no. 1; pp. 53 - 62
• Main Authors: Beheshti, Ben, Braude, Ilan, Marrano, Paula, Thorner, Paul, Zielenska, Maria, Squire, Jeremy A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.01.2003; Elsevier
• Subjects: Algorithms; amplicons; Child, Preschool; Chromosome Aberrations; Chromosomes, Human - genetics; Computational Biology; copy number; DNA microarrays; DNA, Complementary - genetics; DNA, Neoplasm - genetics; Female; Gene Amplification; Gene Dosage; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Genes, myc - genetics; genomic instability; genomic profiling; genomics; high-resolution mapping; HPCAL1 gene; Humans; In Situ Hybridization, Fluorescence; Infant; KIAA0188 gene; LOC151354 gene; LPIN gene; LPIN1 gene; Male; MYCN gene; N-myc; NAG gene; Neuroblastoma - genetics; Neuroblastoma - metabolism; NSE1 gene; NSE1 protein; Nucleic Acid Amplification Techniques; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; genomic profiling; genomics; N-myc; amplicons; genomic instability; high-resolution mapping
• ISSN: 1476-5586; 1522-8002; 1476-5586; 1522-8002
• DOI: 10.1016/S1476-5586(03)80017-9

Conventional comparative genomic hybridization (CGH) profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available) algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb) than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1) no amplifications evident, 2) a small MYCN amplicon as the only detectable imbalance, and 3) a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.