Sequence based high resolution chromosomal CGH

• Published in: Cytogenetic and genome research Vol. 121; no. 1; p. 1
• Main Authors: Kowalska, A, Brunner, B, Bozsaky, E, Chen, Q-R, Stock, C, Lörch, T, Khan, J, Ambros, P F
• Format: Journal Article
• Language: English
• Published: Switzerland 01-01-2008
• Subjects: Base Sequence; Cell Line, Tumor; Chromomycin A3; Chromosome Mapping - methods; Cytogenetics - methods; DNA - genetics; DNA, Neoplasm - genetics; Fluorescent Dyes; Genome, Human; Humans; In Situ Hybridization, Fluorescence - methods; N-Myc Proto-Oncogene Protein; Nuclear Proteins - genetics; Nucleic Acid Hybridization - methods; Oligonucleotide Array Sequence Analysis - methods; Oncogene Proteins - genetics; Protein-Tyrosine Kinases - genetics; Receptor Protein-Tyrosine Kinases
• ISSN: 1424-859X
• DOI: 10.1159/000124373

We aimed to directly align a chromosomal CGH (cCGH) pattern with the gene mapping data by taking advantage of the clustering of the GGCC motif at certain positions in the human genome. The alignment of chromosomal with sequence data was achieved by superimposition of (i) the fluorescence intensity of the sequence specific fluorochrome, Chromomycin A3 (CMA3), (ii) the cCGH fluorescence intensity profile of individual chromosomes and (iii) the GGCC density profile extracted from the Ensembl genome sequence database. The superimposition of these three pieces of information allowed us to precisely localize regions of amplification in the neuroblastoma cell line STA-NB-15. Two prominent cCGH peaks were noted, one at 2p24.3, the position 15.4 mega base (Mb), and the other at 2p23.2, 29.51 Mb. FISH and high resolution array CGH (aCGH) experiments disclosed an amplification of MYCN (16 Mb) and ALK (29.2-29.9 Mb), thus confirming the cCGH data. The combined visualization of sequence information and cCGH data drastically improves the resolution of the method to less than 2 Mb.