Figure 1

Copy number alterations (CNAs) found in a genome of MCF-7 cells with ultra-dense array CGH platforms. Genomic DNA from MCF-7 cells was hybridized to slides containing either 244 K oligonucleotide probes (green) or 1 M oligonucleotide probes (red). (A) The whole genome view of overlaid moving averages (2 Mb window) for log₂ ratios of fluorescence between labeled MCF-7 DNA and the differentially labeled normal human reference. (B) Zoom-in on chromosome 3 showing overlaid moving averages and aberrations found with the ADM-2 algorithm. Aberrations smaller than 1 Mb in genomic length are indicated; those found with both 244 K and 1 M platforms (*) and those found with the 1 M platform only (#). (C) Zoom-in on the smallest aberration, 8 Kb amplification, found only with the 1 M platform. Overlaid data points for log₂ ratios obtained with 1 M platform and 244 K platform are shown (green: values below log₂ = -0.5; red: values above log₂ = 0.5; black: values above log₂ = -0.5 and below log₂ = 0.5). Aberrations called by the ADM-2 algorithm are identified by a shaded area, and the presence of CNVs is indicated with red boxes (bottom).