Figure 1

aCGH profiles of mouse mammary tumors. aCGH profiles typical of (a) Brca1 ^Δ/Δ ;p53 ^Δ/Δ, Brca2 ^Δ/Δ ;p53 ^Δ/Δand p53 ^Δ/Δmammary tumors. Each dot represents the averaged log2 ratio (y-axis) of a BAC clone plotted at its genomic position (x-axis). Red dots (gains) and green dots (losses) represent datapoints with log2 ratios significantly different from 0 as determined by the Rosetta error model [21]; black dots represent datapoints with log2 ratios not significantly different from 0. Blue vertical lines represent chromosome boundaries. (b) aCGH profiles from 35 Brca1 ^Δ/Δ ;p53 ^Δ/Δtumors (blue), 62 Brca2 ^Δ/Δ ;p53 ^Δ/Δtumors (orange) and 33 p53 ^Δ/Δtumors (gray) were analyzed with KC-SMART using a kernel width of 20 Mb, for gains and losses separately. Significant CNAs are depicted in the color matched bars on top (gains) and below (losses) the Kernel Smoothed Estimate curves (KSEs) for each tumor group. (c) The mean percentage of BAC clones ± S.E.M. with absolute log2 ratio > 0.3 is greater across the Brca1 ^Δ/Δ ;p53 ^Δ/Δtumors (blue) and Brca2 ^Δ/Δ ;p53 ^Δ/Δtumors (orange) tumors compared with the p53 ^Δ/Δtumors. P-values are determined by a two-tailed t-test with unequal variance. (d) Each individual tumor aCGH profile was smoothed using KC-SMART (kernel width: 20 Mb). For a range of thresholds, all gains exceeding a positive threshold and losses exceeding the same negative threshold were counted and averaged over each tumor group. Curves are darkened at thresholds for which the average number of CNAs per tumor group is significantly greater in the Brca1/2 ^Δ/Δ ;p53 ^Δ/Δtumors compared with the p53 ^Δ/Δtumors, P < 0.05 determined by a two-tailed t-test with unequal variance.