Figure 2

Frequency of LOH and CNN-AI in HER2-amplified breast cancer. (A) Frequency of LOH across the genome for 99 HER2-amplified cases analyzed by SNP arrays. (B) Frequency of CNN-AI across the genome for the 99 cases. (C) Frequency of combined CN loss and CNN-AI across the genome for the 99 cases, where CN loss calls were obtained from GAP analysis. (D) Fraction of the genome affected by LOH for HER2-amplified cases stratified by different clinicopathological variables. Top-axis indicates number of samples in each group. (E) Fraction of the genome affected by CNN-AI for HER2-amplified cases stratified by different clinicopathological variables. Top-axis indicates number of samples in each group. (F) Variation of FGA values versus GAP-ploidy (n = 99) for CN (black), CNN-AI (red) and LOH (blue). GAP-ploidy estimates were binned in bins of size 0.1 represented by tick marks on the x-axis, and labels for every second bin. For each bin the mean FGA value of included samples are plotted (points) for CN, LOH and CNN-AI. Bins contain different number of samples. P-values were calculated using Wilcoxon's test for indicated groups.