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Figure 3 | Breast Cancer Research

Figure 3

From: Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

Figure 3

Fraction of LOH and CNN-AI in HER2-amplified and HER2-negative breast cancer. (A) Fraction of the genome affected by LOH for HER2-amplified cases stratified by PAM50 subtype and ER-status compared to HER2-negative cases stratified by PAM50 subtypes. Top-axis indicates number of samples in each group. A significant difference in LOH-FGA is observed between HER2-amplified and HER2-negative cases stratified by PAM50 subtype (P = 7 × 10-30, ANOVA). A similar difference was observed when comparing LOH-FGA estimates for all HER2-amplified tumors against HER2-negative cases stratified by PAM50 subtype (P = 3 × 10-33, ANOVA). (B) Fraction of the genome affected by CNN-AI for HER2-amplified cases stratified by PAM50 subtype and ER-status compared to HER2-negative cases stratified by PAM50 subtypes. Top-axis indicates number of samples in each group. A significant difference in CNN-FGA is observed between HER2-amplified and HER2-negative cases stratified by PAM50 subtype (P = 4 × 10-10, ANOVA). A similar difference was observed when comparing CNN-FGA estimates for all HER2-amplified tumors against HER2-negative cases stratified by PAM50 subtype (P = 2 × 10-10, ANOVA).

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