Breast Cancer Res Treat (2012) 135:49–58 Table 2 Correlation between gene copy number gain ([1.3) and clinicopathological features Tumor size and PR were not correlated with any of the studied genes (not shown). p values were calculated with Pearson Chi-square or Fisher’s exact test when appropriate (number of events \5) for categorical variables and ANOVA for continuous variables. Signiﬁcant p values after correction for multiple comparison (Holm–Bonferroni method) are depicted in bold. See Supplementary Table 2 for full data LN meta lymph node metastases Gene ESR1 EGFR FGFR1 ADAM9 IKBKB PRDM14 MTDH MYC CCND1 EMSY CDH1 TRAF4 CPD MED1 HER2 CDC6 TOP2A MAPT BIRC5 CCNE1 AURKA Age (mean) young Mitoses high ([8) Mitoses (mean) high Grade high (3) LN meta negative 0.019 0.043 0.017 0.049 0.019 0.001 0.025 0.045 0.018 0.004 0.005 0.010 <0.001 0.003 0.027 0.025 0.024 0.003 0.003 0.023 0.016 <0.001 0.014 0.013 <0.001 0.010 53 ER negative 0.038 0.033 logistic regression, and these genes were more often gained in male breast cancer. EMSY (p = 0.004) and CPD (p = 0.001) copy number gain were also independent predictors of gender and these genes were more frequently gained in female breast cancer. Two genes, TRAF4 (p = 0.024) and EMSY (p = 0.041) were more often ampliﬁed in female breast cancer. None of the studied genes was signiﬁcantly more frequently ampliﬁed in men. Cluster analysis Unsupervised hierarchical clustering revealed a separate gene cluster, consisting of FGFR1, ADAM9, HER2, MED1, EMSY, and CCND1 (Fig. 3). One small sub-cluster was formed by FGFR1 and ADAM9 which showed simulta- neously copy number gain in 29 % of all cases (31/106). Gains in both genes was correlated with younger age (62 vs 68 years; p = 0.019). No associations with other clinico- pathological features were found. Reasoning from the cases, two major clusters were found (Fig. 3). These clusters were stable according to the approximately unbiased p values calculated with pvclust (p \ 0.001). Cluster A consisted of 55 cases and was characterized by a low rate of gene copy number gain and gene ampliﬁcation. Cluster B consisted of 51 cases and was characterized by CCND1 (73 %), MTDH (69 %), CDC6 (63 %), ADAM9 (57 %), TRAF4 (57 %) and MYC (53 %) copy number gain. The male breast cancers in cluster B showed signiﬁcantly more mitosis compared to the tumors in cluster A (8 vs 14 mitosis; p \ 0.001). Cluster B tumors were also more often grade 3 (p = 0.020) and were larger (2.4 vs 2.0 cm; p = 0.036) compared to cluster A tumors. Survival analysis Grade 3 (p = 0.027), high mitotic count ([8; p = 0.015) and large tumor size ([2.0 cm; p = 0.036) were correlated with a decreased 5 years survival. Chemotherapy was given in 14 % of the cases and 40 % received hormone therapy. Both treatment regimes did not correlate with patients’ survival (p = 0.700 and p = 0.140, respectively). Univariate survival analysis is presented in Fig. 4. Tumors with one or more gains had a poorer outcome compared with tumors without gains (p = 0.039). MED1 and HER2 copy number gain also seem to correlate with poor survival (p = 0.040 and p = 0.017, respectively). In case ampliﬁ- cation was analyzed the genes CCND1 (p = 0.022) and EMSY (p = 0.040) were correlated with decreased sur- vival. However, for EMSY only two cases were ampliﬁed. In case correction for multiple comparisons was performed, no single prognostic factor remained signiﬁcant. On the other hand, tumors with a copy number gain of all genes on chromosome 17 had a poorer survival (p = 0.007). Cluster 123