Gene ESR1 EGFR FGFR1 ADAM9 IKBKB PRDM14 MTDH MYC CCND1 EMSY CDH1 TRAF4 CPD MED1 HER2 CDC6 TOP2A MAPT BIRC5 CCNE1 AURKA Chrom 06q25.1 07p11.2 08p11.23 08p11.23 08p11.21 08q13.3 08q22.1 08q24.21 11q13.2 11q13.5 16q22.1 17q11.2 17q11.2 17q21.2 17q12 17q21.2 17q21.2 17q21.31 17q25.3 19q12 20q13.31 6 22 29 39 32 32 49 36 46 10 6 41 9 23 17 41 26 16 27 2 10 0 1 13 11 6 9 12 10 18 2 0 4 0 4 4 4 2 0 2 0 4 3 0 0 1 0 0 0 0 1 3 9 0 0 0 0 0 0 0 0 1 12 Transcription factor; under debate [40–42] Signal transduction; poor survival [4] Signal transduction; poor survival, tamoxifen resistance [5] Protein metabolism; promotes invasion [38] Signal transduction [43] Transcription regulatory protein; chemoresistance [44] Signal transduction; promoting metastases, chemoresistance, poor survival [36] Transcription factor; poor survival [3] Signal transduction; ER positivity, poor survival [35] Transcription regulatory protein; poor survival [45] Cell adhesion [46] Signal transduction [47] Protein metabolism [48] Transcriptional coactivator; ER positivity [49] Signal transduction; bad survival; trastuzumab response [2] Signal transduction [50] Regulation of the topological status of DNA; poor survival, susceptible for certain chemotherapy [6] Microtubule stabilization; chemoresistance (taxanes) [51] Signal transduction; predict distant recurrence [52] Signal transduction; poor survival [53] Signal transduction [54] Breast Cancer Res Treat (2012) 135:49–58 Table 1 Contents of the ‘‘breast cancer’’ MLPA kit P078-B1 (MRC Holland) 51 Gain (%) Amp (%) Loss (%) Function and clinical relevance For each gene, chromosome location (Chrom), gene copy number gain (Gain;[1.3), ampliﬁcation (Amp;[2.0), gene loss (Loss;\0.7), function and clinical relevance (in female breast cancer) are shown (Applied Biosystems). Mean probe peaks were used for ﬁnal gene copy number analysis with Genescan v4.1 (Applied Biosystems) and Coffalyser v9.4 (MRC-Holland) software. Cut-off values were set as before with 1.3–2.0 for gene copy number gain, [2.0 for ampliﬁcation and \0.7 for lost genes. Values between 0.7 and 1.3 were regarded normal [18, 22]. Control female breast cancers A group of female breast cancer described previously was used to study differences in gene copy number change between male and female breast cancer [18]. This group consists of 104 cases with a mean age of 58 years (range 30–86 years). Tumor size ranged from 0.2 to 6.5 cm (average 2.1 cm) and 46 % of the cases had lymph node metastases. Most cases were diagnosed (according to the WHO) as invasive ductal carcinoma (78 %) or invasive lobular carcinoma (11 %). Mean mitotic activity was 21 per 2 mm2 and according to the modiﬁed Bloom and Richardson score most tumors were grade 2 (34 %) or grade 3 (45 %). ER positivity was common (69 %, 70/101) and 48 % of the tumors were PR positive (48/101). HER2 ampliﬁcation deﬁned by immunohistochemistry and CISH was seen in 19 % of cases (19/102). The same ‘‘breast cancer kit’’ (P078-A1 kit; MRC Holland) was used, but because the gene content of the kit had been updated by the manufacturer in the meanwhile, only 17 genes could be compared between the groups. In addition, for two genes (EGFR and HER2) one of the probes was modiﬁed and for ﬁve genes one probe was deleted. Some reference probes were modiﬁed as well (Supplementary Table 1). Statistics Statistical calculations were performed using SPSS for Windows v15.0. Correction for multiple comparisons was applied by resetting the 0.05 threshold according to the Holm–Bonferroni method. Differences between gene copy number and clinicopathological characteristics were cal- culated with ANOVA for continuous variables and with Pearson Chi-square (or Fisher’s exact test when appropri- ate) for categorical variables. The following clinicopatho- logical features were dichotomized: age ([50 years), tumor size ([2.0 cm), mitotic activity ([8 mitoses/2 mm2), and histological grade (grade 1/2 vs 3). Correlation between 123