<p> 1</p><p>LEGENDS TO SUPPLEMENTARY TABLES</p><p>Supplementary Table 1: Results of microarray-based comparative genomic hybridisation analysis of chromosome 17 of BT474, MDA-MB-361, MDA-MB-453, SKBR3, ZR-75.30 and </p><p>UACC812 breast cancer cell lines. Clone – BAC clone identity; start: mapping position in kb; end: mapping position in kb; AWS smoothed ratios: adaptive weight smoothing processed ratios; categorical data: aws ratios converted into gains and losses (see Material and Methods).</p><p>Supplementary Table 2: Analysis of the expression data from Neve et al. (18) Expression of all genes mapping to the smallest region of overlap as defined in the present study was retrieved. </p><p>Cell phenotypes were retrieved from Neve et al. (18) Analysis of the correlation between HER2 amplification and expression of genes within the SRA of HER2 amplicon was performed with </p><p>Mann-Whitney U test. Analysis of the correlation between HER2/TOP2A co-amplification and expression of genes within the SRA defined in cases harbouring HER2/TOP2A amplification was performed with Mann-Whitney U test. Two-tailed Student’s t test was employed to compare the expression of genes pertaining to the SRA of HER2/TOP2A co-amplified cases in cell lines with </p><p>HER2 amplification versus those with HER2/TOP2A co-amplification due to the limited number of cell lines (n=2 for HER2/TOP2A co-amplified and n=4 for HER2 amplified).</p><p>Supplementary Table 3: Results of microarray-based comparative genomic hybridisation analysis of chromosome 17 of 15 HER2 amplified breast cancers. Clone – BAC clone identity; start: mapping position in kb; end: mapping position in kb; AWS smoothed ratios: adaptive weight smoothing processed ratios; categorical data: aws ratios converted into gains and losses </p><p>(see Material and Methods). 2</p><p>Supplementary Figure 1: Representative genome plots of BT474, MDA-MB-361, MDA-MB-</p><p>453, SKBR3,UACC-812 and ZR-75.30. Log2 ratios are plotted on the Y axis against each clone according to genomic location on the X axis. The centromere is represented by a vertical dotted line. BACs categorised as displaying genomic gains as defined by aws ratios > 0.12 are highlighted in green and those categorised as genomic losses as defined by aws ratios < -0.12 are highlighted in red.</p>