Legends to Supplementary Tables

LEGENDS TO SUPPLEMENTARY TABLES

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

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).

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.

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

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

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).

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

(see Material and Methods). 2

Supplementary Figure 1: Representative genome plots of BT474, MDA-MB-361, MDA-MB-

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.