A C Tumour Chromosome 8 Tumour Chromosome 8 B D Tumour Chromosome 17

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A C Tumour 540 - Chromosome 8 Tumour 540 - Chromosome 8 B D Tumour 540 - Chromosome 17 Tumour 540 - Chromosome 17 Supplementary Figure 6 - Comparison between DNA extraction kits in generating DNA copy number data DNA extracted from tumor 540 using both Roche (A,B) and Qiagen (C,D) methods was shown to be of borderline quality based on QC qPCR assessment and yielded low SNP call rates in the Infinium assay (Supplementary Table 1). BAF plots also demonstrate low quality experimental data. LRR plots and GenoCN plots are also of poor quality in Roche DNA extracted samples (A and B). However, the Qiagen extracted DNA from this challenging sample reveals convincing evidence of DNA copy number aberrations previously highlighted as being common and important in breast tumors (C and D). For instance, on chromosome 8 (A and C) there is a deletion of 8p and copy number gains on 8q including high level amplifications mapping to 8q21, 8q22.3 and 8q24 (arrows). Chromosome 17 (B and D) harbours a deletion at 17p12 along with several complex high-level amplifications (arrows) including at 17p11, 17q11.2 and 17q12-21 (location of ERBB2, see also Figure 2).