Tumour 74 Replicate 1 Tumour 74 Replicate 2

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Tumour 74 Replicate 1 Tumour 74 Replicate 2 CN Estimation LRR BAF 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X CN Estimation LRR BAF 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Tumour 74 Replicate 2 Supplementary Figure 4 - Assessment of assay reproducibility – Tumor 74 Tumor 74 DNA was derived from a post mortem FFPE block taken in 1974. DNA restoration and SNP-CGH was performed in duplicate and the GenoCN output whole genome plots of both replicate arrays are shown. Despite the noise of the arrays, particularly evident on BAF plots, the replicates show reasonable reproducibility in calling copy number gains (CN estimation of 3 and 4); especially for the focal high level gains on chromosomes 2, 8, 15 and 17 (arrows; and see also Supplementary Figure 7 for images of chromosomes 8 and 17). Calling of reduced DNA copy number (CN estimation of 1) however was less reliable.