Chromosome 7

1. Not Restored Restored A B D C E Chromosome 7 Not Restored Restored F G I H J Chromosome 12

2. Not Restored Restored K L P Q N M S R O Chromosome 16 T Not Restored Restored Chromosome 21

3. Supplementary Figure 3 - Assessment of effect of DNA restoration and assay reproducibility – Tumor 007 Tumor 007 FFPE DNA was analyzed in multiple experiments to test the effectiveness and reproducibility of the assay. GenoCN output plots containing BAF, LRR and copy number state are shown for three chromosomes 7, 12,16 and 21 for each of these experiments: Roche extracted DNA without restoration treatment (A, F, K, P), Roche extracted DNA with restoration treatment (B, G, L, Q), Qiagen extracted DNA without restoration treatment (C, H, M, R), Qiagen extracted DNA with restoration treatment replicate 1 (D, I, N, S) and replicate 2 (E, J, O,T). Note that general patterns of copy number alterations are discernable even without restoration (e.g. high level amplifications on chromosomes 7 and 12 and some chromosome breakpoints), however the visual improvements in data quality following restoration is clear using both Roche and Qiagen extracted DNA, and particular with replicate Qiagen extracted DNA samples with which, for example focal amplifications on 16p (arrows) are most pronounced and homozygous deletions on 12p (arrows) are only detected. Replicate samples therefore provide evidence that mapping high level alterations, chromosome breakpoints and a homozygous deletion are reproducible, yet the classification of single copy alterations especially deletions is more variable.