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Q590 Fresh Frozen

Q590 FFPE not restored. Q590 Fresh Frozen. Q590 FFPE replicate 1. Q590 FFPE replicate 2. Chromosome 5. Chromosome 17. Chromosome 19. Chromosome 20. Supplementary Figure 2 - Assessment of assay reproducibility – Tumor Q590

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Q590 Fresh Frozen

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  1. Q590 FFPE not restored Q590 Fresh Frozen Q590 FFPE replicate 1 Q590 FFPE replicate 2 Chromosome 5 Chromosome 17 Chromosome 19 Chromosome 20 Supplementary Figure 2 - Assessment of assay reproducibility – Tumor Q590 GenoCN output plots of selected chromosomes from tumor Q590 DNA derived from a fresh frozen tumor and its matched FFPE surgical tumor block. The FFPE DNA sample was analysed both without restoration and two replicates with restoration. Visual inspection of plots show considerable improvement in performance of FFPE DNA following restoration. The two technical FFPE replicates show good reproducibility in calling copy number gains and losses. Reduced tumor cellularity of the FF sample (50%) compared to the FFPE sample (70%) meant that there was variability in copy number changes between these matched samples. Nevertheless, the same chromosomal breakpoints were detected and where loss was detected in the FFPE sample (green, GenoCN state = 1) copy neutral LOH (dark blue, GenoCN state = 2) was detected in the FF sample.

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