Exome-wide simulated copy number profiles at a range of tumor purities yield expected allelic and copy number ratios.

<p>Allelic ratio for allele-specific copy number gain (A) and loss (B) events at heterozygous SNP loci for haplotypes affected (blue), haplotypes not affected (red), and SNPs not in engineered CNV regions (green) as negative controls at different tumor cellularity levels (x-axis) across all cancers. C) Tumor to normal log2 depth ratio boxplots of copy number gain (red) and loss (blue) segments from Sequenza across all cancers (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006080#pcbi.1006080.t001" target="_blank">Table 1</a>). D) Accuracy of Sequenza copy segment calling gains (red triangles) and losses (blue circles) decreases as simulated tumor content decreases.