Figure 4

Analysis of the 40× coverage breast tumor PD4115a. (A) (Left) Read depth ratios (gray) and the inferred copy number aberrations calculated by our algorithm when n = 3 including the normal population (black), dominant (clonal) tumor population (blue) and subclonal tumor population (red). (Right) A reconstruction of the tumor mixture with the inferred aberrations and estimated fraction of cells in each subpopulation. (B) Distribution of read depth ratios over 50 kb intervals after centering and correction for 24% normal admixture using a simple linear scaling. Several peaks fall near to expected corrected ratios (0.5, 1, 1.5, 2). Two overlapping but distinct peaks can be seen indicating multiple subclonal deletions in similar proportions (labeled D and E). (C) (Top) Read depth ratios in 50 kb bins for chromosomes 5, 9 and 11, each of which has a clonal deletion (purple). (Bottom) Distribution of read depth ratios after correction for the aberration fraction of 76% of the sample. (D) (Top) Read depth ratios in 50 kb bins for chromosomes 3, 4 and 5, each of which has a subclonal deletion (blue). (Bottom) Distribution of read depth ratios after correction for the aberration fraction of 43.3% of the sample. (E) (Top) Read depth ratios as in (D), but a different subclonal deletion is highlighted (red). (Bottom) Distribution of read depth ratios after correction for the aberration fraction of 32.7% of the sample.