SuperFreq: Integrated mutation detection and clonal tracking in cancer
Fig 4
Precision and recall of SuperFreq clonal tracking.
(A) Overview of simulations. As illustrated on the left, the genome is divided into four regions (chr 1–3, 4–8, 9–14 and 15-Y), and the cancer and normal samples are blended to create three samples that contain four clones supported by mutations that reside in different regions of the genome. The expected clonalities across the three samples are shown to the right, where P denotes the purity of the cancer sample. (B) Sensitivity to find clones with a matched normal (WMN) or no matched normal (NMN) in SuperFreq and SciClone, as function of maximum clonality. (C) Recall of the four simulated clones, binned on the purity of the original cancer sample. (D) Number of false clones called. (E) Fraction of mutations associated with a clone originating from the expected chromosomes in panel A. (F) Fraction of mutations called in the cancer-normal recalled by the called clones.