Fig. 2

One versus two samples. a Mutation frequencies in single samples were plotted with respect to ploidy for public (black) or private (red) mutations for four representative tumors (see Additional file 2: Figure S1 for other tumors). Public mutations have a range of frequencies centered around their expected clonal values, which complicates classification because many private mutations also have frequencies that overlap with the public mutations. Black arrows indicate ad hoc cut points to distinguish public from private mutations. The grey shaded areas demonstrate that many private mutations have frequencies within the ranges of the public mutations, indicating that the private mutations are indistinguishable from the public mutations. Data from both single samples from the same tumor are presented. “Clonality” is calculated as: (measured mutation frequency - expected clonal frequency)/expected clonal frequency, with a zero value indicating the measured frequency is at its clonal value. b With two samples, public mutations are typically frequent on both sides. A private mutation frequent on one side is typically absent or rare on the other side. A simple 10/10 rule (<10 % frequency in one side, dotted lines) can usually accurately distinguish public from private mutations. A problematic case (Cancer N) illustrates that distinguishing public from private mutations in well-mixed cancers can be difficult, especially with aneuploid tumors. Blue X’s indicate private mutations found on both tumor sides