Fig. 1

An overview of the eight indices in the algorithm. Var: variation relative to median copy number (J1), steep: steep transitions (J2), curv: curvature or oscillation (J3), dev: deviation from ploidy (J4), gain: gain relative to ploidy (J5), loss: loss relative to ploidy (J6), loh: LOH related allelic skewness (J7), and asym: non-LOH related allelic skewness (J8). The scores can be detected genome-wide or arm-wise in each sample. The red curves represent total copy numbers, while the blue curves represent the number of copies of each allele. Ploidy is defined as the median genome copy number and is shown as a dashed horizontal line