Effects of amplitude-based or length-based filtering of arm-level events on GISTIC results. (a-c) GISTIC amplification (top) and deletion (bottom) plots using all data and a low amplitude threshold (a), using all data and a high amplitude threshold (b), and using the focal data and a low amplitude threshold (c). The genome is oriented vertically from top to bottom, and GISTIC q-values at each locus are plotted from left to right on a log scale. The green line represents the significance threshold (q-value = 0.25). For each plot, known or interesting candidate genes are highlighted in black when identified by all three analyses, in red when identified by the high amplitude or focal length analyses, in purple when identified by the low amplitude or focal length analyses, and in green when identified only in the focal length analysis.