Selection of Statistically Significant Recurrent Copy Number Alterations. a) Genomic Identification of Significant Targets in Cancer (GISTIC) analysis of copy number gains was performed with 32 ovarian serous adenocarcinoma samples. GISTIC calculates the false discovery rate corrected significance (Q-value) of the frequency of gain and the average copy number for samples with gain at each probe position. Each point represents this Q-value for a SNP array probeset. Points are proportionately spaced and arranged in genome order from 1 pter to Xqter. Vertical dashed lines represent chromosome boundaries. b) GISTIC analysis of copy number losses, plotted as above. Gain and loss were specified as log2-transformed cancer/normal copy number ratios of > 0.3 and < -0.3, respectively.