Fig. 3.

Genome-wide allelic imbalance profile. Minor allele frequency of heterozygous SNPs identified from normal tissue in each patient are derived in each tumor sample, enabling assessment of allelic imbalance in ~17,000 loci across the exome. Circular binary segmentation (CBS) is applied to minor allele frequencies of SNPs with minimum coverage of 10× in each tumor sample, and the resulting segment means are shown as a heatmap. Asterisks indicate samples where corresponding mutation analyses were not performed due to low tumor purity (omental metastasis of CGOV279, right ovarian tumor of CGOV278) or miliary pattern of tumor samples (peritoneal metastases of CGOV63). Given the relatively lower number of distinct DNA molecules available from the p53 signature samples from CGOV62 and CGOV63, these samples were subjected to a more sensitive LOH analysis (Methods, Genome-wide imbalance analysis) and are not shown here