Figure 8.

Total number of tumor specific SNPs detected as allelic imbalance in two paired tumor data sets plotted against their mBAF values for five methods. From each tumor, SNPs homozygous in the matched blood were removed. Only SNPs in segments of allelic imbalance >5 SNPs in size and with an average mBAF value ≥0.56 were counted and summarized across all samples in a data set. Lines correspond to the different methods: PennCNV (black), QuantiSNP (green), unpaired segmentation (red), SOMATICs (blue), and dChipSNP (purple). Vertical solid line corresponds to 0.56 in mBAF. (a) Total number of SNPs detected as allelic imbalance at different mBAF levels for the paired urothelial tumor data set (data set 2). (b) Cumulative number of SNPs detected at different mBAF levels for the paired urothelial tumor data set. (c) Total number of SNPs detected as allelic imbalance at different mBAF levels for the paired breast/colon tumor data set (data set 1). (d) Cumulative number of SNPs detected at different mBAF levels for the paired breast/colon tumor data set.