A B TAPS Patchwork Allelic imbalance Allelic imbalance ratio Log R

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A B TAPS Patchwork Allelic imbalance Allelic imbalance ratio Log R Normalized coverage Total and minor Copy number Total and minor Copy number Chromosomal location, chr 13 Chromosomal location, chr 13 Supplemental data 1. Visualizations of TAPS and Patchwork results for cell line HCC1954. Panels A-F illustrate genomic differences affecting whole chromosomes or chromsome arms for chr. 13, 15 and 5. These differences presumably ocurred during culture.These chromosomes were excluded for performance evaluation.

C D TAPS Patchwork Allelic imbalance Allelic imbalance ratio Log R Normalized coverage Total and minor Copy number Total and minor Copy number Chromosomal location, chr 15 Chromosomal location, chr 15

E F TAPS Patchwork Allelic imbalance Allelic imbalance ratio Log R Normalized coverage Total and minor Copy number Total and minor Copy number Chromosomal location, chr 5 Chromosomal location, chr 5

Supplemental Table 1. Segments used for sensitivity and specificity estimates in evaluating Patchwork performance in cell line HCC1954 with TAPS analysis as gold standard. Allele-specific copy number compositions with TP+FN > 15 segments were included. Segments were required to be at least 1Mb in size and have an overlap of 75% or more with the microarray data. [total copy number]m [minor copy number] Sensitivity (%) Specificity (%) True Positive False Negative True Negative False Positive Tumor fraction (%) 30 50 70 100 3m0 10.0 81.0 99.3 99.6 2 17 18 4 273 272 268 1 3m1 95.5 93.3 93.0 96.0 93.6 93.9 93.5 42 40 3 239 234 232 229 10 16 15 4m1 55.1 90.3 91.6 92.9 93.8 94.6 96.8 97.7 38 65 31 7 6 5 210 211 212 214 14 12 4m2 35.3 58.8 68.6 74.5 97.1 28 35 33 21 13 241 237 222 5m1 14.3 75.0 87.5 94.5 97.9 98.9 257 271 270 5m2 37.7 64.8 67.9 58.5 96.3 95.8 97.5 20 36 19 22 227 230 9