Figure 6.

Allelic imbalances in CRL-2324 cells used for estimation of tumor dilution percentage by segmentation. CRL-2324 breast cancer cells were hybridized on Illumina 370k BeadChips in a dilution series with matched normal DNA (data set 3). For all parts, the left panel shows B allele frequency estimates and the right panel log R ratios. Bars indicate allelic imbalances detected by unpaired segmentation (red), SOMATICs (blue), PennCNV (black), QuantiSNP (green) and dChipSNP (purple). (a) Copy neutral LOH on 13q21.31-qter and single copy gain on 13q11-q12.3 in 100% CRL-2324 cells. (b) Copy neutral LOH on 13q21.31-qter and single copy gain on 13q11-q12.3 with 50% tumor fraction. (c) Copy neutral LOH on 13q21.31-qter and single copy gain on 13q11-q12.3 with 30% tumor fraction. (d) Hemizygous loss on chromosome 18q21.32-q22.3 with 50% tumor fraction.