Copy-number and CNN-LOH alterations in PTFL. Frequency of (A) copy number (CN) and (B) CNN-LOH alterations of 40 PTFL analyzed by Oncoscan Copy number molecular inversion probe assay. Each probe is aligned from chromosome 1 to Y and p to q. The vertical axis indicates frequency of the genomic aberration among the analyzed cases. Gains are depicted in blue, losses are depicted in red, and regions of CNN-LOH are represented in yellow. (C) Different patterns of 1p CNN-LOH and loss in 4 cases of PTFL. In the first panel for each case, CN calls are represented. In the second panel, allelic events are displayed along the x-axis. Germ-line homozygosity is given in calls at the 0 and 1 levels, respectively, whereas germ-line heterozygosity is given in calls around 0.5. CNN-LOH in the tumor leads to loss of calls around 0.5 and to the presence of allelic imbalance calls derived from a sum of heterozygous normal cell and homozygous tumor cell calls for a given locus, resulting in values between 0 and 0.5 or 0.5 and 1 depending on the percentage of cells carrying the alteration.