CNAs in 29 BIA-ALCL and ALK⁻nALCL cases. (A) CNA frequencies of 29 BIA-ALCL patient samples. Frequency of gains (red) and losses (blue) are shown on the y-axis, sorted in chromosomal order and by chromosomal position on the x-axis. The top 5 most frequent CNAs in BIA-ALCL are gains of chromosome 2p25-pter (48%) and 8q24-qter (45%) and losses of chromosome 8p (48%), 20p13-p12 (48%), and 20q13.12-q13.2 (66%). Of the 6 paired samples, only CNA of the seromas are included. (The same frequency plot is created for the CNAs of matching tumors; see supplemental Figure 2.) (B) Chromosome 20 CNAs with seroma BIA-ALCL (light blue) and tumor BIA-ALCL (magenta) on the y-axis and gains (red), losses (blue), and blacklisted regions (gray) by chromosomal position on the x-axis. The ideogram of chromosome 20 is given above the graph. The smallest region of overlap and, hence, the most frequently lost region, is at chromosomal band 20q13.13-13.2. (C) Comparison plot for CNAs between BIA-ALCL (filled; n = 29) and ALK⁻ nALCL (lines, n = 24). Gains (positive value, red) and losses (negative value, blue) are depicted, sorted by chromosomal position (x-axis). (D) Frequency plot of P value (pink) calculated with a 2-sided Wilcoxon rank-sum test with 10 000 permutations and false discovery rate (FDR, striped segments) of the difference in CNAs; the horizontal dotted lines show the significance thresholds (red: P < .05; blue: FDR <0.1). If the difference in CNA level crosses the P value, and the FDR level is <0.1, the difference is considered significant. Significant differences are seen for losses at chromosome 19, 20p, and 20q.