Overall picture of CNAs in the RS coding genome. (a) Overall number and frequency of CNAs in RS. (b) Minimal common regions (MCRs) of CN loss (top) or CN gain (bottom) encompassing 1–3 protein-coding genes and altered in ≥10% of RS cases (n = 50; blue and red bars), ranked by chromosome and frequency of alteration. Gray bars represent the frequency of loss (top) or gain (bottom) affecting the genes included in the annotated MCR in a series of 353 CLL cases as reported in Edelmann et al. (2012). All reported MCRs occurred with a significantly different frequency between CLL and RS based on a two-tailed Fisher’s exact test (all with P < 0.001). (c) Frequency of known CLL-associated cytogenetic abnormalities in RS (n = 50 cases, black bars) and in a series of 353 CLL cases as reported in Edelmann et al., 2012 (gray bars). Asterisks indicate lesions present with different frequency between CLL and RS based on a two-tailed Fisher’s exact test (*, P < 0.05; **, P < 0.001). (d) Statistical analysis of CN losses (left, blue) and gains (right, red) in 50 RS cases according to GISTIC. False discovery rates for each aberration (q values, x axis) are plotted at each genomic position across chromosomes 1–22 (y axis). The green line represents the q value cutoff for significance (0.25). Centromere positions in each chromosome are indicated by dotted lines, and the gene names are provided only for focal aberrations encompassing ≤3 genes, unless indicated. (e) Distribution of the total number of CNAs in 50 RS cases (all or grouped according to the presence or absence of TP53 disruption). **, P < 0.001 according to a nonparametric two-tailed Student’s t test.