Fig. 2
Large-scale genomic aberrations dominantly involve losses of ATM on chr.11q and gains of AGO2 and MYC on chr.8q. a Number of differentially sized somatic copy-number alterations (sCNA) in this T-PLL cohort (n = 83) compared to publically available Affymetrix SNP 6.0 primary array data sets (all HapMap controlled, meta-analysis procedure in Methods section). b Ideograms with average abundance of large-scale genomic lesions (Supplementary Fig. 4a, Supplementary Data 6 for GISTIC2.0 analyses). c Minimally deleted region (MDR) on chr.11 centering on ATM and minimally amplified region (MAR) on chr.8 defined by AGO2 (for MDRs on chr.13 and chr.22 see Supplementary Fig. 4c). d Left: verification of AGO2 amplification in T-PLL case TP057 with biallelic MYC (CN = 2) using FISH (scale bar = 5 µm). Right: circular binary segmentation (CBS) with p ≤ 0.01 detects AGO2, but not MYC as significantly amplified. e Total number of significant global gains (red) and losses (blue) in T-PLL ‘monoallelic’ (CN ≤ 1.5), ‘biallelic’ (CN = 2), and ‘multiallelic’ (CN ≥ 2.5) for ATM / AGO2 excluding these affected regions. Representations: boxes as interquartile range (IQR); thick line as the mean, whiskers as lower and upper limits. Lower limit = x0.25–1.5 × IQR. Upper limit = x0.75 + 1.5 × IQR. Values above or below are potential outliers and marked as O (***p < 0.001, *p < 0.05, Wilcoxon rank-sum test with continuity correction). f Different OS across 66 T-PLL subjects stratified by ATM CN (log-rank test)
