Genome-wide screening for recurrent genetic and epigenetic alterations in T-LBL. (A) Overview of the top 50 mutated genes identified by WES in 15 pediatric T-LBL samples including 5 corresponding relapse samples. The relative mutation frequencies (sample-wise) are indicated to the left and the pathways to the far left. Gene names and types of mutation are to the right. The number of mutations is displayed at the top in a bar plot. (B) The top 55 differentially methylated genes enriched by significant CpGs in primary samples in comparison with their corresponding germline samples (TG vs TP 1e⁻⁴). (C) The top 55 differentially methylated genes enriched by significant CpGs in relapse samples in comparison with their corresponding germline samples (TG vs TR 5e⁻⁷). Array used: Infinium MethylationEPIC BeadChip 850K. (D) The frequency of CNAs detected in 22 T-LBL samples including select primary and matched relapse samples. CNAs in the analyzed samples are displayed against the chromosomal numbers and position. The CNA profiles for primary relapse⁻ samples (TP1-10), for primary relapse⁺ samples (TP11-16), and matched relapse samples (TR11-16) are presented separately. Array used: Infinium Omni2.5Exome-8 v1.3. Results validated independently by MLPA for specific regions in Chr 1p, 4q, 6q, 9p, 10q, 11p, and 17q. Red: amplifications; blue: deletions; yellow: loss of heterozygosity.