Whole genome and targeted exome sequencing results for pediatric T-ALL patients at diagnosis.

<p>(A and B) Visualization of chromosomal breakpoint junctions in diagnostic leukemia cells of ETP-ALL patient #10793. (A) Circos plot of somatic structural variations as detected in the diagnostic sample (Dx) along with SNV densities (1-Mb window) and predicted LOH data as explained in the accompanying legend. Interchromosomal junctions are displayed as red lines, and intrachromosomal junctions are displayed as grey lines. (B) Allele-specific copy number variations as determined by Affymetric SNP Array analysis and multiple WGS-predicted chromosomal breakpoints as a consequence of chromothripsis affecting Chromosomes 7 and 14 are displayed. In the copy number plots, black dots indicate the unsmoothed allele-specific copy numbers. Red dots are the smoothed maximal allele-specific copy numbers using a sliding window of 30 SNP probes, while the green dots reflect the smoothed minimal allele-specific copy numbers. Chromosomal breakpoint junctions are displayed for translocations (red arrows), inversions (blue arrows), deletions (green arrows), duplications (purple arrows), and complex rearrangements (grey arrows). Affected (in black) and flanking (in grey) genes for the interchromosomal translocations are indicated. (C) Overview of most deregulated cellular processes among 127 genes carrying mutations/aberrations in the diagnostic material of two or more patients in the expansion cohort of 69 T-ALL patients. The number of patients with each T-ALL subtype is indicated. The <i>p</i>-value for each process represents the significance level for enrichment of mutations/aberrations that affect this pathway in ETP-ALL patients compared to other T-ALL subtypes, and was calculated by two-sided Fisher’s exact test. See also <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1002200#pmed.1002200.s013" target="_blank">S4 Table</a>. ETP-ALL, early thymic progenitor acute lymphoblastic leukemia; LOH, loss of heterozygosity; SNV, single nucleotide variant; T-ALL, T cell acute lymphoblastic leukemia.