REL-truncating SVs in ATL. (A) Introns with significantly enriched SV breakpoints. Introns with q < 0.01, whose breakpoints are found in ≥3 cases, and of gene-wise significant gene, are considered intron-wise significant. Introns with breakpoints in ≥2 cases (n = 888) are shown. (B) REL-truncating SVs in 150 ATL cases. Breakpoint clustered regions (intron 7 and coding sequence in exon 10) are shaded. (C) Expression of REL exon 1-7 in 66 ATL cases analyzed by RNA-seq, according to REL SV status. Numbers of cases are shown in parentheses. Two-sided Brunner-Munzel test. Box plots show the medians (lines), IQRs (boxes), and ± 1.5 × IQR (whiskers). (D) Genomic structure of the rearranged REL locus and transcription in representative ATL cases. In these SV (+) cases, REL open reading frame is terminated within intron 7 and merged into intergenic sequences. Aberrant REL transcripts are shown in red. (E) Effect of REL CN and SV on REL exon 1-7 expression for ATL. Multivariate analysis using linear model. (B,D) mRNA reference sequences are shown in supplemental Table 23.