Genomic alterations during progress from CP to BC. (A) The genomic DNA of 13 paired patients with CML was analyzed by WGS at 2 disease stages, allowing the identification of stage-specific alterations for BC (CP→BC) for each patient. Circos plot shows in the outer layer genomic gains (red) deletions (blue), and inversion/complex rearrangements (black), followed toward the center by SNVs (silent/noncoding in black and putative damaging in red). Each row represents 1 of the 13 samples. Central lines show translocations with individual samples in different colors. (B) Significantly mutated genes by SNV and indels in 13 patients during progression. (C-D) Significantly copy number altered genomic regions acquired during progression by (C) gains and (D) deletions. (E-F) Test for significant (x-axis) and enrichment (y-axis) of genomic alterations acquired from CP to BC for paired (E, by WGS) or unpaired (F, by WES) samples in genes related to cancer and epigenetic pathways (see supplemental Table 11 for gene lists). Dashed lines indicate significance and deviation from the null hypothesis of no enrichment (enrichment = 1).