PAX5 deregulation in a subset of CDX2/UBTF subtype induced by the structural variants at PAX5-ZCCHC7 region. (A) The SVs at PAX5/ZCCHC7 region detected by WGS were shown in green (inversion) and blue (deletion) bars. Below the coverage tracks of 1-dimensional HiChIP and RNA-seq for representative CDX2/UBTF inversion case (SJALL060150_D) are shown. SVs include the promoter and exon 1 of PAX5 (exon 1a) but do not affect the alternative PAX5 exon 1b. (B) Expression of PAX5 by normalized read counts in each B-ALL subtype is shown. CDX2/UBTF cases with PAX5 rearrangements are shown in green (inversion) and blue (deletion). PAX5 is expressed highly in CDX2/UBTF subtype, especially for the case with PAX5/ZCCHC7 inversion. (C) Sashimi plot showing the junctions with the number of reads split across the junction (junction depth) in the PAX5 gene for representative CDX2/UBTF samples: inversion (n = 1, SJALL060150_D), deletion (n = 2, SJBALL016287_D1 and SJBALL020169_D1), and without PAX5 rearrangements (n = 2, SJBALL020165_D1 and SJALL0554518_D1). PAX5 exon 1b is shown in red bar. The ratio of exon 1b usage to exon 1a is shown in the right of plot. The cases with PAX5 rearrangements exhibited higher exon 1b usage ratio than cases without rearrangements.