Figure 3.

Copy number evaluation at the BCOR Xp11.4 locus in hairy-cell leukemia, splenic diffuse red pulp lymphoma and splenic marginal zone lymphoma. (A) Copy number (CN) variation was detected from exon sequencing of the target genes after normalization using DeCovA.^25,24 Each row represents a lymphoma case (HCL: hairy-cell lymphoma; SDRPL: splenic diffuse red pulp lymphoma; SMZL: splenic marginal zone lymphoma). Each column represents an exon of two different genes (BCOR and KDM6A) located at locus Xp11. A progressive gradation of CN variation distinguishes loss (red) and gain (green). Right: mean copy number ratio of the BCOR locus, with some references in brackets corresponding to the next inserts (B–G). (B) Microarray-based comparative genomic hybridization confirmed a monoallelic microdeletion of approximately 669 kb (arr[GRCh37] Xp11.4(39576746_40245183)×1), encompassing the BCOR locus (SDRPL female patient VL_218), whereas the KDM6A gene was unaffected. (C–D) Copy number variation of chromosome X detected by whole-exome sequencing using a circular binary segmentation algorithm and compared to a paired reference genome (log₂ ratio). These two female patients with SDRPL acquired complete monosomy X. (E–G) Detailed karyotype results confirmed monosomy X (E), tetrasomy X (F) or trisomy X (G).