The MCL genome is distinctly methylated compared with normal naive B cells. (A) Three-dimensional principal component analysis of DNA methylation data comparing MCL patient samples (red) and naive B cells (blue). (B) Plot of methylation difference (x-axis) vs significance (on y-axis) shows marked asymmetry with an overall tendency for hypomethylation in patients with MCL compared with NBCs. Blue dots mark probe sets that reached both criteria for differential methylation on our analysis (methylation difference of 1.5 and P < .001). (C) Methylation (HELP data) at the differentially methylated loci identified above from patients with MCL and NBCs represented in a heat map. Scale shows relative methylation (red indicates hypomethylation; blue indicates hypermethylation).