Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

Table 2 Differentially methylated CpG sites in the cytogenetic subtypes of ALL

DMC signature	DMCs^a	Genes^b	Genes unique	DMCs unique	Unique DMCs	Unique DMCs
(number of patients)			to subtype^c	to subtype	+ DNAm (%)^d	-DNAm (%)^e
Constitutive (774)	9,406	2,023	NA	NA	NA	NA
T-ALL (101)	58,157	8,245	895	16,841	15,487 (92.0)	1,365 (8.0)
MLL/11q23 (28)	31,403	7,142	300	1,763	1,285 (72.9)	478 (27.1)
dic(9;20) (20)	53,680	9,009	202	2,370	1,561 (65.9)	809 (34.1)
HeH (187)	42,779	7,773	271	3,014	268 (8.9)	2,746 (91.1)
t(1;19)TCF3/PBX1(23)	21,799	5,956	107	1,110	272 (24.5)	838 (75.5)
t(12;21)ETV6/RUNX1(163)	45,589	7,973	156	2,114	1,126 (53.3)	988 (46.7)
t(9;22)BCR/ABL1(19)	23,871	6,047	36	271	140 (51.7)	131 (48.3)
iAMP21 (10)	44,726	8,614	272	2,656	997 (37.5)	1,659 (62.5)
Undefined (105)	39,262	7,059	3	56	8 (14.3)	48 (85.7)
Non-recurrent (100)	42,109	7,434	2	27	14 (51.9)	13 (48.1)

^aDifferentially methylated CpG sites (DMCs) with mean Δβ-values >0.20 and false discovery rate-corrected Wilcoxon rank-sum P-values <0.01.
^bThe number of gene regions to which the DMCs are annotated.
^cGenes with DMCs are considered unique to a subtype if only that subtype had significant DMCs in the gene region.
^dHypermethylated DMCs, + DNA methylation (DNAm).
^eHypomethylated DMCs, - DNA methylation (DNAm).

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