Table 2

Differentially methylated CpG sites in the cytogenetic subtypes of ALL
DMC signature DMCsa Genesb Genes unique DMCs unique Unique DMCs  Unique DMCs
(number of patients) to subtypec 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).

Nordlund et al.

Nordlund et al. Genome Biology 2013 14:r105   doi:10.1186/gb-2013-14-9-r105

Open Data