Online supplementary table 1: overview of all DNA methylation markers in bladder cancer (reported up to April 2012).
% methylated
in tumours
43 (20/47)
52 (36/69)
57 (31/55)
36 (35/98)
35 (34/98)
35 (34/98)
29 (28/98)
16 (16/98)
15 (15/98)
58 (57/98)
88 (86/98)
63 (62/98)
27 (26/98)
100 (98/98)
69 (35/51)
13 (7/55)
17 (9/55)
11 (6/55)
4 (2/55)
29 (16/55)
13 (7/55)
48 (26/55)
Study
Genes
Bornman 20011
Habuchi 20012
Lee 20013
Maruyama 20014
e-cadherin
DBCCR1
RASSF1A
CDH1
RASSF1A
APC
CDH13
FHIT
RARB
DAPK
RARB
e-cadherin
P16
DAPK, RARB, e-cadherin, P16
e-cadherin
MLH1
MGMT
P16
VHL
DAPK
GSTP1
e-cadherin
MLH1, MGMT, P16, VHL, DAPK, GSTP1,
73 (40/55)
e-cadherin
CDH1
47 (23/49)
APC, RASSF1A, P14
100 (45/45)
Chan 20025
Ribeiro-Filho 20026
Tada 20027
Horikawa 20038
Dulaimi 20049
Satyanarayana 2004
10
% methylated
in normal
66 (6/9)
NA (NA/21)
100 (15/15)
NA
NA
NA
NA
NA
NA
100 (7/7)
43 (3/7)
100 (7/7)
100 (7/7)
43 (3/7)
12 (6/51)
NA (NA/5)
NA (NA/5)
NA (NA/5)
NA (NA/5)
NA (NA/5)
NA (NA/5)
NA (NA/5)
Stage
Grade
Prog1 Sur2
0.02
0.05
0.02
0.02
0.05
0.04
0.04
Rec3
Method4
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
0.001 MSP
MSP
MSP
NA (NA/5)
MSP
NA
100 (5/5)
MSP
MSP
LAMA3, LAMB3, LAMC2
55 (70/128)
100 (10/10)
0.0001 0.0001
MSP
LAMB3
LAMC2
NA (NA/128)
NA (NA/128)
NA (NA/10)
NA (NA/10)
0.01
MSP
MSP
1
0.017
0.002
Catto 200511
Catto 200511
Friedrich 200512
Kim 2005 13
Marsit 200514
200615
Hoque
Christoph 200616
Christoph 200617
Marsit 200618
Neuhausen 200619
Urakami 200620
Boireau 200721
Wu 200722
Yates 200723
RARB
e-cadherin
RASSF1A
TIMP3
RUNX3
SFRP1
SFRP2
SFRP4
SFRP5
SFRP1, SFRP2, SFRP4, SFRP5
TIMP3
DAPK1
APAF1
DAPK1
APAF1
CASP-8
IGFBP3
p16
RASSF1A
PRSS3
SFRP1
APC
RASSF1A
DAPK1
RARB2
CDKN2A
SFRP1,SFRP2, SFRP4, SFRP5, WIF1,
DKK3
CLDN4
LOXL1
LOXL4
LOXL1, LOXL4
RASSF1A,
e-cadherin,
TNFSR25,
EDNRB, APC
25 (23/94)
60 (61/101)
54 (57/106)
NA (NA/105)
73 (91/124)
18 (64/355)
52 (185/355)
9 (32/355)
37 (131/355)
62 (220/355)
175 (121/175)
77 (62/80)
100 (80/80)
74 (81/110)
100 (110/110)
3.6 (4/110)
66 (73/110)
31 (109/351)
32 (112/351)
33 (116/351)
55 (53/96)
45 (43/96)
35 (34/96)
29 (28/96)
19 (18/96)
2 (2/96)
NA
NA
NA
NA
100 (20/20)
NA
NA
NA
NA
NA
25 (0/25)
8 (2/20)
11 (2/20)
20 (4/20)
15 (3/20)
100 (20/20)
10 (2/20)
NA
NA
NA
NA (NA/19)
NA (NA/19)
NA (NA/19)
NA (NA/19)
NA (NA/19)
NA (NA/19)
77 (42/54)
67 (36/54)
NA (NA/39)
70 (45/64)
40 (26/64)
92 (59/64)
NA (NA/39)
67 (8/12)
100 (12/12)
67 (8/12)
97 (93/96)
75 (23/30)
2
0.04
0.04
0.01
0.04
0.01
0.05
0.01
0.04
0.001
0.002
0.01
0.04
0.0001
0.04
0.05
MSP
MSP
0.05
MSP
0.05
0.036 Q-MSP
0.02 MSP
Q-MSP
Q-MSP
Q-MSP
Q-MSP
0.0003
Q-MSP
0.001
Q-MSP
MSP
MSP
0.04 Q-MSP
0.05 Q-MSP
Q-MSP
0.002 Q-MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP, BS-SEQ
MSP
BS-SEQ
BS-SEQ
BS-SEQ
0.05
Q-MSP
Aleman 200824
Aleman 200825
Brait 200826
Jarmalaite 200827
Kim 200828
Shi 200829
Cebrian 200830
Wolff 200831
Mori 200932
Ali Hosseini 201033
Costa 201034
201035
Lin
Lin 201036
Marsit 201037
Matsumoto 201038
Alvarez-Mugica
SOX9
PMF1
CCNA1
MINT1
CRBP
CCND2
PGP9.5
CALCA
AIM1
p16, RARB, RASSF1A, DAPK,MGMT
RUNX3
DBC2
Myopodin
RUNX3
RASSF1A
EDNRB
BCL2
COL1A2
P14ARF, P16INK4a
GDF15, TMEFF2, VIM
TMEFF2
e-cadherin, P16, P14, RASSF1A
e-cadherin
P16
P14
RASSF1A
56.4 (57/101)
83 (421/507)
57 (53/93)
31 (29/93)
39 (36/93)
33 (31/93)
41 (38/93)
28 (26/93)
54 (50/93)
62 (36/58)
72 (85/118)
59 (44/75)
69 (322/466)
39 (133/342)
37 (127/342)
30 (103/342)
28 (96/342)
NA (NA/67)
51.25 (41/80)
100 (50/50)
NA (NA/50)
90 (51/57)
48 (24/50)
64 (32/50)
36 (18/50)
62 (31/50)
90 (9/10)
NA (NA/10)
100 (26/26)
100 (26/26)
96 (25/26)
100 (26/26)
100 (26/26)
88 (23/26)
100 (26/26)
NA (NA/2)
NA
86 (49/57)
NA (NA/20)
NA (NA/10)
NA (NA/10)
NA (NA/10)
NA (NA/10)
NA (NA/10)
NA
100 (20/20)
NA (NA/20)
NA
NA
NA
NA
NA
HOXB2
NA (NA/582)
NA
KRT13
NA (NA/582)
NA
0.0001
FRZB
NA (NA/582)
NA
0.01
FHL1
Myopodin
NA (NA/70)
NA (NA/170)
NA (NA/10)
NA
3
0.032
0.025
0.001
0.025
0.02
0.02
0.04
0.05
0.007
0.02
0.013 0.05
0.0005 0.037
0.026
0.05
0.008
0.005
0.05
0.0001 0.01
0.03
0.028
0.01
MSP
MSP
Q-MSP
Q-MSP
Q-MSP
Q-MSP
Q-MSP
Q-MSP
Q-MSP
MSP
MSP
MSP
MSP
Q-MSP, MS-SNP
Q-MSP, MS-SNP
Q-MSP, MS-SNP
Q-MSP, MS-SNP
Q-MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
MSP
Microarray,
Pyroseq
Microarray,
Pyroseq
Microarray,
Pyroseq
Q-MSP
MSP
201039
Owen 201040
Renard 201041
Serizawa 201142
Sobti 201043
Toki 201044
Cabello 201145
Chung 201146
Duarte-Periera
201147
Reinert 201148
Vinci 201149
Xuan 201150
Kandimalla 201251
Kim 201252
Lin 201236
8 TSG
NID2
TWIST1
FGFR3, APC, RASSF1A, SFRP2
RASSF1A
DAPK
CRBP1
BRCA1
RARB
WT1
THSB1
VHL
MGMT
A2BP1
NPTX2
SOX11
PENK
NKX6-3
DBC1
MYO3A
CA10
NA (NA/76)
73 (66/91)
68 (62/91)
90 (91/101)
NA (NA/101)
38 (39/103)
43 (28/65)
NA (NA/31)
NA (NA/31)
NA (NA/31)
NA (NA/31)
NA (NA/31)
NA (NA/31)
62 (16/26)
88 (23/26)
77 (20/26)
92 (24/26)
69 (18/26)
69 (18/26)
65 (17/26)
85 (22/26)
NA
100 (39/39)
100 (NA/NA)
NA
NA
92 (44/48)
100 (16/16)
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
OPCML
60 (55/91)
96 (24/25)
ZNF154
POU4F2
HOXA9
EMOES
TBX4
BCL2, TERT, DAPK
CD99
TBX2, TBX3, GATA2, ZIC4
RASSF1A
H-Cadherin
85 (89/105)
92 (97/105)
92 (97/105)
88 (92/105)
NA (NA/NA)
91 (98/108)
32 (26/82)
NA (NA/65)
34 (102/301)
35 (47/133)
100 (14/14)
100 (14/14)
100 (14/14)
100 (14/14)
NA
60 (63/105)
100 (10/10)
NA
NA
100 (43/43)
4
0.01
Q-MSP
MSP
MSP
Q-MSP
Q-MSP
MSP
COBRA
MS-MLPA
MS-MLPA
MS-MLPA
MS-MLPA
MS-MLPA
MS-MLPA
Pyroseq
Pyroseq
Pyroseq
Pyroseq
Pyroseq
Pyroseq
Pyroseq
Pyroseq
0.01
0.017
0.025
0.022
0.03
0.022
Q-MSP
0.05
0.05
0.01
0.05
0.05
0.026 0.001
0.0006 0.01
0.003
0.004
0.00 0.007
0.01
MS-HRM
MS-HRM
MS-HRM
MS-HRM
MS-HRM
Q-MSP
MSP
BS-SNP
MSP
MSP
Yan 201253
RUNX3
59 (110/186)
NA
0.05
0.009 0.006
0.04 MSP
- Methylation Specific PCR; Q-MSP - Quantitative MSP; BS-SEQ - Bisulfite Sequencing; MS-SNP Methylation Specific Single Nucleotide Primer Extension; COBRA - Combined Bisulfite Restriction Analysis; MS-MLPA - Methylation Specific Multiplex Ligationdependent Probe Amplification; MS-HRM - Methylation Specific High Resolution Melting; BS-SNP - Bisulfite Specific SNP. NA - Not Available
1Prog-Progression 2Sur-Survival 3Rec-Recurrence 4MSP
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