343-53678-9-4:78;
TRANSCRIPT
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250
500
750
1000
1250
MSI-H MSI-L MSS
# M
SI e
vent
s
CRC (COAD & READ)STADUCEC
0
20
40
60#
MSI
eve
nts
0.0
2.5
5.0
7.5
10.0
12.5
ACVR2A
SLC35F5
TGFBR2
SLAMF1
CASP5
RPL22
PHACTR4
BAX
RNF43
FGFBP1
AIM2
CYHR1
TMEM60
SLC22A9
LMAN1
OR52N5
MNS1
TMEM22
OR6C75
C9orf114
OR6C76
UBR5
JPH4
MARCKS
MSH3
TCEB3
SEC63
TRIM59
PRDM2
MYO1A
MBD6
EIF2B3
FETUB
PPP1R12B
SEC31A
CLOCK
COIL
ARID1A
CRYGA
SLC3A2
0.0
2.5
5.0
7.5
10.0
12.5
ASTE1
OR7E24
SLC22A9
CASP5
SLC35F5
C18orf34
UPF3A
JAK1
TFAM
FAM111B
SEC31A
RNF43
SMAP1
CTCF
PCDHGA10
MCHR2
ACVR2A
C15orf40
PTEN
TMEM97
TBC1D23
PDS5B
XPOT
TAF1B
MNS1
CCDC28A
KIAA2018
RBM27
CD3G
SRPR
AP1S1
SEC63
TTK
FAM18A
TMEM60
ADD3
CCDC150
RAD50
ATR
FAHD2B
0.0
2.5
5.0
7.5
10.0
12.5
ACVR2AINO80EAIM2
SLC22A9OR6C75FGFBP1SLAMF1TGFBR2SEC31ACCDC43
BAXOR7E24
ARV1C4orf6
KIAA1919TCERG1
CCDC150MNS1SYCP1
TMEM97GBP3RPL22
PHACTR4RNF43
PCDHGA10UPF3ACD3G
GOT1L1TEAD2OR7C1SEC63TRIM59
CCDC28APRR11SRPR
SLC35F5BMPR2
SLC23A2EIF2B3SLC3A2ANO10VEGFBOR6C76
EBPLTTK
RARRES3TMBIM4AASDHLMAN1PRRT2
STAD UCEC COAD
a b c-log10 Q value -log10 Q value -log10 Q value
0
20
40
MSH
3RAD
50ATR
PRKD
CMSH
6BLM
RBB
P8MLH
3ATM
FANCM
BRCA1
REV
3LNBN
BRCA2
MLH
1PALB2
POLM
POLQ
REC
QL
SHPR
HTO
PBP1
TP53BP
1ATRIP
TOP2A
DCLR
E1C
LIG3
POLE
USP
1BR
IP1
DCLR
E1A
FANCB
PARP1
PMS1
TP53
WRN
XRCC2
ALKB
H2
CLSPN
DDB1
ERCC2
FANCA
FANCI
LIG4
MBD
4MNAT1
NEIL1
NEIL3
PER1
PMS2
RAD
18REC
QL5
REV
1TD
G
# fra
mes
hift
MSI
eve
nts
0
25
50
75
100
ACVR
2ATG
FBR2
RNF43
RPL22
MLL3
PRDM2
JAK1
ATR
ARID1A
PTEN
CTC
FLR
RK2
MEC
OM
ATM
MLL2
BRCA1
FBXW
7NSD
1USP
9XAP
CATRX
MLL4
SETD
2TB
L1XR
1AX
IN2
BRCA2
POLQ
ARID5B
BRAF NF1
SETB
P1AR
HGAP
35AS
XL1
TAF1
TSHZ3
EPHB6
ERBB
4MAP
3K1
NCOR1
TET2
TP53
ACVR
1BCDH1
DNMT3A
EGR3
EP300
ERCC2
FGFR
3GATA3
IDH1
IDH2
NAV3
NFE
2L2
PBRM1
RB1
SIN3A
SMAD
4SM
C3
TSHZ2
# fra
mes
hift
MSI
eve
nts
COAD
ESCA
READ
STAD
UCEC
190 MSI-H tumors
a
b
0
1
2
3
4
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
% o
f pat
ient
s
0.0
2.5
5.0
7.5
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
% o
f pat
ient
s
0.0
0.5
1.0
1.5
2.0
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
% o
f pat
ient
s
0
10
20
30
40
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
0
20
40
60
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
0
10
20
30
MLH
1: m
si�h
MLH
1: m
si�l
MLH
1: m
ssMLH
3: m
si�h
MLH
3: m
si�l
MLH
3: m
ssMSH
2: m
si�h
MSH
2: m
si�l
MSH
2: m
ssMSH
3: m
si�h
MSH
3: m
si�l
MSH
3: m
ssMSH
6: m
si�h
MSH
6: m
si�l
MSH
6: m
ssPM
S1: m
si�h
PMS1
: msi�l
PMS1
: mss
PMS2
: msi�h
PMS2
: msi�l
PMS2
: mss
POLD
1: m
si�h
POLD
1: m
si�l
POLD
1: m
ssPO
LE: m
si�h
POLE
: msi�l
POLE
: mss
a b
c d
e f
Frameshift Missense Nonsense Splice site
MLH1 MLH3 MSH2 MSH3
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
MSH6
PMS1 PMS2 POLD1 POLE
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
Exp
Met
CN
Mut
MS
I
Exp
Met
Mut
MS
I
Exp (Gene expression)
Met (Methylation)
CN (DNA copy numbers)
-1.5 +1.5
1 0
-1 +1
Missense SNV
Truncating mutations (nonsense/splicing SNVs, frameshift indel) and MSI
* *
*
* * * * * * *
* * *
Pearson correlation < -0.5 (Met), > 0.2 (CN), P < 0.05 (Mann-Whitney test; Mut and MSI)
0
100
200
300
BRCACESC
ESOGBM
HNSCKIRPLIHC
LUSCPHPGPRADSKCMTHCA
LGGPACOV
LUADSTADACC
KIRCBLCAUCECCOADREAD
DPY
SL2
(chr
8:26
5107
91)
ALPK
2 (c
hr18
:562
4644
2)CAR
D9
(chr
9:13
9266
396)
FAM129A
(chr
1:18
4764
498)
OR5K4
(chr
3:98
0735
91)
OR11G2
(chr
14:2
0666
175)
GMIP
(chr
19:1
9741
076)
SULT1A2
(chr
16:2
8603
654)
PRAM
EF4
(chr
1:12
9395
46)
PCDHB5
(chr
5:14
0517
173)
SDC3
(chr
1:31
3515
04)
SLC22A9
(chr
11:6
3149
670)
C4orf43
(chr
4:16
4435
264)
ACVR
2A (c
hr2:
1486
8368
5)KIAA
2018
(chr
3:11
3377
481)
OR1B1
(chr
9:12
5391
770)
ASTE
1 (c
hr3:
1307
3304
6)TG
FBR2
(chr
3:30
6918
71)
OR6C
68 (c
hr12
:558
8648
8)OR13G1
(chr
1:24
7836
000)
MET
TL17
(chr
14:2
1464
874)
NEK
3 (c
hr13
:527
1805
0)LTN1
(chr
21:3
0339
205)
SEC31A
(chr
4:83
7855
64)
AIM2
(chr
1:15
9032
486)
NDUFC
2 (c
hr11
:777
8414
6)MEG
F10
(chr
5:12
6769
145)
C18orf34
(chr
18:3
0913
142)
ABT1
(chr
6:26
5981
87)
OR7E24
(chr
19:9
3617
40)
ATE1
(chr
10:1
2359
6252
)NIPA2
(chr
15:2
3021
238)
RPL22
(chr
1:62
5778
4)OR1J2
(chr
9:12
5273
385)
CCDC150
(chr
2:19
7531
518)
RNF43
(chr
17:5
6435
160)
MLL3
(chr
7:15
1874
147)
SLC35G5
(chr
8:11
1887
57)
RNAS
E8 (c
hr14
:215
2608
1)MSH
3 (c
hr5:
7997
0914
)MIS18BP
1 (c
hr14
:457
1601
8)SLC35F5
(chr
2:11
4500
276)
PTCHD3
(chr
10:2
7702
256)
CAS
P5 (c
hr11
:104
8780
40)
SRPR
(chr
11:1
2613
7086
)PH
ACTR
4 (c
hr1:
2878
5729
)CNTN
5 (c
hr11
:100
2268
81)
CAS
P5 (c
hr11
:104
8796
86)
LMAN
1 (c
hr18
:570
1319
3)OR5K3
(chr
3:98
1104
06)
LRRIQ1
(chr
12:8
5638
645)
Sample count
0 25 50 75 100
0 5 1 0 1 5
Sample percentageb
a
BRCACESC
ESOGBM
HNSCKIRPLIHC
LUSCPHPGPRADSKCMTHCA
LGGPACOV
LUADSTADACC
KIRCBLCAUCECCOADREAD
DPY
SL2
(chr
8:26
5107
91)
ALPK
2 (c
hr18
:562
4644
2)CAR
D9
(chr
9:13
9266
396)
OR5K4
(chr
3:98
0735
91)
OR11G2
(chr
14:2
0666
175)
PRAM
EF4
(chr
1:12
9395
46)
FAM
129A
(chr
1:18
4764
498)
SDC3
(chr
1:31
3515
04)
KIAA
2018
(chr
3:11
3377
481)
SLC22A9
(chr
11:6
3149
670)
ACVR
2A (c
hr2:
1486
8368
5)SU
LT1A2
(chr
16:2
8603
654)
ASTE
1 (c
hr3:
1307
3304
6)AB
T1 (c
hr6:
2659
8187
)PC
DHB5
(chr
5:14
0517
173)
TGFB
R2
(chr
3:30
6918
71)
OR1B1
(chr
9:12
5391
770)
SEC31A
(chr
4:83
7855
64)
OR7E24
(chr
19:9
3617
40)
OR13G1
(chr
1:24
7836
000)
LTN1
(chr
21:3
0339
205)
NDUFC
2 (c
hr11
:777
8414
6)AIM2
(chr
1:15
9032
486)
C18orf34
(chr
18:3
0913
142)
C4orf43
(chr
4:16
4435
264)
GMIP
(chr
19:1
9741
076)
CCDC150
(chr
2:19
7531
518)
PTCHD3
(chr
10:2
7702
256)
RPL22
(chr
1:62
5778
4)RNF43
(chr
17:5
6435
160)
OR6C
68 (c
hr12
:558
8648
8)MEG
F10
(chr
5:12
6769
145)
MSH
3 (c
hr5:
7997
0914
)SR
PR (c
hr11
:126
1370
86)
MLL3
(chr
7:15
1874
147)
SLC22A24
(chr
11:6
2863
517)
SLC35F5
(chr
2:11
4500
276)
PHAC
TR4
(chr
1:28
7857
29)
MIS18BP
1 (c
hr14
:457
1601
8)ATE1
(chr
10:1
2359
6252
)LM
AN1
(chr
18:5
7013
193)
CAS
P5 (c
hr11
:104
8780
40)
SLC35G5
(chr
8:11
1887
57)
RBM
27 (c
hr5:
1456
4731
9)OR1J2
(chr
9:12
5273
385)
CAS
P5 (c
hr11
:104
8796
86)
CNTN
5 (c
hr11
:100
2268
81)
SMAP
1 (c
hr6:
7150
8369
)NIPA2
(chr
15:2
3021
238)
OSB
PL5
(chr
11:3
1417
42)
SLAM
F1 (c
hr1:
1605
8960
0)TM
EM22
(chr
3:13
6573
485)
CLO
CK
(chr
4:56
3369
53)
NEK
3 (c
hr13
:527
1805
0)LG
ALS8
(chr
1:23
6702
201)
OR52N5
(chr
11:5
7996
51)
XPOT
(chr
12:6
4812
754)
OR5K3
(chr
3:98
1104
06)
LRRIQ1
(chr
12:8
5638
645)
MNS1
(chr
15:5
6736
722)
AASD
H (c
hr4:
5722
0268
)UBR
5 (c
hr8:
1032
8934
8)UPF
3A (c
hr13
:115
0572
10)
TMEM
60 (c
hr7:
7742
3459
)TE
AD2
(chr
19:4
9850
472)
RNAS
E8 (c
hr14
:215
2608
1)MET
TL17
(chr
14:2
1464
874)
C4orf6
(chr
4:55
2711
5)SE
C63
(chr
6:10
8214
754)
PSMD9
(chr
12:1
2235
3789
)C15orf40
(chr
15:8
3677
270)
DOCK3
(chr
3:51
4176
03)
PRDM2
(chr
1:14
1087
48)
CCDC168
(chr
13:1
0338
1995
)CELA3B
(chr
1:22
3107
24)
FAM111B
(chr
11:5
8892
376)
BAX
(chr
19:4
9458
970)
SPINK5
(chr
5:14
7499
874)
TMIGD2
(chr
19:4
2928
40)
PCDHGA10
(chr
5:14
0795
208)
KIAA
1919
(chr
6:11
1587
360)
GBP
3 (c
hr1:
8947
3441
)KC
NMA1
(chr
10:7
8729
785)
FGFB
P1 (c
hr4:
1593
8177
)JPH4
(chr
14:2
4040
435)
COBLL1
(chr
2:16
5551
295)
FLRT1
(chr
11:6
3885
305)
ESRP1
(chr
8:95
6866
10)
EIF2B3
(chr
1:45
4071
81)
MIS18BP
1 (c
hr14
:456
9372
1)TR
IM59
(chr
3:16
0156
367)
SMC6
(chr
2:17
8981
25)
LRRIQ3
(chr
1:74
5752
12)
GRK4
(chr
4:30
1546
9)SLC16A4
(chr
1:11
0906
426)
MYO
1A (c
hr12
:574
2257
2)PD
S5B
(chr
13:3
3344
887)
0
2000
4000
6000
0 200 400 600MSI events WXS (coding, 3'UTR and 5'UTR)
MSI
eve
nts
WG
S (c
odin
g, 3
'UTR
and
5'U
TR)
0
1000
2000
3000
4000
0 100 200 300MSI events WXS (3'UTR)
MSI
eve
nts
WG
S (3
'UTR
)
0
100
200
0 20 40 60MSI events WXS (5'UTR)
MSI
eve
nts
WG
S (5
'UTR
)
0
500
1000
0 100 200 300MSI events WXS (coding)
MSI
eve
nts
WG
S (c
odin
g)
a b
c d
0
25
50
75
100
0 25 50 75 100
% of reads subsampled from tumor (82X)
% re
ads
subs
ampl
ed fr
om m
atch
ed n
orm
al (4
8X)
0 1 2 3 4 5log10 # MSI events
0
25
50
75
100
0 25 50 75 100
% of reads subsampled from tumor (82X)
% re
ads
subs
ampl
ed fr
om m
atch
ed n
orm
al (4
8X)
25 50 75 100Percentage of MSI events recovered
a
b
50
75
100
125
40 60 80 100Coverage matched normal
Cov
erag
e tu
mor
BRCACOADGBMHNSCKICHKIRCKIRPLIHCLUADLUSCOVREADSKCMSTADTHCAUCEC
MSI events0e+00
1e+05
2e+05
3e+05
4e+05
0.4
0.6
0.8
1.0
0 2 4log10 # MSI events
Tum
or p
urity
(CPE
, Ara
n et
al.,
201
6 N
at. C
omm
un.)
BRCA
COAD
GBM
HNSC
KICH
KIRC
KIRP
LIHC
LUAD
LUSC
OV
READ
SKCM
THCA
UCEC
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−0.25
0.00
0.25
0.50
0.75
100Kb 1MB 10MB
Pear
son'
s co
r. co
eff.
SNV
vs M
SI e
vent
s
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se2_
Prom
U1_
TssA
12_T
xEnh
W3_
Prom
D115
_Enh
AF18
_Enh
Ac6_
Tx22
_Pro
mP
10_T
xEnh
5'14
_Enh
A223
_Pro
mBi
v16
_Enh
W1
9_Tx
Reg
4_Pr
omD2
13_E
nhA1
20_Z
NF/R
pts
11_T
xEnh
3'
MSI
freq
uenc
y (%
)
TCGA−06−0152 (GBM)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C19
_DNa
se18
_Enh
Ac17
_Enh
W2
15_E
nhAF
21_H
et12
_TxE
nhW
6_Tx
22_P
rom
P14
_Enh
A22_
Prom
U4_
Prom
D216
_Enh
W1
3_Pr
omD1
1_Ts
sA23
_Pro
mBi
v10
_TxE
nh5'
20_Z
NF/R
pts
9_Tx
Reg
11_T
xEnh
3'13
_Enh
A1
MSI
freq
uenc
y (%
)
TCGA−09−2050 (OV)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C18
_Enh
Ac19
_DNa
se17
_Enh
W2
22_P
rom
P12
_TxE
nhW
15_E
nhAF
21_H
et6_
Tx2_
Prom
U1_
TssA
4_Pr
omD2
10_T
xEnh
5'3_
Prom
D114
_Enh
A223
_Pro
mBi
v16
_Enh
W1
20_Z
NF/R
pts
9_Tx
Reg
13_E
nhA1
11_T
xEnh
3'
MSI
freq
uenc
y (%
)
TCGA−13−1491 (OV)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et15
_Enh
AF12
_TxE
nhW
18_E
nhAc
2_Pr
omU
10_T
xEnh
5'14
_Enh
A26_
Tx16
_Enh
W1
3_Pr
omD1
9_Tx
Reg
13_E
nhA1
4_Pr
omD2
22_P
rom
P23
_Pro
mBi
v11
_TxE
nh3'
1_Ts
sA20
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−14−1034 (GBM)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C19
_DNa
se18
_Enh
Ac17
_Enh
W2
21_H
et12
_TxE
nhW
15_E
nhAF
6_Tx
22_P
rom
P10
_TxE
nh5'
14_E
nhA2
2_Pr
omU
1_Ts
sA16
_Enh
W1
23_P
rom
Biv
3_Pr
omD1
4_Pr
omD2
11_T
xEnh
3'9_
TxRe
g13
_Enh
A120
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−24−1557 (OV)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C18
_Enh
Ac19
_DNa
se17
_Enh
W2
6_Tx
12_T
xEnh
W15
_Enh
AF21
_Het
22_P
rom
P23
_Pro
mBi
v2_
Prom
U3_
Prom
D116
_Enh
W1
1_Ts
sA10
_TxE
nh5'
4_Pr
omD2
20_Z
NF/R
pts
14_E
nhA2
11_T
xEnh
3'13
_Enh
A19_
TxRe
g
MSI
freq
uenc
y (%
)
TCGA−24−1614 (OV)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C19
_DNa
se17
_Enh
W2
18_E
nhAc
21_H
et15
_Enh
AF13
_Enh
A122
_Pro
mP
14_E
nhA2
6_Tx
16_E
nhW
110
_TxE
nh5'
9_Tx
Reg
4_Pr
omD2
23_P
rom
Biv
12_T
xEnh
W2_
Prom
U3_
Prom
D111
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−34−2600 (LUSC)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C21
_Het
17_E
nhW
219
_DNa
se18
_Enh
Ac15
_Enh
AF6_
Tx12
_TxE
nhW
2_Pr
omU
14_E
nhA2
13_E
nhA1
3_Pr
omD1
10_T
xEnh
5'9_
TxRe
g22
_Pro
mP
23_P
rom
Biv
16_E
nhW
11_
TssA
4_Pr
omD2
11_T
xEnh
3'20
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−37−4135 (LUSC)
●
●
●●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx19
_DNa
se12
_TxE
nhW
13_E
nhA1
17_E
nhW
29_
TxRe
g15
_Enh
AF14
_Enh
A210
_TxE
nh5'
2_Pr
omU
4_Pr
omD2
22_P
rom
P21
_Het
3_Pr
omD1
16_E
nhW
111
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−A5−A0G9 (UCEC)
●
●
●●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
6_Tx
24_R
eprP
C19
_DNa
se12
_TxE
nhW
13_E
nhA1
10_T
xEnh
5'14
_Enh
A29_
TxRe
g17
_Enh
W2
15_E
nhAF
22_P
rom
P21
_Het
4_Pr
omD2
3_Pr
omD1
2_Pr
omU
16_E
nhW
111
_TxE
nh3'
1_Ts
sA20
_ZNF
/Rpt
s23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−A5−A0GA (UCEC)
●
●
● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
6025
_Qui
es8_
TxW
k5_
Tx5'
7_Tx
3'12
_TxE
nhW
24_R
eprP
C6_
Tx17
_Enh
W2
21_H
et19
_DNa
se10
_TxE
nh5'
15_E
nhAF
18_E
nhAc
14_E
nhA2
4_Pr
omD2
22_P
rom
P9_
TxRe
g2_
Prom
U20
_ZNF
/Rpt
s16
_Enh
W1
3_Pr
omD1
11_T
xEnh
3'13
_Enh
A123
_Pro
mBi
v1_
TssA
MSI
freq
uenc
y (%
)TCGA−A6−6781 (COAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C12
_TxE
nhW
17_E
nhW
26_
Tx19
_DNa
se21
_Het
10_T
xEnh
5'15
_Enh
AF18
_Enh
Ac14
_Enh
A24_
Prom
D222
_Pro
mP
9_Tx
Reg
2_Pr
omU
16_E
nhW
13_
Prom
D120
_ZNF
/Rpt
s13
_Enh
A111
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−AA−3518 (COAD)
a b c
d e f
g h i
j k l
●
●
●●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C12
_TxE
nhW
6_Tx
17_E
nhW
221
_Het
10_T
xEnh
5'15
_Enh
AF4_
Prom
D218
_Enh
Ac19
_DNa
se2_
Prom
U9_
TxRe
g22
_Pro
mP
14_E
nhA2
3_Pr
omD1
20_Z
NF/R
pts
16_E
nhW
111
_TxE
nh3'
13_E
nhA1
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−AA−A00R (COAD)
●
●
● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
12_T
xEnh
W17
_Enh
W2
24_R
eprP
C6_
Tx21
_Het
19_D
Nase
15_E
nhAF
10_T
xEnh
5'18
_Enh
Ac14
_Enh
A222
_Pro
mP
4_Pr
omD2
9_Tx
Reg
2_Pr
omU
16_E
nhW
120
_ZNF
/Rpt
s3_
Prom
D111
_TxE
nh3'
13_E
nhA1
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−AA−A01R (COAD)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et6_
Tx15
_Enh
AF18
_Enh
Ac12
_TxE
nhW
14_E
nhA2
10_T
xEnh
5'13
_Enh
A14_
Prom
D216
_Enh
W1
2_Pr
omU
22_P
rom
P9_
TxRe
g3_
Prom
D123
_Pro
mBi
v20
_ZNF
/Rpt
s1_
TssA
11_T
xEnh
3'
MSI
freq
uenc
y (%
)
TCGA−AC−A2BK (BRCA)
●
●
● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
12_T
xEnh
W6_
Tx17
_Enh
W2
24_R
eprP
C21
_Het
19_D
Nase
10_T
xEnh
5'15
_Enh
AF18
_Enh
Ac14
_Enh
A24_
Prom
D222
_Pro
mP
9_Tx
Reg
2_Pr
omU
20_Z
NF/R
pts
16_E
nhW
13_
Prom
D111
_TxE
nh3'
13_E
nhA1
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−AD−6964 (COAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
12_T
xEnh
W24
_Rep
rPC
6_Tx
17_E
nhW
221
_Het
19_D
Nase
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'4_
Prom
D222
_Pro
mP
14_E
nhA2
2_Pr
omU
9_Tx
Reg
16_E
nhW
120
_ZNF
/Rpt
s3_
Prom
D113
_Enh
A111
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−AD−A5EJ (COAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se6_
Tx15
_Enh
AF12
_TxE
nhW
18_E
nhAc
10_T
xEnh
5'2_
Prom
U14
_Enh
A216
_Enh
W1
9_Tx
Reg
4_Pr
omD2
20_Z
NF/R
pts
13_E
nhA1
3_Pr
omD1
1_Ts
sA23
_Pro
mBi
v22
_Pro
mP
11_T
xEnh
3'
MSI
freq
uenc
y (%
)
TCGA−AO−A124 (BRCA)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx13
_Enh
A112
_TxE
nhW
19_D
Nase
15_E
nhAF
17_E
nhW
29_
TxRe
g10
_TxE
nh5'
14_E
nhA2
2_Pr
omU
4_Pr
omD2
22_P
rom
P3_
Prom
D121
_Het
16_E
nhW
111
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA20
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−AP−A051 (UCEC)
●
●
●●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx19
_DNa
se13
_Enh
A112
_TxE
nhW
17_E
nhW
29_
TxRe
g15
_Enh
AF14
_Enh
A210
_TxE
nh5'
21_H
et2_
Prom
U22
_Pro
mP
4_Pr
omD2
3_Pr
omD1
16_E
nhW
120
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−AP−A054 (UCEC)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C18
_Enh
Ac19
_DNa
se21
_Het
13_E
nhA1
6_Tx
17_E
nhW
23_
Prom
D12_
Prom
U9_
TxRe
g15
_Enh
AF10
_TxE
nh5'
14_E
nhA2
12_T
xEnh
W22
_Pro
mP
1_Ts
sA23
_Pro
mBi
v16
_Enh
W1
4_Pr
omD2
20_Z
NF/R
pts
11_T
xEnh
3'
MSI
freq
uenc
y (%
)
TCGA−AP−A0L8 (UCEC)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C18
_Enh
Ac19
_DNa
se13
_Enh
A117
_Enh
W2
6_Tx
15_E
nhAF
14_E
nhA2
12_T
xEnh
W22
_Pro
mP
9_Tx
Reg
21_H
et10
_TxE
nh5'
2_Pr
omU
4_Pr
omD2
16_E
nhW
13_
Prom
D111
_TxE
nh3'
1_Ts
sA23
_Pro
mBi
v20
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−AP−A0L9 (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
6025
_Qui
es8_
TxW
k5_
Tx5'
7_Tx
3'18
_Enh
Ac24
_Rep
rPC
6_Tx
19_D
Nase
13_E
nhA1
12_T
xEnh
W17
_Enh
W2
15_E
nhAF
9_Tx
Reg
14_E
nhA2
10_T
xEnh
5'21
_Het
22_P
rom
P2_
Prom
U4_
Prom
D23_
Prom
D116
_Enh
W1
11_T
xEnh
3'20
_ZNF
/Rpt
s1_
TssA
23_P
rom
Biv
MSI
freq
uenc
y (%
)TCGA−AP−A0LD (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx19
_DNa
se13
_Enh
A112
_TxE
nhW
17_E
nhW
29_
TxRe
g15
_Enh
AF10
_TxE
nh5'
14_E
nhA2
21_H
et22
_Pro
mP
2_Pr
omU
4_Pr
omD2
3_Pr
omD1
16_E
nhW
111
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−AP−A0LE (UCEC)
a b c
d e f
g h i
j k l
●
●
●●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C18
_Enh
Ac6_
Tx12
_TxE
nhW
13_E
nhA1
9_Tx
Reg
19_D
Nase
17_E
nhW
210
_TxE
nh5'
2_Pr
omU
15_E
nhAF
3_Pr
omD1
4_Pr
omD2
22_P
rom
P21
_Het
14_E
nhA2
16_E
nhW
11_
TssA
20_Z
NF/R
pts
11_T
xEnh
3'23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−AX−A05S (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx19
_DNa
se12
_TxE
nhW
13_E
nhA1
9_Tx
Reg
17_E
nhW
215
_Enh
AF10
_TxE
nh5'
14_E
nhA2
21_H
et22
_Pro
mP
2_Pr
omU
4_Pr
omD2
3_Pr
omD1
16_E
nhW
120
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−AX−A0J1 (UCEC)
●
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C19
_DNa
se6_
Tx12
_TxE
nhW
13_E
nhA1
17_E
nhW
221
_Het
9_Tx
Reg
10_T
xEnh
5'14
_Enh
A215
_Enh
AF22
_Pro
mP
4_Pr
omD2
2_Pr
omU
3_Pr
omD1
16_E
nhW
120
_ZNF
/Rpt
s11
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−B5−A11G (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx19
_DNa
se13
_Enh
A112
_TxE
nhW
17_E
nhW
215
_Enh
AF14
_Enh
A210
_TxE
nh5'
9_Tx
Reg
21_H
et22
_Pro
mP
2_Pr
omU
4_Pr
omD2
3_Pr
omD1
16_E
nhW
120
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−B5−A11H (UCEC)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C17
_Enh
W2
19_D
Nase
6_Tx
21_H
et15
_Enh
AF18
_Enh
Ac12
_TxE
nhW
4_Pr
omD2
10_T
xEnh
5'14
_Enh
A216
_Enh
W1
13_E
nhA1
9_Tx
Reg
2_Pr
omU
22_P
rom
P23
_Pro
mBi
v3_
Prom
D120
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−B6−A0I6 (BRCA)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
6_Tx
12_T
xEnh
W19
_DNa
se21
_Het
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'2_
Prom
U14
_Enh
A23_
Prom
D14_
Prom
D29_
TxRe
g22
_Pro
mP
16_E
nhW
113
_Enh
A111
_TxE
nh3'
23_P
rom
Biv
20_Z
NF/R
pts
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−BR−4280 (STAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
6_Tx
12_T
xEnh
W19
_DNa
se21
_Het
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'2_
Prom
U14
_Enh
A222
_Pro
mP
3_Pr
omD1
4_Pr
omD2
16_E
nhW
19_
TxRe
g13
_Enh
A120
_ZNF
/Rpt
s11
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−BR−6452 (STAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C6_
Tx13
_Enh
A119
_DNa
se12
_TxE
nhW
17_E
nhW
210
_TxE
nh5'
9_Tx
Reg
15_E
nhAF
21_H
et14
_Enh
A22_
Prom
U3_
Prom
D14_
Prom
D222
_Pro
mP
16_E
nhW
120
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−BS−A0TE (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
6_Tx
12_T
xEnh
W19
_DNa
se21
_Het
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'2_
Prom
U14
_Enh
A23_
Prom
D122
_Pro
mP
4_Pr
omD2
16_E
nhW
19_
TxRe
g13
_Enh
A120
_ZNF
/Rpt
s11
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−CG−4442 (STAD)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
6_Tx
12_T
xEnh
W21
_Het
15_E
nhAF
19_D
Nase
18_E
nhAc
10_T
xEnh
5'2_
Prom
U9_
TxRe
g14
_Enh
A213
_Enh
A116
_Enh
W1
11_T
xEnh
3'3_
Prom
D120
_ZNF
/Rpt
s22
_Pro
mP
4_Pr
omD2
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−CG−5723 (STAD)
●
●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
8025
_Qui
es8_
TxW
k5_
Tx5'
7_Tx
3'24
_Rep
rPC
19_D
Nase
17_E
nhW
221
_Het
6_Tx
15_E
nhAF
18_E
nhAc
12_T
xEnh
W14
_Enh
A210
_TxE
nh5'
2_Pr
omU
4_Pr
omD2
16_E
nhW
13_
Prom
D113
_Enh
A19_
TxRe
g22
_Pro
mP
11_T
xEnh
3'23
_Pro
mBi
v20
_ZNF
/Rpt
s1_
TssA
MSI
freq
uenc
y (%
)TCGA−CN−6011 (HNSC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
24_R
eprP
C12
_TxE
nhW
17_E
nhW
26_
Tx21
_Het
19_D
Nase
15_E
nhAF
18_E
nhAc
10_T
xEnh
5'14
_Enh
A24_
Prom
D222
_Pro
mP
2_Pr
omU
9_Tx
Reg
16_E
nhW
120
_ZNF
/Rpt
s3_
Prom
D111
_TxE
nh3'
13_E
nhA1
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−D5−6540 (COAD)
a b c
d e f
g h i
j k l
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
19_D
Nase
24_R
eprP
C17
_Enh
W2
21_H
et6_
Tx15
_Enh
AF18
_Enh
Ac12
_TxE
nhW
14_E
nhA2
10_T
xEnh
5'13
_Enh
A116
_Enh
W1
2_Pr
omU
22_P
rom
P4_
Prom
D23_
Prom
D111
_TxE
nh3'
9_Tx
Reg
20_Z
NF/R
pts
1_Ts
sA23
_Pro
mBi
v
MSI
freq
uenc
y (%
)
TCGA−EW−A1PC (BRCA)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
25
50
75
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
18_E
nhAc
24_R
eprP
C19
_DNa
se21
_Het
6_Tx
2_Pr
omU
22_P
rom
P13
_Enh
A110
_TxE
nh5'
12_T
xEnh
W15
_Enh
AF17
_Enh
W2
9_Tx
Reg
4_Pr
omD2
14_E
nhA2
16_E
nhW
123
_Pro
mBi
v3_
Prom
D111
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−EY−A1GS (UCEC)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
6_Tx
12_T
xEnh
W21
_Het
19_D
Nase
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'2_
Prom
U14
_Enh
A222
_Pro
mP
3_Pr
omD1
4_Pr
omD2
9_Tx
Reg
16_E
nhW
113
_Enh
A111
_TxE
nh3'
20_Z
NF/R
pts
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−F1−6177 (STAD)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se6_
Tx12
_TxE
nhW
18_E
nhAc
15_E
nhAF
2_Pr
omU
10_T
xEnh
5'3_
Prom
D114
_Enh
A216
_Enh
W1
23_P
rom
Biv
22_P
rom
P13
_Enh
A111
_TxE
nh3'
9_Tx
Reg
1_Ts
sA4_
Prom
D220
_ZNF
/Rpt
s
MSI
freq
uenc
y (%
)
TCGA−F1−6875 (STAD)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et18
_Enh
Ac12
_TxE
nhW
6_Tx
15_E
nhAF
4_Pr
omD2
16_E
nhW
12_
Prom
U14
_Enh
A222
_Pro
mP
3_Pr
omD1
23_P
rom
Biv
10_T
xEnh
5'11
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA9_
TxRe
g13
_Enh
A1
MSI
freq
uenc
y (%
)
TCGA−IA−A40Y (KIRP)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et18
_Enh
Ac6_
Tx12
_TxE
nhW
15_E
nhAF
16_E
nhW
14_
Prom
D222
_Pro
mP
2_Pr
omU
14_E
nhA2
10_T
xEnh
5'23
_Pro
mBi
v3_
Prom
D120
_ZNF
/Rpt
s11
_TxE
nh3'
13_E
nhA1
9_Tx
Reg
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−KL−8330 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
17_E
nhW
224
_Rep
rPC
19_D
Nase
21_H
et18
_Enh
Ac6_
Tx12
_TxE
nhW
15_E
nhAF
4_Pr
omD2
14_E
nhA2
16_E
nhW
13_
Prom
D122
_Pro
mP
23_P
rom
Biv
2_Pr
omU
11_T
xEnh
3'10
_TxE
nh5'
20_Z
NF/R
pts
9_Tx
Reg
13_E
nhA1
1_Ts
sA
MSI
freq
uenc
y (%
)TCGA−KL−8337 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
21_H
et18
_Enh
Ac19
_DNa
se12
_TxE
nhW
6_Tx
15_E
nhAF
16_E
nhW
14_
Prom
D220
_ZNF
/Rpt
s22
_Pro
mP
14_E
nhA2
2_Pr
omU
23_P
rom
Biv
9_Tx
Reg
10_T
xEnh
5'11
_TxE
nh3'
3_Pr
omD1
13_E
nhA1
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−KL−8341 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se18
_Enh
Ac6_
Tx12
_TxE
nhW
16_E
nhW
115
_Enh
AF14
_Enh
A222
_Pro
mP
2_Pr
omU
4_Pr
omD2
23_P
rom
Biv
10_T
xEnh
5'20
_ZNF
/Rpt
s3_
Prom
D111
_TxE
nh3'
9_Tx
Reg
13_E
nhA1
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−KL−8346 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et18
_Enh
Ac6_
Tx12
_TxE
nhW
16_E
nhW
115
_Enh
AF2_
Prom
U22
_Pro
mP
3_Pr
omD1
4_Pr
omD2
10_T
xEnh
5'14
_Enh
A223
_Pro
mBi
v9_
TxRe
g20
_ZNF
/Rpt
s11
_TxE
nh3'
1_Ts
sA13
_Enh
A1
MSI
freq
uenc
y (%
)
TCGA−KM−8440 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se6_
Tx18
_Enh
Ac12
_TxE
nhW
15_E
nhAF
16_E
nhW
14_
Prom
D214
_Enh
A210
_TxE
nh5'
22_P
rom
P2_
Prom
U23
_Pro
mBi
v11
_TxE
nh3'
20_Z
NF/R
pts
1_Ts
sA13
_Enh
A13_
Prom
D19_
TxRe
g
MSI
freq
uenc
y (%
)
TCGA−KM−8442 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
80
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
19_D
Nase
21_H
et18
_Enh
Ac12
_TxE
nhW
15_E
nhAF
6_Tx
16_E
nhW
12_
Prom
U4_
Prom
D210
_TxE
nh5'
14_E
nhA2
22_P
rom
P3_
Prom
D123
_Pro
mBi
v1_
TssA
11_T
xEnh
3'13
_Enh
A120
_ZNF
/Rpt
s9_
TxRe
g
MSI
freq
uenc
y (%
)
TCGA−KM−8443 (KICH)
●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20406080
25_Q
uies
8_Tx
Wk
7_Tx
3'5_
Tx5'
24_R
eprP
C17
_Enh
W2
21_H
et19
_DNa
se12
_TxE
nhW
18_E
nhAc
6_Tx
15_E
nhAF
16_E
nhW
12_
Prom
U14
_Enh
A222
_Pro
mP
23_P
rom
Biv
4_Pr
omD2
20_Z
NF/R
pts
3_Pr
omD1
10_T
xEnh
5'11
_TxE
nh3'
9_Tx
Reg
13_E
nhA1
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−KO−8409 (KICH)
●
●
● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●0
20
40
60
25_Q
uies
8_Tx
Wk
5_Tx
5'7_
Tx3'
12_T
xEnh
W6_
Tx17
_Enh
W2
24_R
eprP
C21
_Het
19_D
Nase
18_E
nhAc
15_E
nhAF
10_T
xEnh
5'14
_Enh
A24_
Prom
D222
_Pro
mP
2_Pr
omU
9_Tx
Reg
16_E
nhW
120
_ZNF
/Rpt
s3_
Prom
D113
_Enh
A111
_TxE
nh3'
23_P
rom
Biv
1_Ts
sA
MSI
freq
uenc
y (%
)
TCGA−QG−A5Z2 (COAD)
a b c
d e f
g h i
j k l
m n
25_Quies
24_ReprPC
23_PromBiv
22_PromP
21_Het
20_ZNF/Rpts
19_DNase
18_EnhAc
17_EnhW2
16_EnhW1
15_EnhAF
14_EnhA2
13_EnhA1
12_TxEnhW
11_TxEnh3'
10_TxEnh5'
9_TxReg
8_TxWk
7_Tx3'
6_Tx
5_Tx5'
4_PromD2
3_PromD1
2_PromU
1_TssA
1
2
Odds ratio
25_Quies
24_ReprPC
23_PromBiv
22_PromP
21_Het
20_ZNF/Rpts
19_DNase
18_EnhAc
17_EnhW2
16_EnhW1
15_EnhAF
14_EnhA2
13_EnhA1
12_TxEnhW
11_TxEnh3'
10_TxEnh5'
9_TxReg
8_TxWk
7_Tx3'
6_Tx
5_Tx5'
4_PromD2
3_PromD1
2_PromU
1_TssA
TCG
A−06−0
152
(GBM
) unk
nown
TCG
A−09−2
050
(OV)
unk
nown
TCG
A−13−1
491
(OV)
unk
nown
TCG
A−14−1
034
(GBM
) unk
nown
TCG
A−24−1
557
(OV)
unk
nown
TCG
A−24−1
614
(OV)
unk
nown
TCG
A−34−2
600
(LUS
C) u
nkno
wnTC
GA−
37−4
135
(LUS
C) u
nkno
wnTC
GA−
A5−A
0G9
(UCE
C) M
SI−H
TCG
A−A5−A
0GA
(UCE
C) M
SI−H
TCG
A−A6−6
781
(CO
AD) u
nkno
wnTC
GA−
AA−3
518
(CO
AD) M
SI−H
TCG
A−AA
−A00
R (C
OAD
) MSI−H
TCG
A−AA
−A01
R (C
OAD
) MSI−H
TCG
A−AC
−A2B
K (B
RCA)
unk
nown
TCG
A−AD
−696
4 (C
OAD
) unk
nown
TCG
A−AD
−A5E
J (C
OAD
) unk
nown
TCG
A−AO
−A12
4 (B
RCA)
unk
nown
TCG
A−AP
−A05
1 (U
CEC)
MSI−H
TCG
A−AP
−A05
4 (U
CEC)
MSI−H
TCG
A−AP
−A0L
8 (U
CEC)
MSS
TCG
A−AP
−A0L
9 (U
CEC)
MSS
TCG
A−AP
−A0L
D (U
CEC)
MSI−H
TCG
A−AP
−A0L
E (U
CEC)
MSI−H
TCG
A−AX
−A05
S (U
CEC)
MSI−H
TCG
A−AX
−A0J
1 (U
CEC)
MSI−H
TCG
A−B5−A
11G
(UCE
C) M
SI−H
TCG
A−B5−A
11H
(UCE
C) M
SI−H
TCG
A−B6−A
0I6
(BRC
A) u
nkno
wnTC
GA−
BR−4
280
(STA
D) M
SI−H
TCG
A−BR
−645
2 (S
TAD)
MSI−H
TCG
A−BS
−A0T
E (U
CEC)
MSI−H
TCG
A−CG
−444
2 (S
TAD)
MSI−H
TCG
A−CG
−572
3 (S
TAD)
MSI−H
TCG
A−CN
−601
1 (H
NSC)
unk
nown
TCG
A−D5
−654
0 (C
OAD
) unk
nown
TCG
A−EW
−A1P
C (B
RCA)
unk
nown
TCG
A−EY
−A1G
S (U
CEC)
MSS
TCG
A−F1−6
177
(STA
D) M
SI−H
TCG
A−F1−6
875
(STA
D) M
SSTC
GA−
IA−A
40Y
(KIR
P) u
nkno
wnTC
GA−
KL−8
330
(KIC
H) u
nkno
wnTC
GA−
KL−8
337
(KIC
H) u
nkno
wnTC
GA−
KL−8
341
(KIC
H) u
nkno
wnTC
GA−
KL−8
346
(KIC
H) u
nkno
wnTC
GA−
KM−8
440
(KIC
H) u
nkno
wnTC
GA−
KM−8
442
(KIC
H) u
nkno
wnTC
GA−
KM−8
443
(KIC
H) u
nkno
wnTC
GA−
KO−8
409
(KIC
H) u
nkno
wnTC
GA−
QG−A
5Z2
(CO
AD) u
nkno
wn
P value(Fisher's test)
Non Significant
Significant
a
b
0
5
10
15
20
25
30
Rel
ativ
e fr
eque
ncy
(%)
MSI-H MSI-H (P) MSI-L/MSS
AC
N>A
C
CN
>A
GC
N>A
TC
N>A
AC
N>G
C
CN
>G
GC
N>G
TC
N>G
AC
N>T
C
CN
>T
GC
N>T
TC
N>T
ATN
>A
CTN
>A
GTN
>A
TTN
>A
ATN
>C
CTN
>C
GTN
>C
TTN
>C
ATN
>G
CTN
>G
GTN
>G
TTN
>G