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1.5x109
5x108
1x109
2x108
1x109
2x108
2x109
1.0x109
6x108
6x108
TP53
M WT
M WT
M (n=7)
P=0.08
P=0.06
Supplementary Figure 1
Total AlteraCons Gain Loss
FGFR3
M WT
M WT
M (n=7)
WT (n=34)
P=0.07
1.5x109
5x108
1x109
2x108
1x109
2x108
2x109
1.0x109
6x108
6x108
P=0.05
Grade
High Low
High Low
High (n=13)h
Low (n=11)
P=0.02
1.5x109
5x108
2x108
1x109
2x108
2x109
1.0x109
6x108
6x108
8x108
4x108
P=0.08
Total size of gen
ome altered
Total size of gen
ome gained
To
tal size of gen
ome lost
WT (n=34)
Supplementary Figure 2
LGW01 G600
UM-‐UC-‐14
VM-‐CUB-‐3
UM-‐UC-‐17
VM-‐CUB-‐1
UM-‐UC-‐13
VM-‐CUB-‐2
UM-‐UC-‐11 UM-‐UC-‐18 UM-‐UC-‐12
UM-‐UC-‐6
UM-‐UC-‐7
UM-‐UC-‐9
UM-‐UC-‐1
UM-‐UC-‐5
UM-‐UC-‐3
UM-‐UC-‐4
SW-‐1710
MGH-‐U3
RT4
SW-‐800
HT1376
BC61
MGH-‐U4
T24 SW-‐780 RT112
97-‐1
J82
KU7
TCCSUP
96-‐1 92-‐1
575A HU456 SCaBER 253J
5637 97-‐18
97-‐24
97-‐7
KK47
1 12
11 19 18
17 16
15 14
13 2 4
3 5 10 6
7 8
9 21 22
X 20
Supplementary Figure 3
Male Female Copy Number Loss Copy Number Gain Copy Number Neutral
CNV Frequency
VM-‐CUB-‐3
VM-‐CUB-‐1
UM-‐UC-‐13
VM-‐CUB-‐2
UM-‐UC-‐18
UM-‐UC-‐12
UM-‐UC-‐6 UM-‐UC-‐7
UM-‐UC-‐1
UM-‐UC-‐5
UM-‐UC-‐3 UM-‐UC-‐4
SW-‐1710
MGH-‐U3
RT4
SW-‐800
HT1376 BC61
MGH-‐U4
T24 SW-‐780
RT112
97-‐1
J82
96-‐1 92-‐1
575A
HU456
SCaBER
253J 5637
97-‐18 97-‐24 97-‐7
KK47
639V
UM-‐UC-‐14
A B C
UPD UPD Normal
UPD Normal
DEL
UPD and DUP
AMP
UPD UPD UPD
DEL
D E F
Supplementary Figure 4
A
B
0
5
10
15
20
25
0,00E+00 5,00E+08 1,00E+09 1,50E+09 2,00E+09 2,50E+09
Num
ber o
f UPD
events
Total size CNA (bp)
0
200
400
600
800
1000
1200
0,00E+00 5,00E+08 1,00E+09 1,50E+09 2,00E+09 2,50E+09
Total size UPD
(bp)
Total size CNA (bp)
P=0.09
P=0.08
Supplementary Figure 5
Supplementary Figure 6
BC
Loss Gain Copy Neutral
Supplementary Figure 7
BFTC905 BC3C CAL29 HS172T JMSU1 KMBC2 KU1919 RT11284
1 12
11 19 18
17 16
15 14
13 2 4
3 5 10 6
7 8
9 21 22
X 20
