Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 73 focal events and 13 clinical features across 408 patients, 26 significant findings detected with Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_1q23.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_N_STAGE'.

  • amp_2p25.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_3p25.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • amp_6p22.3 cnv correlated to 'Time to Death'.

  • amp_7p21.1 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'RACE'.

  • amp_11p13 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_3p14.2 cnv correlated to 'PATHOLOGY_N_STAGE' and 'RACE'.

  • del_5q12.1 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_6q21 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_6q27 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_8p23.3 cnv correlated to 'RACE'.

  • del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_12q24.33 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_14q24.1 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_16p13.3 cnv correlated to 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 26 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 3p25 2 190 (47%) 218 0.3
(0.715) 		0.00214
(0.171) 		0.146
(0.56) 		0.0618
(0.434) 		0.00587
(0.223) 		0.757
(0.949) 		0.00469
(0.223) 		0.648
(0.913) 		0.0399
(0.364) 		0.245
(0.671) 		0.00954
(0.279) 		0.0146
(0.317) 		0.514
(0.855)
amp 7p21 1 201 (49%) 207 0.275
(0.695) 		0.0644
(0.434) 		0.00249
(0.171) 		0.13
(0.535) 		0.00297
(0.176) 		1
(1.00) 		0.574
(0.891) 		0.0365
(0.354) 		0.0943
(0.479) 		0.292
(0.712) 		0.0892
(0.479) 		0.00244
(0.171) 		1
(1.00)
del 6q27 190 (47%) 218 0.684
(0.943) 		0.158
(0.576) 		0.00152
(0.171) 		0.244
(0.671) 		0.00038
(0.171) 		0.358
(0.745) 		0.735
(0.949) 		0.363
(0.749) 		0.0375
(0.354) 		0.306
(0.723) 		0.00052
(0.171) 		0.294
(0.712) 		0.312
(0.725)
amp 1q23 3 216 (53%) 192 0.952
(1.00) 		0.00624
(0.228) 		0.0353
(0.354) 		0.576
(0.891) 		0.00255
(0.171) 		0.215
(0.659) 		0.431
(0.811) 		1
(1.00) 		0.0555
(0.418) 		0.354
(0.744) 		0.116
(0.529) 		0.132
(0.537) 		0.743
(0.949)
del 3p14 2 117 (29%) 291 0.719
(0.949) 		0.283
(0.706) 		0.385
(0.773) 		0.293
(0.712) 		0.0014
(0.171) 		0.143
(0.56) 		0.025
(0.352) 		0.803
(0.972) 		0.0828
(0.47) 		0.802
(0.972) 		0.862
(0.998) 		0.0019
(0.171) 		0.126
(0.529)
del 5q12 1 202 (50%) 206 0.0667
(0.443) 		0.00826
(0.27) 		0.0152
(0.317) 		0.159
(0.577) 		0.00166
(0.171) 		0.122
(0.529) 		1
(1.00) 		0.494
(0.847) 		0.285
(0.708) 		0.728
(0.949) 		0.00442
(0.223) 		0.07
(0.443) 		1
(1.00)
del 6q21 190 (47%) 218 0.984
(1.00) 		0.0909
(0.479) 		0.0102
(0.279) 		0.452
(0.841) 		0.00111
(0.171) 		0.116
(0.529) 		0.368
(0.749) 		0.649
(0.913) 		0.0645
(0.434) 		0.585
(0.891) 		0.00139
(0.171) 		0.293
(0.712) 		0.0881
(0.479)
amp 1q21 3 202 (50%) 206 0.458
(0.846) 		0.123
(0.529) 		0.0367
(0.354) 		0.874
(0.999) 		0.00575
(0.223) 		0.127
(0.529) 		0.91
(1.00) 		0.647
(0.913) 		0.0626
(0.434) 		0.495
(0.847) 		0.0163
(0.317) 		0.233
(0.671) 		1
(1.00)
amp 2p25 1 152 (37%) 256 0.555
(0.881) 		0.00525
(0.223) 		0.0528
(0.407) 		0.979
(1.00) 		0.0307
(0.352) 		0.202
(0.64) 		0.0632
(0.434) 		1
(1.00) 		0.973
(1.00) 		0.32
(0.728) 		0.0135
(0.312) 		0.259
(0.671) 		0.728
(0.949)
amp 6p22 3 171 (42%) 237 0.00271
(0.171) 		0.0364
(0.354) 		0.183
(0.603) 		0.237
(0.671) 		0.341
(0.736) 		1
(1.00) 		0.138
(0.55) 		1
(1.00) 		0.0214
(0.322) 		0.853
(0.993) 		0.85
(0.993) 		0.234
(0.671) 		0.17
(0.598)
amp 11p13 51 (12%) 357 0.369
(0.749) 		0.702
(0.943) 		0.0905
(0.479) 		0.707
(0.945) 		0.00214
(0.171) 		1
(1.00) 		0.865
(0.998) 		0.49
(0.847) 		0.254
(0.671) 		0.771
(0.96) 		0.0305
(0.352) 		0.472
(0.847) 		0.339
(0.733)
del 8p23 3 243 (60%) 165 0.701
(0.943) 		0.0281
(0.352) 		0.0464
(0.39) 		0.699
(0.943) 		0.0286
(0.352) 		0.352
(0.744) 		0.567
(0.885) 		0.246
(0.671) 		0.0831
(0.47) 		0.711
(0.948) 		0.254
(0.671) 		0.00575
(0.223) 		1
(1.00)
del 11p15 5 211 (52%) 197 0.463
(0.847) 		0.00242
(0.171) 		0.0752
(0.456) 		0.626
(0.913) 		0.0233
(0.34) 		0.55
(0.877) 		0.911
(1.00) 		0.819
(0.979) 		0.475
(0.847) 		0.806
(0.972) 		0.0498
(0.401) 		0.253
(0.671) 		0.503
(0.847)
del 12q24 33 88 (22%) 320 0.294
(0.712) 		0.306
(0.723) 		0.0801
(0.466) 		0.681
(0.941) 		0.0755
(0.456) 		0.445
(0.833) 		0.494
(0.847) 		0.404
(0.791) 		0.953
(1.00) 		0.884
(1.00) 		0.0056
(0.223) 		0.272
(0.689) 		0.691
(0.943)
del 14q24 1 137 (34%) 271 0.262
(0.677) 		0.0335
(0.354) 		0.326
(0.732) 		0.956
(1.00) 		0.00535
(0.223) 		1
(1.00) 		0.121
(0.529) 		0.0884
(0.479) 		0.0874
(0.479) 		0.0444
(0.386) 		0.0629
(0.434) 		0.618
(0.912) 		1
(1.00)
del 16p13 3 174 (43%) 234 0.745
(0.949) 		0.097
(0.487) 		0.231
(0.671) 		0.0798
(0.466) 		0.014
(0.317) 		1
(1.00) 		0.495
(0.847) 		0.164
(0.589) 		0.191
(0.616) 		0.698
(0.943) 		0.315
(0.725) 		0.00532
(0.223) 		0.738
(0.949)
amp 1p34 2 101 (25%) 307 0.299
(0.715) 		0.0182
(0.317) 		0.184
(0.603) 		0.921
(1.00) 		0.0194
(0.317) 		1
(1.00) 		0.697
(0.943) 		0.793
(0.968) 		0.878
(1) 		0.271
(0.688) 		0.178
(0.603) 		0.0347
(0.354) 		0.695
(0.943)
amp 3q26 33 218 (53%) 190 0.455
(0.845) 		0.179
(0.603) 		0.591
(0.893) 		0.179
(0.603) 		0.185
(0.604) 		0.542
(0.874) 		0.573
(0.891) 		0.492
(0.847) 		0.0369
(0.354) 		0.431
(0.811) 		0.0898
(0.479) 		0.00734
(0.258) 		1
(1.00)
amp 4p16 3 74 (18%) 334 0.0655
(0.438) 		0.518
(0.857) 		0.0316
(0.352) 		0.0343
(0.354) 		0.109
(0.52) 		0.463
(0.847) 		0.884
(1.00) 		0.228
(0.671) 		0.041
(0.37) 		0.868
(0.998) 		0.0749
(0.456) 		0.0585
(0.431) 		0.66
(0.921)
amp 4q13 3 62 (15%) 346 0.108
(0.52) 		0.845
(0.99) 		0.165
(0.589) 		0.126
(0.529) 		0.677
(0.939) 		0.219
(0.666) 		0.0188
(0.317) 		0.751
(0.949) 		0.838
(0.986) 		0.826
(0.979) 		0.868
(0.998) 		0.915
(1.00) 		0.625
(0.913)
amp 5p15 33 206 (50%) 202 0.473
(0.847) 		0.415
(0.799) 		0.872
(0.998) 		0.856
(0.993) 		0.746
(0.949) 		0.0684
(0.443) 		1
(1.00) 		0.369
(0.749) 		0.0792
(0.466) 		0.908
(1.00) 		0.393
(0.782) 		0.0864
(0.479) 		1
(1.00)
amp 6q21 35 (9%) 373 0.0832
(0.47) 		0.495
(0.847) 		0.201
(0.637) 		0.405
(0.791) 		0.637
(0.913) 		1
(1.00) 		0.841
(0.987) 		0.678
(0.939) 		0.52
(0.857) 		0.316
(0.725) 		0.796
(0.97) 		0.494
(0.847) 		0.565
(0.884)
amp 6q23 3 46 (11%) 362 0.756
(0.949) 		0.157
(0.576) 		0.551
(0.877) 		0.949
(1.00) 		0.156
(0.576) 		0.629
(0.913) 		0.594
(0.893) 		1
(1.00) 		0.816
(0.979) 		0.791
(0.968) 		0.839
(0.986) 		0.209
(0.649) 		1
(1.00)
amp 7p11 2 190 (47%) 218 0.866
(0.998) 		0.0477
(0.39) 		0.231
(0.671) 		0.741
(0.949) 		0.0194
(0.317) 		1
(1.00) 		1
(1.00) 		0.167
(0.591) 		0.335
(0.733) 		0.967
(1.00) 		0.182
(0.603) 		0.0283
(0.352) 		0.738
(0.949)
amp 8p11 23 124 (30%) 284 0.751
(0.949) 		0.405
(0.791) 		0.782
(0.965) 		0.557
(0.881) 		0.125
(0.529) 		0.731
(0.949) 		1
(1.00) 		1
(1.00) 		0.256
(0.671) 		0.247
(0.671) 		0.475
(0.847) 		0.356
(0.744) 		0.132
(0.537)
amp 8p11 21 140 (34%) 268 0.0371
(0.354) 		0.52
(0.857) 		0.871
(0.998) 		0.566
(0.885) 		0.29
(0.712) 		0.00866
(0.274) 		0.408
(0.794) 		0.471
(0.847) 		0.357
(0.745) 		0.316
(0.725) 		0.338
(0.733) 		0.329
(0.732) 		0.486
(0.847)
amp 8q22 3 264 (65%) 144 0.697
(0.943) 		0.0687
(0.443) 		0.857
(0.993) 		0.854
(0.993) 		0.398
(0.786) 		1
(1.00) 		0.638
(0.913) 		1
(1.00) 		0.0774
(0.459) 		0.266
(0.682) 		0.308
(0.725) 		0.252
(0.671) 		0.729
(0.949)
amp 8q24 21 254 (62%) 154 0.7
(0.943) 		0.269
(0.686) 		0.885
(1.00) 		0.774
(0.961) 		0.322
(0.73) 		1
(1.00) 		0.563
(0.883) 		1
(1.00) 		0.336
(0.733) 		0.299
(0.715) 		0.33
(0.732) 		0.373
(0.755) 		0.739
(0.949)
amp 9p24 1 88 (22%) 320 0.355
(0.744) 		0.278
(0.697) 		0.871
(0.998) 		0.689
(0.943) 		0.709
(0.946) 		0.425
(0.811) 		0.494
(0.847) 		0.0898
(0.479) 		0.258
(0.671) 		0.172
(0.601) 		0.93
(1.00) 		0.0494
(0.4) 		0.414
(0.799)
amp 10p14 182 (45%) 226 0.728
(0.949) 		0.0082
(0.27) 		0.626
(0.913) 		0.793
(0.968) 		0.0727
(0.454) 		1
(1.00) 		0.429
(0.811) 		0.252
(0.671) 		0.0691
(0.443) 		0.359
(0.745) 		0.293
(0.712) 		0.62
(0.912) 		1
(1.00)
amp 11q13 3 135 (33%) 273 0.479
(0.847) 		0.0117
(0.299) 		0.231
(0.671) 		0.355
(0.744) 		0.321
(0.728) 		1
(1.00) 		0.283
(0.706) 		0.327
(0.732) 		0.541
(0.874) 		0.667
(0.926) 		0.546
(0.874) 		0.0473
(0.39) 		0.724
(0.949)
amp 11q22 2 71 (17%) 337 0.591
(0.893) 		0.0618
(0.434) 		0.11
(0.523) 		0.753
(0.949) 		0.0743
(0.456) 		1
(1.00) 		0.883
(1.00) 		0.22
(0.666) 		0.876
(1) 		0.227
(0.671) 		0.295
(0.712) 		0.128
(0.529) 		1
(1.00)
amp 12p12 1 132 (32%) 276 0.611
(0.907) 		0.0203
(0.321) 		0.168
(0.592) 		0.415
(0.799) 		0.546
(0.874) 		1
(1.00) 		1
(1.00) 		0.476
(0.847) 		0.83
(0.983) 		0.531
(0.873) 		0.584
(0.891) 		0.836
(0.986) 		0.725
(0.949)
amp 12q15 118 (29%) 290 0.734
(0.949) 		0.0155
(0.317) 		0.735
(0.949) 		0.699
(0.943) 		0.951
(1.00) 		0.754
(0.949) 		0.458
(0.846) 		1
(1.00) 		0.551
(0.877) 		0.52
(0.857) 		0.877
(1) 		0.256
(0.671) 		1
(1.00)
amp 13q22 1 128 (31%) 280 0.389
(0.777) 		0.0503
(0.401) 		0.583
(0.891) 		0.563
(0.883) 		0.7
(0.943) 		0.751
(0.949) 		0.0699
(0.443) 		0.629
(0.913) 		0.0319
(0.352) 		0.8
(0.972) 		0.546
(0.874) 		0.0249
(0.352) 		1
(1.00)
amp 16p13 2 87 (21%) 321 0.0866
(0.479) 		0.356
(0.744) 		0.178
(0.603) 		0.0106
(0.279) 		0.115
(0.529) 		0.238
(0.671) 		1
(1.00) 		0.586
(0.891) 		0.213
(0.656) 		0.414
(0.799) 		0.176
(0.603) 		0.245
(0.671) 		0.691
(0.943)
amp 16p11 2 98 (24%) 310 0.429
(0.811) 		0.382
(0.768) 		0.0453
(0.39) 		0.0378
(0.354) 		0.0415
(0.372) 		0.139
(0.55) 		1
(1.00) 		0.792
(0.968) 		0.0575
(0.426) 		0.831
(0.983) 		0.0428
(0.378) 		0.0194
(0.317) 		0.694
(0.943)
amp 16q22 1 108 (26%) 300 0.356
(0.744) 		0.124
(0.529) 		0.109
(0.52) 		0.043
(0.378) 		0.351
(0.744) 		0.135
(0.544) 		0.0561
(0.419) 		0.793
(0.968) 		0.984
(1.00) 		0.978
(1.00) 		0.925
(1.00) 		0.131
(0.537) 		1
(1.00)
amp 17p11 2 88 (22%) 320 0.167
(0.591) 		0.496
(0.847) 		0.339
(0.733) 		0.635
(0.913) 		0.113
(0.527) 		0.456
(0.845) 		0.587
(0.891) 		1
(1.00) 		0.0308
(0.352) 		0.432
(0.811) 		0.148
(0.562) 		0.539
(0.874) 		1
(1.00)
amp 17q11 2 174 (43%) 234 0.537
(0.874) 		0.0326
(0.354) 		0.147
(0.56) 		0.89
(1.00) 		0.0359
(0.354) 		0.536
(0.874) 		0.734
(0.949) 		0.253
(0.671) 		0.214
(0.656) 		0.988
(1.00) 		0.103
(0.513) 		0.241
(0.671) 		0.501
(0.847)
amp 17q12 165 (40%) 243 0.219
(0.666) 		0.064
(0.434) 		0.32
(0.728) 		0.2
(0.637) 		0.105
(0.519) 		1
(1.00) 		0.819
(0.979) 		0.163
(0.589) 		0.0961
(0.485) 		0.229
(0.671) 		0.27
(0.686) 		0.587
(0.891) 		0.164
(0.589)
amp 17q23 3 194 (48%) 214 0.235
(0.671) 		0.0507
(0.401) 		0.0261
(0.352) 		0.315
(0.725) 		0.0233
(0.34) 		1
(1.00) 		0.369
(0.749) 		1
(1.00) 		0.121
(0.529) 		0.503
(0.847) 		0.0302
(0.352) 		0.399
(0.786) 		0.316
(0.725)
amp 19q12 164 (40%) 244 0.205
(0.643) 		0.231
(0.671) 		0.0933
(0.479) 		0.14
(0.55) 		0.108
(0.52) 		0.759
(0.951) 		0.422
(0.81) 		0.241
(0.671) 		0.632
(0.913) 		0.0526
(0.407) 		0.0172
(0.317) 		0.704
(0.944) 		1
(1.00)
amp 19q13 43 155 (38%) 253 0.365
(0.749) 		0.459
(0.847) 		0.0932
(0.479) 		0.0392
(0.361) 		0.0524
(0.407) 		0.539
(0.874) 		0.643
(0.913) 		0.153
(0.572) 		0.636
(0.913) 		0.615
(0.911) 		0.0129
(0.312) 		0.592
(0.893) 		1
(1.00)
amp 20q11 21 263 (64%) 145 0.987
(1.00) 		0.15
(0.566) 		0.31
(0.725) 		0.843
(0.989) 		0.0197
(0.317) 		0.75
(0.949) 		0.29
(0.712) 		0.475
(0.847) 		0.767
(0.958) 		0.945
(1.00) 		0.212
(0.655) 		0.00966
(0.279) 		0.296
(0.714)
amp 22q12 2 87 (21%) 321 0.105
(0.519) 		0.503
(0.847) 		0.144
(0.56) 		0.647
(0.913) 		0.241
(0.671) 		1
(1.00) 		0.891
(1.00) 		1
(1.00) 		0.0833
(0.47) 		0.856
(0.993) 		0.0101
(0.279) 		0.232
(0.671) 		0.399
(0.786)
del 1p36 11 91 (22%) 317 0.863
(0.998) 		0.536
(0.874) 		0.979
(1.00) 		0.337
(0.733) 		0.0318
(0.352) 		0.25
(0.671) 		0.893
(1.00) 		0.585
(0.891) 		0.78
(0.965) 		0.949
(1.00) 		0.606
(0.904) 		0.112
(0.527) 		0.422
(0.81)
del 1q32 1 72 (18%) 336 0.545
(0.874) 		0.978
(1.00) 		0.181
(0.603) 		0.894
(1.00) 		0.0936
(0.479) 		0.686
(0.943) 		0.184
(0.603) 		0.221
(0.667) 		0.931
(1.00) 		0.184
(0.603) 		0.125
(0.529) 		0.478
(0.847) 		0.208
(0.648)
del 2q22 1 134 (33%) 274 0.294
(0.712) 		0.824
(0.979) 		0.93
(1.00) 		0.662
(0.923) 		0.556
(0.881) 		0.186
(0.605) 		0.187
(0.605) 		0.806
(0.972) 		0.784
(0.965) 		0.107
(0.52) 		0.286
(0.71) 		0.631
(0.913) 		0.486
(0.847)
del 2q34 174 (43%) 234 0.618
(0.912) 		0.929
(1.00) 		0.409
(0.794) 		0.467
(0.847) 		0.0609
(0.434) 		0.757
(0.949) 		0.428
(0.811) 		0.644
(0.913) 		0.612
(0.907) 		0.682
(0.942) 		0.0922
(0.479) 		0.199
(0.637) 		0.503
(0.847)
del 2q37 1 207 (51%) 201 0.621
(0.912) 		0.762
(0.953) 		0.125
(0.529) 		0.779
(0.965) 		0.0214
(0.322) 		1
(1.00) 		0.0717
(0.451) 		0.366
(0.749) 		0.719
(0.949) 		0.465
(0.847) 		0.0461
(0.39) 		0.311
(0.725) 		0.175
(0.603)
del 4q22 1 161 (39%) 247 0.302
(0.719) 		0.029
(0.352) 		0.249
(0.671) 		0.312
(0.725) 		0.0596
(0.434) 		0.334
(0.733) 		0.73
(0.949) 		0.488
(0.847) 		0.0938
(0.479) 		0.792
(0.968) 		0.278
(0.697) 		0.0609
(0.434) 		0.493
(0.847)
del 4q34 2 177 (43%) 231 0.888
(1.00) 		0.0684
(0.443) 		0.0933
(0.479) 		0.118
(0.529) 		0.0157
(0.317) 		1
(1.00) 		0.91
(1.00) 		0.821
(0.979) 		0.402
(0.79) 		0.208
(0.648) 		0.224
(0.671) 		0.0805
(0.466) 		0.184
(0.603)
del 6p25 3 106 (26%) 302 0.631
(0.913) 		0.124
(0.529) 		0.586
(0.891) 		0.0733
(0.455) 		0.0768
(0.458) 		1
(1.00) 		0.305
(0.723) 		0.117
(0.529) 		0.0606
(0.434) 		0.846
(0.99) 		0.154
(0.572) 		0.0103
(0.279) 		0.249
(0.671)
del 7q36 3 60 (15%) 348 0.164
(0.589) 		0.752
(0.949) 		0.737
(0.949) 		0.513
(0.855) 		0.361
(0.749) 		1
(1.00) 		0.43
(0.811) 		0.332
(0.733) 		0.519
(0.857) 		0.621
(0.912) 		0.612
(0.907) 		0.636
(0.913) 		0.146
(0.56)
del 8p21 3 252 (62%) 156 0.392
(0.781) 		0.0313
(0.352) 		0.03
(0.352) 		0.151
(0.567) 		0.0555
(0.418) 		0.128
(0.529) 		0.356
(0.744) 		0.349
(0.744) 		0.193
(0.619) 		0.586
(0.891) 		0.259
(0.671) 		0.0381
(0.354) 		1
(1.00)
del 9p23 177 (43%) 231 0.881
(1.00) 		0.321
(0.728) 		0.739
(0.949) 		0.968
(1.00) 		0.803
(0.972) 		1
(1.00) 		0.734
(0.949) 		0.647
(0.913) 		0.276
(0.696) 		0.326
(0.732) 		0.777
(0.964) 		0.955
(1.00) 		1
(1.00)
del 9p21 3 239 (59%) 169 0.433
(0.813) 		0.0546
(0.418) 		0.815
(0.979) 		0.87
(0.998) 		0.819
(0.979) 		0.757
(0.949) 		0.494
(0.847) 		0.648
(0.913) 		0.136
(0.546) 		0.554
(0.881) 		0.587
(0.891) 		0.831
(0.983) 		0.497
(0.847)
del 9q22 33 178 (44%) 230 0.587
(0.891) 		0.25
(0.671) 		0.633
(0.913) 		0.502
(0.847) 		0.707
(0.945) 		0.542
(0.874) 		0.821
(0.979) 		0.648
(0.913) 		0.546
(0.874) 		0.0889
(0.479) 		0.69
(0.943) 		0.43
(0.811) 		0.738
(0.949)
del 10p11 21 74 (18%) 334 0.147
(0.56) 		0.154
(0.572) 		0.983
(1.00) 		0.638
(0.913) 		0.116
(0.529) 		0.407
(0.793) 		0.884
(1.00) 		0.773
(0.961) 		0.466
(0.847) 		0.644
(0.913) 		0.664
(0.924) 		0.0344
(0.354) 		1
(1.00)
del 10q23 31 168 (41%) 240 0.117
(0.529) 		0.0174
(0.317) 		0.601
(0.9) 		0.907
(1.00) 		0.139
(0.55) 		0.339
(0.733) 		1
(1.00) 		0.816
(0.979) 		0.265
(0.68) 		0.802
(0.972) 		0.121
(0.529) 		0.0467
(0.39) 		0.743
(0.949)
del 11q23 3 153 (38%) 255 0.449
(0.838) 		0.241
(0.671) 		0.898
(1.00) 		0.103
(0.513) 		0.467
(0.847) 		0.75
(0.949) 		0.561
(0.883) 		0.242
(0.671) 		0.602
(0.9) 		0.837
(0.986) 		0.352
(0.744) 		0.338
(0.733) 		0.728
(0.949)
del 11q25 144 (35%) 264 0.856
(0.993) 		0.449
(0.838) 		0.783
(0.965) 		0.14
(0.55) 		0.948
(1.00) 		1
(1.00) 		0.48
(0.847) 		0.343
(0.738) 		0.561
(0.883) 		0.378
(0.761) 		0.242
(0.671) 		0.179
(0.603) 		0.504
(0.847)
del 12p13 1 68 (17%) 340 0.478
(0.847) 		0.397
(0.786) 		0.375
(0.757) 		0.134
(0.54) 		0.511
(0.855) 		0.651
(0.914) 		0.228
(0.671) 		1
(1.00) 		0.224
(0.671) 		0.719
(0.949) 		0.258
(0.671) 		0.924
(1.00) 		0.656
(0.92)
del 13q14 2 156 (38%) 252 0.769
(0.959) 		0.204
(0.641) 		0.367
(0.749) 		0.244
(0.671) 		0.176
(0.603) 		0.335
(0.733) 		0.729
(0.949) 		1
(1.00) 		0.66
(0.921) 		0.597
(0.896) 		0.257
(0.671) 		0.0134
(0.312) 		0.298
(0.715)
del 15q13 1 160 (39%) 248 0.633
(0.913) 		0.508
(0.851) 		0.481
(0.847) 		0.355
(0.744) 		0.157
(0.576) 		0.737
(0.949) 		0.646
(0.913) 		0.241
(0.671) 		0.126
(0.529) 		0.182
(0.603) 		0.246
(0.671) 		0.0209
(0.322) 		0.325
(0.732)
del 16q23 1 119 (29%) 289 0.542
(0.874) 		0.264
(0.68) 		0.559
(0.882) 		0.823
(0.979) 		0.203
(0.64) 		0.482
(0.847) 		0.0476
(0.39) 		0.804
(0.972) 		0.0336
(0.354) 		0.328
(0.732) 		0.226
(0.671) 		0.122
(0.529) 		0.128
(0.529)
del 17p12 208 (51%) 200 0.52
(0.857) 		0.0135
(0.312) 		0.593
(0.893) 		0.263
(0.678) 		0.329
(0.732) 		0.538
(0.874) 		0.368
(0.749) 		0.172
(0.601) 		0.794
(0.968) 		0.578
(0.891) 		0.477
(0.847) 		0.545
(0.874) 		0.336
(0.733)
del 18q23 179 (44%) 229 0.118
(0.529) 		0.396
(0.786) 		0.627
(0.913) 		0.595
(0.894) 		0.823
(0.979) 		0.0264
(0.352) 		0.498
(0.847) 		0.252
(0.671) 		0.966
(1.00) 		0.227
(0.671) 		0.856
(0.993) 		0.696
(0.943) 		0.512
(0.855)
del 19p13 3 145 (36%) 263 0.314
(0.725) 		0.495
(0.847) 		0.0148
(0.317) 		0.0167
(0.317) 		0.0267
(0.352) 		0.0171
(0.317) 		0.64
(0.913) 		0.154
(0.572) 		0.0181
(0.317) 		0.576
(0.891) 		0.18
(0.603) 		0.183
(0.603) 		0.0759
(0.456)
del 22q13 32 188 (46%) 220 0.427
(0.811) 		0.106
(0.52) 		0.147
(0.56) 		0.363
(0.749) 		0.0279
(0.352) 		1
(1.00) 		0.822
(0.979) 		0.0692
(0.443) 		0.0269
(0.352) 		0.723
(0.949) 		0.241
(0.671) 		0.0306
(0.352) 		0.313
(0.725)
del xp11 3 91 (22%) 317 0.748
(0.949) 		0.187
(0.605) 		0.921
(1.00) 		0.386
(0.773) 		0.499
(0.847) 		1
(1.00) 		1
(1.00) 		0.784
(0.965) 		0.608
(0.905) 		0.736
(0.949) 		0.918
(1.00) 		0.468
(0.847) 		0.69
(0.943)
del xq21 33 84 (21%) 324 0.111
(0.523) 		0.346
(0.743) 		0.499
(0.847) 		0.659
(0.921) 		0.982
(1.00) 		0.128
(0.529) 		0.58
(0.891) 		0.577
(0.891) 		0.461
(0.847) 		0.7
(0.943) 		0.49
(0.847) 		0.255
(0.671) 		0.0917
(0.479)
'amp_1q21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00575 (Fisher's exact test), Q value = 0.22

Table S1.  Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
AMP PEAK 2(1Q21.3) MUTATED 101 29 41 7
AMP PEAK 2(1Q21.3) WILD-TYPE 135 18 34 1

Figure S1.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1q23.3' versus 'YEARS_TO_BIRTH'

P value = 0.00624 (Wilcoxon-test), Q value = 0.23

Table S2.  Gene #3: 'amp_1q23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
AMP PEAK 3(1Q23.3) MUTATED 215 69.6 (9.9)
AMP PEAK 3(1Q23.3) WILD-TYPE 192 66.4 (11.1)

Figure S2.  Get High-res Image Gene #3: 'amp_1q23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00255 (Fisher's exact test), Q value = 0.17

Table S3.  Gene #3: 'amp_1q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
AMP PEAK 3(1Q23.3) MUTATED 111 30 43 8
AMP PEAK 3(1Q23.3) WILD-TYPE 125 17 32 0

Figure S3.  Get High-res Image Gene #3: 'amp_1q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2p25.1' versus 'YEARS_TO_BIRTH'

P value = 0.00525 (Wilcoxon-test), Q value = 0.22

Table S4.  Gene #4: 'amp_2p25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
AMP PEAK 4(2P25.1) MUTATED 151 70.1 (9.7)
AMP PEAK 4(2P25.1) WILD-TYPE 256 66.9 (11.0)

Figure S4.  Get High-res Image Gene #4: 'amp_2p25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p25.2' versus 'YEARS_TO_BIRTH'

P value = 0.00214 (Wilcoxon-test), Q value = 0.17

Table S5.  Gene #5: 'amp_3p25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
AMP PEAK 5(3P25.2) MUTATED 189 69.8 (10.6)
AMP PEAK 5(3P25.2) WILD-TYPE 218 66.6 (10.5)

Figure S5.  Get High-res Image Gene #5: 'amp_3p25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p25.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00587 (Fisher's exact test), Q value = 0.22

Table S6.  Gene #5: 'amp_3p25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
AMP PEAK 5(3P25.2) MUTATED 94 22 45 6
AMP PEAK 5(3P25.2) WILD-TYPE 142 25 30 2

Figure S6.  Get High-res Image Gene #5: 'amp_3p25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3p25.2' versus 'GENDER'

P value = 0.00469 (Fisher's exact test), Q value = 0.22

Table S7.  Gene #5: 'amp_3p25.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 107 301
AMP PEAK 5(3P25.2) MUTATED 37 153
AMP PEAK 5(3P25.2) WILD-TYPE 70 148

Figure S7.  Get High-res Image Gene #5: 'amp_3p25.2' versus Clinical Feature #7: 'GENDER'

'amp_6p22.3' versus 'Time to Death'

P value = 0.00271 (logrank test), Q value = 0.17

Table S8.  Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 405 178 0.5 - 166.0 (17.6)
AMP PEAK 10(6P22.3) MUTATED 171 61 0.5 - 166.0 (19.1)
AMP PEAK 10(6P22.3) WILD-TYPE 234 117 0.7 - 163.3 (16.7)

Figure S8.  Get High-res Image Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

'amp_7p21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00249 (Fisher's exact test), Q value = 0.17

Table S9.  Gene #13: 'amp_7p21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 2 129 140 135
AMP PEAK 13(7P21.1) MUTATED 1 50 68 82
AMP PEAK 13(7P21.1) WILD-TYPE 1 79 72 53

Figure S9.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7p21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00297 (Fisher's exact test), Q value = 0.18

Table S10.  Gene #13: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
AMP PEAK 13(7P21.1) MUTATED 102 29 44 7
AMP PEAK 13(7P21.1) WILD-TYPE 134 18 31 1

Figure S10.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7p21.1' versus 'RACE'

P value = 0.00244 (Fisher's exact test), Q value = 0.17

Table S11.  Gene #13: 'amp_7p21.1' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
AMP PEAK 13(7P21.1) MUTATED 11 13 171
AMP PEAK 13(7P21.1) WILD-TYPE 32 9 156

Figure S11.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #12: 'RACE'

'amp_11p13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00214 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #21: 'amp_11p13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
AMP PEAK 21(11P13) MUTATED 21 6 15 4
AMP PEAK 21(11P13) WILD-TYPE 215 41 60 4

Figure S12.  Get High-res Image Gene #21: 'amp_11p13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p14.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0014 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #43: 'del_3p14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
DEL PEAK 6(3P14.2) MUTATED 64 21 16 6
DEL PEAK 6(3P14.2) WILD-TYPE 172 26 59 2

Figure S13.  Get High-res Image Gene #43: 'del_3p14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p14.2' versus 'RACE'

P value = 0.0019 (Fisher's exact test), Q value = 0.17

Table S14.  Gene #43: 'del_3p14.2' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
DEL PEAK 6(3P14.2) MUTATED 3 7 101
DEL PEAK 6(3P14.2) WILD-TYPE 40 15 226

Figure S14.  Get High-res Image Gene #43: 'del_3p14.2' versus Clinical Feature #12: 'RACE'

'del_5q12.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00166 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #46: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
DEL PEAK 9(5Q12.1) MUTATED 97 28 46 6
DEL PEAK 9(5Q12.1) WILD-TYPE 139 19 29 2

Figure S15.  Get High-res Image Gene #46: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q12.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00442 (Wilcoxon-test), Q value = 0.22

Table S16.  Gene #46: 'del_5q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
DEL PEAK 9(5Q12.1) MUTATED 151 2.9 (9.2)
DEL PEAK 9(5Q12.1) WILD-TYPE 146 1.2 (3.4)

Figure S16.  Get High-res Image Gene #46: 'del_5q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_6q21' versus 'PATHOLOGY_N_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.17

Table S17.  Gene #48: 'del_6q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
DEL PEAK 11(6Q21) MUTATED 92 24 48 4
DEL PEAK 11(6Q21) WILD-TYPE 144 23 27 4

Figure S17.  Get High-res Image Gene #48: 'del_6q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00139 (Wilcoxon-test), Q value = 0.17

Table S18.  Gene #48: 'del_6q21' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
DEL PEAK 11(6Q21) MUTATED 146 3.0 (9.3)
DEL PEAK 11(6Q21) WILD-TYPE 151 1.2 (3.3)

Figure S18.  Get High-res Image Gene #48: 'del_6q21' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_6q27' versus 'PATHOLOGIC_STAGE'

P value = 0.00152 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #49: 'del_6q27' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 2 129 140 135
DEL PEAK 12(6Q27) MUTATED 0 51 58 80
DEL PEAK 12(6Q27) WILD-TYPE 2 78 82 55

Figure S19.  Get High-res Image Gene #49: 'del_6q27' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q27' versus 'PATHOLOGY_N_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #49: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
DEL PEAK 12(6Q27) MUTATED 93 23 50 5
DEL PEAK 12(6Q27) WILD-TYPE 143 24 25 3

Figure S20.  Get High-res Image Gene #49: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q27' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00052 (Wilcoxon-test), Q value = 0.17

Table S21.  Gene #49: 'del_6q27' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
DEL PEAK 12(6Q27) MUTATED 147 3.2 (9.6)
DEL PEAK 12(6Q27) WILD-TYPE 150 1.0 (2.4)

Figure S21.  Get High-res Image Gene #49: 'del_6q27' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_8p23.3' versus 'RACE'

P value = 0.00575 (Fisher's exact test), Q value = 0.22

Table S22.  Gene #51: 'del_8p23.3' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
DEL PEAK 14(8P23.3) MUTATED 18 18 198
DEL PEAK 14(8P23.3) WILD-TYPE 25 4 129

Figure S22.  Get High-res Image Gene #51: 'del_8p23.3' versus Clinical Feature #12: 'RACE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00242 (Wilcoxon-test), Q value = 0.17

Table S23.  Gene #58: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
DEL PEAK 21(11P15.5) MUTATED 210 69.5 (10.5)
DEL PEAK 21(11P15.5) WILD-TYPE 197 66.6 (10.6)

Figure S23.  Get High-res Image Gene #58: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_12q24.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0056 (Wilcoxon-test), Q value = 0.22

Table S24.  Gene #62: 'del_12q24.33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
DEL PEAK 25(12Q24.33) MUTATED 64 3.1 (6.0)
DEL PEAK 25(12Q24.33) WILD-TYPE 233 1.8 (7.2)

Figure S24.  Get High-res Image Gene #62: 'del_12q24.33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_14q24.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00535 (Fisher's exact test), Q value = 0.22

Table S25.  Gene #64: 'del_14q24.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
DEL PEAK 27(14Q24.1) MUTATED 71 12 38 2
DEL PEAK 27(14Q24.1) WILD-TYPE 165 35 37 6

Figure S25.  Get High-res Image Gene #64: 'del_14q24.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_16p13.3' versus 'RACE'

P value = 0.00532 (Fisher's exact test), Q value = 0.22

Table S26.  Gene #66: 'del_16p13.3' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
DEL PEAK 29(16P13.3) MUTATED 10 6 150
DEL PEAK 29(16P13.3) WILD-TYPE 33 16 177

Figure S26.  Get High-res Image Gene #66: 'del_16p13.3' versus Clinical Feature #12: 'RACE'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22507728/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt

  • Number of patients = 408

  • Number of significantly focal cnvs = 73

  • Number of selected clinical features = 13

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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