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 69 focal events and 12 clinical features across 389 patients, 24 significant findings detected with Q value < 0.25.

  • amp_1q23.3 cnv correlated to 'PATHOLOGY_N_STAGE'.

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

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

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

  • amp_10p14 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_11p13 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_16p13.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_3p14.2 cnv correlated to 'RACE'.

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

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

  • del_6q27 cnv correlated to 'NEOPLASM_DISEASESTAGE',  '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_19p13.3 cnv correlated to 'PATHOLOGY_N_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 24 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER 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 Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 7p21 1 190 (49%) 199 0.391
(0.789) 		0.0621
(0.42) 		0.00685
(0.237) 		0.139
(0.525) 		0.00221
(0.153) 		1
(1.00) 		0.817
(0.986) 		0.143
(0.533) 		0.255
(0.673) 		0.0976
(0.47) 		0.00406
(0.199) 		1
(1.00)
del 6q21 182 (47%) 207 0.735
(0.949) 		0.0479
(0.375) 		0.0024
(0.153) 		0.411
(0.8) 		0.00061
(0.142) 		0.196
(0.611) 		0.132
(0.515) 		0.0857
(0.461) 		0.357
(0.757) 		0.000282
(0.142) 		0.211
(0.623) 		0.0888
(0.467)
del 6q27 179 (46%) 210 0.527
(0.852) 		0.137
(0.524) 		0.00432
(0.199) 		0.365
(0.762) 		0.00039
(0.142) 		0.199
(0.613) 		0.908
(1.00) 		0.081
(0.456) 		0.184
(0.598) 		0.000685
(0.142) 		0.232
(0.64) 		0.31
(0.722)
amp 3p25 2 177 (46%) 212 0.165
(0.578) 		0.00537
(0.212) 		0.335
(0.742) 		0.177
(0.595) 		0.0127
(0.3) 		0.754
(0.951) 		0.00117
(0.153) 		0.0373
(0.343) 		0.255
(0.673) 		0.0295
(0.33) 		0.0198
(0.314) 		0.519
(0.848)
del 5q12 1 190 (49%) 199 0.0345
(0.336) 		0.0109
(0.296) 		0.0475
(0.375) 		0.179
(0.595) 		0.00202
(0.153) 		0.195
(0.611) 		0.908
(1.00) 		0.202
(0.618) 		0.654
(0.936) 		0.00586
(0.22) 		0.0968
(0.469) 		1
(1.00)
amp 1q23 3 205 (53%) 184 0.903
(1.00) 		0.0121
(0.296) 		0.0579
(0.406) 		0.649
(0.932) 		0.00225
(0.153) 		0.332
(0.74) 		0.488
(0.838) 		0.0557
(0.401) 		0.371
(0.769) 		0.152
(0.556) 		0.0863
(0.461) 		0.744
(0.949)
amp 6p22 3 160 (41%) 229 0.00195
(0.153) 		0.0458
(0.375) 		0.115
(0.485) 		0.246
(0.664) 		0.1
(0.476) 		1
(1.00) 		0.199
(0.613) 		0.0513
(0.381) 		0.867
(1.00) 		0.791
(0.972) 		0.342
(0.747) 		0.166
(0.578)
amp 10p14 172 (44%) 217 0.774
(0.961) 		0.0042
(0.199) 		0.715
(0.949) 		0.935
(1.00) 		0.0947
(0.469) 		1
(1.00) 		0.562
(0.875) 		0.0588
(0.406) 		0.21
(0.623) 		0.4
(0.792) 		0.79
(0.972) 		1
(1.00)
amp 11p13 48 (12%) 341 0.0335
(0.336) 		0.887
(1.00) 		0.18
(0.595) 		0.8
(0.977) 		0.00143
(0.153) 		1
(1.00) 		0.6
(0.913) 		0.33
(0.74) 		0.976
(1.00) 		0.0497
(0.381) 		0.505
(0.842) 		0.331
(0.74)
amp 16p13 2 82 (21%) 307 0.226
(0.639) 		0.454
(0.832) 		0.106
(0.485) 		0.00477
(0.208) 		0.105
(0.485) 		0.124
(0.499) 		1
(1.00) 		0.18
(0.595) 		0.511
(0.845) 		0.163
(0.576) 		0.298
(0.718) 		0.692
(0.949)
del 3p14 2 111 (29%) 278 0.96
(1.00) 		0.229
(0.64) 		0.535
(0.855) 		0.467
(0.833) 		0.0148
(0.3) 		0.257
(0.674) 		0.0106
(0.296) 		0.0785
(0.455) 		0.714
(0.949) 		0.524
(0.85) 		0.00228
(0.153) 		0.125
(0.499)
del 8p23 3 227 (58%) 162 0.544
(0.865) 		0.0319
(0.336) 		0.0635
(0.42) 		0.584
(0.895) 		0.0174
(0.314) 		0.35
(0.749) 		0.725
(0.949) 		0.11
(0.485) 		0.946
(1.00) 		0.264
(0.682) 		0.00686
(0.237) 		1
(1.00)
del 11p15 5 198 (51%) 191 0.58
(0.894) 		0.00326
(0.18) 		0.0575
(0.406) 		0.916
(1.00) 		0.0196
(0.314) 		0.346
(0.747) 		1
(1.00) 		0.303
(0.72) 		0.766
(0.956) 		0.0279
(0.322) 		0.154
(0.556) 		0.502
(0.84)
del 12q24 33 83 (21%) 306 0.612
(0.921) 		0.345
(0.747) 		0.0112
(0.296) 		0.749
(0.949) 		0.0448
(0.375) 		0.413
(0.8) 		0.397
(0.79) 		0.943
(1.00) 		0.9
(1.00) 		0.00288
(0.17) 		0.392
(0.789) 		0.691
(0.949)
del 14q24 1 127 (33%) 262 0.532
(0.853) 		0.0711
(0.439) 		0.401
(0.793) 		0.988
(1.00) 		0.00173
(0.153) 		0.505
(0.842) 		0.109
(0.485) 		0.051
(0.381) 		0.0392
(0.356) 		0.111
(0.485) 		0.747
(0.949) 		1
(1.00)
del 19p13 3 139 (36%) 250 0.259
(0.676) 		0.666
(0.941) 		0.025
(0.314) 		0.0471
(0.375) 		0.00508
(0.21) 		0.0104
(0.296) 		0.904
(1.00) 		0.0118
(0.296) 		0.518
(0.848) 		0.0802
(0.455) 		0.185
(0.598) 		0.0775
(0.455)
amp 1p34 2 98 (25%) 291 0.483
(0.836) 		0.0108
(0.296) 		0.264
(0.682) 		0.842
(1.00) 		0.02
(0.314) 		1
(1.00) 		0.691
(0.949) 		0.909
(1.00) 		0.178
(0.595) 		0.263
(0.682) 		0.0322
(0.336) 		0.696
(0.949)
amp 1q21 3 192 (49%) 197 0.468
(0.833) 		0.197
(0.612) 		0.0771
(0.455) 		0.957
(1.00) 		0.0257
(0.314) 		0.205
(0.618) 		0.908
(1.00) 		0.0626
(0.42) 		0.531
(0.853) 		0.0229
(0.314) 		0.205
(0.618) 		1
(1.00)
amp 2p25 1 140 (36%) 249 0.936
(1.00) 		0.00871
(0.277) 		0.0437
(0.375) 		1
(1.00) 		0.0212
(0.314) 		0.311
(0.722) 		0.041
(0.364) 		0.986
(1.00) 		0.374
(0.774) 		0.0138
(0.3) 		0.191
(0.608) 		0.725
(0.949)
amp 3q26 33 206 (53%) 183 0.948
(1.00) 		0.194
(0.61) 		0.699
(0.949) 		0.138
(0.525) 		0.179
(0.595) 		0.75
(0.949) 		0.73
(0.949) 		0.0267
(0.316) 		0.465
(0.833) 		0.207
(0.619) 		0.0172
(0.314) 		1
(1.00)
amp 4p16 3 70 (18%) 319 0.0243
(0.314) 		0.763
(0.955) 		0.0824
(0.461) 		0.0834
(0.461) 		0.135
(0.52) 		0.461
(0.833) 		0.88
(1.00) 		0.0733
(0.449) 		0.695
(0.949) 		0.128
(0.508) 		0.0929
(0.469) 		0.656
(0.936)
amp 4q13 3 58 (15%) 331 0.32
(0.728) 		0.946
(1.00) 		0.217
(0.623) 		0.0773
(0.455) 		0.888
(1.00) 		0.366
(0.762) 		0.0143
(0.3) 		0.605
(0.919) 		0.739
(0.949) 		0.859
(1.00) 		0.954
(1.00) 		0.62
(0.923)
amp 5p15 33 193 (50%) 196 0.824
(0.987) 		0.452
(0.832) 		0.59
(0.901) 		0.719
(0.949) 		0.965
(1.00) 		0.19
(0.606) 		1
(1.00) 		0.0942
(0.469) 		0.873
(1.00) 		0.476
(0.836) 		0.156
(0.56) 		0.75
(0.949)
amp 6q21 33 (8%) 356 0.0787
(0.455) 		0.581
(0.894) 		0.304
(0.72) 		0.354
(0.755) 		0.521
(0.848) 		1
(1.00) 		1
(1.00) 		0.745
(0.949) 		0.388
(0.789) 		0.767
(0.956) 		0.48
(0.836) 		0.559
(0.873)
amp 6q23 3 44 (11%) 345 0.557
(0.873) 		0.17
(0.589) 		0.548
(0.868) 		0.779
(0.963) 		0.125
(0.499) 		0.355
(0.755) 		0.716
(0.949) 		0.588
(0.9) 		0.658
(0.936) 		0.867
(1.00) 		0.276
(0.699) 		1
(1.00)
amp 7p11 2 181 (47%) 208 0.839
(1) 		0.0329
(0.336) 		0.329
(0.74) 		0.744
(0.949) 		0.0213
(0.314) 		1
(1.00) 		0.818
(0.986) 		0.411
(0.8) 		0.771
(0.96) 		0.28
(0.703) 		0.0402
(0.362) 		0.737
(0.949)
amp 8p11 23 118 (30%) 271 0.268
(0.686) 		0.307
(0.722) 		0.583
(0.895) 		0.568
(0.879) 		0.242
(0.656) 		0.729
(0.949) 		0.901
(1.00) 		0.551
(0.868) 		0.217
(0.623) 		0.283
(0.703) 		0.454
(0.832) 		0.132
(0.515)
amp 8p11 21 134 (34%) 255 0.0518
(0.381) 		0.415
(0.8) 		0.893
(1.00) 		0.724
(0.949) 		0.131
(0.515) 		0.0154
(0.303) 		0.274
(0.697) 		0.485
(0.838) 		0.307
(0.722) 		0.316
(0.724) 		0.284
(0.703) 		0.487
(0.838)
amp 8q22 3 250 (64%) 139 0.994
(1.00) 		0.0353
(0.336) 		0.929
(1.00) 		0.814
(0.986) 		0.469
(0.833) 		1
(1.00) 		0.717
(0.949) 		0.101
(0.476) 		0.338
(0.744) 		0.241
(0.656) 		0.366
(0.762) 		0.731
(0.949)
amp 9p24 1 85 (22%) 304 0.166
(0.578) 		0.154
(0.556) 		0.798
(0.977) 		0.722
(0.949) 		0.661
(0.936) 		0.397
(0.79) 		0.675
(0.946) 		0.356
(0.756) 		0.0961
(0.469) 		0.776
(0.961) 		0.0522
(0.381) 		0.417
(0.801)
amp 11q13 3 129 (33%) 260 0.0895
(0.467) 		0.014
(0.3) 		0.186
(0.599) 		0.303
(0.72) 		0.321
(0.728) 		0.726
(0.949) 		0.112
(0.485) 		0.492
(0.84) 		0.723
(0.949) 		0.723
(0.949) 		0.0792
(0.455) 		0.723
(0.949)
amp 11q22 2 69 (18%) 320 0.763
(0.955) 		0.0479
(0.375) 		0.132
(0.515) 		0.62
(0.923) 		0.0485
(0.375) 		1
(1.00) 		0.763
(0.955) 		0.615
(0.923) 		0.347
(0.747) 		0.343
(0.747) 		0.0928
(0.469) 		1
(1.00)
amp 12p12 1 125 (32%) 264 0.254
(0.673) 		0.0121
(0.296) 		0.0855
(0.461) 		0.304
(0.72) 		0.52
(0.848) 		1
(1.00) 		0.712
(0.949) 		0.859
(1.00) 		0.395
(0.789) 		0.214
(0.623) 		0.898
(1.00) 		0.726
(0.949)
amp 12q15 114 (29%) 275 0.992
(1.00) 		0.0191
(0.314) 		0.78
(0.963) 		0.419
(0.801) 		0.789
(0.972) 		0.501
(0.84) 		0.446
(0.831) 		0.415
(0.8) 		0.696
(0.949) 		0.869
(1.00) 		0.394
(0.789) 		0.73
(0.949)
amp 13q22 1 121 (31%) 268 0.292
(0.713) 		0.028
(0.322) 		0.819
(0.986) 		0.566
(0.877) 		0.712
(0.949) 		1
(1.00) 		0.134
(0.517) 		0.0895
(0.467) 		0.959
(1.00) 		0.687
(0.949) 		0.0318
(0.336) 		1
(1.00)
amp 16q22 1 103 (26%) 286 0.379
(0.777) 		0.111
(0.485) 		0.0957
(0.469) 		0.0216
(0.314) 		0.108
(0.485) 		0.063
(0.42) 		0.036
(0.339) 		0.96
(1.00) 		0.855
(1.00) 		0.965
(1.00) 		0.14
(0.525) 		1
(1.00)
amp 17q12 159 (41%) 230 0.441
(0.826) 		0.0483
(0.375) 		0.406
(0.798) 		0.153
(0.556) 		0.115
(0.485) 		1
(1.00) 		0.639
(0.926) 		0.0862
(0.461) 		0.209
(0.622) 		0.261
(0.68) 		0.63
(0.923) 		0.165
(0.578)
amp 17q23 3 186 (48%) 203 0.474
(0.836) 		0.0347
(0.336) 		0.0422
(0.368) 		0.496
(0.84) 		0.0348
(0.336) 		0.757
(0.952) 		0.419
(0.801) 		0.059
(0.406) 		0.546
(0.866) 		0.0243
(0.314) 		0.518
(0.848) 		0.317
(0.726)
amp 19q12 153 (39%) 236 0.068
(0.43) 		0.315
(0.724) 		0.453
(0.832) 		0.246
(0.664) 		0.159
(0.567) 		1
(1.00) 		0.409
(0.8) 		0.39
(0.789) 		0.0676
(0.43) 		0.0562
(0.401) 		0.906
(1.00) 		1
(1.00)
amp 19q13 43 147 (38%) 242 0.112
(0.485) 		0.469
(0.833) 		0.362
(0.762) 		0.0786
(0.455) 		0.0761
(0.455) 		0.501
(0.84) 		0.551
(0.868) 		0.893
(1.00) 		0.513
(0.846) 		0.0317
(0.336) 		0.675
(0.946) 		1
(1.00)
amp 20q11 21 247 (63%) 142 0.541
(0.862) 		0.153
(0.556) 		0.624
(0.923) 		0.954
(1.00) 		0.149
(0.55) 		0.745
(0.949) 		0.28
(0.703) 		0.993
(1.00) 		0.94
(1.00) 		0.436
(0.819) 		0.0333
(0.336) 		0.303
(0.72)
amp 22q12 2 80 (21%) 309 0.0353
(0.336) 		0.638
(0.926) 		0.113
(0.485) 		0.631
(0.923) 		0.457
(0.833) 		0.693
(0.949) 		0.887
(1.00) 		0.117
(0.488) 		0.894
(1.00) 		0.0258
(0.314) 		0.224
(0.637) 		0.387
(0.789)
del 1p36 11 85 (22%) 304 0.492
(0.84) 		0.625
(0.923) 		0.994
(1.00) 		0.626
(0.923) 		0.113
(0.485) 		0.451
(0.832) 		0.889
(1.00) 		1
(1.00) 		0.831
(0.993) 		0.453
(0.832) 		0.121
(0.495) 		0.413
(0.8)
del 1q32 1 71 (18%) 318 0.894
(1.00) 		0.86
(1.00) 		0.23
(0.64) 		1
(1.00) 		0.0795
(0.455) 		0.662
(0.936) 		0.231
(0.64) 		0.997
(1.00) 		0.252
(0.672) 		0.0851
(0.461) 		0.474
(0.836) 		0.379
(0.777)
del 2q22 1 126 (32%) 263 0.483
(0.836) 		0.875
(1.00) 		0.966
(1.00) 		0.61
(0.921) 		0.529
(0.853) 		0.311
(0.722) 		0.217
(0.623) 		0.581
(0.894) 		0.0484
(0.375) 		0.331
(0.74) 		0.707
(0.949) 		0.482
(0.836)
del 2q34 161 (41%) 228 0.66
(0.936) 		0.755
(0.951) 		0.63
(0.923) 		0.456
(0.833) 		0.0353
(0.336) 		1
(1.00) 		0.291
(0.713) 		0.937
(1.00) 		0.646
(0.931) 		0.116
(0.485) 		0.344
(0.747) 		0.497
(0.84)
del 2q37 1 198 (51%) 191 0.608
(0.92) 		0.852
(1.00) 		0.42
(0.801) 		0.81
(0.986) 		0.0196
(0.314) 		0.533
(0.853) 		0.064
(0.42) 		0.869
(1.00) 		0.683
(0.949) 		0.0802
(0.455) 		0.431
(0.815) 		0.175
(0.595)
del 4q22 1 154 (40%) 235 0.231
(0.64) 		0.0212
(0.314) 		0.256
(0.673) 		0.0969
(0.469) 		0.323
(0.731) 		0.5
(0.84) 		0.481
(0.836) 		0.0525
(0.381) 		0.606
(0.92) 		0.434
(0.817) 		0.0651
(0.421) 		0.493
(0.84)
del 4q34 2 169 (43%) 220 0.634
(0.924) 		0.107
(0.485) 		0.0649
(0.421) 		0.0672
(0.43) 		0.0161
(0.309) 		1
(1.00) 		0.816
(0.986) 		0.32
(0.728) 		0.0908
(0.469) 		0.181
(0.595) 		0.092
(0.469) 		0.187
(0.602)
del 6p25 3 97 (25%) 292 0.828
(0.991) 		0.238
(0.65) 		0.709
(0.949) 		0.138
(0.525) 		0.0896
(0.467) 		1
(1.00) 		0.229
(0.64) 		0.0957
(0.469) 		0.847
(1.00) 		0.12
(0.495) 		0.0233
(0.314) 		0.238
(0.65)
del 7q36 3 57 (15%) 332 0.415
(0.8) 		0.897
(1.00) 		0.948
(1.00) 		0.675
(0.946) 		0.447
(0.831) 		1
(1.00) 		0.626
(0.923) 		0.912
(1.00) 		0.78
(0.963) 		0.914
(1.00) 		0.592
(0.903) 		0.144
(0.533)
del 8p21 3 238 (61%) 151 0.376
(0.774) 		0.0178
(0.314) 		0.0364
(0.339) 		0.107
(0.485) 		0.0266
(0.316) 		0.196
(0.611) 		0.553
(0.869) 		0.207
(0.619) 		0.817
(0.986) 		0.213
(0.623) 		0.0685
(0.43) 		1
(1.00)
del 9p23 166 (43%) 223 0.944
(1.00) 		0.673
(0.946) 		0.73
(0.949) 		1
(1.00) 		0.52
(0.848) 		1
(1.00) 		0.907
(1.00) 		0.39
(0.789) 		0.225
(0.637) 		0.619
(0.923) 		0.847
(1.00) 		1
(1.00)
del 9p21 3 226 (58%) 163 0.72
(0.949) 		0.123
(0.499) 		0.698
(0.949) 		0.798
(0.977) 		0.479
(0.836) 		0.525
(0.85) 		0.483
(0.836) 		0.222
(0.633) 		0.647
(0.932) 		0.394
(0.789) 		0.701
(0.949) 		0.498
(0.84)
del 9q22 33 167 (43%) 222 0.267
(0.685) 		0.458
(0.833) 		0.315
(0.724) 		0.298
(0.718) 		0.403
(0.795) 		0.339
(0.744) 		0.727
(0.949) 		0.731
(0.949) 		0.103
(0.478) 		0.985
(1.00) 		0.564
(0.876) 		0.739
(0.949)
del 10p11 21 70 (18%) 319 0.182
(0.595) 		0.236
(0.65) 		0.932
(1.00) 		0.409
(0.8) 		0.108
(0.485) 		0.214
(0.623) 		0.88
(1.00) 		0.799
(0.977) 		0.508
(0.843) 		0.661
(0.936) 		0.0257
(0.314) 		1
(1.00)
del 10q23 31 156 (40%) 233 0.249
(0.668) 		0.0284
(0.322) 		0.661
(0.936) 		0.718
(0.949) 		0.46
(0.833) 		0.336
(0.742) 		1
(1.00) 		0.18
(0.595) 		0.821
(0.987) 		0.203
(0.618) 		0.069
(0.43) 		1
(1.00)
del 11q23 3 145 (37%) 244 0.949
(1.00) 		0.51
(0.845) 		0.362
(0.762) 		0.141
(0.528) 		0.609
(0.921) 		1
(1.00) 		0.811
(0.986) 		0.366
(0.762) 		0.668
(0.942) 		0.376
(0.774) 		0.365
(0.762) 		0.728
(0.949)
del 11q25 134 (34%) 255 0.745
(0.949) 		0.891
(1.00) 		0.463
(0.833) 		0.218
(0.625) 		0.963
(1.00) 		1
(1.00) 		0.627
(0.923) 		0.285
(0.703) 		0.743
(0.949) 		0.35
(0.749) 		0.0925
(0.469) 		0.497
(0.84)
del 12p13 1 62 (16%) 327 0.701
(0.949) 		0.762
(0.955) 		0.344
(0.747) 		0.194
(0.61) 		0.333
(0.74) 		0.632
(0.923) 		0.348
(0.749) 		0.205
(0.618) 		0.842
(1.00) 		0.111
(0.485) 		1
(1.00) 		0.648
(0.932)
del 13q14 2 148 (38%) 241 0.874
(1.00) 		0.23
(0.64) 		0.162
(0.576) 		0.15
(0.551) 		0.0987
(0.472) 		0.499
(0.84) 		0.812
(0.986) 		0.532
(0.853) 		0.47
(0.833) 		0.193
(0.61) 		0.0253
(0.314) 		0.296
(0.718)
del 15q13 1 149 (38%) 240 0.282
(0.703) 		0.488
(0.838) 		0.616
(0.923) 		0.267
(0.685) 		0.252
(0.672) 		1
(1.00) 		1
(1.00) 		0.121
(0.495) 		0.205
(0.618) 		0.287
(0.704) 		0.0511
(0.381) 		0.311
(0.722)
del 16p13 3 163 (42%) 226 0.536
(0.856) 		0.116
(0.485) 		0.394
(0.789) 		0.115
(0.485) 		0.00843
(0.277) 		1
(1.00) 		0.559
(0.873) 		0.185
(0.598) 		0.832
(0.993) 		0.399
(0.792) 		0.0131
(0.3) 		0.739
(0.949)
del 16q23 1 112 (29%) 277 0.699
(0.949) 		0.271
(0.691) 		0.719
(0.949) 		0.803
(0.979) 		0.422
(0.802) 		0.714
(0.949) 		0.0216
(0.314) 		0.0222
(0.314) 		0.314
(0.724) 		0.295
(0.717) 		0.179
(0.595) 		0.127
(0.507)
del 17p12 196 (50%) 193 0.428
(0.81) 		0.0149
(0.3) 		0.55
(0.868) 		0.285
(0.703) 		0.177
(0.595) 		0.748
(0.949) 		0.249
(0.668) 		0.969
(1.00) 		0.285
(0.703) 		0.423
(0.804) 		0.691
(0.949) 		0.332
(0.74)
del 18q23 169 (43%) 220 0.0839
(0.461) 		0.294
(0.717) 		0.774
(0.961) 		0.466
(0.833) 		0.627
(0.923) 		0.046
(0.375) 		0.642
(0.929) 		0.824
(0.987) 		0.0484
(0.375) 		0.632
(0.923) 		0.849
(1.00) 		0.508
(0.843)
del 22q13 32 177 (46%) 212 0.304
(0.72) 		0.102
(0.478) 		0.0593
(0.406) 		0.278
(0.701) 		0.0184
(0.314) 		0.734
(0.949) 		0.908
(1.00) 		0.0228
(0.314) 		0.637
(0.926) 		0.123
(0.499) 		0.0413
(0.364) 		0.311
(0.722)
del xp11 3 87 (22%) 302 0.981
(1.00) 		0.176
(0.595) 		0.881
(1.00) 		0.52
(0.848) 		0.645
(0.931) 		1
(1.00) 		0.891
(1.00) 		0.432
(0.815) 		0.562
(0.875) 		0.871
(1.00) 		0.449
(0.832) 		0.69
(0.949)
del xq21 33 82 (21%) 307 0.171
(0.589) 		0.469
(0.833) 		0.47
(0.833) 		0.74
(0.949) 		0.936
(1.00) 		0.214
(0.623) 		0.479
(0.836) 		0.442
(0.826) 		0.631
(0.923) 		0.497
(0.84) 		0.217
(0.623) 		0.102
(0.478)
'amp_1q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00225 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #3: 'amp_1q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
AMP PEAK 3(1Q23.3) MUTATED 104 27 43 8
AMP PEAK 3(1Q23.3) WILD-TYPE 120 15 32 0

Figure S1.  Get High-res Image Gene #3: 'amp_1q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3p25.2' versus 'YEARS_TO_BIRTH'

P value = 0.00537 (Wilcoxon-test), Q value = 0.21

Table S2.  Gene #5: 'amp_3p25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
AMP PEAK 5(3P25.2) MUTATED 176 69.4 (10.7)
AMP PEAK 5(3P25.2) WILD-TYPE 212 66.4 (10.4)

Figure S2.  Get High-res Image Gene #5: 'amp_3p25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p25.2' versus 'GENDER'

P value = 0.00117 (Fisher's exact test), Q value = 0.15

Table S3.  Gene #5: 'amp_3p25.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 101 288
AMP PEAK 5(3P25.2) MUTATED 32 145
AMP PEAK 5(3P25.2) WILD-TYPE 69 143

Figure S3.  Get High-res Image Gene #5: 'amp_3p25.2' versus Clinical Feature #7: 'GENDER'

'amp_6p22.3' versus 'Time to Death'

P value = 0.00195 (logrank test), Q value = 0.15

Table S4.  Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 383 153 0.1 - 166.0 (15.7)
AMP PEAK 10(6P22.3) MUTATED 160 50 0.4 - 166.0 (17.2)
AMP PEAK 10(6P22.3) WILD-TYPE 223 103 0.1 - 140.8 (15.0)

Figure S4.  Get High-res Image Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

'amp_7p21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00685 (Fisher's exact test), Q value = 0.24

Table S5.  Gene #13: 'amp_7p21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 4 124 127 129
AMP PEAK 13(7P21.1) MUTATED 2 48 61 77
AMP PEAK 13(7P21.1) WILD-TYPE 2 76 66 52

Figure S5.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_7p21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00221 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #13: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
AMP PEAK 13(7P21.1) MUTATED 95 26 44 7
AMP PEAK 13(7P21.1) WILD-TYPE 129 16 31 1

Figure S6.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7p21.1' versus 'RACE'

P value = 0.00406 (Fisher's exact test), Q value = 0.2

Table S7.  Gene #13: 'amp_7p21.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 42 21 311
AMP PEAK 13(7P21.1) MUTATED 11 13 160
AMP PEAK 13(7P21.1) WILD-TYPE 31 8 151

Figure S7.  Get High-res Image Gene #13: 'amp_7p21.1' versus Clinical Feature #11: 'RACE'

'amp_10p14' versus 'YEARS_TO_BIRTH'

P value = 0.0042 (Wilcoxon-test), Q value = 0.2

Table S8.  Gene #19: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
AMP PEAK 19(10P14) MUTATED 171 69.5 (10.0)
AMP PEAK 19(10P14) WILD-TYPE 217 66.4 (10.9)

Figure S8.  Get High-res Image Gene #19: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11p13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00143 (Fisher's exact test), Q value = 0.15

Table S9.  Gene #20: 'amp_11p13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
AMP PEAK 20(11P13) MUTATED 19 5 15 4
AMP PEAK 20(11P13) WILD-TYPE 205 37 60 4

Figure S9.  Get High-res Image Gene #20: 'amp_11p13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_16p13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00477 (Fisher's exact test), Q value = 0.21

Table S10.  Gene #26: 'amp_16p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1+T2 T3 T4
ALL 121 184 53
AMP PEAK 26(16P13.2) MUTATED 19 35 20
AMP PEAK 26(16P13.2) WILD-TYPE 102 149 33

Figure S10.  Get High-res Image Gene #26: 'amp_16p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p14.2' versus 'RACE'

P value = 0.00228 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #39: 'del_3p14.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 42 21 311
DEL PEAK 6(3P14.2) MUTATED 3 7 95
DEL PEAK 6(3P14.2) WILD-TYPE 39 14 216

Figure S11.  Get High-res Image Gene #39: 'del_3p14.2' versus Clinical Feature #11: 'RACE'

'del_5q12.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00202 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #42: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
DEL PEAK 9(5Q12.1) MUTATED 90 24 46 6
DEL PEAK 9(5Q12.1) WILD-TYPE 134 18 29 2

Figure S12.  Get High-res Image Gene #42: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q12.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00586 (Wilcoxon-test), Q value = 0.22

Table S13.  Gene #42: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
DEL PEAK 9(5Q12.1) MUTATED 141 2.8 (9.1)
DEL PEAK 9(5Q12.1) WILD-TYPE 143 1.3 (3.4)

Figure S13.  Get High-res Image Gene #42: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_6q21' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0024 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #44: 'del_6q21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 4 124 127 129
DEL PEAK 11(6Q21) MUTATED 0 53 50 75
DEL PEAK 11(6Q21) WILD-TYPE 4 71 77 54

Figure S14.  Get High-res Image Gene #44: 'del_6q21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q21' versus 'PATHOLOGY_N_STAGE'

P value = 0.00061 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #44: 'del_6q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
DEL PEAK 11(6Q21) MUTATED 87 21 49 4
DEL PEAK 11(6Q21) WILD-TYPE 137 21 26 4

Figure S15.  Get High-res Image Gene #44: 'del_6q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000282 (Wilcoxon-test), Q value = 0.14

Table S16.  Gene #44: 'del_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
DEL PEAK 11(6Q21) MUTATED 139 3.2 (9.6)
DEL PEAK 11(6Q21) WILD-TYPE 145 0.9 (1.9)

Figure S16.  Get High-res Image Gene #44: 'del_6q21' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_6q27' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00432 (Fisher's exact test), Q value = 0.2

Table S17.  Gene #45: 'del_6q27' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 4 124 127 129
DEL PEAK 12(6Q27) MUTATED 1 48 52 75
DEL PEAK 12(6Q27) WILD-TYPE 3 76 75 54

Figure S17.  Get High-res Image Gene #45: 'del_6q27' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q27' versus 'PATHOLOGY_N_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.14

Table S18.  Gene #45: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
DEL PEAK 12(6Q27) MUTATED 87 19 50 4
DEL PEAK 12(6Q27) WILD-TYPE 137 23 25 4

Figure S18.  Get High-res Image Gene #45: 'del_6q27' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q27' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000685 (Wilcoxon-test), Q value = 0.14

Table S19.  Gene #45: 'del_6q27' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
DEL PEAK 12(6Q27) MUTATED 137 3.1 (9.5)
DEL PEAK 12(6Q27) WILD-TYPE 147 1.0 (2.4)

Figure S19.  Get High-res Image Gene #45: 'del_6q27' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_8p23.3' versus 'RACE'

P value = 0.00686 (Fisher's exact test), Q value = 0.24

Table S20.  Gene #47: 'del_8p23.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 42 21 311
DEL PEAK 14(8P23.3) MUTATED 17 17 184
DEL PEAK 14(8P23.3) WILD-TYPE 25 4 127

Figure S20.  Get High-res Image Gene #47: 'del_8p23.3' versus Clinical Feature #11: 'RACE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00326 (Wilcoxon-test), Q value = 0.18

Table S21.  Gene #54: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
DEL PEAK 21(11P15.5) MUTATED 197 69.2 (10.6)
DEL PEAK 21(11P15.5) WILD-TYPE 191 66.3 (10.5)

Figure S21.  Get High-res Image Gene #54: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_12q24.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00288 (Wilcoxon-test), Q value = 0.17

Table S22.  Gene #58: 'del_12q24.33' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
DEL PEAK 25(12Q24.33) MUTATED 63 3.2 (6.0)
DEL PEAK 25(12Q24.33) WILD-TYPE 221 1.7 (7.1)

Figure S22.  Get High-res Image Gene #58: 'del_12q24.33' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'del_14q24.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.15

Table S23.  Gene #60: 'del_14q24.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
DEL PEAK 27(14Q24.1) MUTATED 67 9 38 1
DEL PEAK 27(14Q24.1) WILD-TYPE 157 33 37 7

Figure S23.  Get High-res Image Gene #60: 'del_14q24.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00508 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #66: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
DEL PEAK 33(19P13.3) MUTATED 68 23 30 5
DEL PEAK 33(19P13.3) WILD-TYPE 156 19 45 3

Figure S24.  Get High-res Image Gene #66: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

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/15082908/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/15076720/BLCA-TP.merged_data.txt

  • Number of patients = 389

  • Number of significantly focal cnvs = 69

  • Number of selected clinical features = 12

  • 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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