Correlation between copy number variations of arm-level result and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 13 clinical features across 408 patients, 22 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 3p gain cnv correlated to 'YEARS_TO_BIRTH' and 'NUMBER_OF_LYMPH_NODES'.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 7q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 10q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_N_STAGE'.

  • 14q gain cnv correlated to 'RACE'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3p loss cnv correlated to 'GENDER'.

  • 4p loss cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_N_STAGE'.

  • 4q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 5q loss cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 6q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 15q loss cnv correlated to 'RACE'.

  • 21q loss 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 82 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 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
3q gain 178 (44%) 230 0.637
(0.994) 		0.00375
(0.233) 		0.0238
(0.4) 		0.428
(0.922) 		0.00473
(0.233) 		0.211
(0.754) 		0.91
(1.00) 		1
(1.00) 		0.109
(0.665) 		0.302
(0.814) 		0.0001
(0.0789) 		0.131
(0.679) 		1
(1.00)
3p gain 142 (35%) 266 0.415
(0.91) 		0.00133
(0.158) 		0.0756
(0.571) 		0.163
(0.696) 		0.0268
(0.4) 		0.186
(0.729) 		0.238
(0.773) 		0.806
(1.00) 		0.0898
(0.614) 		0.0239
(0.4) 		0.000228
(0.0789) 		0.0953
(0.627) 		1
(1.00)
11q gain 48 (12%) 360 0.0185
(0.371) 		0.00469
(0.233) 		0.0472
(0.521) 		0.663
(0.994) 		0.00378
(0.233) 		0.275
(0.797) 		0.0552
(0.528) 		0.709
(0.994) 		0.892
(1.00) 		0.846
(1.00) 		0.0971
(0.631) 		0.333
(0.842) 		1
(1.00)
4p loss 143 (35%) 265 0.081
(0.596) 		0.181
(0.727) 		0.00146
(0.158) 		0.147
(0.68) 		0.00028
(0.0789) 		0.744
(0.994) 		0.637
(0.994) 		1
(1.00) 		0.577
(0.977) 		0.198
(0.739) 		0.00796
(0.272) 		0.0087
(0.273) 		0.504
(0.943)
6q loss 159 (39%) 249 0.848
(1.00) 		0.615
(0.987) 		0.0055
(0.251) 		0.316
(0.818) 		0.00332
(0.233) 		0.539
(0.969) 		0.645
(0.994) 		0.336
(0.847) 		0.0348
(0.454) 		0.653
(0.994) 		0.00148
(0.158) 		0.0376
(0.472) 		0.0961
(0.628)
2p gain 111 (27%) 297 0.546
(0.972) 		0.112
(0.665) 		0.0877
(0.614) 		0.85
(1.00) 		0.0154
(0.353) 		0.18
(0.724) 		0.016
(0.353) 		1
(1.00) 		0.739
(0.994) 		0.116
(0.67) 		0.00416
(0.233) 		0.44
(0.93) 		0.702
(0.994)
7q gain 150 (37%) 258 0.684
(0.994) 		0.0397
(0.493) 		0.118
(0.67) 		0.0853
(0.609) 		0.00037
(0.0789) 		0.51
(0.949) 		0.56
(0.977) 		0.636
(0.994) 		0.269
(0.797) 		0.704
(0.994) 		0.146
(0.68) 		0.0476
(0.521) 		1
(1.00)
10q gain 45 (11%) 363 0.0597
(0.528) 		0.822
(1.00) 		0.0458
(0.521) 		0.238
(0.773) 		0.00403
(0.233) 		1
(1.00) 		0.859
(1.00) 		0.708
(0.994) 		0.688
(0.994) 		0.581
(0.978) 		0.0232
(0.4) 		0.791
(1.00) 		1
(1.00)
14q gain 58 (14%) 350 0.0251
(0.4) 		0.533
(0.964) 		0.414
(0.91) 		0.0419
(0.507) 		0.892
(1.00) 		0.296
(0.814) 		0.0358
(0.455) 		1
(1.00) 		0.528
(0.961) 		0.702
(0.994) 		0.513
(0.949) 		0.00231
(0.205) 		0.358
(0.87)
21q gain 115 (28%) 293 0.413
(0.91) 		0.000736
(0.131) 		0.764
(1.00) 		0.272
(0.797) 		0.463
(0.934) 		1
(1.00) 		0.213
(0.754) 		0.609
(0.984) 		0.351
(0.861) 		0.905
(1.00) 		0.301
(0.814) 		0.563
(0.977) 		1
(1.00)
3p loss 53 (13%) 355 0.44
(0.93) 		0.341
(0.85) 		0.238
(0.773) 		0.37
(0.878) 		0.69
(0.994) 		1
(1.00) 		0.00401
(0.233) 		1
(1.00) 		0.778
(1.00) 		0.616
(0.987) 		0.635
(0.994) 		0.0675
(0.542) 		1
(1.00)
4q loss 136 (33%) 272 0.651
(0.994) 		0.00481
(0.233) 		0.0548
(0.528) 		0.574
(0.977) 		0.073
(0.567) 		0.739
(0.994) 		1
(1.00) 		1
(1.00) 		0.342
(0.85) 		0.959
(1.00) 		0.183
(0.728) 		0.102
(0.644) 		0.483
(0.94)
5p loss 56 (14%) 352 0.708
(0.994) 		0.00253
(0.208) 		0.266
(0.796) 		0.792
(1.00) 		0.254
(0.789) 		0.0679
(0.542) 		0.744
(0.994) 		1
(1.00) 		0.613
(0.987) 		0.974
(1.00) 		0.416
(0.91) 		0.719
(0.994) 		1
(1.00)
5q loss 159 (39%) 249 0.404
(0.906) 		0.111
(0.665) 		0.0424
(0.507) 		0.222
(0.763) 		0.00201
(0.195) 		0.102
(0.644) 		0.908
(1.00) 		0.632
(0.994) 		0.0209
(0.391) 		0.0476
(0.521) 		0.00822
(0.272) 		0.00655
(0.251) 		0.742
(0.994)
15q loss 145 (36%) 263 0.597
(0.984) 		0.296
(0.814) 		0.402
(0.906) 		0.144
(0.68) 		0.971
(1.00) 		0.507
(0.946) 		0.35
(0.861) 		0.223
(0.763) 		0.0896
(0.614) 		0.297
(0.814) 		0.609
(0.984) 		0.00091
(0.139) 		0.291
(0.814)
21q loss 79 (19%) 329 0.417
(0.91) 		0.159
(0.696) 		0.303
(0.814) 		0.768
(1.00) 		0.00035
(0.0789) 		1
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.602
(0.984) 		0.601
(0.984) 		0.469
(0.934) 		0.0635
(0.542) 		0.687
(0.994)
1p gain 90 (22%) 318 0.538
(0.969) 		0.461
(0.934) 		0.454
(0.934) 		0.578
(0.977) 		0.0172
(0.36) 		0.698
(0.994) 		0.501
(0.943) 		0.775
(1.00) 		0.633
(0.994) 		0.165
(0.699) 		0.305
(0.814) 		0.111
(0.665) 		1
(1.00)
1q gain 128 (31%) 280 0.683
(0.994) 		0.93
(1.00) 		0.121
(0.67) 		0.866
(1.00) 		0.0498
(0.521) 		0.311
(0.814) 		0.718
(0.994) 		0.608
(0.984) 		0.3
(0.814) 		0.0849
(0.609) 		0.0584
(0.528) 		0.311
(0.814) 		0.727
(0.994)
2q gain 57 (14%) 351 0.498
(0.943) 		0.82
(1.00) 		0.71
(0.994) 		0.809
(1.00) 		0.649
(0.994) 		0.629
(0.994) 		0.332
(0.842) 		0.494
(0.943) 		0.808
(1.00) 		0.669
(0.994) 		0.128
(0.679) 		0.955
(1.00) 		1
(1.00)
4p gain 38 (9%) 370 0.056
(0.528) 		0.528
(0.961) 		0.367
(0.876) 		0.0586
(0.528) 		0.17
(0.707) 		0.368
(0.876) 		0.124
(0.677) 		1
(1.00) 		0.215
(0.76) 		0.964
(1.00) 		0.233
(0.77) 		0.643
(0.994) 		0.553
(0.976)
4q gain 26 (6%) 382 0.157
(0.694) 		0.133
(0.68) 		0.255
(0.789) 		0.0172
(0.36) 		0.669
(0.994) 		1
(1.00) 		0.645
(0.994) 		1
(1.00) 		0.406
(0.909) 		0.974
(1.00) 		0.288
(0.814) 		0.592
(0.984) 		0.421
(0.917)
5p gain 166 (41%) 242 0.937
(1.00) 		0.919
(1.00) 		0.545
(0.972) 		0.832
(1.00) 		0.446
(0.933) 		0.102
(0.644) 		0.819
(1.00) 		1
(1.00) 		0.417
(0.91) 		0.999
(1.00) 		0.589
(0.984) 		0.0999
(0.644) 		0.741
(0.994)
5q gain 53 (13%) 355 0.903
(1.00) 		0.0632
(0.542) 		0.772
(1.00) 		0.83
(1.00) 		0.411
(0.91) 		0.604
(0.984) 		1
(1.00) 		0.728
(0.994) 		0.923
(1.00) 		0.0722
(0.566) 		0.482
(0.94) 		0.578
(0.977) 		1
(1.00)
6p gain 78 (19%) 330 0.839
(1.00) 		0.139
(0.68) 		0.72
(0.994) 		0.712
(0.994) 		0.576
(0.977) 		0.686
(0.994) 		0.252
(0.786) 		0.362
(0.87) 		0.491
(0.943) 		0.0527
(0.528) 		0.783
(1.00) 		0.267
(0.797) 		0.683
(0.994)
6q gain 41 (10%) 367 0.262
(0.793) 		0.389
(0.9) 		0.838
(1.00) 		0.696
(0.994) 		0.211
(0.754) 		1
(1.00) 		0.0917
(0.614) 		0.0272
(0.4) 		0.617
(0.987) 		0.16
(0.696) 		0.608
(0.984) 		0.258
(0.793) 		1
(1.00)
7p gain 171 (42%) 237 0.875
(1.00) 		0.0592
(0.528) 		0.0107
(0.3) 		0.0293
(0.412) 		0.00658
(0.251) 		0.755
(0.999) 		0.82
(1.00) 		0.0598
(0.528) 		0.157
(0.694) 		0.714
(0.994) 		0.22
(0.763) 		0.0682
(0.542) 		1
(1.00)
8p gain 90 (22%) 318 0.229
(0.77) 		0.47
(0.934) 		0.818
(1.00) 		0.837
(1.00) 		0.473
(0.934) 		0.729
(0.994) 		0.587
(0.984) 		1
(1.00) 		0.162
(0.696) 		0.577
(0.977) 		0.123
(0.677) 		0.875
(1.00) 		1
(1.00)
8q gain 203 (50%) 205 0.276
(0.797) 		0.659
(0.994) 		0.591
(0.984) 		0.94
(1.00) 		0.735
(0.994) 		0.767
(1.00) 		1
(1.00) 		0.347
(0.859) 		0.209
(0.749) 		0.872
(1.00) 		0.232
(0.77) 		0.306
(0.814) 		0.742
(0.994)
9p gain 68 (17%) 340 0.137
(0.68) 		0.986
(1.00) 		0.897
(1.00) 		0.827
(1.00) 		0.231
(0.77) 		0.392
(0.9) 		0.452
(0.934) 		0.75
(0.994) 		0.187
(0.729) 		0.567
(0.977) 		0.972
(1.00) 		0.0659
(0.542) 		0.646
(0.994)
9q gain 56 (14%) 352 0.315
(0.818) 		0.304
(0.814) 		0.508
(0.946) 		0.24
(0.775) 		0.741
(0.994) 		0.0328
(0.442) 		0.513
(0.949) 		0.489
(0.943) 		0.887
(1.00) 		0.275
(0.797) 		0.25
(0.785) 		0.156
(0.694) 		0.339
(0.847)
10p gain 116 (28%) 292 0.26
(0.793) 		0.739
(0.994) 		0.522
(0.957) 		0.797
(1.00) 		0.0193
(0.38) 		1
(1.00) 		0.212
(0.754) 		0.608
(0.984) 		0.206
(0.746) 		0.396
(0.904) 		0.0605
(0.529) 		0.057
(0.528) 		0.707
(0.994)
11p gain 28 (7%) 380 0.0662
(0.542) 		0.777
(1.00) 		0.807
(1.00) 		0.821
(1.00) 		0.00615
(0.251) 		0.401
(0.906) 		0.0142
(0.337) 		1
(1.00) 		0.575
(0.977) 		0.974
(1.00) 		0.701
(0.994) 		0.25
(0.785) 		0.504
(0.943)
12p gain 115 (28%) 293 0.603
(0.984) 		0.0118
(0.301) 		0.339
(0.847) 		0.39
(0.9) 		0.485
(0.941) 		1
(1.00) 		0.708
(0.994) 		1
(1.00) 		0.521
(0.957) 		0.748
(0.994) 		0.878
(1.00) 		0.872
(1.00) 		0.713
(0.994)
12q gain 92 (23%) 316 0.547
(0.973) 		0.309
(0.814) 		0.194
(0.739) 		0.441
(0.93) 		0.87
(1.00) 		1
(1.00) 		0.501
(0.943) 		0.784
(1.00) 		0.661
(0.994) 		0.759
(1) 		0.88
(1.00) 		0.828
(1.00) 		1
(1.00)
13q gain 100 (25%) 308 0.651
(0.994) 		0.466
(0.934) 		0.379
(0.891) 		0.787
(1.00) 		0.00955
(0.283) 		0.148
(0.68) 		0.297
(0.814) 		1
(1.00) 		0.186
(0.729) 		0.935
(1.00) 		0.0734
(0.567) 		0.163
(0.696) 		0.119
(0.67)
15q gain 35 (9%) 373 0.55
(0.975) 		0.283
(0.81) 		0.205
(0.746) 		0.0264
(0.4) 		0.426
(0.921) 		1
(1.00) 		0.841
(1.00) 		0.205
(0.746) 		0.0952
(0.627) 		0.835
(1.00) 		0.328
(0.836) 		0.868
(1.00) 		0.553
(0.976)
16p gain 74 (18%) 334 0.19
(0.731) 		0.222
(0.763) 		0.113
(0.665) 		0.0162
(0.353) 		0.184
(0.728) 		0.128
(0.679) 		0.308
(0.814) 		1
(1.00) 		0.393
(0.902) 		0.6
(0.984) 		0.156
(0.694) 		0.306
(0.814) 		1
(1.00)
16q gain 83 (20%) 325 0.263
(0.793) 		0.147
(0.68) 		0.324
(0.829) 		0.103
(0.644) 		0.262
(0.793) 		0.118
(0.67) 		0.0504
(0.522) 		1
(1.00) 		0.665
(0.994) 		0.796
(1.00) 		0.89
(1.00) 		0.12
(0.67) 		0.693
(0.994)
17p gain 58 (14%) 350 0.219
(0.763) 		0.174
(0.718) 		0.847
(1.00) 		0.425
(0.921) 		0.671
(0.994) 		0.167
(0.702) 		1
(1.00) 		1
(1.00) 		0.4
(0.906) 		0.199
(0.739) 		0.957
(1.00) 		0.139
(0.68) 		0.348
(0.859)
17q gain 136 (33%) 272 0.268
(0.797) 		0.144
(0.68) 		0.0652
(0.542) 		0.878
(1.00) 		0.0347
(0.454) 		0.737
(0.994) 		0.811
(1.00) 		0.321
(0.822) 		0.0807
(0.596) 		0.198
(0.739) 		0.0581
(0.528) 		0.317
(0.818) 		0.0641
(0.542)
18p gain 117 (29%) 291 0.908
(1.00) 		0.468
(0.934) 		0.681
(0.994) 		0.724
(0.994) 		0.287
(0.814) 		0.467
(0.934) 		0.619
(0.987) 		0.606
(0.984) 		0.044
(0.521) 		0.163
(0.696) 		0.855
(1.00) 		0.0251
(0.4) 		0.721
(0.994)
18q gain 63 (15%) 345 0.563
(0.977) 		0.288
(0.814) 		0.638
(0.994) 		0.606
(0.984) 		0.558
(0.976) 		1
(1.00) 		0.877
(1.00) 		0.75
(0.994) 		0.144
(0.68) 		0.696
(0.994) 		0.467
(0.934) 		0.0162
(0.353) 		0.636
(0.994)
19p gain 87 (21%) 321 0.582
(0.978) 		0.877
(1.00) 		0.898
(1.00) 		0.503
(0.943) 		0.442
(0.93) 		0.707
(0.994) 		0.494
(0.943) 		0.558
(0.976) 		0.965
(1.00) 		0.784
(1.00) 		0.0754
(0.571) 		0.148
(0.68) 		0.691
(0.994)
19q gain 134 (33%) 274 0.31
(0.814) 		0.558
(0.976) 		0.184
(0.728) 		0.32
(0.822) 		0.14
(0.68) 		0.334
(0.845) 		1
(1.00) 		0.449
(0.933) 		0.728
(0.994) 		0.155
(0.694) 		0.00761
(0.271) 		0.633
(0.994) 		1
(1.00)
20p gain 201 (49%) 207 0.399
(0.906) 		0.121
(0.67) 		0.12
(0.67) 		0.281
(0.806) 		0.0354
(0.454) 		0.117
(0.67) 		1
(1.00) 		0.159
(0.696) 		0.223
(0.763) 		0.397
(0.904) 		0.0868
(0.613) 		0.00843
(0.272) 		0.175
(0.722)
20q gain 229 (56%) 179 0.842
(1.00) 		0.223
(0.763) 		0.237
(0.773) 		0.467
(0.934) 		0.0857
(0.609) 		0.542
(0.971) 		0.307
(0.814) 		0.816
(1.00) 		0.827
(1.00) 		0.737
(0.994) 		0.199
(0.739) 		0.0297
(0.412) 		0.309
(0.814)
22q gain 49 (12%) 359 0.805
(1.00) 		0.616
(0.987) 		0.656
(0.994) 		0.575
(0.977) 		0.195
(0.739) 		1
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.747
(0.994) 		0.566
(0.977) 		0.163
(0.696) 		0.594
(0.984) 		0.606
(0.984)
xp gain 66 (16%) 342 0.843
(1.00) 		0.256
(0.789) 		0.802
(1.00) 		1
(1.00) 		0.711
(0.994) 		0.368
(0.876) 		0.445
(0.933) 		0.0533
(0.528) 		0.582
(0.978) 		0.273
(0.797) 		0.678
(0.994) 		0.447
(0.933) 		0.14
(0.68)
xq gain 47 (12%) 361 0.65
(0.994) 		0.0594
(0.528) 		0.836
(1.00) 		0.839
(1.00) 		0.605
(0.984) 		1
(1.00) 		0.597
(0.984) 		0.147
(0.68) 		0.86
(1.00) 		0.396
(0.904) 		0.43
(0.922) 		0.72
(0.994) 		1
(1.00)
1p loss 34 (8%) 374 0.519
(0.956) 		0.938
(1.00) 		0.0352
(0.454) 		0.144
(0.68) 		0.221
(0.763) 		0.19
(0.731) 		0.543
(0.972) 		0.674
(0.994) 		0.845
(1.00) 		0.191
(0.731) 		0.314
(0.817) 		0.265
(0.796) 		1
(1.00)
1q loss 34 (8%) 374 0.5
(0.943) 		0.748
(0.994) 		0.0104
(0.299) 		0.118
(0.67) 		0.458
(0.934) 		0.58
(0.978) 		1
(1.00) 		0.388
(0.9) 		1
(1.00) 		0.0271
(0.4) 		0.436
(0.927) 		0.749
(0.994) 		1
(1.00)
2p loss 45 (11%) 363 0.633
(0.994) 		0.96
(1.00) 		0.374
(0.883) 		0.61
(0.984) 		0.68
(0.994) 		0.623
(0.991) 		0.372
(0.881) 		0.133
(0.68) 		0.145
(0.68) 		0.853
(1.00) 		0.877
(1.00) 		0.619
(0.987) 		1
(1.00)
2q loss 91 (22%) 317 0.512
(0.949) 		0.654
(0.994) 		0.636
(0.994) 		0.534
(0.964) 		0.25
(0.785) 		0.467
(0.934) 		0.787
(1.00) 		0.391
(0.9) 		0.0599
(0.528) 		0.646
(0.994) 		0.201
(0.743) 		1
(1.00) 		1
(1.00)
3q loss 24 (6%) 384 0.988
(1.00) 		0.436
(0.927) 		0.127
(0.679) 		0.57
(0.977) 		0.749
(0.994) 		0.526
(0.961) 		0.473
(0.934) 		1
(1.00) 		0.813
(1.00) 		0.303
(0.814) 		0.5
(0.943) 		0.81
(1.00) 		1
(1.00)
6p loss 100 (25%) 308 0.0854
(0.609) 		0.503
(0.943) 		0.248
(0.785) 		0.114
(0.665) 		0.0252
(0.4) 		1
(1.00) 		0.36
(0.87) 		1
(1.00) 		0.276
(0.797) 		0.847
(1.00) 		0.156
(0.694) 		0.27
(0.797) 		0.235
(0.77)
7p loss 21 (5%) 387 0.981
(1.00) 		0.993
(1.00) 		0.106
(0.658) 		0.471
(0.934) 		0.023
(0.4) 		1
(1.00) 		0.307
(0.814) 		0.241
(0.777) 		0.928
(1.00) 		0.569
(0.977) 		0.141
(0.68) 		0.807
(1.00) 		1
(1.00)
7q loss 27 (7%) 381 0.998
(1.00) 		0.321
(0.822) 		0.23
(0.77) 		0.96
(1.00) 		0.274
(0.797) 		1
(1.00) 		0.256
(0.789) 		1
(1.00) 		0.482
(0.94) 		0.0417
(0.507) 		0.671
(0.994) 		0.533
(0.964) 		0.13
(0.679)
8p loss 188 (46%) 220 0.897
(1.00) 		0.546
(0.972) 		0.0494
(0.521) 		0.776
(1.00) 		0.142
(0.68) 		0.352
(0.863) 		1
(1.00) 		0.637
(0.994) 		0.403
(0.906) 		0.297
(0.814) 		0.0616
(0.534) 		0.0451
(0.521) 		1
(1.00)
8q loss 38 (9%) 370 0.983
(1.00) 		0.33
(0.839) 		0.0952
(0.627) 		0.00756
(0.271) 		0.36
(0.87) 		0.275
(0.797) 		0.441
(0.93) 		0.391
(0.9) 		0.777
(1.00) 		0.818
(1.00) 		0.0908
(0.614) 		0.683
(0.994) 		0.607
(0.984)
9p loss 175 (43%) 233 0.957
(1.00) 		0.0235
(0.4) 		0.28
(0.805) 		0.958
(1.00) 		0.49
(0.943) 		0.759
(1) 		0.733
(0.994) 		0.48
(0.94) 		0.164
(0.696) 		0.481
(0.94) 		0.569
(0.977) 		0.85
(1.00) 		1
(1.00)
9q loss 170 (42%) 238 0.462
(0.934) 		0.232
(0.77) 		0.177
(0.722) 		0.684
(0.994) 		0.455
(0.934) 		0.554
(0.976) 		0.733
(0.994) 		0.354
(0.864) 		0.422
(0.918) 		0.132
(0.679) 		0.992
(1.00) 		0.339
(0.847) 		0.742
(0.994)
10p loss 74 (18%) 334 0.54
(0.969) 		0.721
(0.994) 		0.477
(0.939) 		0.711
(0.994) 		0.875
(1.00) 		0.416
(0.91) 		0.884
(1.00) 		0.142
(0.68) 		0.244
(0.778) 		0.0496
(0.521) 		0.806
(1.00) 		0.00926
(0.282) 		0.671
(0.994)
10q loss 128 (31%) 280 0.197
(0.739) 		0.023
(0.4) 		0.503
(0.943) 		0.851
(1.00) 		0.708
(0.994) 		0.303
(0.814) 		1
(1.00) 		0.13
(0.679) 		0.576
(0.977) 		0.745
(0.994) 		0.446
(0.933) 		0.158
(0.694) 		0.473
(0.934)
11p loss 181 (44%) 227 0.501
(0.943) 		0.0118
(0.301) 		0.0535
(0.528) 		0.939
(1.00) 		0.0599
(0.528) 		0.358
(0.87) 		0.91
(1.00) 		0.482
(0.94) 		0.561
(0.977) 		0.43
(0.922) 		0.0284
(0.409) 		0.114
(0.665) 		0.512
(0.949)
11q loss 131 (32%) 277 0.735
(0.994) 		0.515
(0.95) 		0.643
(0.994) 		0.73
(0.994) 		0.403
(0.906) 		1
(1.00) 		0.186
(0.729) 		0.205
(0.746) 		0.93
(1.00) 		0.767
(1.00) 		0.811
(1.00) 		0.277
(0.797) 		1
(1.00)
12p loss 56 (14%) 352 0.574
(0.977) 		0.853
(1.00) 		0.144
(0.68) 		0.0915
(0.614) 		0.0907
(0.614) 		1
(1.00) 		0.744
(0.994) 		0.732
(0.994) 		0.743
(0.994) 		0.391
(0.9) 		0.0486
(0.521) 		0.49
(0.943) 		0.367
(0.876)
12q loss 60 (15%) 348 0.916
(1.00) 		0.197
(0.739) 		0.0777
(0.583) 		0.233
(0.77) 		0.049
(0.521) 		1
(1.00) 		0.875
(1.00) 		0.169
(0.706) 		0.316
(0.818) 		0.797
(1.00) 		0.0298
(0.412) 		0.671
(0.994) 		1
(1.00)
13q loss 86 (21%) 322 0.877
(1.00) 		0.264
(0.796) 		0.389
(0.9) 		0.566
(0.977) 		0.466
(0.934) 		0.466
(0.934) 		0.408
(0.91) 		0.564
(0.977) 		0.905
(1.00) 		0.808
(1.00) 		0.616
(0.987) 		0.0672
(0.542) 		0.0811
(0.596)
14q loss 122 (30%) 286 0.129
(0.679) 		0.0269
(0.4) 		0.536
(0.967) 		0.753
(0.996) 		0.00565
(0.251) 		1
(1.00) 		0.11
(0.665) 		0.204
(0.746) 		0.373
(0.882) 		0.0528
(0.528) 		0.141
(0.68) 		0.785
(1.00) 		0.287
(0.814)
16p loss 107 (26%) 301 0.245
(0.778) 		0.759
(1) 		0.698
(0.994) 		0.142
(0.68) 		0.304
(0.814) 		1
(1.00) 		0.522
(0.957) 		0.178
(0.722) 		0.556
(0.976) 		0.728
(0.994) 		0.784
(1.00) 		0.00605
(0.251) 		0.701
(0.994)
16q loss 103 (25%) 305 0.244
(0.778) 		0.25
(0.785) 		0.386
(0.9) 		0.96
(1.00) 		0.128
(0.679) 		1
(1.00) 		0.154
(0.694) 		0.425
(0.921) 		0.17
(0.707) 		0.979
(1.00) 		0.137
(0.68) 		0.0122
(0.302) 		0.0459
(0.521)
17p loss 180 (44%) 228 0.732
(0.994) 		0.0198
(0.38) 		0.415
(0.91) 		0.301
(0.814) 		0.27
(0.797) 		0.531
(0.963) 		0.428
(0.922) 		1
(1.00) 		0.956
(1.00) 		0.8
(1.00) 		0.235
(0.77) 		0.894
(1.00) 		1
(1.00)
17q loss 43 (11%) 365 0.503
(0.943) 		0.474
(0.934) 		0.379
(0.891) 		0.11
(0.665) 		0.19
(0.731) 		1
(1.00) 		0.359
(0.87) 		0.442
(0.93) 		0.835
(1.00) 		0.593
(0.984) 		0.748
(0.994) 		0.409
(0.91) 		0.606
(0.984)
18p loss 99 (24%) 309 0.907
(1.00) 		0.861
(1.00) 		0.0184
(0.371) 		0.846
(1.00) 		0.0142
(0.337) 		0.294
(0.814) 		0.433
(0.925) 		0.788
(1.00) 		0.149
(0.68) 		0.297
(0.814) 		0.0464
(0.521) 		0.857
(1.00) 		0.45
(0.933)
18q loss 146 (36%) 262 0.388
(0.9) 		0.555
(0.976) 		0.661
(0.994) 		0.77
(1.00) 		0.311
(0.814) 		0.219
(0.763) 		0.412
(0.91) 		0.466
(0.934) 		0.782
(1.00) 		0.18
(0.724) 		0.206
(0.746) 		0.953
(1.00) 		0.289
(0.814)
19p loss 94 (23%) 314 0.208
(0.748) 		0.0533
(0.528) 		0.102
(0.644) 		0.0274
(0.4) 		0.125
(0.677) 		0.232
(0.77) 		1
(1.00) 		0.0886
(0.614) 		0.233
(0.77) 		0.853
(1.00) 		0.666
(0.994) 		0.0743
(0.57) 		0.222
(0.763)
19q loss 57 (14%) 351 0.107
(0.661) 		0.644
(0.994) 		0.809
(1.00) 		0.252
(0.786) 		0.758
(1) 		0.361
(0.87) 		1
(1.00) 		0.492
(0.943) 		0.125
(0.677) 		0.201
(0.743) 		0.492
(0.943) 		0.6
(0.984) 		0.367
(0.876)
20p loss 33 (8%) 375 0.233
(0.77) 		0.821
(1.00) 		0.714
(0.994) 		0.45
(0.933) 		0.523
(0.957) 		1
(1.00) 		0.152
(0.693) 		0.646
(0.994) 		0.457
(0.934) 		0.0665
(0.542) 		0.639
(0.994) 		0.26
(0.793) 		1
(1.00)
20q loss 14 (3%) 394 0.178
(0.722) 		0.699
(0.994) 		0.0834
(0.609) 		0.191
(0.731) 		0.131
(0.679) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.465
(0.934) 		0.642
(0.994) 		0.188
(0.729) 		0.856
(1.00) 		1
(1.00)
22q loss 159 (39%) 249 0.23
(0.77) 		0.176
(0.722) 		0.0263
(0.4) 		0.105
(0.656) 		0.0114
(0.301) 		1
(1.00) 		1
(1.00) 		0.337
(0.847) 		0.114
(0.667) 		0.433
(0.925) 		0.0199
(0.38) 		0.0118
(0.301) 		0.0311
(0.425)
xp loss 71 (17%) 337 0.74
(0.994) 		0.472
(0.934) 		0.737
(0.994) 		0.964
(1.00) 		0.706
(0.994) 		0.686
(0.994) 		0.767
(1.00) 		0.348
(0.859) 		0.262
(0.793) 		0.698
(0.994) 		0.79
(1.00) 		0.733
(0.994) 		0.66
(0.994)
xq loss 80 (20%) 328 0.302
(0.814) 		0.243
(0.778) 		0.733
(0.994) 		0.672
(0.994) 		0.819
(1.00) 		0.693
(0.994) 		0.671
(0.994) 		0.551
(0.976) 		0.168
(0.706) 		0.466
(0.934) 		0.496
(0.943) 		0.806
(1.00) 		0.0712
(0.562)
'2p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00416 (Wilcoxon-test), Q value = 0.23

Table S1.  Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
2P GAIN MUTATED 79 2.7 (5.2)
2P GAIN WILD-TYPE 218 1.9 (7.6)

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00133 (Wilcoxon-test), Q value = 0.16

Table S2.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
3P GAIN MUTATED 141 70.4 (10.2)
3P GAIN WILD-TYPE 266 66.9 (10.7)

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000228 (Wilcoxon-test), Q value = 0.079

Table S3.  Gene #5: '3p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
3P GAIN MUTATED 99 3.7 (11.0)
3P GAIN WILD-TYPE 198 1.3 (3.5)

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00375 (Wilcoxon-test), Q value = 0.23

Table S4.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
3Q GAIN MUTATED 177 69.9 (10.3)
3Q GAIN WILD-TYPE 230 66.7 (10.7)

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00473 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
3Q GAIN MUTATED 84 24 43 4
3Q GAIN WILD-TYPE 151 23 32 5

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 1e-04 (Wilcoxon-test), Q value = 0.079

Table S6.  Gene #6: '3q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
3Q GAIN MUTATED 129 3.4 (9.8)
3Q GAIN WILD-TYPE 168 1.1 (3.2)

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.079

Table S7.  Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
7Q GAIN MUTATED 77 19 31 9
7Q GAIN WILD-TYPE 158 28 44 0

Figure S7.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00403 (Fisher's exact test), Q value = 0.23

Table S8.  Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
10Q GAIN MUTATED 17 11 11 2
10Q GAIN WILD-TYPE 218 36 64 7

Figure S8.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00469 (Wilcoxon-test), Q value = 0.23

Table S9.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
11Q GAIN MUTATED 48 72.0 (11.0)
11Q GAIN WILD-TYPE 359 67.6 (10.5)

Figure S9.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00378 (Fisher's exact test), Q value = 0.23

Table S10.  Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
11Q GAIN MUTATED 21 5 15 4
11Q GAIN WILD-TYPE 214 42 60 5

Figure S10.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q gain' versus 'RACE'

P value = 0.00231 (Fisher's exact test), Q value = 0.21

Table S11.  Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
14Q GAIN MUTATED 0 5 47
14Q GAIN WILD-TYPE 43 17 280

Figure S11.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000736 (Wilcoxon-test), Q value = 0.13

Table S12.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
21Q GAIN MUTATED 115 71.0 (9.9)
21Q GAIN WILD-TYPE 292 66.9 (10.7)

Figure S12.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'GENDER'

P value = 0.00401 (Fisher's exact test), Q value = 0.23

Table S13.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 107 301
3P LOSS MUTATED 23 30
3P LOSS WILD-TYPE 84 271

Figure S13.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00146 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 2 129 140 135
4P LOSS MUTATED 1 35 43 64
4P LOSS WILD-TYPE 1 94 97 71

Figure S14.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.079

Table S15.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
4P LOSS MUTATED 62 23 37 2
4P LOSS WILD-TYPE 173 24 38 7

Figure S15.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00481 (Wilcoxon-test), Q value = 0.23

Table S16.  Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
4Q LOSS MUTATED 136 70.3 (9.4)
4Q LOSS WILD-TYPE 271 67.0 (11.0)

Figure S16.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00253 (Wilcoxon-test), Q value = 0.21

Table S17.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
5P LOSS MUTATED 56 72.1 (8.2)
5P LOSS WILD-TYPE 351 67.5 (10.8)

Figure S17.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00201 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
5Q LOSS MUTATED 74 21 36 7
5Q LOSS WILD-TYPE 161 26 39 2

Figure S18.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00332 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
6Q LOSS MUTATED 76 20 41 5
6Q LOSS WILD-TYPE 159 27 34 4

Figure S19.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00148 (Wilcoxon-test), Q value = 0.16

Table S20.  Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
6Q LOSS MUTATED 122 2.5 (5.2)
6Q LOSS WILD-TYPE 175 1.8 (8.0)

Figure S20.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'15q loss' versus 'RACE'

P value = 0.00091 (Fisher's exact test), Q value = 0.14

Table S21.  Gene #68: '15q loss' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
15Q LOSS MUTATED 6 4 127
15Q LOSS WILD-TYPE 37 18 200

Figure S21.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #12: 'RACE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.079

Table S22.  Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 235 47 75 9
21Q LOSS MUTATED 40 20 11 0
21Q LOSS WILD-TYPE 195 27 64 9

Figure S22.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/19780561/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/19775034/BLCA-TP.merged_data.txt

  • Number of patients = 408

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 13

  • Exclude regions 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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