Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1SN0859
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SN0859
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 12 clinical features across 528 patients, 133 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death'.

  • 1q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 5p gain cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • 5q gain cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • 7p gain cnv correlated to 'PATHOLOGY_M_STAGE',  'GENDER', and 'RACE'.

  • 7q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER', and 'RACE'.

  • 8p gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 8q gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 9p gain cnv correlated to 'GENDER'.

  • 9q gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 10q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 11p gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 12p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 12q gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 14q gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 17p gain cnv correlated to 'PATHOLOGY_M_STAGE' and 'RACE'.

  • 19p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 19q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'RACE'.

  • 20p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • 20q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • xp gain cnv correlated to 'PATHOLOGIC_STAGE'.

  • xq gain cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 1p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 3p loss cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.

  • 3q loss cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • 4p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 4q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'RACE'.

  • 5p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 5q loss cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 6p loss cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

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

  • 7p loss cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.

  • 7q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 8q loss cnv correlated to 'GENDER'.

  • 9p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • 9q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • 10p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 10q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 11p loss cnv correlated to 'Time to Death'.

  • 11q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 13q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 14q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER', and 'RACE'.

  • 15q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 16p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 16q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 18p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 18q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 19p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 19q loss cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.

  • 21q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 22q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'ETHNICITY'.

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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 133 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		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
14q loss 216 (41%) 312 0.000776
(0.0201) 		0.257
(0.733) 		1e-05
(0.00141) 		3e-05
(0.00204) 		0.000724
(0.0194) 		0.00111
(0.0237) 		0.0266
(0.213) 		0.0441
(0.31) 		0.201
(0.68) 		0.073
(0.411) 		0.0192
(0.168) 		0.686
(1.00)
12p gain 121 (23%) 407 0.00603
(0.0761) 		0.185
(0.661) 		0.00028
(0.00984) 		0.00144
(0.0283) 		0.0479
(0.32) 		0.0193
(0.168) 		0.388
(0.882) 		0.018
(0.166) 		0.311
(0.804) 		0.109
(0.499) 		0.225
(0.711)
12q gain 122 (23%) 406 0.00918
(0.105) 		0.334
(0.835) 		0.00018
(0.00757) 		0.0008
(0.0202) 		0.0479
(0.32) 		0.0199
(0.172) 		0.334
(0.835) 		0.018
(0.166) 		0.311
(0.804) 		0.112
(0.506) 		0.225
(0.711)
4q loss 65 (12%) 463 4.24e-06
(0.00141) 		0.828
(1.00) 		3e-05
(0.00204) 		2e-05
(0.00179) 		0.438
(0.918) 		0.00293
(0.0471) 		0.27
(0.752) 		0.827
(1.00) 		0.0216
(0.182) 		0.55
(1.00)
9p loss 149 (28%) 379 1.89e-05
(0.00179) 		0.0573
(0.355) 		2e-05
(0.00179) 		6e-05
(0.00328) 		0.0854
(0.45) 		0.0016
(0.0303) 		0.000887
(0.0203) 		0.673
(1.00) 		1
(1.00) 		0.872
(1.00) 		0.135
(0.551) 		0.655
(1.00)
9q loss 150 (28%) 378 0.000295
(0.01) 		0.0404
(0.286) 		1e-05
(0.00141) 		1e-05
(0.00141) 		0.0941
(0.472) 		0.00411
(0.0586) 		0.00086
(0.0203) 		0.437
(0.918) 		1
(1.00) 		0.872
(1.00) 		0.124
(0.534) 		0.823
(1.00)
3q gain 61 (12%) 467 0.194
(0.669) 		0.905
(1.00) 		0.00017
(0.00757) 		5e-05
(0.00307) 		0.00655
(0.0815) 		0.0074
(0.0899) 		0.671
(1.00) 		0.671
(1.00) 		0.479
(0.962) 		1
(1.00)
7q gain 172 (33%) 356 0.549
(1.00) 		0.261
(0.737) 		0.0143
(0.149) 		0.0512
(0.331) 		0.296
(0.792) 		0.00255
(0.0427) 		0.00897
(0.104) 		0.663
(1.00) 		0.275
(0.761) 		0.0635
(0.378) 		0.0185
(0.168) 		0.271
(0.752)
19q gain 57 (11%) 471 0.814
(1.00) 		0.392
(0.884) 		0.00087
(0.0203) 		0.00494
(0.0671) 		0.416
(0.903) 		0.00354
(0.0531) 		0.242
(0.716) 		0.494
(0.98) 		0.0313
(0.235) 		1
(1.00)
20p gain 112 (21%) 416 0.141
(0.564) 		0.233
(0.711) 		3e-05
(0.00204) 		1e-05
(0.00141) 		0.375
(0.877) 		0.0167
(0.16) 		0.00035
(0.0108) 		0.965
(1.00) 		0.498
(0.982) 		0.328
(0.833) 		0.442
(0.919)
20q gain 115 (22%) 413 0.104
(0.487) 		0.0787
(0.431) 		2e-05
(0.00179) 		1e-05
(0.00141) 		0.225
(0.711) 		0.0188
(0.168) 		0.00199
(0.0363) 		0.965
(1.00) 		0.498
(0.982) 		0.316
(0.811) 		0.319
(0.815)
4p loss 72 (14%) 456 5.55e-05
(0.00321) 		0.743
(1.00) 		0.0002
(0.00757) 		0.00025
(0.00911) 		0.718
(1.00) 		0.0216
(0.182) 		0.895
(1.00) 		0.874
(1.00) 		0.0449
(0.313) 		0.399
(0.891)
13q loss 71 (13%) 457 0.00157
(0.0303) 		0.928
(1.00) 		0.00019
(0.00757) 		1e-05
(0.00141) 		0.3
(0.795) 		0.0333
(0.248) 		0.425
(0.914) 		0.874
(1.00) 		0.209
(0.693) 		0.228
(0.711)
15q loss 36 (7%) 492 0.000934
(0.0204) 		0.965
(1.00) 		0.00126
(0.0253) 		0.00053
(0.0153) 		1
(1.00) 		0.0142
(0.149) 		0.104
(0.487) 		0.599
(1.00) 		0.179
(0.651) 		0.385
(0.877)
5p gain 193 (37%) 335 0.0616
(0.375) 		0.000108
(0.00536) 		0.129
(0.542) 		0.175
(0.648) 		0.803
(1.00) 		1
(1.00) 		0.0144
(0.149) 		0.343
(0.836) 		0.919
(1.00) 		0.781
(1.00) 		0.0306
(0.233) 		0.833
(1.00)
5q gain 207 (39%) 321 0.0641
(0.378) 		0.000331
(0.0108) 		0.371
(0.877) 		0.287
(0.777) 		0.619
(1.00) 		1
(1.00) 		0.0158
(0.157) 		0.462
(0.937) 		0.967
(1.00) 		0.781
(1.00) 		0.0274
(0.214) 		0.836
(1.00)
7p gain 171 (32%) 357 0.987
(1.00) 		0.228
(0.711) 		0.059
(0.363) 		0.104
(0.487) 		0.306
(0.8) 		0.0255
(0.207) 		0.00356
(0.0531) 		0.984
(1.00) 		0.182
(0.653) 		0.0635
(0.378) 		0.0189
(0.168) 		0.655
(1.00)
19p gain 51 (10%) 477 0.776
(1.00) 		0.676
(1.00) 		0.00302
(0.0472) 		0.013
(0.141) 		0.232
(0.711) 		0.00781
(0.0937) 		0.22
(0.709) 		0.494
(0.98) 		0.0739
(0.411) 		0.727
(1.00)
5p loss 7 (1%) 521 0.0232
(0.193) 		0.252
(0.727) 		0.00168
(0.0312) 		0.0002
(0.00757) 		1
(1.00) 		0.0816
(0.439) 		0.256
(0.733) 		1
(1.00) 		1
(1.00)
6p loss 100 (19%) 428 0.376
(0.877) 		0.271
(0.752) 		0.0481
(0.32) 		0.0169
(0.16) 		0.0156
(0.157) 		0.279
(0.765) 		0.00118
(0.0244) 		0.114
(0.506) 		0.51
(0.996) 		0.643
(1.00) 		0.0362
(0.266) 		1
(1.00)
18p loss 93 (18%) 435 0.00093
(0.0204) 		0.0927
(0.468) 		0.00034
(0.0108) 		0.0002
(0.00757) 		1
(1.00) 		0.0797
(0.431) 		0.234
(0.711) 		0.911
(1.00) 		0.233
(0.711) 		0.0978
(0.476)
18q loss 95 (18%) 433 0.0046
(0.0637) 		0.113
(0.506) 		0.00897
(0.104) 		0.00417
(0.0586) 		1
(1.00) 		0.113
(0.506) 		0.193
(0.669) 		0.77
(1.00) 		0.214
(0.701) 		0.28
(0.766)
19p loss 11 (2%) 517 3.11e-05
(0.00204) 		0.0927
(0.468) 		0.0254
(0.207) 		0.0006
(0.0169) 		1
(1.00) 		0.391
(0.884) 		0.754
(1.00) 		0.121
(0.524) 		1
(1.00)
22q loss 39 (7%) 489 0.00725
(0.0892) 		0.242
(0.716) 		0.019
(0.168) 		0.159
(0.608) 		1
(1.00) 		0.1
(0.48) 		0.863
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.00959
(0.109)
8p gain 31 (6%) 497 0.503
(0.987) 		0.176
(0.65) 		0.00086
(0.0203) 		0.00073
(0.0194) 		1
(1.00) 		0.194
(0.669) 		0.563
(1.00) 		0.241
(0.716) 		0.524
(1.00) 		0.382
(0.877)
8q gain 62 (12%) 466 0.113
(0.506) 		0.0457
(0.315) 		0.00341
(0.0524) 		0.00509
(0.0677) 		0.438
(0.918) 		0.0855
(0.45) 		0.0911
(0.464) 		0.286
(0.775) 		0.8
(1.00) 		0.738
(1.00) 		0.496
(0.982)
11p gain 31 (6%) 497 0.563
(1.00) 		0.986
(1.00) 		0.0276
(0.214) 		0.0126
(0.138) 		1
(1.00) 		0.116
(0.506) 		0.847
(1.00) 		0.288
(0.777) 		0.731
(1.00) 		1
(1.00)
17p gain 26 (5%) 502 0.766
(1.00) 		0.557
(1.00) 		0.297
(0.792) 		0.825
(1.00) 		0.191
(0.668) 		0.0213
(0.182) 		1
(1.00) 		0.679
(1.00) 		0.0266
(0.213) 		0.612
(1.00)
3p loss 380 (72%) 148 0.606
(1.00) 		0.815
(1.00) 		0.0392
(0.279) 		0.0271
(0.214) 		0.593
(1.00) 		0.1
(0.48) 		0.0114
(0.127) 		0.643
(1.00) 		0.522
(1.00) 		0.458
(0.936) 		0.183
(0.655) 		0.655
(1.00)
3q loss 99 (19%) 429 0.993
(1.00) 		0.0135
(0.145) 		0.482
(0.966) 		0.233
(0.711) 		0.485
(0.968) 		0.876
(1.00) 		0.000109
(0.00536) 		0.0791
(0.431) 		0.694
(1.00) 		0.783
(1.00)
5q loss 6 (1%) 522 0.0664
(0.389) 		0.15
(0.583) 		0.00557
(0.0721) 		0.00037
(0.011) 		1
(1.00) 		0.24
(0.716) 		0.672
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 128 (24%) 400 0.431
(0.916) 		0.666
(1.00) 		0.304
(0.8) 		0.182
(0.653) 		0.00363
(0.0532) 		0.669
(1.00) 		0.0717
(0.408) 		0.501
(0.986) 		0.0337
(0.249) 		0.643
(1.00) 		0.0711
(0.407) 		0.476
(0.96)
7p loss 3 (1%) 525 0.0307
(0.233) 		0.695
(1.00) 		0.0738
(0.411) 		0.0175
(0.164) 		0.131
(0.542) 		1
(1.00) 		0.556
(1.00) 		0.326
(0.828) 		1
(1.00)
11q loss 23 (4%) 505 0.00256
(0.0427) 		0.0059
(0.0755) 		0.453
(0.932) 		0.516
(1.00) 		0.217
(0.704) 		0.385
(0.877) 		0.38
(0.877) 		0.378
(0.877) 		0.644
(1.00) 		1
(1.00)
19q loss 4 (1%) 524 0.00244
(0.042) 		0.844
(1.00) 		0.195
(0.669) 		0.00297
(0.0471) 		1
(1.00) 		0.118
(0.513) 		1
(1.00) 		1
(1.00) 		1
(1.00)
1p gain 24 (5%) 504 0.00237
(0.042) 		0.168
(0.629) 		0.152
(0.59) 		0.262
(0.738) 		0.191
(0.668) 		0.385
(0.877) 		1
(1.00) 		0.177
(0.65) 		0.431
(0.916) 		1
(1.00)
1q gain 51 (10%) 477 0.0503
(0.329) 		0.0297
(0.228) 		0.0571
(0.355) 		0.0798
(0.431) 		0.406
(0.894) 		0.682
(1.00) 		0.541
(1.00) 		0.426
(0.914) 		0.634
(1.00) 		0.727
(1.00)
9p gain 13 (2%) 515 0.171
(0.636) 		0.674
(1.00) 		0.902
(1.00) 		0.0469
(0.32) 		1
(1.00) 		0.237
(0.713) 		0.0166
(0.16) 		0.709
(1.00) 		0.55
(1.00)
9q gain 12 (2%) 516 0.633
(1.00) 		0.337
(0.836) 		0.241
(0.716) 		0.00282
(0.0462) 		1
(1.00) 		1
(1.00) 		0.128
(0.542) 		1
(1.00) 		0.55
(1.00)
10q gain 12 (2%) 516 0.73
(1.00) 		0.0152
(0.154) 		0.847
(1.00) 		0.88
(1.00) 		0.246
(0.716) 		1
(1.00) 		0.364
(0.873) 		0.578
(1.00) 		0.486
(0.968) 		1
(1.00)
14q gain 16 (3%) 512 0.131
(0.542) 		0.473
(0.957) 		0.226
(0.711) 		0.00531
(0.0697) 		1
(1.00) 		0.295
(0.792) 		0.796
(1.00) 		1
(1.00) 		1
(1.00)
xp gain 32 (6%) 496 0.53
(1.00) 		0.558
(1.00) 		0.0239
(0.198) 		0.0959
(0.474) 		1
(1.00) 		0.0369
(0.269) 		0.851
(1.00) 		0.943
(1.00) 		0.108
(0.499) 		0.383
(0.877)
xq gain 31 (6%) 497 0.877
(1.00) 		0.781
(1.00) 		0.0537
(0.342) 		0.116
(0.506) 		1
(1.00) 		0.0274
(0.214) 		0.704
(1.00) 		0.558
(1.00) 		0.534
(1.00) 		0.383
(0.877)
1p loss 57 (11%) 471 0.536
(1.00) 		0.131
(0.542) 		0.436
(0.918) 		0.0152
(0.154) 		1
(1.00) 		0.431
(0.916) 		0.381
(0.877) 		0.72
(1.00) 		0.45
(0.929) 		0.209
(0.693)
7q loss 4 (1%) 524 0.265
(0.746) 		0.712
(1.00) 		0.0452
(0.313) 		0.016
(0.157) 		0.131
(0.542) 		1
(1.00) 		0.302
(0.797) 		0.408
(0.895) 		0.194
(0.669)
8q loss 64 (12%) 464 0.459
(0.936) 		0.805
(1.00) 		0.629
(1.00) 		0.244
(0.716) 		1
(1.00) 		1
(1.00) 		0.0125
(0.138) 		0.653
(1.00) 		0.229
(0.711) 		0.0504
(0.329)
10p loss 67 (13%) 461 0.363
(0.873) 		0.358
(0.867) 		0.0734
(0.411) 		0.00902
(0.104) 		0.236
(0.713) 		0.583
(1.00) 		0.34
(0.836) 		0.145
(0.574) 		0.593
(1.00) 		0.209
(0.693)
10q loss 89 (17%) 439 0.519
(1.00) 		0.536
(1.00) 		0.0992
(0.48) 		0.00242
(0.042) 		0.485
(0.968) 		0.627
(1.00) 		0.115
(0.506) 		0.187
(0.666) 		0.285
(0.775) 		0.278
(0.765)
11p loss 18 (3%) 510 0.00389
(0.0563) 		0.0538
(0.342) 		0.279
(0.765) 		0.403
(0.891) 		0.141
(0.564) 		0.505
(0.987) 		1
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00)
16p loss 10 (2%) 518 0.091
(0.464) 		0.652
(1.00) 		0.395
(0.887) 		0.0169
(0.16) 		0.346
(0.844) 		1
(1.00) 		1
(1.00) 		0.401
(0.891) 		1
(1.00)
16q loss 16 (3%) 512 0.139
(0.561) 		0.332
(0.834) 		0.412
(0.899) 		0.00498
(0.0671) 		0.434
(0.918) 		1
(1.00) 		0.796
(1.00) 		0.166
(0.629) 		1
(1.00)
21q loss 55 (10%) 473 0.726
(1.00) 		0.723
(1.00) 		0.107
(0.497) 		0.00119
(0.0244) 		0.0844
(0.449) 		1
(1.00) 		0.461
(0.937) 		0.842
(1.00) 		0.581
(1.00) 		1
(1.00)
2p gain 77 (15%) 451 0.505
(0.987) 		0.134
(0.547) 		0.236
(0.713) 		0.425
(0.914) 		0.739
(1.00) 		0.231
(0.711) 		1
(1.00) 		0.776
(1.00) 		0.543
(1.00) 		0.406
(0.894) 		0.761
(1.00)
2q gain 79 (15%) 449 0.519
(1.00) 		0.217
(0.704) 		0.462
(0.937) 		0.546
(1.00) 		1
(1.00) 		0.392
(0.884) 		0.525
(1.00) 		0.829
(1.00) 		0.543
(1.00) 		0.337
(0.836) 		0.374
(0.877)
3p gain 19 (4%) 509 0.101
(0.484) 		0.516
(1.00) 		0.149
(0.583) 		0.194
(0.669) 		0.0389
(0.279) 		0.0978
(0.476) 		0.332
(0.834) 		0.821
(1.00) 		0.784
(1.00) 		1
(1.00)
4p gain 13 (2%) 515 0.146
(0.577) 		0.774
(1.00) 		0.381
(0.877) 		0.171
(0.636) 		0.474
(0.957) 		1
(1.00) 		0.396
(0.887) 		1
(1.00) 		1
(1.00)
4q gain 13 (2%) 515 0.383
(0.877) 		0.774
(1.00) 		0.456
(0.936) 		0.678
(1.00) 		0.434
(0.918) 		0.702
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00)
6p gain 11 (2%) 517 0.916
(1.00) 		0.793
(1.00) 		0.312
(0.804) 		0.232
(0.711) 		1
(1.00) 		0.686
(1.00) 		0.342
(0.836) 		1
(1.00) 		1
(1.00)
6q gain 9 (2%) 519 0.741
(1.00) 		0.359
(0.867) 		0.218
(0.704) 		0.283
(0.771) 		1
(1.00) 		1
(1.00) 		0.168
(0.629) 		1
(1.00) 		1
(1.00)
10p gain 17 (3%) 511 0.724
(1.00) 		0.095
(0.472) 		0.171
(0.637) 		0.102
(0.484) 		0.0951
(0.472) 		0.739
(1.00) 		0.798
(1.00) 		0.9
(1.00) 		0.416
(0.903) 		1
(1.00)
11q gain 29 (5%) 499 0.215
(0.701) 		0.946
(1.00) 		0.163
(0.619) 		0.0841
(0.449) 		1
(1.00) 		0.42
(0.909) 		1
(1.00) 		0.848
(1.00) 		1
(1.00)
13q gain 22 (4%) 506 0.126
(0.541) 		0.254
(0.73) 		0.129
(0.542) 		0.206
(0.692) 		1
(1.00) 		0.367
(0.877) 		0.257
(0.733) 		0.0977
(0.476) 		0.09
(0.464)
15q gain 26 (5%) 502 0.538
(1.00) 		0.451
(0.929) 		0.448
(0.929) 		0.371
(0.877) 		0.191
(0.668) 		0.582
(1.00) 		0.678
(1.00) 		0.0531
(0.341) 		0.565
(1.00) 		1
(1.00)
16p gain 107 (20%) 421 0.371
(0.877) 		0.245
(0.716) 		0.157
(0.607) 		0.0711
(0.407) 		0.21
(0.694) 		0.648
(1.00) 		0.652
(1.00) 		0.669
(1.00) 		0.0641
(0.378) 		0.238
(0.715) 		1
(1.00)
16q gain 99 (19%) 429 0.247
(0.716) 		0.338
(0.836) 		0.222
(0.711) 		0.0485
(0.32) 		0.208
(0.693) 		1
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.0641
(0.378) 		0.42
(0.909) 		0.787
(1.00)
17q gain 33 (6%) 495 0.441
(0.919) 		0.341
(0.836) 		0.687
(1.00) 		0.658
(1.00) 		0.296
(0.792) 		0.202
(0.68) 		0.709
(1.00) 		0.559
(1.00) 		0.389
(0.882) 		0.0617
(0.375) 		0.383
(0.877)
18p gain 25 (5%) 503 0.0688
(0.4) 		0.804
(1.00) 		0.929
(1.00) 		0.872
(1.00) 		0.607
(1.00) 		0.401
(0.891) 		0.0907
(0.464) 		0.669
(1.00) 		0.332
(0.834)
18q gain 25 (5%) 503 0.132
(0.544) 		0.617
(1.00) 		0.833
(1.00) 		0.765
(1.00) 		0.577
(1.00) 		0.401
(0.891) 		0.0907
(0.464) 		0.667
(1.00) 		0.332
(0.834)
21q gain 50 (9%) 478 0.691
(1.00) 		0.116
(0.506) 		0.226
(0.711) 		0.113
(0.506) 		1
(1.00) 		0.533
(1.00) 		0.439
(0.919) 		0.112
(0.506) 		0.478
(0.962) 		0.22
(0.709) 		0.719
(1.00)
22q gain 40 (8%) 488 0.364
(0.873) 		0.563
(1.00) 		0.704
(1.00) 		0.0882
(0.462) 		1
(1.00) 		0.82
(1.00) 		0.305
(0.8) 		0.422
(0.911) 		0.213
(0.701) 		1
(1.00)
1q loss 36 (7%) 492 0.832
(1.00) 		0.655
(1.00) 		0.843
(1.00) 		0.0757
(0.418) 		1
(1.00) 		0.338
(0.836) 		0.591
(1.00) 		0.76
(1.00) 		0.374
(0.877) 		0.45
(0.929)
2p loss 14 (3%) 514 0.815
(1.00) 		0.839
(1.00) 		0.43
(0.916) 		0.139
(0.561) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.0557
(0.35) 		1
(1.00)
2q loss 14 (3%) 514 0.804
(1.00) 		0.814
(1.00) 		0.539
(1.00) 		0.221
(0.709) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.179
(0.651) 		1
(1.00)
8p loss 137 (26%) 391 0.18
(0.651) 		0.674
(1.00) 		0.32
(0.815) 		0.19
(0.668) 		1
(1.00) 		0.267
(0.748) 		0.0389
(0.279) 		0.841
(1.00) 		0.964
(1.00) 		0.458
(0.936) 		0.13
(0.542) 		0.0559
(0.35)
12p loss 4 (1%) 524 0.258
(0.735) 		0.69
(1.00) 		0.772
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.41
(0.897) 		1
(1.00)
12q loss 4 (1%) 524 0.829
(1.00) 		0.312
(0.804) 		0.159
(0.608) 		0.408
(0.895) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 46 (9%) 482 0.342
(0.836) 		0.3
(0.795) 		0.144
(0.574) 		0.134
(0.547) 		0.375
(0.877) 		0.0474
(0.32) 		0.197
(0.67) 		0.299
(0.794) 		1
(1.00) 		0.713
(1.00)
17q loss 28 (5%) 500 0.441
(0.919) 		0.787
(1.00) 		0.307
(0.802) 		0.26
(0.736) 		1
(1.00) 		0.18
(0.651) 		0.311
(0.804) 		0.841
(1.00) 		1
(1.00)
20p loss 8 (2%) 520 0.732
(1.00) 		0.701
(1.00) 		0.791
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.366
(0.876) 		1
(1.00) 		0.158
(0.607) 		0.25
(0.724)
20q loss 3 (1%) 525 0.873
(1.00) 		0.115
(0.506) 		0.234
(0.711) 		0.108
(0.499) 		0.402
(0.891) 		1
(1.00) 		1
(1.00) 		0.0691
(0.4)
xp loss 46 (9%) 482 0.317
(0.813) 		0.977
(1.00) 		0.901
(1.00) 		0.541
(1.00) 		0.243
(0.716) 		0.826
(1.00) 		0.197
(0.67) 		0.359
(0.867) 		0.809
(1.00) 		0.149
(0.583)
xq loss 46 (9%) 482 0.244
(0.716) 		0.607
(1.00) 		0.901
(1.00) 		0.538
(1.00) 		0.269
(0.752) 		1
(1.00) 		0.197
(0.67) 		0.696
(1.00) 		0.586
(1.00) 		0.15
(0.583)
'1p gain' versus 'Time to Death'

P value = 0.00237 (logrank test), Q value = 0.042

Table S1.  Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
1P GAIN MUTATED 24 14 0.5 - 118.8 (22.9)
1P GAIN WILD-TYPE 502 161 0.1 - 149.2 (38.8)

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0297 (Wilcoxon-test), Q value = 0.23

Table S2.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
1Q GAIN MUTATED 51 63.6 (11.8)
1Q GAIN WILD-TYPE 476 60.2 (12.1)

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0076

Table S3.  Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
3Q GAIN MUTATED 17 5 20 19
3Q GAIN WILD-TYPE 246 52 105 64

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0031

Table S4.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
3Q GAIN MUTATED 17 6 34 4
3Q GAIN WILD-TYPE 251 63 146 7

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00655 (Fisher's exact test), Q value = 0.082

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

nPatients 0 1
ALL 234 17
3Q GAIN MUTATED 31 7
3Q GAIN WILD-TYPE 203 10

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

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0074 (Fisher's exact test), Q value = 0.09

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

nPatients 0 1
ALL 418 78
3Q GAIN MUTATED 43 17
3Q GAIN WILD-TYPE 375 61

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

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000108 (Wilcoxon-test), Q value = 0.0054

Table S7.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
5P GAIN MUTATED 193 63.2 (11.8)
5P GAIN WILD-TYPE 334 59.0 (12.0)

Figure S7.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'GENDER'

P value = 0.0144 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #9: '5p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
5P GAIN MUTATED 56 137
5P GAIN WILD-TYPE 133 202

Figure S8.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'GENDER'

'5p gain' versus 'RACE'

P value = 0.0306 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #9: '5p gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
5P GAIN MUTATED 3 12 176
5P GAIN WILD-TYPE 5 44 281

Figure S9.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #11: 'RACE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000331 (Wilcoxon-test), Q value = 0.011

Table S10.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
5Q GAIN MUTATED 206 62.9 (12.2)
5Q GAIN WILD-TYPE 321 59.0 (11.8)

Figure S10.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'GENDER'

P value = 0.0158 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
5Q GAIN MUTATED 61 146
5Q GAIN WILD-TYPE 128 193

Figure S11.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

'5q gain' versus 'RACE'

P value = 0.0274 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
5Q GAIN MUTATED 3 13 189
5Q GAIN WILD-TYPE 5 43 268

Figure S12.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0255 (Fisher's exact test), Q value = 0.21

Table S13.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
7P GAIN MUTATED 130 35
7P GAIN WILD-TYPE 288 43

Figure S13.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'GENDER'

P value = 0.00356 (Fisher's exact test), Q value = 0.053

Table S14.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
7P GAIN MUTATED 46 125
7P GAIN WILD-TYPE 143 214

Figure S14.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7p gain' versus 'RACE'

P value = 0.0189 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #13: '7p gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
7P GAIN MUTATED 4 10 155
7P GAIN WILD-TYPE 4 46 302

Figure S15.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #11: 'RACE'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0143 (Fisher's exact test), Q value = 0.15

Table S16.  Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
7Q GAIN MUTATED 72 17 45 38
7Q GAIN WILD-TYPE 191 40 80 45

Figure S16.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00255 (Fisher's exact test), Q value = 0.043

Table S17.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
7Q GAIN MUTATED 128 38
7Q GAIN WILD-TYPE 290 40

Figure S17.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'GENDER'

P value = 0.00897 (Fisher's exact test), Q value = 0.1

Table S18.  Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
7Q GAIN MUTATED 48 124
7Q GAIN WILD-TYPE 141 215

Figure S18.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'RACE'

P value = 0.0185 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #14: '7q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
7Q GAIN MUTATED 4 10 156
7Q GAIN WILD-TYPE 4 46 301

Figure S19.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #11: 'RACE'

'8p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00086 (Fisher's exact test), Q value = 0.02

Table S20.  Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
8P GAIN MUTATED 6 8 9 8
8P GAIN WILD-TYPE 257 49 116 75

Figure S20.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00073 (Fisher's exact test), Q value = 0.019

Table S21.  Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
8P GAIN MUTATED 6 9 16 0
8P GAIN WILD-TYPE 262 60 164 11

Figure S21.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00341 (Fisher's exact test), Q value = 0.052

Table S22.  Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
8Q GAIN MUTATED 18 11 19 14
8Q GAIN WILD-TYPE 245 46 106 69

Figure S22.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00509 (Fisher's exact test), Q value = 0.068

Table S23.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
8Q GAIN MUTATED 19 12 30 1
8Q GAIN WILD-TYPE 249 57 150 10

Figure S23.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'GENDER'

P value = 0.0166 (Fisher's exact test), Q value = 0.16

Table S24.  Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
9P GAIN MUTATED 9 4
9P GAIN WILD-TYPE 180 335

Figure S24.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00282 (Fisher's exact test), Q value = 0.046

Table S25.  Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
9Q GAIN MUTATED 4 2 3 3
9Q GAIN WILD-TYPE 264 67 177 8

Figure S25.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0152 (Wilcoxon-test), Q value = 0.15

Table S26.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
10Q GAIN MUTATED 12 68.6 (12.2)
10Q GAIN WILD-TYPE 515 60.3 (12.0)

Figure S26.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0276 (Fisher's exact test), Q value = 0.21

Table S27.  Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
11P GAIN MUTATED 8 4 11 8
11P GAIN WILD-TYPE 255 53 114 75

Figure S27.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0126 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
11P GAIN MUTATED 8 4 18 1
11P GAIN WILD-TYPE 260 65 162 10

Figure S28.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12p gain' versus 'Time to Death'

P value = 0.00603 (logrank test), Q value = 0.076

Table S29.  Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
12P GAIN MUTATED 121 51 0.1 - 133.7 (31.9)
12P GAIN WILD-TYPE 405 124 0.1 - 149.2 (40.7)

Figure S29.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0098

Table S30.  Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
12P GAIN MUTATED 44 9 38 30
12P GAIN WILD-TYPE 219 48 87 53

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00144 (Fisher's exact test), Q value = 0.028

Table S31.  Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
12P GAIN MUTATED 46 13 58 4
12P GAIN WILD-TYPE 222 56 122 7

Figure S31.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0193 (Fisher's exact test), Q value = 0.17

Table S32.  Gene #23: '12p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
12P GAIN MUTATED 90 27
12P GAIN WILD-TYPE 328 51

Figure S32.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.018 (Wilcoxon-test), Q value = 0.17

Table S33.  Gene #23: '12p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 53 85.3 (26.0)
12P GAIN MUTATED 13 69.2 (39.9)
12P GAIN WILD-TYPE 40 90.5 (17.2)

Figure S33.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'12q gain' versus 'Time to Death'

P value = 0.00918 (logrank test), Q value = 0.11

Table S34.  Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
12Q GAIN MUTATED 122 51 0.1 - 133.7 (32.7)
12Q GAIN WILD-TYPE 404 124 0.1 - 149.2 (40.4)

Figure S34.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0076

Table S35.  Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
12Q GAIN MUTATED 44 9 39 30
12Q GAIN WILD-TYPE 219 48 86 53

Figure S35.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.02

Table S36.  Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
12Q GAIN MUTATED 46 13 59 4
12Q GAIN WILD-TYPE 222 56 121 7

Figure S36.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0199 (Fisher's exact test), Q value = 0.17

Table S37.  Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
12Q GAIN MUTATED 91 27
12Q GAIN WILD-TYPE 327 51

Figure S37.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.018 (Wilcoxon-test), Q value = 0.17

Table S38.  Gene #24: '12q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 53 85.3 (26.0)
12Q GAIN MUTATED 13 69.2 (39.9)
12Q GAIN WILD-TYPE 40 90.5 (17.2)

Figure S38.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00531 (Fisher's exact test), Q value = 0.07

Table S39.  Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
14Q GAIN MUTATED 5 2 6 3
14Q GAIN WILD-TYPE 263 67 174 8

Figure S39.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0213 (Fisher's exact test), Q value = 0.18

Table S40.  Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
17P GAIN MUTATED 25 0
17P GAIN WILD-TYPE 393 78

Figure S40.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p gain' versus 'RACE'

P value = 0.0266 (Fisher's exact test), Q value = 0.21

Table S41.  Gene #30: '17p gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
17P GAIN MUTATED 2 4 20
17P GAIN WILD-TYPE 6 52 437

Figure S41.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'RACE'

'19p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00302 (Fisher's exact test), Q value = 0.047

Table S42.  Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
19P GAIN MUTATED 15 7 13 16
19P GAIN WILD-TYPE 248 50 112 67

Figure S42.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.013 (Fisher's exact test), Q value = 0.14

Table S43.  Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
19P GAIN MUTATED 16 7 26 2
19P GAIN WILD-TYPE 252 62 154 9

Figure S43.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00781 (Fisher's exact test), Q value = 0.094

Table S44.  Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
19P GAIN MUTATED 36 15
19P GAIN WILD-TYPE 382 63

Figure S44.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00087 (Fisher's exact test), Q value = 0.02

Table S45.  Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
19Q GAIN MUTATED 16 7 16 18
19Q GAIN WILD-TYPE 247 50 109 65

Figure S45.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00494 (Fisher's exact test), Q value = 0.067

Table S46.  Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
19Q GAIN MUTATED 17 9 29 2
19Q GAIN WILD-TYPE 251 60 151 9

Figure S46.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00354 (Fisher's exact test), Q value = 0.053

Table S47.  Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
19Q GAIN MUTATED 40 17
19Q GAIN WILD-TYPE 378 61

Figure S47.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'RACE'

P value = 0.0313 (Fisher's exact test), Q value = 0.23

Table S48.  Gene #35: '19q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
19Q GAIN MUTATED 1 1 55
19Q GAIN WILD-TYPE 7 55 402

Figure S48.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #11: 'RACE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S49.  Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
20P GAIN MUTATED 34 12 38 28
20P GAIN WILD-TYPE 229 45 87 55

Figure S49.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S50.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
20P GAIN MUTATED 35 13 58 6
20P GAIN WILD-TYPE 233 56 122 5

Figure S50.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0167 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
20P GAIN MUTATED 84 26
20P GAIN WILD-TYPE 334 52

Figure S51.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'GENDER'

P value = 0.00035 (Fisher's exact test), Q value = 0.011

Table S52.  Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
20P GAIN MUTATED 24 88
20P GAIN WILD-TYPE 165 251

Figure S52.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0018

Table S53.  Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
20Q GAIN MUTATED 35 12 40 28
20Q GAIN WILD-TYPE 228 45 85 55

Figure S53.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S54.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
20Q GAIN MUTATED 37 13 60 5
20Q GAIN WILD-TYPE 231 56 120 6

Figure S54.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0188 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
20Q GAIN MUTATED 87 26
20Q GAIN WILD-TYPE 331 52

Figure S55.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'GENDER'

P value = 0.00199 (Fisher's exact test), Q value = 0.036

Table S56.  Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
20Q GAIN MUTATED 27 88
20Q GAIN WILD-TYPE 162 251

Figure S56.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0239 (Fisher's exact test), Q value = 0.2

Table S57.  Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
XP GAIN MUTATED 10 4 7 11
XP GAIN WILD-TYPE 253 53 118 72

Figure S57.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.21

Table S58.  Gene #41: 'xq gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
XQ GAIN MUTATED 19 9
XQ GAIN WILD-TYPE 399 69

Figure S58.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0152 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
1P LOSS MUTATED 32 9 12 4
1P LOSS WILD-TYPE 236 60 168 7

Figure S59.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0271 (Fisher's exact test), Q value = 0.21

Table S60.  Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
3P LOSS MUTATED 187 51 138 4
3P LOSS WILD-TYPE 81 18 42 7

Figure S60.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'GENDER'

P value = 0.0114 (Fisher's exact test), Q value = 0.13

Table S61.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
3P LOSS MUTATED 123 257
3P LOSS WILD-TYPE 66 82

Figure S61.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0135 (Wilcoxon-test), Q value = 0.14

Table S62.  Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
3Q LOSS MUTATED 99 63.5 (12.7)
3Q LOSS WILD-TYPE 428 59.8 (11.9)

Figure S62.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'GENDER'

P value = 0.000109 (Fisher's exact test), Q value = 0.0054

Table S63.  Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
3Q LOSS MUTATED 19 80
3Q LOSS WILD-TYPE 170 259

Figure S63.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'Time to Death'

P value = 5.55e-05 (logrank test), Q value = 0.0032

Table S64.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
4P LOSS MUTATED 72 39 0.5 - 133.7 (37.6)
4P LOSS WILD-TYPE 454 136 0.1 - 149.2 (38.6)

Figure S64.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0076

Table S65.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
4P LOSS MUTATED 21 6 25 20
4P LOSS WILD-TYPE 242 51 100 63

Figure S65.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0091

Table S66.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
4P LOSS MUTATED 22 8 38 4
4P LOSS WILD-TYPE 246 61 142 7

Figure S66.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0216 (Fisher's exact test), Q value = 0.18

Table S67.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
4P LOSS MUTATED 53 18
4P LOSS WILD-TYPE 365 60

Figure S67.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'Time to Death'

P value = 4.24e-06 (logrank test), Q value = 0.0014

Table S68.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
4Q LOSS MUTATED 65 37 1.2 - 133.7 (32.6)
4Q LOSS WILD-TYPE 461 138 0.1 - 149.2 (39.2)

Figure S68.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S69.  Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
4Q LOSS MUTATED 15 6 23 21
4Q LOSS WILD-TYPE 248 51 102 62

Figure S69.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0018

Table S70.  Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
4Q LOSS MUTATED 16 8 36 5
4Q LOSS WILD-TYPE 252 61 144 6

Figure S70.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00293 (Fisher's exact test), Q value = 0.047

Table S71.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
4Q LOSS MUTATED 46 19
4Q LOSS WILD-TYPE 372 59

Figure S71.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'RACE'

P value = 0.0216 (Fisher's exact test), Q value = 0.18

Table S72.  Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
4Q LOSS MUTATED 1 1 61
4Q LOSS WILD-TYPE 7 55 396

Figure S72.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'Time to Death'

P value = 0.0232 (logrank test), Q value = 0.19

Table S73.  Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
5P LOSS MUTATED 7 5 3.3 - 112.1 (30.5)
5P LOSS WILD-TYPE 519 170 0.1 - 149.2 (38.6)

Figure S73.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00168 (Fisher's exact test), Q value = 0.031

Table S74.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
5P LOSS MUTATED 0 2 1 4
5P LOSS WILD-TYPE 263 55 124 79

Figure S74.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0076

Table S75.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
5P LOSS MUTATED 0 3 2 2
5P LOSS WILD-TYPE 268 66 178 9

Figure S75.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00557 (Fisher's exact test), Q value = 0.072

Table S76.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
5Q LOSS MUTATED 0 2 1 3
5Q LOSS WILD-TYPE 263 55 124 80

Figure S76.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.011

Table S77.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
5Q LOSS MUTATED 0 2 2 2
5Q LOSS WILD-TYPE 268 67 178 9

Figure S77.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0169 (Fisher's exact test), Q value = 0.16

Table S78.  Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
6P LOSS MUTATED 38 15 43 4
6P LOSS WILD-TYPE 230 54 137 7

Figure S78.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0156 (Fisher's exact test), Q value = 0.16

Table S79.  Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
6P LOSS MUTATED 37 7
6P LOSS WILD-TYPE 197 10

Figure S79.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p loss' versus 'GENDER'

P value = 0.00118 (Fisher's exact test), Q value = 0.024

Table S80.  Gene #52: '6p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
6P LOSS MUTATED 22 78
6P LOSS WILD-TYPE 167 261

Figure S80.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'GENDER'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.053

Table S81.  Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
6Q LOSS MUTATED 46 9
6Q LOSS WILD-TYPE 188 8

Figure S81.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0337 (Wilcoxon-test), Q value = 0.25

Table S82.  Gene #53: '6q loss' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 21 28.3 (16.1)
6Q LOSS MUTATED 5 16.0 (13.7)
6Q LOSS WILD-TYPE 16 32.2 (15.2)

Figure S82.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'7p loss' versus 'Time to Death'

P value = 0.0307 (logrank test), Q value = 0.23

Table S83.  Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
7P LOSS MUTATED 3 2 1.4 - 53.5 (6.0)
7P LOSS WILD-TYPE 523 173 0.1 - 149.2 (38.5)

Figure S83.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

'7p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0175 (Fisher's exact test), Q value = 0.16

Table S84.  Gene #54: '7p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
7P LOSS MUTATED 0 0 2 1
7P LOSS WILD-TYPE 268 69 178 10

Figure S84.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'7q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.016 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #55: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
7Q LOSS MUTATED 0 1 2 1
7Q LOSS WILD-TYPE 268 68 178 10

Figure S85.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q loss' versus 'GENDER'

P value = 0.0125 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #57: '8q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
8Q LOSS MUTATED 14 50
8Q LOSS WILD-TYPE 175 289

Figure S86.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'Time to Death'

P value = 1.89e-05 (logrank test), Q value = 0.0018

Table S87.  Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
9P LOSS MUTATED 148 72 0.5 - 133.7 (38.6)
9P LOSS WILD-TYPE 378 103 0.1 - 149.2 (38.3)

Figure S87.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0018

Table S88.  Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
9P LOSS MUTATED 53 11 49 36
9P LOSS WILD-TYPE 210 46 76 47

Figure S88.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0033

Table S89.  Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
9P LOSS MUTATED 56 15 73 5
9P LOSS WILD-TYPE 212 54 107 6

Figure S89.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0016 (Fisher's exact test), Q value = 0.03

Table S90.  Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
9P LOSS MUTATED 109 35
9P LOSS WILD-TYPE 309 43

Figure S90.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'GENDER'

P value = 0.000887 (Fisher's exact test), Q value = 0.02

Table S91.  Gene #58: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
9P LOSS MUTATED 37 112
9P LOSS WILD-TYPE 152 227

Figure S91.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'Time to Death'

P value = 0.000295 (logrank test), Q value = 0.01

Table S92.  Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
9Q LOSS MUTATED 149 70 0.5 - 133.7 (38.6)
9Q LOSS WILD-TYPE 377 105 0.1 - 149.2 (38.3)

Figure S92.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S93.  Gene #59: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
9Q LOSS MUTATED 50 14 51 35
9Q LOSS WILD-TYPE 213 43 74 48

Figure S93.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S94.  Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
9Q LOSS MUTATED 52 18 76 4
9Q LOSS WILD-TYPE 216 51 104 7

Figure S94.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00411 (Fisher's exact test), Q value = 0.059

Table S95.  Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
9Q LOSS MUTATED 111 34
9Q LOSS WILD-TYPE 307 44

Figure S95.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'GENDER'

P value = 0.00086 (Fisher's exact test), Q value = 0.02

Table S96.  Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
9Q LOSS MUTATED 37 113
9Q LOSS WILD-TYPE 152 226

Figure S96.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'GENDER'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00902 (Fisher's exact test), Q value = 0.1

Table S97.  Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
10P LOSS MUTATED 25 7 31 4
10P LOSS WILD-TYPE 243 62 149 7

Figure S97.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00242 (Fisher's exact test), Q value = 0.042

Table S98.  Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
10Q LOSS MUTATED 34 12 37 6
10Q LOSS WILD-TYPE 234 57 143 5

Figure S98.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'Time to Death'

P value = 0.00389 (logrank test), Q value = 0.056

Table S99.  Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
11P LOSS MUTATED 18 10 1.7 - 84.3 (25.0)
11P LOSS WILD-TYPE 508 165 0.1 - 149.2 (39.1)

Figure S99.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'Time to Death'

P value = 0.00256 (logrank test), Q value = 0.043

Table S100.  Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
11Q LOSS MUTATED 23 12 1.7 - 109.9 (21.6)
11Q LOSS WILD-TYPE 503 163 0.1 - 149.2 (39.5)

Figure S100.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0059 (Wilcoxon-test), Q value = 0.075

Table S101.  Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
11Q LOSS MUTATED 23 66.7 (12.3)
11Q LOSS WILD-TYPE 504 60.2 (12.0)

Figure S101.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'Time to Death'

P value = 0.00157 (logrank test), Q value = 0.03

Table S102.  Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
13Q LOSS MUTATED 70 34 0.5 - 112.1 (31.5)
13Q LOSS WILD-TYPE 456 141 0.1 - 149.2 (39.1)

Figure S102.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0076

Table S103.  Gene #66: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
13Q LOSS MUTATED 25 2 24 20
13Q LOSS WILD-TYPE 238 55 101 63

Figure S103.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S104.  Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
13Q LOSS MUTATED 27 3 34 7
13Q LOSS WILD-TYPE 241 66 146 4

Figure S104.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0333 (Fisher's exact test), Q value = 0.25

Table S105.  Gene #66: '13q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
13Q LOSS MUTATED 52 17
13Q LOSS WILD-TYPE 366 61

Figure S105.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'Time to Death'

P value = 0.000776 (logrank test), Q value = 0.02

Table S106.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
14Q LOSS MUTATED 215 92 0.4 - 133.7 (36.2)
14Q LOSS WILD-TYPE 311 83 0.1 - 149.2 (41.9)

Figure S106.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S107.  Gene #67: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
14Q LOSS MUTATED 80 26 63 47
14Q LOSS WILD-TYPE 183 31 62 36

Figure S107.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S108.  Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
14Q LOSS MUTATED 85 34 94 3
14Q LOSS WILD-TYPE 183 35 86 8

Figure S108.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000724 (Fisher's exact test), Q value = 0.019

Table S109.  Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
14Q LOSS MUTATED 93 14
14Q LOSS WILD-TYPE 141 3

Figure S109.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.024

Table S110.  Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
14Q LOSS MUTATED 162 46
14Q LOSS WILD-TYPE 256 32

Figure S110.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'GENDER'

P value = 0.0266 (Fisher's exact test), Q value = 0.21

Table S111.  Gene #67: '14q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
14Q LOSS MUTATED 65 151
14Q LOSS WILD-TYPE 124 188

Figure S111.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'GENDER'

'14q loss' versus 'RACE'

P value = 0.0192 (Fisher's exact test), Q value = 0.17

Table S112.  Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
14Q LOSS MUTATED 2 14 196
14Q LOSS WILD-TYPE 6 42 261

Figure S112.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'Time to Death'

P value = 0.000934 (logrank test), Q value = 0.02

Table S113.  Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
15Q LOSS MUTATED 36 19 1.4 - 90.5 (32.0)
15Q LOSS WILD-TYPE 490 156 0.1 - 149.2 (39.1)

Figure S113.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00126 (Fisher's exact test), Q value = 0.025

Table S114.  Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
15Q LOSS MUTATED 9 2 13 12
15Q LOSS WILD-TYPE 254 55 112 71

Figure S114.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.015

Table S115.  Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
15Q LOSS MUTATED 10 2 21 3
15Q LOSS WILD-TYPE 258 67 159 8

Figure S115.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0142 (Fisher's exact test), Q value = 0.15

Table S116.  Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
15Q LOSS MUTATED 24 11
15Q LOSS WILD-TYPE 394 67

Figure S116.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0169 (Fisher's exact test), Q value = 0.16

Table S117.  Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
16P LOSS MUTATED 3 2 3 2
16P LOSS WILD-TYPE 265 67 177 9

Figure S117.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00498 (Fisher's exact test), Q value = 0.067

Table S118.  Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
16Q LOSS MUTATED 6 3 4 3
16Q LOSS WILD-TYPE 262 66 176 8

Figure S118.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'Time to Death'

P value = 0.00093 (logrank test), Q value = 0.02

Table S119.  Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
18P LOSS MUTATED 92 42 0.4 - 118.8 (31.3)
18P LOSS WILD-TYPE 434 133 0.1 - 149.2 (39.7)

Figure S119.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.011

Table S120.  Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
18P LOSS MUTATED 31 7 33 22
18P LOSS WILD-TYPE 232 50 92 61

Figure S120.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0076

Table S121.  Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
18P LOSS MUTATED 33 9 46 5
18P LOSS WILD-TYPE 235 60 134 6

Figure S121.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'Time to Death'

P value = 0.0046 (logrank test), Q value = 0.064

Table S122.  Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
18Q LOSS MUTATED 94 41 0.4 - 119.6 (31.5)
18Q LOSS WILD-TYPE 432 134 0.1 - 149.2 (39.7)

Figure S122.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00897 (Fisher's exact test), Q value = 0.1

Table S123.  Gene #74: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
18Q LOSS MUTATED 35 8 30 22
18Q LOSS WILD-TYPE 228 49 95 61

Figure S123.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00417 (Fisher's exact test), Q value = 0.059

Table S124.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
18Q LOSS MUTATED 37 10 43 5
18Q LOSS WILD-TYPE 231 59 137 6

Figure S124.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'Time to Death'

P value = 3.11e-05 (logrank test), Q value = 0.002

Table S125.  Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
19P LOSS MUTATED 11 9 1.4 - 109.9 (28.5)
19P LOSS WILD-TYPE 515 166 0.1 - 149.2 (38.7)

Figure S125.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0254 (Fisher's exact test), Q value = 0.21

Table S126.  Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
19P LOSS MUTATED 2 0 5 4
19P LOSS WILD-TYPE 261 57 120 79

Figure S126.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 6e-04 (Fisher's exact test), Q value = 0.017

Table S127.  Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
19P LOSS MUTATED 2 1 5 3
19P LOSS WILD-TYPE 266 68 175 8

Figure S127.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.00244 (logrank test), Q value = 0.042

Table S128.  Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
19Q LOSS MUTATED 4 3 1.4 - 37.1 (19.7)
19Q LOSS WILD-TYPE 522 172 0.1 - 149.2 (38.6)

Figure S128.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00297 (Fisher's exact test), Q value = 0.047

Table S129.  Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
19Q LOSS MUTATED 1 0 1 2
19Q LOSS WILD-TYPE 267 69 179 9

Figure S129.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00119 (Fisher's exact test), Q value = 0.024

Table S130.  Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
21Q LOSS MUTATED 20 5 25 5
21Q LOSS WILD-TYPE 248 64 155 6

Figure S130.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'Time to Death'

P value = 0.00725 (logrank test), Q value = 0.089

Table S131.  Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
22Q LOSS MUTATED 39 21 1.7 - 114.4 (33.5)
22Q LOSS WILD-TYPE 487 154 0.1 - 149.2 (38.6)

Figure S131.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.019 (Fisher's exact test), Q value = 0.17

Table S132.  Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
22Q LOSS MUTATED 11 4 14 10
22Q LOSS WILD-TYPE 252 53 111 73

Figure S132.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'ETHNICITY'

P value = 0.00959 (Fisher's exact test), Q value = 0.11

Table S133.  Gene #80: '22q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 350
22Q LOSS MUTATED 6 23
22Q LOSS WILD-TYPE 20 327

Figure S133.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #12: 'ETHNICITY'

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/KIRC-TP/19781827/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/19775258/KIRC-TP.merged_data.txt

  • Number of patients = 528

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 12

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle