Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1N015K1
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/C1N015K1
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 81 arm-level events and 12 clinical features across 524 patients, 120 significant findings detected with Q value < 0.25.

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

  • 3p gain cnv correlated to 'Time to Death'.

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

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

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

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

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

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

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

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

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

  • 14q gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 17p gain cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

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

  • xq gain cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 1p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

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

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

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

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

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

  • 5q loss cnv correlated to 'NEOPLASM_DISEASESTAGE' 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'.

  • 7q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 8q loss cnv correlated to 'GENDER'.

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

  • 9q loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  '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',  'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_T_STAGE'.

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

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

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

  • 19p loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE', 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',  'NEOPLASM_DISEASESTAGE', and 'ETHNICITY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 120 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		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 214 (41%) 310 0.000797
(0.0209) 		0.254
(0.772) 		3e-05
(0.00194) 		9e-05
(0.00515) 		0.00227
(0.0394) 		0.00111
(0.0262) 		0.0331
(0.263) 		0.242
(0.751) 		0.217
(0.74) 		0.23
(0.75) 		0.0119
(0.126) 		0.686
(1.00)
4q loss 65 (12%) 459 1.48e-06
(0.00144) 		0.871
(1.00) 		1e-05
(0.00162) 		1e-05
(0.00162) 		0.461
(0.97) 		0.00293
(0.0467) 		0.27
(0.78) 		0.437
(0.954) 		0.0282
(0.233) 		0.758
(1.00)
9p loss 149 (28%) 375 1.97e-05
(0.00162) 		0.0706
(0.432) 		2e-05
(0.00162) 		2e-05
(0.00162) 		0.102
(0.507) 		0.0016
(0.0305) 		0.000854
(0.0209) 		0.523
(1.00) 		0.805
(1.00) 		0.764
(1.00) 		0.241
(0.751) 		0.655
(1.00)
9q loss 150 (29%) 374 0.000358
(0.012) 		0.0505
(0.34) 		1e-05
(0.00162) 		2e-05
(0.00162) 		0.172
(0.654) 		0.00411
(0.0605) 		0.000846
(0.0209) 		0.307
(0.826) 		0.843
(1.00) 		0.764
(1.00) 		0.222
(0.749) 		0.824
(1.00)
3q gain 60 (11%) 464 0.265
(0.778) 		0.884
(1.00) 		0.00067
(0.0186) 		4e-05
(0.00243) 		0.00829
(0.0972) 		0.0074
(0.0911) 		0.775
(1.00) 		0.437
(0.954) 		0.324
(0.85) 		1
(1.00)
12p gain 119 (23%) 405 0.00374
(0.056) 		0.164
(0.65) 		0.00027
(0.0101) 		0.00135
(0.0277) 		0.0879
(0.486) 		0.0193
(0.176) 		0.448
(0.959) 		0.0343
(0.265) 		0.0449
(0.328) 		0.225
(0.749)
12q gain 120 (23%) 404 0.00609
(0.08) 		0.302
(0.823) 		0.00028
(0.0101) 		0.00086
(0.0209) 		0.0879
(0.486) 		0.0199
(0.176) 		0.448
(0.959) 		0.0343
(0.265) 		0.0348
(0.266) 		0.224
(0.749)
20p gain 111 (21%) 413 0.153
(0.626) 		0.258
(0.773) 		3e-05
(0.00194) 		1e-05
(0.00162) 		0.548
(1.00) 		0.0167
(0.158) 		0.000349
(0.012) 		0.684
(1.00) 		0.281
(0.792) 		0.441
(0.956)
20q gain 114 (22%) 410 0.114
(0.538) 		0.0894
(0.488) 		2e-05
(0.00162) 		2e-05
(0.00162) 		0.241
(0.751) 		0.0188
(0.174) 		0.00199
(0.0361) 		0.684
(1.00) 		0.288
(0.806) 		0.319
(0.847)
4p loss 72 (14%) 452 2.19e-05
(0.00164) 		0.785
(1.00) 		0.00028
(0.0101) 		0.00013
(0.00602) 		0.73
(1.00) 		0.0216
(0.188) 		0.895
(1.00) 		0.551
(1.00) 		0.0608
(0.381) 		0.561
(1.00)
15q loss 36 (7%) 488 0.000853
(0.0209) 		0.999
(1.00) 		0.00122
(0.0274) 		0.00046
(0.014) 		1
(1.00) 		0.0142
(0.143) 		0.104
(0.515) 		0.537
(1.00) 		0.227
(0.749) 		0.385
(0.905)
5q gain 206 (39%) 318 0.093
(0.488) 		0.000456
(0.014) 		0.349
(0.865) 		0.353
(0.874) 		1
(1.00) 		1
(1.00) 		0.0196
(0.176) 		0.846
(1.00) 		0.0306
(0.248) 		0.836
(1.00)
7q gain 172 (33%) 352 0.583
(1.00) 		0.306
(0.825) 		0.0161
(0.155) 		0.0569
(0.362) 		0.443
(0.956) 		0.00255
(0.0432) 		0.00877
(0.0996) 		0.243
(0.751) 		0.123
(0.55) 		0.0432
(0.32) 		0.271
(0.78)
19p gain 51 (10%) 473 0.92
(1.00) 		0.712
(1.00) 		0.00533
(0.074) 		0.0139
(0.142) 		0.403
(0.921) 		0.00781
(0.0949) 		0.22
(0.745) 		0.427
(0.942) 		0.0853
(0.486) 		0.729
(1.00)
19q gain 57 (11%) 467 0.498
(1.00) 		0.42
(0.942) 		0.00147
(0.0286) 		0.00496
(0.0709) 		0.435
(0.954) 		0.00354
(0.0537) 		0.242
(0.751) 		0.427
(0.942) 		0.0494
(0.34) 		1
(1.00)
5p loss 7 (1%) 517 0.0159
(0.155) 		0.247
(0.763) 		0.00137
(0.0277) 		0.00012
(0.00591) 		1
(1.00) 		0.0816
(0.477) 		0.257
(0.773) 		1
(1.00) 		1
(1.00)
6p loss 100 (19%) 424 0.413
(0.936) 		0.301
(0.823) 		0.0547
(0.357) 		0.0198
(0.176) 		0.0055
(0.0752) 		0.279
(0.792) 		0.00115
(0.0266) 		0.0455
(0.328) 		0.716
(1.00) 		0.881
(1.00) 		0.0602
(0.38) 		1
(1.00)
13q loss 71 (14%) 453 0.00128
(0.0274) 		0.972
(1.00) 		0.00016
(0.00697) 		1e-05
(0.00162) 		0.491
(1.00) 		0.0333
(0.263) 		0.425
(0.942) 		1
(1.00) 		0.279
(0.792) 		0.229
(0.749)
18p loss 93 (18%) 431 0.00201
(0.0361) 		0.107
(0.525) 		0.00049
(0.0144) 		0.00019
(0.00769) 		1
(1.00) 		0.0797
(0.469) 		0.234
(0.751) 		0.868
(1.00) 		0.345
(0.865) 		0.0986
(0.504)
18q loss 95 (18%) 429 0.00831
(0.0972) 		0.131
(0.571) 		0.00881
(0.0996) 		0.00454
(0.0659) 		1
(1.00) 		0.113
(0.538) 		0.158
(0.637) 		0.809
(1.00) 		0.336
(0.862) 		0.281
(0.792)
19p loss 11 (2%) 513 0.000122
(0.00591) 		0.0977
(0.503) 		0.0235
(0.202) 		0.00057
(0.0163) 		1
(1.00) 		0.391
(0.91) 		0.754
(1.00) 		0.117
(0.538) 		1
(1.00)
22q loss 39 (7%) 485 0.0021
(0.0372) 		0.259
(0.774) 		0.0197
(0.176) 		0.164
(0.65) 		1
(1.00) 		0.1
(0.504) 		0.863
(1.00) 		0.34
(0.862) 		1
(1.00) 		0.0102
(0.113)
5p gain 193 (37%) 331 0.0866
(0.486) 		0.000165
(0.00697) 		0.114
(0.538) 		0.196
(0.709) 		0.623
(1.00) 		1
(1.00) 		0.0141
(0.142) 		0.846
(1.00) 		0.0909
(0.488) 		0.835
(1.00)
7p gain 171 (33%) 353 0.936
(1.00) 		0.27
(0.78) 		0.0657
(0.407) 		0.117
(0.538) 		0.449
(0.959) 		0.0255
(0.215) 		0.0035
(0.0537) 		0.486
(1.00) 		0.123
(0.55) 		0.0501
(0.34) 		0.655
(1.00)
8p gain 30 (6%) 494 0.554
(1.00) 		0.17
(0.654) 		0.00127
(0.0274) 		0.00145
(0.0286) 		1
(1.00) 		0.194
(0.709) 		0.561
(1.00) 		0.538
(1.00) 		0.426
(0.942) 		0.382
(0.905)
8q gain 61 (12%) 463 0.229
(0.749) 		0.0471
(0.331) 		0.00533
(0.074) 		0.00808
(0.097) 		0.448
(0.959) 		0.0855
(0.486) 		0.118
(0.538) 		0.952
(1.00) 		0.61
(1.00) 		0.495
(1.00)
11p gain 31 (6%) 493 0.969
(1.00) 		0.978
(1.00) 		0.0291
(0.238) 		0.0132
(0.137) 		1
(1.00) 		0.116
(0.538) 		0.705
(1.00) 		0.895
(1.00) 		0.854
(1.00) 		1
(1.00)
3p loss 378 (72%) 146 0.588
(1.00) 		0.734
(1.00) 		0.0244
(0.208) 		0.0315
(0.253) 		0.791
(1.00) 		0.1
(0.504) 		0.0113
(0.12) 		0.379
(0.905) 		0.387
(0.905) 		0.262
(0.778) 		0.655
(1.00)
3q loss 98 (19%) 426 0.992
(1.00) 		0.0107
(0.116) 		0.473
(0.987) 		0.237
(0.751) 		0.747
(1.00) 		0.876
(1.00) 		0.00011
(0.00591) 		0.347
(0.865) 		0.614
(1.00) 		0.783
(1.00)
5q loss 6 (1%) 518 0.0467
(0.331) 		0.147
(0.615) 		0.00564
(0.0761) 		0.00039
(0.0126) 		1
(1.00) 		0.24
(0.751) 		0.672
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 23 (4%) 501 0.00741
(0.0911) 		0.0064
(0.0829) 		0.62
(1.00) 		0.514
(1.00) 		0.238
(0.751) 		0.385
(0.905) 		0.379
(0.905) 		0.281
(0.792) 		0.796
(1.00) 		1
(1.00)
19q loss 4 (1%) 520 0.00319
(0.05) 		0.859
(1.00) 		0.195
(0.709) 		0.00279
(0.0457) 		1
(1.00) 		0.118
(0.538) 		1
(1.00) 		1
(1.00) 		1
(1.00)
1p gain 24 (5%) 500 0.00706
(0.0891) 		0.179
(0.678) 		0.153
(0.626) 		0.267
(0.778) 		0.21
(0.729) 		0.385
(0.905) 		1
(1.00) 		0.498
(1.00) 		0.426
(0.942) 		1
(1.00)
3p gain 19 (4%) 505 0.0266
(0.223) 		0.532
(1.00) 		0.141
(0.592) 		0.197
(0.709) 		0.0459
(0.328) 		0.0978
(0.503) 		0.332
(0.862) 		0.96
(1.00) 		0.785
(1.00) 		1
(1.00)
9p gain 13 (2%) 511 0.281
(0.792) 		0.693
(1.00) 		0.901
(1.00) 		0.0507
(0.34) 		1
(1.00) 		0.237
(0.751) 		0.0168
(0.158) 		0.699
(1.00) 		0.555
(1.00)
9q gain 12 (2%) 512 0.987
(1.00) 		0.347
(0.865) 		0.212
(0.73) 		0.00258
(0.0432) 		1
(1.00) 		1
(1.00) 		0.129
(0.566) 		1
(1.00) 		0.555
(1.00)
10q gain 12 (2%) 512 0.65
(1.00) 		0.0159
(0.155) 		0.825
(1.00) 		0.882
(1.00) 		0.26
(0.774) 		1
(1.00) 		0.364
(0.892) 		0.67
(1.00) 		0.683
(1.00) 		1
(1.00)
14q gain 16 (3%) 508 0.136
(0.581) 		0.457
(0.964) 		0.209
(0.729) 		0.00652
(0.0834) 		1
(1.00) 		0.295
(0.811) 		0.796
(1.00) 		1
(1.00) 		1
(1.00)
17p gain 25 (5%) 499 0.96
(1.00) 		0.414
(0.936) 		0.0847
(0.486) 		0.833
(1.00) 		0.21
(0.729) 		0.0213
(0.187) 		0.832
(1.00) 		0.184
(0.687) 		0.0528
(0.349) 		0.611
(1.00)
xq gain 30 (6%) 494 0.83
(1.00) 		0.778
(1.00) 		0.0938
(0.49) 		0.166
(0.65) 		1
(1.00) 		0.0274
(0.227) 		0.696
(1.00) 		0.96
(1.00) 		0.442
(0.956) 		0.626
(1.00)
1p loss 56 (11%) 468 0.335
(0.862) 		0.101
(0.504) 		0.578
(1.00) 		0.0158
(0.155) 		0.702
(1.00) 		0.431
(0.949) 		0.242
(0.751) 		0.769
(1.00) 		0.529
(1.00) 		0.205
(0.726)
6q loss 128 (24%) 396 0.479
(0.995) 		0.727
(1.00) 		0.348
(0.865) 		0.198
(0.709) 		0.0013
(0.0274) 		0.669
(1.00) 		0.0713
(0.433) 		0.528
(1.00) 		0.0556
(0.361) 		0.881
(1.00) 		0.13
(0.571) 		0.479
(0.995)
7q loss 3 (1%) 521 0.505
(1.00) 		0.605
(1.00) 		0.118
(0.538) 		0.0105
(0.115) 		0.072
(0.435) 		1
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.135
(0.58)
8q loss 64 (12%) 460 0.526
(1.00) 		0.764
(1.00) 		0.561
(1.00) 		0.254
(0.772) 		0.435
(0.954) 		1
(1.00) 		0.0124
(0.129) 		0.387
(0.905) 		0.292
(0.809) 		0.0534
(0.351)
10p loss 67 (13%) 457 0.252
(0.772) 		0.387
(0.905) 		0.082
(0.477) 		0.0102
(0.113) 		0.141
(0.592) 		0.583
(1.00) 		0.34
(0.862) 		0.168
(0.65) 		0.686
(1.00) 		0.215
(0.738)
10q loss 89 (17%) 435 0.342
(0.862) 		0.581
(1.00) 		0.109
(0.525) 		0.00282
(0.0457) 		0.322
(0.848) 		0.627
(1.00) 		0.114
(0.538) 		0.511
(1.00) 		0.316
(0.844) 		0.404
(0.921)
11p loss 18 (3%) 506 0.0084
(0.0972) 		0.0567
(0.362) 		0.367
(0.892) 		0.414
(0.936) 		0.156
(0.633) 		0.505
(1.00) 		1
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.612
(1.00)
16p loss 10 (2%) 514 0.118
(0.538) 		0.664
(1.00) 		0.38
(0.905) 		0.0169
(0.158) 		0.364
(0.892) 		1
(1.00) 		1
(1.00) 		0.376
(0.905) 		1
(1.00)
16q loss 16 (3%) 508 0.134
(0.576) 		0.347
(0.865) 		0.395
(0.912) 		0.00575
(0.0766) 		0.455
(0.962) 		1
(1.00) 		0.796
(1.00) 		0.153
(0.626) 		1
(1.00)
21q loss 54 (10%) 470 0.603
(1.00) 		0.737
(1.00) 		0.162
(0.648) 		0.00195
(0.0361) 		0.0905
(0.488) 		1
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.454
(0.962) 		1
(1.00)
1q gain 51 (10%) 473 0.0774
(0.459) 		0.0335
(0.263) 		0.0522
(0.348) 		0.0848
(0.486) 		0.423
(0.942) 		0.682
(1.00) 		0.541
(1.00) 		0.796
(1.00) 		0.693
(1.00) 		0.729
(1.00)
2p gain 76 (15%) 448 0.71
(1.00) 		0.142
(0.596) 		0.133
(0.576) 		0.531
(1.00) 		1
(1.00) 		0.231
(0.75) 		1
(1.00) 		0.628
(1.00) 		0.289
(0.806) 		0.76
(1.00)
2q gain 78 (15%) 446 0.708
(1.00) 		0.229
(0.749) 		0.321
(0.848) 		0.666
(1.00) 		0.747
(1.00) 		0.392
(0.91) 		0.445
(0.959) 		0.943
(1.00) 		0.255
(0.773) 		0.372
(0.898)
4p gain 13 (2%) 511 0.0895
(0.488) 		0.754
(1.00) 		0.384
(0.905) 		0.171
(0.654) 		0.495
(1.00) 		1
(1.00) 		0.395
(0.912) 		1
(1.00) 		1
(1.00)
4q gain 13 (2%) 511 0.277
(0.792) 		0.754
(1.00) 		0.535
(1.00) 		0.713
(1.00) 		0.455
(0.962) 		0.702
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00)
6p gain 11 (2%) 513 0.707
(1.00) 		0.812
(1.00) 		0.312
(0.835) 		0.232
(0.751) 		1
(1.00) 		0.686
(1.00) 		0.342
(0.862) 		1
(1.00) 		1
(1.00)
6q gain 9 (2%) 515 0.504
(1.00) 		0.372
(0.898) 		0.228
(0.749) 		0.284
(0.797) 		1
(1.00) 		1
(1.00) 		0.167
(0.65) 		1
(1.00) 		1
(1.00)
10p gain 17 (3%) 507 0.754
(1.00) 		0.0996
(0.504) 		0.342
(0.862) 		0.106
(0.521) 		0.106
(0.521) 		0.739
(1.00) 		0.798
(1.00) 		0.281
(0.792) 		0.42
(0.942) 		1
(1.00)
11q gain 29 (6%) 495 0.51
(1.00) 		0.913
(1.00) 		0.167
(0.65) 		0.087
(0.486) 		1
(1.00) 		0.42
(0.942) 		1
(1.00) 		0.845
(1.00) 		1
(1.00)
13q gain 22 (4%) 502 0.184
(0.687) 		0.242
(0.751) 		0.128
(0.566) 		0.208
(0.729) 		1
(1.00) 		0.367
(0.892) 		0.257
(0.773) 		0.0928
(0.488) 		0.0929
(0.488)
15q gain 26 (5%) 498 0.289
(0.806) 		0.471
(0.987) 		0.559
(1.00) 		0.389
(0.907) 		0.21
(0.729) 		0.582
(1.00) 		0.678
(1.00) 		0.0351
(0.267) 		0.671
(1.00) 		1
(1.00)
16p gain 106 (20%) 418 0.355
(0.875) 		0.266
(0.778) 		0.182
(0.681) 		0.0946
(0.492) 		0.134
(0.576) 		0.648
(1.00) 		0.734
(1.00) 		0.831
(1.00) 		0.167
(0.65) 		0.198
(0.709) 		1
(1.00)
16q gain 98 (19%) 426 0.219
(0.745) 		0.361
(0.888) 		0.197
(0.709) 		0.0642
(0.4) 		0.211
(0.729) 		1
(1.00) 		1
(1.00) 		0.956
(1.00) 		0.167
(0.65) 		0.326
(0.853) 		0.786
(1.00)
17q gain 32 (6%) 492 0.679
(1.00) 		0.25
(0.767) 		0.531
(1.00) 		0.706
(1.00) 		0.323
(0.848) 		0.202
(0.718) 		0.851
(1.00) 		0.519
(1.00) 		0.0755
(0.453) 		0.626
(1.00)
18p gain 25 (5%) 499 0.0497
(0.34) 		0.83
(1.00) 		0.674
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.401
(0.92) 		0.0914
(0.488) 		0.664
(1.00) 		0.338
(0.862)
18q gain 25 (5%) 499 0.119
(0.538) 		0.641
(1.00) 		0.525
(1.00) 		0.768
(1.00) 		0.601
(1.00) 		0.401
(0.92) 		0.0914
(0.488) 		0.663
(1.00) 		0.338
(0.862)
21q gain 50 (10%) 474 0.642
(1.00) 		0.127
(0.565) 		0.243
(0.751) 		0.114
(0.538) 		1
(1.00) 		0.533
(1.00) 		0.439
(0.956) 		0.876
(1.00) 		0.319
(0.847) 		0.72
(1.00)
22q gain 40 (8%) 484 0.524
(1.00) 		0.589
(1.00) 		0.721
(1.00) 		0.0876
(0.486) 		1
(1.00) 		0.82
(1.00) 		0.305
(0.825) 		0.34
(0.862) 		0.233
(0.751) 		1
(1.00)
xp gain 31 (6%) 493 0.471
(0.987) 		0.554
(1.00) 		0.0458
(0.328) 		0.128
(0.566) 		1
(1.00) 		0.0369
(0.278) 		0.847
(1.00) 		0.96
(1.00) 		0.0451
(0.328) 		0.626
(1.00)
1q loss 36 (7%) 488 0.654
(1.00) 		0.685
(1.00) 		0.831
(1.00) 		0.076
(0.453) 		1
(1.00) 		0.338
(0.862) 		0.59
(1.00) 		0.895
(1.00) 		0.417
(0.94) 		0.455
(0.962)
2p loss 14 (3%) 510 0.966
(1.00) 		0.815
(1.00) 		0.453
(0.962) 		0.139
(0.59) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.0504
(0.34) 		1
(1.00)
2q loss 14 (3%) 510 0.98
(1.00) 		0.791
(1.00) 		0.557
(1.00) 		0.223
(0.749) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.169
(0.65) 		1
(1.00)
8p loss 137 (26%) 387 0.265
(0.778) 		0.739
(1.00) 		0.339
(0.862) 		0.198
(0.709) 		0.775
(1.00) 		0.267
(0.778) 		0.0383
(0.287) 		0.698
(1.00) 		0.843
(1.00) 		0.653
(1.00) 		0.217
(0.74) 		0.057
(0.362)
12p loss 3 (1%) 521 0.328
(0.854) 		0.823
(1.00) 		0.472
(0.987) 		0.738
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 4 (1%) 520 0.978
(1.00) 		0.32
(0.847) 		0.162
(0.648) 		0.411
(0.936) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 45 (9%) 479 0.441
(0.956) 		0.303
(0.823) 		0.205
(0.726) 		0.18
(0.678) 		0.375
(0.904) 		0.0474
(0.331) 		0.197
(0.709) 		0.302
(0.823) 		1
(1.00) 		0.711
(1.00)
17q loss 28 (5%) 496 0.492
(1.00) 		0.813
(1.00) 		0.29
(0.806) 		0.265
(0.778) 		1
(1.00) 		0.18
(0.678) 		0.311
(0.835) 		1
(1.00) 		1
(1.00)
20p loss 8 (2%) 516 0.801
(1.00) 		0.687
(1.00) 		0.724
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.366
(0.892) 		1
(1.00) 		0.155
(0.628) 		0.253
(0.772)
20q loss 3 (1%) 521 0.818
(1.00) 		0.113
(0.538) 		0.227
(0.749) 		0.108
(0.525) 		0.402
(0.921) 		1
(1.00) 		1
(1.00) 		0.0701
(0.431)
xp loss 46 (9%) 478 0.382
(0.905) 		0.936
(1.00) 		0.878
(1.00) 		0.557
(1.00) 		0.266
(0.778) 		0.826
(1.00) 		0.197
(0.709) 		0.547
(1.00) 		0.577
(1.00) 		0.149
(0.618)
xq loss 46 (9%) 478 0.293
(0.81) 		0.644
(1.00) 		0.876
(1.00) 		0.559
(1.00) 		0.295
(0.811) 		1
(1.00) 		0.197
(0.709) 		0.547
(1.00) 		0.645
(1.00) 		0.149
(0.618)
'1p gain' versus 'Time to Death'

P value = 0.00706 (logrank test), Q value = 0.089

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

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
1P GAIN MUTATED 24 13 0.5 - 83.9 (22.9)
1P GAIN WILD-TYPE 498 155 0.1 - 120.6 (36.8)

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

'3p gain' versus 'Time to Death'

P value = 0.0266 (logrank test), Q value = 0.22

Table S2.  Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
3P GAIN MUTATED 19 9 0.1 - 59.4 (30.6)
3P GAIN WILD-TYPE 503 159 0.1 - 120.6 (36.5)

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.019

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
3Q GAIN MUTATED 17 5 21 17
3Q GAIN WILD-TYPE 243 52 106 63

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

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0024

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

nPatients T1 T2 T3 T4
ALL 265 69 179 11
3Q GAIN MUTATED 17 6 33 4
3Q GAIN WILD-TYPE 248 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 = 0.00829 (Fisher's exact test), Q value = 0.097

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

nPatients 0 1
ALL 232 18
3Q GAIN MUTATED 30 7
3Q GAIN WILD-TYPE 202 11

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 = 0.091

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 = 0.000165 (Wilcoxon-test), Q value = 0.007

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

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
5P GAIN MUTATED 193 63.2 (11.8)
5P GAIN WILD-TYPE 330 59.0 (12.1)

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

'5p gain' versus 'GENDER'

P value = 0.0141 (Fisher's exact test), Q value = 0.14

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

nPatients FEMALE MALE
ALL 188 336
5P GAIN MUTATED 56 137
5P GAIN WILD-TYPE 132 199

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

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000456 (Wilcoxon-test), Q value = 0.014

Table S9.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
5Q GAIN MUTATED 205 63.0 (12.2)
5Q GAIN WILD-TYPE 318 59.1 (11.8)

Figure S9.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'GENDER'

P value = 0.0196 (Fisher's exact test), Q value = 0.18

Table S10.  Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
5Q GAIN MUTATED 61 145
5Q GAIN WILD-TYPE 127 191

Figure S10.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

'5q gain' versus 'RACE'

P value = 0.0306 (Fisher's exact test), Q value = 0.25

Table S11.  Gene #10: '5q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
5Q GAIN MUTATED 3 12 189
5Q GAIN WILD-TYPE 5 40 268

Figure S11.  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 = 0.22

Table S12.  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 S12.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'GENDER'

P value = 0.0035 (Fisher's exact test), Q value = 0.054

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

nPatients FEMALE MALE
ALL 188 336
7P GAIN MUTATED 46 125
7P GAIN WILD-TYPE 142 211

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

'7q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0161 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
7Q GAIN MUTATED 72 17 46 37
7Q GAIN WILD-TYPE 188 40 81 43

Figure S14.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

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

Table S15.  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 S15.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'GENDER'

P value = 0.00877 (Fisher's exact test), Q value = 0.1

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

nPatients FEMALE MALE
ALL 188 336
7Q GAIN MUTATED 48 124
7Q GAIN WILD-TYPE 140 212

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

'8p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00127 (Fisher's exact test), Q value = 0.027

Table S17.  Gene #15: '8p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
8P GAIN MUTATED 6 8 9 7
8P GAIN WILD-TYPE 254 49 118 73

Figure S17.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00145 (Fisher's exact test), Q value = 0.029

Table S18.  Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
8P GAIN MUTATED 6 9 15 0
8P GAIN WILD-TYPE 259 60 164 11

Figure S18.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00533 (Fisher's exact test), Q value = 0.074

Table S19.  Gene #16: '8q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
8Q GAIN MUTATED 18 11 19 13
8Q GAIN WILD-TYPE 242 46 108 67

Figure S19.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00808 (Fisher's exact test), Q value = 0.097

Table S20.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
8Q GAIN MUTATED 19 12 29 1
8Q GAIN WILD-TYPE 246 57 150 10

Figure S20.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'GENDER'

P value = 0.0168 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
9P GAIN MUTATED 9 4
9P GAIN WILD-TYPE 179 332

Figure S21.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00258 (Fisher's exact test), Q value = 0.043

Table S22.  Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
9Q GAIN MUTATED 4 2 3 3
9Q GAIN WILD-TYPE 261 67 176 8

Figure S22.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0159 (Wilcoxon-test), Q value = 0.15

Table S23.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
10Q GAIN MUTATED 12 68.6 (12.2)
10Q GAIN WILD-TYPE 511 60.4 (12.1)

Figure S23.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0291 (Fisher's exact test), Q value = 0.24

Table S24.  Gene #21: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
11P GAIN MUTATED 8 4 11 8
11P GAIN WILD-TYPE 252 53 116 72

Figure S24.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.14

Table S25.  Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
11P GAIN MUTATED 8 4 18 1
11P GAIN WILD-TYPE 257 65 161 10

Figure S25.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12p gain' versus 'Time to Death'

P value = 0.00374 (logrank test), Q value = 0.056

Table S26.  Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
12P GAIN MUTATED 119 49 0.1 - 109.9 (30.5)
12P GAIN WILD-TYPE 403 119 0.1 - 120.6 (37.1)

Figure S26.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.01

Table S27.  Gene #23: '12p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
12P GAIN MUTATED 43 9 39 28
12P GAIN WILD-TYPE 217 48 88 52

Figure S27.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'12p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00135 (Fisher's exact test), Q value = 0.028

Table S28.  Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
12P GAIN MUTATED 45 13 57 4
12P GAIN WILD-TYPE 220 56 122 7

Figure S28.  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 = 0.18

Table S29.  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 S29.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12q gain' versus 'Time to Death'

P value = 0.00609 (logrank test), Q value = 0.08

Table S30.  Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
12Q GAIN MUTATED 120 49 0.1 - 109.9 (30.6)
12Q GAIN WILD-TYPE 402 119 0.1 - 120.6 (37.1)

Figure S30.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.01

Table S31.  Gene #24: '12q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
12Q GAIN MUTATED 43 9 40 28
12Q GAIN WILD-TYPE 217 48 87 52

Figure S31.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00086 (Fisher's exact test), Q value = 0.021

Table S32.  Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
12Q GAIN MUTATED 45 13 58 4
12Q GAIN WILD-TYPE 220 56 121 7

Figure S32.  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 = 0.18

Table S33.  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 S33.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00652 (Fisher's exact test), Q value = 0.083

Table S34.  Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
14Q GAIN MUTATED 5 2 6 3
14Q GAIN WILD-TYPE 260 67 173 8

Figure S34.  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 = 0.19

Table S35.  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 S35.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00533 (Fisher's exact test), Q value = 0.074

Table S36.  Gene #34: '19p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
19P GAIN MUTATED 15 7 14 15
19P GAIN WILD-TYPE 245 50 113 65

Figure S36.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.14

Table S37.  Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
19P GAIN MUTATED 16 7 26 2
19P GAIN WILD-TYPE 249 62 153 9

Figure S37.  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 = 0.095

Table S38.  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 S38.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00147 (Fisher's exact test), Q value = 0.029

Table S39.  Gene #35: '19q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
19Q GAIN MUTATED 16 7 17 17
19Q GAIN WILD-TYPE 244 50 110 63

Figure S39.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00496 (Fisher's exact test), Q value = 0.071

Table S40.  Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
19Q GAIN MUTATED 17 9 29 2
19Q GAIN WILD-TYPE 248 60 150 9

Figure S40.  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 = 0.054

Table S41.  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 S41.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0019

Table S42.  Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
20P GAIN MUTATED 34 12 39 26
20P GAIN WILD-TYPE 226 45 88 54

Figure S42.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S43.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
20P GAIN MUTATED 35 13 57 6
20P GAIN WILD-TYPE 230 56 122 5

Figure S43.  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 S44.  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 S44.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'GENDER'

P value = 0.000349 (Fisher's exact test), Q value = 0.012

Table S45.  Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
20P GAIN MUTATED 24 87
20P GAIN WILD-TYPE 164 249

Figure S45.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S46.  Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
20Q GAIN MUTATED 35 12 41 26
20Q GAIN WILD-TYPE 225 45 86 54

Figure S46.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S47.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
20Q GAIN MUTATED 37 13 59 5
20Q GAIN WILD-TYPE 228 56 120 6

Figure S47.  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 S48.  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 S48.  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 S49.  Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
20Q GAIN MUTATED 27 87
20Q GAIN WILD-TYPE 161 249

Figure S49.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.23

Table S50.  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 S50.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.15

Table S51.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
1P LOSS MUTATED 31 9 12 4
1P LOSS WILD-TYPE 234 60 167 7

Figure S51.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0244 (Fisher's exact test), Q value = 0.21

Table S52.  Gene #46: '3p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
3P LOSS MUTATED 183 42 103 50
3P LOSS WILD-TYPE 77 15 24 30

Figure S52.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'3p loss' versus 'GENDER'

P value = 0.0113 (Fisher's exact test), Q value = 0.12

Table S53.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
3P LOSS MUTATED 123 255
3P LOSS WILD-TYPE 65 81

Figure S53.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0107 (Wilcoxon-test), Q value = 0.12

Table S54.  Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
3Q LOSS MUTATED 98 63.7 (12.7)
3Q LOSS WILD-TYPE 425 59.9 (11.9)

Figure S54.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'GENDER'

P value = 0.00011 (Fisher's exact test), Q value = 0.0059

Table S55.  Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
3Q LOSS MUTATED 19 79
3Q LOSS WILD-TYPE 169 257

Figure S55.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'Time to Death'

P value = 2.19e-05 (logrank test), Q value = 0.0016

Table S56.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
4P LOSS MUTATED 72 38 0.5 - 90.3 (31.5)
4P LOSS WILD-TYPE 450 130 0.1 - 120.6 (36.9)

Figure S56.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.01

Table S57.  Gene #48: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
4P LOSS MUTATED 21 6 26 19
4P LOSS WILD-TYPE 239 51 101 61

Figure S57.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.006

Table S58.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
4P LOSS MUTATED 22 8 38 4
4P LOSS WILD-TYPE 243 61 141 7

Figure S58.  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 = 0.19

Table S59.  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 S59.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'Time to Death'

P value = 1.48e-06 (logrank test), Q value = 0.0014

Table S60.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
4Q LOSS MUTATED 65 36 1.2 - 90.3 (25.7)
4Q LOSS WILD-TYPE 457 132 0.1 - 120.6 (37.0)

Figure S60.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S61.  Gene #49: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
4Q LOSS MUTATED 15 6 24 20
4Q LOSS WILD-TYPE 245 51 103 60

Figure S61.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S62.  Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
4Q LOSS MUTATED 16 8 36 5
4Q LOSS WILD-TYPE 249 61 143 6

Figure S62.  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 S63.  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 S63.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'RACE'

P value = 0.0282 (Fisher's exact test), Q value = 0.23

Table S64.  Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
4Q LOSS MUTATED 1 1 61
4Q LOSS WILD-TYPE 7 51 396

Figure S64.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'Time to Death'

P value = 0.0159 (logrank test), Q value = 0.15

Table S65.  Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
5P LOSS MUTATED 7 5 3.3 - 72.1 (30.5)
5P LOSS WILD-TYPE 515 163 0.1 - 120.6 (36.5)

Figure S65.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00137 (Fisher's exact test), Q value = 0.028

Table S66.  Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
5P LOSS MUTATED 0 2 1 4
5P LOSS WILD-TYPE 260 55 126 76

Figure S66.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0059

Table S67.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
5P LOSS MUTATED 0 3 2 2
5P LOSS WILD-TYPE 265 66 177 9

Figure S67.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00564 (Fisher's exact test), Q value = 0.076

Table S68.  Gene #51: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
5Q LOSS MUTATED 0 2 1 3
5Q LOSS WILD-TYPE 260 55 126 77

Figure S68.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.013

Table S69.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
5Q LOSS MUTATED 0 2 2 2
5Q LOSS WILD-TYPE 265 67 177 9

Figure S69.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0198 (Fisher's exact test), Q value = 0.18

Table S70.  Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
6P LOSS MUTATED 38 15 43 4
6P LOSS WILD-TYPE 227 54 136 7

Figure S70.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0055 (Fisher's exact test), Q value = 0.075

Table S71.  Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
6P LOSS MUTATED 36 8
6P LOSS WILD-TYPE 196 10

Figure S71.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p loss' versus 'GENDER'

P value = 0.00115 (Fisher's exact test), Q value = 0.027

Table S72.  Gene #52: '6p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
6P LOSS MUTATED 22 78
6P LOSS WILD-TYPE 166 258

Figure S72.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'GENDER'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0013 (Fisher's exact test), Q value = 0.027

Table S73.  Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
6Q LOSS MUTATED 45 10
6Q LOSS WILD-TYPE 187 8

Figure S73.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0105 (Fisher's exact test), Q value = 0.12

Table S74.  Gene #54: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
7Q LOSS MUTATED 0 1 1 1
7Q LOSS WILD-TYPE 265 68 178 10

Figure S74.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q loss' versus 'GENDER'

P value = 0.0124 (Fisher's exact test), Q value = 0.13

Table S75.  Gene #56: '8q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
8Q LOSS MUTATED 14 50
8Q LOSS WILD-TYPE 174 286

Figure S75.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'Time to Death'

P value = 1.97e-05 (logrank test), Q value = 0.0016

Table S76.  Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
9P LOSS MUTATED 148 69 0.2 - 109.9 (34.9)
9P LOSS WILD-TYPE 374 99 0.1 - 120.6 (36.7)

Figure S76.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S77.  Gene #57: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
9P LOSS MUTATED 53 11 50 35
9P LOSS WILD-TYPE 207 46 77 45

Figure S77.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S78.  Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
9P LOSS MUTATED 56 15 73 5
9P LOSS WILD-TYPE 209 54 106 6

Figure S78.  Get High-res Image Gene #57: '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 = 0.031

Table S79.  Gene #57: '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 S79.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'GENDER'

P value = 0.000854 (Fisher's exact test), Q value = 0.021

Table S80.  Gene #57: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
9P LOSS MUTATED 37 112
9P LOSS WILD-TYPE 151 224

Figure S80.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'Time to Death'

P value = 0.000358 (logrank test), Q value = 0.012

Table S81.  Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
9Q LOSS MUTATED 149 67 0.2 - 109.9 (36.5)
9Q LOSS WILD-TYPE 373 101 0.1 - 120.6 (36.1)

Figure S81.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S82.  Gene #58: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
9Q LOSS MUTATED 50 14 52 34
9Q LOSS WILD-TYPE 210 43 75 46

Figure S82.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S83.  Gene #58: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
9Q LOSS MUTATED 52 18 76 4
9Q LOSS WILD-TYPE 213 51 103 7

Figure S83.  Get High-res Image Gene #58: '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 = 0.061

Table S84.  Gene #58: '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 S84.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'GENDER'

P value = 0.000846 (Fisher's exact test), Q value = 0.021

Table S85.  Gene #58: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
9Q LOSS MUTATED 37 113
9Q LOSS WILD-TYPE 151 223

Figure S85.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #7: 'GENDER'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.11

Table S86.  Gene #59: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
10P LOSS MUTATED 25 7 31 4
10P LOSS WILD-TYPE 240 62 148 7

Figure S86.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

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

Table S87.  Gene #60: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
10Q LOSS MUTATED 34 12 37 6
10Q LOSS WILD-TYPE 231 57 142 5

Figure S87.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'Time to Death'

P value = 0.0084 (logrank test), Q value = 0.097

Table S88.  Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
11P LOSS MUTATED 18 9 1.8 - 66.3 (25.0)
11P LOSS WILD-TYPE 504 159 0.1 - 120.6 (36.9)

Figure S88.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'Time to Death'

P value = 0.00741 (logrank test), Q value = 0.091

Table S89.  Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
11Q LOSS MUTATED 23 11 0.2 - 109.9 (21.6)
11Q LOSS WILD-TYPE 499 157 0.1 - 120.6 (37.0)

Figure S89.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0064 (Wilcoxon-test), Q value = 0.083

Table S90.  Gene #62: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
11Q LOSS MUTATED 23 66.7 (12.3)
11Q LOSS WILD-TYPE 500 60.3 (12.0)

Figure S90.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'Time to Death'

P value = 0.00128 (logrank test), Q value = 0.027

Table S91.  Gene #65: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
13Q LOSS MUTATED 70 33 0.2 - 94.0 (30.9)
13Q LOSS WILD-TYPE 452 135 0.1 - 120.6 (36.8)

Figure S91.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.007

Table S92.  Gene #65: '13q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
13Q LOSS MUTATED 25 2 25 19
13Q LOSS WILD-TYPE 235 55 102 61

Figure S92.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0016

Table S93.  Gene #65: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
13Q LOSS MUTATED 27 3 34 7
13Q LOSS WILD-TYPE 238 66 145 4

Figure S93.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'Time to Death'

P value = 0.000797 (logrank test), Q value = 0.021

Table S94.  Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
14Q LOSS MUTATED 213 88 0.2 - 96.4 (34.0)
14Q LOSS WILD-TYPE 309 80 0.1 - 120.6 (37.0)

Figure S94.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0019

Table S95.  Gene #66: '14q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
14Q LOSS MUTATED 79 26 64 45
14Q LOSS WILD-TYPE 181 31 63 35

Figure S95.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0051

Table S96.  Gene #66: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
14Q LOSS MUTATED 84 34 93 3
14Q LOSS WILD-TYPE 181 35 86 8

Figure S96.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00227 (Fisher's exact test), Q value = 0.039

Table S97.  Gene #66: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
14Q LOSS MUTATED 92 14
14Q LOSS WILD-TYPE 140 4

Figure S97.  Get High-res Image Gene #66: '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 = 0.026

Table S98.  Gene #66: '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 S98.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'RACE'

P value = 0.0119 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #66: '14q loss' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
14Q LOSS MUTATED 2 12 196
14Q LOSS WILD-TYPE 6 40 261

Figure S99.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'Time to Death'

P value = 0.000853 (logrank test), Q value = 0.021

Table S100.  Gene #67: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
15Q LOSS MUTATED 36 19 0.2 - 89.4 (31.2)
15Q LOSS WILD-TYPE 486 149 0.1 - 120.6 (36.9)

Figure S100.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00122 (Fisher's exact test), Q value = 0.027

Table S101.  Gene #67: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
15Q LOSS MUTATED 9 2 13 12
15Q LOSS WILD-TYPE 251 55 114 68

Figure S101.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.014

Table S102.  Gene #67: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
15Q LOSS MUTATED 10 2 21 3
15Q LOSS WILD-TYPE 255 67 158 8

Figure S102.  Get High-res Image Gene #67: '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 = 0.14

Table S103.  Gene #67: '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 S103.  Get High-res Image Gene #67: '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 S104.  Gene #68: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
16P LOSS MUTATED 3 2 3 2
16P LOSS WILD-TYPE 262 67 176 9

Figure S104.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00575 (Fisher's exact test), Q value = 0.077

Table S105.  Gene #69: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
16Q LOSS MUTATED 6 3 4 3
16Q LOSS WILD-TYPE 259 66 175 8

Figure S105.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'Time to Death'

P value = 0.00201 (logrank test), Q value = 0.036

Table S106.  Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
18P LOSS MUTATED 92 41 0.2 - 109.9 (31.0)
18P LOSS WILD-TYPE 430 127 0.1 - 120.6 (37.1)

Figure S106.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.014

Table S107.  Gene #72: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
18P LOSS MUTATED 31 7 33 22
18P LOSS WILD-TYPE 229 50 94 58

Figure S107.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0077

Table S108.  Gene #72: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
18P LOSS MUTATED 33 9 46 5
18P LOSS WILD-TYPE 232 60 133 6

Figure S108.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'Time to Death'

P value = 0.00831 (logrank test), Q value = 0.097

Table S109.  Gene #73: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
18Q LOSS MUTATED 94 40 0.2 - 109.9 (31.3)
18Q LOSS WILD-TYPE 428 128 0.1 - 120.6 (37.0)

Figure S109.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00881 (Fisher's exact test), Q value = 0.1

Table S110.  Gene #73: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
18Q LOSS MUTATED 35 8 30 22
18Q LOSS WILD-TYPE 225 49 97 58

Figure S110.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00454 (Fisher's exact test), Q value = 0.066

Table S111.  Gene #73: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
18Q LOSS MUTATED 37 10 43 5
18Q LOSS WILD-TYPE 228 59 136 6

Figure S111.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'Time to Death'

P value = 0.000122 (logrank test), Q value = 0.0059

Table S112.  Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
19P LOSS MUTATED 11 9 1.4 - 109.9 (28.5)
19P LOSS WILD-TYPE 511 159 0.1 - 120.6 (36.5)

Figure S112.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0235 (Fisher's exact test), Q value = 0.2

Table S113.  Gene #74: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
19P LOSS MUTATED 2 0 5 4
19P LOSS WILD-TYPE 258 57 122 76

Figure S113.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00057 (Fisher's exact test), Q value = 0.016

Table S114.  Gene #74: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
19P LOSS MUTATED 2 1 5 3
19P LOSS WILD-TYPE 263 68 174 8

Figure S114.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.00319 (logrank test), Q value = 0.05

Table S115.  Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
19Q LOSS MUTATED 4 3 1.4 - 37.1 (19.7)
19Q LOSS WILD-TYPE 518 165 0.1 - 120.6 (36.5)

Figure S115.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00279 (Fisher's exact test), Q value = 0.046

Table S116.  Gene #75: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
19Q LOSS MUTATED 1 0 1 2
19Q LOSS WILD-TYPE 264 69 178 9

Figure S116.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00195 (Fisher's exact test), Q value = 0.036

Table S117.  Gene #78: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
21Q LOSS MUTATED 20 5 24 5
21Q LOSS WILD-TYPE 245 64 155 6

Figure S117.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'Time to Death'

P value = 0.0021 (logrank test), Q value = 0.037

Table S118.  Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
22Q LOSS MUTATED 39 21 1.7 - 73.2 (31.3)
22Q LOSS WILD-TYPE 483 147 0.1 - 120.6 (36.5)

Figure S118.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0197 (Fisher's exact test), Q value = 0.18

Table S119.  Gene #79: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
22Q LOSS MUTATED 11 4 14 10
22Q LOSS WILD-TYPE 249 53 113 70

Figure S119.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'22q loss' versus 'ETHNICITY'

P value = 0.0102 (Fisher's exact test), Q value = 0.11

Table S120.  Gene #79: '22q loss' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 345
22Q LOSS MUTATED 6 23
22Q LOSS WILD-TYPE 20 322

Figure S120.  Get High-res Image Gene #79: '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/15087101/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/15081616/KIRC-TP.merged_data.txt

  • Number of patients = 524

  • Number of significantly arm-level cnvs = 81

  • 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)
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