Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C19P311R
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C19P311R
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 80 arm-level events and 12 clinical features across 528 patients, 127 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' and 'GENDER'.

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

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

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

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

  • 8q gain cnv correlated to 'YEARS_TO_BIRTH',  '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 'Time to Death',  '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'.

  • 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 80 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 127 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 0.000738
(0.0185) 		0.257
(0.741) 		1e-05
(0.0016) 		0.00013
(0.00657) 		0.000724
(0.0185) 		0.00111
(0.0231) 		0.0266
(0.217) 		0.0362
(0.266) 		0.201
(0.677) 		0.073
(0.404) 		0.019
(0.169) 		0.686
(1.00)
12p gain 121 (23%) 407 0.00703
(0.0865) 		0.185
(0.667) 		0.00021
(0.00916) 		0.00142
(0.0273) 		0.0479
(0.315) 		0.0193
(0.17) 		0.388
(0.885) 		0.0148
(0.145) 		0.311
(0.807) 		0.11
(0.503) 		0.225
(0.699)
12q gain 122 (23%) 406 0.0106
(0.115) 		0.334
(0.834) 		0.0002
(0.00914) 		0.00073
(0.0185) 		0.0479
(0.315) 		0.0199
(0.174) 		0.334
(0.834) 		0.0148
(0.145) 		0.311
(0.807) 		0.111
(0.503) 		0.225
(0.699)
4q loss 65 (12%) 463 6.83e-06
(0.0016) 		0.828
(1.00) 		2e-05
(0.0016) 		2e-05
(0.0016) 		0.438
(0.923) 		0.00293
(0.0469) 		0.27
(0.76) 		0.877
(1.00) 		0.0218
(0.185) 		0.55
(1.00)
9p loss 149 (28%) 379 1.68e-05
(0.0016) 		0.0573
(0.348) 		1e-05
(0.0016) 		6e-05
(0.00384) 		0.0854
(0.436) 		0.0016
(0.0301) 		0.000887
(0.0203) 		0.613
(1.00) 		1
(1.00) 		0.872
(1.00) 		0.133
(0.548) 		0.655
(1.00)
9q loss 151 (29%) 377 0.000345
(0.0112) 		0.0565
(0.345) 		1e-05
(0.0016) 		1e-05
(0.0016) 		0.0941
(0.459) 		0.00425
(0.0598) 		0.00128
(0.0251) 		0.392
(0.885) 		1
(1.00) 		0.872
(1.00) 		0.12
(0.513) 		0.823
(1.00)
3q gain 60 (11%) 468 0.135
(0.548) 		0.788
(1.00) 		0.00046
(0.0138) 		0.00016
(0.00768) 		0.00469
(0.0634) 		0.0061
(0.076) 		0.568
(1.00) 		0.918
(1.00) 		0.467
(0.944) 		1
(1.00)
19q gain 57 (11%) 471 0.826
(1.00) 		0.392
(0.885) 		0.00075
(0.0185) 		0.00468
(0.0634) 		0.416
(0.893) 		0.00354
(0.0534) 		0.242
(0.722) 		0.456
(0.937) 		0.0319
(0.241) 		1
(1.00)
20p gain 112 (21%) 416 0.162
(0.615) 		0.233
(0.709) 		2e-05
(0.0016) 		1e-05
(0.0016) 		0.375
(0.884) 		0.0167
(0.154) 		0.00035
(0.0112) 		0.991
(1.00) 		0.498
(0.978) 		0.329
(0.832) 		0.442
(0.928)
20q gain 115 (22%) 413 0.12
(0.513) 		0.0787
(0.42) 		6e-05
(0.00384) 		2e-05
(0.0016) 		0.225
(0.699) 		0.0188
(0.169) 		0.00199
(0.036) 		0.991
(1.00) 		0.498
(0.978) 		0.316
(0.812) 		0.319
(0.819)
4p loss 72 (14%) 456 7.8e-05
(0.00468) 		0.743
(1.00) 		0.00026
(0.00998) 		0.00013
(0.00657) 		0.718
(1.00) 		0.0216
(0.185) 		0.895
(1.00) 		0.929
(1.00) 		0.0458
(0.307) 		0.399
(0.885)
13q loss 70 (13%) 458 0.000967
(0.0216) 		0.812
(1.00) 		0.00012
(0.00657) 		2e-05
(0.0016) 		0.289
(0.785) 		0.0309
(0.237) 		0.349
(0.854) 		0.929
(1.00) 		0.241
(0.722) 		0.226
(0.7)
15q loss 35 (7%) 493 0.00172
(0.0318) 		0.989
(1.00) 		0.00054
(0.0157) 		0.00033
(0.0112) 		1
(1.00) 		0.0142
(0.142) 		0.0458
(0.307) 		0.949
(1.00) 		0.0368
(0.266) 		0.382
(0.884)
7q gain 173 (33%) 355 0.517
(0.997) 		0.269
(0.76) 		0.00874
(0.102) 		0.0373
(0.268) 		0.301
(0.803) 		0.00255
(0.0422) 		0.0089
(0.102) 		0.309
(0.807) 		0.154
(0.6) 		0.0635
(0.368) 		0.0445
(0.303) 		0.27
(0.76)
8q gain 61 (12%) 467 0.146
(0.573) 		0.0117
(0.125) 		0.008
(0.096) 		0.00361
(0.0534) 		0.416
(0.893) 		0.177
(0.648) 		0.202
(0.677) 		0.523
(1.00) 		0.8
(1.00) 		0.859
(1.00) 		0.494
(0.974)
19p gain 51 (10%) 477 0.761
(1.00) 		0.676
(1.00) 		0.00338
(0.0523) 		0.0132
(0.134) 		0.232
(0.709) 		0.00781
(0.0949) 		0.22
(0.699) 		0.456
(0.937) 		0.071
(0.399) 		0.727
(1.00)
5p loss 8 (2%) 520 0.0109
(0.117) 		0.413
(0.893) 		0.0122
(0.127) 		0.00102
(0.0218) 		1
(1.00) 		0.116
(0.509) 		0.465
(0.943) 		0.571
(1.00) 		1
(1.00) 		1
(1.00)
5q loss 7 (1%) 521 0.0314
(0.239) 		0.288
(0.783) 		0.0276
(0.219) 		0.00231
(0.0397) 		1
(1.00) 		0.304
(0.803) 		0.705
(1.00) 		0.571
(1.00) 		1
(1.00) 		1
(1.00)
6p loss 100 (19%) 428 0.426
(0.907) 		0.271
(0.76) 		0.0348
(0.259) 		0.0184
(0.168) 		0.0156
(0.15) 		0.279
(0.773) 		0.00118
(0.0241) 		0.0998
(0.471) 		0.51
(0.993) 		0.643
(1.00) 		0.0353
(0.261) 		1
(1.00)
18p loss 93 (18%) 435 0.00101
(0.0218) 		0.0927
(0.454) 		0.00031
(0.0112) 		0.00025
(0.00998) 		1
(1.00) 		0.0797
(0.42) 		0.234
(0.709) 		0.869
(1.00) 		0.234
(0.709) 		0.0978
(0.468)
18q loss 95 (18%) 433 0.00595
(0.0751) 		0.113
(0.508) 		0.00889
(0.102) 		0.0043
(0.0598) 		1
(1.00) 		0.113
(0.508) 		0.193
(0.674) 		0.815
(1.00) 		0.213
(0.694) 		0.28
(0.773)
19p loss 11 (2%) 517 2.78e-05
(0.00205) 		0.0927
(0.454) 		0.0245
(0.205) 		0.0006
(0.0169) 		1
(1.00) 		0.391
(0.885) 		0.754
(1.00) 		0.12
(0.513) 		1
(1.00)
22q loss 39 (7%) 489 0.009
(0.102) 		0.242
(0.722) 		0.019
(0.169) 		0.157
(0.604) 		1
(1.00) 		0.1
(0.471) 		0.863
(1.00) 		0.911
(1.00) 		1
(1.00) 		0.00959
(0.107)
5p gain 191 (36%) 337 0.0752
(0.406) 		0.000241
(0.00998) 		0.0989
(0.47) 		0.215
(0.697) 		0.798
(1.00) 		0.899
(1.00) 		0.0233
(0.196) 		0.596
(1.00) 		0.0403
(0.28) 		0.832
(1.00)
5q gain 210 (40%) 318 0.0616
(0.368) 		0.00064
(0.0175) 		0.42
(0.899) 		0.398
(0.885) 		0.621
(1.00) 		1
(1.00) 		0.0159
(0.152) 		0.523
(1.00) 		0.588
(1.00) 		0.404
(0.885) 		0.0486
(0.315) 		0.836
(1.00)
7p gain 173 (33%) 355 0.993
(1.00) 		0.247
(0.729) 		0.0391
(0.274) 		0.0641
(0.368) 		0.432
(0.918) 		0.0259
(0.212) 		0.00379
(0.0543) 		0.541
(1.00) 		0.0979
(0.468) 		0.0635
(0.368) 		0.0851
(0.436) 		0.512
(0.993)
8p gain 31 (6%) 497 0.55
(1.00) 		0.176
(0.648) 		0.00088
(0.0203) 		0.00079
(0.019) 		1
(1.00) 		0.194
(0.674) 		0.563
(1.00) 		0.225
(0.699) 		0.528
(1.00) 		0.382
(0.884)
11p gain 31 (6%) 497 0.531
(1.00) 		0.986
(1.00) 		0.0285
(0.225) 		0.0128
(0.131) 		1
(1.00) 		0.116
(0.509) 		0.847
(1.00) 		0.305
(0.803) 		0.732
(1.00) 		1
(1.00)
17p gain 26 (5%) 502 0.834
(1.00) 		0.557
(1.00) 		0.303
(0.803) 		0.825
(1.00) 		0.191
(0.668) 		0.0213
(0.185) 		1
(1.00) 		0.646
(1.00) 		0.0269
(0.217) 		0.612
(1.00)
3p loss 379 (72%) 149 0.559
(1.00) 		0.792
(1.00) 		0.0433
(0.297) 		0.0288
(0.225) 		0.593
(1.00) 		0.103
(0.48) 		0.0118
(0.125) 		0.32
(0.819) 		0.522
(1.00) 		0.458
(0.937) 		0.219
(0.699) 		0.655
(1.00)
3q loss 102 (19%) 426 0.989
(1.00) 		0.0125
(0.129) 		0.757
(1.00) 		0.37
(0.884) 		0.322
(0.819) 		1
(1.00) 		0.000333
(0.0112) 		0.18
(0.652) 		0.63
(1.00) 		0.789
(1.00)
11q loss 23 (4%) 505 0.00236
(0.0397) 		0.0059
(0.0751) 		0.457
(0.937) 		0.512
(0.993) 		0.217
(0.697) 		0.385
(0.884) 		0.38
(0.884) 		0.358
(0.87) 		0.643
(1.00) 		1
(1.00)
19q loss 4 (1%) 524 0.00235
(0.0397) 		0.844
(1.00) 		0.194
(0.674) 		0.00273
(0.0444) 		1
(1.00) 		0.118
(0.512) 		1
(1.00) 		1
(1.00) 		1
(1.00)
1p gain 22 (4%) 506 0.000378
(0.0117) 		0.0753
(0.406) 		0.129
(0.541) 		0.206
(0.684) 		0.191
(0.668) 		0.352
(0.86) 		1
(1.00) 		0.168
(0.627) 		0.403
(0.885) 		0.612
(1.00)
1q gain 51 (10%) 477 0.0489
(0.315) 		0.0297
(0.23) 		0.0552
(0.344) 		0.08
(0.42) 		0.406
(0.885) 		0.682
(1.00) 		0.541
(1.00) 		0.401
(0.885) 		0.637
(1.00) 		0.727
(1.00)
9p gain 14 (3%) 514 0.118
(0.511) 		0.493
(0.973) 		0.89
(1.00) 		0.0587
(0.355) 		1
(1.00) 		0.141
(0.56) 		0.00842
(0.0998) 		0.724
(1.00) 		0.582
(1.00)
9q gain 13 (2%) 515 0.461
(0.937) 		0.225
(0.699) 		0.275
(0.771) 		0.00313
(0.0493) 		1
(1.00) 		1
(1.00) 		0.0751
(0.406) 		1
(1.00) 		0.582
(1.00)
10q gain 12 (2%) 516 0.84
(1.00) 		0.0152
(0.147) 		0.848
(1.00) 		0.88
(1.00) 		0.246
(0.726) 		1
(1.00) 		0.364
(0.88) 		0.599
(1.00) 		0.486
(0.964) 		1
(1.00)
14q gain 16 (3%) 512 0.124
(0.525) 		0.473
(0.951) 		0.227
(0.7) 		0.00566
(0.0734) 		1
(1.00) 		0.295
(0.798) 		0.796
(1.00) 		1
(1.00) 		1
(1.00)
xp gain 32 (6%) 496 0.578
(1.00) 		0.558
(1.00) 		0.0253
(0.209) 		0.0928
(0.454) 		1
(1.00) 		0.0369
(0.266) 		0.851
(1.00) 		0.587
(1.00) 		0.108
(0.498) 		0.383
(0.884)
xq gain 31 (6%) 497 0.928
(1.00) 		0.781
(1.00) 		0.0538
(0.34) 		0.117
(0.51) 		1
(1.00) 		0.0274
(0.219) 		0.704
(1.00) 		0.331
(0.832) 		0.532
(1.00) 		0.383
(0.884)
1p loss 60 (11%) 468 0.529
(1.00) 		0.303
(0.803) 		0.305
(0.803) 		0.0163
(0.152) 		1
(1.00) 		0.564
(1.00) 		0.252
(0.734) 		0.764
(1.00) 		0.615
(1.00) 		0.112
(0.506)
6q loss 128 (24%) 400 0.385
(0.884) 		0.666
(1.00) 		0.279
(0.773) 		0.179
(0.652) 		0.00363
(0.0534) 		0.669
(1.00) 		0.0717
(0.4) 		0.444
(0.93) 		0.0337
(0.253) 		0.643
(1.00) 		0.07
(0.398) 		0.476
(0.952)
8q loss 65 (12%) 463 0.505
(0.986) 		0.459
(0.937) 		0.57
(1.00) 		0.159
(0.61) 		1
(1.00) 		1
(1.00) 		0.00536
(0.0705) 		0.988
(1.00) 		0.199
(0.676) 		0.056
(0.345)
10p loss 68 (13%) 460 0.299
(0.803) 		0.265
(0.756) 		0.0799
(0.42) 		0.0104
(0.114) 		0.142
(0.56) 		0.586
(1.00) 		0.279
(0.773) 		0.163
(0.617) 		0.551
(1.00) 		0.209
(0.69)
10q loss 89 (17%) 439 0.555
(1.00) 		0.536
(1.00) 		0.098
(0.468) 		0.00233
(0.0397) 		0.485
(0.964) 		0.627
(1.00) 		0.115
(0.509) 		0.212
(0.694) 		0.285
(0.781) 		0.278
(0.773)
11p loss 18 (3%) 510 0.00367
(0.0534) 		0.0538
(0.34) 		0.286
(0.781) 		0.404
(0.885) 		0.141
(0.56) 		0.505
(0.986) 		1
(1.00) 		0.762
(1.00) 		1
(1.00) 		1
(1.00)
16p loss 10 (2%) 518 0.0881
(0.445) 		0.652
(1.00) 		0.395
(0.885) 		0.0164
(0.152) 		0.346
(0.853) 		1
(1.00) 		1
(1.00) 		0.403
(0.885) 		1
(1.00)
16q loss 16 (3%) 512 0.135
(0.548) 		0.332
(0.832) 		0.414
(0.893) 		0.00508
(0.0677) 		0.434
(0.918) 		1
(1.00) 		0.796
(1.00) 		0.166
(0.626) 		1
(1.00)
21q loss 55 (10%) 473 0.697
(1.00) 		0.723
(1.00) 		0.0764
(0.41) 		0.00126
(0.0251) 		0.0844
(0.436) 		1
(1.00) 		0.461
(0.937) 		0.804
(1.00) 		0.582
(1.00) 		1
(1.00)
2p gain 78 (15%) 450 0.656
(1.00) 		0.177
(0.648) 		0.261
(0.745) 		0.349
(0.854) 		0.746
(1.00) 		0.393
(0.885) 		1
(1.00) 		0.71
(1.00) 		0.543
(1.00) 		0.359
(0.87) 		0.764
(1.00)
2q gain 79 (15%) 449 0.539
(1.00) 		0.217
(0.697) 		0.448
(0.935) 		0.547
(1.00) 		1
(1.00) 		0.392
(0.885) 		0.525
(1.00) 		0.899
(1.00) 		0.543
(1.00) 		0.338
(0.838) 		0.374
(0.884)
3p gain 20 (4%) 508 0.0418
(0.288) 		0.482
(0.96) 		0.0852
(0.436) 		0.129
(0.541) 		0.0389
(0.274) 		0.107
(0.498) 		0.476
(0.952) 		0.469
(0.945) 		0.79
(1.00) 		1
(1.00)
4p gain 13 (2%) 515 0.14
(0.56) 		0.774
(1.00) 		0.385
(0.884) 		0.169
(0.63) 		0.474
(0.951) 		1
(1.00) 		0.396
(0.885) 		1
(1.00) 		1
(1.00)
4q gain 13 (2%) 515 0.372
(0.884) 		0.774
(1.00) 		0.459
(0.937) 		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 0.931
(1.00) 		0.793
(1.00) 		0.313
(0.808) 		0.231
(0.709) 		1
(1.00) 		0.686
(1.00) 		0.342
(0.845) 		1
(1.00) 		1
(1.00)
6q gain 9 (2%) 519 0.728
(1.00) 		0.359
(0.87) 		0.204
(0.681) 		0.281
(0.774) 		1
(1.00) 		1
(1.00) 		0.168
(0.627) 		1
(1.00) 		1
(1.00)
10p gain 16 (3%) 512 0.949
(1.00) 		0.183
(0.662) 		0.366
(0.881) 		0.186
(0.667) 		0.0742
(0.406) 		0.726
(1.00) 		0.796
(1.00) 		0.874
(1.00) 		0.406
(0.885) 		1
(1.00)
11q gain 29 (5%) 499 0.199
(0.676) 		0.946
(1.00) 		0.162
(0.615) 		0.084
(0.436) 		1
(1.00) 		0.42
(0.899) 		1
(1.00) 		0.851
(1.00) 		1
(1.00)
13q gain 22 (4%) 506 0.134
(0.548) 		0.254
(0.736) 		0.131
(0.543) 		0.205
(0.683) 		1
(1.00) 		0.367
(0.881) 		0.257
(0.741) 		0.0957
(0.464) 		0.09
(0.451)
15q gain 26 (5%) 502 0.503
(0.985) 		0.451
(0.937) 		0.456
(0.937) 		0.368
(0.882) 		0.191
(0.668) 		0.582
(1.00) 		0.678
(1.00) 		0.0499
(0.32) 		0.561
(1.00) 		1
(1.00)
16p gain 107 (20%) 421 0.379
(0.884) 		0.245
(0.726) 		0.195
(0.674) 		0.0705
(0.398) 		0.21
(0.691) 		0.648
(1.00) 		0.652
(1.00) 		0.742
(1.00) 		0.0641
(0.368) 		0.238
(0.718) 		1
(1.00)
16q gain 99 (19%) 429 0.252
(0.734) 		0.338
(0.838) 		0.286
(0.781) 		0.0485
(0.315) 		0.208
(0.687) 		1
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.0641
(0.368) 		0.423
(0.902) 		0.787
(1.00)
17q gain 33 (6%) 495 0.492
(0.973) 		0.341
(0.843) 		0.687
(1.00) 		0.661
(1.00) 		0.296
(0.798) 		0.202
(0.677) 		0.709
(1.00) 		0.523
(1.00) 		0.389
(0.885) 		0.0624
(0.368) 		0.383
(0.884)
18p gain 25 (5%) 503 0.0624
(0.368) 		0.804
(1.00) 		0.927
(1.00) 		0.87
(1.00) 		0.607
(1.00) 		0.401
(0.885) 		0.0907
(0.451) 		0.665
(1.00) 		0.332
(0.832)
18q gain 25 (5%) 503 0.138
(0.56) 		0.617
(1.00) 		0.82
(1.00) 		0.768
(1.00) 		0.577
(1.00) 		0.401
(0.885) 		0.0907
(0.451) 		0.668
(1.00) 		0.332
(0.832)
21q gain 50 (9%) 478 0.713
(1.00) 		0.116
(0.509) 		0.221
(0.699) 		0.111
(0.503) 		1
(1.00) 		0.533
(1.00) 		0.439
(0.925) 		0.126
(0.533) 		0.478
(0.954) 		0.22
(0.699) 		0.719
(1.00)
22q gain 40 (8%) 488 0.383
(0.884) 		0.563
(1.00) 		0.7
(1.00) 		0.0873
(0.444) 		1
(1.00) 		0.82
(1.00) 		0.305
(0.803) 		0.407
(0.885) 		0.213
(0.694) 		1
(1.00)
1q loss 37 (7%) 491 0.651
(1.00) 		0.537
(1.00) 		0.834
(1.00) 		0.0732
(0.404) 		1
(1.00) 		0.243
(0.722) 		0.725
(1.00) 		0.791
(1.00) 		0.584
(1.00) 		0.463
(0.939)
2p loss 14 (3%) 514 0.828
(1.00) 		0.839
(1.00) 		0.445
(0.93) 		0.139
(0.56) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.0552
(0.344) 		1
(1.00)
2q loss 14 (3%) 514 0.817
(1.00) 		0.814
(1.00) 		0.539
(1.00) 		0.223
(0.699) 		1
(1.00) 		0.707
(1.00) 		0.779
(1.00) 		0.175
(0.647) 		1
(1.00)
8p loss 137 (26%) 391 0.189
(0.668) 		0.674
(1.00) 		0.329
(0.832) 		0.19
(0.668) 		1
(1.00) 		0.267
(0.758) 		0.0389
(0.274) 		0.78
(1.00) 		0.964
(1.00) 		0.458
(0.937) 		0.13
(0.543) 		0.0559
(0.345)
12p loss 4 (1%) 524 0.261
(0.745) 		0.69
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.408
(0.885) 		1
(1.00)
12q loss 4 (1%) 524 0.836
(1.00) 		0.312
(0.808) 		0.16
(0.612) 		0.407
(0.885) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 46 (9%) 482 0.4
(0.885) 		0.3
(0.803) 		0.141
(0.56) 		0.132
(0.546) 		0.375
(0.884) 		0.0474
(0.315) 		0.197
(0.674) 		0.321
(0.819) 		1
(1.00) 		0.713
(1.00)
17q loss 28 (5%) 500 0.459
(0.937) 		0.787
(1.00) 		0.308
(0.807) 		0.261
(0.745) 		1
(1.00) 		0.18
(0.652) 		0.311
(0.807) 		0.843
(1.00) 		1
(1.00)
20p loss 8 (2%) 520 0.724
(1.00) 		0.701
(1.00) 		0.79
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.366
(0.881) 		1
(1.00) 		0.156
(0.604) 		0.25
(0.732)
20q loss 3 (1%) 525 0.878
(1.00) 		0.115
(0.509) 		0.23
(0.706) 		0.107
(0.498) 		0.402
(0.885) 		1
(1.00) 		1
(1.00) 		0.0691
(0.395)
xp loss 45 (9%) 483 0.25
(0.732) 		0.898
(1.00) 		0.951
(1.00) 		0.515
(0.995) 		0.217
(0.697) 		0.823
(1.00) 		0.197
(0.674) 		0.377
(0.884) 		0.809
(1.00) 		0.149
(0.585)
xq loss 45 (9%) 483 0.188
(0.668) 		0.673
(1.00) 		0.95
(1.00) 		0.515
(0.995) 		0.243
(0.722) 		1
(1.00) 		0.197
(0.674) 		0.716
(1.00) 		0.585
(1.00) 		0.15
(0.585)
'1p gain' versus 'Time to Death'

P value = 0.000378 (logrank test), Q value = 0.012

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 (38.8)
1P GAIN MUTATED 22 14 0.5 - 118.8 (22.4)
1P GAIN WILD-TYPE 504 161 0.1 - 149.2 (40.0)

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

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
3Q GAIN MUTATED 17 6 18 19
3Q GAIN WILD-TYPE 245 51 106 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 = 0.00016 (Fisher's exact test), Q value = 0.0077

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 7 32 4
3Q GAIN WILD-TYPE 251 62 148 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 = 0.00469 (Fisher's exact test), Q value = 0.063

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

nPatients 0 1
ALL 234 17
3Q GAIN MUTATED 29 7
3Q GAIN WILD-TYPE 205 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 = 0.0061 (Fisher's exact test), Q value = 0.076

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

nPatients 0 1
ALL 418 78
3Q GAIN MUTATED 41 17
3Q GAIN WILD-TYPE 377 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 = 0.000241 (Wilcoxon-test), Q value = 0.01

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 191 63.1 (11.9)
5P GAIN WILD-TYPE 336 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 = 0.0233 (Fisher's exact test), Q value = 0.2

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

nPatients FEMALE MALE
ALL 189 339
5P GAIN MUTATED 56 135
5P GAIN WILD-TYPE 133 204

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

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00064 (Wilcoxon-test), Q value = 0.018

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

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
5Q GAIN MUTATED 209 62.8 (12.2)
5Q GAIN WILD-TYPE 318 59.0 (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 = 0.0159 (Fisher's exact test), Q value = 0.15

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

nPatients FEMALE MALE
ALL 189 339
5Q GAIN MUTATED 62 148
5Q GAIN WILD-TYPE 127 191

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

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0259 (Fisher's exact test), Q value = 0.21

Table S11.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
7P GAIN MUTATED 131 35
7P GAIN WILD-TYPE 287 43

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'GENDER'

P value = 0.00379 (Fisher's exact test), Q value = 0.054

Table S12.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
7P GAIN MUTATED 47 126
7P GAIN WILD-TYPE 142 213

Figure S12.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00874 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
7Q GAIN MUTATED 72 17 44 39
7Q GAIN WILD-TYPE 190 40 80 44

Figure S13.  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 = 0.042

Table S14.  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 S14.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'GENDER'

P value = 0.0089 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
7Q GAIN MUTATED 48 125
7Q GAIN WILD-TYPE 141 214

Figure S15.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'8p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00088 (Fisher's exact test), Q value = 0.02

Table S16.  Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
8P GAIN MUTATED 6 8 9 8
8P GAIN WILD-TYPE 256 49 115 75

Figure S16.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00079 (Fisher's exact test), Q value = 0.019

Table S17.  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 S17.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0117 (Wilcoxon-test), Q value = 0.12

Table S18.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
8Q GAIN MUTATED 61 64.0 (11.5)
8Q GAIN WILD-TYPE 466 60.1 (12.1)

Figure S18.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.008 (Fisher's exact test), Q value = 0.096

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
8Q GAIN MUTATED 18 10 19 13
8Q GAIN WILD-TYPE 244 47 105 70

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

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00361 (Fisher's exact test), Q value = 0.053

Table S20.  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 11 31 0
8Q GAIN WILD-TYPE 249 58 149 11

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

'9p gain' versus 'GENDER'

P value = 0.00842 (Fisher's exact test), Q value = 0.1

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

nPatients FEMALE MALE
ALL 189 339
9P GAIN MUTATED 10 4
9P GAIN WILD-TYPE 179 335

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

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00313 (Fisher's exact test), Q value = 0.049

Table S22.  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 4 3
9Q GAIN WILD-TYPE 264 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 = 0.0152 (Wilcoxon-test), Q value = 0.15

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

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0285 (Fisher's exact test), Q value = 0.22

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
11P GAIN MUTATED 8 4 11 8
11P GAIN WILD-TYPE 254 53 113 75

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

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0128 (Fisher's exact test), Q value = 0.13

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

'12p gain' versus 'Time to Death'

P value = 0.00703 (logrank test), Q value = 0.087

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

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
12P GAIN MUTATED 121 51 0.1 - 133.7 (33.5)
12P GAIN WILD-TYPE 405 124 0.1 - 149.2 (41.6)

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

'12p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0092

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
12P GAIN MUTATED 44 9 38 30
12P GAIN WILD-TYPE 218 48 86 53

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

'12p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00142 (Fisher's exact test), Q value = 0.027

Table S28.  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 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 = 0.17

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'

'12p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0148 (Wilcoxon-test), Q value = 0.15

Table S30.  Gene #23: '12p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 54 85.6 (25.8)
12P GAIN MUTATED 13 69.2 (39.9)
12P GAIN WILD-TYPE 41 90.7 (17.1)

Figure S30.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'12q gain' versus 'Time to Death'

P value = 0.0106 (logrank test), Q value = 0.12

Table S31.  Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
12Q GAIN MUTATED 122 51 0.1 - 133.7 (34.2)
12Q GAIN WILD-TYPE 404 124 0.1 - 149.2 (41.2)

Figure S31.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0091

Table S32.  Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
12Q GAIN MUTATED 44 9 39 30
12Q GAIN WILD-TYPE 218 48 85 53

Figure S32.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00073 (Fisher's exact test), Q value = 0.018

Table S33.  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 S33.  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 S34.  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 S34.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0148 (Wilcoxon-test), Q value = 0.15

Table S35.  Gene #24: '12q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 54 85.6 (25.8)
12Q GAIN MUTATED 13 69.2 (39.9)
12Q GAIN WILD-TYPE 41 90.7 (17.1)

Figure S35.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00566 (Fisher's exact test), Q value = 0.073

Table S36.  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 S36.  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 S37.  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 S37.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p gain' versus 'RACE'

P value = 0.0269 (Fisher's exact test), Q value = 0.22

Table S38.  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 S38.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'RACE'

'19p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00338 (Fisher's exact test), Q value = 0.052

Table S39.  Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
19P GAIN MUTATED 15 7 13 16
19P GAIN WILD-TYPE 247 50 111 67

Figure S39.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.13

Table S40.  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 S40.  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 S41.  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 S41.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00075 (Fisher's exact test), Q value = 0.018

Table S42.  Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
19Q GAIN MUTATED 16 7 16 18
19Q GAIN WILD-TYPE 246 50 108 65

Figure S42.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00468 (Fisher's exact test), Q value = 0.063

Table S43.  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 S43.  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 S44.  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 S44.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'RACE'

P value = 0.0319 (Fisher's exact test), Q value = 0.24

Table S45.  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 S45.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #11: 'RACE'

'20p gain' versus 'PATHOLOGIC_STAGE'

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

Table S46.  Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
20P GAIN MUTATED 34 12 37 28
20P GAIN WILD-TYPE 228 45 87 55

Figure S46.  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 = 0.0016

Table S47.  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 S47.  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 = 0.15

Table S48.  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 S48.  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 S49.  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 S49.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0038

Table S50.  Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
20Q GAIN MUTATED 35 12 39 28
20Q GAIN WILD-TYPE 227 45 85 55

Figure S50.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

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

Table S51.  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 S51.  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 S52.  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 S52.  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 S53.  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 S53.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0253 (Fisher's exact test), Q value = 0.21

Table S54.  Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
XP GAIN MUTATED 10 4 7 11
XP GAIN WILD-TYPE 252 53 117 72

Figure S54.  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 = 0.22

Table S55.  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 S55.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0163 (Fisher's exact test), Q value = 0.15

Table S56.  Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
1P LOSS MUTATED 33 10 13 4
1P LOSS WILD-TYPE 235 59 167 7

Figure S56.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0288 (Fisher's exact test), Q value = 0.22

Table S57.  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 50 138 4
3P LOSS WILD-TYPE 81 19 42 7

Figure S57.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'GENDER'

P value = 0.0118 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
3P LOSS MUTATED 123 256
3P LOSS WILD-TYPE 66 83

Figure S58.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0125 (Wilcoxon-test), Q value = 0.13

Table S59.  Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
3Q LOSS MUTATED 102 63.4 (13.1)
3Q LOSS WILD-TYPE 425 59.8 (11.8)

Figure S59.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'GENDER'

P value = 0.000333 (Fisher's exact test), Q value = 0.011

Table S60.  Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
3Q LOSS MUTATED 21 81
3Q LOSS WILD-TYPE 168 258

Figure S60.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'Time to Death'

P value = 7.8e-05 (logrank test), Q value = 0.0047

Table S61.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
4P LOSS MUTATED 72 39 0.5 - 133.7 (38.5)
4P LOSS WILD-TYPE 454 136 0.1 - 149.2 (39.3)

Figure S61.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.01

Table S62.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
4P LOSS MUTATED 21 6 25 20
4P LOSS WILD-TYPE 241 51 99 63

Figure S62.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0066

Table S63.  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 S63.  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 S64.  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 S64.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'Time to Death'

P value = 6.83e-06 (logrank test), Q value = 0.0016

Table S65.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
4Q LOSS MUTATED 65 37 1.2 - 133.7 (33.5)
4Q LOSS WILD-TYPE 461 138 0.1 - 149.2 (40.0)

Figure S65.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'PATHOLOGIC_STAGE'

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

Table S66.  Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
4Q LOSS MUTATED 15 6 23 21
4Q LOSS WILD-TYPE 247 51 101 62

Figure S66.  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 = 0.0016

Table S67.  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 S67.  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 S68.  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 S68.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'RACE'

P value = 0.0218 (Fisher's exact test), Q value = 0.19

Table S69.  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 S69.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'Time to Death'

P value = 0.0109 (logrank test), Q value = 0.12

Table S70.  Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
5P LOSS MUTATED 8 6 3.3 - 112.1 (30.8)
5P LOSS WILD-TYPE 518 169 0.1 - 149.2 (39.1)

Figure S70.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.13

Table S71.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
5P LOSS MUTATED 1 2 1 4
5P LOSS WILD-TYPE 261 55 123 79

Figure S71.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00102 (Fisher's exact test), Q value = 0.022

Table S72.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
5P LOSS MUTATED 1 3 2 2
5P LOSS WILD-TYPE 267 66 178 9

Figure S72.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'Time to Death'

P value = 0.0314 (logrank test), Q value = 0.24

Table S73.  Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
5Q LOSS MUTATED 7 5 3.3 - 112.1 (31.1)
5Q LOSS WILD-TYPE 519 170 0.1 - 149.2 (39.0)

Figure S73.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0276 (Fisher's exact test), Q value = 0.22

Table S74.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
5Q LOSS MUTATED 1 2 1 3
5Q LOSS WILD-TYPE 261 55 123 80

Figure S74.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00231 (Fisher's exact test), Q value = 0.04

Table S75.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
5Q LOSS MUTATED 1 2 2 2
5Q LOSS WILD-TYPE 267 67 178 9

Figure S75.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0184 (Fisher's exact test), Q value = 0.17

Table S76.  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 S76.  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 = 0.15

Table S77.  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 S77.  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 S78.  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 S78.  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 S79.  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 S79.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q loss' versus 'GENDER'

P value = 0.00536 (Fisher's exact test), Q value = 0.071

Table S80.  Gene #55: '8q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
8Q LOSS MUTATED 13 52
8Q LOSS WILD-TYPE 176 287

Figure S80.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'Time to Death'

P value = 1.68e-05 (logrank test), Q value = 0.0016

Table S81.  Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
9P LOSS MUTATED 148 72 0.5 - 133.7 (38.9)
9P LOSS WILD-TYPE 378 103 0.1 - 149.2 (38.8)

Figure S81.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'PATHOLOGIC_STAGE'

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

Table S82.  Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
9P LOSS MUTATED 52 11 48 36
9P LOSS WILD-TYPE 210 46 76 47

Figure S82.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0038

Table S83.  Gene #56: '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 S83.  Get High-res Image Gene #56: '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 S84.  Gene #56: '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 S84.  Get High-res Image Gene #56: '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 S85.  Gene #56: '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 S85.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'Time to Death'

P value = 0.000345 (logrank test), Q value = 0.011

Table S86.  Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
9Q LOSS MUTATED 150 70 0.5 - 133.7 (39.3)
9Q LOSS WILD-TYPE 376 105 0.1 - 149.2 (38.6)

Figure S86.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'PATHOLOGIC_STAGE'

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

Table S87.  Gene #57: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
9Q LOSS MUTATED 50 14 50 35
9Q LOSS WILD-TYPE 212 43 74 48

Figure S87.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

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

Table S88.  Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
9Q LOSS MUTATED 53 18 76 4
9Q LOSS WILD-TYPE 215 51 104 7

Figure S88.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00425 (Fisher's exact test), Q value = 0.06

Table S89.  Gene #57: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
9Q LOSS MUTATED 112 34
9Q LOSS WILD-TYPE 306 44

Figure S89.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'GENDER'

P value = 0.00128 (Fisher's exact test), Q value = 0.025

Table S90.  Gene #57: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
9Q LOSS MUTATED 38 113
9Q LOSS WILD-TYPE 151 226

Figure S90.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #7: 'GENDER'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0104 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
10P LOSS MUTATED 25 8 31 4
10P LOSS WILD-TYPE 243 61 149 7

Figure S91.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00233 (Fisher's exact test), Q value = 0.04

Table S92.  Gene #59: '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 S92.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'Time to Death'

P value = 0.00367 (logrank test), Q value = 0.053

Table S93.  Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
11P LOSS MUTATED 18 10 2.0 - 84.3 (25.0)
11P LOSS WILD-TYPE 508 165 0.1 - 149.2 (40.0)

Figure S93.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'Time to Death'

P value = 0.00236 (logrank test), Q value = 0.04

Table S94.  Gene #61: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
11Q LOSS MUTATED 23 12 1.9 - 109.9 (21.6)
11Q LOSS WILD-TYPE 503 163 0.1 - 149.2 (40.4)

Figure S94.  Get High-res Image Gene #61: '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 S95.  Gene #61: '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 S95.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'Time to Death'

P value = 0.000967 (logrank test), Q value = 0.022

Table S96.  Gene #64: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
13Q LOSS MUTATED 69 34 0.5 - 112.1 (31.3)
13Q LOSS WILD-TYPE 457 141 0.1 - 149.2 (40.0)

Figure S96.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0066

Table S97.  Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
13Q LOSS MUTATED 24 2 24 20
13Q LOSS WILD-TYPE 238 55 100 63

Figure S97.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

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

Table S98.  Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
13Q LOSS MUTATED 26 3 34 7
13Q LOSS WILD-TYPE 242 66 146 4

Figure S98.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0309 (Fisher's exact test), Q value = 0.24

Table S99.  Gene #64: '13q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
13Q LOSS MUTATED 51 17
13Q LOSS WILD-TYPE 367 61

Figure S99.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'Time to Death'

P value = 0.000738 (logrank test), Q value = 0.018

Table S100.  Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
14Q LOSS MUTATED 215 92 0.4 - 133.7 (36.4)
14Q LOSS WILD-TYPE 311 83 0.1 - 149.2 (43.0)

Figure S100.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGIC_STAGE'

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

Table S101.  Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
14Q LOSS MUTATED 79 26 62 47
14Q LOSS WILD-TYPE 183 31 62 36

Figure S101.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0066

Table S102.  Gene #65: '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 S102.  Get High-res Image Gene #65: '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 = 0.018

Table S103.  Gene #65: '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 S103.  Get High-res Image Gene #65: '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 = 0.023

Table S104.  Gene #65: '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 S104.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'GENDER'

P value = 0.0266 (Fisher's exact test), Q value = 0.22

Table S105.  Gene #65: '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 S105.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #7: 'GENDER'

'14q loss' versus 'RACE'

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

Table S106.  Gene #65: '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 S106.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #11: 'RACE'

'15q loss' versus 'Time to Death'

P value = 0.00172 (logrank test), Q value = 0.032

Table S107.  Gene #66: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
15Q LOSS MUTATED 35 18 1.4 - 90.5 (31.3)
15Q LOSS WILD-TYPE 491 157 0.1 - 149.2 (40.0)

Figure S107.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00054 (Fisher's exact test), Q value = 0.016

Table S108.  Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
15Q LOSS MUTATED 8 2 13 12
15Q LOSS WILD-TYPE 254 55 111 71

Figure S108.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.011

Table S109.  Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
15Q LOSS MUTATED 9 2 21 3
15Q LOSS WILD-TYPE 259 67 159 8

Figure S109.  Get High-res Image Gene #66: '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 S110.  Gene #66: '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 S110.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.15

Table S111.  Gene #67: '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 S111.  Get High-res Image Gene #67: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00508 (Fisher's exact test), Q value = 0.068

Table S112.  Gene #68: '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 S112.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'Time to Death'

P value = 0.00101 (logrank test), Q value = 0.022

Table S113.  Gene #71: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
18P LOSS MUTATED 92 42 0.4 - 118.8 (31.3)
18P LOSS WILD-TYPE 434 133 0.1 - 149.2 (41.7)

Figure S113.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00031 (Fisher's exact test), Q value = 0.011

Table S114.  Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
18P LOSS MUTATED 31 7 33 22
18P LOSS WILD-TYPE 231 50 91 61

Figure S114.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.01

Table S115.  Gene #71: '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 S115.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'Time to Death'

P value = 0.00595 (logrank test), Q value = 0.075

Table S116.  Gene #72: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
18Q LOSS MUTATED 94 41 0.4 - 119.6 (32.2)
18Q LOSS WILD-TYPE 432 134 0.1 - 149.2 (41.2)

Figure S116.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00889 (Fisher's exact test), Q value = 0.1

Table S117.  Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
18Q LOSS MUTATED 35 8 30 22
18Q LOSS WILD-TYPE 227 49 94 61

Figure S117.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0043 (Fisher's exact test), Q value = 0.06

Table S118.  Gene #72: '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 S118.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'Time to Death'

P value = 2.78e-05 (logrank test), Q value = 0.0021

Table S119.  Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
19P LOSS MUTATED 11 9 1.4 - 109.9 (28.5)
19P LOSS WILD-TYPE 515 166 0.1 - 149.2 (39.5)

Figure S119.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0245 (Fisher's exact test), Q value = 0.2

Table S120.  Gene #73: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
19P LOSS MUTATED 2 0 5 4
19P LOSS WILD-TYPE 260 57 119 79

Figure S120.  Get High-res Image Gene #73: '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 S121.  Gene #73: '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 S121.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.00235 (logrank test), Q value = 0.04

Table S122.  Gene #74: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
19Q LOSS MUTATED 4 3 1.4 - 37.1 (19.7)
19Q LOSS WILD-TYPE 522 172 0.1 - 149.2 (39.3)

Figure S122.  Get High-res Image Gene #74: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00273 (Fisher's exact test), Q value = 0.044

Table S123.  Gene #74: '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 S123.  Get High-res Image Gene #74: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

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

Table S124.  Gene #77: '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 S124.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'Time to Death'

P value = 0.009 (logrank test), Q value = 0.1

Table S125.  Gene #78: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.8)
22Q LOSS MUTATED 39 21 1.7 - 114.4 (33.5)
22Q LOSS WILD-TYPE 487 154 0.1 - 149.2 (39.5)

Figure S125.  Get High-res Image Gene #78: '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 S126.  Gene #78: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 262 57 124 83
22Q LOSS MUTATED 11 4 14 10
22Q LOSS WILD-TYPE 251 53 110 73

Figure S126.  Get High-res Image Gene #78: '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 S127.  Gene #78: '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 S127.  Get High-res Image Gene #78: '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/22531285/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/22506714/KIRC-TP.merged_data.txt

  • Number of patients = 528

  • Number of significantly arm-level cnvs = 80

  • 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)
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