Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1CC1030
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/C1CC1030
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 74 arm-level events and 12 clinical features across 288 patients, 234 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • 1q gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 2p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 2q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 3p gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

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

  • 5p gain cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 5q gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 6p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 6q gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 7p gain cnv correlated to 'PATHOLOGIC_STAGE',  'GENDER', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

  • 8p gain cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.

  • 8q gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • 9p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 10p gain cnv correlated to 'RACE'.

  • 10q gain cnv correlated to 'RACE'.

  • 11p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 11q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'GENDER'.

  • 12p gain cnv correlated to 'GENDER'.

  • 12q gain cnv correlated to 'GENDER'.

  • 14q gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 16p gain cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • 16q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • 17p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'ETHNICITY'.

  • 17q gain cnv correlated to 'PATHOLOGIC_STAGE'.

  • 18q gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 21q gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • xp gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • xq gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • 1p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 2p loss cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • 3p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • 3q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • 4p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • 4q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

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

  • 5q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • 6p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 6q loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 8p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 8q loss cnv correlated to 'GENDER'.

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

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

  • 10p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 10q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 11p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • 11q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 13q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

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

  • 16p loss cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • 16q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • 17p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

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

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

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

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

  • 21q loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 22q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • xp loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

  • xq loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 234 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
22q loss 60 (21%) 228 0.00125
(0.0132) 		0.0636
(0.245) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00561
(0.0415) 		0.043
(0.188) 		0.000466
(0.00636) 		0.00113
(0.0126) 		0.559
(0.898) 		0.216
(0.524) 		0.299
(0.63) 		0.707
(1.00)
9q loss 34 (12%) 254 2.55e-05
(0.000551) 		0.416
(0.756) 		5e-05
(0.000906) 		2e-05
(0.000444) 		0.00609
(0.0436) 		0.353
(0.699) 		0.00167
(0.0161) 		0.001
(0.0114) 		0.941
(1.00) 		0.57
(0.911) 		0.0379
(0.172) 		0.371
(0.711)
13q loss 24 (8%) 264 1.33e-07
(1.47e-05) 		0.00291
(0.0256) 		0.00023
(0.00358) 		2e-05
(0.000444) 		0.00378
(0.0311) 		0.532
(0.878) 		1.74e-05
(0.000428) 		0.064
(0.245) 		0.746
(1.00) 		0.447
(0.788) 		0.175
(0.468) 		1
(1.00)
1q gain 17 (6%) 271 4.2e-08
(6.21e-06) 		0.654
(0.969) 		3e-05
(0.00062) 		1e-05
(0.000269) 		0.0301
(0.15) 		0.114
(0.353) 		0.0195
(0.11) 		0.0219
(0.117) 		0.236
(0.549) 		0.109
(0.347) 		1
(1.00)
17p gain 172 (60%) 116 0.0579
(0.229) 		0.0535
(0.22) 		1e-05
(0.000269) 		7e-05
(0.00122) 		0.673
(0.988) 		0.504
(0.848) 		0.0139
(0.0846) 		0.321
(0.66) 		0.741
(1.00) 		0.139
(0.406) 		0.0841
(0.294) 		0.0614
(0.239)
4p loss 25 (9%) 263 8.66e-09
(2.27e-06) 		0.00351
(0.0297) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00106
(0.0119) 		0.576
(0.919) 		3.8e-05
(0.000767) 		0.0768
(0.275) 		0.96
(1.00) 		0.192
(0.491) 		0.173
(0.468) 		1
(1.00)
4q loss 26 (9%) 262 7.78e-09
(2.27e-06) 		0.0203
(0.11) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00976
(0.0646) 		0.211
(0.518) 		0.000614
(0.00798) 		0.067
(0.253) 		0.611
(0.93) 		0.282
(0.606) 		0.172
(0.468) 		1
(1.00)
5q loss 8 (3%) 280 9.36e-08
(1.19e-05) 		0.0121
(0.076) 		0.0381
(0.173) 		0.00396
(0.0323) 		0.0257
(0.133) 		0.242
(0.552) 		0.0322
(0.158) 		1
(1.00) 		0.256
(0.571)
9p loss 33 (11%) 255 6.49e-07
(4.8e-05) 		0.294
(0.624) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00092
(0.0111) 		0.0685
(0.254) 		0.00122
(0.0132) 		0.000832
(0.0103) 		0.388
(0.725) 		0.478
(0.814) 		0.149
(0.427) 		0.37
(0.711)
14q loss 47 (16%) 241 0.000118
(0.00198) 		0.348
(0.693) 		0.00191
(0.0182) 		6e-05
(0.00107) 		0.00138
(0.0142) 		0.123
(0.371) 		0.00338
(0.0289) 		0.00896
(0.0617) 		0.476
(0.812) 		0.0756
(0.272) 		1
(1.00) 		0.697
(1.00)
18p loss 42 (15%) 246 1.08e-06
(7.35e-05) 		0.073
(0.265) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.0162
(0.0967) 		0.0577
(0.229) 		0.0359
(0.17) 		0.244
(0.552) 		0.222
(0.527) 		0.0832
(0.292) 		0.464
(0.801) 		0.676
(0.988)
xp loss 33 (11%) 255 1.09e-05
(0.000284) 		0.12
(0.368) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.0174
(0.102) 		0.211
(0.518) 		0.0919
(0.31) 		0.00532
(0.0404) 		0.568
(0.909) 		0.354
(0.699) 		0.0406
(0.181) 		0.619
(0.932)
xq loss 29 (10%) 259 6.17e-07
(4.8e-05) 		0.0832
(0.292) 		2e-05
(0.000444) 		2e-05
(0.000444) 		0.00986
(0.0646) 		0.177
(0.468) 		0.0735
(0.265) 		0.00532
(0.0404) 		0.772
(1.00) 		0.354
(0.699) 		0.0415
(0.184) 		0.609
(0.93)
1p gain 10 (3%) 278 9.48e-09
(2.27e-06) 		0.505
(0.848) 		0.0003
(0.00459) 		0.0004
(0.00582) 		0.00014
(0.00226) 		0.168
(0.463) 		0.0236
(0.123) 		0.117
(0.361) 		0.331
(0.671) 		1
(1.00)
6p gain 10 (3%) 278 0.00158
(0.0158) 		0.21
(0.518) 		9e-05
(0.00154) 		5e-05
(0.000906) 		0.0365
(0.17) 		0.0374
(0.171) 		0.727
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.779
(1.00) 		1
(1.00)
6q gain 7 (2%) 281 3.81e-08
(6.21e-06) 		0.0684
(0.254) 		0.00131
(0.0137) 		0.00095
(0.0111) 		0.0261
(0.134) 		0.0196
(0.11) 		0.385
(0.725) 		0.871
(1.00) 		0.323
(0.66) 		0.726
(1.00) 		1
(1.00)
8q gain 25 (9%) 263 2.43e-06
(0.000154) 		0.808
(1.00) 		0.00017
(0.0027) 		3e-05
(0.00062) 		0.00079
(0.00988) 		0.144
(0.415) 		0.0547
(0.223) 		0.24
(0.552) 		0.551
(0.897) 		0.743
(1.00) 		0.193
(0.491) 		1
(1.00)
5p loss 7 (2%) 281 1.02e-08
(2.27e-06) 		0.0101
(0.0648) 		0.00923
(0.0629) 		0.00095
(0.0111) 		0.0175
(0.102) 		0.242
(0.552) 		0.0815
(0.29) 		1
(1.00) 		0.218
(0.524)
10q loss 18 (6%) 270 0.00037
(0.00548) 		0.393
(0.73) 		1e-05
(0.000269) 		0.00068
(0.00863) 		0.0466
(0.199) 		0.373
(0.711) 		0.581
(0.922) 		0.0116
(0.0736) 		0.11
(0.348) 		0.151
(0.43) 		0.427
(0.767) 		1
(1.00)
11q loss 21 (7%) 267 0.000608
(0.00798) 		0.893
(1.00) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00125
(0.0132) 		0.177
(0.468) 		0.448
(0.788) 		0.0121
(0.076) 		0.846
(1.00) 		0.856
(1.00) 		0.153
(0.434) 		1
(1.00)
17p loss 13 (5%) 275 3.64e-07
(3.23e-05) 		0.854
(1.00) 		0.00241
(0.0218) 		0.00153
(0.0154) 		0.047
(0.2) 		0.0595
(0.234) 		0.112
(0.349) 		0.143
(0.412) 		0.921
(1.00) 		0.418
(0.758) 		0.356
(0.7) 		1
(1.00)
11p gain 12 (4%) 276 0.00457
(0.0362) 		0.221
(0.527) 		0.0263
(0.134) 		0.0228
(0.12) 		0.172
(0.468) 		0.0374
(0.171) 		0.312
(0.648) 		0.688
(0.998) 		0.582
(0.922) 		0.356
(0.7) 		1
(1.00)
16q gain 148 (51%) 140 0.0403
(0.181) 		0.0363
(0.17) 		0.483
(0.82) 		0.222
(0.527) 		0.856
(1.00) 		0.183
(0.476) 		0.00334
(0.0288) 		0.92
(1.00) 		0.602
(0.93) 		0.167
(0.462) 		0.0128
(0.0791) 		0.241
(0.552)
3p loss 21 (7%) 267 0.00226
(0.0209) 		0.0209
(0.113) 		5e-05
(0.000906) 		0.00014
(0.00226) 		0.255
(0.571) 		0.085
(0.294) 		1
(1.00) 		0.685
(0.998) 		0.787
(1.00) 		0.271
(0.593) 		0.605
(0.93) 		1
(1.00)
3q loss 6 (2%) 282 0.000439
(0.00609) 		0.166
(0.462) 		0.0418
(0.185) 		0.0494
(0.207) 		0.0654
(0.248) 		0.168
(0.463) 		0.656
(0.969) 		1
(1.00) 		1
(1.00)
6q loss 27 (9%) 261 0.751
(1.00) 		0.825
(1.00) 		0.00993
(0.0646) 		0.00418
(0.0337) 		0.111
(0.349) 		0.594
(0.93) 		0.0371
(0.171) 		0.0184
(0.106) 		0.821
(1.00) 		0.929
(1.00) 		0.125
(0.376) 		0.607
(0.93)
8p loss 16 (6%) 272 0.00198
(0.0187) 		0.195
(0.492) 		0.0357
(0.17) 		0.275
(0.597) 		0.0348
(0.168) 		0.0138
(0.0846) 		0.141
(0.408) 		0.803
(1.00) 		0.978
(1.00) 		0.0937
(0.312) 		1
(1.00)
10p loss 17 (6%) 271 0.00759
(0.0526) 		0.946
(1.00) 		0.00049
(0.00659) 		0.00165
(0.0161) 		0.182
(0.476) 		0.31
(0.647) 		0.401
(0.74) 		0.0282
(0.142) 		0.11
(0.348) 		0.151
(0.43) 		0.855
(1.00) 		1
(1.00)
11p loss 17 (6%) 271 0.000923
(0.0111) 		0.527
(0.875) 		0.0107
(0.0684) 		0.00062
(0.00798) 		0.00361
(0.03) 		0.373
(0.711) 		0.163
(0.456) 		0.102
(0.333) 		0.703
(1.00) 		1
(1.00)
15q loss 31 (11%) 257 0.0152
(0.0911) 		0.0706
(0.259) 		0.00163
(0.0161) 		0.00034
(0.00512) 		0.00575
(0.0417) 		0.281
(0.606) 		0.28
(0.604) 		0.131
(0.389) 		0.387
(0.725) 		0.511
(0.853) 		1
(1.00)
16q loss 7 (2%) 281 1.43e-05
(0.000363) 		0.745
(1.00) 		0.00442
(0.0354) 		0.0127
(0.0791) 		0.0652
(0.248) 		1
(1.00) 		0.385
(0.725) 		0.912
(1.00) 		0.985
(1.00) 		0.648
(0.963) 		1
(1.00)
18q loss 44 (15%) 244 3.44e-07
(3.23e-05) 		0.172
(0.468) 		1e-05
(0.000269) 		1e-05
(0.000269) 		0.00097
(0.0112) 		0.0689
(0.254) 		0.136
(0.399) 		0.207
(0.513) 		0.412
(0.756) 		0.18
(0.475) 		0.141
(0.408) 		1
(1.00)
19q loss 15 (5%) 273 0.00206
(0.0193) 		0.421
(0.76) 		4e-05
(0.000789) 		5e-05
(0.000906) 		0.0428
(0.188) 		1
(1.00) 		0.234
(0.549) 		0.131
(0.389) 		0.627
(0.938) 		0.227
(0.535) 		0.844
(1.00) 		1
(1.00)
2p gain 42 (15%) 246 0.248
(0.559) 		0.235
(0.549) 		0.062
(0.24) 		0.291
(0.623) 		0.0314
(0.156) 		0.00302
(0.0263) 		0.455
(0.79) 		0.294
(0.624) 		0.163
(0.456) 		0.617
(0.932) 		0.953
(1.00) 		0.699
(1.00)
2q gain 47 (16%) 241 0.27
(0.593) 		0.324
(0.661) 		0.0341
(0.165) 		0.259
(0.574) 		0.00553
(0.0413) 		0.00577
(0.0417) 		0.589
(0.929) 		0.251
(0.565) 		0.313
(0.648) 		0.954
(1.00) 		0.955
(1.00) 		1
(1.00)
5p gain 34 (12%) 254 0.0606
(0.237) 		0.607
(0.93) 		0.0732
(0.265) 		0.0243
(0.126) 		0.183
(0.476) 		0.616
(0.932) 		1
(1.00) 		0.045
(0.193) 		0.589
(0.929) 		0.591
(0.93) 		0.442
(0.78) 		1
(1.00)
7p gain 171 (59%) 117 0.34
(0.679) 		0.71
(1.00) 		0.00929
(0.0629) 		0.117
(0.36) 		0.462
(0.798) 		0.728
(1.00) 		0.00282
(0.025) 		0.112
(0.349) 		0.804
(1.00) 		0.0072
(0.0504) 		0.218
(0.524) 		0.547
(0.895)
7q gain 172 (60%) 116 0.332
(0.671) 		0.615
(0.932) 		0.00674
(0.0479) 		0.0928
(0.311) 		0.507
(0.85) 		0.728
(1.00) 		0.00261
(0.0234) 		0.112
(0.349) 		0.804
(1.00) 		0.0072
(0.0504) 		0.203
(0.506) 		0.546
(0.895)
9p gain 3 (1%) 285 0.0481
(0.204) 		0.516
(0.86) 		0.0449
(0.193) 		0.0361
(0.17) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 10 (3%) 278 0.055
(0.223) 		0.0495
(0.207) 		0.141
(0.408) 		0.124
(0.375) 		0.673
(0.988) 		0.242
(0.552) 		0.0236
(0.123) 		0.91
(1.00) 		0.582
(0.922) 		0.273
(0.597) 		0.356
(0.7) 		1
(1.00)
16p gain 153 (53%) 135 0.341
(0.679) 		0.0169
(0.0992) 		0.834
(1.00) 		0.661
(0.975) 		0.852
(1.00) 		0.489
(0.826) 		0.00123
(0.0132) 		0.602
(0.93) 		0.896
(1.00) 		0.167
(0.462) 		0.00151
(0.0154) 		0.235
(0.549)
xp gain 88 (31%) 200 0.258
(0.574) 		0.196
(0.493) 		0.00476
(0.0368) 		0.00472
(0.0368) 		0.705
(1.00) 		1
(1.00) 		0.0199
(0.11) 		0.192
(0.491) 		0.838
(1.00) 		0.0991
(0.325) 		0.181
(0.475) 		1
(1.00)
xq gain 92 (32%) 196 0.194
(0.491) 		0.182
(0.476) 		0.0326
(0.159) 		0.0196
(0.11) 		0.554
(0.897) 		1
(1.00) 		0.0214
(0.115) 		0.192
(0.491) 		0.995
(1.00) 		0.0991
(0.325) 		0.224
(0.531) 		1
(1.00)
6p loss 21 (7%) 267 0.331
(0.671) 		0.566
(0.907) 		0.00996
(0.0646) 		0.0199
(0.11) 		0.0865
(0.296) 		1
(1.00) 		0.207
(0.513) 		0.0364
(0.17) 		0.787
(1.00) 		0.754
(1.00) 		0.176
(0.468) 		1
(1.00)
16p loss 4 (1%) 284 0.000422
(0.00595) 		0.884
(1.00) 		0.0946
(0.313) 		0.0641
(0.245) 		1
(1.00) 		0.0577
(0.229) 		1
(1.00)
19p loss 16 (6%) 272 0.0897
(0.304) 		0.595
(0.93) 		0.00476
(0.0368) 		0.00568
(0.0417) 		0.0436
(0.19) 		1
(1.00) 		0.38
(0.72) 		0.131
(0.389) 		0.496
(0.837) 		1
(1.00) 		1
(1.00)
21q loss 43 (15%) 245 0.259
(0.574) 		0.132
(0.389) 		0.00358
(0.03) 		0.00041
(0.00587) 		0.0866
(0.296) 		0.103
(0.335) 		0.0923
(0.311) 		0.00554
(0.0413) 		0.547
(0.895) 		0.362
(0.707) 		0.323
(0.66) 		1
(1.00)
3p gain 75 (26%) 213 0.606
(0.93) 		0.768
(1.00) 		0.0185
(0.106) 		0.0145
(0.0877) 		0.488
(0.825) 		0.107
(0.345) 		0.649
(0.963) 		0.105
(0.34) 		0.732
(1.00) 		0.555
(0.897) 		0.621
(0.932) 		1
(1.00)
3q gain 95 (33%) 193 0.938
(1.00) 		0.376
(0.715) 		0.0541
(0.222) 		0.0689
(0.254) 		0.898
(1.00) 		0.0581
(0.229) 		0.398
(0.737) 		0.298
(0.63) 		0.442
(0.78) 		0.511
(0.853) 		0.13
(0.389) 		1
(1.00)
8p gain 20 (7%) 268 0.00241
(0.0218) 		0.816
(1.00) 		0.0673
(0.253) 		0.0165
(0.0978) 		0.0687
(0.254) 		1
(1.00) 		0.187
(0.485) 		0.803
(1.00) 		0.762
(1.00) 		0.194
(0.491) 		0.598
(0.93)
14q gain 3 (1%) 285 0.391
(0.728) 		0.0351
(0.168) 		0.0201
(0.11) 		1
(1.00) 		0.171
(0.468) 		1
(1.00)
2p loss 5 (2%) 283 0.92
(1.00) 		0.599
(0.93) 		0.0278
(0.141) 		0.0497
(0.207) 		1
(1.00) 		0.61
(0.93) 		0.624
(0.935) 		1
(1.00)
5q gain 31 (11%) 257 0.714
(1.00) 		0.433
(0.768) 		0.0847
(0.294) 		0.109
(0.347) 		0.216
(0.524) 		0.616
(0.932) 		1
(1.00) 		0.045
(0.193) 		0.589
(0.929) 		0.765
(1.00) 		0.621
(0.932) 		0.619
(0.932)
10p gain 8 (3%) 280 0.407
(0.748) 		0.365
(0.708) 		0.244
(0.552) 		0.455
(0.79) 		0.176
(0.468) 		0.431
(0.768) 		0.214
(0.521) 		0.389
(0.725) 		0.00935
(0.0629) 		1
(1.00)
10q gain 8 (3%) 280 0.407
(0.748) 		0.365
(0.708) 		0.24
(0.552) 		0.454
(0.79) 		0.175
(0.468) 		0.431
(0.768) 		0.214
(0.521) 		0.389
(0.725) 		0.00961
(0.0642) 		1
(1.00)
12p gain 112 (39%) 176 0.838
(1.00) 		0.76
(1.00) 		0.293
(0.624) 		0.85
(1.00) 		0.177
(0.468) 		0.473
(0.809) 		0.0201
(0.11) 		0.415
(0.756) 		0.92
(1.00) 		0.121
(0.368) 		0.901
(1.00) 		0.373
(0.711)
12q gain 112 (39%) 176 0.838
(1.00) 		0.76
(1.00) 		0.294
(0.624) 		0.85
(1.00) 		0.176
(0.468) 		0.473
(0.809) 		0.0201
(0.11) 		0.415
(0.756) 		0.92
(1.00) 		0.121
(0.368) 		0.902
(1.00) 		0.373
(0.711)
17q gain 191 (66%) 97 0.694
(1.00) 		0.0862
(0.296) 		0.032
(0.158) 		0.0716
(0.262) 		0.3
(0.63) 		1
(1.00) 		0.157
(0.442) 		0.771
(1.00) 		0.615
(0.932) 		0.282
(0.606) 		0.0849
(0.294) 		0.201
(0.503)
18q gain 9 (3%) 279 0.199
(0.5) 		0.597
(0.93) 		0.527
(0.875) 		0.432
(0.768) 		1
(1.00) 		0.453
(0.79) 		0.0286
(0.144) 		0.333
(0.673) 		1
(1.00)
19p gain 5 (2%) 283 0.558
(0.898) 		0.0529
(0.218) 		0.687
(0.998) 		0.631
(0.941) 		1
(1.00) 		1
(1.00) 		0.61
(0.93) 		0.107
(0.345) 		1
(1.00)
19q gain 5 (2%) 283 0.558
(0.898) 		0.0529
(0.218) 		0.687
(0.998) 		0.631
(0.941) 		1
(1.00) 		1
(1.00) 		0.61
(0.93) 		0.105
(0.34) 		1
(1.00)
21q gain 19 (7%) 269 0.864
(1.00) 		0.13
(0.389) 		1
(1.00) 		1
(1.00) 		0.674
(0.988) 		0.31
(0.647) 		1
(1.00) 		0.299
(0.63) 		0.058
(0.229) 		0.098
(0.324) 		0.598
(0.93)
1p loss 30 (10%) 258 0.485
(0.822) 		0.461
(0.798) 		0.0832
(0.292) 		0.0386
(0.174) 		0.367
(0.708) 		1
(1.00) 		0.384
(0.725) 		0.397
(0.736) 		0.755
(1.00) 		0.474
(0.809) 		1
(1.00)
8q loss 9 (3%) 279 0.366
(0.708) 		0.551
(0.897) 		0.36
(0.703) 		1
(1.00) 		0.366
(0.708) 		0.242
(0.552) 		0.0576
(0.229) 		0.262
(0.579) 		1
(1.00)
4p gain 10 (3%) 278 0.318
(0.655) 		0.0935
(0.312) 		0.077
(0.275) 		0.543
(0.893) 		0.277
(0.6) 		0.242
(0.552) 		1
(1.00) 		0.326
(0.665) 		0.871
(1.00) 		0.834
(1.00) 		0.605
(0.93) 		1
(1.00)
4q gain 9 (3%) 279 0.986
(1.00) 		0.219
(0.524) 		0.252
(0.565) 		0.433
(0.768) 		0.177
(0.468) 		1
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.388
(0.725) 		0.834
(1.00) 		0.765
(1.00) 		1
(1.00)
13q gain 28 (10%) 260 0.452
(0.79) 		0.358
(0.702) 		0.94
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.594
(0.93) 		1
(1.00) 		0.53
(0.878) 		0.931
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.338
(0.679)
15q gain 5 (2%) 283 0.996
(1.00) 		0.832
(1.00) 		0.274
(0.597) 		0.246
(0.556) 		1
(1.00) 		0.117
(0.36) 		0.42
(0.759) 		1
(1.00)
18p gain 12 (4%) 276 0.958
(1.00) 		0.806
(1.00) 		0.275
(0.597) 		0.808
(1.00) 		0.675
(0.988) 		0.431
(0.768) 		0.194
(0.491) 		0.213
(0.521) 		0.719
(1.00) 		0.195
(0.492) 		1
(1.00)
20p gain 99 (34%) 189 0.957
(1.00) 		0.303
(0.634) 		0.454
(0.79) 		0.336
(0.676) 		0.454
(0.79) 		1
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.244
(0.552) 		0.787
(1.00) 		0.434
(0.768) 		0.552
(0.897)
20q gain 101 (35%) 187 0.768
(1.00) 		0.318
(0.655) 		0.54
(0.89) 		0.415
(0.756) 		0.317
(0.655) 		1
(1.00) 		0.889
(1.00) 		0.91
(1.00) 		0.34
(0.679) 		0.642
(0.955) 		0.231
(0.544) 		0.55
(0.897)
22q gain 5 (2%) 283 0.265
(0.584) 		0.472
(0.809) 		0.14
(0.408) 		0.0884
(0.301) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.218
(0.524)
1q loss 21 (7%) 267 0.779
(1.00) 		0.968
(1.00) 		0.466
(0.803) 		0.832
(1.00) 		0.559
(0.898) 		0.532
(0.878) 		0.207
(0.513) 		0.678
(0.99) 		0.418
(0.758) 		1
(1.00)
2q loss 3 (1%) 285 0.425
(0.766) 		0.155
(0.44) 		1
(1.00) 		1
(1.00) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 9.48e-09 (logrank test), Q value = 2.3e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
1P GAIN MUTATED 10 6 2.0 - 58.2 (14.9)
1P GAIN WILD-TYPE 275 38 0.1 - 194.8 (25.6)

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

'1p gain' versus 'PATHOLOGIC_STAGE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0046

Table S2.  Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
1P GAIN MUTATED 1 0 6 2
1P GAIN WILD-TYPE 170 21 46 13

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0058

Table S3.  Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
1P GAIN MUTATED 2 0 8
1P GAIN WILD-TYPE 189 33 54

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0023

Table S4.  Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
1P GAIN MUTATED 0 5 2
1P GAIN WILD-TYPE 49 19 2

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p gain' versus 'GENDER'

P value = 0.0236 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #1: '1p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
1P GAIN MUTATED 6 4
1P GAIN WILD-TYPE 70 208

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #7: 'GENDER'

'1q gain' versus 'Time to Death'

P value = 4.2e-08 (logrank test), Q value = 6.2e-06

Table S6.  Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
1Q GAIN MUTATED 17 8 0.9 - 59.0 (16.9)
1Q GAIN WILD-TYPE 268 36 0.1 - 194.8 (25.7)

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00062

Table S7.  Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
1Q GAIN MUTATED 3 0 10 3
1Q GAIN WILD-TYPE 168 21 42 12

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S8.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
1Q GAIN MUTATED 4 0 13
1Q GAIN WILD-TYPE 187 33 49

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0301 (Fisher's exact test), Q value = 0.15

Table S9.  Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
1Q GAIN MUTATED 4 6 2
1Q GAIN WILD-TYPE 45 18 2

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'GENDER'

P value = 0.0195 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #2: '1q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
1Q GAIN MUTATED 9 8
1Q GAIN WILD-TYPE 67 204

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'GENDER'

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0219 (Wilcoxon-test), Q value = 0.12

Table S11.  Gene #2: '1q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
1Q GAIN MUTATED 4 45.0 (52.0)
1Q GAIN WILD-TYPE 72 89.9 (17.1)

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'2p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.062 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #3: '2p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
2P GAIN MUTATED 24 4 6 6
2P GAIN WILD-TYPE 147 17 46 9

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0314 (Fisher's exact test), Q value = 0.16

Table S13.  Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
2P GAIN MUTATED 5 7 2
2P GAIN WILD-TYPE 44 17 2

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00302 (Fisher's exact test), Q value = 0.026

Table S14.  Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
2P GAIN MUTATED 10 5
2P GAIN WILD-TYPE 84 4

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0341 (Fisher's exact test), Q value = 0.17

Table S15.  Gene #4: '2q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
2Q GAIN MUTATED 27 4 7 7
2Q GAIN WILD-TYPE 144 17 45 8

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00553 (Fisher's exact test), Q value = 0.041

Table S16.  Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
2Q GAIN MUTATED 6 8 3
2Q GAIN WILD-TYPE 43 16 1

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00577 (Fisher's exact test), Q value = 0.042

Table S17.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
2Q GAIN MUTATED 12 5
2Q GAIN WILD-TYPE 82 4

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0185 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
3P GAIN MUTATED 50 8 6 2
3P GAIN WILD-TYPE 121 13 46 13

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.088

Table S19.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
3P GAIN MUTATED 54 12 8
3P GAIN WILD-TYPE 137 21 54

Figure S19.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0541 (Fisher's exact test), Q value = 0.22

Table S20.  Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
3Q GAIN MUTATED 58 11 13 2
3Q GAIN WILD-TYPE 113 10 39 13

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0581 (Fisher's exact test), Q value = 0.23

Table S21.  Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
3Q GAIN MUTATED 29 0
3Q GAIN WILD-TYPE 65 9

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'5p gain' versus 'Time to Death'

P value = 0.0606 (logrank test), Q value = 0.24

Table S22.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
5P GAIN MUTATED 33 7 0.2 - 99.1 (18.4)
5P GAIN WILD-TYPE 252 37 0.1 - 194.8 (26.0)

Figure S22.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0243 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
5P GAIN MUTATED 16 5 13
5P GAIN WILD-TYPE 175 28 49

Figure S23.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.045 (Wilcoxon-test), Q value = 0.19

Table S24.  Gene #9: '5p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
5P GAIN MUTATED 13 76.2 (34.5)
5P GAIN WILD-TYPE 63 89.8 (18.0)

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'5q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.045 (Wilcoxon-test), Q value = 0.19

Table S25.  Gene #10: '5q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
5Q GAIN MUTATED 13 76.2 (34.5)
5Q GAIN WILD-TYPE 63 89.8 (18.0)

Figure S25.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'6p gain' versus 'Time to Death'

P value = 0.00158 (logrank test), Q value = 0.016

Table S26.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
6P GAIN MUTATED 10 5 6.6 - 93.3 (13.8)
6P GAIN WILD-TYPE 275 39 0.1 - 194.8 (25.6)

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0015

Table S27.  Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
6P GAIN MUTATED 1 0 6 3
6P GAIN WILD-TYPE 170 21 46 12

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p gain' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S28.  Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
6P GAIN MUTATED 1 1 8
6P GAIN WILD-TYPE 190 32 54

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0365 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
6P GAIN MUTATED 1 5 0
6P GAIN WILD-TYPE 48 19 4

Figure S29.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0374 (Fisher's exact test), Q value = 0.17

Table S30.  Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
6P GAIN MUTATED 2 2
6P GAIN WILD-TYPE 92 7

Figure S30.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'6q gain' versus 'Time to Death'

P value = 3.81e-08 (logrank test), Q value = 6.2e-06

Table S31.  Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
6Q GAIN MUTATED 7 4 6.6 - 49.2 (12.8)
6Q GAIN WILD-TYPE 278 40 0.1 - 194.8 (25.6)

Figure S31.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00131 (Fisher's exact test), Q value = 0.014

Table S32.  Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
6Q GAIN MUTATED 1 0 3 3
6Q GAIN WILD-TYPE 170 21 49 12

Figure S32.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00095 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
6Q GAIN MUTATED 1 0 6
6Q GAIN WILD-TYPE 190 33 56

Figure S33.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0261 (Fisher's exact test), Q value = 0.13

Table S34.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
6Q GAIN MUTATED 0 4 0
6Q GAIN WILD-TYPE 49 20 4

Figure S34.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0196 (Fisher's exact test), Q value = 0.11

Table S35.  Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
6Q GAIN MUTATED 1 2
6Q GAIN WILD-TYPE 93 7

Figure S35.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00929 (Fisher's exact test), Q value = 0.063

Table S36.  Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
7P GAIN MUTATED 111 11 21 11
7P GAIN WILD-TYPE 60 10 31 4

Figure S36.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7p gain' versus 'GENDER'

P value = 0.00282 (Fisher's exact test), Q value = 0.025

Table S37.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
7P GAIN MUTATED 34 137
7P GAIN WILD-TYPE 42 75

Figure S37.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7p gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0072 (Wilcoxon-test), Q value = 0.05

Table S38.  Gene #13: '7p gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
7P GAIN MUTATED 31 1967.6 (14.7)
7P GAIN WILD-TYPE 23 1979.0 (14.8)

Figure S38.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00674 (Fisher's exact test), Q value = 0.048

Table S39.  Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
7Q GAIN MUTATED 112 11 21 11
7Q GAIN WILD-TYPE 59 10 31 4

Figure S39.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'GENDER'

P value = 0.00261 (Fisher's exact test), Q value = 0.023

Table S40.  Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
7Q GAIN MUTATED 34 138
7Q GAIN WILD-TYPE 42 74

Figure S40.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0072 (Wilcoxon-test), Q value = 0.05

Table S41.  Gene #14: '7q gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
7Q GAIN MUTATED 31 1967.6 (14.7)
7Q GAIN WILD-TYPE 23 1979.0 (14.8)

Figure S41.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'8p gain' versus 'Time to Death'

P value = 0.00241 (logrank test), Q value = 0.022

Table S42.  Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
8P GAIN MUTATED 20 6 0.2 - 59.0 (21.2)
8P GAIN WILD-TYPE 265 38 0.1 - 194.8 (25.6)

Figure S42.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0165 (Fisher's exact test), Q value = 0.098

Table S43.  Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
8P GAIN MUTATED 8 3 9
8P GAIN WILD-TYPE 183 30 53

Figure S43.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'Time to Death'

P value = 2.43e-06 (logrank test), Q value = 0.00015

Table S44.  Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
8Q GAIN MUTATED 25 9 0.2 - 59.0 (16.0)
8Q GAIN WILD-TYPE 260 35 0.1 - 194.8 (25.9)

Figure S44.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0027

Table S45.  Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
8Q GAIN MUTATED 7 4 8 5
8Q GAIN WILD-TYPE 164 17 44 10

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00062

Table S46.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
8Q GAIN MUTATED 7 4 14
8Q GAIN WILD-TYPE 184 29 48

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00079 (Fisher's exact test), Q value = 0.0099

Table S47.  Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
8Q GAIN MUTATED 3 7 3
8Q GAIN WILD-TYPE 46 17 1

Figure S47.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q gain' versus 'GENDER'

P value = 0.0547 (Fisher's exact test), Q value = 0.22

Table S48.  Gene #16: '8q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
8Q GAIN MUTATED 11 14
8Q GAIN WILD-TYPE 65 198

Figure S48.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'GENDER'

'9p gain' versus 'Time to Death'

P value = 0.0481 (logrank test), Q value = 0.2

Table S49.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
9P GAIN MUTATED 3 1 3.7 - 34.5 (11.3)
9P GAIN WILD-TYPE 282 43 0.1 - 194.8 (25.3)

Figure S49.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0449 (Fisher's exact test), Q value = 0.19

Table S50.  Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
9P GAIN MUTATED 0 1 2 0
9P GAIN WILD-TYPE 171 20 50 15

Figure S50.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0361 (Fisher's exact test), Q value = 0.17

Table S51.  Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
9P GAIN MUTATED 0 1 2
9P GAIN WILD-TYPE 191 32 60

Figure S51.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p gain' versus 'RACE'

P value = 0.00935 (Fisher's exact test), Q value = 0.063

Table S52.  Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
10P GAIN MUTATED 0 2 2 3
10P GAIN WILD-TYPE 2 4 59 201

Figure S52.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

'10q gain' versus 'RACE'

P value = 0.00961 (Fisher's exact test), Q value = 0.064

Table S53.  Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
10Q GAIN MUTATED 0 2 2 3
10Q GAIN WILD-TYPE 2 4 59 201

Figure S53.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

'11p gain' versus 'Time to Death'

P value = 0.00457 (logrank test), Q value = 0.036

Table S54.  Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
11P GAIN MUTATED 11 4 0.5 - 99.1 (11.9)
11P GAIN WILD-TYPE 274 40 0.1 - 194.8 (25.7)

Figure S54.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0263 (Fisher's exact test), Q value = 0.13

Table S55.  Gene #20: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
11P GAIN MUTATED 4 0 5 2
11P GAIN WILD-TYPE 167 21 47 13

Figure S55.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0228 (Fisher's exact test), Q value = 0.12

Table S56.  Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
11P GAIN MUTATED 4 2 6
11P GAIN WILD-TYPE 187 31 56

Figure S56.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0374 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
11P GAIN MUTATED 2 2
11P GAIN WILD-TYPE 92 7

Figure S57.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11q gain' versus 'Time to Death'

P value = 0.055 (logrank test), Q value = 0.22

Table S58.  Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
11Q GAIN MUTATED 10 3 0.5 - 99.1 (12.5)
11Q GAIN WILD-TYPE 275 41 0.1 - 194.8 (25.6)

Figure S58.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0495 (Wilcoxon-test), Q value = 0.21

Table S59.  Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
11Q GAIN MUTATED 10 53.6 (14.8)
11Q GAIN WILD-TYPE 273 61.8 (11.9)

Figure S59.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'GENDER'

P value = 0.0236 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
11Q GAIN MUTATED 6 4
11Q GAIN WILD-TYPE 70 208

Figure S60.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

'12p gain' versus 'GENDER'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S61.  Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
12P GAIN MUTATED 21 91
12P GAIN WILD-TYPE 55 121

Figure S61.  Get High-res Image Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'GENDER'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S62.  Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
12Q GAIN MUTATED 21 91
12Q GAIN WILD-TYPE 55 121

Figure S62.  Get High-res Image Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

'14q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0351 (Fisher's exact test), Q value = 0.17

Table S63.  Gene #25: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
14Q GAIN MUTATED 0 0 3 0
14Q GAIN WILD-TYPE 171 21 49 15

Figure S63.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
14Q GAIN MUTATED 0 0 3
14Q GAIN WILD-TYPE 191 33 59

Figure S64.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0169 (Wilcoxon-test), Q value = 0.099

Table S65.  Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
16P GAIN MUTATED 151 63.0 (11.6)
16P GAIN WILD-TYPE 132 59.7 (12.4)

Figure S65.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'GENDER'

P value = 0.00123 (Fisher's exact test), Q value = 0.013

Table S66.  Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
16P GAIN MUTATED 28 125
16P GAIN WILD-TYPE 48 87

Figure S66.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

'16p gain' versus 'RACE'

P value = 0.00151 (Fisher's exact test), Q value = 0.015

Table S67.  Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
16P GAIN MUTATED 2 3 21 120
16P GAIN WILD-TYPE 0 3 40 84

Figure S67.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

'16q gain' versus 'Time to Death'

P value = 0.0403 (logrank test), Q value = 0.18

Table S68.  Gene #28: '16q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
16Q GAIN MUTATED 145 17 0.1 - 194.8 (25.2)
16Q GAIN WILD-TYPE 140 27 0.1 - 103.6 (25.6)

Figure S68.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #1: 'Time to Death'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0363 (Wilcoxon-test), Q value = 0.17

Table S69.  Gene #28: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
16Q GAIN MUTATED 146 62.9 (11.6)
16Q GAIN WILD-TYPE 137 59.9 (12.5)

Figure S69.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'GENDER'

P value = 0.00334 (Fisher's exact test), Q value = 0.029

Table S70.  Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
16Q GAIN MUTATED 28 120
16Q GAIN WILD-TYPE 48 92

Figure S70.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

'16q gain' versus 'RACE'

P value = 0.0128 (Fisher's exact test), Q value = 0.079

Table S71.  Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
16Q GAIN MUTATED 2 3 22 115
16Q GAIN WILD-TYPE 0 3 39 89

Figure S71.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

'17p gain' versus 'Time to Death'

P value = 0.0579 (logrank test), Q value = 0.23

Table S72.  Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
17P GAIN MUTATED 169 20 0.1 - 194.8 (25.3)
17P GAIN WILD-TYPE 116 24 0.1 - 123.6 (25.6)

Figure S72.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0535 (Wilcoxon-test), Q value = 0.22

Table S73.  Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
17P GAIN MUTATED 169 60.4 (11.8)
17P GAIN WILD-TYPE 114 63.1 (12.5)

Figure S73.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S74.  Gene #29: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
17P GAIN MUTATED 117 15 17 6
17P GAIN WILD-TYPE 54 6 35 9

Figure S74.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0012

Table S75.  Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
17P GAIN MUTATED 127 22 22
17P GAIN WILD-TYPE 64 11 40

Figure S75.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'GENDER'

P value = 0.0139 (Fisher's exact test), Q value = 0.085

Table S76.  Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
17P GAIN MUTATED 36 136
17P GAIN WILD-TYPE 40 76

Figure S76.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'ETHNICITY'

P value = 0.0614 (Fisher's exact test), Q value = 0.24

Table S77.  Gene #29: '17p gain' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 12 240
17P GAIN MUTATED 4 154
17P GAIN WILD-TYPE 8 86

Figure S77.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #12: 'ETHNICITY'

'17q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.032 (Fisher's exact test), Q value = 0.16

Table S78.  Gene #30: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
17Q GAIN MUTATED 121 16 26 9
17Q GAIN WILD-TYPE 50 5 26 6

Figure S78.  Get High-res Image Gene #30: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0286 (Wilcoxon-test), Q value = 0.14

Table S79.  Gene #32: '18q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
18Q GAIN MUTATED 5 100.0 (0.0)
18Q GAIN WILD-TYPE 71 86.6 (22.5)

Figure S79.  Get High-res Image Gene #32: '18q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0529 (Wilcoxon-test), Q value = 0.22

Table S80.  Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
19P GAIN MUTATED 5 48.0 (15.2)
19P GAIN WILD-TYPE 278 61.7 (11.9)

Figure S80.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0529 (Wilcoxon-test), Q value = 0.22

Table S81.  Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
19Q GAIN MUTATED 5 48.0 (15.2)
19Q GAIN WILD-TYPE 278 61.7 (11.9)

Figure S81.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.058 (Wilcoxon-test), Q value = 0.23

Table S82.  Gene #37: '21q gain' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 74 32.3 (27.3)
21Q GAIN MUTATED 3 12.3 (4.6)
21Q GAIN WILD-TYPE 71 33.2 (27.5)

Figure S82.  Get High-res Image Gene #37: '21q gain' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00476 (Fisher's exact test), Q value = 0.037

Table S83.  Gene #39: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
XP GAIN MUTATED 62 7 6 4
XP GAIN WILD-TYPE 109 14 46 11

Figure S83.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00472 (Fisher's exact test), Q value = 0.037

Table S84.  Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
XP GAIN MUTATED 68 11 9
XP GAIN WILD-TYPE 123 22 53

Figure S84.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'GENDER'

P value = 0.0199 (Fisher's exact test), Q value = 0.11

Table S85.  Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
XP GAIN MUTATED 15 73
XP GAIN WILD-TYPE 61 139

Figure S85.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0326 (Fisher's exact test), Q value = 0.16

Table S86.  Gene #40: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
XQ GAIN MUTATED 62 7 8 4
XQ GAIN WILD-TYPE 109 14 44 11

Figure S86.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0196 (Fisher's exact test), Q value = 0.11

Table S87.  Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
XQ GAIN MUTATED 69 12 11
XQ GAIN WILD-TYPE 122 21 51

Figure S87.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'GENDER'

P value = 0.0214 (Fisher's exact test), Q value = 0.11

Table S88.  Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
XQ GAIN MUTATED 16 76
XQ GAIN WILD-TYPE 60 136

Figure S88.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0386 (Fisher's exact test), Q value = 0.17

Table S89.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
1P LOSS MUTATED 14 5 11
1P LOSS WILD-TYPE 177 28 51

Figure S89.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'2p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0278 (Fisher's exact test), Q value = 0.14

Table S90.  Gene #43: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
2P LOSS MUTATED 0 0 2 1
2P LOSS WILD-TYPE 171 21 50 14

Figure S90.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0497 (Fisher's exact test), Q value = 0.21

Table S91.  Gene #43: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
2P LOSS MUTATED 1 1 3
2P LOSS WILD-TYPE 190 32 59

Figure S91.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'Time to Death'

P value = 0.00226 (logrank test), Q value = 0.021

Table S92.  Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
3P LOSS MUTATED 21 7 2.0 - 86.3 (14.1)
3P LOSS WILD-TYPE 264 37 0.1 - 194.8 (25.7)

Figure S92.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0209 (Wilcoxon-test), Q value = 0.11

Table S93.  Gene #45: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
3P LOSS MUTATED 20 54.6 (12.7)
3P LOSS WILD-TYPE 263 62.0 (11.9)

Figure S93.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'PATHOLOGIC_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S94.  Gene #45: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
3P LOSS MUTATED 5 1 12 3
3P LOSS WILD-TYPE 166 20 40 12

Figure S94.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0023

Table S95.  Gene #45: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
3P LOSS MUTATED 6 3 12
3P LOSS WILD-TYPE 185 30 50

Figure S95.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'Time to Death'

P value = 0.000439 (logrank test), Q value = 0.0061

Table S96.  Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
3Q LOSS MUTATED 6 3 3.7 - 54.6 (15.3)
3Q LOSS WILD-TYPE 279 41 0.1 - 194.8 (25.6)

Figure S96.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0418 (Fisher's exact test), Q value = 0.18

Table S97.  Gene #46: '3q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
3Q LOSS MUTATED 2 0 2 2
3Q LOSS WILD-TYPE 169 21 50 13

Figure S97.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0494 (Fisher's exact test), Q value = 0.21

Table S98.  Gene #46: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
3Q LOSS MUTATED 2 0 4
3Q LOSS WILD-TYPE 189 33 58

Figure S98.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0654 (Fisher's exact test), Q value = 0.25

Table S99.  Gene #46: '3q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
3Q LOSS MUTATED 1 2 1
3Q LOSS WILD-TYPE 48 22 3

Figure S99.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'Time to Death'

P value = 8.66e-09 (logrank test), Q value = 2.3e-06

Table S100.  Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
4P LOSS MUTATED 25 12 2.0 - 79.9 (19.4)
4P LOSS WILD-TYPE 260 32 0.1 - 194.8 (25.9)

Figure S100.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00351 (Wilcoxon-test), Q value = 0.03

Table S101.  Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
4P LOSS MUTATED 24 53.1 (15.1)
4P LOSS WILD-TYPE 259 62.2 (11.5)

Figure S101.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S102.  Gene #47: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
4P LOSS MUTATED 4 1 15 2
4P LOSS WILD-TYPE 167 20 37 13

Figure S102.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S103.  Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
4P LOSS MUTATED 5 3 17
4P LOSS WILD-TYPE 186 30 45

Figure S103.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00106 (Fisher's exact test), Q value = 0.012

Table S104.  Gene #47: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
4P LOSS MUTATED 3 10 1
4P LOSS WILD-TYPE 46 14 3

Figure S104.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'GENDER'

P value = 3.8e-05 (Fisher's exact test), Q value = 0.00077

Table S105.  Gene #47: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
4P LOSS MUTATED 16 9
4P LOSS WILD-TYPE 60 203

Figure S105.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'Time to Death'

P value = 7.78e-09 (logrank test), Q value = 2.3e-06

Table S106.  Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
4Q LOSS MUTATED 26 12 2.0 - 79.9 (18.6)
4Q LOSS WILD-TYPE 259 32 0.1 - 194.8 (26.0)

Figure S106.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0203 (Wilcoxon-test), Q value = 0.11

Table S107.  Gene #48: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
4Q LOSS MUTATED 25 55.0 (14.7)
4Q LOSS WILD-TYPE 258 62.1 (11.7)

Figure S107.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S108.  Gene #48: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
4Q LOSS MUTATED 5 1 14 3
4Q LOSS WILD-TYPE 166 20 38 12

Figure S108.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S109.  Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
4Q LOSS MUTATED 6 4 16
4Q LOSS WILD-TYPE 185 29 46

Figure S109.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00976 (Fisher's exact test), Q value = 0.065

Table S110.  Gene #48: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
4Q LOSS MUTATED 4 9 1
4Q LOSS WILD-TYPE 45 15 3

Figure S110.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'GENDER'

P value = 0.000614 (Fisher's exact test), Q value = 0.008

Table S111.  Gene #48: '4q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
4Q LOSS MUTATED 15 11
4Q LOSS WILD-TYPE 61 201

Figure S111.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #7: 'GENDER'

'5p loss' versus 'Time to Death'

P value = 1.02e-08 (logrank test), Q value = 2.3e-06

Table S112.  Gene #49: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
5P LOSS MUTATED 7 4 2.8 - 30.5 (11.1)
5P LOSS WILD-TYPE 278 40 0.1 - 194.8 (25.6)

Figure S112.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0101 (Wilcoxon-test), Q value = 0.065

Table S113.  Gene #49: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
5P LOSS MUTATED 7 47.4 (13.1)
5P LOSS WILD-TYPE 276 61.8 (11.9)

Figure S113.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00923 (Fisher's exact test), Q value = 0.063

Table S114.  Gene #49: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
5P LOSS MUTATED 1 0 3 2
5P LOSS WILD-TYPE 170 21 49 13

Figure S114.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00095 (Fisher's exact test), Q value = 0.011

Table S115.  Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
5P LOSS MUTATED 1 0 6
5P LOSS WILD-TYPE 190 33 56

Figure S115.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0175 (Fisher's exact test), Q value = 0.1

Table S116.  Gene #49: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
5P LOSS MUTATED 0 3 1
5P LOSS WILD-TYPE 49 21 3

Figure S116.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'Time to Death'

P value = 9.36e-08 (logrank test), Q value = 1.2e-05

Table S117.  Gene #50: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
5Q LOSS MUTATED 8 4 2.8 - 30.5 (14.4)
5Q LOSS WILD-TYPE 277 40 0.1 - 194.8 (25.6)

Figure S117.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0121 (Wilcoxon-test), Q value = 0.076

Table S118.  Gene #50: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
5Q LOSS MUTATED 8 46.9 (17.0)
5Q LOSS WILD-TYPE 275 61.9 (11.7)

Figure S118.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0381 (Fisher's exact test), Q value = 0.17

Table S119.  Gene #50: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
5Q LOSS MUTATED 2 0 4 1
5Q LOSS WILD-TYPE 169 21 48 14

Figure S119.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00396 (Fisher's exact test), Q value = 0.032

Table S120.  Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
5Q LOSS MUTATED 2 0 6
5Q LOSS WILD-TYPE 189 33 56

Figure S120.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0257 (Fisher's exact test), Q value = 0.13

Table S121.  Gene #50: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
5Q LOSS MUTATED 0 4 0
5Q LOSS WILD-TYPE 49 20 4

Figure S121.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'GENDER'

P value = 0.0322 (Fisher's exact test), Q value = 0.16

Table S122.  Gene #50: '5q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
5Q LOSS MUTATED 5 3
5Q LOSS WILD-TYPE 71 209

Figure S122.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #7: 'GENDER'

'6p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00996 (Fisher's exact test), Q value = 0.065

Table S123.  Gene #51: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
6P LOSS MUTATED 8 0 9 2
6P LOSS WILD-TYPE 163 21 43 13

Figure S123.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0199 (Fisher's exact test), Q value = 0.11

Table S124.  Gene #51: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
6P LOSS MUTATED 10 1 10
6P LOSS WILD-TYPE 181 32 52

Figure S124.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0364 (Wilcoxon-test), Q value = 0.17

Table S125.  Gene #51: '6p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
6P LOSS MUTATED 10 70.0 (37.1)
6P LOSS WILD-TYPE 66 90.2 (17.8)

Figure S125.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00993 (Fisher's exact test), Q value = 0.065

Table S126.  Gene #52: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
6Q LOSS MUTATED 12 0 11 2
6Q LOSS WILD-TYPE 159 21 41 13

Figure S126.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00418 (Fisher's exact test), Q value = 0.034

Table S127.  Gene #52: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
6Q LOSS MUTATED 13 1 13
6Q LOSS WILD-TYPE 178 32 49

Figure S127.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'GENDER'

P value = 0.0371 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #52: '6q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
6Q LOSS MUTATED 12 15
6Q LOSS WILD-TYPE 64 197

Figure S128.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #7: 'GENDER'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0184 (Wilcoxon-test), Q value = 0.11

Table S129.  Gene #52: '6q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
6Q LOSS MUTATED 10 69.0 (36.7)
6Q LOSS WILD-TYPE 66 90.3 (17.7)

Figure S129.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'8p loss' versus 'Time to Death'

P value = 0.00198 (logrank test), Q value = 0.019

Table S130.  Gene #53: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
8P LOSS MUTATED 16 6 1.2 - 67.2 (20.5)
8P LOSS WILD-TYPE 269 38 0.1 - 194.8 (25.4)

Figure S130.  Get High-res Image Gene #53: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0357 (Fisher's exact test), Q value = 0.17

Table S131.  Gene #53: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
8P LOSS MUTATED 6 2 2 3
8P LOSS WILD-TYPE 165 19 50 12

Figure S131.  Get High-res Image Gene #53: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0348 (Fisher's exact test), Q value = 0.17

Table S132.  Gene #53: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
8P LOSS MUTATED 1 5 0
8P LOSS WILD-TYPE 48 19 4

Figure S132.  Get High-res Image Gene #53: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.085

Table S133.  Gene #53: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
8P LOSS MUTATED 4 3
8P LOSS WILD-TYPE 90 6

Figure S133.  Get High-res Image Gene #53: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8q loss' versus 'GENDER'

P value = 0.0576 (Fisher's exact test), Q value = 0.23

Table S134.  Gene #54: '8q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
8Q LOSS MUTATED 5 4
8Q LOSS WILD-TYPE 71 208

Figure S134.  Get High-res Image Gene #54: '8q loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'Time to Death'

P value = 6.49e-07 (logrank test), Q value = 4.8e-05

Table S135.  Gene #55: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
9P LOSS MUTATED 33 14 2.0 - 93.3 (19.4)
9P LOSS WILD-TYPE 252 30 0.1 - 194.8 (26.0)

Figure S135.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S136.  Gene #55: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
9P LOSS MUTATED 9 0 15 6
9P LOSS WILD-TYPE 162 21 37 9

Figure S136.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S137.  Gene #55: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
9P LOSS MUTATED 10 3 20
9P LOSS WILD-TYPE 181 30 42

Figure S137.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00092 (Fisher's exact test), Q value = 0.011

Table S138.  Gene #55: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
9P LOSS MUTATED 6 10 3
9P LOSS WILD-TYPE 43 14 1

Figure S138.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'GENDER'

P value = 0.00122 (Fisher's exact test), Q value = 0.013

Table S139.  Gene #55: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
9P LOSS MUTATED 17 16
9P LOSS WILD-TYPE 59 196

Figure S139.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000832 (Wilcoxon-test), Q value = 0.01

Table S140.  Gene #55: '9p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
9P LOSS MUTATED 13 66.9 (36.6)
9P LOSS WILD-TYPE 63 91.7 (14.9)

Figure S140.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'Time to Death'

P value = 2.55e-05 (logrank test), Q value = 0.00055

Table S141.  Gene #56: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
9Q LOSS MUTATED 34 12 2.0 - 93.3 (19.0)
9Q LOSS WILD-TYPE 251 32 0.1 - 194.8 (26.0)

Figure S141.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'PATHOLOGIC_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S142.  Gene #56: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
9Q LOSS MUTATED 11 1 15 5
9Q LOSS WILD-TYPE 160 20 37 10

Figure S142.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S143.  Gene #56: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
9Q LOSS MUTATED 12 1 21
9Q LOSS WILD-TYPE 179 32 41

Figure S143.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00609 (Fisher's exact test), Q value = 0.044

Table S144.  Gene #56: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
9Q LOSS MUTATED 6 8 3
9Q LOSS WILD-TYPE 43 16 1

Figure S144.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'GENDER'

P value = 0.00167 (Fisher's exact test), Q value = 0.016

Table S145.  Gene #56: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
9Q LOSS MUTATED 17 17
9Q LOSS WILD-TYPE 59 195

Figure S145.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.001 (Wilcoxon-test), Q value = 0.011

Table S146.  Gene #56: '9q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
9Q LOSS MUTATED 11 62.7 (38.5)
9Q LOSS WILD-TYPE 65 91.7 (14.6)

Figure S146.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'RACE'

P value = 0.0379 (Fisher's exact test), Q value = 0.17

Table S147.  Gene #56: '9q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
9Q LOSS MUTATED 0 3 4 26
9Q LOSS WILD-TYPE 2 3 57 178

Figure S147.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #11: 'RACE'

'10p loss' versus 'Time to Death'

P value = 0.00759 (logrank test), Q value = 0.053

Table S148.  Gene #57: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
10P LOSS MUTATED 17 6 3.7 - 91.7 (20.5)
10P LOSS WILD-TYPE 268 38 0.1 - 194.8 (25.8)

Figure S148.  Get High-res Image Gene #57: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0066

Table S149.  Gene #57: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
10P LOSS MUTATED 4 0 9 2
10P LOSS WILD-TYPE 167 21 43 13

Figure S149.  Get High-res Image Gene #57: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00165 (Fisher's exact test), Q value = 0.016

Table S150.  Gene #57: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
10P LOSS MUTATED 6 1 10
10P LOSS WILD-TYPE 185 32 52

Figure S150.  Get High-res Image Gene #57: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0282 (Wilcoxon-test), Q value = 0.14

Table S151.  Gene #57: '10p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
10P LOSS MUTATED 7 45.7 (48.3)
10P LOSS WILD-TYPE 69 91.7 (11.5)

Figure S151.  Get High-res Image Gene #57: '10p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'Time to Death'

P value = 0.00037 (logrank test), Q value = 0.0055

Table S152.  Gene #58: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
10Q LOSS MUTATED 18 8 3.7 - 91.7 (19.9)
10Q LOSS WILD-TYPE 267 36 0.1 - 194.8 (25.6)

Figure S152.  Get High-res Image Gene #58: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S153.  Gene #58: '10q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
10Q LOSS MUTATED 4 0 11 2
10Q LOSS WILD-TYPE 167 21 41 13

Figure S153.  Get High-res Image Gene #58: '10q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00068 (Fisher's exact test), Q value = 0.0086

Table S154.  Gene #58: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
10Q LOSS MUTATED 6 1 11
10Q LOSS WILD-TYPE 185 32 51

Figure S154.  Get High-res Image Gene #58: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0466 (Fisher's exact test), Q value = 0.2

Table S155.  Gene #58: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
10Q LOSS MUTATED 3 6 1
10Q LOSS WILD-TYPE 46 18 3

Figure S155.  Get High-res Image Gene #58: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0116 (Wilcoxon-test), Q value = 0.074

Table S156.  Gene #58: '10q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
10Q LOSS MUTATED 8 50.0 (46.3)
10Q LOSS WILD-TYPE 68 91.9 (11.5)

Figure S156.  Get High-res Image Gene #58: '10q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'11p loss' versus 'Time to Death'

P value = 0.000923 (logrank test), Q value = 0.011

Table S157.  Gene #59: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
11P LOSS MUTATED 17 6 2.0 - 58.2 (19.4)
11P LOSS WILD-TYPE 268 38 0.1 - 194.8 (25.6)

Figure S157.  Get High-res Image Gene #59: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0107 (Fisher's exact test), Q value = 0.068

Table S158.  Gene #59: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
11P LOSS MUTATED 5 2 5 3
11P LOSS WILD-TYPE 166 19 47 12

Figure S158.  Get High-res Image Gene #59: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00062 (Fisher's exact test), Q value = 0.008

Table S159.  Gene #59: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
11P LOSS MUTATED 5 2 10
11P LOSS WILD-TYPE 186 31 52

Figure S159.  Get High-res Image Gene #59: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00361 (Fisher's exact test), Q value = 0.03

Table S160.  Gene #59: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
11P LOSS MUTATED 1 4 2
11P LOSS WILD-TYPE 48 20 2

Figure S160.  Get High-res Image Gene #59: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'Time to Death'

P value = 0.000608 (logrank test), Q value = 0.008

Table S161.  Gene #60: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
11Q LOSS MUTATED 21 8 0.4 - 123.6 (18.6)
11Q LOSS WILD-TYPE 264 36 0.1 - 194.8 (25.8)

Figure S161.  Get High-res Image Gene #60: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S162.  Gene #60: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
11Q LOSS MUTATED 3 1 11 5
11Q LOSS WILD-TYPE 168 20 41 10

Figure S162.  Get High-res Image Gene #60: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S163.  Gene #60: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
11Q LOSS MUTATED 3 2 16
11Q LOSS WILD-TYPE 188 31 46

Figure S163.  Get High-res Image Gene #60: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00125 (Fisher's exact test), Q value = 0.013

Table S164.  Gene #60: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
11Q LOSS MUTATED 3 6 3
11Q LOSS WILD-TYPE 46 18 1

Figure S164.  Get High-res Image Gene #60: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0121 (Wilcoxon-test), Q value = 0.076

Table S165.  Gene #60: '11q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
11Q LOSS MUTATED 6 66.7 (36.1)
11Q LOSS WILD-TYPE 70 89.3 (19.8)

Figure S165.  Get High-res Image Gene #60: '11q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'13q loss' versus 'Time to Death'

P value = 1.33e-07 (logrank test), Q value = 1.5e-05

Table S166.  Gene #61: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
13Q LOSS MUTATED 24 10 0.2 - 86.8 (17.5)
13Q LOSS WILD-TYPE 261 34 0.1 - 194.8 (26.0)

Figure S166.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00291 (Wilcoxon-test), Q value = 0.026

Table S167.  Gene #61: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
13Q LOSS MUTATED 24 52.8 (15.3)
13Q LOSS WILD-TYPE 259 62.3 (11.5)

Figure S167.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0036

Table S168.  Gene #61: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
13Q LOSS MUTATED 7 1 12 3
13Q LOSS WILD-TYPE 164 20 40 12

Figure S168.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S169.  Gene #61: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
13Q LOSS MUTATED 7 2 15
13Q LOSS WILD-TYPE 184 31 47

Figure S169.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00378 (Fisher's exact test), Q value = 0.031

Table S170.  Gene #61: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
13Q LOSS MUTATED 3 7 2
13Q LOSS WILD-TYPE 46 17 2

Figure S170.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'GENDER'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.00043

Table S171.  Gene #61: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
13Q LOSS MUTATED 16 8
13Q LOSS WILD-TYPE 60 204

Figure S171.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #7: 'GENDER'

'13q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.064 (Wilcoxon-test), Q value = 0.25

Table S172.  Gene #61: '13q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
13Q LOSS MUTATED 9 75.6 (32.1)
13Q LOSS WILD-TYPE 67 89.1 (20.1)

Figure S172.  Get High-res Image Gene #61: '13q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q loss' versus 'Time to Death'

P value = 0.000118 (logrank test), Q value = 0.002

Table S173.  Gene #62: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
14Q LOSS MUTATED 47 14 0.1 - 80.9 (19.6)
14Q LOSS WILD-TYPE 238 30 0.1 - 194.8 (26.0)

Figure S173.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00191 (Fisher's exact test), Q value = 0.018

Table S174.  Gene #62: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
14Q LOSS MUTATED 18 3 14 6
14Q LOSS WILD-TYPE 153 18 38 9

Figure S174.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S175.  Gene #62: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
14Q LOSS MUTATED 20 5 22
14Q LOSS WILD-TYPE 171 28 40

Figure S175.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00138 (Fisher's exact test), Q value = 0.014

Table S176.  Gene #62: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
14Q LOSS MUTATED 8 8 4
14Q LOSS WILD-TYPE 41 16 0

Figure S176.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'GENDER'

P value = 0.00338 (Fisher's exact test), Q value = 0.029

Table S177.  Gene #62: '14q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
14Q LOSS MUTATED 21 26
14Q LOSS WILD-TYPE 55 186

Figure S177.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #7: 'GENDER'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00896 (Wilcoxon-test), Q value = 0.062

Table S178.  Gene #62: '14q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
14Q LOSS MUTATED 15 71.3 (35.8)
14Q LOSS WILD-TYPE 61 91.5 (15.0)

Figure S178.  Get High-res Image Gene #62: '14q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'15q loss' versus 'Time to Death'

P value = 0.0152 (logrank test), Q value = 0.091

Table S179.  Gene #63: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
15Q LOSS MUTATED 31 9 0.1 - 194.8 (19.4)
15Q LOSS WILD-TYPE 254 35 0.1 - 129.9 (26.0)

Figure S179.  Get High-res Image Gene #63: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.016

Table S180.  Gene #63: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
15Q LOSS MUTATED 11 1 10 5
15Q LOSS WILD-TYPE 160 20 42 10

Figure S180.  Get High-res Image Gene #63: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0051

Table S181.  Gene #63: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
15Q LOSS MUTATED 13 2 16
15Q LOSS WILD-TYPE 178 31 46

Figure S181.  Get High-res Image Gene #63: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00575 (Fisher's exact test), Q value = 0.042

Table S182.  Gene #63: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
15Q LOSS MUTATED 4 8 2
15Q LOSS WILD-TYPE 45 16 2

Figure S182.  Get High-res Image Gene #63: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p loss' versus 'Time to Death'

P value = 0.000422 (logrank test), Q value = 0.006

Table S183.  Gene #64: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
16P LOSS MUTATED 4 3 11.1 - 58.2 (20.6)
16P LOSS WILD-TYPE 281 41 0.1 - 194.8 (25.4)

Figure S183.  Get High-res Image Gene #64: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0641 (Fisher's exact test), Q value = 0.25

Table S184.  Gene #64: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
16P LOSS MUTATED 1 0 3
16P LOSS WILD-TYPE 190 33 59

Figure S184.  Get High-res Image Gene #64: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p loss' versus 'GENDER'

P value = 0.0577 (Fisher's exact test), Q value = 0.23

Table S185.  Gene #64: '16p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
16P LOSS MUTATED 3 1
16P LOSS WILD-TYPE 73 211

Figure S185.  Get High-res Image Gene #64: '16p loss' versus Clinical Feature #7: 'GENDER'

'16q loss' versus 'Time to Death'

P value = 1.43e-05 (logrank test), Q value = 0.00036

Table S186.  Gene #65: '16q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
16Q LOSS MUTATED 7 5 11.1 - 58.2 (19.6)
16Q LOSS WILD-TYPE 278 39 0.1 - 194.8 (25.5)

Figure S186.  Get High-res Image Gene #65: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00442 (Fisher's exact test), Q value = 0.035

Table S187.  Gene #65: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
16Q LOSS MUTATED 1 0 5 1
16Q LOSS WILD-TYPE 170 21 47 14

Figure S187.  Get High-res Image Gene #65: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0127 (Fisher's exact test), Q value = 0.079

Table S188.  Gene #65: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
16Q LOSS MUTATED 2 0 5
16Q LOSS WILD-TYPE 189 33 57

Figure S188.  Get High-res Image Gene #65: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0652 (Fisher's exact test), Q value = 0.25

Table S189.  Gene #65: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
16Q LOSS MUTATED 1 2 1
16Q LOSS WILD-TYPE 48 22 3

Figure S189.  Get High-res Image Gene #65: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'Time to Death'

P value = 3.64e-07 (logrank test), Q value = 3.2e-05

Table S190.  Gene #66: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
17P LOSS MUTATED 13 7 0.2 - 67.4 (14.1)
17P LOSS WILD-TYPE 272 37 0.1 - 194.8 (25.7)

Figure S190.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00241 (Fisher's exact test), Q value = 0.022

Table S191.  Gene #66: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
17P LOSS MUTATED 2 1 4 3
17P LOSS WILD-TYPE 169 20 48 12

Figure S191.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00153 (Fisher's exact test), Q value = 0.015

Table S192.  Gene #66: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
17P LOSS MUTATED 3 3 7
17P LOSS WILD-TYPE 188 30 55

Figure S192.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.047 (Fisher's exact test), Q value = 0.2

Table S193.  Gene #66: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
17P LOSS MUTATED 3 1 2
17P LOSS WILD-TYPE 46 23 2

Figure S193.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0595 (Fisher's exact test), Q value = 0.23

Table S194.  Gene #66: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
17P LOSS MUTATED 3 2
17P LOSS WILD-TYPE 91 7

Figure S194.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'Time to Death'

P value = 1.08e-06 (logrank test), Q value = 7.4e-05

Table S195.  Gene #67: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
18P LOSS MUTATED 42 15 2.0 - 123.6 (18.8)
18P LOSS WILD-TYPE 243 29 0.1 - 194.8 (26.2)

Figure S195.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S196.  Gene #67: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
18P LOSS MUTATED 13 1 17 6
18P LOSS WILD-TYPE 158 20 35 9

Figure S196.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S197.  Gene #67: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
18P LOSS MUTATED 14 4 24
18P LOSS WILD-TYPE 177 29 38

Figure S197.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0162 (Fisher's exact test), Q value = 0.097

Table S198.  Gene #67: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
18P LOSS MUTATED 6 9 2
18P LOSS WILD-TYPE 43 15 2

Figure S198.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0577 (Fisher's exact test), Q value = 0.23

Table S199.  Gene #67: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
18P LOSS MUTATED 15 4
18P LOSS WILD-TYPE 79 5

Figure S199.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'GENDER'

P value = 0.0359 (Fisher's exact test), Q value = 0.17

Table S200.  Gene #67: '18p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
18P LOSS MUTATED 17 25
18P LOSS WILD-TYPE 59 187

Figure S200.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #7: 'GENDER'

'18q loss' versus 'Time to Death'

P value = 3.44e-07 (logrank test), Q value = 3.2e-05

Table S201.  Gene #68: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
18Q LOSS MUTATED 44 16 0.4 - 123.6 (17.6)
18Q LOSS WILD-TYPE 241 28 0.1 - 194.8 (26.3)

Figure S201.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S202.  Gene #68: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
18Q LOSS MUTATED 13 1 19 6
18Q LOSS WILD-TYPE 158 20 33 9

Figure S202.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S203.  Gene #68: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
18Q LOSS MUTATED 15 5 24
18Q LOSS WILD-TYPE 176 28 38

Figure S203.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00097 (Fisher's exact test), Q value = 0.011

Table S204.  Gene #68: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
18Q LOSS MUTATED 6 12 2
18Q LOSS WILD-TYPE 43 12 2

Figure S204.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00476 (Fisher's exact test), Q value = 0.037

Table S205.  Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
19P LOSS MUTATED 4 1 8 1
19P LOSS WILD-TYPE 167 20 44 14

Figure S205.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00568 (Fisher's exact test), Q value = 0.042

Table S206.  Gene #69: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
19P LOSS MUTATED 6 1 9
19P LOSS WILD-TYPE 185 32 53

Figure S206.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0436 (Fisher's exact test), Q value = 0.19

Table S207.  Gene #69: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
19P LOSS MUTATED 1 3 1
19P LOSS WILD-TYPE 48 21 3

Figure S207.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.00206 (logrank test), Q value = 0.019

Table S208.  Gene #70: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
19Q LOSS MUTATED 15 5 0.9 - 54.6 (16.9)
19Q LOSS WILD-TYPE 270 39 0.1 - 194.8 (25.5)

Figure S208.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00079

Table S209.  Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
19Q LOSS MUTATED 2 1 10 1
19Q LOSS WILD-TYPE 169 20 42 14

Figure S209.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S210.  Gene #70: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
19Q LOSS MUTATED 3 1 11
19Q LOSS WILD-TYPE 188 32 51

Figure S210.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0428 (Fisher's exact test), Q value = 0.19

Table S211.  Gene #70: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
19Q LOSS MUTATED 1 3 1
19Q LOSS WILD-TYPE 48 21 3

Figure S211.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00358 (Fisher's exact test), Q value = 0.03

Table S212.  Gene #71: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
21Q LOSS MUTATED 17 3 14 5
21Q LOSS WILD-TYPE 154 18 38 10

Figure S212.  Get High-res Image Gene #71: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.0059

Table S213.  Gene #71: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
21Q LOSS MUTATED 18 6 19
21Q LOSS WILD-TYPE 173 27 43

Figure S213.  Get High-res Image Gene #71: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00554 (Wilcoxon-test), Q value = 0.041

Table S214.  Gene #71: '21q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
21Q LOSS MUTATED 11 79.1 (26.6)
21Q LOSS WILD-TYPE 65 88.9 (21.1)

Figure S214.  Get High-res Image Gene #71: '21q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'Time to Death'

P value = 0.00125 (logrank test), Q value = 0.013

Table S215.  Gene #72: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
22Q LOSS MUTATED 60 15 0.9 - 123.6 (19.9)
22Q LOSS WILD-TYPE 225 29 0.1 - 194.8 (26.0)

Figure S215.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0636 (Wilcoxon-test), Q value = 0.25

Table S216.  Gene #72: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
22Q LOSS MUTATED 59 58.4 (13.8)
22Q LOSS WILD-TYPE 224 62.3 (11.5)

Figure S216.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S217.  Gene #72: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
22Q LOSS MUTATED 20 3 25 8
22Q LOSS WILD-TYPE 151 18 27 7

Figure S217.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S218.  Gene #72: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
22Q LOSS MUTATED 24 5 31
22Q LOSS WILD-TYPE 167 28 31

Figure S218.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00561 (Fisher's exact test), Q value = 0.042

Table S219.  Gene #72: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
22Q LOSS MUTATED 11 14 2
22Q LOSS WILD-TYPE 38 10 2

Figure S219.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.043 (Fisher's exact test), Q value = 0.19

Table S220.  Gene #72: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
22Q LOSS MUTATED 21 5
22Q LOSS WILD-TYPE 73 4

Figure S220.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'GENDER'

P value = 0.000466 (Fisher's exact test), Q value = 0.0064

Table S221.  Gene #72: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
22Q LOSS MUTATED 27 33
22Q LOSS WILD-TYPE 49 179

Figure S221.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #7: 'GENDER'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00113 (Wilcoxon-test), Q value = 0.013

Table S222.  Gene #72: '22q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
22Q LOSS MUTATED 19 70.5 (35.5)
22Q LOSS WILD-TYPE 57 93.2 (10.7)

Figure S222.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xp loss' versus 'Time to Death'

P value = 1.09e-05 (logrank test), Q value = 0.00028

Table S223.  Gene #73: 'xp loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
XP LOSS MUTATED 33 13 0.4 - 91.7 (19.6)
XP LOSS WILD-TYPE 252 31 0.1 - 194.8 (26.0)

Figure S223.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #1: 'Time to Death'

'xp loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S224.  Gene #73: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
XP LOSS MUTATED 7 1 15 4
XP LOSS WILD-TYPE 164 20 37 11

Figure S224.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S225.  Gene #73: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
XP LOSS MUTATED 10 4 19
XP LOSS WILD-TYPE 181 29 43

Figure S225.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.1

Table S226.  Gene #73: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
XP LOSS MUTATED 5 9 1
XP LOSS WILD-TYPE 44 15 3

Figure S226.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00532 (Wilcoxon-test), Q value = 0.04

Table S227.  Gene #73: 'xp loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
XP LOSS MUTATED 9 66.7 (35.4)
XP LOSS WILD-TYPE 67 90.3 (18.3)

Figure S227.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xp loss' versus 'RACE'

P value = 0.0406 (Fisher's exact test), Q value = 0.18

Table S228.  Gene #73: 'xp loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
XP LOSS MUTATED 0 3 9 20
XP LOSS WILD-TYPE 2 3 52 184

Figure S228.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #11: 'RACE'

'xq loss' versus 'Time to Death'

P value = 6.17e-07 (logrank test), Q value = 4.8e-05

Table S229.  Gene #74: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
XQ LOSS MUTATED 29 13 0.4 - 91.7 (19.3)
XQ LOSS WILD-TYPE 256 31 0.1 - 194.8 (26.0)

Figure S229.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S230.  Gene #74: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
XQ LOSS MUTATED 7 1 13 4
XQ LOSS WILD-TYPE 164 20 39 11

Figure S230.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S231.  Gene #74: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
XQ LOSS MUTATED 9 3 17
XQ LOSS WILD-TYPE 182 30 45

Figure S231.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00986 (Fisher's exact test), Q value = 0.065

Table S232.  Gene #74: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
XQ LOSS MUTATED 4 9 1
XQ LOSS WILD-TYPE 45 15 3

Figure S232.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00532 (Wilcoxon-test), Q value = 0.04

Table S233.  Gene #74: 'xq loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
XQ LOSS MUTATED 9 66.7 (35.4)
XQ LOSS WILD-TYPE 67 90.3 (18.3)

Figure S233.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'RACE'

P value = 0.0415 (Fisher's exact test), Q value = 0.18

Table S234.  Gene #74: 'xq loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
XQ LOSS MUTATED 0 3 7 18
XQ LOSS WILD-TYPE 2 3 54 186

Figure S234.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #11: 'RACE'

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/KIRP-TP/22533934/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/22507257/KIRP-TP.merged_data.txt

  • Number of patients = 288

  • Number of significantly arm-level cnvs = 74

  • 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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