Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1028QSS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1028QSS
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 287 patients, 235 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 '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 'PATHOLOGY_T_STAGE' and 'PATHOLOGY_M_STAGE'.

  • 5p gain cnv correlated to 'PATHOLOGIC_STAGE',  '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',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • 7q gain cnv correlated to 'PATHOLOGIC_STAGE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE', 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 'Time to Death' and 'RACE'.

  • 10q gain cnv correlated to 'Time to Death' and '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 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • 17q gain cnv correlated to 'PATHOLOGIC_STAGE'.

  • 18q gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 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',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • 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',  'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

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

  • 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', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 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', and 'PATHOLOGY_T_STAGE'.

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

  • 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 'Time to Death',  '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',  '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',  'YEARS_TO_BIRTH',  '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, 235 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
13q loss 24 (8%) 263 9.42e-08
(8.36e-06) 		0.00304
(0.0276) 		0.00029
(0.00422) 		2e-05
(0.000433) 		0.00572
(0.0423) 		0.536
(0.882) 		1.82e-05
(0.000433) 		0.064
(0.245) 		0.746
(1.00) 		0.447
(0.786) 		0.124
(0.369) 		1
(1.00)
22q loss 60 (21%) 227 0.00122
(0.0137) 		0.0687
(0.252) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.0113
(0.072) 		0.0448
(0.188) 		0.000481
(0.00638) 		0.00113
(0.0131) 		0.559
(0.906) 		0.216
(0.524) 		0.197
(0.504) 		0.708
(1.00)
xq loss 30 (10%) 257 6.38e-07
(4.05e-05) 		0.0579
(0.227) 		3e-05
(0.000605) 		2e-05
(0.000433) 		0.00936
(0.0607) 		0.214
(0.524) 		0.0834
(0.288) 		0.0192
(0.105) 		0.912
(1.00) 		0.361
(0.692) 		0.0175
(0.0998) 		0.612
(0.93)
1q gain 17 (6%) 270 6.48e-10
(9.59e-08) 		0.669
(0.985) 		2e-05
(0.000433) 		1e-05
(0.000254) 		0.0464
(0.193) 		0.116
(0.352) 		0.0197
(0.105) 		0.0219
(0.111) 		0.236
(0.559) 		0.104
(0.335) 		1
(1.00)
4p loss 25 (9%) 262 3.89e-10
(8.63e-08) 		0.00368
(0.0311) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00061
(0.00785) 		0.58
(0.924) 		3.99e-05
(0.00074) 		0.0768
(0.274) 		0.96
(1.00) 		0.192
(0.497) 		0.106
(0.338) 		1
(1.00)
4q loss 26 (9%) 261 3.35e-10
(8.63e-08) 		0.0211
(0.109) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00914
(0.0598) 		0.214
(0.524) 		0.000623
(0.00791) 		0.067
(0.25) 		0.611
(0.93) 		0.282
(0.595) 		0.124
(0.371) 		1
(1.00)
5p loss 8 (3%) 279 1.74e-10
(7.72e-08) 		0.0507
(0.206) 		0.0218
(0.111) 		0.00387
(0.0321) 		0.0102
(0.0654) 		0.244
(0.559) 		0.0327
(0.154) 		1
(1.00) 		0.257
(0.572)
5q loss 8 (3%) 279 1.47e-07
(1.09e-05) 		0.0124
(0.0757) 		0.0358
(0.163) 		0.00438
(0.035) 		0.0183
(0.103) 		0.244
(0.559) 		0.0327
(0.154) 		1
(1.00) 		0.257
(0.572)
9p loss 33 (11%) 254 1.47e-07
(1.09e-05) 		0.306
(0.63) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00332
(0.0292) 		0.0702
(0.255) 		0.00125
(0.0137) 		0.000832
(0.0101) 		0.388
(0.715) 		0.478
(0.82) 		0.114
(0.351) 		0.37
(0.702)
9q loss 33 (11%) 254 4.88e-06
(0.000254) 		0.301
(0.62) 		4e-05
(0.00074) 		1e-05
(0.000254) 		0.00478
(0.0369) 		0.322
(0.639) 		0.00125
(0.0137) 		0.001
(0.0118) 		0.941
(1.00) 		0.57
(0.919) 		0.114
(0.351) 		0.373
(0.702)
14q loss 47 (16%) 240 0.00014
(0.0023) 		0.364
(0.694) 		0.00206
(0.0195) 		4e-05
(0.00074) 		0.00628
(0.0446) 		0.125
(0.373) 		0.00345
(0.03) 		0.00896
(0.0594) 		0.476
(0.82) 		0.0756
(0.271) 		0.956
(1.00) 		0.697
(1.00)
17p loss 11 (4%) 276 6.36e-10
(9.59e-08) 		0.563
(0.91) 		0.00092
(0.011) 		0.00186
(0.018) 		0.00419
(0.0341) 		0.0381
(0.167) 		0.167
(0.451) 		0.0251
(0.124) 		0.612
(0.93) 		1
(1.00) 		0.587
(0.924) 		1
(1.00)
18p loss 42 (15%) 245 3.05e-07
(2.09e-05) 		0.0778
(0.276) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00643
(0.0453) 		0.0596
(0.231) 		0.0363
(0.163) 		0.244
(0.559) 		0.222
(0.532) 		0.0832
(0.288) 		0.294
(0.612) 		0.677
(0.993)
xp loss 34 (12%) 253 9.66e-06
(0.000254) 		0.0874
(0.295) 		1e-05
(0.000254) 		2e-05
(0.000433) 		0.0153
(0.0882) 		0.25
(0.563) 		0.102
(0.332) 		0.0192
(0.105) 		0.698
(1.00) 		0.361
(0.692) 		0.0158
(0.0907) 		0.373
(0.702)
1p gain 9 (3%) 278 1.13e-10
(7.72e-08) 		0.296
(0.614) 		0.00114
(0.0131) 		0.00162
(0.016) 		0.00067
(0.00838) 		0.169
(0.453) 		0.0122
(0.075) 		0.352
(0.679) 		1
(1.00)
6p gain 10 (3%) 277 0.00194
(0.0185) 		0.216
(0.524) 		4e-05
(0.00074) 		6e-05
(0.00102) 		0.0255
(0.125) 		0.0381
(0.167) 		0.728
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.771
(1.00) 		1
(1.00)
6q gain 8 (3%) 279 7.04e-06
(0.000254) 		0.0688
(0.252) 		0.00038
(0.00519) 		0.00154
(0.0157) 		0.00422
(0.0341) 		0.02
(0.106) 		0.44
(0.779) 		0.871
(1.00) 		0.323
(0.639) 		0.503
(0.848) 		1
(1.00)
8q gain 25 (9%) 262 3.93e-06
(0.000233) 		0.825
(1.00) 		0.00011
(0.00184) 		6e-05
(0.00102) 		0.00146
(0.0154) 		0.147
(0.41) 		0.0552
(0.22) 		0.24
(0.559) 		0.551
(0.899) 		0.743
(1.00) 		0.192
(0.497) 		1
(1.00)
6q loss 26 (9%) 261 0.839
(1.00) 		0.752
(1.00) 		0.021
(0.109) 		0.00071
(0.00876) 		0.169
(0.453) 		0.594
(0.924) 		0.033
(0.154) 		0.0184
(0.103) 		0.821
(1.00) 		0.929
(1.00) 		0.0484
(0.201) 		0.607
(0.93)
8p loss 16 (6%) 271 0.00157
(0.0159) 		0.2
(0.505) 		0.0365
(0.163) 		0.278
(0.594) 		0.0251
(0.124) 		0.0142
(0.084) 		0.142
(0.402) 		0.803
(1.00) 		0.978
(1.00) 		0.0516
(0.208) 		1
(1.00)
10q loss 17 (6%) 270 0.00247
(0.0231) 		0.505
(0.85) 		0.00019
(0.00286) 		0.00142
(0.0152) 		0.0266
(0.13) 		0.313
(0.636) 		0.402
(0.729) 		0.0116
(0.0731) 		0.11
(0.346) 		0.151
(0.419) 		0.402
(0.729) 		1
(1.00)
11q loss 21 (7%) 266 0.000161
(0.00255) 		0.876
(1.00) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00411
(0.0338) 		0.18
(0.475) 		0.449
(0.786) 		0.0121
(0.075) 		0.846
(1.00) 		0.856
(1.00) 		0.111
(0.349) 		1
(1.00)
7p gain 172 (60%) 115 0.346
(0.67) 		0.661
(0.975) 		0.00469
(0.0369) 		0.086
(0.295) 		0.758
(1.00) 		0.728
(1.00) 		0.00253
(0.0232) 		0.0656
(0.248) 		0.804
(1.00) 		0.0072
(0.0491) 		0.382
(0.715) 		0.545
(0.895)
7q gain 173 (60%) 114 0.338
(0.659) 		0.568
(0.918) 		0.00348
(0.03) 		0.0675
(0.251) 		0.704
(1.00) 		0.728
(1.00) 		0.00162
(0.016) 		0.0656
(0.248) 		0.804
(1.00) 		0.0072
(0.0491) 		0.348
(0.671) 		0.544
(0.895)
11p gain 11 (4%) 276 0.0038
(0.0318) 		0.131
(0.381) 		0.0491
(0.203) 		0.0614
(0.236) 		0.201
(0.506) 		0.0381
(0.167) 		0.167
(0.451) 		0.688
(1.00) 		0.902
(1.00) 		0.183
(0.481) 		1
(1.00)
16q gain 148 (52%) 139 0.0384
(0.167) 		0.0291
(0.139) 		0.53
(0.879) 		0.217
(0.524) 		0.611
(0.93) 		0.179
(0.475) 		0.0032
(0.0284) 		0.92
(1.00) 		0.602
(0.929) 		0.167
(0.451) 		0.00956
(0.0615) 		0.239
(0.559)
3p loss 22 (8%) 265 0.000325
(0.00465) 		0.0205
(0.107) 		3e-05
(0.000605) 		6e-05
(0.00102) 		0.114
(0.351) 		0.0866
(0.295) 		1
(1.00) 		0.685
(1.00) 		0.787
(1.00) 		0.271
(0.59) 		0.532
(0.879) 		0.608
(0.93)
3q loss 7 (2%) 280 1.25e-05
(0.000308) 		0.16
(0.442) 		0.0423
(0.18) 		0.0143
(0.0841) 		0.0137
(0.0826) 		0.169
(0.453) 		0.386
(0.715) 		1
(1.00) 		1
(1.00)
10p loss 16 (6%) 271 0.0365
(0.163) 		0.885
(1.00) 		0.00165
(0.0161) 		0.00513
(0.0389) 		0.115
(0.351) 		0.244
(0.559) 		0.38
(0.713) 		0.0282
(0.137) 		0.11
(0.346) 		0.151
(0.419) 		0.848
(1.00) 		1
(1.00)
11p loss 18 (6%) 269 0.000186
(0.00286) 		0.403
(0.729) 		0.00665
(0.0465) 		0.00028
(0.00414) 		0.00725
(0.0491) 		0.376
(0.706) 		0.268
(0.588) 		0.102
(0.332) 		0.826
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 31 (11%) 256 0.0071
(0.0491) 		0.0734
(0.264) 		0.00151
(0.0156) 		0.00036
(0.00499) 		0.0117
(0.0731) 		0.286
(0.601) 		0.28
(0.594) 		0.131
(0.381) 		0.387
(0.715) 		0.449
(0.786) 		1
(1.00)
18q loss 45 (16%) 242 2.16e-08
(2.74e-06) 		0.146
(0.409) 		1e-05
(0.000254) 		1e-05
(0.000254) 		0.00059
(0.0077) 		0.0712
(0.257) 		0.0677
(0.251) 		0.207
(0.517) 		0.412
(0.742) 		0.18
(0.475) 		0.0816
(0.287) 		0.699
(1.00)
19p loss 17 (6%) 270 0.0188
(0.104) 		0.653
(0.965) 		0.00478
(0.0369) 		0.0015
(0.0156) 		0.00841
(0.0566) 		1
(1.00) 		0.164
(0.449) 		0.131
(0.381) 		0.496
(0.841) 		0.853
(1.00) 		1
(1.00)
19q loss 16 (6%) 271 0.00016
(0.00255) 		0.395
(0.723) 		5e-05
(0.000906) 		3e-05
(0.000605) 		0.00893
(0.0594) 		1
(1.00) 		0.142
(0.402) 		0.131
(0.381) 		0.627
(0.938) 		0.227
(0.541) 		0.847
(1.00) 		1
(1.00)
2q gain 47 (16%) 240 0.292
(0.612) 		0.338
(0.659) 		0.0345
(0.16) 		0.26
(0.577) 		0.0145
(0.0849) 		0.00604
(0.0443) 		0.59
(0.924) 		0.251
(0.563) 		0.313
(0.636) 		0.954
(1.00) 		0.911
(1.00) 		1
(1.00)
5p gain 33 (11%) 254 0.113
(0.351) 		0.461
(0.799) 		0.0495
(0.204) 		0.0141
(0.084) 		0.329
(0.645) 		0.617
(0.93) 		0.837
(1.00) 		0.045
(0.188) 		0.589
(0.924) 		0.591
(0.924) 		0.402
(0.729) 		1
(1.00)
9p gain 3 (1%) 284 0.0525
(0.21) 		0.515
(0.859) 		0.0449
(0.188) 		0.0355
(0.162) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 10 (3%) 277 0.0605
(0.234) 		0.0505
(0.206) 		0.144
(0.407) 		0.123
(0.369) 		0.693
(1.00) 		0.244
(0.559) 		0.024
(0.12) 		0.91
(1.00) 		0.582
(0.924) 		0.273
(0.593) 		0.275
(0.594) 		1
(1.00)
16p gain 153 (53%) 134 0.329
(0.645) 		0.013
(0.0793) 		0.902
(1.00) 		0.652
(0.965) 		0.817
(1.00) 		0.488
(0.831) 		0.00121
(0.0137) 		0.602
(0.929) 		0.896
(1.00) 		0.167
(0.451) 		0.00141
(0.0152) 		0.234
(0.558)
17p gain 174 (61%) 113 0.0957
(0.315) 		0.0994
(0.326) 		0.00019
(0.00286) 		0.00047
(0.00632) 		0.454
(0.791) 		0.501
(0.846) 		0.0142
(0.084) 		0.213
(0.524) 		0.59
(0.924) 		0.29
(0.608) 		0.0917
(0.307) 		0.127
(0.375)
xp gain 87 (30%) 200 0.319
(0.639) 		0.137
(0.394) 		0.00474
(0.0369) 		0.00563
(0.042) 		0.648
(0.962) 		1
(1.00) 		0.0201
(0.106) 		0.279
(0.594) 		0.937
(1.00) 		0.0872
(0.295) 		0.146
(0.409) 		1
(1.00)
xq gain 91 (32%) 196 0.248
(0.561) 		0.127
(0.375) 		0.0339
(0.158) 		0.0225
(0.113) 		0.589
(0.924) 		1
(1.00) 		0.0216
(0.11) 		0.279
(0.594) 		0.895
(1.00) 		0.0872
(0.295) 		0.215
(0.524) 		1
(1.00)
6p loss 21 (7%) 266 0.215
(0.524) 		0.575
(0.924) 		0.00916
(0.0598) 		0.0208
(0.108) 		0.138
(0.396) 		1
(1.00) 		0.209
(0.519) 		0.0364
(0.163) 		0.787
(1.00) 		0.754
(1.00) 		0.131
(0.381) 		1
(1.00)
16p loss 4 (1%) 283 2.51e-08
(2.79e-06) 		0.878
(1.00) 		0.0957
(0.315) 		0.0656
(0.248) 		1
(1.00) 		0.0582
(0.227) 		1
(1.00)
16q loss 7 (2%) 280 7.13e-08
(7.03e-06) 		0.736
(1.00) 		0.00495
(0.0379) 		0.0149
(0.0867) 		0.0833
(0.288) 		1
(1.00) 		0.386
(0.715) 		0.912
(1.00) 		0.985
(1.00) 		0.642
(0.957) 		1
(1.00)
21q loss 43 (15%) 244 0.2
(0.505) 		0.14
(0.4) 		0.00362
(0.0309) 		0.00035
(0.00493) 		0.114
(0.351) 		0.105
(0.338) 		0.0932
(0.31) 		0.00554
(0.0417) 		0.547
(0.895) 		0.362
(0.693) 		0.28
(0.594) 		0.699
(1.00)
2p gain 42 (15%) 245 0.266
(0.585) 		0.246
(0.56) 		0.0667
(0.25) 		0.293
(0.612) 		0.0506
(0.206) 		0.00316
(0.0284) 		0.456
(0.793) 		0.294
(0.612) 		0.163
(0.447) 		0.617
(0.93) 		0.799
(1.00) 		1
(1.00)
3p gain 74 (26%) 213 0.479
(0.82) 		0.701
(1.00) 		0.0188
(0.104) 		0.00612
(0.0445) 		0.845
(1.00) 		0.107
(0.339) 		0.45
(0.786) 		0.105
(0.338) 		0.732
(1.00) 		0.555
(0.902) 		0.645
(0.96) 		1
(1.00)
3q gain 94 (33%) 193 0.915
(1.00) 		0.325
(0.642) 		0.0683
(0.252) 		0.0348
(0.16) 		0.649
(0.962) 		0.0572
(0.227) 		0.319
(0.639) 		0.298
(0.617) 		0.442
(0.78) 		0.511
(0.856) 		0.163
(0.447) 		1
(1.00)
8p gain 20 (7%) 267 0.0025
(0.0231) 		0.801
(1.00) 		0.079
(0.28) 		0.0185
(0.103) 		0.0932
(0.31) 		1
(1.00) 		0.188
(0.49) 		0.803
(1.00) 		0.762
(1.00) 		0.174
(0.462) 		0.599
(0.928)
10p gain 9 (3%) 278 0.042
(0.18) 		0.262
(0.577) 		0.214
(0.524) 		0.194
(0.498) 		0.319
(0.639) 		0.487
(0.83) 		0.251
(0.563) 		0.389
(0.715) 		0.00626
(0.0446) 		1
(1.00)
10q gain 9 (3%) 278 0.042
(0.18) 		0.262
(0.577) 		0.216
(0.524) 		0.193
(0.497) 		0.318
(0.639) 		0.487
(0.83) 		0.251
(0.563) 		0.389
(0.715) 		0.00625
(0.0446) 		1
(1.00)
14q gain 3 (1%) 284 0.0367
(0.163) 		0.0195
(0.105) 		1
(1.00) 		0.172
(0.459) 		1
(1.00)
2p loss 5 (2%) 282 0.877
(1.00) 		0.593
(0.924) 		0.0288
(0.138) 		0.0521
(0.209) 		1
(1.00) 		0.611
(0.93) 		0.621
(0.93) 		1
(1.00)
5q gain 31 (11%) 256 0.594
(0.924) 		0.447
(0.786) 		0.0869
(0.295) 		0.114
(0.351) 		0.311
(0.636) 		0.617
(0.93) 		1
(1.00) 		0.045
(0.188) 		0.589
(0.924) 		0.765
(1.00) 		0.547
(0.895) 		0.62
(0.93)
12p gain 112 (39%) 175 0.842
(1.00) 		0.807
(1.00) 		0.24
(0.559) 		0.835
(1.00) 		0.321
(0.639) 		0.477
(0.82) 		0.0198
(0.105) 		0.415
(0.742) 		0.92
(1.00) 		0.121
(0.364) 		0.925
(1.00) 		0.372
(0.702)
12q gain 112 (39%) 175 0.842
(1.00) 		0.807
(1.00) 		0.24
(0.559) 		0.838
(1.00) 		0.321
(0.639) 		0.477
(0.82) 		0.0198
(0.105) 		0.415
(0.742) 		0.92
(1.00) 		0.121
(0.364) 		0.924
(1.00) 		0.372
(0.702)
17q gain 191 (67%) 96 0.676
(0.993) 		0.106
(0.338) 		0.0327
(0.154) 		0.0694
(0.253) 		0.202
(0.506) 		1
(1.00) 		0.121
(0.364) 		0.771
(1.00) 		0.615
(0.93) 		0.282
(0.595) 		0.0667
(0.25) 		0.199
(0.505)
18q gain 9 (3%) 278 0.2
(0.505) 		0.585
(0.924) 		0.532
(0.879) 		0.435
(0.772) 		1
(1.00) 		0.453
(0.79) 		0.0286
(0.138) 		0.309
(0.634) 		1
(1.00)
21q gain 19 (7%) 268 0.861
(1.00) 		0.135
(0.39) 		1
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.313
(0.636) 		1
(1.00) 		0.299
(0.618) 		0.058
(0.227) 		0.1
(0.327) 		0.599
(0.928)
1p loss 30 (10%) 257 0.493
(0.837) 		0.474
(0.82) 		0.0829
(0.288) 		0.0387
(0.168) 		0.32
(0.639) 		1
(1.00) 		0.385
(0.715) 		0.397
(0.725) 		0.755
(1.00) 		0.415
(0.742) 		1
(1.00)
8q loss 9 (3%) 278 0.319
(0.639) 		0.558
(0.906) 		0.369
(0.702) 		1
(1.00) 		0.394
(0.722) 		0.244
(0.559) 		0.0584
(0.227) 		0.238
(0.559) 		1
(1.00)
4p gain 10 (3%) 277 0.338
(0.659) 		0.0952
(0.315) 		0.0817
(0.287) 		0.62
(0.93) 		0.318
(0.639) 		0.244
(0.559) 		1
(1.00) 		0.326
(0.643) 		0.871
(1.00) 		0.834
(1.00) 		0.588
(0.924) 		1
(1.00)
4q gain 9 (3%) 278 0.991
(1.00) 		0.222
(0.532) 		0.24
(0.559) 		0.434
(0.771) 		0.132
(0.383) 		1
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.388
(0.715) 		0.834
(1.00) 		0.755
(1.00) 		1
(1.00)
13q gain 28 (10%) 259 0.512
(0.857) 		0.371
(0.702) 		0.939
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.594
(0.924) 		1
(1.00) 		0.53
(0.879) 		0.931
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.34
(0.66)
15q gain 5 (2%) 282 0.978
(1.00) 		0.838
(1.00) 		0.279
(0.594) 		0.247
(0.561) 		1
(1.00) 		0.118
(0.358) 		0.407
(0.735) 		1
(1.00)
18p gain 12 (4%) 275 0.96
(1.00) 		0.792
(1.00) 		0.279
(0.594) 		0.807
(1.00) 		0.69
(1.00) 		0.434
(0.771) 		0.193
(0.497) 		0.213
(0.524) 		0.719
(1.00) 		0.261
(0.577) 		1
(1.00)
19p gain 4 (1%) 283 0.588
(0.924) 		0.185
(0.483) 		0.588
(0.924) 		0.272
(0.593) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.62
(0.93) 		1
(1.00)
19q gain 4 (1%) 283 0.588
(0.924) 		0.185
(0.483) 		0.585
(0.924) 		0.274
(0.594) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.619
(0.93) 		1
(1.00)
20p gain 98 (34%) 189 0.957
(1.00) 		0.256
(0.572) 		0.516
(0.859) 		0.326
(0.643) 		0.508
(0.853) 		1
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.244
(0.559) 		0.787
(1.00) 		0.423
(0.755) 		0.756
(1.00)
20q gain 100 (35%) 187 0.769
(1.00) 		0.27
(0.59) 		0.612
(0.93) 		0.415
(0.742) 		0.246
(0.56) 		1
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.34
(0.66) 		0.642
(0.957) 		0.2
(0.505) 		0.551
(0.899)
22q gain 5 (2%) 282 0.277
(0.594) 		0.479
(0.82) 		0.143
(0.405) 		0.0884
(0.297) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.219
(0.527)
1q loss 21 (7%) 266 0.793
(1.00) 		0.978
(1.00) 		0.501
(0.846) 		0.83
(1.00) 		0.6
(0.929) 		0.536
(0.882) 		0.209
(0.519) 		0.678
(0.993) 		0.399
(0.728) 		1
(1.00)
2q loss 3 (1%) 284 0.158
(0.436) 		1
(1.00) 		1
(1.00) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 1.13e-10 (logrank test), Q value = 7.7e-08

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
1P GAIN MUTATED 8 5 2.0 - 49.2 (10.5)
1P GAIN WILD-TYPE 274 39 0.1 - 194.8 (25.0)

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

'1p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00114 (Fisher's exact test), Q value = 0.013

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
1P GAIN MUTATED 1 0 5 2
1P GAIN WILD-TYPE 170 22 47 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 = 0.00162 (Fisher's exact test), Q value = 0.016

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

nPatients T1 T2 T3+T4
ALL 190 33 62
1P GAIN MUTATED 2 0 7
1P GAIN WILD-TYPE 188 33 55

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 = 0.00067 (Fisher's exact test), Q value = 0.0084

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

nPatients N0 N1 N2
ALL 48 24 5
1P GAIN MUTATED 0 4 2
1P GAIN WILD-TYPE 48 20 3

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

'1p gain' versus 'GENDER'

P value = 0.0122 (Fisher's exact test), Q value = 0.075

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

nPatients FEMALE MALE
ALL 76 211
1P GAIN MUTATED 6 3
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 = 6.48e-10 (logrank test), Q value = 9.6e-08

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
1Q GAIN MUTATED 16 8 0.9 - 59.0 (14.9)
1Q GAIN WILD-TYPE 266 36 0.1 - 194.8 (25.2)

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

'1q gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00043

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
1Q GAIN MUTATED 3 0 10 3
1Q GAIN WILD-TYPE 168 22 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 = 0.00025

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

nPatients T1 T2 T3+T4
ALL 190 33 62
1Q GAIN MUTATED 4 0 13
1Q GAIN WILD-TYPE 186 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 = 0.0464 (Fisher's exact test), Q value = 0.19

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

nPatients N0 N1 N2
ALL 48 24 5
1Q GAIN MUTATED 4 6 2
1Q GAIN WILD-TYPE 44 18 3

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

'1q gain' versus 'GENDER'

P value = 0.0197 (Fisher's exact test), Q value = 0.11

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

nPatients FEMALE MALE
ALL 76 211
1Q GAIN MUTATED 9 8
1Q GAIN WILD-TYPE 67 203

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 = 0.11

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 'PATHOLOGY_N_STAGE'

P value = 0.0506 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
2P GAIN MUTATED 5 7 2
2P GAIN WILD-TYPE 43 17 3

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00316 (Fisher's exact test), Q value = 0.028

Table S13.  Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
2P GAIN MUTATED 10 5
2P GAIN WILD-TYPE 83 4

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0345 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #4: '2q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
2Q GAIN MUTATED 27 4 7 7
2Q GAIN WILD-TYPE 144 18 45 8

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.085

Table S15.  Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
2Q GAIN MUTATED 6 8 3
2Q GAIN WILD-TYPE 42 16 2

Figure S15.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00604 (Fisher's exact test), Q value = 0.044

Table S16.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
2Q GAIN MUTATED 12 5
2Q GAIN WILD-TYPE 81 4

Figure S16.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0188 (Fisher's exact test), Q value = 0.1

Table S17.  Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
3P GAIN MUTATED 51 8 6 2
3P GAIN WILD-TYPE 120 14 46 13

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00612 (Fisher's exact test), Q value = 0.045

Table S18.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
3P GAIN MUTATED 54 12 7
3P GAIN WILD-TYPE 136 21 55

Figure S18.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0348 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
3Q GAIN MUTATED 65 15 13
3Q GAIN WILD-TYPE 125 18 49

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0572 (Fisher's exact test), Q value = 0.23

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

nPatients 0 1
ALL 93 9
3Q GAIN MUTATED 29 0
3Q GAIN WILD-TYPE 64 9

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

'5p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0495 (Fisher's exact test), Q value = 0.2

Table S21.  Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
5P GAIN MUTATED 14 3 9 4
5P GAIN WILD-TYPE 157 19 43 11

Figure S21.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0141 (Fisher's exact test), Q value = 0.084

Table S22.  Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
5P GAIN MUTATED 15 5 13
5P GAIN WILD-TYPE 175 28 49

Figure S22.  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 S23.  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 S23.  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 S24.  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 S24.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'6p gain' versus 'Time to Death'

P value = 0.00194 (logrank test), Q value = 0.019

Table S25.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
6P GAIN MUTATED 10 5 6.6 - 93.3 (13.8)
6P GAIN WILD-TYPE 272 39 0.1 - 194.8 (25.0)

Figure S25.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00074

Table S26.  Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
6P GAIN MUTATED 1 0 6 3
6P GAIN WILD-TYPE 170 22 46 12

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p gain' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S27.  Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
6P GAIN MUTATED 1 1 8
6P GAIN WILD-TYPE 189 32 54

Figure S27.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0255 (Fisher's exact test), Q value = 0.13

Table S28.  Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
6P GAIN MUTATED 1 5 0
6P GAIN WILD-TYPE 47 19 5

Figure S28.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'PATHOLOGY_M_STAGE'

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

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

nPatients 0 1
ALL 93 9
6P GAIN MUTATED 2 2
6P GAIN WILD-TYPE 91 7

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

'6q gain' versus 'Time to Death'

P value = 7.04e-06 (logrank test), Q value = 0.00025

Table S30.  Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
6Q GAIN MUTATED 8 5 6.6 - 86.3 (13.2)
6Q GAIN WILD-TYPE 274 39 0.1 - 194.8 (25.0)

Figure S30.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.0052

Table S31.  Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
6Q GAIN MUTATED 1 0 4 3
6Q GAIN WILD-TYPE 170 22 48 12

Figure S31.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00154 (Fisher's exact test), Q value = 0.016

Table S32.  Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
6Q GAIN MUTATED 1 1 6
6Q GAIN WILD-TYPE 189 32 56

Figure S32.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00422 (Fisher's exact test), Q value = 0.034

Table S33.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
6Q GAIN MUTATED 0 5 0
6Q GAIN WILD-TYPE 48 19 5

Figure S33.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.02 (Fisher's exact test), Q value = 0.11

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

nPatients 0 1
ALL 93 9
6Q GAIN MUTATED 1 2
6Q GAIN WILD-TYPE 92 7

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

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00469 (Fisher's exact test), Q value = 0.037

Table S35.  Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
7P GAIN MUTATED 113 11 21 11
7P GAIN WILD-TYPE 58 11 31 4

Figure S35.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7p gain' versus 'GENDER'

P value = 0.00253 (Fisher's exact test), Q value = 0.023

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

nPatients FEMALE MALE
ALL 76 211
7P GAIN MUTATED 34 138
7P GAIN WILD-TYPE 42 73

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

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0656 (Wilcoxon-test), Q value = 0.25

Table S37.  Gene #13: '7p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
7P GAIN MUTATED 52 90.4 (19.1)
7P GAIN WILD-TYPE 24 81.2 (26.8)

Figure S37.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'7p gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0072 (Wilcoxon-test), Q value = 0.049

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 = 0.00348 (Fisher's exact test), Q value = 0.03

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
7Q GAIN MUTATED 114 11 21 11
7Q GAIN WILD-TYPE 57 11 31 4

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

'7q gain' versus 'GENDER'

P value = 0.00162 (Fisher's exact test), Q value = 0.016

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

nPatients FEMALE MALE
ALL 76 211
7Q GAIN MUTATED 34 139
7Q GAIN WILD-TYPE 42 72

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

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0656 (Wilcoxon-test), Q value = 0.25

Table S41.  Gene #14: '7q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
7Q GAIN MUTATED 52 90.4 (19.1)
7Q GAIN WILD-TYPE 24 81.2 (26.8)

Figure S41.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'7q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0072 (Wilcoxon-test), Q value = 0.049

Table S42.  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 S42.  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 = 0.0025 (logrank test), Q value = 0.023

Table S43.  Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
8P GAIN MUTATED 20 6 0.2 - 59.0 (19.7)
8P GAIN WILD-TYPE 262 38 0.1 - 194.8 (25.0)

Figure S43.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0185 (Fisher's exact test), Q value = 0.1

Table S44.  Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
8P GAIN MUTATED 8 3 9
8P GAIN WILD-TYPE 182 30 53

Figure S44.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'Time to Death'

P value = 3.93e-06 (logrank test), Q value = 0.00023

Table S45.  Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
8Q GAIN MUTATED 25 9 0.2 - 59.0 (16.0)
8Q GAIN WILD-TYPE 257 35 0.1 - 194.8 (25.2)

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0018

Table S46.  Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
8Q GAIN MUTATED 7 4 8 5
8Q GAIN WILD-TYPE 164 18 44 10

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S47.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
8Q GAIN MUTATED 7 4 14
8Q GAIN WILD-TYPE 183 29 48

Figure S47.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00146 (Fisher's exact test), Q value = 0.015

Table S48.  Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
8Q GAIN MUTATED 3 7 3
8Q GAIN WILD-TYPE 45 17 2

Figure S48.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q gain' versus 'GENDER'

P value = 0.0552 (Fisher's exact test), Q value = 0.22

Table S49.  Gene #16: '8q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
8Q GAIN MUTATED 11 14
8Q GAIN WILD-TYPE 65 197

Figure S49.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'GENDER'

'9p gain' versus 'Time to Death'

P value = 0.0525 (logrank test), Q value = 0.21

Table S50.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
9P GAIN MUTATED 3 1 3.7 - 34.5 (11.3)
9P GAIN WILD-TYPE 279 43 0.1 - 194.8 (24.6)

Figure S50.  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 S51.  Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
9P GAIN MUTATED 0 1 2 0
9P GAIN WILD-TYPE 171 21 50 15

Figure S51.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0355 (Fisher's exact test), Q value = 0.16

Table S52.  Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
9P GAIN MUTATED 0 1 2
9P GAIN WILD-TYPE 190 32 60

Figure S52.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p gain' versus 'Time to Death'

P value = 0.042 (logrank test), Q value = 0.18

Table S53.  Gene #18: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
10P GAIN MUTATED 8 3 1.1 - 76.6 (20.5)
10P GAIN WILD-TYPE 274 41 0.1 - 194.8 (24.7)

Figure S53.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'RACE'

P value = 0.00626 (Fisher's exact test), Q value = 0.045

Table S54.  Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
10P GAIN MUTATED 0 2 2 3
10P GAIN WILD-TYPE 2 3 59 201

Figure S54.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

'10q gain' versus 'Time to Death'

P value = 0.042 (logrank test), Q value = 0.18

Table S55.  Gene #19: '10q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
10Q GAIN MUTATED 8 3 1.1 - 76.6 (20.5)
10Q GAIN WILD-TYPE 274 41 0.1 - 194.8 (24.7)

Figure S55.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'RACE'

P value = 0.00625 (Fisher's exact test), Q value = 0.045

Table S56.  Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
10Q GAIN MUTATED 0 2 2 3
10Q GAIN WILD-TYPE 2 3 59 201

Figure S56.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

'11p gain' versus 'Time to Death'

P value = 0.0038 (logrank test), Q value = 0.032

Table S57.  Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
11P GAIN MUTATED 10 4 0.5 - 99.1 (11.4)
11P GAIN WILD-TYPE 272 40 0.1 - 194.8 (25.2)

Figure S57.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0491 (Fisher's exact test), Q value = 0.2

Table S58.  Gene #20: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
11P GAIN MUTATED 4 0 4 2
11P GAIN WILD-TYPE 167 22 48 13

Figure S58.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

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

Table S59.  Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
11P GAIN MUTATED 4 2 5
11P GAIN WILD-TYPE 186 31 57

Figure S59.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

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

Table S60.  Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
11P GAIN MUTATED 2 2
11P GAIN WILD-TYPE 91 7

Figure S60.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11q gain' versus 'Time to Death'

P value = 0.0605 (logrank test), Q value = 0.23

Table S61.  Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
11Q GAIN MUTATED 10 3 0.5 - 99.1 (12.5)
11Q GAIN WILD-TYPE 272 41 0.1 - 194.8 (25.2)

Figure S61.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0505 (Wilcoxon-test), Q value = 0.21

Table S62.  Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
11Q GAIN MUTATED 10 53.6 (14.8)
11Q GAIN WILD-TYPE 272 61.7 (11.9)

Figure S62.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'GENDER'

P value = 0.024 (Fisher's exact test), Q value = 0.12

Table S63.  Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
11Q GAIN MUTATED 6 4
11Q GAIN WILD-TYPE 70 207

Figure S63.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

'12p gain' versus 'GENDER'

P value = 0.0198 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
12P GAIN MUTATED 21 91
12P GAIN WILD-TYPE 55 120

Figure S64.  Get High-res Image Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'GENDER'

P value = 0.0198 (Fisher's exact test), Q value = 0.11

Table S65.  Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
12Q GAIN MUTATED 21 91
12Q GAIN WILD-TYPE 55 120

Figure S65.  Get High-res Image Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

'14q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0367 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #25: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
14Q GAIN MUTATED 0 0 3 0
14Q GAIN WILD-TYPE 171 22 49 15

Figure S66.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

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

Table S67.  Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
14Q GAIN MUTATED 0 0 3
14Q GAIN WILD-TYPE 190 33 59

Figure S67.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.079

Table S68.  Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
16P GAIN MUTATED 151 63.0 (11.6)
16P GAIN WILD-TYPE 131 59.6 (12.4)

Figure S68.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'GENDER'

P value = 0.00121 (Fisher's exact test), Q value = 0.014

Table S69.  Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
16P GAIN MUTATED 28 125
16P GAIN WILD-TYPE 48 86

Figure S69.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

'16p gain' versus 'RACE'

P value = 0.00141 (Fisher's exact test), Q value = 0.015

Table S70.  Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
16P GAIN MUTATED 2 3 21 120
16P GAIN WILD-TYPE 0 2 40 84

Figure S70.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

'16q gain' versus 'Time to Death'

P value = 0.0384 (logrank test), Q value = 0.17

Table S71.  Gene #28: '16q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
16Q GAIN MUTATED 144 17 0.1 - 194.8 (25.0)
16Q GAIN WILD-TYPE 138 27 0.1 - 103.6 (23.8)

Figure S71.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #1: 'Time to Death'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0291 (Wilcoxon-test), Q value = 0.14

Table S72.  Gene #28: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
16Q GAIN MUTATED 146 62.9 (11.6)
16Q GAIN WILD-TYPE 136 59.8 (12.5)

Figure S72.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'GENDER'

P value = 0.0032 (Fisher's exact test), Q value = 0.028

Table S73.  Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
16Q GAIN MUTATED 28 120
16Q GAIN WILD-TYPE 48 91

Figure S73.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

'16q gain' versus 'RACE'

P value = 0.00956 (Fisher's exact test), Q value = 0.062

Table S74.  Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
16Q GAIN MUTATED 2 3 22 115
16Q GAIN WILD-TYPE 0 2 39 89

Figure S74.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

'17p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0029

Table S75.  Gene #29: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
17P GAIN MUTATED 118 15 19 6
17P GAIN WILD-TYPE 53 7 33 9

Figure S75.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0063

Table S76.  Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
17P GAIN MUTATED 127 22 24
17P GAIN WILD-TYPE 63 11 38

Figure S76.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'GENDER'

P value = 0.0142 (Fisher's exact test), Q value = 0.084

Table S77.  Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
17P GAIN MUTATED 37 137
17P GAIN WILD-TYPE 39 74

Figure S77.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

'17q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0327 (Fisher's exact test), Q value = 0.15

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
17Q GAIN MUTATED 122 16 26 9
17Q GAIN WILD-TYPE 49 6 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'

'21q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

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

Table S80.  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 S80.  Get High-res Image Gene #37: '21q gain' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00474 (Fisher's exact test), Q value = 0.037

Table S81.  Gene #39: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
XP GAIN MUTATED 62 6 6 4
XP GAIN WILD-TYPE 109 16 46 11

Figure S81.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00563 (Fisher's exact test), Q value = 0.042

Table S82.  Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
XP GAIN MUTATED 67 11 9
XP GAIN WILD-TYPE 123 22 53

Figure S82.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'GENDER'

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

Table S83.  Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
XP GAIN MUTATED 15 72
XP GAIN WILD-TYPE 61 139

Figure S83.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0339 (Fisher's exact test), Q value = 0.16

Table S84.  Gene #40: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
XQ GAIN MUTATED 62 6 8 4
XQ GAIN WILD-TYPE 109 16 44 11

Figure S84.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0225 (Fisher's exact test), Q value = 0.11

Table S85.  Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
XQ GAIN MUTATED 68 12 11
XQ GAIN WILD-TYPE 122 21 51

Figure S85.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'GENDER'

P value = 0.0216 (Fisher's exact test), Q value = 0.11

Table S86.  Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
XQ GAIN MUTATED 16 75
XQ GAIN WILD-TYPE 60 136

Figure S86.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0387 (Fisher's exact test), Q value = 0.17

Table S87.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
1P LOSS MUTATED 14 5 11
1P LOSS WILD-TYPE 176 28 51

Figure S87.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'2p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0288 (Fisher's exact test), Q value = 0.14

Table S88.  Gene #43: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
2P LOSS MUTATED 0 0 2 1
2P LOSS WILD-TYPE 171 22 50 14

Figure S88.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0521 (Fisher's exact test), Q value = 0.21

Table S89.  Gene #43: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
2P LOSS MUTATED 1 1 3
2P LOSS WILD-TYPE 189 32 59

Figure S89.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'Time to Death'

P value = 0.000325 (logrank test), Q value = 0.0047

Table S90.  Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
3P LOSS MUTATED 22 8 2.0 - 86.3 (14.5)
3P LOSS WILD-TYPE 260 36 0.1 - 194.8 (25.2)

Figure S90.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0205 (Wilcoxon-test), Q value = 0.11

Table S91.  Gene #45: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
3P LOSS MUTATED 21 54.8 (12.4)
3P LOSS WILD-TYPE 261 61.9 (11.9)

Figure S91.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S92.  Gene #45: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
3P LOSS MUTATED 5 1 12 3
3P LOSS WILD-TYPE 166 21 40 12

Figure S92.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S93.  Gene #45: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
3P LOSS MUTATED 6 3 13
3P LOSS WILD-TYPE 184 30 49

Figure S93.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'Time to Death'

P value = 1.25e-05 (logrank test), Q value = 0.00031

Table S94.  Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
3Q LOSS MUTATED 7 4 3.7 - 54.6 (19.4)
3Q LOSS WILD-TYPE 275 40 0.1 - 194.8 (25.1)

Figure S94.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0423 (Fisher's exact test), Q value = 0.18

Table S95.  Gene #46: '3q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
3Q LOSS MUTATED 2 0 2 2
3Q LOSS WILD-TYPE 169 22 50 13

Figure S95.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0143 (Fisher's exact test), Q value = 0.084

Table S96.  Gene #46: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
3Q LOSS MUTATED 2 0 5
3Q LOSS WILD-TYPE 188 33 57

Figure S96.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0137 (Fisher's exact test), Q value = 0.083

Table S97.  Gene #46: '3q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
3Q LOSS MUTATED 1 2 2
3Q LOSS WILD-TYPE 47 22 3

Figure S97.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'Time to Death'

P value = 3.89e-10 (logrank test), Q value = 8.6e-08

Table S98.  Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
4P LOSS MUTATED 24 12 2.0 - 79.9 (17.5)
4P LOSS WILD-TYPE 258 32 0.1 - 194.8 (25.5)

Figure S98.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00368 (Wilcoxon-test), Q value = 0.031

Table S99.  Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
4P LOSS MUTATED 24 53.1 (15.1)
4P LOSS WILD-TYPE 258 62.2 (11.5)

Figure S99.  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 = 0.00025

Table S100.  Gene #47: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
4P LOSS MUTATED 4 1 15 2
4P LOSS WILD-TYPE 167 21 37 13

Figure S100.  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 = 0.00025

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

nPatients T1 T2 T3+T4
ALL 190 33 62
4P LOSS MUTATED 5 3 17
4P LOSS WILD-TYPE 185 30 45

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

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00061 (Fisher's exact test), Q value = 0.0079

Table S102.  Gene #47: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
4P LOSS MUTATED 3 10 1
4P LOSS WILD-TYPE 45 14 4

Figure S102.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'GENDER'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.00074

Table S103.  Gene #47: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
4P LOSS MUTATED 16 9
4P LOSS WILD-TYPE 60 202

Figure S103.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'Time to Death'

P value = 3.35e-10 (logrank test), Q value = 8.6e-08

Table S104.  Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
4Q LOSS MUTATED 25 12 2.0 - 79.9 (16.9)
4Q LOSS WILD-TYPE 257 32 0.1 - 194.8 (25.6)

Figure S104.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0211 (Wilcoxon-test), Q value = 0.11

Table S105.  Gene #48: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
4Q LOSS MUTATED 25 55.0 (14.7)
4Q LOSS WILD-TYPE 257 62.0 (11.7)

Figure S105.  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 = 0.00025

Table S106.  Gene #48: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
4Q LOSS MUTATED 5 1 14 3
4Q LOSS WILD-TYPE 166 21 38 12

Figure S106.  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 = 0.00025

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

nPatients T1 T2 T3+T4
ALL 190 33 62
4Q LOSS MUTATED 6 4 16
4Q LOSS WILD-TYPE 184 29 46

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

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00914 (Fisher's exact test), Q value = 0.06

Table S108.  Gene #48: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
4Q LOSS MUTATED 4 9 1
4Q LOSS WILD-TYPE 44 15 4

Figure S108.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'GENDER'

P value = 0.000623 (Fisher's exact test), Q value = 0.0079

Table S109.  Gene #48: '4q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
4Q LOSS MUTATED 15 11
4Q LOSS WILD-TYPE 61 200

Figure S109.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #7: 'GENDER'

'5p loss' versus 'Time to Death'

P value = 1.74e-10 (logrank test), Q value = 7.7e-08

Table S110.  Gene #49: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
5P LOSS MUTATED 8 5 2.8 - 30.5 (14.6)
5P LOSS WILD-TYPE 274 39 0.1 - 194.8 (25.2)

Figure S110.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0507 (Wilcoxon-test), Q value = 0.21

Table S111.  Gene #49: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
5P LOSS MUTATED 8 50.9 (15.6)
5P LOSS WILD-TYPE 274 61.7 (11.9)

Figure S111.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.11

Table S112.  Gene #49: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
5P LOSS MUTATED 2 0 3 2
5P LOSS WILD-TYPE 169 22 49 13

Figure S112.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00387 (Fisher's exact test), Q value = 0.032

Table S113.  Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
5P LOSS MUTATED 2 0 6
5P LOSS WILD-TYPE 188 33 56

Figure S113.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.065

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

nPatients N0 N1 N2
ALL 48 24 5
5P LOSS MUTATED 0 3 1
5P LOSS WILD-TYPE 48 21 4

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

'5p loss' versus 'GENDER'

P value = 0.0327 (Fisher's exact test), Q value = 0.15

Table S115.  Gene #49: '5p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
5P LOSS MUTATED 5 3
5P LOSS WILD-TYPE 71 208

Figure S115.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #7: 'GENDER'

'5q loss' versus 'Time to Death'

P value = 1.47e-07 (logrank test), Q value = 1.1e-05

Table S116.  Gene #50: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
5Q LOSS MUTATED 8 4 2.8 - 30.5 (14.4)
5Q LOSS WILD-TYPE 274 40 0.1 - 194.8 (25.2)

Figure S116.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0124 (Wilcoxon-test), Q value = 0.076

Table S117.  Gene #50: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
5Q LOSS MUTATED 8 46.9 (17.0)
5Q LOSS WILD-TYPE 274 61.8 (11.7)

Figure S117.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0358 (Fisher's exact test), Q value = 0.16

Table S118.  Gene #50: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
5Q LOSS MUTATED 2 0 4 1
5Q LOSS WILD-TYPE 169 22 48 14

Figure S118.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00438 (Fisher's exact test), Q value = 0.035

Table S119.  Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
5Q LOSS MUTATED 2 0 6
5Q LOSS WILD-TYPE 188 33 56

Figure S119.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0183 (Fisher's exact test), Q value = 0.1

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

nPatients N0 N1 N2
ALL 48 24 5
5Q LOSS MUTATED 0 4 0
5Q LOSS WILD-TYPE 48 20 5

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

'5q loss' versus 'GENDER'

P value = 0.0327 (Fisher's exact test), Q value = 0.15

Table S121.  Gene #50: '5q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
5Q LOSS MUTATED 5 3
5Q LOSS WILD-TYPE 71 208

Figure S121.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #7: 'GENDER'

'6p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00916 (Fisher's exact test), Q value = 0.06

Table S122.  Gene #51: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
6P LOSS MUTATED 8 0 9 2
6P LOSS WILD-TYPE 163 22 43 13

Figure S122.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0208 (Fisher's exact test), Q value = 0.11

Table S123.  Gene #51: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
6P LOSS MUTATED 10 1 10
6P LOSS WILD-TYPE 180 32 52

Figure S123.  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 = 0.16

Table S124.  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 S124.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.021 (Fisher's exact test), Q value = 0.11

Table S125.  Gene #52: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
6Q LOSS MUTATED 12 0 10 2
6Q LOSS WILD-TYPE 159 22 42 13

Figure S125.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00071 (Fisher's exact test), Q value = 0.0088

Table S126.  Gene #52: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
6Q LOSS MUTATED 13 0 13
6Q LOSS WILD-TYPE 177 33 49

Figure S126.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'GENDER'

P value = 0.033 (Fisher's exact test), Q value = 0.15

Table S127.  Gene #52: '6q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
6Q LOSS MUTATED 12 14
6Q LOSS WILD-TYPE 64 197

Figure S127.  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 = 0.1

Table S128.  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 S128.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'RACE'

P value = 0.0484 (Fisher's exact test), Q value = 0.2

Table S129.  Gene #52: '6q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
6Q LOSS MUTATED 0 2 2 19
6Q LOSS WILD-TYPE 2 3 59 185

Figure S129.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #11: 'RACE'

'8p loss' versus 'Time to Death'

P value = 0.00157 (logrank test), Q value = 0.016

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
8P LOSS MUTATED 16 6 1.2 - 67.2 (17.5)
8P LOSS WILD-TYPE 266 38 0.1 - 194.8 (25.0)

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

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0365 (Fisher's exact test), Q value = 0.16

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
8P LOSS MUTATED 6 2 2 3
8P LOSS WILD-TYPE 165 20 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 = 0.0251 (Fisher's exact test), Q value = 0.12

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

nPatients N0 N1 N2
ALL 48 24 5
8P LOSS MUTATED 1 5 0
8P LOSS WILD-TYPE 47 19 5

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 = 0.0142 (Fisher's exact test), Q value = 0.084

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

nPatients 0 1
ALL 93 9
8P LOSS MUTATED 4 3
8P LOSS WILD-TYPE 89 6

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

'8p loss' versus 'RACE'

P value = 0.0516 (Fisher's exact test), Q value = 0.21

Table S134.  Gene #53: '8p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
8P LOSS MUTATED 0 2 2 12
8P LOSS WILD-TYPE 2 3 59 192

Figure S134.  Get High-res Image Gene #53: '8p loss' versus Clinical Feature #11: 'RACE'

'8q loss' versus 'GENDER'

P value = 0.0584 (Fisher's exact test), Q value = 0.23

Table S135.  Gene #54: '8q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
8Q LOSS MUTATED 5 4
8Q LOSS WILD-TYPE 71 207

Figure S135.  Get High-res Image Gene #54: '8q loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'Time to Death'

P value = 1.47e-07 (logrank test), Q value = 1.1e-05

Table S136.  Gene #55: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
9P LOSS MUTATED 32 14 2.0 - 93.3 (18.4)
9P LOSS WILD-TYPE 250 30 0.1 - 194.8 (25.7)

Figure S136.  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 = 0.00025

Table S137.  Gene #55: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
9P LOSS MUTATED 9 0 15 6
9P LOSS WILD-TYPE 162 22 37 9

Figure S137.  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 = 0.00025

Table S138.  Gene #55: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
9P LOSS MUTATED 10 3 20
9P LOSS WILD-TYPE 180 30 42

Figure S138.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00332 (Fisher's exact test), Q value = 0.029

Table S139.  Gene #55: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
9P LOSS MUTATED 6 10 3
9P LOSS WILD-TYPE 42 14 2

Figure S139.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'GENDER'

P value = 0.00125 (Fisher's exact test), Q value = 0.014

Table S140.  Gene #55: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
9P LOSS MUTATED 17 16
9P LOSS WILD-TYPE 59 195

Figure S140.  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 S141.  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 S141.  Get High-res Image Gene #55: '9p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'Time to Death'

P value = 4.88e-06 (logrank test), Q value = 0.00025

Table S142.  Gene #56: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
9Q LOSS MUTATED 32 12 2.0 - 93.3 (18.4)
9Q LOSS WILD-TYPE 250 32 0.1 - 194.8 (25.6)

Figure S142.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00074

Table S143.  Gene #56: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
9Q LOSS MUTATED 10 1 15 5
9Q LOSS WILD-TYPE 161 21 37 10

Figure S143.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S144.  Gene #56: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
9Q LOSS MUTATED 11 1 21
9Q LOSS WILD-TYPE 179 32 41

Figure S144.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00478 (Fisher's exact test), Q value = 0.037

Table S145.  Gene #56: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
9Q LOSS MUTATED 5 8 3
9Q LOSS WILD-TYPE 43 16 2

Figure S145.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'GENDER'

P value = 0.00125 (Fisher's exact test), Q value = 0.014

Table S146.  Gene #56: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
9Q LOSS MUTATED 17 16
9Q LOSS WILD-TYPE 59 195

Figure S146.  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 = 0.012

Table S147.  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 S147.  Get High-res Image Gene #56: '9q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'Time to Death'

P value = 0.0365 (logrank test), Q value = 0.16

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
10P LOSS MUTATED 16 5 2.1 - 91.7 (19.9)
10P LOSS WILD-TYPE 266 39 0.1 - 194.8 (25.2)

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

'10p loss' versus 'PATHOLOGIC_STAGE'

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

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
10P LOSS MUTATED 4 0 8 2
10P LOSS WILD-TYPE 167 22 44 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 = 0.00513 (Fisher's exact test), Q value = 0.039

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

nPatients T1 T2 T3+T4
ALL 190 33 62
10P LOSS MUTATED 6 1 9
10P LOSS WILD-TYPE 184 32 53

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 = 0.00247 (logrank test), Q value = 0.023

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
10Q LOSS MUTATED 17 7 2.1 - 91.7 (19.3)
10Q LOSS WILD-TYPE 265 37 0.1 - 194.8 (25.1)

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

'10q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0029

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
10Q LOSS MUTATED 4 0 10 2
10Q LOSS WILD-TYPE 167 22 42 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 = 0.00142 (Fisher's exact test), Q value = 0.015

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

nPatients T1 T2 T3+T4
ALL 190 33 62
10Q LOSS MUTATED 6 1 10
10Q LOSS WILD-TYPE 184 32 52

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 = 0.0266 (Fisher's exact test), Q value = 0.13

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

nPatients N0 N1 N2
ALL 48 24 5
10Q LOSS MUTATED 2 6 1
10Q LOSS WILD-TYPE 46 18 4

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 = 0.073

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 = 0.000186 (logrank test), Q value = 0.0029

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
11P LOSS MUTATED 17 6 2.0 - 54.6 (19.3)
11P LOSS WILD-TYPE 265 38 0.1 - 194.8 (25.2)

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

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00665 (Fisher's exact test), Q value = 0.046

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
11P LOSS MUTATED 5 2 6 3
11P LOSS WILD-TYPE 166 20 46 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 = 0.00028 (Fisher's exact test), Q value = 0.0041

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

nPatients T1 T2 T3+T4
ALL 190 33 62
11P LOSS MUTATED 5 2 11
11P LOSS WILD-TYPE 185 31 51

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 = 0.00725 (Fisher's exact test), Q value = 0.049

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

nPatients N0 N1 N2
ALL 48 24 5
11P LOSS MUTATED 1 4 2
11P LOSS WILD-TYPE 47 20 3

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 = 0.000161 (logrank test), Q value = 0.0025

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
11Q LOSS MUTATED 20 8 0.4 - 123.6 (15.7)
11Q LOSS WILD-TYPE 262 36 0.1 - 194.8 (25.2)

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 = 0.00025

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
11Q LOSS MUTATED 3 1 11 5
11Q LOSS WILD-TYPE 168 21 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 = 0.00025

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

nPatients T1 T2 T3+T4
ALL 190 33 62
11Q LOSS MUTATED 3 2 16
11Q LOSS WILD-TYPE 187 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 = 0.00411 (Fisher's exact test), Q value = 0.034

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

nPatients N0 N1 N2
ALL 48 24 5
11Q LOSS MUTATED 3 6 3
11Q LOSS WILD-TYPE 45 18 2

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 = 0.075

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 = 9.42e-08 (logrank test), Q value = 8.4e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
13Q LOSS MUTATED 24 10 0.2 - 86.8 (15.5)
13Q LOSS WILD-TYPE 258 34 0.1 - 194.8 (25.5)

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 = 0.00304 (Wilcoxon-test), Q value = 0.028

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

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
13Q LOSS MUTATED 24 52.8 (15.3)
13Q LOSS WILD-TYPE 258 62.2 (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 = 0.00029 (Fisher's exact test), Q value = 0.0042

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
13Q LOSS MUTATED 7 1 12 3
13Q LOSS WILD-TYPE 164 21 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 = 0.00043

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

nPatients T1 T2 T3+T4
ALL 190 33 62
13Q LOSS MUTATED 7 2 15
13Q LOSS WILD-TYPE 183 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 = 0.00572 (Fisher's exact test), Q value = 0.042

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

nPatients N0 N1 N2
ALL 48 24 5
13Q LOSS MUTATED 3 7 2
13Q LOSS WILD-TYPE 45 17 3

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

'13q loss' versus 'GENDER'

P value = 1.82e-05 (Fisher's exact test), Q value = 0.00043

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

nPatients FEMALE MALE
ALL 76 211
13Q LOSS MUTATED 16 8
13Q LOSS WILD-TYPE 60 203

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 = 0.24

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 = 0.00014 (logrank test), Q value = 0.0023

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
14Q LOSS MUTATED 47 14 0.1 - 80.9 (19.4)
14Q LOSS WILD-TYPE 235 30 0.1 - 194.8 (25.4)

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

'14q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00206 (Fisher's exact test), Q value = 0.019

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
14Q LOSS MUTATED 18 3 14 6
14Q LOSS WILD-TYPE 153 19 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 = 4e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients T1 T2 T3+T4
ALL 190 33 62
14Q LOSS MUTATED 20 5 22
14Q LOSS WILD-TYPE 170 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 = 0.00628 (Fisher's exact test), Q value = 0.045

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

nPatients N0 N1 N2
ALL 48 24 5
14Q LOSS MUTATED 8 8 4
14Q LOSS WILD-TYPE 40 16 1

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

'14q loss' versus 'GENDER'

P value = 0.00345 (Fisher's exact test), Q value = 0.03

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

nPatients FEMALE MALE
ALL 76 211
14Q LOSS MUTATED 21 26
14Q LOSS WILD-TYPE 55 185

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 = 0.059

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 = 0.0071 (logrank test), Q value = 0.049

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
15Q LOSS MUTATED 30 9 0.1 - 194.8 (18.4)
15Q LOSS WILD-TYPE 252 35 0.1 - 129.9 (25.6)

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

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00151 (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 22 52 15
15Q LOSS MUTATED 11 1 10 5
15Q LOSS WILD-TYPE 160 21 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 = 0.00036 (Fisher's exact test), Q value = 0.005

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

nPatients T1 T2 T3+T4
ALL 190 33 62
15Q LOSS MUTATED 13 2 16
15Q LOSS WILD-TYPE 177 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 = 0.0117 (Fisher's exact test), Q value = 0.073

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

nPatients N0 N1 N2
ALL 48 24 5
15Q LOSS MUTATED 4 8 2
15Q LOSS WILD-TYPE 44 16 3

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 = 2.51e-08 (logrank test), Q value = 2.8e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
16P LOSS MUTATED 3 3 11.1 - 21.6 (19.6)
16P LOSS WILD-TYPE 279 41 0.1 - 194.8 (24.9)

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 = 0.0656 (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 190 33 62
16P LOSS MUTATED 1 0 3
16P LOSS WILD-TYPE 189 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 = 0.0582 (Fisher's exact test), Q value = 0.23

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

nPatients FEMALE MALE
ALL 76 211
16P LOSS MUTATED 3 1
16P LOSS WILD-TYPE 73 210

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

'16q loss' versus 'Time to Death'

P value = 7.13e-08 (logrank test), Q value = 7e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
16Q LOSS MUTATED 6 5 11.1 - 51.5 (18.3)
16Q LOSS WILD-TYPE 276 39 0.1 - 194.8 (25.0)

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

'16q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00495 (Fisher's exact test), Q value = 0.038

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
16Q LOSS MUTATED 1 0 5 1
16Q LOSS WILD-TYPE 170 22 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 = 0.0149 (Fisher's exact test), Q value = 0.087

Table S188.  Gene #65: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
16Q LOSS MUTATED 2 0 5
16Q LOSS WILD-TYPE 188 33 57

Figure S188.  Get High-res Image Gene #65: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'Time to Death'

P value = 6.36e-10 (logrank test), Q value = 9.6e-08

Table S189.  Gene #66: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
17P LOSS MUTATED 10 7 0.2 - 67.4 (13.4)
17P LOSS WILD-TYPE 272 37 0.1 - 194.8 (25.2)

Figure S189.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'PATHOLOGIC_STAGE'

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

Table S190.  Gene #66: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
17P LOSS MUTATED 1 1 3 3
17P LOSS WILD-TYPE 170 21 49 12

Figure S190.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00186 (Fisher's exact test), Q value = 0.018

Table S191.  Gene #66: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
17P LOSS MUTATED 2 3 6
17P LOSS WILD-TYPE 188 30 56

Figure S191.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00419 (Fisher's exact test), Q value = 0.034

Table S192.  Gene #66: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
17P LOSS MUTATED 2 1 3
17P LOSS WILD-TYPE 46 23 2

Figure S192.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

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

Table S193.  Gene #66: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
17P LOSS MUTATED 2 2
17P LOSS WILD-TYPE 91 7

Figure S193.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0251 (Wilcoxon-test), Q value = 0.12

Table S194.  Gene #66: '17p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
17P LOSS MUTATED 3 46.7 (45.1)
17P LOSS WILD-TYPE 73 89.2 (19.4)

Figure S194.  Get High-res Image Gene #66: '17p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'18p loss' versus 'Time to Death'

P value = 3.05e-07 (logrank test), Q value = 2.1e-05

Table S195.  Gene #67: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
18P LOSS MUTATED 41 15 2.0 - 123.6 (16.0)
18P LOSS WILD-TYPE 241 29 0.1 - 194.8 (26.0)

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 = 0.00025

Table S196.  Gene #67: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
18P LOSS MUTATED 13 1 17 6
18P LOSS WILD-TYPE 158 21 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 = 0.00025

Table S197.  Gene #67: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
18P LOSS MUTATED 14 4 24
18P LOSS WILD-TYPE 176 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 = 0.00643 (Fisher's exact test), Q value = 0.045

Table S198.  Gene #67: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
18P LOSS MUTATED 6 9 3
18P LOSS WILD-TYPE 42 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 = 0.0596 (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 93 9
18P LOSS MUTATED 15 4
18P LOSS WILD-TYPE 78 5

Figure S199.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'GENDER'

P value = 0.0363 (Fisher's exact test), Q value = 0.16

Table S200.  Gene #67: '18p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
18P LOSS MUTATED 17 25
18P LOSS WILD-TYPE 59 186

Figure S200.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #7: 'GENDER'

'18q loss' versus 'Time to Death'

P value = 2.16e-08 (logrank test), Q value = 2.7e-06

Table S201.  Gene #68: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
18Q LOSS MUTATED 44 17 0.4 - 123.6 (16.2)
18Q LOSS WILD-TYPE 238 27 0.1 - 194.8 (26.0)

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 = 0.00025

Table S202.  Gene #68: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
18Q LOSS MUTATED 13 1 20 6
18Q LOSS WILD-TYPE 158 21 32 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 = 0.00025

Table S203.  Gene #68: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
18Q LOSS MUTATED 15 5 25
18Q LOSS WILD-TYPE 175 28 37

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 = 0.00059 (Fisher's exact test), Q value = 0.0077

Table S204.  Gene #68: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
18Q LOSS MUTATED 6 12 3
18Q LOSS WILD-TYPE 42 12 2

Figure S204.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'Time to Death'

P value = 0.0188 (logrank test), Q value = 0.1

Table S205.  Gene #69: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
19P LOSS MUTATED 17 5 0.9 - 99.1 (18.2)
19P LOSS WILD-TYPE 265 39 0.1 - 194.8 (25.1)

Figure S205.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00478 (Fisher's exact test), Q value = 0.037

Table S206.  Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
19P LOSS MUTATED 4 1 8 1
19P LOSS WILD-TYPE 167 21 44 14

Figure S206.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0015 (Fisher's exact test), Q value = 0.016

Table S207.  Gene #69: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
19P LOSS MUTATED 6 1 10
19P LOSS WILD-TYPE 184 32 52

Figure S207.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00841 (Fisher's exact test), Q value = 0.057

Table S208.  Gene #69: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
19P LOSS MUTATED 1 3 2
19P LOSS WILD-TYPE 47 21 3

Figure S208.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.00016 (logrank test), Q value = 0.0025

Table S209.  Gene #70: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
19Q LOSS MUTATED 16 6 0.9 - 54.6 (17.6)
19Q LOSS WILD-TYPE 266 38 0.1 - 194.8 (25.0)

Figure S209.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGIC_STAGE'

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

Table S210.  Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
19Q LOSS MUTATED 2 1 10 1
19Q LOSS WILD-TYPE 169 21 42 14

Figure S210.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S211.  Gene #70: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
19Q LOSS MUTATED 3 1 12
19Q LOSS WILD-TYPE 187 32 50

Figure S211.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00893 (Fisher's exact test), Q value = 0.059

Table S212.  Gene #70: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
19Q LOSS MUTATED 1 3 2
19Q LOSS WILD-TYPE 47 21 3

Figure S212.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00362 (Fisher's exact test), Q value = 0.031

Table S213.  Gene #71: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
21Q LOSS MUTATED 17 3 14 5
21Q LOSS WILD-TYPE 154 19 38 10

Figure S213.  Get High-res Image Gene #71: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0049

Table S214.  Gene #71: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
21Q LOSS MUTATED 18 6 19
21Q LOSS WILD-TYPE 172 27 43

Figure S214.  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 = 0.042

Table S215.  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 S215.  Get High-res Image Gene #71: '21q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'Time to Death'

P value = 0.00122 (logrank test), Q value = 0.014

Table S216.  Gene #72: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
22Q LOSS MUTATED 60 15 0.9 - 123.6 (18.8)
22Q LOSS WILD-TYPE 222 29 0.1 - 194.8 (25.6)

Figure S216.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S217.  Gene #72: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
22Q LOSS MUTATED 20 3 25 8
22Q LOSS WILD-TYPE 151 19 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 = 0.00025

Table S218.  Gene #72: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
22Q LOSS MUTATED 24 5 31
22Q LOSS WILD-TYPE 166 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 = 0.0113 (Fisher's exact test), Q value = 0.072

Table S219.  Gene #72: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
22Q LOSS MUTATED 11 14 2
22Q LOSS WILD-TYPE 37 10 3

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 = 0.0448 (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 93 9
22Q LOSS MUTATED 21 5
22Q LOSS WILD-TYPE 72 4

Figure S220.  Get High-res Image Gene #72: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'GENDER'

P value = 0.000481 (Fisher's exact test), Q value = 0.0064

Table S221.  Gene #72: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
22Q LOSS MUTATED 27 33
22Q LOSS WILD-TYPE 49 178

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 = 9.66e-06 (logrank test), Q value = 0.00025

Table S223.  Gene #73: 'xp loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
XP LOSS MUTATED 34 13 0.4 - 91.7 (18.1)
XP LOSS WILD-TYPE 248 31 0.1 - 194.8 (25.7)

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 = 0.00025

Table S224.  Gene #73: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
XP LOSS MUTATED 8 1 15 4
XP LOSS WILD-TYPE 163 21 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 = 2e-05 (Fisher's exact test), Q value = 0.00043

Table S225.  Gene #73: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
XP LOSS MUTATED 11 4 19
XP LOSS WILD-TYPE 179 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 = 0.0153 (Fisher's exact test), Q value = 0.088

Table S226.  Gene #73: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
XP LOSS MUTATED 5 9 1
XP LOSS WILD-TYPE 43 15 4

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 = 0.0192 (Wilcoxon-test), Q value = 0.1

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 10 70.0 (35.0)
XP LOSS WILD-TYPE 66 90.2 (18.4)

Figure S227.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xp loss' versus 'RACE'

P value = 0.0158 (Fisher's exact test), Q value = 0.091

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 5 61 204
XP LOSS MUTATED 0 3 10 20
XP LOSS WILD-TYPE 2 2 51 184

Figure S228.  Get High-res Image Gene #73: 'xp loss' versus Clinical Feature #11: 'RACE'

'xq loss' versus 'Time to Death'

P value = 6.38e-07 (logrank test), Q value = 4e-05

Table S229.  Gene #74: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
XQ LOSS MUTATED 30 13 0.4 - 91.7 (17.5)
XQ LOSS WILD-TYPE 252 31 0.1 - 194.8 (25.6)

Figure S229.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.0579 (Wilcoxon-test), Q value = 0.23

Table S230.  Gene #74: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
XQ LOSS MUTATED 30 56.4 (14.7)
XQ LOSS WILD-TYPE 252 62.0 (11.6)

Figure S230.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S231.  Gene #74: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
XQ LOSS MUTATED 8 1 13 4
XQ LOSS WILD-TYPE 163 21 39 11

Figure S231.  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 = 0.00043

Table S232.  Gene #74: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
XQ LOSS MUTATED 10 3 17
XQ LOSS WILD-TYPE 180 30 45

Figure S232.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00936 (Fisher's exact test), Q value = 0.061

Table S233.  Gene #74: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
XQ LOSS MUTATED 4 9 1
XQ LOSS WILD-TYPE 44 15 4

Figure S233.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0192 (Wilcoxon-test), Q value = 0.1

Table S234.  Gene #74: 'xq loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
XQ LOSS MUTATED 10 70.0 (35.0)
XQ LOSS WILD-TYPE 66 90.2 (18.4)

Figure S234.  Get High-res Image Gene #74: 'xq loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'RACE'

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

Table S235.  Gene #74: 'xq loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 61 204
XQ LOSS MUTATED 0 3 8 18
XQ LOSS WILD-TYPE 2 2 53 186

Figure S235.  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/19781623/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/19775272/KIRP-TP.merged_data.txt

  • Number of patients = 287

  • 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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