Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1PN94PV
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/C1PN94PV
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 73 arm-level events and 12 clinical features across 269 patients, 219 significant findings detected with Q value < 0.25.

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

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

  • 2p gain cnv correlated to 'PATHOLOGY_M_STAGE'.

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

  • 3p gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 3q gain cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

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

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

  • 8q gain cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'RACE'.

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

  • 10p gain cnv correlated to 'RACE'.

  • 10q gain cnv correlated to 'RACE'.

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

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

  • 16q gain cnv correlated to 'GENDER' and 'RACE'.

  • 17p gain cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

  • 17q gain cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'RACE'.

  • xp gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • xq gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

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

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

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

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

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

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

  • 6q loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

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

  • 8q loss cnv correlated to 'Time to Death'.

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

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

  • 10p loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • xq loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 219 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
4q loss 24 (9%) 245 4.13e-05
(0.000963) 		0.0271
(0.151) 		2e-05
(0.000604) 		4e-05
(0.000963) 		0.0242
(0.139) 		0.225
(0.552) 		0.000999
(0.0133) 		0.061
(0.244) 		0.838
(1.00) 		0.274
(0.597) 		0.106
(0.347) 		1
(1.00)
22q loss 57 (21%) 212 0.0581
(0.236) 		0.0357
(0.178) 		1e-05
(0.000412) 		1e-05
(0.000412) 		0.00664
(0.0529) 		0.0427
(0.194) 		0.000624
(0.00927) 		0.164
(0.454) 		0.986
(1.00) 		0.135
(0.409) 		0.208
(0.52) 		0.706
(1.00)
4p loss 23 (9%) 246 4.18e-05
(0.000963) 		0.00449
(0.0385) 		1e-05
(0.000412) 		1e-05
(0.000412) 		0.00198
(0.0231) 		0.592
(0.936) 		5.85e-05
(0.00125) 		0.0967
(0.327) 		0.767
(1.00) 		0.189
(0.491) 		0.0877
(0.307) 		1
(1.00)
5p loss 8 (3%) 261 1.28e-10
(1.12e-07) 		0.0535
(0.223) 		0.0202
(0.125) 		0.00334
(0.0332) 		0.02
(0.125) 		0.251
(0.573) 		0.0341
(0.173) 		1
(1.00) 		0.275
(0.597)
5q loss 8 (3%) 261 1.06e-07
(1.33e-05) 		0.013
(0.0889) 		0.0284
(0.154) 		0.00339
(0.0332) 		0.0284
(0.154) 		0.251
(0.573) 		0.0341
(0.173) 		1
(1.00) 		0.275
(0.597)
9p loss 32 (12%) 237 0.000127
(0.00236) 		0.356
(0.699) 		2e-05
(0.000604) 		2e-05
(0.000604) 		0.0142
(0.0949) 		0.0758
(0.283) 		0.00271
(0.0286) 		0.00288
(0.03) 		0.35
(0.698) 		0.64
(0.975) 		0.115
(0.367) 		0.369
(0.712)
9q loss 32 (12%) 237 0.00162
(0.0203) 		0.348
(0.697) 		2e-05
(0.000604) 		1e-05
(0.000412) 		0.0258
(0.147) 		0.336
(0.687) 		0.00271
(0.0286) 		0.00798
(0.0603) 		0.937
(1.00) 		0.766
(1.00) 		0.115
(0.367) 		0.37
(0.712)
13q loss 23 (9%) 246 1.06e-06
(0.000105) 		0.00584
(0.0483) 		0.0002
(0.0035) 		4e-05
(0.000963) 		0.00335
(0.0332) 		0.547
(0.899) 		5.85e-05
(0.00125) 		0.233
(0.554) 		0.707
(1.00) 		0.222
(0.547) 		0.136
(0.41) 		1
(1.00)
14q loss 44 (16%) 225 0.004
(0.035) 		0.56
(0.912) 		0.00111
(0.0143) 		0.00021
(0.00354) 		0.0231
(0.136) 		0.135
(0.409) 		0.00941
(0.0693) 		0.0732
(0.278) 		0.265
(0.594) 		0.0369
(0.184) 		0.954
(1.00) 		0.696
(1.00)
xq loss 27 (10%) 242 2.53e-05
(0.000739) 		0.0535
(0.223) 		0.0001
(0.00195) 		7e-05
(0.00146) 		0.019
(0.122) 		0.225
(0.552) 		0.107
(0.349) 		0.153
(0.434) 		0.624
(0.954) 		0.233
(0.554) 		0.0121
(0.0844) 		0.608
(0.954)
1p gain 8 (3%) 261 3.35e-08
(7.34e-06) 		0.334
(0.685) 		0.0007
(0.0101) 		0.0035
(0.0332) 		0.00576
(0.0481) 		0.174
(0.467) 		0.0341
(0.173) 		0.346
(0.697) 		1
(1.00)
1q gain 16 (6%) 253 4.64e-08
(8.13e-06) 		0.746
(1.00) 		3e-05
(0.000796) 		1e-05
(0.000412) 		0.078
(0.289) 		0.122
(0.379) 		0.0411
(0.191) 		0.0413
(0.191) 		0.268
(0.594) 		0.102
(0.336) 		1
(1.00)
6q gain 8 (3%) 261 3.56e-05
(0.000916) 		0.0746
(0.279) 		0.00188
(0.0224) 		0.00363
(0.0332) 		0.0272
(0.151) 		0.0212
(0.128) 		0.445
(0.792) 		0.656
(0.99) 		0.355
(0.699) 		0.525
(0.884) 		1
(1.00)
8q gain 23 (9%) 246 8.89e-05
(0.00177) 		0.8
(1.00) 		0.00212
(0.0244) 		0.00086
(0.0122) 		0.00345
(0.0332) 		0.154
(0.437) 		0.082
(0.296) 		0.716
(1.00) 		0.505
(0.868) 		0.483
(0.843) 		0.0553
(0.226) 		1
(1.00)
17p gain 165 (61%) 104 0.167
(0.46) 		0.056
(0.228) 		0.00012
(0.00229) 		0.00111
(0.0143) 		0.668
(0.998) 		0.498
(0.859) 		0.024
(0.139) 		0.926
(1.00) 		0.387
(0.727) 		0.206
(0.519) 		0.0479
(0.209) 		0.12
(0.376)
xp gain 82 (30%) 187 0.278
(0.602) 		0.27
(0.594) 		0.00041
(0.00641) 		0.00167
(0.0206) 		0.589
(0.936) 		1
(1.00) 		0.0512
(0.219) 		0.0194
(0.123) 		0.763
(1.00) 		0.041
(0.191) 		0.123
(0.382) 		1
(1.00)
xq gain 85 (32%) 184 0.249
(0.573) 		0.207
(0.519) 		0.00556
(0.0468) 		0.0123
(0.0846) 		0.454
(0.802) 		1
(1.00) 		0.0541
(0.225) 		0.0194
(0.123) 		0.937
(1.00) 		0.041
(0.191) 		0.18
(0.473) 		1
(1.00)
8p loss 13 (5%) 256 4.7e-05
(0.00106) 		0.524
(0.884) 		0.0309
(0.164) 		0.415
(0.765) 		0.0204
(0.125) 		0.0154
(0.103) 		0.116
(0.369) 		0.438
(0.791) 		0.0528
(0.223) 		1
(1.00)
10q loss 15 (6%) 254 0.023
(0.136) 		0.145
(0.423) 		0.00039
(0.00621) 		0.00246
(0.0276) 		0.00624
(0.0506) 		0.251
(0.573) 		0.239
(0.56) 		0.0333
(0.173) 		0.361
(0.703) 		0.155
(0.437) 		0.38
(0.72) 		1
(1.00)
15q loss 29 (11%) 240 0.00993
(0.0719) 		0.0428
(0.194) 		0.00432
(0.0375) 		0.00089
(0.0124) 		0.0404
(0.191) 		0.299
(0.632) 		0.374
(0.715) 		0.0646
(0.255) 		0.355
(0.699) 		0.479
(0.84) 		1
(1.00)
17p loss 8 (3%) 261 4.28e-10
(1.87e-07) 		0.356
(0.699) 		0.00067
(0.00978) 		0.0026
(0.0285) 		0.0275
(0.151) 		0.0403
(0.191) 		0.216
(0.536) 		0.299
(0.632) 		0.913
(1.00) 		1
(1.00) 		1
(1.00)
18p loss 39 (14%) 230 1.04e-05
(0.000412) 		0.0859
(0.305) 		2e-05
(0.000604) 		2e-05
(0.000604) 		0.0106
(0.0755) 		0.0658
(0.256) 		0.0487
(0.209) 		0.233
(0.554) 		0.357
(0.699) 		0.0841
(0.302) 		0.299
(0.632) 		0.674
(1)
xp loss 30 (11%) 239 7.23e-05
(0.00147) 		0.111
(0.36) 		1e-05
(0.000412) 		1e-05
(0.000412) 		0.0471
(0.208) 		0.261
(0.59) 		0.123
(0.382) 		0.153
(0.434) 		0.452
(0.8) 		0.233
(0.554) 		0.0088
(0.0653) 		0.614
(0.954)
6p gain 10 (4%) 259 0.00717
(0.056) 		0.227
(0.554) 		0.00033
(0.00545) 		0.0002
(0.0035) 		0.0731
(0.278) 		0.0403
(0.191) 		0.73
(1.00) 		0.656
(0.99) 		0.967
(1.00) 		0.904
(1.00) 		0.781
(1.00) 		1
(1.00)
7p gain 161 (60%) 108 0.144
(0.422) 		0.411
(0.762) 		0.00094
(0.0129) 		0.0218
(0.131) 		0.668
(0.998) 		0.727
(1.00) 		0.00301
(0.031) 		0.142
(0.418) 		0.764
(1.00) 		0.00359
(0.0332) 		0.307
(0.646) 		0.545
(0.899)
7q gain 162 (60%) 107 0.138
(0.412) 		0.339
(0.687) 		0.00062
(0.00927) 		0.0185
(0.121) 		0.614
(0.954) 		0.728
(1.00) 		0.00189
(0.0224) 		0.142
(0.418) 		0.764
(1.00) 		0.00359
(0.0332) 		0.275
(0.597) 		0.544
(0.898)
11p gain 11 (4%) 258 0.000593
(0.00911) 		0.138
(0.412) 		0.0442
(0.199) 		0.0534
(0.223) 		0.178
(0.472) 		0.0403
(0.191) 		0.17
(0.465) 		0.987
(1.00) 		0.229
(0.554) 		1
(1.00)
3p loss 21 (8%) 248 0.0101
(0.0723) 		0.0239
(0.139) 		2e-05
(0.000604) 		0.00013
(0.00237) 		0.313
(0.654) 		0.0914
(0.318) 		1
(1.00) 		0.351
(0.698) 		0.704
(1.00) 		0.266
(0.594) 		0.535
(0.893) 		0.606
(0.953)
6q loss 24 (9%) 245 0.977
(1.00) 		0.785
(1.00) 		0.0371
(0.184) 		0.0012
(0.0152) 		0.0957
(0.327) 		0.592
(0.936) 		0.0135
(0.0911) 		0.233
(0.554) 		0.351
(0.698) 		0.847
(1.00) 		0.0446
(0.2) 		0.606
(0.953)
10p loss 14 (5%) 255 0.0399
(0.191) 		0.537
(0.893) 		0.00311
(0.0317) 		0.00723
(0.056) 		0.0289
(0.156) 		0.174
(0.467) 		0.212
(0.529) 		0.118
(0.371) 		0.361
(0.703) 		0.155
(0.437) 		0.833
(1.00) 		1
(1.00)
11p loss 16 (6%) 253 0.000207
(0.00354) 		0.195
(0.498) 		0.0194
(0.123) 		0.00651
(0.0523) 		0.0482
(0.209) 		0.386
(0.726) 		0.771
(1.00) 		0.102
(0.336) 		0.754
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 20 (7%) 249 0.0098
(0.0716) 		0.785
(1.00) 		1e-05
(0.000412) 		1e-05
(0.000412) 		0.0196
(0.123) 		0.189
(0.491) 		0.794
(1.00) 		0.153
(0.434) 		0.816
(1.00) 		0.904
(1.00) 		0.115
(0.367) 		1
(1.00)
18q loss 42 (16%) 227 1.08e-06
(0.000105) 		0.164
(0.454) 		1e-05
(0.000412) 		1e-05
(0.000412) 		0.00265
(0.0286) 		0.0785
(0.29) 		0.0874
(0.307) 		0.158
(0.441) 		0.561
(0.912) 		0.18
(0.473) 		0.0817
(0.296) 		1
(1.00)
19q loss 15 (6%) 254 0.0107
(0.0756) 		0.448
(0.795) 		3e-05
(0.000796) 		3e-05
(0.000796) 		0.048
(0.209) 		1
(1.00) 		0.239
(0.56) 		0.0967
(0.327) 		0.739
(1.00) 		0.222
(0.547) 		0.845
(1.00) 		1
(1.00)
2q gain 45 (17%) 224 0.472
(0.829) 		0.338
(0.687) 		0.027
(0.151) 		0.405
(0.755) 		0.0331
(0.173) 		0.00692
(0.0546) 		0.715
(1.00) 		0.381
(0.72) 		0.43
(0.783) 		0.907
(1.00) 		0.75
(1.00) 		1
(1.00)
3p gain 70 (26%) 199 0.234
(0.554) 		0.866
(1.00) 		0.0424
(0.194) 		0.0207
(0.126) 		0.832
(1.00) 		0.107
(0.349) 		0.64
(0.975) 		0.0296
(0.158) 		0.586
(0.936) 		0.341
(0.689) 		0.527
(0.886) 		1
(1.00)
9p gain 3 (1%) 266 0.048
(0.209) 		0.51
(0.87) 		0.0423
(0.194) 		0.0343
(0.173) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 10 (4%) 259 0.0219
(0.131) 		0.0543
(0.225) 		0.127
(0.389) 		0.0989
(0.332) 		0.679
(1.00) 		0.251
(0.573) 		0.0251
(0.144) 		0.691
(1.00) 		0.671
(0.998) 		0.271
(0.594) 		0.341
(0.689) 		1
(1.00)
16p gain 143 (53%) 126 0.427
(0.779) 		0.0275
(0.151) 		0.883
(1.00) 		0.66
(0.994) 		1
(1.00) 		0.487
(0.848) 		0.00233
(0.0265) 		0.875
(1.00) 		0.506
(0.868) 		0.102
(0.336) 		0.00096
(0.0129) 		0.234
(0.554)
3q loss 6 (2%) 263 0.000345
(0.00559) 		0.174
(0.467) 		0.0392
(0.191) 		0.0451
(0.201) 		0.0714
(0.274) 		0.174
(0.467) 		0.66
(0.994) 		1
(1.00) 		1
(1.00)
6p loss 19 (7%) 250 0.0944
(0.326) 		0.206
(0.519) 		0.0163
(0.108) 		0.0295
(0.158) 		0.0516
(0.219) 		1
(1.00) 		0.175
(0.467) 		0.847
(1.00) 		0.24
(0.56) 		1
(1.00) 		0.159
(0.441) 		1
(1.00)
16p loss 4 (1%) 265 2.08e-08
(6.08e-06) 		0.864
(1.00) 		0.0743
(0.279) 		0.06
(0.241) 		1
(1.00) 		0.0599
(0.241) 		1
(1.00)
16q loss 7 (3%) 262 8.59e-08
(1.25e-05) 		0.721
(1.00) 		0.00396
(0.035) 		0.0116
(0.081) 		0.07
(0.27) 		1
(1.00) 		0.389
(0.73) 		0.427
(0.779) 		1
(1.00)
19p loss 15 (6%) 254 0.147
(0.426) 		0.378
(0.72) 		0.00357
(0.0332) 		0.00249
(0.0276) 		0.0484
(0.209) 		1
(1.00) 		0.555
(0.906) 		0.0967
(0.327) 		0.613
(0.954) 		1
(1.00) 		1
(1.00)
21q loss 41 (15%) 228 0.955
(1.00) 		0.0972
(0.327) 		0.00591
(0.0484) 		0.00184
(0.0224) 		0.469
(0.825) 		0.113
(0.367) 		0.129
(0.394) 		0.0383
(0.187) 		0.539
(0.893) 		0.649
(0.983) 		0.269
(0.594) 		1
(1.00)
8p gain 18 (7%) 251 0.0332
(0.173) 		0.822
(1.00) 		0.305
(0.643) 		0.182
(0.478) 		0.216
(0.536) 		1
(1.00) 		0.27
(0.594) 		0.338
(0.687) 		0.707
(1.00) 		0.0327
(0.172) 		0.585
(0.935)
14q gain 3 (1%) 266 0.0336
(0.173) 		0.0186
(0.121) 		1
(1.00) 		0.176
(0.467) 		1
(1.00)
16q gain 139 (52%) 130 0.0869
(0.307) 		0.0639
(0.253) 		0.53
(0.89) 		0.319
(0.661) 		0.669
(0.998) 		0.176
(0.468) 		0.0131
(0.0892) 		0.38
(0.72) 		0.974
(1.00) 		0.102
(0.336) 		0.00495
(0.0421) 		0.239
(0.56)
17q gain 180 (67%) 89 0.515
(0.875) 		0.0744
(0.279) 		0.045
(0.201) 		0.117
(0.371) 		0.404
(0.754) 		1
(1.00) 		0.144
(0.422) 		0.509
(0.87) 		0.243
(0.565) 		0.271
(0.594) 		0.0378
(0.186) 		0.195
(0.498)
2p gain 40 (15%) 229 0.503
(0.866) 		0.241
(0.562) 		0.0632
(0.252) 		0.481
(0.841) 		0.0806
(0.293) 		0.00364
(0.0332) 		0.699
(1.00) 		0.516
(0.875) 		0.235
(0.556) 		0.565
(0.916) 		0.671
(0.998) 		1
(1.00)
3q gain 88 (33%) 181 0.668
(0.998) 		0.288
(0.621) 		0.115
(0.367) 		0.0718
(0.275) 		0.892
(1.00) 		0.0549
(0.226) 		0.309
(0.648) 		0.228
(0.554) 		0.385
(0.726) 		0.347
(0.697) 		0.136
(0.41) 		1
(1.00)
10p gain 8 (3%) 261 0.851
(1.00) 		0.293
(0.626) 		0.204
(0.515) 		0.443
(0.792) 		1
(1.00) 		0.498
(0.859) 		0.445
(0.792) 		0.00388
(0.0347) 		1
(1.00)
10q gain 8 (3%) 261 0.851
(1.00) 		0.293
(0.626) 		0.202
(0.512) 		0.44
(0.792) 		1
(1.00) 		0.498
(0.859) 		0.445
(0.792) 		0.00378
(0.0341) 		1
(1.00)
12p gain 107 (40%) 162 0.865
(1.00) 		0.831
(1.00) 		0.125
(0.385) 		0.759
(1.00) 		0.539
(0.893) 		0.489
(0.848) 		0.00745
(0.0568) 		0.437
(0.791) 		0.727
(1.00) 		0.0652
(0.255) 		0.864
(1.00) 		0.368
(0.712)
12q gain 107 (40%) 162 0.865
(1.00) 		0.831
(1.00) 		0.126
(0.387) 		0.758
(1.00) 		0.539
(0.893) 		0.489
(0.848) 		0.00745
(0.0568) 		0.437
(0.791) 		0.727
(1.00) 		0.0652
(0.255) 		0.864
(1.00) 		0.368
(0.712)
8q loss 7 (3%) 262 0.0088
(0.0653) 		0.808
(1.00) 		0.357
(0.699) 		1
(1.00) 		0.371
(0.712) 		0.251
(0.573) 		0.0852
(0.304) 		0.144
(0.422) 		1
(1.00)
4p gain 10 (4%) 259 0.0901
(0.314) 		0.101
(0.336) 		0.0803
(0.293) 		0.531
(0.89) 		0.293
(0.626) 		0.251
(0.573) 		1
(1.00) 		0.299
(0.632) 		0.754
(1.00) 		0.779
(1.00) 		0.592
(0.936) 		1
(1.00)
4q gain 9 (3%) 260 0.624
(0.954) 		0.232
(0.554) 		0.269
(0.594) 		0.419
(0.769) 		0.189
(0.491) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.76
(1.00) 		1
(1.00)
5p gain 32 (12%) 237 0.138
(0.412) 		0.524
(0.884) 		0.139
(0.413) 		0.0922
(0.319) 		0.375
(0.715) 		0.622
(0.954) 		0.671
(0.998) 		0.0796
(0.292) 		0.439
(0.791) 		0.579
(0.927) 		0.41
(0.761) 		1
(1.00)
5q gain 30 (11%) 239 0.785
(1.00) 		0.51
(0.87) 		0.166
(0.458) 		0.267
(0.594) 		0.739
(1.00) 		0.622
(0.954) 		0.827
(1.00) 		0.0796
(0.292) 		0.439
(0.791) 		0.763
(1.00) 		0.602
(0.95) 		0.372
(0.713)
13q gain 26 (10%) 243 0.841
(1.00) 		0.407
(0.757) 		0.332
(0.684) 		0.417
(0.768) 		1
(1.00) 		0.592
(0.936) 		1
(1.00) 		0.643
(0.977) 		0.99
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.338
(0.687)
15q gain 5 (2%) 264 0.725
(1.00) 		0.852
(1.00) 		0.266
(0.594) 		0.233
(0.554) 		1
(1.00) 		0.121
(0.379) 		0.648
(0.983) 		1
(1.00)
18p gain 12 (4%) 257 0.829
(1.00) 		0.77
(1.00) 		0.258
(0.588) 		0.803
(1.00) 		0.68
(1.00) 		0.444
(0.792) 		0.191
(0.493) 		0.711
(1.00) 		0.712
(1.00) 		0.194
(0.498) 		1
(1.00)
18q gain 9 (3%) 260 0.234
(0.554) 		0.574
(0.923) 		0.566
(0.916) 		0.421
(0.772) 		1
(1.00) 		0.452
(0.8) 		0.2
(0.509) 		0.318
(0.661) 		1
(1.00)
19p gain 4 (1%) 265 0.611
(0.954) 		0.191
(0.493) 		0.575
(0.923) 		0.262
(0.59) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.619
(0.954) 		1
(1.00)
19q gain 4 (1%) 265 0.611
(0.954) 		0.191
(0.493) 		0.574
(0.923) 		0.26
(0.589) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.622
(0.954) 		1
(1.00)
20p gain 91 (34%) 178 0.829
(1.00) 		0.157
(0.439) 		0.693
(1.00) 		0.323
(0.667) 		0.902
(1.00) 		1
(1.00) 		0.885
(1.00) 		0.616
(0.954) 		0.351
(0.698) 		0.831
(1.00) 		0.325
(0.67) 		0.756
(1.00)
20q gain 93 (35%) 176 0.624
(0.954) 		0.168
(0.46) 		0.791
(1.00) 		0.414
(0.765) 		0.818
(1.00) 		1
(1.00) 		1
(1.00) 		0.616
(0.954) 		0.468
(0.825) 		0.679
(1.00) 		0.149
(0.428) 		0.552
(0.905)
21q gain 19 (7%) 250 0.539
(0.893) 		0.147
(0.426) 		1
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.321
(0.665) 		1
(1.00) 		0.704
(1.00) 		0.0666
(0.258) 		0.0964
(0.327) 		1
(1.00)
22q gain 3 (1%) 266 0.289
(0.621) 		0.26
(0.589) 		0.4
(0.748) 		1
(1.00) 		0.567
(0.916) 		1
(1.00) 		0.148
(0.426)
1p loss 26 (10%) 243 0.91
(1.00) 		0.315
(0.656) 		0.0845
(0.302) 		0.157
(0.439) 		0.572
(0.923) 		1
(1.00) 		0.356
(0.699) 		0.555
(0.906) 		0.839
(1.00) 		0.295
(0.628) 		1
(1.00)
1q loss 19 (7%) 250 0.621
(0.954) 		0.516
(0.875) 		0.781
(1.00) 		1
(1.00) 		1
(1.00) 		0.547
(0.899) 		0.175
(0.467) 		0.555
(0.906) 		0.369
(0.712) 		1
(1.00)
2p loss 3 (1%) 266 1
(1.00) 		0.176
(0.467) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 3.35e-08 (logrank test), Q value = 7.3e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
1P GAIN MUTATED 7 4 2.0 - 49.2 (7.9)
1P GAIN WILD-TYPE 249 30 0.1 - 194.8 (21.6)

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

'1p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 7e-04 (Fisher's exact test), Q value = 0.01

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
1P GAIN MUTATED 1 0 5 2
1P GAIN WILD-TYPE 166 21 44 12

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

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0035 (Fisher's exact test), Q value = 0.033

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

nPatients T1 T2 T3+T4
ALL 176 29 56
1P GAIN MUTATED 2 0 6
1P GAIN WILD-TYPE 174 29 50

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 = 0.00576 (Fisher's exact test), Q value = 0.048

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

nPatients N0 N1 N2
ALL 45 22 4
1P GAIN MUTATED 0 4 1
1P GAIN WILD-TYPE 45 18 3

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

'1p gain' versus 'GENDER'

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

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

nPatients FEMALE MALE
ALL 72 197
1P GAIN MUTATED 5 3
1P GAIN WILD-TYPE 67 194

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

'1q gain' versus 'Time to Death'

P value = 4.64e-08 (logrank test), Q value = 8.1e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
1Q GAIN MUTATED 15 7 0.9 - 59.0 (13.0)
1Q GAIN WILD-TYPE 241 27 0.1 - 194.8 (21.7)

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

'1q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 8e-04

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
1Q GAIN MUTATED 3 0 10 3
1Q GAIN WILD-TYPE 164 21 39 11

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

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

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

nPatients T1 T2 T3+T4
ALL 176 29 56
1Q GAIN MUTATED 4 0 12
1Q GAIN WILD-TYPE 172 29 44

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

'1q gain' versus 'GENDER'

P value = 0.0411 (Fisher's exact test), Q value = 0.19

Table S9.  Gene #2: '1q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
1Q GAIN MUTATED 8 8
1Q GAIN WILD-TYPE 64 189

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'GENDER'

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0413 (Wilcoxon-test), Q value = 0.19

Table S10.  Gene #2: '1q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
1Q GAIN MUTATED 3 60.0 (52.0)
1Q GAIN WILD-TYPE 57 93.7 (10.1)

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'2p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00364 (Fisher's exact test), Q value = 0.033

Table S11.  Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
2P GAIN MUTATED 10 5
2P GAIN WILD-TYPE 80 4

Figure S11.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.027 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #4: '2q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
2Q GAIN MUTATED 27 3 7 7
2Q GAIN WILD-TYPE 140 18 42 7

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0331 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
2Q GAIN MUTATED 6 8 2
2Q GAIN WILD-TYPE 39 14 2

Figure S13.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00692 (Fisher's exact test), Q value = 0.055

Table S14.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
2Q GAIN MUTATED 12 5
2Q GAIN WILD-TYPE 78 4

Figure S14.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0424 (Fisher's exact test), Q value = 0.19

Table S15.  Gene #5: '3p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
3P GAIN MUTATED 50 7 6 2
3P GAIN WILD-TYPE 117 14 43 12

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0207 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
3P GAIN MUTATED 51 10 7
3P GAIN WILD-TYPE 125 19 49

Figure S16.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0296 (Wilcoxon-test), Q value = 0.16

Table S17.  Gene #5: '3p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
3P GAIN MUTATED 17 97.1 (5.9)
3P GAIN WILD-TYPE 43 90.0 (17.7)

Figure S17.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0549 (Fisher's exact test), Q value = 0.23

Table S18.  Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
3Q GAIN MUTATED 29 0
3Q GAIN WILD-TYPE 61 9

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'6p gain' versus 'Time to Death'

P value = 0.00717 (logrank test), Q value = 0.056

Table S19.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
6P GAIN MUTATED 10 5 6.6 - 93.3 (13.8)
6P GAIN WILD-TYPE 246 29 0.1 - 194.8 (21.6)

Figure S19.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0055

Table S20.  Gene #11: '6p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
6P GAIN MUTATED 1 0 6 2
6P GAIN WILD-TYPE 166 21 43 12

Figure S20.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'6p gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0035

Table S21.  Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
6P GAIN MUTATED 1 1 7
6P GAIN WILD-TYPE 175 28 49

Figure S21.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0403 (Fisher's exact test), Q value = 0.19

Table S22.  Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
6P GAIN MUTATED 2 2
6P GAIN WILD-TYPE 88 7

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'6q gain' versus 'Time to Death'

P value = 3.56e-05 (logrank test), Q value = 0.00092

Table S23.  Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
6Q GAIN MUTATED 8 5 6.6 - 86.3 (13.2)
6Q GAIN WILD-TYPE 248 29 0.1 - 194.8 (21.6)

Figure S23.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'6q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00188 (Fisher's exact test), Q value = 0.022

Table S24.  Gene #12: '6q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
6Q GAIN MUTATED 1 0 4 2
6Q GAIN WILD-TYPE 166 21 45 12

Figure S24.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'6q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.033

Table S25.  Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
6Q GAIN MUTATED 1 1 5
6Q GAIN WILD-TYPE 175 28 51

Figure S25.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0272 (Fisher's exact test), Q value = 0.15

Table S26.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
6Q GAIN MUTATED 0 4 0
6Q GAIN WILD-TYPE 45 18 4

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0212 (Fisher's exact test), Q value = 0.13

Table S27.  Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
6Q GAIN MUTATED 1 2
6Q GAIN WILD-TYPE 89 7

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00094 (Fisher's exact test), Q value = 0.013

Table S28.  Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
7P GAIN MUTATED 112 10 18 10
7P GAIN WILD-TYPE 55 11 31 4

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.13

Table S29.  Gene #13: '7p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
7P GAIN MUTATED 115 17 25
7P GAIN WILD-TYPE 61 12 31

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'7p gain' versus 'GENDER'

P value = 0.00301 (Fisher's exact test), Q value = 0.031

Table S30.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
7P GAIN MUTATED 32 129
7P GAIN WILD-TYPE 40 68

Figure S30.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7p gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00359 (Wilcoxon-test), Q value = 0.033

Table S31.  Gene #13: '7p gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
7P GAIN MUTATED 29 1966.8 (14.7)
7P GAIN WILD-TYPE 22 1979.7 (14.8)

Figure S31.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'7q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00062 (Fisher's exact test), Q value = 0.0093

Table S32.  Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
7Q GAIN MUTATED 113 10 18 10
7Q GAIN WILD-TYPE 54 11 31 4

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0185 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #14: '7q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
7Q GAIN MUTATED 116 17 25
7Q GAIN WILD-TYPE 60 12 31

Figure S33.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'7q gain' versus 'GENDER'

P value = 0.00189 (Fisher's exact test), Q value = 0.022

Table S34.  Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
7Q GAIN MUTATED 32 130
7Q GAIN WILD-TYPE 40 67

Figure S34.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00359 (Wilcoxon-test), Q value = 0.033

Table S35.  Gene #14: '7q gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
7Q GAIN MUTATED 29 1966.8 (14.7)
7Q GAIN WILD-TYPE 22 1979.7 (14.8)

Figure S35.  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 = 0.0332 (logrank test), Q value = 0.17

Table S36.  Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
8P GAIN MUTATED 18 4 0.2 - 59.0 (16.4)
8P GAIN WILD-TYPE 238 30 0.1 - 194.8 (21.6)

Figure S36.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8p gain' versus 'RACE'

P value = 0.0327 (Fisher's exact test), Q value = 0.17

Table S37.  Gene #15: '8p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
8P GAIN MUTATED 0 0 0 18
8P GAIN WILD-TYPE 2 5 60 169

Figure S37.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #11: 'RACE'

'8q gain' versus 'Time to Death'

P value = 8.89e-05 (logrank test), Q value = 0.0018

Table S38.  Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
8Q GAIN MUTATED 23 7 0.2 - 59.0 (14.1)
8Q GAIN WILD-TYPE 233 27 0.1 - 194.8 (21.9)

Figure S38.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'8q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00212 (Fisher's exact test), Q value = 0.024

Table S39.  Gene #16: '8q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
8Q GAIN MUTATED 7 3 7 4
8Q GAIN WILD-TYPE 160 18 42 10

Figure S39.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00086 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
8Q GAIN MUTATED 7 3 11
8Q GAIN WILD-TYPE 169 26 45

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00345 (Fisher's exact test), Q value = 0.033

Table S41.  Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
8Q GAIN MUTATED 2 6 2
8Q GAIN WILD-TYPE 43 16 2

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q gain' versus 'RACE'

P value = 0.0553 (Fisher's exact test), Q value = 0.23

Table S42.  Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
8Q GAIN MUTATED 0 1 1 21
8Q GAIN WILD-TYPE 2 4 59 166

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #11: 'RACE'

'9p gain' versus 'Time to Death'

P value = 0.048 (logrank test), Q value = 0.21

Table S43.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
9P GAIN MUTATED 3 1 3.7 - 34.5 (11.3)
9P GAIN WILD-TYPE 253 33 0.1 - 194.8 (21.4)

Figure S43.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0423 (Fisher's exact test), Q value = 0.19

Table S44.  Gene #17: '9p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
9P GAIN MUTATED 0 1 2 0
9P GAIN WILD-TYPE 167 20 47 14

Figure S44.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0343 (Fisher's exact test), Q value = 0.17

Table S45.  Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
9P GAIN MUTATED 0 1 2
9P GAIN WILD-TYPE 176 28 54

Figure S45.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p gain' versus 'RACE'

P value = 0.00388 (Fisher's exact test), Q value = 0.035

Table S46.  Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
10P GAIN MUTATED 0 2 2 2
10P GAIN WILD-TYPE 2 3 58 185

Figure S46.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #11: 'RACE'

'10q gain' versus 'RACE'

P value = 0.00378 (Fisher's exact test), Q value = 0.034

Table S47.  Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
10Q GAIN MUTATED 0 2 2 2
10Q GAIN WILD-TYPE 2 3 58 185

Figure S47.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #11: 'RACE'

'11p gain' versus 'Time to Death'

P value = 0.000593 (logrank test), Q value = 0.0091

Table S48.  Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
11P GAIN MUTATED 10 4 0.5 - 85.0 (11.4)
11P GAIN WILD-TYPE 246 30 0.1 - 194.8 (21.8)

Figure S48.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0442 (Fisher's exact test), Q value = 0.2

Table S49.  Gene #20: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
11P GAIN MUTATED 4 0 4 2
11P GAIN WILD-TYPE 163 21 45 12

Figure S49.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0534 (Fisher's exact test), Q value = 0.22

Table S50.  Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
11P GAIN MUTATED 4 2 5
11P GAIN WILD-TYPE 172 27 51

Figure S50.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0403 (Fisher's exact test), Q value = 0.19

Table S51.  Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
11P GAIN MUTATED 2 2
11P GAIN WILD-TYPE 88 7

Figure S51.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11q gain' versus 'Time to Death'

P value = 0.0219 (logrank test), Q value = 0.13

Table S52.  Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
11Q GAIN MUTATED 10 3 0.5 - 85.0 (12.5)
11Q GAIN WILD-TYPE 246 31 0.1 - 194.8 (21.8)

Figure S52.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0543 (Wilcoxon-test), Q value = 0.22

Table S53.  Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
11Q GAIN MUTATED 10 53.6 (14.8)
11Q GAIN WILD-TYPE 254 61.6 (12.0)

Figure S53.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'GENDER'

P value = 0.0251 (Fisher's exact test), Q value = 0.14

Table S54.  Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
11Q GAIN MUTATED 6 4
11Q GAIN WILD-TYPE 66 193

Figure S54.  Get High-res Image Gene #21: '11q gain' versus Clinical Feature #7: 'GENDER'

'12p gain' versus 'GENDER'

P value = 0.00745 (Fisher's exact test), Q value = 0.057

Table S55.  Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
12P GAIN MUTATED 19 88
12P GAIN WILD-TYPE 53 109

Figure S55.  Get High-res Image Gene #22: '12p gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'GENDER'

P value = 0.00745 (Fisher's exact test), Q value = 0.057

Table S56.  Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
12Q GAIN MUTATED 19 88
12Q GAIN WILD-TYPE 53 109

Figure S56.  Get High-res Image Gene #23: '12q gain' versus Clinical Feature #7: 'GENDER'

'14q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0336 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #25: '14q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
14Q GAIN MUTATED 0 0 3 0
14Q GAIN WILD-TYPE 167 21 46 14

Figure S57.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0186 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
14Q GAIN MUTATED 0 0 3
14Q GAIN WILD-TYPE 176 29 53

Figure S58.  Get High-res Image Gene #25: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0275 (Wilcoxon-test), Q value = 0.15

Table S59.  Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
16P GAIN MUTATED 141 62.8 (11.9)
16P GAIN WILD-TYPE 123 59.5 (12.4)

Figure S59.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'GENDER'

P value = 0.00233 (Fisher's exact test), Q value = 0.026

Table S60.  Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
16P GAIN MUTATED 27 116
16P GAIN WILD-TYPE 45 81

Figure S60.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #7: 'GENDER'

'16p gain' versus 'RACE'

P value = 0.00096 (Fisher's exact test), Q value = 0.013

Table S61.  Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
16P GAIN MUTATED 2 3 20 111
16P GAIN WILD-TYPE 0 2 40 76

Figure S61.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #11: 'RACE'

'16q gain' versus 'GENDER'

P value = 0.0131 (Fisher's exact test), Q value = 0.089

Table S62.  Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
16Q GAIN MUTATED 28 111
16Q GAIN WILD-TYPE 44 86

Figure S62.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #7: 'GENDER'

'16q gain' versus 'RACE'

P value = 0.00495 (Fisher's exact test), Q value = 0.042

Table S63.  Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
16Q GAIN MUTATED 2 3 21 107
16Q GAIN WILD-TYPE 0 2 39 80

Figure S63.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #11: 'RACE'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.056 (Wilcoxon-test), Q value = 0.23

Table S64.  Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
17P GAIN MUTATED 162 60.3 (11.9)
17P GAIN WILD-TYPE 102 62.9 (12.5)

Figure S64.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0023

Table S65.  Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
17P GAIN MUTATED 117 14 18 6
17P GAIN WILD-TYPE 50 7 31 8

Figure S65.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.014

Table S66.  Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
17P GAIN MUTATED 120 20 23
17P GAIN WILD-TYPE 56 9 33

Figure S66.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'GENDER'

P value = 0.024 (Fisher's exact test), Q value = 0.14

Table S67.  Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
17P GAIN MUTATED 36 129
17P GAIN WILD-TYPE 36 68

Figure S67.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'RACE'

P value = 0.0479 (Fisher's exact test), Q value = 0.21

Table S68.  Gene #29: '17p gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
17P GAIN MUTATED 2 4 29 122
17P GAIN WILD-TYPE 0 1 31 65

Figure S68.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #11: 'RACE'

'17q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.045 (Fisher's exact test), Q value = 0.2

Table S69.  Gene #30: '17q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
17Q GAIN MUTATED 121 15 25 9
17Q GAIN WILD-TYPE 46 6 24 5

Figure S69.  Get High-res Image Gene #30: '17q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17q gain' versus 'RACE'

P value = 0.0378 (Fisher's exact test), Q value = 0.19

Table S70.  Gene #30: '17q gain' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
17Q GAIN MUTATED 2 4 32 133
17Q GAIN WILD-TYPE 0 1 28 54

Figure S70.  Get High-res Image Gene #30: '17q gain' versus Clinical Feature #11: 'RACE'

'xp gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.0064

Table S71.  Gene #39: 'xp gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
XP GAIN MUTATED 62 5 4 4
XP GAIN WILD-TYPE 105 16 45 10

Figure S71.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00167 (Fisher's exact test), Q value = 0.021

Table S72.  Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
XP GAIN MUTATED 64 9 7
XP GAIN WILD-TYPE 112 20 49

Figure S72.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'GENDER'

P value = 0.0512 (Fisher's exact test), Q value = 0.22

Table S73.  Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
XP GAIN MUTATED 15 67
XP GAIN WILD-TYPE 57 130

Figure S73.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0194 (Wilcoxon-test), Q value = 0.12

Table S74.  Gene #39: 'xp gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
XP GAIN MUTATED 19 96.3 (8.3)
XP GAIN WILD-TYPE 41 90.0 (17.7)

Figure S74.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xp gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.041 (Wilcoxon-test), Q value = 0.19

Table S75.  Gene #39: 'xp gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
XP GAIN MUTATED 13 1965.3 (13.9)
XP GAIN WILD-TYPE 38 1974.8 (16.0)

Figure S75.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'xq gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00556 (Fisher's exact test), Q value = 0.047

Table S76.  Gene #40: 'xq gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
XQ GAIN MUTATED 62 5 6 4
XQ GAIN WILD-TYPE 105 16 43 10

Figure S76.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0123 (Fisher's exact test), Q value = 0.085

Table S77.  Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
XQ GAIN MUTATED 64 10 9
XQ GAIN WILD-TYPE 112 19 47

Figure S77.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'GENDER'

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

Table S78.  Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
XQ GAIN MUTATED 16 69
XQ GAIN WILD-TYPE 56 128

Figure S78.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0194 (Wilcoxon-test), Q value = 0.12

Table S79.  Gene #40: 'xq gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
XQ GAIN MUTATED 19 96.3 (8.3)
XQ GAIN WILD-TYPE 41 90.0 (17.7)

Figure S79.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.041 (Wilcoxon-test), Q value = 0.19

Table S80.  Gene #40: 'xq gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
XQ GAIN MUTATED 13 1965.3 (13.9)
XQ GAIN WILD-TYPE 38 1974.8 (16.0)

Figure S80.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'3p loss' versus 'Time to Death'

P value = 0.0101 (logrank test), Q value = 0.072

Table S81.  Gene #44: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
3P LOSS MUTATED 21 6 0.1 - 86.3 (14.1)
3P LOSS WILD-TYPE 235 28 0.1 - 194.8 (21.9)

Figure S81.  Get High-res Image Gene #44: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0239 (Wilcoxon-test), Q value = 0.14

Table S82.  Gene #44: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
3P LOSS MUTATED 20 54.6 (12.7)
3P LOSS WILD-TYPE 244 61.8 (12.0)

Figure S82.  Get High-res Image Gene #44: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S83.  Gene #44: '3p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
3P LOSS MUTATED 5 1 12 3
3P LOSS WILD-TYPE 162 20 37 11

Figure S83.  Get High-res Image Gene #44: '3p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0024

Table S84.  Gene #44: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
3P LOSS MUTATED 6 3 12
3P LOSS WILD-TYPE 170 26 44

Figure S84.  Get High-res Image Gene #44: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3q loss' versus 'Time to Death'

P value = 0.000345 (logrank test), Q value = 0.0056

Table S85.  Gene #45: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
3Q LOSS MUTATED 6 3 3.7 - 54.6 (13.1)
3Q LOSS WILD-TYPE 250 31 0.1 - 194.8 (21.6)

Figure S85.  Get High-res Image Gene #45: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0392 (Fisher's exact test), Q value = 0.19

Table S86.  Gene #45: '3q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
3Q LOSS MUTATED 2 0 2 2
3Q LOSS WILD-TYPE 165 21 47 12

Figure S86.  Get High-res Image Gene #45: '3q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'3q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0451 (Fisher's exact test), Q value = 0.2

Table S87.  Gene #45: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
3Q LOSS MUTATED 2 0 4
3Q LOSS WILD-TYPE 174 29 52

Figure S87.  Get High-res Image Gene #45: '3q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'Time to Death'

P value = 4.18e-05 (logrank test), Q value = 0.00096

Table S88.  Gene #46: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
4P LOSS MUTATED 22 8 0.1 - 79.9 (13.9)
4P LOSS WILD-TYPE 234 26 0.1 - 194.8 (22.2)

Figure S88.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00449 (Wilcoxon-test), Q value = 0.039

Table S89.  Gene #46: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
4P LOSS MUTATED 22 52.5 (15.7)
4P LOSS WILD-TYPE 242 62.1 (11.6)

Figure S89.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S90.  Gene #46: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
4P LOSS MUTATED 4 1 15 1
4P LOSS WILD-TYPE 163 20 34 13

Figure S90.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S91.  Gene #46: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
4P LOSS MUTATED 5 2 15
4P LOSS WILD-TYPE 171 27 41

Figure S91.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00198 (Fisher's exact test), Q value = 0.023

Table S92.  Gene #46: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
4P LOSS MUTATED 3 9 0
4P LOSS WILD-TYPE 42 13 4

Figure S92.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'GENDER'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.0012

Table S93.  Gene #46: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
4P LOSS MUTATED 15 8
4P LOSS WILD-TYPE 57 189

Figure S93.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'Time to Death'

P value = 4.13e-05 (logrank test), Q value = 0.00096

Table S94.  Gene #47: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
4Q LOSS MUTATED 23 8 0.1 - 79.9 (13.7)
4Q LOSS WILD-TYPE 233 26 0.1 - 194.8 (22.5)

Figure S94.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0271 (Wilcoxon-test), Q value = 0.15

Table S95.  Gene #47: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
4Q LOSS MUTATED 23 54.7 (15.3)
4Q LOSS WILD-TYPE 241 61.9 (11.7)

Figure S95.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S96.  Gene #47: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
4Q LOSS MUTATED 5 1 14 2
4Q LOSS WILD-TYPE 162 20 35 12

Figure S96.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00096

Table S97.  Gene #47: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
4Q LOSS MUTATED 6 3 14
4Q LOSS WILD-TYPE 170 26 42

Figure S97.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0242 (Fisher's exact test), Q value = 0.14

Table S98.  Gene #47: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
4Q LOSS MUTATED 4 8 0
4Q LOSS WILD-TYPE 41 14 4

Figure S98.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'GENDER'

P value = 0.000999 (Fisher's exact test), Q value = 0.013

Table S99.  Gene #47: '4q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
4Q LOSS MUTATED 14 10
4Q LOSS WILD-TYPE 58 187

Figure S99.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.061 (Wilcoxon-test), Q value = 0.24

Table S100.  Gene #47: '4q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
4Q LOSS MUTATED 7 90.0 (5.8)
4Q LOSS WILD-TYPE 53 92.3 (16.5)

Figure S100.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'5p loss' versus 'Time to Death'

P value = 1.28e-10 (logrank test), Q value = 1.1e-07

Table S101.  Gene #48: '5p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
5P LOSS MUTATED 8 5 2.8 - 30.5 (14.6)
5P LOSS WILD-TYPE 248 29 0.1 - 194.8 (21.6)

Figure S101.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'YEARS_TO_BIRTH'

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

Table S102.  Gene #48: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
5P LOSS MUTATED 8 50.9 (15.6)
5P LOSS WILD-TYPE 256 61.6 (12.0)

Figure S102.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0202 (Fisher's exact test), Q value = 0.12

Table S103.  Gene #48: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
5P LOSS MUTATED 2 0 3 2
5P LOSS WILD-TYPE 165 21 46 12

Figure S103.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00334 (Fisher's exact test), Q value = 0.033

Table S104.  Gene #48: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
5P LOSS MUTATED 2 0 6
5P LOSS WILD-TYPE 174 29 50

Figure S104.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.02 (Fisher's exact test), Q value = 0.12

Table S105.  Gene #48: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
5P LOSS MUTATED 0 3 1
5P LOSS WILD-TYPE 45 19 3

Figure S105.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'GENDER'

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

Table S106.  Gene #48: '5p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
5P LOSS MUTATED 5 3
5P LOSS WILD-TYPE 67 194

Figure S106.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #7: 'GENDER'

'5q loss' versus 'Time to Death'

P value = 1.06e-07 (logrank test), Q value = 1.3e-05

Table S107.  Gene #49: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
5Q LOSS MUTATED 8 4 2.8 - 30.5 (14.4)
5Q LOSS WILD-TYPE 248 30 0.1 - 194.8 (21.6)

Figure S107.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.089

Table S108.  Gene #49: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
5Q LOSS MUTATED 8 46.9 (17.0)
5Q LOSS WILD-TYPE 256 61.7 (11.8)

Figure S108.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0284 (Fisher's exact test), Q value = 0.15

Table S109.  Gene #49: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
5Q LOSS MUTATED 2 0 4 1
5Q LOSS WILD-TYPE 165 21 45 13

Figure S109.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00339 (Fisher's exact test), Q value = 0.033

Table S110.  Gene #49: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
5Q LOSS MUTATED 2 0 6
5Q LOSS WILD-TYPE 174 29 50

Figure S110.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0284 (Fisher's exact test), Q value = 0.15

Table S111.  Gene #49: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
5Q LOSS MUTATED 0 4 0
5Q LOSS WILD-TYPE 45 18 4

Figure S111.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'GENDER'

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

Table S112.  Gene #49: '5q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
5Q LOSS MUTATED 5 3
5Q LOSS WILD-TYPE 67 194

Figure S112.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #7: 'GENDER'

'6p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0163 (Fisher's exact test), Q value = 0.11

Table S113.  Gene #50: '6p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
6P LOSS MUTATED 8 0 8 2
6P LOSS WILD-TYPE 159 21 41 12

Figure S113.  Get High-res Image Gene #50: '6p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0295 (Fisher's exact test), Q value = 0.16

Table S114.  Gene #50: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
6P LOSS MUTATED 9 1 9
6P LOSS WILD-TYPE 167 28 47

Figure S114.  Get High-res Image Gene #50: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0516 (Fisher's exact test), Q value = 0.22

Table S115.  Gene #50: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
6P LOSS MUTATED 3 2 2
6P LOSS WILD-TYPE 42 20 2

Figure S115.  Get High-res Image Gene #50: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0371 (Fisher's exact test), Q value = 0.18

Table S116.  Gene #51: '6q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
6Q LOSS MUTATED 12 0 9 2
6Q LOSS WILD-TYPE 155 21 40 12

Figure S116.  Get High-res Image Gene #51: '6q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0012 (Fisher's exact test), Q value = 0.015

Table S117.  Gene #51: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
6Q LOSS MUTATED 12 0 12
6Q LOSS WILD-TYPE 164 29 44

Figure S117.  Get High-res Image Gene #51: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'GENDER'

P value = 0.0135 (Fisher's exact test), Q value = 0.091

Table S118.  Gene #51: '6q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
6Q LOSS MUTATED 12 12
6Q LOSS WILD-TYPE 60 185

Figure S118.  Get High-res Image Gene #51: '6q loss' versus Clinical Feature #7: 'GENDER'

'6q loss' versus 'RACE'

P value = 0.0446 (Fisher's exact test), Q value = 0.2

Table S119.  Gene #51: '6q loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
6Q LOSS MUTATED 0 2 2 17
6Q LOSS WILD-TYPE 2 3 58 170

Figure S119.  Get High-res Image Gene #51: '6q loss' versus Clinical Feature #11: 'RACE'

'8p loss' versus 'Time to Death'

P value = 4.7e-05 (logrank test), Q value = 0.0011

Table S120.  Gene #52: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
8P LOSS MUTATED 13 5 1.2 - 58.2 (13.0)
8P LOSS WILD-TYPE 243 29 0.1 - 194.8 (22.1)

Figure S120.  Get High-res Image Gene #52: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0309 (Fisher's exact test), Q value = 0.16

Table S121.  Gene #52: '8p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
8P LOSS MUTATED 6 2 2 3
8P LOSS WILD-TYPE 161 19 47 11

Figure S121.  Get High-res Image Gene #52: '8p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0204 (Fisher's exact test), Q value = 0.13

Table S122.  Gene #52: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
8P LOSS MUTATED 1 5 0
8P LOSS WILD-TYPE 44 17 4

Figure S122.  Get High-res Image Gene #52: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0154 (Fisher's exact test), Q value = 0.1

Table S123.  Gene #52: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
8P LOSS MUTATED 4 3
8P LOSS WILD-TYPE 86 6

Figure S123.  Get High-res Image Gene #52: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'RACE'

P value = 0.0528 (Fisher's exact test), Q value = 0.22

Table S124.  Gene #52: '8p loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
8P LOSS MUTATED 0 2 2 9
8P LOSS WILD-TYPE 2 3 58 178

Figure S124.  Get High-res Image Gene #52: '8p loss' versus Clinical Feature #11: 'RACE'

'8q loss' versus 'Time to Death'

P value = 0.0088 (logrank test), Q value = 0.065

Table S125.  Gene #53: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
8Q LOSS MUTATED 7 2 7.3 - 18.0 (13.0)
8Q LOSS WILD-TYPE 249 32 0.1 - 194.8 (21.9)

Figure S125.  Get High-res Image Gene #53: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'Time to Death'

P value = 0.000127 (logrank test), Q value = 0.0024

Table S126.  Gene #54: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
9P LOSS MUTATED 31 11 0.1 - 93.3 (17.3)
9P LOSS WILD-TYPE 225 23 0.1 - 194.8 (22.5)

Figure S126.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S127.  Gene #54: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
9P LOSS MUTATED 9 0 15 5
9P LOSS WILD-TYPE 158 21 34 9

Figure S127.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S128.  Gene #54: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
9P LOSS MUTATED 10 3 18
9P LOSS WILD-TYPE 166 26 38

Figure S128.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0142 (Fisher's exact test), Q value = 0.095

Table S129.  Gene #54: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
9P LOSS MUTATED 6 9 2
9P LOSS WILD-TYPE 39 13 2

Figure S129.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'GENDER'

P value = 0.00271 (Fisher's exact test), Q value = 0.029

Table S130.  Gene #54: '9p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
9P LOSS MUTATED 16 16
9P LOSS WILD-TYPE 56 181

Figure S130.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00288 (Wilcoxon-test), Q value = 0.03

Table S131.  Gene #54: '9p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
9P LOSS MUTATED 11 81.8 (27.5)
9P LOSS WILD-TYPE 49 94.3 (10.6)

Figure S131.  Get High-res Image Gene #54: '9p loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'Time to Death'

P value = 0.00162 (logrank test), Q value = 0.02

Table S132.  Gene #55: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
9Q LOSS MUTATED 31 9 0.1 - 93.3 (17.3)
9Q LOSS WILD-TYPE 225 25 0.1 - 194.8 (22.3)

Figure S132.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S133.  Gene #55: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
9Q LOSS MUTATED 10 1 15 4
9Q LOSS WILD-TYPE 157 20 34 10

Figure S133.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S134.  Gene #55: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
9Q LOSS MUTATED 11 1 19
9Q LOSS WILD-TYPE 165 28 37

Figure S134.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0258 (Fisher's exact test), Q value = 0.15

Table S135.  Gene #55: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
9Q LOSS MUTATED 5 7 2
9Q LOSS WILD-TYPE 40 15 2

Figure S135.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'GENDER'

P value = 0.00271 (Fisher's exact test), Q value = 0.029

Table S136.  Gene #55: '9q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
9Q LOSS MUTATED 16 16
9Q LOSS WILD-TYPE 56 181

Figure S136.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #7: 'GENDER'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00798 (Wilcoxon-test), Q value = 0.06

Table S137.  Gene #55: '9q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
9Q LOSS MUTATED 9 80.0 (30.4)
9Q LOSS WILD-TYPE 51 94.1 (10.4)

Figure S137.  Get High-res Image Gene #55: '9q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'Time to Death'

P value = 0.0399 (logrank test), Q value = 0.19

Table S138.  Gene #56: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
10P LOSS MUTATED 14 4 2.1 - 79.9 (15.7)
10P LOSS WILD-TYPE 242 30 0.1 - 194.8 (21.8)

Figure S138.  Get High-res Image Gene #56: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00311 (Fisher's exact test), Q value = 0.032

Table S139.  Gene #56: '10p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
10P LOSS MUTATED 4 0 7 2
10P LOSS WILD-TYPE 163 21 42 12

Figure S139.  Get High-res Image Gene #56: '10p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00723 (Fisher's exact test), Q value = 0.056

Table S140.  Gene #56: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
10P LOSS MUTATED 5 1 8
10P LOSS WILD-TYPE 171 28 48

Figure S140.  Get High-res Image Gene #56: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0289 (Fisher's exact test), Q value = 0.16

Table S141.  Gene #56: '10p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
10P LOSS MUTATED 1 4 1
10P LOSS WILD-TYPE 44 18 3

Figure S141.  Get High-res Image Gene #56: '10p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'Time to Death'

P value = 0.023 (logrank test), Q value = 0.14

Table S142.  Gene #57: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
10Q LOSS MUTATED 15 5 0.1 - 86.3 (14.1)
10Q LOSS WILD-TYPE 241 29 0.1 - 194.8 (21.7)

Figure S142.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.0062

Table S143.  Gene #57: '10q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
10Q LOSS MUTATED 4 0 9 2
10Q LOSS WILD-TYPE 163 21 40 12

Figure S143.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00246 (Fisher's exact test), Q value = 0.028

Table S144.  Gene #57: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
10Q LOSS MUTATED 5 1 9
10Q LOSS WILD-TYPE 171 28 47

Figure S144.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00624 (Fisher's exact test), Q value = 0.051

Table S145.  Gene #57: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
10Q LOSS MUTATED 1 6 1
10Q LOSS WILD-TYPE 44 16 3

Figure S145.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0333 (Wilcoxon-test), Q value = 0.17

Table S146.  Gene #57: '10q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
10Q LOSS MUTATED 6 75.0 (37.3)
10Q LOSS WILD-TYPE 54 93.9 (10.2)

Figure S146.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'11p loss' versus 'Time to Death'

P value = 0.000207 (logrank test), Q value = 0.0035

Table S147.  Gene #58: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
11P LOSS MUTATED 15 5 2.0 - 54.6 (16.9)
11P LOSS WILD-TYPE 241 29 0.1 - 194.8 (22.1)

Figure S147.  Get High-res Image Gene #58: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #58: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
11P LOSS MUTATED 5 2 6 2
11P LOSS WILD-TYPE 162 19 43 12

Figure S148.  Get High-res Image Gene #58: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00651 (Fisher's exact test), Q value = 0.052

Table S149.  Gene #58: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
11P LOSS MUTATED 5 2 8
11P LOSS WILD-TYPE 171 27 48

Figure S149.  Get High-res Image Gene #58: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0482 (Fisher's exact test), Q value = 0.21

Table S150.  Gene #58: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
11P LOSS MUTATED 1 3 1
11P LOSS WILD-TYPE 44 19 3

Figure S150.  Get High-res Image Gene #58: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'Time to Death'

P value = 0.0098 (logrank test), Q value = 0.072

Table S151.  Gene #59: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
11Q LOSS MUTATED 19 6 0.1 - 123.6 (11.1)
11Q LOSS WILD-TYPE 237 28 0.1 - 194.8 (22.1)

Figure S151.  Get High-res Image Gene #59: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S152.  Gene #59: '11q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
11Q LOSS MUTATED 3 1 11 4
11Q LOSS WILD-TYPE 164 20 38 10

Figure S152.  Get High-res Image Gene #59: '11q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S153.  Gene #59: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
11Q LOSS MUTATED 3 2 14
11Q LOSS WILD-TYPE 173 27 42

Figure S153.  Get High-res Image Gene #59: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0196 (Fisher's exact test), Q value = 0.12

Table S154.  Gene #59: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
11Q LOSS MUTATED 3 5 2
11Q LOSS WILD-TYPE 42 17 2

Figure S154.  Get High-res Image Gene #59: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'Time to Death'

P value = 1.06e-06 (logrank test), Q value = 1e-04

Table S155.  Gene #60: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
13Q LOSS MUTATED 23 9 0.1 - 86.8 (14.1)
13Q LOSS WILD-TYPE 233 25 0.1 - 194.8 (22.3)

Figure S155.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00584 (Wilcoxon-test), Q value = 0.048

Table S156.  Gene #60: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
13Q LOSS MUTATED 23 52.9 (15.6)
13Q LOSS WILD-TYPE 241 62.1 (11.6)

Figure S156.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0035

Table S157.  Gene #60: '13q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
13Q LOSS MUTATED 7 1 12 3
13Q LOSS WILD-TYPE 160 20 37 11

Figure S157.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00096

Table S158.  Gene #60: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
13Q LOSS MUTATED 7 2 14
13Q LOSS WILD-TYPE 169 27 42

Figure S158.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00335 (Fisher's exact test), Q value = 0.033

Table S159.  Gene #60: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
13Q LOSS MUTATED 3 7 2
13Q LOSS WILD-TYPE 42 15 2

Figure S159.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'GENDER'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.0012

Table S160.  Gene #60: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
13Q LOSS MUTATED 15 8
13Q LOSS WILD-TYPE 57 189

Figure S160.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #7: 'GENDER'

'14q loss' versus 'Time to Death'

P value = 0.004 (logrank test), Q value = 0.035

Table S161.  Gene #61: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
14Q LOSS MUTATED 44 10 0.1 - 80.9 (17.1)
14Q LOSS WILD-TYPE 212 24 0.1 - 194.8 (22.7)

Figure S161.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.014

Table S162.  Gene #61: '14q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
14Q LOSS MUTATED 18 3 14 6
14Q LOSS WILD-TYPE 149 18 35 8

Figure S162.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0035

Table S163.  Gene #61: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
14Q LOSS MUTATED 20 4 20
14Q LOSS WILD-TYPE 156 25 36

Figure S163.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0231 (Fisher's exact test), Q value = 0.14

Table S164.  Gene #61: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
14Q LOSS MUTATED 8 8 3
14Q LOSS WILD-TYPE 37 14 1

Figure S164.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'GENDER'

P value = 0.00941 (Fisher's exact test), Q value = 0.069

Table S165.  Gene #61: '14q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
14Q LOSS MUTATED 19 25
14Q LOSS WILD-TYPE 53 172

Figure S165.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #7: 'GENDER'

'14q loss' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0369 (Wilcoxon-test), Q value = 0.18

Table S166.  Gene #61: '14q loss' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
14Q LOSS MUTATED 8 1983.8 (15.3)
14Q LOSS WILD-TYPE 43 1970.3 (15.3)

Figure S166.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'15q loss' versus 'Time to Death'

P value = 0.00993 (logrank test), Q value = 0.072

Table S167.  Gene #62: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
15Q LOSS MUTATED 28 7 0.1 - 194.8 (13.2)
15Q LOSS WILD-TYPE 228 27 0.1 - 129.9 (22.9)

Figure S167.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0428 (Wilcoxon-test), Q value = 0.19

Table S168.  Gene #62: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
15Q LOSS MUTATED 28 56.1 (14.5)
15Q LOSS WILD-TYPE 236 61.9 (11.8)

Figure S168.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00432 (Fisher's exact test), Q value = 0.037

Table S169.  Gene #62: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
15Q LOSS MUTATED 11 1 10 4
15Q LOSS WILD-TYPE 156 20 39 10

Figure S169.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00089 (Fisher's exact test), Q value = 0.012

Table S170.  Gene #62: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
15Q LOSS MUTATED 13 1 14
15Q LOSS WILD-TYPE 163 28 42

Figure S170.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0404 (Fisher's exact test), Q value = 0.19

Table S171.  Gene #62: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
15Q LOSS MUTATED 4 7 1
15Q LOSS WILD-TYPE 41 15 3

Figure S171.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p loss' versus 'Time to Death'

P value = 2.08e-08 (logrank test), Q value = 6.1e-06

Table S172.  Gene #63: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
16P LOSS MUTATED 3 3 11.1 - 21.6 (19.6)
16P LOSS WILD-TYPE 253 31 0.1 - 194.8 (21.4)

Figure S172.  Get High-res Image Gene #63: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.06 (Fisher's exact test), Q value = 0.24

Table S173.  Gene #63: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
16P LOSS MUTATED 1 0 3
16P LOSS WILD-TYPE 175 29 53

Figure S173.  Get High-res Image Gene #63: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p loss' versus 'GENDER'

P value = 0.0599 (Fisher's exact test), Q value = 0.24

Table S174.  Gene #63: '16p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
16P LOSS MUTATED 3 1
16P LOSS WILD-TYPE 69 196

Figure S174.  Get High-res Image Gene #63: '16p loss' versus Clinical Feature #7: 'GENDER'

'16q loss' versus 'Time to Death'

P value = 8.59e-08 (logrank test), Q value = 1.3e-05

Table S175.  Gene #64: '16q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
16Q LOSS MUTATED 6 5 11.1 - 51.5 (18.3)
16Q LOSS WILD-TYPE 250 29 0.1 - 194.8 (21.6)

Figure S175.  Get High-res Image Gene #64: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00396 (Fisher's exact test), Q value = 0.035

Table S176.  Gene #64: '16q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
16Q LOSS MUTATED 1 0 5 1
16Q LOSS WILD-TYPE 166 21 44 13

Figure S176.  Get High-res Image Gene #64: '16q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.081

Table S177.  Gene #64: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
16Q LOSS MUTATED 2 0 5
16Q LOSS WILD-TYPE 174 29 51

Figure S177.  Get High-res Image Gene #64: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'Time to Death'

P value = 4.28e-10 (logrank test), Q value = 1.9e-07

Table S178.  Gene #65: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
17P LOSS MUTATED 7 5 0.2 - 51.5 (11.1)
17P LOSS WILD-TYPE 249 29 0.1 - 194.8 (21.7)

Figure S178.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0098

Table S179.  Gene #65: '17p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
17P LOSS MUTATED 1 1 3 3
17P LOSS WILD-TYPE 166 20 46 11

Figure S179.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0026 (Fisher's exact test), Q value = 0.028

Table S180.  Gene #65: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
17P LOSS MUTATED 1 2 5
17P LOSS WILD-TYPE 175 27 51

Figure S180.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0275 (Fisher's exact test), Q value = 0.15

Table S181.  Gene #65: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
17P LOSS MUTATED 2 1 2
17P LOSS WILD-TYPE 43 21 2

Figure S181.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0403 (Fisher's exact test), Q value = 0.19

Table S182.  Gene #65: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
17P LOSS MUTATED 2 2
17P LOSS WILD-TYPE 88 7

Figure S182.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'Time to Death'

P value = 1.04e-05 (logrank test), Q value = 0.00041

Table S183.  Gene #66: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
18P LOSS MUTATED 38 12 0.1 - 123.6 (13.2)
18P LOSS WILD-TYPE 218 22 0.1 - 194.8 (22.9)

Figure S183.  Get High-res Image Gene #66: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S184.  Gene #66: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
18P LOSS MUTATED 13 1 16 5
18P LOSS WILD-TYPE 154 20 33 9

Figure S184.  Get High-res Image Gene #66: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 6e-04

Table S185.  Gene #66: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
18P LOSS MUTATED 13 3 21
18P LOSS WILD-TYPE 163 26 35

Figure S185.  Get High-res Image Gene #66: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0106 (Fisher's exact test), Q value = 0.075

Table S186.  Gene #66: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
18P LOSS MUTATED 5 8 2
18P LOSS WILD-TYPE 40 14 2

Figure S186.  Get High-res Image Gene #66: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'GENDER'

P value = 0.0487 (Fisher's exact test), Q value = 0.21

Table S187.  Gene #66: '18p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
18P LOSS MUTATED 16 23
18P LOSS WILD-TYPE 56 174

Figure S187.  Get High-res Image Gene #66: '18p loss' versus Clinical Feature #7: 'GENDER'

'18q loss' versus 'Time to Death'

P value = 1.08e-06 (logrank test), Q value = 1e-04

Table S188.  Gene #67: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
18Q LOSS MUTATED 41 14 0.1 - 123.6 (13.1)
18Q LOSS WILD-TYPE 215 20 0.1 - 194.8 (23.3)

Figure S188.  Get High-res Image Gene #67: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S189.  Gene #67: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
18Q LOSS MUTATED 13 1 20 5
18Q LOSS WILD-TYPE 154 20 29 9

Figure S189.  Get High-res Image Gene #67: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S190.  Gene #67: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
18Q LOSS MUTATED 14 4 23
18Q LOSS WILD-TYPE 162 25 33

Figure S190.  Get High-res Image Gene #67: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00265 (Fisher's exact test), Q value = 0.029

Table S191.  Gene #67: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
18Q LOSS MUTATED 6 11 2
18Q LOSS WILD-TYPE 39 11 2

Figure S191.  Get High-res Image Gene #67: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00357 (Fisher's exact test), Q value = 0.033

Table S192.  Gene #68: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
19P LOSS MUTATED 4 1 8 1
19P LOSS WILD-TYPE 163 20 41 13

Figure S192.  Get High-res Image Gene #68: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00249 (Fisher's exact test), Q value = 0.028

Table S193.  Gene #68: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
19P LOSS MUTATED 5 1 9
19P LOSS WILD-TYPE 171 28 47

Figure S193.  Get High-res Image Gene #68: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0484 (Fisher's exact test), Q value = 0.21

Table S194.  Gene #68: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
19P LOSS MUTATED 1 3 1
19P LOSS WILD-TYPE 44 19 3

Figure S194.  Get High-res Image Gene #68: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'Time to Death'

P value = 0.0107 (logrank test), Q value = 0.076

Table S195.  Gene #69: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
19Q LOSS MUTATED 15 4 0.9 - 54.6 (14.1)
19Q LOSS WILD-TYPE 241 30 0.1 - 194.8 (21.7)

Figure S195.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 8e-04

Table S196.  Gene #69: '19q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
19Q LOSS MUTATED 2 1 10 1
19Q LOSS WILD-TYPE 165 20 39 13

Figure S196.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 8e-04

Table S197.  Gene #69: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
19Q LOSS MUTATED 3 1 11
19Q LOSS WILD-TYPE 173 28 45

Figure S197.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.048 (Fisher's exact test), Q value = 0.21

Table S198.  Gene #69: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
19Q LOSS MUTATED 1 3 1
19Q LOSS WILD-TYPE 44 19 3

Figure S198.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00591 (Fisher's exact test), Q value = 0.048

Table S199.  Gene #70: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
21Q LOSS MUTATED 17 3 14 4
21Q LOSS WILD-TYPE 150 18 35 10

Figure S199.  Get High-res Image Gene #70: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00184 (Fisher's exact test), Q value = 0.022

Table S200.  Gene #70: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
21Q LOSS MUTATED 18 5 17
21Q LOSS WILD-TYPE 158 24 39

Figure S200.  Get High-res Image Gene #70: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0383 (Wilcoxon-test), Q value = 0.19

Table S201.  Gene #70: '21q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
21Q LOSS MUTATED 8 90.0 (5.3)
21Q LOSS WILD-TYPE 52 92.3 (16.6)

Figure S201.  Get High-res Image Gene #70: '21q loss' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'Time to Death'

P value = 0.0581 (logrank test), Q value = 0.24

Table S202.  Gene #71: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
22Q LOSS MUTATED 57 11 0.1 - 123.6 (18.0)
22Q LOSS WILD-TYPE 199 23 0.1 - 194.8 (22.5)

Figure S202.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0357 (Wilcoxon-test), Q value = 0.18

Table S203.  Gene #71: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
22Q LOSS MUTATED 56 57.7 (13.5)
22Q LOSS WILD-TYPE 208 62.3 (11.7)

Figure S203.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S204.  Gene #71: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
22Q LOSS MUTATED 19 3 24 7
22Q LOSS WILD-TYPE 148 18 25 7

Figure S204.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S205.  Gene #71: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
22Q LOSS MUTATED 22 4 29
22Q LOSS WILD-TYPE 154 25 27

Figure S205.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00664 (Fisher's exact test), Q value = 0.053

Table S206.  Gene #71: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
22Q LOSS MUTATED 10 13 2
22Q LOSS WILD-TYPE 35 9 2

Figure S206.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0427 (Fisher's exact test), Q value = 0.19

Table S207.  Gene #71: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
22Q LOSS MUTATED 20 5
22Q LOSS WILD-TYPE 70 4

Figure S207.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'GENDER'

P value = 0.000624 (Fisher's exact test), Q value = 0.0093

Table S208.  Gene #71: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
22Q LOSS MUTATED 26 31
22Q LOSS WILD-TYPE 46 166

Figure S208.  Get High-res Image Gene #71: '22q loss' versus Clinical Feature #7: 'GENDER'

'xp loss' versus 'Time to Death'

P value = 7.23e-05 (logrank test), Q value = 0.0015

Table S209.  Gene #72: 'xp loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
XP LOSS MUTATED 30 10 0.1 - 86.3 (14.6)
XP LOSS WILD-TYPE 226 24 0.1 - 194.8 (23.3)

Figure S209.  Get High-res Image Gene #72: 'xp loss' versus Clinical Feature #1: 'Time to Death'

'xp loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S210.  Gene #72: 'xp loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
XP LOSS MUTATED 8 1 15 3
XP LOSS WILD-TYPE 159 20 34 11

Figure S210.  Get High-res Image Gene #72: 'xp loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xp loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00041

Table S211.  Gene #72: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
XP LOSS MUTATED 9 3 17
XP LOSS WILD-TYPE 167 26 39

Figure S211.  Get High-res Image Gene #72: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0471 (Fisher's exact test), Q value = 0.21

Table S212.  Gene #72: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
XP LOSS MUTATED 5 8 1
XP LOSS WILD-TYPE 40 14 3

Figure S212.  Get High-res Image Gene #72: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'RACE'

P value = 0.0088 (Fisher's exact test), Q value = 0.065

Table S213.  Gene #72: 'xp loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
XP LOSS MUTATED 0 3 10 16
XP LOSS WILD-TYPE 2 2 50 171

Figure S213.  Get High-res Image Gene #72: 'xp loss' versus Clinical Feature #11: 'RACE'

'xq loss' versus 'Time to Death'

P value = 2.53e-05 (logrank test), Q value = 0.00074

Table S214.  Gene #73: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
XQ LOSS MUTATED 27 10 0.1 - 86.3 (14.1)
XQ LOSS WILD-TYPE 229 24 0.1 - 194.8 (23.3)

Figure S214.  Get High-res Image Gene #73: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'YEARS_TO_BIRTH'

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

Table S215.  Gene #73: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
XQ LOSS MUTATED 27 55.8 (14.9)
XQ LOSS WILD-TYPE 237 61.9 (11.8)

Figure S215.  Get High-res Image Gene #73: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0019

Table S216.  Gene #73: 'xq loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
XQ LOSS MUTATED 8 1 13 3
XQ LOSS WILD-TYPE 159 20 36 11

Figure S216.  Get High-res Image Gene #73: 'xq loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0015

Table S217.  Gene #73: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
XQ LOSS MUTATED 9 2 15
XQ LOSS WILD-TYPE 167 27 41

Figure S217.  Get High-res Image Gene #73: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.019 (Fisher's exact test), Q value = 0.12

Table S218.  Gene #73: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
XQ LOSS MUTATED 4 8 1
XQ LOSS WILD-TYPE 41 14 3

Figure S218.  Get High-res Image Gene #73: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'RACE'

P value = 0.0121 (Fisher's exact test), Q value = 0.084

Table S219.  Gene #73: 'xq loss' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
XQ LOSS MUTATED 0 3 8 15
XQ LOSS WILD-TYPE 2 2 52 172

Figure S219.  Get High-res Image Gene #73: '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/15087099/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/15081779/KIRP-TP.merged_data.txt

  • Number of patients = 269

  • Number of significantly arm-level cnvs = 73

  • Number of selected clinical features = 12

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
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