Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 31 focal events and 12 clinical features across 269 patients, 127 significant findings detected with Q value < 0.25.

  • amp_2p23.2 cnv correlated to 'PATHOLOGY_N_STAGE' and 'PATHOLOGY_M_STAGE'.

  • amp_2q32.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • amp_3q27.1 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_5q35.2 cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • amp_7q31.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • amp_17q25.2 cnv correlated to 'GENDER' and 'RACE'.

  • amp_19p13.2 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.

  • del_1p36.31 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_2p12 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • del_2q22.1 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • del_2q37.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • del_3p22.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • del_4q34.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

  • del_5p15.33 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • del_5q35.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • del_6p12.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • del_6q22.31 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • del_6q25.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • del_9p21.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_10q21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • del_11q22.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • del_11q23.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • del_14q11.2 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • del_14q24.2 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • del_15q13.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_16q24.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_T_STAGE'.

  • del_19p13.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_19q13.42 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • del_22q12.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • del_xp11.4 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'RACE'.

  • del_xq28 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 31 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 127 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		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
del 9p21 3 38 (14%) 231 1.91e-07
(3.56e-05) 		0.55
(0.819) 		1e-05
(0.000266) 		1e-05
(0.000266) 		0.00022
(0.00292) 		0.0215
(0.0929) 		0.00483
(0.0264) 		0.00947
(0.0476) 		0.35
(0.64) 		0.64
(0.858) 		0.143
(0.374) 		1
(1.00)
del 14q24 2 47 (17%) 222 0.00158
(0.0128) 		0.964
(1.00) 		0.00155
(0.0128) 		0.00021
(0.00289) 		0.0146
(0.0677) 		0.182
(0.442) 		0.0286
(0.113) 		0.0732
(0.23) 		0.265
(0.543) 		0.0369
(0.136) 		0.957
(1.00) 		0.697
(0.892)
del 22q12 2 60 (22%) 209 0.0398
(0.143) 		0.0559
(0.187) 		1e-05
(0.000266) 		1e-05
(0.000266) 		0.00195
(0.0144) 		0.0596
(0.195) 		0.00158
(0.0128) 		0.164
(0.409) 		0.879
(1.00) 		0.135
(0.361) 		0.208
(0.479) 		0.713
(0.899)
del xq28 25 (9%) 244 4.42e-05
(0.000865) 		0.0253
(0.104) 		0.00073
(0.00734) 		0.00317
(0.0203) 		0.0221
(0.0935) 		0.592
(0.842) 		0.0171
(0.0768) 		0.153
(0.389) 		0.658
(0.868) 		0.168
(0.413) 		0.085
(0.249) 		0.606
(0.842)
del 1p36 31 50 (19%) 219 0.0182
(0.08) 		0.16
(0.404) 		1e-05
(0.000266) 		1e-05
(0.000266) 		0.00346
(0.0215) 		0.368
(0.644) 		0.0528
(0.182) 		0.00253
(0.0175) 		0.68
(0.888) 		0.2
(0.464) 		0.527
(0.796) 		0.697
(0.892)
del 5q35 2 11 (4%) 258 8.06e-05
(0.00125) 		0.00481
(0.0264) 		0.00028
(0.00347) 		3e-05
(0.000656) 		0.0733
(0.23) 		0.321
(0.619) 		0.00979
(0.0486) 		0.762
(0.932) 		0.314
(0.615)
del 15q13 3 33 (12%) 236 0.000304
(0.00353) 		0.0746
(0.231) 		0.0004
(0.00438) 		8e-05
(0.00125) 		0.00281
(0.0187) 		0.0937
(0.268) 		0.402
(0.665) 		0.00476
(0.0264) 		0.843
(0.982) 		1
(1.00) 		0.539
(0.806) 		1
(1.00)
del xp11 4 30 (11%) 239 0.00181
(0.0141) 		0.169
(0.413) 		1e-05
(0.000266) 		5e-05
(0.000886) 		0.0787
(0.236) 		1
(1.00) 		0.0147
(0.0677) 		0.431
(0.685) 		0.704
(0.896) 		0.214
(0.488) 		0.0132
(0.063) 		0.611
(0.842)
amp 7q31 2 165 (61%) 104 0.236
(0.508) 		0.388
(0.647) 		0.0005
(0.00517) 		0.0328
(0.123) 		0.369
(0.644) 		0.728
(0.902) 		0.00477
(0.0264) 		0.0812
(0.242) 		0.764
(0.932) 		0.00359
(0.0216) 		0.325
(0.62) 		0.369
(0.644)
del 3p22 1 23 (9%) 246 0.00217
(0.0152) 		0.0343
(0.128) 		1e-05
(0.000266) 		2e-05
(0.000465) 		0.078
(0.236) 		0.0914
(0.266) 		1
(1.00) 		0.153
(0.389) 		0.806
(0.957) 		0.294
(0.594) 		0.576
(0.842) 		0.606
(0.842)
del 4q34 3 30 (11%) 239 0.00153
(0.0128) 		0.489
(0.758) 		2e-05
(0.000465) 		8e-05
(0.00125) 		0.108
(0.295) 		0.611
(0.842) 		0.0147
(0.0677) 		0.431
(0.685) 		0.791
(0.95) 		0.935
(1.00) 		0.0283
(0.113) 		0.358
(0.644)
del 11q22 3 30 (11%) 239 0.00095
(0.00906) 		0.354
(0.64) 		1e-05
(0.000266) 		1e-05
(0.000266) 		0.00197
(0.0144) 		0.0758
(0.231) 		0.666
(0.874) 		0.0967
(0.27) 		0.441
(0.698) 		0.324
(0.62) 		0.191
(0.451) 		0.372
(0.645)
del 11q23 3 28 (10%) 241 4.06e-05
(0.00084) 		0.354
(0.64) 		1e-05
(0.000266) 		1e-05
(0.000266) 		0.00203
(0.0145) 		0.0598
(0.195) 		1
(1.00) 		0.0967
(0.27) 		0.937
(1.00) 		0.727
(0.902) 		0.137
(0.364) 		0.614
(0.842)
del 14q11 2 48 (18%) 221 0.00498
(0.0269) 		0.811
(0.961) 		0.00647
(0.0339) 		0.00162
(0.0128) 		0.0423
(0.15) 		0.395
(0.656) 		0.0317
(0.12) 		0.144
(0.376) 		0.366
(0.644) 		0.188
(0.446) 		1
(1.00) 		0.698
(0.892)
del 19p13 3 20 (7%) 249 0.0106
(0.052) 		0.762
(0.932) 		0.00139
(0.0126) 		0.00029
(0.00348) 		0.0315
(0.12) 		0.386
(0.646) 		0.794
(0.95) 		0.00532
(0.0283) 		0.355
(0.64) 		0.539
(0.806) 		0.606
(0.842)
del 5p15 33 13 (5%) 256 0.163
(0.409) 		0.184
(0.442) 		0.0382
(0.139) 		0.0218
(0.0933) 		0.00272
(0.0184) 		0.386
(0.646) 		0.047
(0.163) 		0.216
(0.489) 		0.904
(1.00) 		1
(1.00) 		0.385
(0.646)
del 6q22 31 27 (10%) 242 0.419
(0.684) 		0.773
(0.94) 		0.00357
(0.0216) 		0.00048
(0.0051) 		0.0754
(0.231) 		1
(1.00) 		0.0117
(0.0566) 		0.431
(0.685) 		0.581
(0.842) 		0.366
(0.644) 		0.125
(0.339) 		0.608
(0.842)
amp 2q32 1 51 (19%) 218 0.496
(0.758) 		0.493
(0.758) 		0.0269
(0.11) 		0.0841
(0.248) 		0.0997
(0.275) 		0.0154
(0.0697) 		0.725
(0.902) 		0.381
(0.646) 		0.827
(0.974) 		0.618
(0.842) 		0.593
(0.842) 		1
(1.00)
del 2q37 3 11 (4%) 258 0.857
(0.99) 		0.79
(0.95) 		0.00905
(0.0461) 		0.00403
(0.0234) 		1
(1.00) 		1
(1.00) 		0.0737
(0.23) 		0.497
(0.758) 		0.837
(0.982) 		0.781
(0.947) 		1
(1.00)
del 6p12 3 23 (9%) 246 0.234
(0.508) 		0.429
(0.685) 		0.00162
(0.0128) 		0.00198
(0.0144) 		0.0598
(0.195) 		0.592
(0.842) 		0.459
(0.724) 		0.847
(0.982) 		0.226
(0.501) 		0.847
(0.982) 		0.246
(0.526) 		0.606
(0.842)
del 6q25 3 29 (11%) 240 0.497
(0.758) 		0.711
(0.899) 		0.00025
(0.00321) 		5e-05
(0.000886) 		0.0982
(0.273) 		0.595
(0.842) 		0.00303
(0.0197) 		0.299
(0.598) 		0.581
(0.842) 		0.366
(0.644) 		0.138
(0.364) 		0.614
(0.842)
del 10q21 1 17 (6%) 252 0.308
(0.606) 		0.422
(0.685) 		9e-05
(0.00134) 		0.00079
(0.00773) 		0.0314
(0.12) 		1
(1.00) 		0.168
(0.413) 		0.153
(0.389) 		0.743
(0.918) 		0.649
(0.86) 		0.381
(0.646) 		1
(1.00)
del 16q24 1 11 (4%) 258 1.05e-08
(3.91e-06) 		0.409
(0.673) 		0.00381
(0.0225) 		0.00733
(0.0379) 		0.13
(0.35) 		0.321
(0.619) 		0.492
(0.758) 		0.571
(0.842) 		0.707
(0.897) 		0.795
(0.95) 		0.255
(0.527) 		1
(1.00)
amp 2p23 2 42 (16%) 227 0.533
(0.803) 		0.338
(0.636) 		0.266
(0.543) 		0.418
(0.684) 		0.0183
(0.08) 		0.028
(0.113) 		0.343
(0.64) 		0.516
(0.783) 		0.344
(0.64) 		0.726
(0.902) 		0.647
(0.86) 		1
(1.00)
amp 17q25 2 189 (70%) 80 0.87
(0.999) 		0.188
(0.446) 		0.219
(0.491) 		0.308
(0.606) 		0.84
(0.982) 		1
(1.00) 		0.0247
(0.103) 		0.696
(0.892) 		0.347
(0.64) 		0.231
(0.505) 		0.0428
(0.15) 		0.329
(0.625)
amp 19p13 2 30 (11%) 239 0.621
(0.844) 		0.0542
(0.185) 		0.977
(1.00) 		0.0653
(0.209) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.716
(0.9) 		0.383
(0.646) 		0.469
(0.734) 		0.636
(0.857)
del 2p12 6 (2%) 263 0.608
(0.842) 		0.431
(0.685) 		0.04
(0.143) 		0.0307
(0.12) 		1
(1.00) 		0.251
(0.527) 		1
(1.00) 		0.691
(0.892) 		1
(1.00)
del 2q22 1 9 (3%) 260 0.252
(0.527) 		0.667
(0.874) 		0.0012
(0.0112) 		0.00346
(0.0215) 		0.198
(0.464) 		0.321
(0.619) 		0.255
(0.527) 		0.299
(0.598) 		0.816
(0.964) 		0.561
(0.832) 		0.745
(0.918) 		1
(1.00)
del 19q13 42 19 (7%) 250 0.201
(0.465) 		0.618
(0.842) 		0.00035
(0.00395) 		0.0002
(0.00286) 		0.218
(0.491) 		1
(1.00) 		0.599
(0.842) 		0.0967
(0.27) 		0.989
(1.00) 		0.222
(0.494) 		0.251
(0.527) 		0.606
(0.842)
amp 3q27 1 93 (35%) 176 0.864
(0.995) 		0.29
(0.589) 		0.333
(0.628) 		0.236
(0.508) 		1
(1.00) 		0.0549
(0.186) 		0.47
(0.734) 		0.228
(0.502) 		0.354
(0.64) 		0.385
(0.646) 		0.183
(0.442) 		1
(1.00)
amp 5q35 2 35 (13%) 234 0.934
(1.00) 		0.641
(0.858) 		0.0644
(0.208) 		0.0927
(0.267) 		1
(1.00) 		0.65
(0.86) 		0.685
(0.89) 		0.307
(0.606) 		0.634
(0.857) 		0.804
(0.957) 		0.252
(0.527) 		0.373
(0.645)
'amp_2p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0183 (Fisher's exact test), Q value = 0.08

Table S1.  Gene #1: 'amp_2p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
AMP PEAK 1(2P23.2) MUTATED 4 8 1
AMP PEAK 1(2P23.2) WILD-TYPE 41 14 3

Figure S1.  Get High-res Image Gene #1: 'amp_2p23.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2p23.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.028 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #1: 'amp_2p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
AMP PEAK 1(2P23.2) MUTATED 11 4
AMP PEAK 1(2P23.2) WILD-TYPE 79 5

Figure S2.  Get High-res Image Gene #1: 'amp_2p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_2q32.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0269 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #2: 'amp_2q32.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
AMP PEAK 2(2Q32.1) MUTATED 28 3 12 7
AMP PEAK 2(2Q32.1) WILD-TYPE 139 18 37 7

Figure S3.  Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_2q32.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0841 (Fisher's exact test), Q value = 0.25

Table S4.  Gene #2: 'amp_2q32.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
AMP PEAK 2(2Q32.1) MUTATED 28 7 16
AMP PEAK 2(2Q32.1) WILD-TYPE 148 22 40

Figure S4.  Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_2q32.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0154 (Fisher's exact test), Q value = 0.07

Table S5.  Gene #2: 'amp_2q32.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
AMP PEAK 2(2Q32.1) MUTATED 15 5
AMP PEAK 2(2Q32.1) WILD-TYPE 75 4

Figure S5.  Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_3q27.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0549 (Fisher's exact test), Q value = 0.19

Table S6.  Gene #3: 'amp_3q27.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
AMP PEAK 3(3Q27.1) MUTATED 29 0
AMP PEAK 3(3Q27.1) WILD-TYPE 61 9

Figure S6.  Get High-res Image Gene #3: 'amp_3q27.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0644 (Fisher's exact test), Q value = 0.21

Table S7.  Gene #4: 'amp_5q35.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
AMP PEAK 4(5Q35.2) MUTATED 16 2 11 3
AMP PEAK 4(5Q35.2) WILD-TYPE 151 19 38 11

Figure S7.  Get High-res Image Gene #4: 'amp_5q35.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_7q31.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0052

Table S8.  Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
AMP PEAK 5(7Q31.2) MUTATED 113 11 18 11
AMP PEAK 5(7Q31.2) WILD-TYPE 54 10 31 3

Figure S8.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_7q31.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0328 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #5: 'amp_7q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
AMP PEAK 5(7Q31.2) MUTATED 116 19 26
AMP PEAK 5(7Q31.2) WILD-TYPE 60 10 30

Figure S9.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 0.00477 (Fisher's exact test), Q value = 0.026

Table S10.  Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
AMP PEAK 5(7Q31.2) MUTATED 34 131
AMP PEAK 5(7Q31.2) WILD-TYPE 38 66

Figure S10.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0812 (Wilcoxon-test), Q value = 0.24

Table S11.  Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
AMP PEAK 5(7Q31.2) MUTATED 42 95.0 (7.1)
AMP PEAK 5(7Q31.2) WILD-TYPE 18 85.0 (25.5)

Figure S11.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q31.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00359 (Wilcoxon-test), Q value = 0.022

Table S12.  Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
AMP PEAK 5(7Q31.2) MUTATED 29 1966.8 (14.7)
AMP PEAK 5(7Q31.2) WILD-TYPE 22 1979.7 (14.8)

Figure S12.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q25.2' versus 'GENDER'

P value = 0.0247 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #6: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
AMP PEAK 6(17Q25.2) MUTATED 43 146
AMP PEAK 6(17Q25.2) WILD-TYPE 29 51

Figure S13.  Get High-res Image Gene #6: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

'amp_17q25.2' versus 'RACE'

P value = 0.0428 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #6: 'amp_17q25.2' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
AMP PEAK 6(17Q25.2) MUTATED 2 4 34 139
AMP PEAK 6(17Q25.2) WILD-TYPE 0 1 26 48

Figure S14.  Get High-res Image Gene #6: 'amp_17q25.2' versus Clinical Feature #11: 'RACE'

'amp_19p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0542 (Wilcoxon-test), Q value = 0.19

Table S15.  Gene #7: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
AMP PEAK 7(19P13.2) MUTATED 29 57.1 (12.6)
AMP PEAK 7(19P13.2) WILD-TYPE 235 61.8 (12.1)

Figure S15.  Get High-res Image Gene #7: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0653 (Fisher's exact test), Q value = 0.21

Table S16.  Gene #7: 'amp_19p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
AMP PEAK 7(19P13.2) MUTATED 18 7 4
AMP PEAK 7(19P13.2) WILD-TYPE 158 22 52

Figure S16.  Get High-res Image Gene #7: 'amp_19p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.31' versus 'Time to Death'

P value = 0.0182 (logrank test), Q value = 0.08

Table S17.  Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 1(1P36.31) MUTATED 50 11 0.1 - 123.6 (16.3)
DEL PEAK 1(1P36.31) WILD-TYPE 206 23 0.1 - 194.8 (23.3)

Figure S17.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'NEOPLASM_DISEASESTAGE'

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

Table S18.  Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 1(1P36.31) MUTATED 16 3 22 4
DEL PEAK 1(1P36.31) WILD-TYPE 151 18 27 10

Figure S18.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p36.31' versus 'PATHOLOGY_T_STAGE'

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

Table S19.  Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 1(1P36.31) MUTATED 19 5 24
DEL PEAK 1(1P36.31) WILD-TYPE 157 24 32

Figure S19.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.00346 (Fisher's exact test), Q value = 0.021

Table S20.  Gene #8: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 1(1P36.31) MUTATED 7 12 1
DEL PEAK 1(1P36.31) WILD-TYPE 38 10 3

Figure S20.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.31' versus 'GENDER'

P value = 0.0528 (Fisher's exact test), Q value = 0.18

Table S21.  Gene #8: 'del_1p36.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 1(1P36.31) MUTATED 19 31
DEL PEAK 1(1P36.31) WILD-TYPE 53 166

Figure S21.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #7: 'GENDER'

'del_1p36.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00253 (Wilcoxon-test), Q value = 0.017

Table S22.  Gene #8: 'del_1p36.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
DEL PEAK 1(1P36.31) MUTATED 13 83.1 (25.6)
DEL PEAK 1(1P36.31) WILD-TYPE 47 94.5 (10.6)

Figure S22.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2p12' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.04 (Fisher's exact test), Q value = 0.14

Table S23.  Gene #9: 'del_2p12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 2(2P12) MUTATED 1 0 3 1
DEL PEAK 2(2P12) WILD-TYPE 166 21 46 13

Figure S23.  Get High-res Image Gene #9: 'del_2p12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_2p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.0307 (Fisher's exact test), Q value = 0.12

Table S24.  Gene #9: 'del_2p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 2(2P12) MUTATED 1 2 2
DEL PEAK 2(2P12) WILD-TYPE 175 27 54

Figure S24.  Get High-res Image Gene #9: 'del_2p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q22.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0012 (Fisher's exact test), Q value = 0.011

Table S25.  Gene #10: 'del_2q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 3(2Q22.1) MUTATED 1 0 6 1
DEL PEAK 3(2Q22.1) WILD-TYPE 166 21 43 13

Figure S25.  Get High-res Image Gene #10: 'del_2q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00346 (Fisher's exact test), Q value = 0.021

Table S26.  Gene #10: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 3(2Q22.1) MUTATED 2 0 6
DEL PEAK 3(2Q22.1) WILD-TYPE 174 29 50

Figure S26.  Get High-res Image Gene #10: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00905 (Fisher's exact test), Q value = 0.046

Table S27.  Gene #11: 'del_2q37.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 4(2Q37.3) MUTATED 2 2 5 0
DEL PEAK 4(2Q37.3) WILD-TYPE 165 19 44 14

Figure S27.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00403 (Fisher's exact test), Q value = 0.023

Table S28.  Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 4(2Q37.3) MUTATED 2 3 5
DEL PEAK 4(2Q37.3) WILD-TYPE 174 26 51

Figure S28.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'GENDER'

P value = 0.0737 (Fisher's exact test), Q value = 0.23

Table S29.  Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 4(2Q37.3) MUTATED 6 5
DEL PEAK 4(2Q37.3) WILD-TYPE 66 192

Figure S29.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

'del_3p22.1' versus 'Time to Death'

P value = 0.00217 (logrank test), Q value = 0.015

Table S30.  Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 5(3P22.1) MUTATED 23 7 0.1 - 86.3 (14.1)
DEL PEAK 5(3P22.1) WILD-TYPE 233 27 0.1 - 194.8 (22.1)

Figure S30.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

'del_3p22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0343 (Wilcoxon-test), Q value = 0.13

Table S31.  Gene #12: 'del_3p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
DEL PEAK 5(3P22.1) MUTATED 22 55.4 (12.6)
DEL PEAK 5(3P22.1) WILD-TYPE 242 61.8 (12.1)

Figure S31.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p22.1' versus 'NEOPLASM_DISEASESTAGE'

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

Table S32.  Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 5(3P22.1) MUTATED 5 1 14 3
DEL PEAK 5(3P22.1) WILD-TYPE 162 20 35 11

Figure S32.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00046

Table S33.  Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 5(3P22.1) MUTATED 6 3 14
DEL PEAK 5(3P22.1) WILD-TYPE 170 26 42

Figure S33.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.078 (Fisher's exact test), Q value = 0.24

Table S34.  Gene #12: 'del_3p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 5(3P22.1) MUTATED 6 8 1
DEL PEAK 5(3P22.1) WILD-TYPE 39 14 3

Figure S34.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q34.3' versus 'Time to Death'

P value = 0.00153 (logrank test), Q value = 0.013

Table S35.  Gene #13: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 6(4Q34.3) MUTATED 29 8 0.1 - 79.9 (13.7)
DEL PEAK 6(4Q34.3) WILD-TYPE 227 26 0.1 - 194.8 (22.3)

Figure S35.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00046

Table S36.  Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 6(4Q34.3) MUTATED 7 2 16 2
DEL PEAK 6(4Q34.3) WILD-TYPE 160 19 33 12

Figure S36.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S37.  Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 6(4Q34.3) MUTATED 9 4 15
DEL PEAK 6(4Q34.3) WILD-TYPE 167 25 41

Figure S37.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'GENDER'

P value = 0.0147 (Fisher's exact test), Q value = 0.068

Table S38.  Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 6(4Q34.3) MUTATED 14 16
DEL PEAK 6(4Q34.3) WILD-TYPE 58 181

Figure S38.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'RACE'

P value = 0.0283 (Fisher's exact test), Q value = 0.11

Table S39.  Gene #13: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
DEL PEAK 6(4Q34.3) MUTATED 0 3 6 17
DEL PEAK 6(4Q34.3) WILD-TYPE 2 2 54 170

Figure S39.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_5p15.33' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0382 (Fisher's exact test), Q value = 0.14

Table S40.  Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 7(5P15.33) MUTATED 5 0 5 2
DEL PEAK 7(5P15.33) WILD-TYPE 162 21 44 12

Figure S40.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.093

Table S41.  Gene #14: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 7(5P15.33) MUTATED 5 1 7
DEL PEAK 7(5P15.33) WILD-TYPE 171 28 49

Figure S41.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.00272 (Fisher's exact test), Q value = 0.018

Table S42.  Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 7(5P15.33) MUTATED 0 5 1
DEL PEAK 7(5P15.33) WILD-TYPE 45 17 3

Figure S42.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'GENDER'

P value = 0.047 (Fisher's exact test), Q value = 0.16

Table S43.  Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 7(5P15.33) MUTATED 7 6
DEL PEAK 7(5P15.33) WILD-TYPE 65 191

Figure S43.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

'del_5q35.2' versus 'Time to Death'

P value = 8.06e-05 (logrank test), Q value = 0.0012

Table S44.  Gene #15: 'del_5q35.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 8(5Q35.2) MUTATED 10 5 2.8 - 79.9 (18.9)
DEL PEAK 8(5Q35.2) WILD-TYPE 246 29 0.1 - 194.8 (21.5)

Figure S44.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #1: 'Time to Death'

'del_5q35.2' versus 'YEARS_TO_BIRTH'

P value = 0.00481 (Wilcoxon-test), Q value = 0.026

Table S45.  Gene #15: 'del_5q35.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
DEL PEAK 8(5Q35.2) MUTATED 10 46.8 (17.3)
DEL PEAK 8(5Q35.2) WILD-TYPE 254 61.9 (11.7)

Figure S45.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q35.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0035

Table S46.  Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 8(5Q35.2) MUTATED 1 1 7 1
DEL PEAK 8(5Q35.2) WILD-TYPE 166 20 42 13

Figure S46.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5q35.2' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S47.  Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 8(5Q35.2) MUTATED 1 1 9
DEL PEAK 8(5Q35.2) WILD-TYPE 175 28 47

Figure S47.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5q35.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0733 (Fisher's exact test), Q value = 0.23

Table S48.  Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 8(5Q35.2) MUTATED 1 4 0
DEL PEAK 8(5Q35.2) WILD-TYPE 44 18 4

Figure S48.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q35.2' versus 'GENDER'

P value = 0.00979 (Fisher's exact test), Q value = 0.049

Table S49.  Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 8(5Q35.2) MUTATED 7 4
DEL PEAK 8(5Q35.2) WILD-TYPE 65 193

Figure S49.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

'del_6p12.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00162 (Fisher's exact test), Q value = 0.013

Table S50.  Gene #16: 'del_6p12.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 9(6P12.3) MUTATED 9 0 11 2
DEL PEAK 9(6P12.3) WILD-TYPE 158 21 38 12

Figure S50.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6p12.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00198 (Fisher's exact test), Q value = 0.014

Table S51.  Gene #16: 'del_6p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 9(6P12.3) MUTATED 10 1 12
DEL PEAK 9(6P12.3) WILD-TYPE 166 28 44

Figure S51.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6p12.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0598 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #16: 'del_6p12.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 9(6P12.3) MUTATED 5 1 2
DEL PEAK 9(6P12.3) WILD-TYPE 40 21 2

Figure S52.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q22.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00357 (Fisher's exact test), Q value = 0.022

Table S53.  Gene #17: 'del_6q22.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 10(6Q22.31) MUTATED 12 0 11 3
DEL PEAK 10(6Q22.31) WILD-TYPE 155 21 38 11

Figure S53.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q22.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00048 (Fisher's exact test), Q value = 0.0051

Table S54.  Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 10(6Q22.31) MUTATED 12 1 14
DEL PEAK 10(6Q22.31) WILD-TYPE 164 28 42

Figure S54.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q22.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0754 (Fisher's exact test), Q value = 0.23

Table S55.  Gene #17: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 10(6Q22.31) MUTATED 4 4 2
DEL PEAK 10(6Q22.31) WILD-TYPE 41 18 2

Figure S55.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q22.31' versus 'GENDER'

P value = 0.0117 (Fisher's exact test), Q value = 0.057

Table S56.  Gene #17: 'del_6q22.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 10(6Q22.31) MUTATED 13 14
DEL PEAK 10(6Q22.31) WILD-TYPE 59 183

Figure S56.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #7: 'GENDER'

'del_6q25.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0032

Table S57.  Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 11(6Q25.3) MUTATED 12 0 14 2
DEL PEAK 11(6Q25.3) WILD-TYPE 155 21 35 12

Figure S57.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q25.3' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00089

Table S58.  Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 11(6Q25.3) MUTATED 12 1 16
DEL PEAK 11(6Q25.3) WILD-TYPE 164 28 40

Figure S58.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q25.3' versus 'GENDER'

P value = 0.00303 (Fisher's exact test), Q value = 0.02

Table S59.  Gene #18: 'del_6q25.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 11(6Q25.3) MUTATED 15 14
DEL PEAK 11(6Q25.3) WILD-TYPE 57 183

Figure S59.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'Time to Death'

P value = 1.91e-07 (logrank test), Q value = 3.6e-05

Table S60.  Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 12(9P21.3) MUTATED 36 14 0.1 - 93.3 (16.5)
DEL PEAK 12(9P21.3) WILD-TYPE 220 20 0.1 - 194.8 (23.3)

Figure S60.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM_DISEASESTAGE'

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

Table S61.  Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 12(9P21.3) MUTATED 10 0 18 6
DEL PEAK 12(9P21.3) WILD-TYPE 157 21 31 8

Figure S61.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

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

Table S62.  Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 12(9P21.3) MUTATED 11 3 22
DEL PEAK 12(9P21.3) WILD-TYPE 165 26 34

Figure S62.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0029

Table S63.  Gene #19: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 12(9P21.3) MUTATED 6 13 2
DEL PEAK 12(9P21.3) WILD-TYPE 39 9 2

Figure S63.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0215 (Fisher's exact test), Q value = 0.093

Table S64.  Gene #19: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
DEL PEAK 12(9P21.3) MUTATED 10 4
DEL PEAK 12(9P21.3) WILD-TYPE 80 5

Figure S64.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.00483 (Fisher's exact test), Q value = 0.026

Table S65.  Gene #19: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 12(9P21.3) MUTATED 18 20
DEL PEAK 12(9P21.3) WILD-TYPE 54 177

Figure S65.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00947 (Wilcoxon-test), Q value = 0.048

Table S66.  Gene #19: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
DEL PEAK 12(9P21.3) MUTATED 12 83.3 (26.7)
DEL PEAK 12(9P21.3) WILD-TYPE 48 94.2 (10.7)

Figure S66.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0013

Table S67.  Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 13(10Q21.1) MUTATED 4 0 11 1
DEL PEAK 13(10Q21.1) WILD-TYPE 163 21 38 13

Figure S67.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00079 (Fisher's exact test), Q value = 0.0077

Table S68.  Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 13(10Q21.1) MUTATED 6 0 10
DEL PEAK 13(10Q21.1) WILD-TYPE 170 29 46

Figure S68.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0314 (Fisher's exact test), Q value = 0.12

Table S69.  Gene #20: 'del_10q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 13(10Q21.1) MUTATED 2 5 1
DEL PEAK 13(10Q21.1) WILD-TYPE 43 17 3

Figure S69.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 0.00095 (logrank test), Q value = 0.0091

Table S70.  Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 14(11Q22.3) MUTATED 28 9 0.1 - 123.6 (13.1)
DEL PEAK 14(11Q22.3) WILD-TYPE 228 25 0.1 - 194.8 (22.4)

Figure S70.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM_DISEASESTAGE'

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

Table S71.  Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 14(11Q22.3) MUTATED 7 3 14 5
DEL PEAK 14(11Q22.3) WILD-TYPE 160 18 35 9

Figure S71.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_11q22.3' versus 'PATHOLOGY_T_STAGE'

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

Table S72.  Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 14(11Q22.3) MUTATED 8 5 16
DEL PEAK 14(11Q22.3) WILD-TYPE 168 24 40

Figure S72.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00197 (Fisher's exact test), Q value = 0.014

Table S73.  Gene #21: 'del_11q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 14(11Q22.3) MUTATED 3 8 2
DEL PEAK 14(11Q22.3) WILD-TYPE 42 14 2

Figure S73.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q22.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0758 (Fisher's exact test), Q value = 0.23

Table S74.  Gene #21: 'del_11q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
DEL PEAK 14(11Q22.3) MUTATED 9 3
DEL PEAK 14(11Q22.3) WILD-TYPE 81 6

Figure S74.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q23.3' versus 'Time to Death'

P value = 4.06e-05 (logrank test), Q value = 0.00084

Table S75.  Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 15(11Q23.3) MUTATED 26 10 0.1 - 123.6 (13.1)
DEL PEAK 15(11Q23.3) WILD-TYPE 230 24 0.1 - 194.8 (22.2)

Figure S75.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

'del_11q23.3' versus 'NEOPLASM_DISEASESTAGE'

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

Table S76.  Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 15(11Q23.3) MUTATED 5 2 15 5
DEL PEAK 15(11Q23.3) WILD-TYPE 162 19 34 9

Figure S76.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_11q23.3' versus 'PATHOLOGY_T_STAGE'

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

Table S77.  Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 15(11Q23.3) MUTATED 6 4 17
DEL PEAK 15(11Q23.3) WILD-TYPE 170 25 39

Figure S77.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00203 (Fisher's exact test), Q value = 0.015

Table S78.  Gene #22: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 15(11Q23.3) MUTATED 3 8 2
DEL PEAK 15(11Q23.3) WILD-TYPE 42 14 2

Figure S78.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0598 (Fisher's exact test), Q value = 0.2

Table S79.  Gene #22: 'del_11q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
DEL PEAK 15(11Q23.3) MUTATED 8 3
DEL PEAK 15(11Q23.3) WILD-TYPE 82 6

Figure S79.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q11.2' versus 'Time to Death'

P value = 0.00498 (logrank test), Q value = 0.027

Table S80.  Gene #23: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 16(14Q11.2) MUTATED 47 10 0.1 - 80.9 (17.3)
DEL PEAK 16(14Q11.2) WILD-TYPE 209 24 0.1 - 194.8 (22.3)

Figure S80.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

'del_14q11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00647 (Fisher's exact test), Q value = 0.034

Table S81.  Gene #23: 'del_14q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 16(14Q11.2) MUTATED 22 3 14 6
DEL PEAK 16(14Q11.2) WILD-TYPE 145 18 35 8

Figure S81.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_14q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00162 (Fisher's exact test), Q value = 0.013

Table S82.  Gene #23: 'del_14q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 16(14Q11.2) MUTATED 24 4 20
DEL PEAK 16(14Q11.2) WILD-TYPE 152 25 36

Figure S82.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0423 (Fisher's exact test), Q value = 0.15

Table S83.  Gene #23: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 16(14Q11.2) MUTATED 9 8 3
DEL PEAK 16(14Q11.2) WILD-TYPE 36 14 1

Figure S83.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q11.2' versus 'GENDER'

P value = 0.0317 (Fisher's exact test), Q value = 0.12

Table S84.  Gene #23: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 16(14Q11.2) MUTATED 19 29
DEL PEAK 16(14Q11.2) WILD-TYPE 53 168

Figure S84.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

'del_14q24.2' versus 'Time to Death'

P value = 0.00158 (logrank test), Q value = 0.013

Table S85.  Gene #24: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 17(14Q24.2) MUTATED 47 11 0.1 - 80.9 (17.3)
DEL PEAK 17(14Q24.2) WILD-TYPE 209 23 0.1 - 194.8 (22.5)

Figure S85.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

'del_14q24.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00155 (Fisher's exact test), Q value = 0.013

Table S86.  Gene #24: 'del_14q24.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 17(14Q24.2) MUTATED 20 3 15 6
DEL PEAK 17(14Q24.2) WILD-TYPE 147 18 34 8

Figure S86.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_14q24.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0029

Table S87.  Gene #24: 'del_14q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 17(14Q24.2) MUTATED 22 4 21
DEL PEAK 17(14Q24.2) WILD-TYPE 154 25 35

Figure S87.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q24.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.068

Table S88.  Gene #24: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 17(14Q24.2) MUTATED 8 9 3
DEL PEAK 17(14Q24.2) WILD-TYPE 37 13 1

Figure S88.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q24.2' versus 'GENDER'

P value = 0.0286 (Fisher's exact test), Q value = 0.11

Table S89.  Gene #24: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 17(14Q24.2) MUTATED 19 28
DEL PEAK 17(14Q24.2) WILD-TYPE 53 169

Figure S89.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

'del_14q24.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0732 (Wilcoxon-test), Q value = 0.23

Table S90.  Gene #24: 'del_14q24.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
DEL PEAK 17(14Q24.2) MUTATED 12 85.0 (27.1)
DEL PEAK 17(14Q24.2) WILD-TYPE 48 93.8 (10.8)

Figure S90.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q24.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0369 (Wilcoxon-test), Q value = 0.14

Table S91.  Gene #24: 'del_14q24.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 51 1972.4 (15.9)
DEL PEAK 17(14Q24.2) MUTATED 8 1983.8 (15.3)
DEL PEAK 17(14Q24.2) WILD-TYPE 43 1970.3 (15.3)

Figure S91.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_15q13.3' versus 'Time to Death'

P value = 0.000304 (logrank test), Q value = 0.0035

Table S92.  Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 18(15Q13.3) MUTATED 32 9 0.1 - 194.8 (13.0)
DEL PEAK 18(15Q13.3) WILD-TYPE 224 25 0.1 - 129.9 (23.6)

Figure S92.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'YEARS_TO_BIRTH'

P value = 0.0746 (Wilcoxon-test), Q value = 0.23

Table S93.  Gene #25: 'del_15q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
DEL PEAK 18(15Q13.3) MUTATED 32 57.0 (14.6)
DEL PEAK 18(15Q13.3) WILD-TYPE 232 61.9 (11.8)

Figure S93.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q13.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0044

Table S94.  Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 18(15Q13.3) MUTATED 12 1 12 5
DEL PEAK 18(15Q13.3) WILD-TYPE 155 20 37 9

Figure S94.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_15q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S95.  Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 18(15Q13.3) MUTATED 14 1 17
DEL PEAK 18(15Q13.3) WILD-TYPE 162 28 39

Figure S95.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_15q13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00281 (Fisher's exact test), Q value = 0.019

Table S96.  Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 18(15Q13.3) MUTATED 4 10 1
DEL PEAK 18(15Q13.3) WILD-TYPE 41 12 3

Figure S96.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q13.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00476 (Wilcoxon-test), Q value = 0.026

Table S97.  Gene #25: 'del_15q13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
DEL PEAK 18(15Q13.3) MUTATED 8 78.8 (31.8)
DEL PEAK 18(15Q13.3) WILD-TYPE 52 94.0 (10.5)

Figure S97.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_16q24.1' versus 'Time to Death'

P value = 1.05e-08 (logrank test), Q value = 3.9e-06

Table S98.  Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 19(16Q24.1) MUTATED 10 6 0.4 - 51.5 (14.9)
DEL PEAK 19(16Q24.1) WILD-TYPE 246 28 0.1 - 194.8 (22.0)

Figure S98.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_16q24.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00381 (Fisher's exact test), Q value = 0.022

Table S99.  Gene #26: 'del_16q24.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 19(16Q24.1) MUTATED 3 0 6 2
DEL PEAK 19(16Q24.1) WILD-TYPE 164 21 43 12

Figure S99.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_16q24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00733 (Fisher's exact test), Q value = 0.038

Table S100.  Gene #26: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 19(16Q24.1) MUTATED 4 0 7
DEL PEAK 19(16Q24.1) WILD-TYPE 172 29 49

Figure S100.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'Time to Death'

P value = 0.0106 (logrank test), Q value = 0.052

Table S101.  Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 20(19P13.3) MUTATED 20 4 0.1 - 54.6 (13.5)
DEL PEAK 20(19P13.3) WILD-TYPE 236 30 0.1 - 194.8 (22.7)

Figure S101.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00139 (Fisher's exact test), Q value = 0.013

Table S102.  Gene #27: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 20(19P13.3) MUTATED 6 1 10 2
DEL PEAK 20(19P13.3) WILD-TYPE 161 20 39 12

Figure S102.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00029 (Fisher's exact test), Q value = 0.0035

Table S103.  Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 20(19P13.3) MUTATED 7 1 12
DEL PEAK 20(19P13.3) WILD-TYPE 169 28 44

Figure S103.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0315 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #27: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 20(19P13.3) MUTATED 2 5 1
DEL PEAK 20(19P13.3) WILD-TYPE 43 17 3

Figure S104.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00532 (Wilcoxon-test), Q value = 0.028

Table S105.  Gene #27: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 60 92.0 (15.6)
DEL PEAK 20(19P13.3) MUTATED 8 77.5 (32.0)
DEL PEAK 20(19P13.3) WILD-TYPE 52 94.2 (10.2)

Figure S105.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.42' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0039

Table S106.  Gene #28: 'del_19q13.42' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 21(19Q13.42) MUTATED 5 1 11 1
DEL PEAK 21(19Q13.42) WILD-TYPE 162 20 38 13

Figure S106.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_19q13.42' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0029

Table S107.  Gene #28: 'del_19q13.42' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 21(19Q13.42) MUTATED 6 1 12
DEL PEAK 21(19Q13.42) WILD-TYPE 170 28 44

Figure S107.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q12.2' versus 'Time to Death'

P value = 0.0398 (logrank test), Q value = 0.14

Table S108.  Gene #29: 'del_22q12.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 22(22Q12.2) MUTATED 59 12 0.1 - 123.6 (18.2)
DEL PEAK 22(22Q12.2) WILD-TYPE 197 22 0.1 - 194.8 (22.3)

Figure S108.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #1: 'Time to Death'

'del_22q12.2' versus 'YEARS_TO_BIRTH'

P value = 0.0559 (Wilcoxon-test), Q value = 0.19

Table S109.  Gene #29: 'del_22q12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
DEL PEAK 22(22Q12.2) MUTATED 58 58.1 (13.6)
DEL PEAK 22(22Q12.2) WILD-TYPE 206 62.2 (11.7)

Figure S109.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q12.2' versus 'NEOPLASM_DISEASESTAGE'

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

Table S110.  Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 22(22Q12.2) MUTATED 21 3 25 7
DEL PEAK 22(22Q12.2) WILD-TYPE 146 18 24 7

Figure S110.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_22q12.2' versus 'PATHOLOGY_T_STAGE'

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

Table S111.  Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 22(22Q12.2) MUTATED 23 6 29
DEL PEAK 22(22Q12.2) WILD-TYPE 153 23 27

Figure S111.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q12.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00195 (Fisher's exact test), Q value = 0.014

Table S112.  Gene #29: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 22(22Q12.2) MUTATED 10 14 2
DEL PEAK 22(22Q12.2) WILD-TYPE 35 8 2

Figure S112.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_22q12.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0596 (Fisher's exact test), Q value = 0.2

Table S113.  Gene #29: 'del_22q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 90 9
DEL PEAK 22(22Q12.2) MUTATED 22 5
DEL PEAK 22(22Q12.2) WILD-TYPE 68 4

Figure S113.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_22q12.2' versus 'GENDER'

P value = 0.00158 (Fisher's exact test), Q value = 0.013

Table S114.  Gene #29: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 22(22Q12.2) MUTATED 26 34
DEL PEAK 22(22Q12.2) WILD-TYPE 46 163

Figure S114.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

'del_xp11.4' versus 'Time to Death'

P value = 0.00181 (logrank test), Q value = 0.014

Table S115.  Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 23(XP11.4) MUTATED 29 9 0.1 - 86.3 (18.0)
DEL PEAK 23(XP11.4) WILD-TYPE 227 25 0.1 - 194.8 (22.3)

Figure S115.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

'del_xp11.4' versus 'NEOPLASM_DISEASESTAGE'

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

Table S116.  Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 23(XP11.4) MUTATED 8 1 16 2
DEL PEAK 23(XP11.4) WILD-TYPE 159 20 33 12

Figure S116.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xp11.4' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00089

Table S117.  Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 23(XP11.4) MUTATED 10 3 16
DEL PEAK 23(XP11.4) WILD-TYPE 166 26 40

Figure S117.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xp11.4' versus 'PATHOLOGY_N_STAGE'

P value = 0.0787 (Fisher's exact test), Q value = 0.24

Table S118.  Gene #30: 'del_xp11.4' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 23(XP11.4) MUTATED 5 7 1
DEL PEAK 23(XP11.4) WILD-TYPE 40 15 3

Figure S118.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xp11.4' versus 'GENDER'

P value = 0.0147 (Fisher's exact test), Q value = 0.068

Table S119.  Gene #30: 'del_xp11.4' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 23(XP11.4) MUTATED 14 16
DEL PEAK 23(XP11.4) WILD-TYPE 58 181

Figure S119.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #7: 'GENDER'

'del_xp11.4' versus 'RACE'

P value = 0.0132 (Fisher's exact test), Q value = 0.063

Table S120.  Gene #30: 'del_xp11.4' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
DEL PEAK 23(XP11.4) MUTATED 0 3 9 16
DEL PEAK 23(XP11.4) WILD-TYPE 2 2 51 171

Figure S120.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #11: 'RACE'

'del_xq28' versus 'Time to Death'

P value = 4.42e-05 (logrank test), Q value = 0.00086

Table S121.  Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 256 34 0.1 - 194.8 (21.4)
DEL PEAK 24(XQ28) MUTATED 24 9 0.1 - 86.3 (15.5)
DEL PEAK 24(XQ28) WILD-TYPE 232 25 0.1 - 194.8 (22.4)

Figure S121.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

'del_xq28' versus 'YEARS_TO_BIRTH'

P value = 0.0253 (Wilcoxon-test), Q value = 0.1

Table S122.  Gene #31: 'del_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 264 61.3 (12.2)
DEL PEAK 24(XQ28) MUTATED 24 55.0 (13.9)
DEL PEAK 24(XQ28) WILD-TYPE 240 61.9 (11.9)

Figure S122.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xq28' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00073 (Fisher's exact test), Q value = 0.0073

Table S123.  Gene #31: 'del_xq28' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 167 21 49 14
DEL PEAK 24(XQ28) MUTATED 8 1 12 2
DEL PEAK 24(XQ28) WILD-TYPE 159 20 37 12

Figure S123.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 0.00317 (Fisher's exact test), Q value = 0.02

Table S124.  Gene #31: 'del_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 176 29 56
DEL PEAK 24(XQ28) MUTATED 10 2 12
DEL PEAK 24(XQ28) WILD-TYPE 166 27 44

Figure S124.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xq28' versus 'PATHOLOGY_N_STAGE'

P value = 0.0221 (Fisher's exact test), Q value = 0.093

Table S125.  Gene #31: 'del_xq28' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 45 22 4
DEL PEAK 24(XQ28) MUTATED 3 7 1
DEL PEAK 24(XQ28) WILD-TYPE 42 15 3

Figure S125.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xq28' versus 'GENDER'

P value = 0.0171 (Fisher's exact test), Q value = 0.077

Table S126.  Gene #31: 'del_xq28' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 72 197
DEL PEAK 24(XQ28) MUTATED 12 13
DEL PEAK 24(XQ28) WILD-TYPE 60 184

Figure S126.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #7: 'GENDER'

'del_xq28' versus 'RACE'

P value = 0.085 (Fisher's exact test), Q value = 0.25

Table S127.  Gene #31: 'del_xq28' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 5 60 187
DEL PEAK 24(XQ28) MUTATED 0 2 7 14
DEL PEAK 24(XQ28) WILD-TYPE 2 3 53 173

Figure S127.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #11: 'RACE'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/15087100/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 focal cnvs = 31

  • Number of selected clinical features = 12

  • Exclude genes 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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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