Correlation between copy number variation genes (focal events) and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1V9879W
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1V9879W
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 287 patients, 139 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 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • amp_3q27.1 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_5q35.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • amp_7q31.2 cnv correlated to 'PATHOLOGIC_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'.

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

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

  • del_2q22.1 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

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

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

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

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

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

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

  • del_6q22.31 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_6q25.3 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

  • del_10q21.1 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

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

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

  • del_14q24.2 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  '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',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

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

  • del_19q13.42 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_22q12.2 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

  • del_xq28 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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, 139 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
del 9p21 3 39 (14%) 248 5.46e-11
(2.03e-08) 		0.486
(0.739) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.0002
(0.00213) 		0.0193
(0.0781) 		0.00147
(0.00911) 		0.00303
(0.0163) 		0.388
(0.647) 		0.478
(0.736) 		0.139
(0.342) 		1
(1.00)
del 14q24 2 50 (17%) 237 6.65e-05
(0.000883) 		0.703
(0.883) 		0.00268
(0.0147) 		8e-05
(0.00093) 		0.00526
(0.0257) 		0.17
(0.403) 		0.00826
(0.0389) 		0.00896
(0.0411) 		0.476
(0.735) 		0.0756
(0.213) 		0.959
(1.00) 		0.697
(0.882)
del xp11 4 34 (12%) 253 0.000231
(0.00239) 		0.133
(0.331) 		2e-05
(0.000323) 		5e-05
(0.000689) 		0.0557
(0.163) 		1
(1.00) 		0.0212
(0.0844) 		0.0213
(0.0844) 		0.968
(1.00) 		0.354
(0.623) 		0.0239
(0.0916) 		0.62
(0.82)
del xq28 28 (10%) 259 1.16e-06
(7.19e-05) 		0.0292
(0.102) 		0.00051
(0.00395) 		0.00145
(0.00911) 		0.00695
(0.0336) 		0.58
(0.818) 		0.0218
(0.0855) 		0.00491
(0.0247) 		1
(1.00) 		0.308
(0.578) 		0.114
(0.295) 		0.609
(0.818)
del 1p36 31 55 (19%) 232 3.06e-05
(0.000455) 		0.215
(0.466) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.00125
(0.00845) 		0.363
(0.629) 		0.0404
(0.134) 		0.00146
(0.00911) 		0.848
(0.974) 		0.201
(0.453) 		0.583
(0.818) 		0.699
(0.882)
del 3p22 1 25 (9%) 262 2.44e-07
(2.73e-05) 		0.0272
(0.0993) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.0443
(0.141) 		0.0866
(0.237) 		0.816
(0.958) 		0.264
(0.523) 		0.648
(0.842) 		0.3
(0.573) 		0.644
(0.84) 		0.608
(0.818)
del 4q34 3 32 (11%) 255 4e-07
(2.98e-05) 		0.399
(0.662) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.0343
(0.117) 		0.607
(0.818) 		0.00962
(0.0431) 		0.2
(0.453) 		0.577
(0.818) 		0.959
(1.00) 		0.0294
(0.102) 		0.359
(0.629)
del 5q35 2 11 (4%) 276 7.56e-05
(0.00093) 		0.00448
(0.0228) 		0.00046
(0.00372) 		1e-05
(0.000177) 		0.0873
(0.237) 		0.313
(0.578) 		0.00926
(0.042) 		0.754
(0.924) 		0.293
(0.567)
del 11q22 3 31 (11%) 256 2.44e-05
(0.000378) 		0.424
(0.686) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.00033
(0.00307) 		0.0702
(0.199) 		0.518
(0.774) 		0.044
(0.141) 		0.417
(0.68) 		0.503
(0.757) 		0.173
(0.406) 		0.62
(0.82)
del 11q23 3 29 (10%) 258 2.93e-07
(2.73e-05) 		0.423
(0.686) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.00051
(0.00395) 		0.0553
(0.163) 		0.828
(0.964) 		0.044
(0.141) 		0.897
(1.00) 		0.967
(1.00) 		0.144
(0.352) 		0.612
(0.819)
del 14q11 2 51 (18%) 236 0.000374
(0.00324) 		0.572
(0.818) 		0.0115
(0.0487) 		0.00046
(0.00372) 		0.0111
(0.0475) 		0.386
(0.647) 		0.0135
(0.0556) 		0.0224
(0.0867) 		0.659
(0.851) 		0.315
(0.578) 		1
(1.00) 		0.698
(0.882)
del 15q13 3 35 (12%) 252 0.000318
(0.00304) 		0.115
(0.296) 		0.00017
(0.00186) 		4e-05
(0.000572) 		0.00106
(0.00744) 		0.087
(0.237) 		0.307
(0.578) 		0.0278
(0.1) 		0.914
(1.00) 		0.985
(1.00) 		0.539
(0.788) 		1
(1.00)
del 22q12 2 63 (22%) 224 0.00127
(0.00847) 		0.101
(0.268) 		1e-05
(0.000177) 		1e-05
(0.000177) 		0.00261
(0.0145) 		0.11
(0.286) 		0.00188
(0.0111) 		0.00113
(0.00781) 		0.468
(0.728) 		0.216
(0.466) 		0.205
(0.454) 		0.714
(0.894)
del 6q25 3 32 (11%) 255 0.198
(0.451) 		0.921
(1.00) 		0.00014
(0.00158) 		2e-05
(0.000323) 		0.0457
(0.142) 		0.599
(0.818) 		0.00256
(0.0144) 		0.0429
(0.14) 		0.941
(1.00) 		0.572
(0.818) 		0.126
(0.318) 		0.62
(0.82)
del 19p13 3 23 (8%) 264 0.000729
(0.00542) 		0.778
(0.931) 		0.00063
(0.00478) 		7e-05
(0.000898) 		0.0405
(0.134) 		0.434
(0.696) 		0.335
(0.607) 		0.00144
(0.00911) 		0.104
(0.273) 		0.516
(0.774) 		0.608
(0.818)
amp 2q32 1 53 (18%) 234 0.315
(0.578) 		0.487
(0.739) 		0.0463
(0.142) 		0.0516
(0.155) 		0.0536
(0.16) 		0.0135
(0.0556) 		0.495
(0.748) 		0.251
(0.505) 		0.989
(1.00) 		0.591
(0.818) 		0.752
(0.924) 		1
(1.00)
amp 7q31 2 177 (62%) 110 0.308
(0.578) 		0.538
(0.788) 		0.00248
(0.0142) 		0.104
(0.273) 		0.329
(0.6) 		0.728
(0.906) 		0.00876
(0.0407) 		0.0843
(0.236) 		0.76
(0.924) 		0.0042
(0.0217) 		0.368
(0.63) 		0.365
(0.629)
del 5p15 33 13 (5%) 274 0.18
(0.413) 		0.177
(0.41) 		0.0456
(0.142) 		0.0257
(0.0957) 		0.00371
(0.0194) 		0.376
(0.636) 		0.0463
(0.142) 		0.245
(0.498) 		0.882
(1.00) 		1
(1.00) 		0.361
(0.629)
del 6p12 3 26 (9%) 261 0.159
(0.382) 		0.81
(0.954) 		0.0009
(0.00656) 		0.00035
(0.0031) 		0.0106
(0.0464) 		0.592
(0.818) 		0.353
(0.623) 		0.0364
(0.123) 		0.65
(0.843) 		0.929
(1.00) 		0.202
(0.453) 		0.608
(0.818)
del 6q22 31 29 (10%) 258 0.341
(0.613) 		0.792
(0.941) 		0.00164
(0.00984) 		0.00034
(0.00308) 		0.148
(0.359) 		1
(1.00) 		0.0256
(0.0957) 		0.0506
(0.153) 		0.941
(1.00) 		0.572
(0.818) 		0.134
(0.333) 		0.609
(0.818)
del 10q21 1 19 (7%) 268 0.0686
(0.196) 		0.949
(1.00) 		8e-05
(0.00093) 		0.00096
(0.00687) 		0.117
(0.298) 		1
(1.00) 		0.29
(0.566) 		0.0496
(0.151) 		0.262
(0.52) 		0.644
(0.84) 		0.401
(0.662) 		1
(1.00)
del 19q13 42 19 (7%) 268 0.0564
(0.164) 		0.598
(0.818) 		0.0004
(0.00338) 		0.00026
(0.00261) 		0.242
(0.498) 		1
(1.00) 		0.596
(0.818) 		0.0267
(0.0984) 		0.924
(1.00) 		0.227
(0.482) 		0.235
(0.496) 		1
(1.00)
del 2q22 1 10 (3%) 277 0.452
(0.719) 		0.402
(0.662) 		0.00031
(0.00303) 		0.00353
(0.0188) 		0.0864
(0.237) 		0.313
(0.578) 		0.464
(0.726) 		0.455
(0.719) 		0.765
(0.926) 		0.571
(0.818) 		0.756
(0.924) 		1
(1.00)
del 2q37 3 12 (4%) 275 0.911
(1.00) 		0.521
(0.776) 		0.0073
(0.0348) 		0.00513
(0.0254) 		0.695
(0.882) 		1
(1.00) 		0.0887
(0.237) 		0.567
(0.818) 		0.834
(0.967) 		0.79
(0.941) 		1
(1.00)
del 16q24 1 12 (4%) 275 2.9e-08
(5.4e-06) 		0.212
(0.465) 		0.00155
(0.00945) 		0.00219
(0.0127) 		0.243
(0.498) 		0.376
(0.636) 		0.524
(0.777) 		0.153
(0.371) 		0.31
(0.578) 		0.96
(1.00) 		0.273
(0.535) 		1
(1.00)
amp 2p23 2 45 (16%) 242 0.365
(0.629) 		0.253
(0.507) 		0.299
(0.573) 		0.344
(0.616) 		0.0108
(0.0466) 		0.0252
(0.0956) 		0.272
(0.535) 		0.294
(0.567) 		0.237
(0.498) 		0.772
(0.929) 		0.769
(0.929) 		1
(1.00)
amp 5q35 2 37 (13%) 250 0.487
(0.739) 		0.529
(0.781) 		0.0418
(0.138) 		0.0293
(0.102) 		0.54
(0.788) 		0.643
(0.84) 		0.844
(0.973) 		0.177
(0.41) 		0.939
(1.00) 		0.804
(0.95) 		0.251
(0.505) 		0.373
(0.636)
amp 17q25 2 200 (70%) 87 0.727
(0.906) 		0.243
(0.498) 		0.164
(0.392) 		0.172
(0.406) 		0.473
(0.733) 		0.737
(0.911) 		0.0285
(0.102) 		0.82
(0.959) 		0.776
(0.931) 		0.239
(0.498) 		0.0883
(0.237) 		0.339
(0.612)
del 2p12 8 (3%) 279 0.414
(0.679) 		0.731
(0.907) 		0.00981
(0.0434) 		0.0136
(0.0556) 		0.694
(0.882) 		0.244
(0.498) 		0.686
(0.88) 		0.447
(0.713) 		0.216
(0.466) 		1
(1.00) 		1
(1.00)
amp 3q27 1 100 (35%) 187 0.684
(0.88) 		0.351
(0.623) 		0.221
(0.472) 		0.205
(0.454) 		0.76
(0.924) 		0.0572
(0.165) 		0.575
(0.818) 		0.596
(0.818) 		0.433
(0.696) 		0.456
(0.719) 		0.211
(0.464) 		1
(1.00)
amp 19p13 2 31 (11%) 256 0.799
(0.947) 		0.0312
(0.107) 		1
(1.00) 		0.131
(0.329) 		0.845
(0.973) 		1
(1.00) 		0.829
(0.964) 		0.861
(0.986) 		0.591
(0.818) 		0.386
(0.647) 		0.462
(0.726) 		0.63
(0.83)
'amp_2p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.047

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

nPatients N0 N1 N2
ALL 48 24 5
AMP PEAK 1(2P23.2) MUTATED 4 8 2
AMP PEAK 1(2P23.2) WILD-TYPE 44 16 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 = 0.0252 (Fisher's exact test), Q value = 0.096

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

nPatients 0 1
ALL 93 9
AMP PEAK 1(2P23.2) MUTATED 11 4
AMP PEAK 1(2P23.2) WILD-TYPE 82 5

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

'amp_2q32.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0463 (Fisher's exact test), Q value = 0.14

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
AMP PEAK 2(2Q32.1) MUTATED 28 4 12 7
AMP PEAK 2(2Q32.1) WILD-TYPE 143 18 40 8

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

'amp_2q32.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0516 (Fisher's exact test), Q value = 0.15

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

nPatients T1 T2 T3+T4
ALL 190 33 62
AMP PEAK 2(2Q32.1) MUTATED 28 8 17
AMP PEAK 2(2Q32.1) WILD-TYPE 162 25 45

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

'amp_2q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0536 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
AMP PEAK 2(2Q32.1) MUTATED 9 9 3
AMP PEAK 2(2Q32.1) WILD-TYPE 39 15 2

Figure S5.  Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2q32.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.056

Table S6.  Gene #2: 'amp_2q32.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
AMP PEAK 2(2Q32.1) MUTATED 15 5
AMP PEAK 2(2Q32.1) WILD-TYPE 78 4

Figure S6.  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 = 0.0572 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #3: 'amp_3q27.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
AMP PEAK 3(3Q27.1) MUTATED 29 0
AMP PEAK 3(3Q27.1) WILD-TYPE 64 9

Figure S7.  Get High-res Image Gene #3: 'amp_3q27.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0418 (Fisher's exact test), Q value = 0.14

Table S8.  Gene #4: 'amp_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
AMP PEAK 4(5Q35.2) MUTATED 16 2 11 4
AMP PEAK 4(5Q35.2) WILD-TYPE 155 20 41 11

Figure S8.  Get High-res Image Gene #4: 'amp_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q35.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0293 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #4: 'amp_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
AMP PEAK 4(5Q35.2) MUTATED 18 5 14
AMP PEAK 4(5Q35.2) WILD-TYPE 172 28 48

Figure S9.  Get High-res Image Gene #4: 'amp_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7q31.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00248 (Fisher's exact test), Q value = 0.014

Table S10.  Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
AMP PEAK 5(7Q31.2) MUTATED 114 12 21 12
AMP PEAK 5(7Q31.2) WILD-TYPE 57 10 31 3

Figure S10.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 0.00876 (Fisher's exact test), Q value = 0.041

Table S11.  Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
AMP PEAK 5(7Q31.2) MUTATED 37 140
AMP PEAK 5(7Q31.2) WILD-TYPE 39 71

Figure S11.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0843 (Wilcoxon-test), Q value = 0.24

Table S12.  Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
AMP PEAK 5(7Q31.2) MUTATED 54 89.8 (19.6)
AMP PEAK 5(7Q31.2) WILD-TYPE 22 81.8 (26.8)

Figure S12.  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 = 0.0042 (Wilcoxon-test), Q value = 0.022

Table S13.  Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
AMP PEAK 5(7Q31.2) MUTATED 32 1967.6 (14.5)
AMP PEAK 5(7Q31.2) WILD-TYPE 22 1979.7 (14.8)

Figure S13.  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 = 0.0285 (Fisher's exact test), Q value = 0.1

Table S14.  Gene #6: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
AMP PEAK 6(17Q25.2) MUTATED 45 155
AMP PEAK 6(17Q25.2) WILD-TYPE 31 56

Figure S14.  Get High-res Image Gene #6: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

'amp_17q25.2' versus 'RACE'

P value = 0.0883 (Fisher's exact test), Q value = 0.24

Table S15.  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 61 204
AMP PEAK 6(17Q25.2) MUTATED 2 4 35 149
AMP PEAK 6(17Q25.2) WILD-TYPE 0 1 26 55

Figure S15.  Get High-res Image Gene #6: 'amp_17q25.2' versus Clinical Feature #11: 'RACE'

'amp_19p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0312 (Wilcoxon-test), Q value = 0.11

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

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
AMP PEAK 7(19P13.2) MUTATED 30 56.9 (12.4)
AMP PEAK 7(19P13.2) WILD-TYPE 252 61.9 (12.0)

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

'del_1p36.31' versus 'Time to Death'

P value = 3.06e-05 (logrank test), Q value = 0.00045

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

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 1(1P36.31) MUTATED 55 17 0.1 - 123.6 (19.4)
DEL PEAK 1(1P36.31) WILD-TYPE 227 27 0.1 - 194.8 (25.6)

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

'del_1p36.31' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 1(1P36.31) MUTATED 17 3 22 5
DEL PEAK 1(1P36.31) WILD-TYPE 154 19 30 10

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

'del_1p36.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 1(1P36.31) MUTATED 21 7 27
DEL PEAK 1(1P36.31) WILD-TYPE 169 26 35

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 = 0.00125 (Fisher's exact test), Q value = 0.0085

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

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 1(1P36.31) MUTATED 7 13 2
DEL PEAK 1(1P36.31) WILD-TYPE 41 11 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 = 0.0404 (Fisher's exact test), Q value = 0.13

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

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 1(1P36.31) MUTATED 21 34
DEL PEAK 1(1P36.31) WILD-TYPE 55 177

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 = 0.00146 (Wilcoxon-test), Q value = 0.0091

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

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 1(1P36.31) MUTATED 16 73.1 (33.8)
DEL PEAK 1(1P36.31) WILD-TYPE 60 91.3 (16.0)

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

'del_2p12' versus 'PATHOLOGIC_STAGE'

P value = 0.00981 (Fisher's exact test), Q value = 0.043

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 2(2P12) MUTATED 1 0 3 2
DEL PEAK 2(2P12) WILD-TYPE 170 22 49 13

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

'del_2p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.0136 (Fisher's exact test), Q value = 0.056

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

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 2(2P12) MUTATED 2 3 3
DEL PEAK 2(2P12) WILD-TYPE 188 30 59

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

'del_2q22.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00031 (Fisher's exact test), Q value = 0.003

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 3(2Q22.1) MUTATED 1 0 6 2
DEL PEAK 3(2Q22.1) WILD-TYPE 170 22 46 13

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

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00353 (Fisher's exact test), Q value = 0.019

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

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 3(2Q22.1) MUTATED 3 0 7
DEL PEAK 3(2Q22.1) WILD-TYPE 187 33 55

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

'del_2q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0864 (Fisher's exact test), Q value = 0.24

Table S27.  Gene #10: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 3(2Q22.1) MUTATED 1 4 0
DEL PEAK 3(2Q22.1) WILD-TYPE 47 20 5

Figure S27.  Get High-res Image Gene #10: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0073 (Fisher's exact test), Q value = 0.035

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 4(2Q37.3) MUTATED 2 2 5 1
DEL PEAK 4(2Q37.3) WILD-TYPE 169 20 47 14

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

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00513 (Fisher's exact test), Q value = 0.025

Table S29.  Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 4(2Q37.3) MUTATED 3 3 6
DEL PEAK 4(2Q37.3) WILD-TYPE 187 30 56

Figure S29.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'GENDER'

P value = 0.0887 (Fisher's exact test), Q value = 0.24

Table S30.  Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 4(2Q37.3) MUTATED 6 6
DEL PEAK 4(2Q37.3) WILD-TYPE 70 205

Figure S30.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

'del_3p22.1' versus 'Time to Death'

P value = 2.44e-07 (logrank test), Q value = 2.7e-05

Table S31.  Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 5(3P22.1) MUTATED 25 11 2.0 - 86.3 (15.5)
DEL PEAK 5(3P22.1) WILD-TYPE 257 33 0.1 - 194.8 (25.4)

Figure S31.  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 = 0.0272 (Wilcoxon-test), Q value = 0.099

Table S32.  Gene #12: 'del_3p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
DEL PEAK 5(3P22.1) MUTATED 24 55.7 (12.1)
DEL PEAK 5(3P22.1) WILD-TYPE 258 61.9 (12.0)

Figure S32.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p22.1' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S33.  Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 5(3P22.1) MUTATED 5 1 14 3
DEL PEAK 5(3P22.1) WILD-TYPE 166 21 38 12

Figure S33.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p22.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S34.  Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 5(3P22.1) MUTATED 6 4 15
DEL PEAK 5(3P22.1) WILD-TYPE 184 29 47

Figure S34.  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 = 0.0443 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #12: 'del_3p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 5(3P22.1) MUTATED 6 8 2
DEL PEAK 5(3P22.1) WILD-TYPE 42 16 3

Figure S35.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p22.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0866 (Fisher's exact test), Q value = 0.24

Table S36.  Gene #12: 'del_3p22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
DEL PEAK 5(3P22.1) MUTATED 4 2
DEL PEAK 5(3P22.1) WILD-TYPE 89 7

Figure S36.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'Time to Death'

P value = 4e-07 (logrank test), Q value = 3e-05

Table S37.  Gene #13: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 6(4Q34.3) MUTATED 31 12 0.4 - 79.9 (18.0)
DEL PEAK 6(4Q34.3) WILD-TYPE 251 32 0.1 - 194.8 (25.4)

Figure S37.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 6(4Q34.3) MUTATED 7 2 17 3
DEL PEAK 6(4Q34.3) WILD-TYPE 164 20 35 12

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

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S39.  Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 6(4Q34.3) MUTATED 9 5 18
DEL PEAK 6(4Q34.3) WILD-TYPE 181 28 44

Figure S39.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0343 (Fisher's exact test), Q value = 0.12

Table S40.  Gene #13: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 6(4Q34.3) MUTATED 7 10 1
DEL PEAK 6(4Q34.3) WILD-TYPE 41 14 4

Figure S40.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q34.3' versus 'GENDER'

P value = 0.00962 (Fisher's exact test), Q value = 0.043

Table S41.  Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 6(4Q34.3) MUTATED 15 17
DEL PEAK 6(4Q34.3) WILD-TYPE 61 194

Figure S41.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'RACE'

P value = 0.0294 (Fisher's exact test), Q value = 0.1

Table S42.  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 61 204
DEL PEAK 6(4Q34.3) MUTATED 0 3 6 19
DEL PEAK 6(4Q34.3) WILD-TYPE 2 2 55 185

Figure S42.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_5p15.33' versus 'PATHOLOGIC_STAGE'

P value = 0.0456 (Fisher's exact test), Q value = 0.14

Table S43.  Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 7(5P15.33) MUTATED 5 0 5 2
DEL PEAK 7(5P15.33) WILD-TYPE 166 22 47 13

Figure S43.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.0257 (Fisher's exact test), Q value = 0.096

Table S44.  Gene #14: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 7(5P15.33) MUTATED 5 1 7
DEL PEAK 7(5P15.33) WILD-TYPE 185 32 55

Figure S44.  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 = 0.00371 (Fisher's exact test), Q value = 0.019

Table S45.  Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 7(5P15.33) MUTATED 0 5 1
DEL PEAK 7(5P15.33) WILD-TYPE 48 19 4

Figure S45.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'GENDER'

P value = 0.0463 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 7(5P15.33) MUTATED 7 6
DEL PEAK 7(5P15.33) WILD-TYPE 69 205

Figure S46.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

'del_5q35.2' versus 'Time to Death'

P value = 7.56e-05 (logrank test), Q value = 0.00093

Table S47.  Gene #15: 'del_5q35.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 8(5Q35.2) MUTATED 10 5 2.8 - 79.9 (18.9)
DEL PEAK 8(5Q35.2) WILD-TYPE 272 39 0.1 - 194.8 (25.0)

Figure S47.  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 = 0.00448 (Wilcoxon-test), Q value = 0.023

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

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
DEL PEAK 8(5Q35.2) MUTATED 10 46.8 (17.3)
DEL PEAK 8(5Q35.2) WILD-TYPE 272 62.0 (11.6)

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

'del_5q35.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.0037

Table S49.  Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 8(5Q35.2) MUTATED 1 1 7 1
DEL PEAK 8(5Q35.2) WILD-TYPE 170 21 45 14

Figure S49.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5q35.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S50.  Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 8(5Q35.2) MUTATED 1 1 9
DEL PEAK 8(5Q35.2) WILD-TYPE 189 32 53

Figure S50.  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 = 0.0873 (Fisher's exact test), Q value = 0.24

Table S51.  Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 8(5Q35.2) MUTATED 1 4 0
DEL PEAK 8(5Q35.2) WILD-TYPE 47 20 5

Figure S51.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q35.2' versus 'GENDER'

P value = 0.00926 (Fisher's exact test), Q value = 0.042

Table S52.  Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 8(5Q35.2) MUTATED 7 4
DEL PEAK 8(5Q35.2) WILD-TYPE 69 207

Figure S52.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

'del_6p12.3' versus 'PATHOLOGIC_STAGE'

P value = 9e-04 (Fisher's exact test), Q value = 0.0066

Table S53.  Gene #16: 'del_6p12.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 9(6P12.3) MUTATED 9 0 12 2
DEL PEAK 9(6P12.3) WILD-TYPE 162 22 40 13

Figure S53.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6p12.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0031

Table S54.  Gene #16: 'del_6p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 9(6P12.3) MUTATED 11 1 14
DEL PEAK 9(6P12.3) WILD-TYPE 179 32 48

Figure S54.  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 = 0.0106 (Fisher's exact test), Q value = 0.046

Table S55.  Gene #16: 'del_6p12.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 9(6P12.3) MUTATED 6 1 3
DEL PEAK 9(6P12.3) WILD-TYPE 42 23 2

Figure S55.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6p12.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0364 (Wilcoxon-test), Q value = 0.12

Table S56.  Gene #16: 'del_6p12.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 9(6P12.3) MUTATED 10 70.0 (37.1)
DEL PEAK 9(6P12.3) WILD-TYPE 66 90.2 (17.8)

Figure S56.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'PATHOLOGIC_STAGE'

P value = 0.00164 (Fisher's exact test), Q value = 0.0098

Table S57.  Gene #17: 'del_6q22.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 10(6Q22.31) MUTATED 12 0 12 3
DEL PEAK 10(6Q22.31) WILD-TYPE 159 22 40 12

Figure S57.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q22.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0031

Table S58.  Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 10(6Q22.31) MUTATED 13 1 15
DEL PEAK 10(6Q22.31) WILD-TYPE 177 32 47

Figure S58.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q22.31' versus 'GENDER'

P value = 0.0256 (Fisher's exact test), Q value = 0.096

Table S59.  Gene #17: 'del_6q22.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 10(6Q22.31) MUTATED 13 16
DEL PEAK 10(6Q22.31) WILD-TYPE 63 195

Figure S59.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #7: 'GENDER'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0506 (Wilcoxon-test), Q value = 0.15

Table S60.  Gene #17: 'del_6q22.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 10(6Q22.31) MUTATED 11 71.8 (36.0)
DEL PEAK 10(6Q22.31) WILD-TYPE 65 90.2 (17.8)

Figure S60.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q25.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0016

Table S61.  Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 11(6Q25.3) MUTATED 12 0 15 2
DEL PEAK 11(6Q25.3) WILD-TYPE 159 22 37 13

Figure S61.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q25.3' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S62.  Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 11(6Q25.3) MUTATED 13 1 18
DEL PEAK 11(6Q25.3) WILD-TYPE 177 32 44

Figure S62.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q25.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0457 (Fisher's exact test), Q value = 0.14

Table S63.  Gene #18: 'del_6q25.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 11(6Q25.3) MUTATED 6 4 3
DEL PEAK 11(6Q25.3) WILD-TYPE 42 20 2

Figure S63.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q25.3' versus 'GENDER'

P value = 0.00256 (Fisher's exact test), Q value = 0.014

Table S64.  Gene #18: 'del_6q25.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 11(6Q25.3) MUTATED 16 16
DEL PEAK 11(6Q25.3) WILD-TYPE 60 195

Figure S64.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #7: 'GENDER'

'del_6q25.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0429 (Wilcoxon-test), Q value = 0.14

Table S65.  Gene #18: 'del_6q25.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 11(6Q25.3) MUTATED 12 73.3 (34.7)
DEL PEAK 11(6Q25.3) WILD-TYPE 64 90.2 (17.9)

Figure S65.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'Time to Death'

P value = 5.46e-11 (logrank test), Q value = 2e-08

Table S66.  Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 12(9P21.3) MUTATED 37 17 2.0 - 93.3 (18.0)
DEL PEAK 12(9P21.3) WILD-TYPE 245 27 0.1 - 194.8 (26.0)

Figure S66.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S67.  Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 12(9P21.3) MUTATED 10 0 19 7
DEL PEAK 12(9P21.3) WILD-TYPE 161 22 33 8

Figure S67.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S68.  Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 12(9P21.3) MUTATED 11 3 25
DEL PEAK 12(9P21.3) WILD-TYPE 179 30 37

Figure S68.  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 = 2e-04 (Fisher's exact test), Q value = 0.0021

Table S69.  Gene #19: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 12(9P21.3) MUTATED 7 14 3
DEL PEAK 12(9P21.3) WILD-TYPE 41 10 2

Figure S69.  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 = 0.0193 (Fisher's exact test), Q value = 0.078

Table S70.  Gene #19: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
DEL PEAK 12(9P21.3) MUTATED 10 4
DEL PEAK 12(9P21.3) WILD-TYPE 83 5

Figure S70.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.00147 (Fisher's exact test), Q value = 0.0091

Table S71.  Gene #19: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 12(9P21.3) MUTATED 19 20
DEL PEAK 12(9P21.3) WILD-TYPE 57 191

Figure S71.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00303 (Wilcoxon-test), Q value = 0.016

Table S72.  Gene #19: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 12(9P21.3) MUTATED 14 69.3 (36.3)
DEL PEAK 12(9P21.3) WILD-TYPE 62 91.6 (15.0)

Figure S72.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q21.1' versus 'Time to Death'

P value = 0.0686 (logrank test), Q value = 0.2

Table S73.  Gene #20: 'del_10q21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 13(10Q21.1) MUTATED 18 6 2.1 - 99.8 (21.1)
DEL PEAK 13(10Q21.1) WILD-TYPE 264 38 0.1 - 194.8 (25.0)

Figure S73.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #1: 'Time to Death'

'del_10q21.1' versus 'PATHOLOGIC_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00093

Table S74.  Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 13(10Q21.1) MUTATED 5 0 12 1
DEL PEAK 13(10Q21.1) WILD-TYPE 166 22 40 14

Figure S74.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00096 (Fisher's exact test), Q value = 0.0069

Table S75.  Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 13(10Q21.1) MUTATED 8 0 11
DEL PEAK 13(10Q21.1) WILD-TYPE 182 33 51

Figure S75.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q21.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0496 (Wilcoxon-test), Q value = 0.15

Table S76.  Gene #20: 'del_10q21.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 13(10Q21.1) MUTATED 7 57.1 (45.0)
DEL PEAK 13(10Q21.1) WILD-TYPE 69 90.6 (15.9)

Figure S76.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q22.3' versus 'Time to Death'

P value = 2.44e-05 (logrank test), Q value = 0.00038

Table S77.  Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 14(11Q22.3) MUTATED 29 11 0.4 - 123.6 (18.6)
DEL PEAK 14(11Q22.3) WILD-TYPE 253 33 0.1 - 194.8 (25.4)

Figure S77.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S78.  Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 14(11Q22.3) MUTATED 7 3 14 6
DEL PEAK 14(11Q22.3) WILD-TYPE 164 19 38 9

Figure S78.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q22.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S79.  Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 14(11Q22.3) MUTATED 8 5 18
DEL PEAK 14(11Q22.3) WILD-TYPE 182 28 44

Figure S79.  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 = 0.00033 (Fisher's exact test), Q value = 0.0031

Table S80.  Gene #21: 'del_11q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 14(11Q22.3) MUTATED 3 9 3
DEL PEAK 14(11Q22.3) WILD-TYPE 45 15 2

Figure S80.  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 = 0.0702 (Fisher's exact test), Q value = 0.2

Table S81.  Gene #21: 'del_11q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
DEL PEAK 14(11Q22.3) MUTATED 9 3
DEL PEAK 14(11Q22.3) WILD-TYPE 84 6

Figure S81.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q22.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.044 (Wilcoxon-test), Q value = 0.14

Table S82.  Gene #21: 'del_11q22.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 14(11Q22.3) MUTATED 8 73.8 (33.4)
DEL PEAK 14(11Q22.3) WILD-TYPE 68 89.1 (20.1)

Figure S82.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q23.3' versus 'Time to Death'

P value = 2.93e-07 (logrank test), Q value = 2.7e-05

Table S83.  Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 15(11Q23.3) MUTATED 27 12 0.4 - 123.6 (16.9)
DEL PEAK 15(11Q23.3) WILD-TYPE 255 32 0.1 - 194.8 (25.3)

Figure S83.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

'del_11q23.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S84.  Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 15(11Q23.3) MUTATED 5 2 15 6
DEL PEAK 15(11Q23.3) WILD-TYPE 166 20 37 9

Figure S84.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S85.  Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 15(11Q23.3) MUTATED 6 4 19
DEL PEAK 15(11Q23.3) WILD-TYPE 184 29 43

Figure S85.  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 = 0.00051 (Fisher's exact test), Q value = 0.004

Table S86.  Gene #22: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 15(11Q23.3) MUTATED 3 9 3
DEL PEAK 15(11Q23.3) WILD-TYPE 45 15 2

Figure S86.  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 = 0.0553 (Fisher's exact test), Q value = 0.16

Table S87.  Gene #22: 'del_11q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
DEL PEAK 15(11Q23.3) MUTATED 8 3
DEL PEAK 15(11Q23.3) WILD-TYPE 85 6

Figure S87.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q23.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.044 (Wilcoxon-test), Q value = 0.14

Table S88.  Gene #22: 'del_11q23.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 15(11Q23.3) MUTATED 8 73.8 (33.4)
DEL PEAK 15(11Q23.3) WILD-TYPE 68 89.1 (20.1)

Figure S88.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q11.2' versus 'Time to Death'

P value = 0.000374 (logrank test), Q value = 0.0032

Table S89.  Gene #23: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 16(14Q11.2) MUTATED 50 14 0.1 - 80.9 (20.1)
DEL PEAK 16(14Q11.2) WILD-TYPE 232 30 0.1 - 194.8 (25.2)

Figure S89.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

'del_14q11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.049

Table S90.  Gene #23: 'del_14q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 16(14Q11.2) MUTATED 22 3 14 6
DEL PEAK 16(14Q11.2) WILD-TYPE 149 19 38 9

Figure S90.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.0037

Table S91.  Gene #23: 'del_14q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 16(14Q11.2) MUTATED 24 5 22
DEL PEAK 16(14Q11.2) WILD-TYPE 166 28 40

Figure S91.  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 = 0.0111 (Fisher's exact test), Q value = 0.047

Table S92.  Gene #23: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 16(14Q11.2) MUTATED 9 8 4
DEL PEAK 16(14Q11.2) WILD-TYPE 39 16 1

Figure S92.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q11.2' versus 'GENDER'

P value = 0.0135 (Fisher's exact test), Q value = 0.056

Table S93.  Gene #23: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 16(14Q11.2) MUTATED 21 30
DEL PEAK 16(14Q11.2) WILD-TYPE 55 181

Figure S93.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

'del_14q11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0224 (Wilcoxon-test), Q value = 0.087

Table S94.  Gene #23: 'del_14q11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 16(14Q11.2) MUTATED 16 73.1 (35.3)
DEL PEAK 16(14Q11.2) WILD-TYPE 60 91.3 (15.1)

Figure S94.  Get High-res Image Gene #23: 'del_14q11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q24.2' versus 'Time to Death'

P value = 6.65e-05 (logrank test), Q value = 0.00088

Table S95.  Gene #24: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 17(14Q24.2) MUTATED 50 15 0.1 - 80.9 (19.5)
DEL PEAK 17(14Q24.2) WILD-TYPE 232 29 0.1 - 194.8 (25.3)

Figure S95.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

'del_14q24.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00268 (Fisher's exact test), Q value = 0.015

Table S96.  Gene #24: 'del_14q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 17(14Q24.2) MUTATED 20 3 15 6
DEL PEAK 17(14Q24.2) WILD-TYPE 151 19 37 9

Figure S96.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q24.2' versus 'PATHOLOGY_T_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00093

Table S97.  Gene #24: 'del_14q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 17(14Q24.2) MUTATED 22 5 23
DEL PEAK 17(14Q24.2) WILD-TYPE 168 28 39

Figure S97.  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 = 0.00526 (Fisher's exact test), Q value = 0.026

Table S98.  Gene #24: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 17(14Q24.2) MUTATED 8 9 4
DEL PEAK 17(14Q24.2) WILD-TYPE 40 15 1

Figure S98.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q24.2' versus 'GENDER'

P value = 0.00826 (Fisher's exact test), Q value = 0.039

Table S99.  Gene #24: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 17(14Q24.2) MUTATED 21 29
DEL PEAK 17(14Q24.2) WILD-TYPE 55 182

Figure S99.  Get High-res Image Gene #24: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

'del_14q24.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00896 (Wilcoxon-test), Q value = 0.041

Table S100.  Gene #24: 'del_14q24.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 17(14Q24.2) MUTATED 15 71.3 (35.8)
DEL PEAK 17(14Q24.2) WILD-TYPE 61 91.5 (15.0)

Figure S100.  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 = 0.0756 (Wilcoxon-test), Q value = 0.21

Table S101.  Gene #24: 'del_14q24.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
DEL PEAK 17(14Q24.2) MUTATED 9 1981.7 (15.6)
DEL PEAK 17(14Q24.2) WILD-TYPE 45 1970.7 (15.2)

Figure S101.  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 = 0.000318 (logrank test), Q value = 0.003

Table S102.  Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 18(15Q13.3) MUTATED 34 11 0.1 - 194.8 (17.6)
DEL PEAK 18(15Q13.3) WILD-TYPE 248 33 0.1 - 129.9 (26.0)

Figure S102.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0019

Table S103.  Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 18(15Q13.3) MUTATED 12 1 12 6
DEL PEAK 18(15Q13.3) WILD-TYPE 159 21 40 9

Figure S103.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_15q13.3' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00057

Table S104.  Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 18(15Q13.3) MUTATED 14 2 19
DEL PEAK 18(15Q13.3) WILD-TYPE 176 31 43

Figure S104.  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 = 0.00106 (Fisher's exact test), Q value = 0.0074

Table S105.  Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 18(15Q13.3) MUTATED 4 11 2
DEL PEAK 18(15Q13.3) WILD-TYPE 44 13 3

Figure S105.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q13.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.087 (Fisher's exact test), Q value = 0.24

Table S106.  Gene #25: 'del_15q13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 93 9
DEL PEAK 18(15Q13.3) MUTATED 10 3
DEL PEAK 18(15Q13.3) WILD-TYPE 83 6

Figure S106.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q13.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0278 (Wilcoxon-test), Q value = 0.1

Table S107.  Gene #25: 'del_15q13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 18(15Q13.3) MUTATED 10 72.0 (38.2)
DEL PEAK 18(15Q13.3) WILD-TYPE 66 89.8 (17.8)

Figure S107.  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 = 2.9e-08 (logrank test), Q value = 5.4e-06

Table S108.  Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 19(16Q24.1) MUTATED 11 6 0.4 - 51.5 (13.0)
DEL PEAK 19(16Q24.1) WILD-TYPE 271 38 0.1 - 194.8 (25.3)

Figure S108.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_16q24.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00155 (Fisher's exact test), Q value = 0.0095

Table S109.  Gene #26: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 19(16Q24.1) MUTATED 3 0 7 2
DEL PEAK 19(16Q24.1) WILD-TYPE 168 22 45 13

Figure S109.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00219 (Fisher's exact test), Q value = 0.013

Table S110.  Gene #26: 'del_16q24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 19(16Q24.1) MUTATED 4 0 8
DEL PEAK 19(16Q24.1) WILD-TYPE 186 33 54

Figure S110.  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 = 0.000729 (logrank test), Q value = 0.0054

Table S111.  Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 20(19P13.3) MUTATED 23 7 0.9 - 99.0 (16.9)
DEL PEAK 20(19P13.3) WILD-TYPE 259 37 0.1 - 194.8 (25.4)

Figure S111.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0048

Table S112.  Gene #27: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 20(19P13.3) MUTATED 6 1 11 2
DEL PEAK 20(19P13.3) WILD-TYPE 165 21 41 13

Figure S112.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 9e-04

Table S113.  Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 20(19P13.3) MUTATED 8 1 14
DEL PEAK 20(19P13.3) WILD-TYPE 182 32 48

Figure S113.  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 = 0.0405 (Fisher's exact test), Q value = 0.13

Table S114.  Gene #27: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 20(19P13.3) MUTATED 3 5 2
DEL PEAK 20(19P13.3) WILD-TYPE 45 19 3

Figure S114.  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 = 0.00144 (Wilcoxon-test), Q value = 0.0091

Table S115.  Gene #27: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 20(19P13.3) MUTATED 11 64.5 (39.8)
DEL PEAK 20(19P13.3) WILD-TYPE 65 91.4 (14.7)

Figure S115.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.42' versus 'Time to Death'

P value = 0.0564 (logrank test), Q value = 0.16

Table S116.  Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 21(19Q13.42) MUTATED 19 5 0.9 - 93.3 (19.6)
DEL PEAK 21(19Q13.42) WILD-TYPE 263 39 0.1 - 194.8 (24.6)

Figure S116.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'PATHOLOGIC_STAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0034

Table S117.  Gene #28: 'del_19q13.42' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 21(19Q13.42) MUTATED 5 1 11 1
DEL PEAK 21(19Q13.42) WILD-TYPE 166 21 41 14

Figure S117.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19q13.42' versus 'PATHOLOGY_T_STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0026

Table S118.  Gene #28: 'del_19q13.42' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 21(19Q13.42) MUTATED 6 1 12
DEL PEAK 21(19Q13.42) WILD-TYPE 184 32 50

Figure S118.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19q13.42' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0267 (Wilcoxon-test), Q value = 0.098

Table S119.  Gene #28: 'del_19q13.42' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 21(19Q13.42) MUTATED 9 77.8 (29.9)
DEL PEAK 21(19Q13.42) WILD-TYPE 67 88.8 (20.7)

Figure S119.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_22q12.2' versus 'Time to Death'

P value = 0.00127 (logrank test), Q value = 0.0085

Table S120.  Gene #29: 'del_22q12.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 22(22Q12.2) MUTATED 62 16 0.9 - 123.6 (19.3)
DEL PEAK 22(22Q12.2) WILD-TYPE 220 28 0.1 - 194.8 (25.5)

Figure S120.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #1: 'Time to Death'

'del_22q12.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S121.  Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 22(22Q12.2) MUTATED 22 3 26 8
DEL PEAK 22(22Q12.2) WILD-TYPE 149 19 26 7

Figure S121.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_22q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S122.  Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 22(22Q12.2) MUTATED 25 7 31
DEL PEAK 22(22Q12.2) WILD-TYPE 165 26 31

Figure S122.  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 = 0.00261 (Fisher's exact test), Q value = 0.014

Table S123.  Gene #29: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 22(22Q12.2) MUTATED 11 15 2
DEL PEAK 22(22Q12.2) WILD-TYPE 37 9 3

Figure S123.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_22q12.2' versus 'GENDER'

P value = 0.00188 (Fisher's exact test), Q value = 0.011

Table S124.  Gene #29: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 22(22Q12.2) MUTATED 27 36
DEL PEAK 22(22Q12.2) WILD-TYPE 49 175

Figure S124.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

'del_22q12.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00113 (Wilcoxon-test), Q value = 0.0078

Table S125.  Gene #29: 'del_22q12.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 22(22Q12.2) MUTATED 19 70.5 (35.5)
DEL PEAK 22(22Q12.2) WILD-TYPE 57 93.2 (10.7)

Figure S125.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_xp11.4' versus 'Time to Death'

P value = 0.000231 (logrank test), Q value = 0.0024

Table S126.  Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 23(XP11.4) MUTATED 33 12 0.4 - 91.7 (19.6)
DEL PEAK 23(XP11.4) WILD-TYPE 249 32 0.1 - 194.8 (25.6)

Figure S126.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

'del_xp11.4' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00032

Table S127.  Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 23(XP11.4) MUTATED 8 1 16 3
DEL PEAK 23(XP11.4) WILD-TYPE 163 21 36 12

Figure S127.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xp11.4' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00069

Table S128.  Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 23(XP11.4) MUTATED 12 4 18
DEL PEAK 23(XP11.4) WILD-TYPE 178 29 44

Figure S128.  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 = 0.0557 (Fisher's exact test), Q value = 0.16

Table S129.  Gene #30: 'del_xp11.4' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 23(XP11.4) MUTATED 5 8 1
DEL PEAK 23(XP11.4) WILD-TYPE 43 16 4

Figure S129.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xp11.4' versus 'GENDER'

P value = 0.0212 (Fisher's exact test), Q value = 0.084

Table S130.  Gene #30: 'del_xp11.4' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 23(XP11.4) MUTATED 15 19
DEL PEAK 23(XP11.4) WILD-TYPE 61 192

Figure S130.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #7: 'GENDER'

'del_xp11.4' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0213 (Wilcoxon-test), Q value = 0.084

Table S131.  Gene #30: 'del_xp11.4' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 23(XP11.4) MUTATED 9 76.7 (25.5)
DEL PEAK 23(XP11.4) WILD-TYPE 67 89.0 (21.3)

Figure S131.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_xp11.4' versus 'RACE'

P value = 0.0239 (Fisher's exact test), Q value = 0.092

Table S132.  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 61 204
DEL PEAK 23(XP11.4) MUTATED 0 3 9 20
DEL PEAK 23(XP11.4) WILD-TYPE 2 2 52 184

Figure S132.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #11: 'RACE'

'del_xq28' versus 'Time to Death'

P value = 1.16e-06 (logrank test), Q value = 7.2e-05

Table S133.  Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 282 44 0.1 - 194.8 (24.5)
DEL PEAK 24(XQ28) MUTATED 27 12 0.1 - 91.7 (18.2)
DEL PEAK 24(XQ28) WILD-TYPE 255 32 0.1 - 194.8 (25.6)

Figure S133.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

'del_xq28' versus 'YEARS_TO_BIRTH'

P value = 0.0292 (Wilcoxon-test), Q value = 0.1

Table S134.  Gene #31: 'del_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 282 61.4 (12.1)
DEL PEAK 24(XQ28) MUTATED 27 55.8 (13.8)
DEL PEAK 24(XQ28) WILD-TYPE 255 62.0 (11.8)

Figure S134.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xq28' versus 'PATHOLOGIC_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.004

Table S135.  Gene #31: 'del_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 22 52 15
DEL PEAK 24(XQ28) MUTATED 8 1 12 3
DEL PEAK 24(XQ28) WILD-TYPE 163 21 40 12

Figure S135.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 0.00145 (Fisher's exact test), Q value = 0.0091

Table S136.  Gene #31: 'del_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 190 33 62
DEL PEAK 24(XQ28) MUTATED 11 3 14
DEL PEAK 24(XQ28) WILD-TYPE 179 30 48

Figure S136.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xq28' versus 'PATHOLOGY_N_STAGE'

P value = 0.00695 (Fisher's exact test), Q value = 0.034

Table S137.  Gene #31: 'del_xq28' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 48 24 5
DEL PEAK 24(XQ28) MUTATED 3 8 1
DEL PEAK 24(XQ28) WILD-TYPE 45 16 4

Figure S137.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xq28' versus 'GENDER'

P value = 0.0218 (Fisher's exact test), Q value = 0.086

Table S138.  Gene #31: 'del_xq28' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 211
DEL PEAK 24(XQ28) MUTATED 13 15
DEL PEAK 24(XQ28) WILD-TYPE 63 196

Figure S138.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #7: 'GENDER'

'del_xq28' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00491 (Wilcoxon-test), Q value = 0.025

Table S139.  Gene #31: 'del_xq28' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 24(XQ28) MUTATED 10 69.0 (34.1)
DEL PEAK 24(XQ28) WILD-TYPE 66 90.3 (18.4)

Figure S139.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

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/19781624/transformed.cor.cli.txt

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

  • Number of patients = 287

  • Number of significantly 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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