Correlation between copy number variation genes (focal events) and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C17M07BT
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 28 focal events and 12 clinical features across 288 patients, 124 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_3q26.31 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_5q35.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • amp_7p11.2 cnv correlated to 'PATHOLOGIC_STAGE',  'GENDER', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

  • amp_17q23.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'GENDER'.

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

  • del_10q21.1 cnv correlated to '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_16q24.2 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',  'PATHOLOGY_M_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 28 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 124 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 40 (14%) 248 4.65e-10
(1.56e-07)
0.617
(0.816)
1e-05
(0.000187)
1e-05
(0.000187)
0.00018
(0.00195)
0.0243
(0.0908)
0.00187
(0.011)
0.00303
(0.0159)
0.388
(0.623)
0.478
(0.702)
0.0577
(0.171)
1
(1.00)
del 14q24 2 50 (17%) 238 5.44e-05
(0.000761)
0.679
(0.86)
0.0028
(0.0149)
0.0001
(0.00116)
0.00063
(0.00504)
0.166
(0.399)
0.00805
(0.0361)
0.00896
(0.0393)
0.476
(0.702)
0.0756
(0.213)
0.957
(1.00)
0.697
(0.867)
del 22q12 2 63 (22%) 225 0.00238
(0.0136)
0.0937
(0.252)
1e-05
(0.000187)
1e-05
(0.000187)
0.00176
(0.0106)
0.0591
(0.173)
0.0012
(0.00775)
0.00113
(0.00747)
0.468
(0.701)
0.216
(0.479)
0.332
(0.58)
0.713
(0.881)
del 1p36 31 54 (19%) 234 2.28e-05
(0.000349)
0.225
(0.493)
1e-05
(0.000187)
1e-05
(0.000187)
0.00087
(0.00635)
0.19
(0.449)
0.026
(0.0927)
0.00173
(0.0106)
0.848
(0.983)
0.201
(0.462)
0.681
(0.86)
0.699
(0.867)
del 3p22 1 25 (9%) 263 2.24e-07
(3.76e-05)
0.0257
(0.0927)
1e-05
(0.000187)
1e-05
(0.000187)
0.0249
(0.0918)
0.085
(0.232)
0.816
(0.962)
0.264
(0.528)
0.648
(0.84)
0.3
(0.548)
0.672
(0.858)
0.607
(0.813)
del 4q34 3 32 (11%) 256 2.2e-06
(0.000184)
0.387
(0.623)
1e-05
(0.000187)
2e-05
(0.00032)
0.0268
(0.0927)
0.353
(0.605)
0.00947
(0.0398)
0.2
(0.462)
0.577
(0.801)
0.959
(1.00)
0.0523
(0.158)
0.357
(0.609)
del 5q35 2 11 (4%) 277 0.000775
(0.00579)
0.0044
(0.0211)
0.0003
(0.0028)
5e-05
(0.00073)
0.0708
(0.202)
0.31
(0.555)
0.00907
(0.0393)
0.765
(0.918)
0.292
(0.544)
del 11q22 3 31 (11%) 257 7.11e-05
(0.000919)
0.442
(0.681)
1e-05
(0.000187)
1e-05
(0.000187)
0.0001
(0.00116)
0.0685
(0.198)
0.517
(0.749)
0.044
(0.141)
0.417
(0.657)
0.503
(0.731)
0.274
(0.538)
0.619
(0.816)
del 11q23 3 29 (10%) 259 1.38e-06
(0.000154)
0.44
(0.681)
1e-05
(0.000187)
1e-05
(0.000187)
9e-05
(0.00112)
0.0539
(0.162)
0.828
(0.966)
0.044
(0.141)
0.897
(1.00)
0.967
(1.00)
0.195
(0.455)
0.612
(0.816)
del 14q11 2 51 (18%) 237 0.000625
(0.00504)
0.55
(0.784)
0.0113
(0.0471)
0.00046
(0.00396)
0.00244
(0.0137)
0.384
(0.623)
0.0134
(0.0542)
0.0224
(0.0854)
0.659
(0.848)
0.315
(0.56)
1
(1.00)
0.698
(0.867)
del 15q13 3 35 (12%) 253 0.00092
(0.00644)
0.111
(0.281)
0.00023
(0.00241)
2e-05
(0.00032)
0.00029
(0.00278)
0.0849
(0.232)
0.306
(0.555)
0.0278
(0.0952)
0.914
(1.00)
0.985
(1.00)
0.567
(0.797)
1
(1.00)
del 6q25 3 32 (11%) 256 0.27
(0.536)
0.94
(1.00)
0.00024
(0.00244)
2e-05
(0.00032)
0.02
(0.0771)
0.598
(0.811)
0.00249
(0.0137)
0.0429
(0.14)
0.941
(1.00)
0.572
(0.798)
0.164
(0.397)
0.619
(0.816)
del 19p13 3 23 (8%) 265 0.000719
(0.00549)
0.762
(0.918)
0.00067
(0.00524)
0.00012
(0.00134)
0.0157
(0.062)
0.431
(0.673)
0.333
(0.58)
0.00144
(0.00911)
0.104
(0.272)
0.548
(0.783)
0.607
(0.813)
amp 2q32 1 53 (18%) 235 0.288
(0.544)
0.467
(0.701)
0.0467
(0.147)
0.0493
(0.152)
0.0171
(0.067)
0.0129
(0.0528)
0.493
(0.721)
0.251
(0.511)
0.989
(1.00)
0.591
(0.81)
0.854
(0.986)
1
(1.00)
amp 7q31 2 177 (61%) 111 0.287
(0.544)
0.477
(0.702)
0.00396
(0.0201)
0.111
(0.281)
0.106
(0.275)
0.728
(0.893)
0.00911
(0.0393)
0.0843
(0.232)
0.76
(0.918)
0.0042
(0.0205)
0.291
(0.544)
0.368
(0.62)
del 5p15 33 13 (5%) 275 0.285
(0.544)
0.173
(0.412)
0.0285
(0.0969)
0.0263
(0.0927)
0.00258
(0.014)
0.373
(0.62)
0.0461
(0.146)
0.245
(0.505)
0.882
(1.00)
1
(1.00)
0.36
(0.611)
del 6p12 3 26 (9%) 262 0.238
(0.505)
0.795
(0.944)
0.00101
(0.0069)
0.00051
(0.00428)
0.00459
(0.0217)
0.592
(0.81)
0.352
(0.605)
0.0364
(0.122)
0.65
(0.84)
0.929
(1.00)
0.245
(0.505)
0.607
(0.813)
del 19q13 42 19 (7%) 269 0.0489
(0.152)
0.583
(0.806)
0.00036
(0.00318)
0.00026
(0.00257)
0.209
(0.472)
1
(1.00)
0.595
(0.81)
0.0267
(0.0927)
0.924
(1.00)
0.227
(0.494)
0.25
(0.511)
1
(1.00)
amp 7p11 2 175 (61%) 113 0.378
(0.62)
0.372
(0.62)
0.004
(0.0201)
0.128
(0.322)
0.688
(0.863)
0.294
(0.544)
0.00103
(0.0069)
0.0947
(0.253)
0.956
(1.00)
0.0072
(0.0332)
0.236
(0.505)
0.377
(0.62)
del 2q22 1 10 (3%) 278 0.626
(0.82)
0.409
(0.651)
0.00036
(0.00318)
0.00312
(0.0161)
0.0708
(0.202)
0.31
(0.555)
0.299
(0.548)
0.455
(0.69)
0.765
(0.918)
0.571
(0.798)
0.763
(0.918)
1
(1.00)
del 2q37 3 12 (4%) 276 0.75
(0.916)
0.53
(0.761)
0.00787
(0.0357)
0.00421
(0.0205)
0.674
(0.858)
1
(1.00)
0.088
(0.238)
0.567
(0.797)
0.834
(0.97)
0.8
(0.946)
1
(1.00)
del 10q21 1 19 (7%) 269 0.107
(0.276)
0.937
(1.00)
6e-05
(0.000806)
0.00089
(0.00636)
0.11
(0.281)
1
(1.00)
0.289
(0.544)
0.0496
(0.152)
0.262
(0.526)
0.644
(0.838)
0.429
(0.673)
1
(1.00)
del 16q24 2 12 (4%) 276 2.88e-06
(0.000187)
0.216
(0.479)
0.00177
(0.0106)
0.00218
(0.0126)
0.209
(0.472)
0.373
(0.62)
0.523
(0.754)
0.153
(0.379)
0.31
(0.555)
0.96
(1.00)
0.351
(0.605)
1
(1.00)
amp 2p23 2 45 (16%) 243 0.415
(0.657)
0.242
(0.505)
0.287
(0.544)
0.325
(0.574)
0.00549
(0.0256)
0.0243
(0.0908)
0.271
(0.536)
0.294
(0.544)
0.237
(0.505)
0.772
(0.923)
0.909
(1.00)
1
(1.00)
amp 5q35 3 37 (13%) 251 0.161
(0.394)
0.451
(0.689)
0.0405
(0.135)
0.0268
(0.0927)
0.293
(0.544)
0.627
(0.82)
0.554
(0.785)
0.15
(0.373)
0.918
(1.00)
0.918
(1.00)
0.382
(0.623)
0.375
(0.62)
amp 17q23 2 199 (69%) 89 0.825
(0.966)
0.257
(0.519)
0.0839
(0.232)
0.203
(0.464)
0.475
(0.702)
1
(1.00)
0.0422
(0.139)
0.82
(0.963)
0.776
(0.925)
0.239
(0.505)
0.103
(0.272)
0.191
(0.449)
del 2p12 8 (3%) 280 0.391
(0.625)
0.722
(0.889)
0.00928
(0.0395)
0.0142
(0.0567)
0.671
(0.858)
0.242
(0.505)
0.686
(0.863)
0.447
(0.685)
0.216
(0.479)
1
(1.00)
1
(1.00)
amp 3q26 31 101 (35%) 187 0.927
(1.00)
0.476
(0.702)
0.244
(0.505)
0.282
(0.544)
1
(1.00)
0.0581
(0.171)
0.33
(0.58)
0.596
(0.81)
0.433
(0.673)
0.456
(0.69)
0.164
(0.397)
1
(1.00)
'amp_2p23.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00549 (Fisher's exact test), Q value = 0.026

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

nPatients N0 N1 N2
ALL 49 24 4
AMP PEAK 1(2P23.2) MUTATED 4 8 2
AMP PEAK 1(2P23.2) WILD-TYPE 45 16 2

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 = 0.0243 (Fisher's exact test), Q value = 0.091

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

nPatients 0 1
ALL 94 9
AMP PEAK 1(2P23.2) MUTATED 11 4
AMP PEAK 1(2P23.2) WILD-TYPE 83 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 = 0.0467 (Fisher's exact test), Q value = 0.15

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
AMP PEAK 2(2Q32.1) MUTATED 28 4 12 7
AMP PEAK 2(2Q32.1) WILD-TYPE 143 17 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 = 0.0493 (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 191 33 62
AMP PEAK 2(2Q32.1) MUTATED 28 8 17
AMP PEAK 2(2Q32.1) WILD-TYPE 163 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 = 0.0171 (Fisher's exact test), Q value = 0.067

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

nPatients N0 N1 N2
ALL 49 24 4
AMP PEAK 2(2Q32.1) MUTATED 9 9 3
AMP PEAK 2(2Q32.1) WILD-TYPE 40 15 1

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 = 0.0129 (Fisher's exact test), Q value = 0.053

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

nPatients 0 1
ALL 94 9
AMP PEAK 2(2Q32.1) MUTATED 15 5
AMP PEAK 2(2Q32.1) WILD-TYPE 79 4

Figure S6.  Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_3q26.31' versus 'PATHOLOGY_M_STAGE'

P value = 0.0581 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #3: 'amp_3q26.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
AMP PEAK 3(3Q26.31) MUTATED 29 0
AMP PEAK 3(3Q26.31) WILD-TYPE 65 9

Figure S7.  Get High-res Image Gene #3: 'amp_3q26.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0405 (Fisher's exact test), Q value = 0.13

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
AMP PEAK 4(5Q35.3) MUTATED 16 2 11 4
AMP PEAK 4(5Q35.3) WILD-TYPE 155 19 41 11

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

'amp_5q35.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0268 (Fisher's exact test), Q value = 0.093

Table S9.  Gene #4: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
AMP PEAK 4(5Q35.3) MUTATED 18 5 14
AMP PEAK 4(5Q35.3) WILD-TYPE 173 28 48

Figure S9.  Get High-res Image Gene #4: 'amp_5q35.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7p11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.004 (Fisher's exact test), Q value = 0.02

Table S10.  Gene #5: 'amp_7p11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
AMP PEAK 5(7P11.2) MUTATED 113 12 21 12
AMP PEAK 5(7P11.2) WILD-TYPE 58 9 31 3

Figure S10.  Get High-res Image Gene #5: 'amp_7p11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7p11.2' versus 'GENDER'

P value = 0.00103 (Fisher's exact test), Q value = 0.0069

Table S11.  Gene #5: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
AMP PEAK 5(7P11.2) MUTATED 34 141
AMP PEAK 5(7P11.2) WILD-TYPE 42 71

Figure S11.  Get High-res Image Gene #5: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

'amp_7p11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0072 (Wilcoxon-test), Q value = 0.033

Table S12.  Gene #5: 'amp_7p11.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
AMP PEAK 5(7P11.2) MUTATED 31 1967.6 (14.7)
AMP PEAK 5(7P11.2) WILD-TYPE 23 1979.0 (14.8)

Figure S12.  Get High-res Image Gene #5: 'amp_7p11.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_7q31.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00396 (Fisher's exact test), Q value = 0.02

Table S13.  Gene #6: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
AMP PEAK 6(7Q31.2) MUTATED 113 12 21 12
AMP PEAK 6(7Q31.2) WILD-TYPE 58 9 31 3

Figure S13.  Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 0.00911 (Fisher's exact test), Q value = 0.039

Table S14.  Gene #6: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
AMP PEAK 6(7Q31.2) MUTATED 37 140
AMP PEAK 6(7Q31.2) WILD-TYPE 39 72

Figure S14.  Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0843 (Wilcoxon-test), Q value = 0.23

Table S15.  Gene #6: 'amp_7q31.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
AMP PEAK 6(7Q31.2) MUTATED 54 89.8 (19.6)
AMP PEAK 6(7Q31.2) WILD-TYPE 22 81.8 (26.8)

Figure S15.  Get High-res Image Gene #6: '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 = 0.021

Table S16.  Gene #6: 'amp_7q31.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
AMP PEAK 6(7Q31.2) MUTATED 32 1967.6 (14.5)
AMP PEAK 6(7Q31.2) WILD-TYPE 22 1979.7 (14.8)

Figure S16.  Get High-res Image Gene #6: 'amp_7q31.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q23.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0839 (Fisher's exact test), Q value = 0.23

Table S17.  Gene #7: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
AMP PEAK 7(17Q23.2) MUTATED 124 17 29 10
AMP PEAK 7(17Q23.2) WILD-TYPE 47 4 23 5

Figure S17.  Get High-res Image Gene #7: 'amp_17q23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q23.2' versus 'GENDER'

P value = 0.0422 (Fisher's exact test), Q value = 0.14

Table S18.  Gene #7: 'amp_17q23.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
AMP PEAK 7(17Q23.2) MUTATED 45 154
AMP PEAK 7(17Q23.2) WILD-TYPE 31 58

Figure S18.  Get High-res Image Gene #7: 'amp_17q23.2' versus Clinical Feature #7: 'GENDER'

'del_1p36.31' versus 'Time to Death'

P value = 2.28e-05 (logrank test), Q value = 0.00035

Table S19.  Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 1(1P36.31) MUTATED 54 17 0.1 - 123.6 (20.1)
DEL PEAK 1(1P36.31) WILD-TYPE 231 27 0.1 - 194.8 (26.0)

Figure S19.  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 = 0.00019

Table S20.  Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 1(1P36.31) MUTATED 16 3 22 5
DEL PEAK 1(1P36.31) WILD-TYPE 155 18 30 10

Figure S20.  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 = 0.00019

Table S21.  Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 1(1P36.31) MUTATED 20 7 27
DEL PEAK 1(1P36.31) WILD-TYPE 171 26 35

Figure S21.  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 = 0.00087 (Fisher's exact test), Q value = 0.0064

Table S22.  Gene #8: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 1(1P36.31) MUTATED 7 13 2
DEL PEAK 1(1P36.31) WILD-TYPE 42 11 2

Figure S22.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.31' versus 'GENDER'

P value = 0.026 (Fisher's exact test), Q value = 0.093

Table S23.  Gene #8: 'del_1p36.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 1(1P36.31) MUTATED 21 33
DEL PEAK 1(1P36.31) WILD-TYPE 55 179

Figure S23.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #7: 'GENDER'

'del_1p36.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00173 (Wilcoxon-test), Q value = 0.011

Table S24.  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 15 72.0 (34.7)
DEL PEAK 1(1P36.31) WILD-TYPE 61 91.3 (15.9)

Figure S24.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2p12' versus 'PATHOLOGIC_STAGE'

P value = 0.00928 (Fisher's exact test), Q value = 0.039

Table S25.  Gene #9: 'del_2p12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 2(2P12) MUTATED 1 0 3 2
DEL PEAK 2(2P12) WILD-TYPE 170 21 49 13

Figure S25.  Get High-res Image Gene #9: 'del_2p12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2p12' versus 'PATHOLOGY_T_STAGE'

P value = 0.0142 (Fisher's exact test), Q value = 0.057

Table S26.  Gene #9: 'del_2p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 2(2P12) MUTATED 2 3 3
DEL PEAK 2(2P12) WILD-TYPE 189 30 59

Figure S26.  Get High-res Image Gene #9: 'del_2p12' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q22.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0032

Table S27.  Gene #10: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 3(2Q22.1) MUTATED 1 0 6 2
DEL PEAK 3(2Q22.1) WILD-TYPE 170 21 46 13

Figure S27.  Get High-res Image Gene #10: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00312 (Fisher's exact test), Q value = 0.016

Table S28.  Gene #10: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 3(2Q22.1) MUTATED 3 0 7
DEL PEAK 3(2Q22.1) WILD-TYPE 188 33 55

Figure S28.  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 = 0.0708 (Fisher's exact test), Q value = 0.2

Table S29.  Gene #10: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 3(2Q22.1) MUTATED 1 4 0
DEL PEAK 3(2Q22.1) WILD-TYPE 48 20 4

Figure S29.  Get High-res Image Gene #10: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00787 (Fisher's exact test), Q value = 0.036

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 4(2Q37.3) MUTATED 2 2 5 1
DEL PEAK 4(2Q37.3) WILD-TYPE 169 19 47 14

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

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00421 (Fisher's exact test), Q value = 0.021

Table S31.  Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 4(2Q37.3) MUTATED 3 3 6
DEL PEAK 4(2Q37.3) WILD-TYPE 188 30 56

Figure S31.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'GENDER'

P value = 0.088 (Fisher's exact test), Q value = 0.24

Table S32.  Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 4(2Q37.3) MUTATED 6 6
DEL PEAK 4(2Q37.3) WILD-TYPE 70 206

Figure S32.  Get High-res Image Gene #11: 'del_2q37.3' versus Clinical Feature #7: 'GENDER'

'del_3p22.1' versus 'Time to Death'

P value = 2.24e-07 (logrank test), Q value = 3.8e-05

Table S33.  Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 5(3P22.1) MUTATED 25 11 2.0 - 86.3 (15.5)
DEL PEAK 5(3P22.1) WILD-TYPE 260 33 0.1 - 194.8 (26.0)

Figure S33.  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 = 0.0257 (Wilcoxon-test), Q value = 0.093

Table S34.  Gene #12: 'del_3p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
DEL PEAK 5(3P22.1) MUTATED 24 55.7 (12.1)
DEL PEAK 5(3P22.1) WILD-TYPE 259 62.0 (12.0)

Figure S34.  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 = 0.00019

Table S35.  Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 5(3P22.1) MUTATED 5 1 14 3
DEL PEAK 5(3P22.1) WILD-TYPE 166 20 38 12

Figure S35.  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 = 0.00019

Table S36.  Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 5(3P22.1) MUTATED 6 4 15
DEL PEAK 5(3P22.1) WILD-TYPE 185 29 47

Figure S36.  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 = 0.0249 (Fisher's exact test), Q value = 0.092

Table S37.  Gene #12: 'del_3p22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 5(3P22.1) MUTATED 6 8 2
DEL PEAK 5(3P22.1) WILD-TYPE 43 16 2

Figure S37.  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 = 0.085 (Fisher's exact test), Q value = 0.23

Table S38.  Gene #12: 'del_3p22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 5(3P22.1) MUTATED 4 2
DEL PEAK 5(3P22.1) WILD-TYPE 90 7

Figure S38.  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 = 2.2e-06 (logrank test), Q value = 0.00018

Table S39.  Gene #13: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 6(4Q34.3) MUTATED 32 12 0.4 - 79.9 (19.3)
DEL PEAK 6(4Q34.3) WILD-TYPE 253 32 0.1 - 194.8 (25.8)

Figure S39.  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 = 0.00019

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 6(4Q34.3) MUTATED 7 2 17 3
DEL PEAK 6(4Q34.3) WILD-TYPE 164 19 35 12

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

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

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

Table S41.  Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 6(4Q34.3) MUTATED 9 5 18
DEL PEAK 6(4Q34.3) WILD-TYPE 182 28 44

Figure S41.  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 = 0.0268 (Fisher's exact test), Q value = 0.093

Table S42.  Gene #13: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 6(4Q34.3) MUTATED 7 10 1
DEL PEAK 6(4Q34.3) WILD-TYPE 42 14 3

Figure S42.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q34.3' versus 'GENDER'

P value = 0.00947 (Fisher's exact test), Q value = 0.04

Table S43.  Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 6(4Q34.3) MUTATED 15 17
DEL PEAK 6(4Q34.3) WILD-TYPE 61 195

Figure S43.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'RACE'

P value = 0.0523 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #13: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
DEL PEAK 6(4Q34.3) MUTATED 0 3 6 19
DEL PEAK 6(4Q34.3) WILD-TYPE 2 3 55 185

Figure S44.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_5p15.33' versus 'PATHOLOGIC_STAGE'

P value = 0.0285 (Fisher's exact test), Q value = 0.097

Table S45.  Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 7(5P15.33) MUTATED 4 1 5 2
DEL PEAK 7(5P15.33) WILD-TYPE 167 20 47 13

Figure S45.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.0263 (Fisher's exact test), Q value = 0.093

Table S46.  Gene #14: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 7(5P15.33) MUTATED 5 1 7
DEL PEAK 7(5P15.33) WILD-TYPE 186 32 55

Figure S46.  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 = 0.00258 (Fisher's exact test), Q value = 0.014

Table S47.  Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 7(5P15.33) MUTATED 0 5 1
DEL PEAK 7(5P15.33) WILD-TYPE 49 19 3

Figure S47.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'GENDER'

P value = 0.0461 (Fisher's exact test), Q value = 0.15

Table S48.  Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 7(5P15.33) MUTATED 7 6
DEL PEAK 7(5P15.33) WILD-TYPE 69 206

Figure S48.  Get High-res Image Gene #14: 'del_5p15.33' versus Clinical Feature #7: 'GENDER'

'del_5q35.2' versus 'Time to Death'

P value = 0.000775 (logrank test), Q value = 0.0058

Table S49.  Gene #15: 'del_5q35.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 8(5Q35.2) MUTATED 11 5 2.8 - 79.9 (19.6)
DEL PEAK 8(5Q35.2) WILD-TYPE 274 39 0.1 - 194.8 (25.5)

Figure S49.  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 = 0.0044 (Wilcoxon-test), Q value = 0.021

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

nPatients Mean (Std.Dev)
ALL 283 61.5 (12.1)
DEL PEAK 8(5Q35.2) MUTATED 10 46.8 (17.3)
DEL PEAK 8(5Q35.2) WILD-TYPE 273 62.0 (11.6)

Figure S50.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q35.2' versus 'PATHOLOGIC_STAGE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0028

Table S51.  Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 8(5Q35.2) MUTATED 1 1 7 1
DEL PEAK 8(5Q35.2) WILD-TYPE 170 20 45 14

Figure S51.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5q35.2' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00073

Table S52.  Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 8(5Q35.2) MUTATED 1 1 9
DEL PEAK 8(5Q35.2) WILD-TYPE 190 32 53

Figure S52.  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 = 0.0708 (Fisher's exact test), Q value = 0.2

Table S53.  Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 8(5Q35.2) MUTATED 1 4 0
DEL PEAK 8(5Q35.2) WILD-TYPE 48 20 4

Figure S53.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q35.2' versus 'GENDER'

P value = 0.00907 (Fisher's exact test), Q value = 0.039

Table S54.  Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 8(5Q35.2) MUTATED 7 4
DEL PEAK 8(5Q35.2) WILD-TYPE 69 208

Figure S54.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #7: 'GENDER'

'del_6p12.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.0069

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 9(6P12.3) MUTATED 9 0 12 2
DEL PEAK 9(6P12.3) WILD-TYPE 162 21 40 13

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

'del_6p12.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0043

Table S56.  Gene #16: 'del_6p12.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 9(6P12.3) MUTATED 11 1 14
DEL PEAK 9(6P12.3) WILD-TYPE 180 32 48

Figure S56.  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 = 0.00459 (Fisher's exact test), Q value = 0.022

Table S57.  Gene #16: 'del_6p12.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 9(6P12.3) MUTATED 6 1 3
DEL PEAK 9(6P12.3) WILD-TYPE 43 23 1

Figure S57.  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 S58.  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 S58.  Get High-res Image Gene #16: 'del_6p12.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q25.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.0024

Table S59.  Gene #17: 'del_6q25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 10(6Q25.3) MUTATED 12 0 15 2
DEL PEAK 10(6Q25.3) WILD-TYPE 159 21 37 13

Figure S59.  Get High-res Image Gene #17: '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 S60.  Gene #17: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 10(6Q25.3) MUTATED 13 1 18
DEL PEAK 10(6Q25.3) WILD-TYPE 178 32 44

Figure S60.  Get High-res Image Gene #17: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q25.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.02 (Fisher's exact test), Q value = 0.077

Table S61.  Gene #17: 'del_6q25.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 10(6Q25.3) MUTATED 6 4 3
DEL PEAK 10(6Q25.3) WILD-TYPE 43 20 1

Figure S61.  Get High-res Image Gene #17: 'del_6q25.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q25.3' versus 'GENDER'

P value = 0.00249 (Fisher's exact test), Q value = 0.014

Table S62.  Gene #17: 'del_6q25.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 10(6Q25.3) MUTATED 16 16
DEL PEAK 10(6Q25.3) WILD-TYPE 60 196

Figure S62.  Get High-res Image Gene #17: '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 S63.  Gene #17: 'del_6q25.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 10(6Q25.3) MUTATED 12 73.3 (34.7)
DEL PEAK 10(6Q25.3) WILD-TYPE 64 90.2 (17.9)

Figure S63.  Get High-res Image Gene #17: 'del_6q25.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'Time to Death'

P value = 4.65e-10 (logrank test), Q value = 1.6e-07

Table S64.  Gene #18: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 11(9P21.3) MUTATED 39 17 2.0 - 93.3 (18.2)
DEL PEAK 11(9P21.3) WILD-TYPE 246 27 0.1 - 194.8 (26.1)

Figure S64.  Get High-res Image Gene #18: '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 = 0.00019

Table S65.  Gene #18: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 11(9P21.3) MUTATED 11 0 19 7
DEL PEAK 11(9P21.3) WILD-TYPE 160 21 33 8

Figure S65.  Get High-res Image Gene #18: '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 = 0.00019

Table S66.  Gene #18: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 11(9P21.3) MUTATED 12 3 25
DEL PEAK 11(9P21.3) WILD-TYPE 179 30 37

Figure S66.  Get High-res Image Gene #18: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.002

Table S67.  Gene #18: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 11(9P21.3) MUTATED 8 14 3
DEL PEAK 11(9P21.3) WILD-TYPE 41 10 1

Figure S67.  Get High-res Image Gene #18: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0243 (Fisher's exact test), Q value = 0.091

Table S68.  Gene #18: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 11(9P21.3) MUTATED 11 4
DEL PEAK 11(9P21.3) WILD-TYPE 83 5

Figure S68.  Get High-res Image Gene #18: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.00187 (Fisher's exact test), Q value = 0.011

Table S69.  Gene #18: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 11(9P21.3) MUTATED 19 21
DEL PEAK 11(9P21.3) WILD-TYPE 57 191

Figure S69.  Get High-res Image Gene #18: '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 S70.  Gene #18: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 11(9P21.3) MUTATED 14 69.3 (36.3)
DEL PEAK 11(9P21.3) WILD-TYPE 62 91.6 (15.0)

Figure S70.  Get High-res Image Gene #18: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'RACE'

P value = 0.0577 (Fisher's exact test), Q value = 0.17

Table S71.  Gene #18: 'del_9p21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 6 61 204
DEL PEAK 11(9P21.3) MUTATED 0 3 5 31
DEL PEAK 11(9P21.3) WILD-TYPE 2 3 56 173

Figure S71.  Get High-res Image Gene #18: 'del_9p21.3' versus Clinical Feature #11: 'RACE'

'del_10q21.1' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00081

Table S72.  Gene #19: 'del_10q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 12(10Q21.1) MUTATED 5 0 12 1
DEL PEAK 12(10Q21.1) WILD-TYPE 166 21 40 14

Figure S72.  Get High-res Image Gene #19: 'del_10q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00089 (Fisher's exact test), Q value = 0.0064

Table S73.  Gene #19: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 12(10Q21.1) MUTATED 8 0 11
DEL PEAK 12(10Q21.1) WILD-TYPE 183 33 51

Figure S73.  Get High-res Image Gene #19: '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 S74.  Gene #19: 'del_10q21.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 12(10Q21.1) MUTATED 7 57.1 (45.0)
DEL PEAK 12(10Q21.1) WILD-TYPE 69 90.6 (15.9)

Figure S74.  Get High-res Image Gene #19: 'del_10q21.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q22.3' versus 'Time to Death'

P value = 7.11e-05 (logrank test), Q value = 0.00092

Table S75.  Gene #20: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 13(11Q22.3) MUTATED 30 11 0.4 - 123.6 (18.6)
DEL PEAK 13(11Q22.3) WILD-TYPE 255 33 0.1 - 194.8 (26.0)

Figure S75.  Get High-res Image Gene #20: '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 = 0.00019

Table S76.  Gene #20: 'del_11q22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 13(11Q22.3) MUTATED 7 3 14 6
DEL PEAK 13(11Q22.3) WILD-TYPE 164 18 38 9

Figure S76.  Get High-res Image Gene #20: '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 = 0.00019

Table S77.  Gene #20: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 13(11Q22.3) MUTATED 8 5 18
DEL PEAK 13(11Q22.3) WILD-TYPE 183 28 44

Figure S77.  Get High-res Image Gene #20: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q22.3' versus 'PATHOLOGY_N_STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S78.  Gene #20: 'del_11q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 13(11Q22.3) MUTATED 3 9 3
DEL PEAK 13(11Q22.3) WILD-TYPE 46 15 1

Figure S78.  Get High-res Image Gene #20: 'del_11q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q22.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0685 (Fisher's exact test), Q value = 0.2

Table S79.  Gene #20: 'del_11q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 13(11Q22.3) MUTATED 9 3
DEL PEAK 13(11Q22.3) WILD-TYPE 85 6

Figure S79.  Get High-res Image Gene #20: '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 S80.  Gene #20: 'del_11q22.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 13(11Q22.3) MUTATED 8 73.8 (33.4)
DEL PEAK 13(11Q22.3) WILD-TYPE 68 89.1 (20.1)

Figure S80.  Get High-res Image Gene #20: 'del_11q22.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q23.3' versus 'Time to Death'

P value = 1.38e-06 (logrank test), Q value = 0.00015

Table S81.  Gene #21: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 14(11Q23.3) MUTATED 28 12 0.4 - 123.6 (17.8)
DEL PEAK 14(11Q23.3) WILD-TYPE 257 32 0.1 - 194.8 (26.0)

Figure S81.  Get High-res Image Gene #21: '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 = 0.00019

Table S82.  Gene #21: 'del_11q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 14(11Q23.3) MUTATED 5 2 15 6
DEL PEAK 14(11Q23.3) WILD-TYPE 166 19 37 9

Figure S82.  Get High-res Image Gene #21: '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 = 0.00019

Table S83.  Gene #21: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 14(11Q23.3) MUTATED 6 4 19
DEL PEAK 14(11Q23.3) WILD-TYPE 185 29 43

Figure S83.  Get High-res Image Gene #21: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

Table S84.  Gene #21: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 14(11Q23.3) MUTATED 3 9 3
DEL PEAK 14(11Q23.3) WILD-TYPE 46 15 1

Figure S84.  Get High-res Image Gene #21: 'del_11q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0539 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #21: 'del_11q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 14(11Q23.3) MUTATED 8 3
DEL PEAK 14(11Q23.3) WILD-TYPE 86 6

Figure S85.  Get High-res Image Gene #21: '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 S86.  Gene #21: 'del_11q23.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 14(11Q23.3) MUTATED 8 73.8 (33.4)
DEL PEAK 14(11Q23.3) WILD-TYPE 68 89.1 (20.1)

Figure S86.  Get High-res Image Gene #21: 'del_11q23.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q11.2' versus 'Time to Death'

P value = 0.000625 (logrank test), Q value = 0.005

Table S87.  Gene #22: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 15(14Q11.2) MUTATED 51 14 0.1 - 80.9 (20.6)
DEL PEAK 15(14Q11.2) WILD-TYPE 234 30 0.1 - 194.8 (25.5)

Figure S87.  Get High-res Image Gene #22: 'del_14q11.2' versus Clinical Feature #1: 'Time to Death'

'del_14q11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0113 (Fisher's exact test), Q value = 0.047

Table S88.  Gene #22: 'del_14q11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 15(14Q11.2) MUTATED 22 3 14 6
DEL PEAK 15(14Q11.2) WILD-TYPE 149 18 38 9

Figure S88.  Get High-res Image Gene #22: '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 = 0.004

Table S89.  Gene #22: 'del_14q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 15(14Q11.2) MUTATED 24 5 22
DEL PEAK 15(14Q11.2) WILD-TYPE 167 28 40

Figure S89.  Get High-res Image Gene #22: 'del_14q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00244 (Fisher's exact test), Q value = 0.014

Table S90.  Gene #22: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 15(14Q11.2) MUTATED 9 8 4
DEL PEAK 15(14Q11.2) WILD-TYPE 40 16 0

Figure S90.  Get High-res Image Gene #22: 'del_14q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q11.2' versus 'GENDER'

P value = 0.0134 (Fisher's exact test), Q value = 0.054

Table S91.  Gene #22: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 15(14Q11.2) MUTATED 21 30
DEL PEAK 15(14Q11.2) WILD-TYPE 55 182

Figure S91.  Get High-res Image Gene #22: 'del_14q11.2' versus Clinical Feature #7: 'GENDER'

'del_14q11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0224 (Wilcoxon-test), Q value = 0.085

Table S92.  Gene #22: 'del_14q11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 15(14Q11.2) MUTATED 16 73.1 (35.3)
DEL PEAK 15(14Q11.2) WILD-TYPE 60 91.3 (15.1)

Figure S92.  Get High-res Image Gene #22: 'del_14q11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q24.2' versus 'Time to Death'

P value = 5.44e-05 (logrank test), Q value = 0.00076

Table S93.  Gene #23: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 16(14Q24.2) MUTATED 50 15 0.1 - 80.9 (19.7)
DEL PEAK 16(14Q24.2) WILD-TYPE 235 29 0.1 - 194.8 (26.0)

Figure S93.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

'del_14q24.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0028 (Fisher's exact test), Q value = 0.015

Table S94.  Gene #23: 'del_14q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 16(14Q24.2) MUTATED 20 3 15 6
DEL PEAK 16(14Q24.2) WILD-TYPE 151 18 37 9

Figure S94.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q24.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0012

Table S95.  Gene #23: 'del_14q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 16(14Q24.2) MUTATED 22 5 23
DEL PEAK 16(14Q24.2) WILD-TYPE 169 28 39

Figure S95.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q24.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00063 (Fisher's exact test), Q value = 0.005

Table S96.  Gene #23: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 16(14Q24.2) MUTATED 8 9 4
DEL PEAK 16(14Q24.2) WILD-TYPE 41 15 0

Figure S96.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q24.2' versus 'GENDER'

P value = 0.00805 (Fisher's exact test), Q value = 0.036

Table S97.  Gene #23: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 16(14Q24.2) MUTATED 21 29
DEL PEAK 16(14Q24.2) WILD-TYPE 55 183

Figure S97.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #7: 'GENDER'

'del_14q24.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00896 (Wilcoxon-test), Q value = 0.039

Table S98.  Gene #23: 'del_14q24.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 16(14Q24.2) MUTATED 15 71.3 (35.8)
DEL PEAK 16(14Q24.2) WILD-TYPE 61 91.5 (15.0)

Figure S98.  Get High-res Image Gene #23: '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 S99.  Gene #23: 'del_14q24.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 54 1972.5 (15.7)
DEL PEAK 16(14Q24.2) MUTATED 9 1981.7 (15.6)
DEL PEAK 16(14Q24.2) WILD-TYPE 45 1970.7 (15.2)

Figure S99.  Get High-res Image Gene #23: 'del_14q24.2' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_15q13.3' versus 'Time to Death'

P value = 0.00092 (logrank test), Q value = 0.0064

Table S100.  Gene #24: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 17(15Q13.3) MUTATED 35 11 0.1 - 194.8 (18.2)
DEL PEAK 17(15Q13.3) WILD-TYPE 250 33 0.1 - 129.9 (26.0)

Figure S100.  Get High-res Image Gene #24: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0024

Table S101.  Gene #24: 'del_15q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 17(15Q13.3) MUTATED 12 1 12 6
DEL PEAK 17(15Q13.3) WILD-TYPE 159 20 40 9

Figure S101.  Get High-res Image Gene #24: 'del_15q13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_15q13.3' versus 'PATHOLOGY_T_STAGE'

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

Table S102.  Gene #24: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 17(15Q13.3) MUTATED 14 2 19
DEL PEAK 17(15Q13.3) WILD-TYPE 177 31 43

Figure S102.  Get High-res Image Gene #24: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_15q13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00029 (Fisher's exact test), Q value = 0.0028

Table S103.  Gene #24: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 17(15Q13.3) MUTATED 4 11 2
DEL PEAK 17(15Q13.3) WILD-TYPE 45 13 2

Figure S103.  Get High-res Image Gene #24: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q13.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0849 (Fisher's exact test), Q value = 0.23

Table S104.  Gene #24: 'del_15q13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 17(15Q13.3) MUTATED 10 3
DEL PEAK 17(15Q13.3) WILD-TYPE 84 6

Figure S104.  Get High-res Image Gene #24: '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 = 0.095

Table S105.  Gene #24: 'del_15q13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 17(15Q13.3) MUTATED 10 72.0 (38.2)
DEL PEAK 17(15Q13.3) WILD-TYPE 66 89.8 (17.8)

Figure S105.  Get High-res Image Gene #24: 'del_15q13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_16q24.2' versus 'Time to Death'

P value = 2.88e-06 (logrank test), Q value = 0.00019

Table S106.  Gene #25: 'del_16q24.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 18(16Q24.2) MUTATED 12 6 0.4 - 58.2 (14.9)
DEL PEAK 18(16Q24.2) WILD-TYPE 273 38 0.1 - 194.8 (25.8)

Figure S106.  Get High-res Image Gene #25: 'del_16q24.2' versus Clinical Feature #1: 'Time to Death'

'del_16q24.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00177 (Fisher's exact test), Q value = 0.011

Table S107.  Gene #25: 'del_16q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 18(16Q24.2) MUTATED 3 0 7 2
DEL PEAK 18(16Q24.2) WILD-TYPE 168 21 45 13

Figure S107.  Get High-res Image Gene #25: 'del_16q24.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q24.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00218 (Fisher's exact test), Q value = 0.013

Table S108.  Gene #25: 'del_16q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 18(16Q24.2) MUTATED 4 0 8
DEL PEAK 18(16Q24.2) WILD-TYPE 187 33 54

Figure S108.  Get High-res Image Gene #25: 'del_16q24.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'Time to Death'

P value = 0.000719 (logrank test), Q value = 0.0055

Table S109.  Gene #26: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 19(19P13.3) MUTATED 23 7 0.9 - 99.0 (16.9)
DEL PEAK 19(19P13.3) WILD-TYPE 262 37 0.1 - 194.8 (26.0)

Figure S109.  Get High-res Image Gene #26: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0052

Table S110.  Gene #26: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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

Figure S110.  Get High-res Image Gene #26: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0013

Table S111.  Gene #26: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 19(19P13.3) MUTATED 8 1 14
DEL PEAK 19(19P13.3) WILD-TYPE 183 32 48

Figure S111.  Get High-res Image Gene #26: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0157 (Fisher's exact test), Q value = 0.062

Table S112.  Gene #26: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 19(19P13.3) MUTATED 3 5 2
DEL PEAK 19(19P13.3) WILD-TYPE 46 19 2

Figure S112.  Get High-res Image Gene #26: '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 S113.  Gene #26: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

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

Figure S113.  Get High-res Image Gene #26: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.42' versus 'Time to Death'

P value = 0.0489 (logrank test), Q value = 0.15

Table S114.  Gene #27: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 20(19Q13.42) MUTATED 19 5 0.9 - 93.3 (19.6)
DEL PEAK 20(19Q13.42) WILD-TYPE 266 39 0.1 - 194.8 (25.3)

Figure S114.  Get High-res Image Gene #27: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'PATHOLOGIC_STAGE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0032

Table S115.  Gene #27: 'del_19q13.42' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 20(19Q13.42) MUTATED 5 1 11 1
DEL PEAK 20(19Q13.42) WILD-TYPE 166 20 41 14

Figure S115.  Get High-res Image Gene #27: '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 S116.  Gene #27: 'del_19q13.42' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 20(19Q13.42) MUTATED 6 1 12
DEL PEAK 20(19Q13.42) WILD-TYPE 185 32 50

Figure S116.  Get High-res Image Gene #27: '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 = 0.093

Table S117.  Gene #27: 'del_19q13.42' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 20(19Q13.42) MUTATED 9 77.8 (29.9)
DEL PEAK 20(19Q13.42) WILD-TYPE 67 88.8 (20.7)

Figure S117.  Get High-res Image Gene #27: 'del_19q13.42' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_22q12.2' versus 'Time to Death'

P value = 0.00238 (logrank test), Q value = 0.014

Table S118.  Gene #28: 'del_22q12.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 285 44 0.1 - 194.8 (25.3)
DEL PEAK 21(22Q12.2) MUTATED 63 16 0.9 - 123.6 (20.5)
DEL PEAK 21(22Q12.2) WILD-TYPE 222 28 0.1 - 194.8 (25.8)

Figure S118.  Get High-res Image Gene #28: '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 = 0.00019

Table S119.  Gene #28: 'del_22q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 171 21 52 15
DEL PEAK 21(22Q12.2) MUTATED 21 4 26 8
DEL PEAK 21(22Q12.2) WILD-TYPE 150 17 26 7

Figure S119.  Get High-res Image Gene #28: '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 = 0.00019

Table S120.  Gene #28: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3+T4
ALL 191 33 62
DEL PEAK 21(22Q12.2) MUTATED 25 7 31
DEL PEAK 21(22Q12.2) WILD-TYPE 166 26 31

Figure S120.  Get High-res Image Gene #28: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q12.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00176 (Fisher's exact test), Q value = 0.011

Table S121.  Gene #28: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 49 24 4
DEL PEAK 21(22Q12.2) MUTATED 11 15 2
DEL PEAK 21(22Q12.2) WILD-TYPE 38 9 2

Figure S121.  Get High-res Image Gene #28: 'del_22q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_22q12.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0591 (Fisher's exact test), Q value = 0.17

Table S122.  Gene #28: 'del_22q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 94 9
DEL PEAK 21(22Q12.2) MUTATED 23 5
DEL PEAK 21(22Q12.2) WILD-TYPE 71 4

Figure S122.  Get High-res Image Gene #28: 'del_22q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_22q12.2' versus 'GENDER'

P value = 0.0012 (Fisher's exact test), Q value = 0.0078

Table S123.  Gene #28: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 76 212
DEL PEAK 21(22Q12.2) MUTATED 27 36
DEL PEAK 21(22Q12.2) WILD-TYPE 49 176

Figure S123.  Get High-res Image Gene #28: 'del_22q12.2' versus Clinical Feature #7: 'GENDER'

'del_22q12.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00113 (Wilcoxon-test), Q value = 0.0075

Table S124.  Gene #28: 'del_22q12.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 76 87.5 (22.0)
DEL PEAK 21(22Q12.2) MUTATED 19 70.5 (35.5)
DEL PEAK 21(22Q12.2) WILD-TYPE 57 93.2 (10.7)

Figure S124.  Get High-res Image Gene #28: 'del_22q12.2' 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/22533930/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/22507257/KIRP-TP.merged_data.txt

  • Number of patients = 288

  • Number of significantly focal cnvs = 28

  • 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)