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

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

Summary

Testing the association between copy number variation 76 focal events and 14 clinical features across 522 patients, 73 significant findings detected with Q value < 0.25.

  • amp_2q11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_3q26.33 cnv correlated to 'GENDER'.

  • amp_7p11.2 cnv correlated to 'Time to Death'.

  • amp_7q21.3 cnv correlated to 'Time to Death' and 'RACE'.

  • amp_8p11.23 cnv correlated to 'RACE'.

  • amp_8q24.21 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • amp_9p24.1 cnv correlated to 'GENDER'.

  • amp_9p23 cnv correlated to 'GENDER' and 'NUMBER_PACK_YEARS_SMOKED'.

  • amp_9q34.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_13q34 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_18p11.31 cnv correlated to 'GENDER'.

  • amp_18q11.2 cnv correlated to 'GENDER'.

  • amp_xq28 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_1p36.21 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_1p13.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_2q21.2 cnv correlated to 'GENDER'.

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

  • del_2q36.2 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'NUMBER_PACK_YEARS_SMOKED',  'RACE', and 'ETHNICITY'.

  • del_3p26.2 cnv correlated to 'GENDER',  'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.

  • del_3p24.1 cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'GENDER',  'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.

  • del_3p14.2 cnv correlated to 'Time to Death',  'GENDER',  'NUMBER_PACK_YEARS_SMOKED',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_3p12.1 cnv correlated to 'Time to Death',  'GENDER',  'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.

  • del_4p15.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_5q12.1 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.

  • del_5q15 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.

  • del_5q35.3 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_7q31.1 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_8p23.2 cnv correlated to 'Time to Death'.

  • del_9p23 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_9p21.3 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_10p15.3 cnv correlated to 'Time to Death' and 'NUMBER_OF_LYMPH_NODES'.

  • del_10p11.21 cnv correlated to 'RACE'.

  • del_11q23.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE',  'GENDER',  'RADIATION_THERAPY', and 'NUMBER_OF_LYMPH_NODES'.

  • del_13q14.2 cnv correlated to 'RACE'.

  • del_14q11.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_14q32.32 cnv correlated to 'RADIATION_THERAPY'.

  • del_17p11.2 cnv correlated to 'RACE'.

  • del_17q25.3 cnv correlated to 'ETHNICITY'.

  • del_18q23 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.

  • del_19p13.3 cnv correlated to 'Time to Death'.

  • del_21q22.3 cnv correlated to 'RACE'.

  • del_xp22.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'NUMBER_OF_LYMPH_NODES'.

  • del_xp21.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_xq21.33 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 73 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		NUMBER
OF
LYMPH
NODES 		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 Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
del 2q36 2 157 (30%) 365 0.438
(0.797) 		0.627
(0.9) 		0.012
(0.225) 		0.00207
(0.11) 		0.428
(0.786) 		1
(1.00) 		0.747
(0.963) 		0.337
(0.715) 		1
(1.00) 		0.0113
(0.215) 		0.319
(0.707) 		0.905
(1.00) 		0.0093
(0.198) 		0.0141
(0.238)
del 3p24 1 368 (70%) 154 0.00893
(0.198) 		0.217
(0.63) 		0.423
(0.784) 		0.00534
(0.165) 		0.146
(0.574) 		1
(1.00) 		0.0035
(0.13) 		0.916
(1.00) 		0.0719
(0.436) 		7.33e-05
(0.0189) 		0.589
(0.883) 		0.0614
(0.399) 		0.00023
(0.0223) 		1
(1.00)
del 3p14 2 372 (71%) 150 0.0027
(0.125) 		0.21
(0.629) 		0.447
(0.801) 		0.129
(0.544) 		0.0554
(0.376) 		1
(1.00) 		0.00635
(0.171) 		0.673
(0.922) 		0.0465
(0.349) 		0.000107
(0.0189) 		0.495
(0.832) 		0.014
(0.238) 		0.00173
(0.1) 		1
(1.00)
del 11q23 1 246 (47%) 276 0.885
(1.00) 		0.00342
(0.13) 		0.856
(0.997) 		0.917
(1.00) 		0.0006
(0.0479) 		1
(1.00) 		4.97e-06
(0.00529) 		0.00124
(0.0824) 		0.432
(0.788) 		0.216
(0.63) 		0.245
(0.664) 		0.000219
(0.0223) 		0.0388
(0.338) 		0.314
(0.704)
del 3p12 1 343 (66%) 179 0.00438
(0.15) 		0.909
(1.00) 		0.272
(0.68) 		0.229
(0.641) 		0.153
(0.579) 		1
(1.00) 		0.0165
(0.246) 		0.839
(0.988) 		0.557
(0.861) 		8.33e-05
(0.0189) 		0.336
(0.715) 		0.157
(0.58) 		0.00179
(0.1) 		1
(1.00)
del 3p26 2 348 (67%) 174 0.0328
(0.326) 		0.836
(0.987) 		0.607
(0.89) 		0.0279
(0.309) 		0.375
(0.745) 		1
(1.00) 		0.00331
(0.13) 		0.682
(0.929) 		0.121
(0.524) 		0.00116
(0.0824) 		0.429
(0.786) 		0.102
(0.481) 		9e-05
(0.0189) 		0.833
(0.987)
amp 7q21 3 169 (32%) 353 0.00354
(0.13) 		0.175
(0.604) 		0.775
(0.967) 		0.0618
(0.399) 		0.284
(0.683) 		1
(1.00) 		0.673
(0.922) 		0.752
(0.963) 		0.0811
(0.457) 		0.0427
(0.348) 		0.791
(0.97) 		0.634
(0.904) 		0.00055
(0.0479) 		0.525
(0.844)
amp 9p23 124 (24%) 398 0.113
(0.502) 		0.034
(0.326) 		0.925
(1.00) 		0.671
(0.922) 		0.0525
(0.363) 		1
(1.00) 		0.00241
(0.116) 		0.172
(0.599) 		0.592
(0.884) 		0.0102
(0.204) 		0.263
(0.676) 		0.0439
(0.349) 		0.877
(1.00) 		0.485
(0.83)
del 2q22 1 121 (23%) 401 0.612
(0.892) 		0.0729
(0.436) 		0.0127
(0.23) 		0.00725
(0.18) 		0.747
(0.963) 		0.288
(0.687) 		0.0346
(0.326) 		0.169
(0.599) 		0.775
(0.967) 		0.181
(0.609) 		0.552
(0.859) 		0.693
(0.929) 		0.382
(0.746) 		0.631
(0.902)
del 5q12 1 215 (41%) 307 0.867
(1.00) 		0.45
(0.801) 		0.809
(0.975) 		0.0514
(0.363) 		0.325
(0.71) 		1
(1.00) 		0.0352
(0.326) 		0.552
(0.859) 		0.61
(0.89) 		0.00626
(0.171) 		0.357
(0.728) 		0.308
(0.704) 		0.00217
(0.11) 		0.15
(0.574)
del 5q15 226 (43%) 296 0.669
(0.922) 		0.27
(0.68) 		0.742
(0.963) 		0.0307
(0.324) 		0.765
(0.966) 		1
(1.00) 		0.0587
(0.39) 		0.768
(0.967) 		0.521
(0.844) 		0.0111
(0.215) 		0.701
(0.931) 		0.793
(0.97) 		0.00968
(0.202) 		0.224
(0.635)
del 10p15 3 170 (33%) 352 0.0077
(0.182) 		0.588
(0.883) 		0.211
(0.629) 		0.0223
(0.276) 		0.0413
(0.346) 		1
(1.00) 		0.345
(0.723) 		0.532
(0.849) 		0.0347
(0.326) 		0.749
(0.963) 		0.787
(0.97) 		0.0132
(0.233) 		0.0456
(0.349) 		0.668
(0.922)
del 18q23 288 (55%) 234 0.186
(0.616) 		0.171
(0.599) 		0.954
(1.00) 		0.1
(0.479) 		0.896
(1.00) 		1
(1.00) 		0.321
(0.709) 		0.495
(0.832) 		0.0479
(0.349) 		0.017
(0.247) 		0.331
(0.711) 		0.247
(0.666) 		0.00435
(0.15) 		0.156
(0.58)
del xp22 2 157 (30%) 365 0.0439
(0.349) 		0.87
(1.00) 		0.292
(0.691) 		0.0607
(0.399) 		0.107
(0.499) 		0.257
(0.675) 		0.133
(0.548) 		0.524
(0.844) 		0.346
(0.723) 		0.0157
(0.245) 		0.505
(0.838) 		0.00063
(0.0479) 		0.346
(0.723) 		0.661
(0.921)
amp 2q11 2 107 (20%) 415 0.471
(0.814) 		0.851
(0.994) 		0.264
(0.676) 		0.00586
(0.171) 		0.255
(0.672) 		1
(1.00) 		0.18
(0.609) 		0.218
(0.63) 		0.759
(0.963) 		0.087
(0.462) 		0.405
(0.765) 		0.428
(0.786) 		0.452
(0.802) 		0.449
(0.801)
amp 3q26 33 380 (73%) 142 0.52
(0.844) 		0.0525
(0.363) 		0.111
(0.502) 		0.718
(0.944) 		0.21
(0.629) 		1
(1.00) 		0.00541
(0.165) 		0.195
(0.622) 		0.377
(0.746) 		0.0343
(0.326) 		0.419
(0.78) 		0.0398
(0.343) 		0.46
(0.807) 		0.822
(0.981)
amp 7p11 2 222 (43%) 300 3.54e-05
(0.0188) 		0.493
(0.832) 		0.778
(0.968) 		0.031
(0.324) 		0.785
(0.97) 		0.403
(0.765) 		0.842
(0.988) 		0.323
(0.71) 		0.149
(0.574) 		0.134
(0.549) 		0.446
(0.801) 		0.606
(0.89) 		0.0469
(0.349) 		0.689
(0.929)
amp 8p11 23 161 (31%) 361 0.312
(0.704) 		0.834
(0.987) 		0.0194
(0.262) 		0.0895
(0.462) 		0.217
(0.63) 		0.298
(0.693) 		0.67
(0.922) 		0.753
(0.963) 		0.109
(0.502) 		0.149
(0.574) 		0.609
(0.89) 		0.208
(0.629) 		0.00643
(0.171) 		1
(1.00)
amp 8q24 21 386 (74%) 136 0.0697
(0.434) 		0.541
(0.854) 		0.17
(0.599) 		0.199
(0.622) 		0.0615
(0.399) 		0.215
(0.63) 		1
(1.00) 		0.741
(0.963) 		0.478
(0.821) 		0.823
(0.981) 		0.0408
(0.345) 		0.0162
(0.246) 		0.875
(1.00) 		0.254
(0.672)
amp 9p24 1 126 (24%) 396 0.188
(0.617) 		0.0379
(0.336) 		0.886
(1.00) 		0.745
(0.963) 		0.196
(0.622) 		1
(1.00) 		0.000125
(0.019) 		0.211
(0.629) 		0.592
(0.884) 		0.0188
(0.256) 		0.167
(0.599) 		0.0906
(0.462) 		0.979
(1.00) 		0.252
(0.669)
amp 9q34 3 177 (34%) 345 0.0766
(0.443) 		0.0793
(0.449) 		0.133
(0.548) 		0.00851
(0.193) 		0.248
(0.666) 		1
(1.00) 		0.917
(1.00) 		0.836
(0.987) 		1
(1.00) 		0.775
(0.967) 		0.917
(1.00) 		0.444
(0.801) 		0.692
(0.929) 		0.203
(0.627)
amp 13q34 106 (20%) 416 0.0281
(0.309) 		0.0143
(0.238) 		0.277
(0.681) 		0.153
(0.579) 		0.155
(0.58) 		1
(1.00) 		0.326
(0.711) 		0.72
(0.945) 		1
(1.00) 		0.726
(0.951) 		0.131
(0.547) 		0.693
(0.929) 		0.769
(0.967) 		0.212
(0.629)
amp 18p11 31 156 (30%) 366 0.12
(0.523) 		0.451
(0.801) 		0.0533
(0.364) 		0.0478
(0.349) 		0.192
(0.62) 		0.262
(0.676) 		0.00023
(0.0223) 		0.24
(0.655) 		0.647
(0.913) 		0.0408
(0.345) 		0.787
(0.97) 		0.443
(0.801) 		0.257
(0.675) 		0.276
(0.681)
amp 18q11 2 106 (20%) 416 0.6
(0.889) 		0.0775
(0.443) 		0.33
(0.711) 		0.827
(0.985) 		0.857
(0.997) 		0.168
(0.599) 		0.00993
(0.203) 		0.331
(0.711) 		0.113
(0.502) 		0.285
(0.683) 		0.702
(0.931) 		0.847
(0.991) 		0.129
(0.544) 		0.323
(0.71)
amp xq28 150 (29%) 372 0.177
(0.608) 		0.408
(0.768) 		0.553
(0.859) 		0.106
(0.494) 		0.233
(0.648) 		0.246
(0.666) 		0.384
(0.746) 		1
(1.00) 		0.807
(0.974) 		0.861
(0.998) 		0.548
(0.859) 		0.014
(0.238) 		0.76
(0.963) 		0.509
(0.841)
del 1p36 21 95 (18%) 427 0.364
(0.734) 		0.0531
(0.364) 		0.277
(0.681) 		0.528
(0.844) 		0.657
(0.918) 		1
(1.00) 		0.609
(0.89) 		0.306
(0.704) 		0.0331
(0.326) 		0.00326
(0.13) 		0.111
(0.502) 		0.925
(1.00) 		0.376
(0.745) 		0.794
(0.97)
del 1p13 2 133 (25%) 389 0.0868
(0.462) 		0.0351
(0.326) 		0.54
(0.854) 		0.313
(0.704) 		0.96
(1.00) 		0.241
(0.655) 		0.91
(1.00) 		0.499
(0.832) 		0.464
(0.809) 		0.00612
(0.171) 		0.609
(0.89) 		0.709
(0.936) 		0.191
(0.619) 		0.817
(0.979)
del 2q21 2 78 (15%) 444 0.676
(0.925) 		0.262
(0.676) 		0.113
(0.502) 		0.803
(0.973) 		0.263
(0.676) 		1
(1.00) 		0.00804
(0.186) 		0.893
(1.00) 		0.703
(0.931) 		0.366
(0.736) 		0.0476
(0.349) 		0.262
(0.676) 		0.555
(0.859) 		0.262
(0.676)
del 4p15 2 208 (40%) 314 0.286
(0.683) 		0.51
(0.841) 		0.748
(0.963) 		0.385
(0.746) 		0.498
(0.832) 		1
(1.00) 		0.0202
(0.264) 		0.274
(0.68) 		0.718
(0.944) 		0.0152
(0.242) 		0.317
(0.706) 		0.282
(0.683) 		0.174
(0.602) 		1
(1.00)
del 5q35 3 199 (38%) 323 0.731
(0.955) 		0.223
(0.633) 		0.792
(0.97) 		0.0654
(0.417) 		0.641
(0.911) 		1
(1.00) 		0.222
(0.633) 		0.548
(0.859) 		0.314
(0.704) 		0.0126
(0.23) 		0.493
(0.832) 		0.558
(0.861) 		0.138
(0.555) 		0.404
(0.765)
del 7q31 1 77 (15%) 445 0.41
(0.772) 		0.0338
(0.326) 		0.593
(0.884) 		0.755
(0.963) 		0.0164
(0.246) 		1
(1.00) 		1
(1.00) 		0.593
(0.884) 		0.7
(0.931) 		0.0246
(0.292) 		0.114
(0.505) 		0.149
(0.574) 		0.404
(0.765) 		0.782
(0.97)
del 8p23 2 305 (58%) 217 0.00729
(0.18) 		0.0203
(0.264) 		0.787
(0.97) 		0.206
(0.629) 		0.345
(0.723) 		1
(1.00) 		0.23
(0.642) 		0.235
(0.648) 		0.0728
(0.436) 		0.554
(0.859) 		0.978
(1.00) 		0.15
(0.574) 		0.393
(0.751) 		0.152
(0.579)
del 9p23 239 (46%) 283 0.52
(0.844) 		0.504
(0.838) 		0.762
(0.963) 		0.278
(0.681) 		0.814
(0.978) 		0.466
(0.809) 		0.0478
(0.349) 		0.845
(0.99) 		0.869
(1.00) 		0.000175
(0.0223) 		0.239
(0.652) 		0.836
(0.987) 		0.123
(0.53) 		0.32
(0.707)
del 9p21 3 302 (58%) 220 0.0174
(0.25) 		0.525
(0.844) 		0.29
(0.69) 		0.0318
(0.326) 		0.651
(0.916) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.333
(0.712) 		0.00135
(0.0847) 		0.208
(0.629) 		0.78
(0.97) 		0.0855
(0.462) 		0.687
(0.929)
del 10p11 21 163 (31%) 359 0.0714
(0.436) 		0.76
(0.963) 		0.333
(0.712) 		0.132
(0.548) 		0.373
(0.742) 		1
(1.00) 		0.11
(0.502) 		0.092
(0.462) 		0.112
(0.502) 		0.733
(0.955) 		0.953
(1.00) 		0.138
(0.555) 		0.00512
(0.165) 		0.669
(0.922)
del 13q14 2 217 (42%) 305 0.327
(0.711) 		0.0942
(0.462) 		0.429
(0.786) 		0.854
(0.997) 		0.278
(0.681) 		0.393
(0.751) 		0.0451
(0.349) 		0.277
(0.681) 		0.198
(0.622) 		0.669
(0.922) 		0.574
(0.876) 		0.202
(0.626) 		0.0152
(0.242) 		0.217
(0.63)
del 14q11 2 75 (14%) 447 0.616
(0.895) 		0.352
(0.728) 		0.522
(0.844) 		0.496
(0.832) 		0.772
(0.967) 		1
(1.00) 		0.161
(0.59) 		0.0518
(0.363) 		0.283
(0.683) 		0.0111
(0.215) 		0.656
(0.917) 		0.286
(0.683) 		0.353
(0.728) 		0.0358
(0.329)
del 14q32 32 75 (14%) 447 0.196
(0.622) 		0.349
(0.723) 		0.314
(0.704) 		0.521
(0.844) 		0.596
(0.886) 		1
(1.00) 		0.0487
(0.353) 		0.0166
(0.246) 		0.693
(0.929) 		0.816
(0.979) 		0.578
(0.878) 		0.878
(1.00) 		0.343
(0.722) 		0.558
(0.861)
del 17p11 2 99 (19%) 423 0.198
(0.622) 		0.803
(0.973) 		0.182
(0.609) 		0.776
(0.967) 		0.359
(0.731) 		0.188
(0.617) 		0.614
(0.893) 		0.215
(0.63) 		0.525
(0.844) 		0.355
(0.728) 		0.928
(1.00) 		0.654
(0.917) 		0.00283
(0.125) 		0.124
(0.53)
del 17q25 3 71 (14%) 451 0.842
(0.988) 		0.324
(0.71) 		0.686
(0.929) 		0.0755
(0.439) 		0.089
(0.462) 		1
(1.00) 		0.313
(0.704) 		0.259
(0.676) 		0.166
(0.597) 		0.299
(0.693) 		0.459
(0.807) 		0.619
(0.895) 		0.83
(0.987) 		0.0145
(0.238)
del 19p13 3 175 (34%) 347 0.00756
(0.182) 		0.607
(0.89) 		0.0852
(0.462) 		0.296
(0.693) 		0.102
(0.481) 		0.33
(0.711) 		0.601
(0.889) 		0.531
(0.849) 		0.223
(0.633) 		0.297
(0.693) 		0.0902
(0.462) 		0.164
(0.594) 		0.775
(0.967) 		0.394
(0.751)
del 21q22 3 208 (40%) 314 0.749
(0.963) 		0.847
(0.991) 		0.975
(1.00) 		0.0966
(0.469) 		0.383
(0.746) 		1
(1.00) 		0.268
(0.678) 		0.367
(0.737) 		1
(1.00) 		0.0179
(0.254) 		0.788
(0.97) 		0.44
(0.799) 		0.00694
(0.18) 		0.683
(0.929)
del xp21 3 159 (30%) 363 0.343
(0.722) 		0.728
(0.952) 		0.279
(0.682) 		0.123
(0.53) 		0.212
(0.629) 		0.283
(0.683) 		0.336
(0.715) 		0.596
(0.886) 		0.348
(0.723) 		0.0729
(0.436) 		0.7
(0.931) 		0.0092
(0.198) 		0.884
(1.00) 		0.382
(0.746)
del xq21 33 80 (15%) 442 0.805
(0.973) 		0.968
(1.00) 		0.102
(0.481) 		0.669
(0.922) 		0.148
(0.574) 		0.141
(0.563) 		0.784
(0.97) 		0.507
(0.839) 		0.103
(0.481) 		0.717
(0.944) 		0.491
(0.832) 		0.00524
(0.165) 		0.634
(0.904) 		0.574
(0.876)
amp 2q31 2 112 (21%) 410 0.198
(0.622) 		0.522
(0.844) 		0.454
(0.803) 		0.393
(0.751) 		0.189
(0.617) 		1
(1.00) 		0.0936
(0.462) 		0.026
(0.297) 		0.762
(0.963) 		0.0524
(0.363) 		0.907
(1.00) 		0.138
(0.555) 		0.206
(0.629) 		0.0871
(0.462)
amp 5p15 33 240 (46%) 282 0.833
(0.987) 		0.0187
(0.256) 		0.293
(0.692) 		0.579
(0.878) 		0.0331
(0.326) 		0.445
(0.801) 		0.0473
(0.349) 		0.0642
(0.412) 		0.742
(0.963) 		0.29
(0.69) 		0.173
(0.602) 		0.0934
(0.462) 		0.044
(0.349) 		0.156
(0.58)
amp 5p12 205 (39%) 317 0.576
(0.878) 		0.118
(0.516) 		0.373
(0.742) 		0.411
(0.772) 		0.0596
(0.394) 		1
(1.00) 		0.188
(0.617) 		0.0739
(0.439) 		0.591
(0.884) 		0.543
(0.854) 		0.769
(0.967) 		0.102
(0.481) 		0.758
(0.963) 		0.15
(0.574)
amp 6p12 1 110 (21%) 412 0.79
(0.97) 		0.134
(0.549) 		0.796
(0.972) 		0.266
(0.676) 		0.688
(0.929) 		1
(1.00) 		0.468
(0.81) 		0.812
(0.977) 		1
(1.00) 		0.472
(0.814) 		0.909
(1.00) 		0.697
(0.931) 		0.0579
(0.389) 		1
(1.00)
amp 6q12 96 (18%) 426 0.431
(0.788) 		0.192
(0.62) 		0.894
(1.00) 		0.347
(0.723) 		0.804
(0.973) 		1
(1.00) 		0.799
(0.973) 		0.385
(0.746) 		0.364
(0.734) 		0.75
(0.963) 		0.0228
(0.279) 		0.564
(0.866) 		0.183
(0.609) 		0.297
(0.693)
amp 8q11 21 310 (59%) 212 0.947
(1.00) 		0.891
(1.00) 		0.13
(0.546) 		0.329
(0.711) 		0.525
(0.844) 		0.356
(0.728) 		0.841
(0.988) 		0.113
(0.502) 		0.724
(0.948) 		0.863
(0.999) 		0.228
(0.639) 		0.369
(0.739) 		0.569
(0.871) 		0.31
(0.704)
amp 9p13 3 139 (27%) 383 0.542
(0.854) 		0.254
(0.672) 		0.54
(0.854) 		0.92
(1.00) 		0.406
(0.766) 		1
(1.00) 		0.0939
(0.462) 		0.583
(0.882) 		0.804
(0.973) 		0.295
(0.693) 		0.115
(0.507) 		0.202
(0.626) 		0.876
(1.00) 		0.182
(0.609)
amp 11p13 102 (20%) 420 0.278
(0.681) 		0.448
(0.801) 		0.183
(0.609) 		0.868
(1.00) 		0.0989
(0.476) 		1
(1.00) 		0.619
(0.895) 		0.0909
(0.462) 		0.755
(0.963) 		0.0673
(0.424) 		0.311
(0.704) 		0.881
(1.00) 		0.379
(0.746) 		0.201
(0.626)
amp 11q13 3 229 (44%) 293 0.0452
(0.349) 		0.16
(0.59) 		0.5
(0.833) 		0.517
(0.844) 		0.211
(0.629) 		1
(1.00) 		0.426
(0.785) 		0.922
(1.00) 		0.196
(0.622) 		0.0342
(0.326) 		0.604
(0.89) 		0.182
(0.609) 		0.27
(0.68) 		1
(1.00)
amp 12p13 33 167 (32%) 355 0.931
(1.00) 		0.962
(1.00) 		0.92
(1.00) 		0.983
(1.00) 		0.536
(0.854) 		1
(1.00) 		0.0718
(0.436) 		0.833
(0.987) 		1
(1.00) 		0.553
(0.859) 		0.62
(0.895) 		0.247
(0.666) 		0.183
(0.609) 		0.669
(0.922)
amp 12q15 103 (20%) 419 0.872
(1.00) 		0.0385
(0.338) 		0.614
(0.893) 		0.662
(0.921) 		0.216
(0.63) 		1
(1.00) 		0.902
(1.00) 		0.9
(1.00) 		0.755
(0.963) 		0.0752
(0.439) 		0.38
(0.746) 		0.0914
(0.462) 		0.0954
(0.466) 		0.799
(0.973)
amp 13q22 1 105 (20%) 417 0.0299
(0.322) 		0.0898
(0.462) 		0.835
(0.987) 		0.207
(0.629) 		0.561
(0.863) 		1
(1.00) 		0.462
(0.809) 		1
(1.00) 		0.758
(0.963) 		0.537
(0.854) 		0.162
(0.591) 		0.934
(1.00) 		0.273
(0.68) 		0.316
(0.706)
amp 15q26 3 105 (20%) 417 0.0308
(0.324) 		0.671
(0.922) 		0.759
(0.963) 		0.125
(0.53) 		0.889
(1.00) 		1
(1.00) 		0.902
(1.00) 		0.466
(0.809) 		0.3
(0.693) 		0.368
(0.738) 		0.389
(0.749) 		0.956
(1.00) 		0.622
(0.895) 		0.8
(0.973)
amp 17q12 91 (17%) 431 0.199
(0.622) 		0.0749
(0.439) 		0.128
(0.543) 		0.193
(0.62) 		0.743
(0.963) 		0.194
(0.621) 		0.435
(0.793) 		0.898
(1.00) 		0.186
(0.615) 		0.0249
(0.292) 		0.226
(0.636) 		0.718
(0.944) 		0.82
(0.98) 		0.0287
(0.312)
amp 20q11 22 227 (43%) 295 0.52
(0.844) 		0.212
(0.629) 		0.541
(0.854) 		0.495
(0.832) 		0.962
(1.00) 		1
(1.00) 		0.486
(0.83) 		0.492
(0.832) 		0.623
(0.895) 		0.79
(0.97) 		0.171
(0.599) 		0.672
(0.922) 		0.583
(0.882) 		0.542
(0.854)
del 1q44 48 (9%) 474 0.0375
(0.336) 		0.421
(0.783) 		0.806
(0.974) 		0.478
(0.821) 		0.864
(0.999) 		1
(1.00) 		0.495
(0.832) 		0.0211
(0.27) 		0.646
(0.913) 		0.695
(0.929) 		0.145
(0.574) 		0.273
(0.68) 		0.481
(0.825) 		0.295
(0.693)
del 4p16 3 205 (39%) 317 0.138
(0.555) 		0.475
(0.818) 		0.36
(0.731) 		0.273
(0.68) 		0.762
(0.963) 		0.351
(0.726) 		0.0266
(0.301) 		0.37
(0.74) 		0.251
(0.669) 		0.0511
(0.363) 		0.342
(0.722) 		0.301
(0.694) 		0.387
(0.747) 		0.684
(0.929)
del 4q21 3 156 (30%) 366 0.82
(0.98) 		0.231
(0.644) 		0.222
(0.633) 		0.0451
(0.349) 		0.917
(1.00) 		1
(1.00) 		1
(1.00) 		0.398
(0.757) 		0.506
(0.838) 		0.17
(0.599) 		0.0467
(0.349) 		0.425
(0.784) 		0.332
(0.712) 		0.0775
(0.443)
del 4q22 1 169 (32%) 353 0.319
(0.707) 		0.549
(0.859) 		0.309
(0.704) 		0.312
(0.704) 		0.882
(1.00) 		1
(1.00) 		0.527
(0.844) 		0.348
(0.723) 		0.22
(0.633) 		0.0918
(0.462) 		0.085
(0.462) 		0.515
(0.844) 		0.356
(0.728) 		0.137
(0.555)
del 4q35 2 213 (41%) 309 0.643
(0.911) 		0.653
(0.917) 		0.0824
(0.457) 		0.068
(0.426) 		0.494
(0.832) 		0.393
(0.751) 		0.0874
(0.462) 		0.236
(0.648) 		0.26
(0.676) 		0.443
(0.801) 		0.499
(0.832) 		0.623
(0.895) 		0.521
(0.844) 		0.841
(0.988)
del 6p25 3 96 (18%) 426 0.0744
(0.439) 		0.283
(0.683) 		0.183
(0.609) 		0.0931
(0.462) 		0.526
(0.844) 		1
(1.00) 		0.0975
(0.472) 		0.899
(1.00) 		1
(1.00) 		0.317
(0.706) 		0.362
(0.734) 		0.638
(0.908) 		0.0419
(0.346) 		0.794
(0.97)
del 7q36 1 132 (25%) 390 0.0508
(0.363) 		0.691
(0.929) 		0.415
(0.775) 		0.577
(0.878) 		0.164
(0.594) 		1
(1.00) 		0.364
(0.734) 		0.265
(0.676) 		0.792
(0.97) 		0.148
(0.574) 		0.237
(0.649) 		0.38
(0.746) 		0.327
(0.711) 		0.643
(0.911)
del 9q21 11 108 (21%) 414 0.451
(0.801) 		0.234
(0.648) 		0.569
(0.871) 		0.607
(0.89) 		0.684
(0.929) 		0.262
(0.676) 		0.393
(0.751) 		0.904
(1.00) 		0.386
(0.747) 		0.0369
(0.336) 		0.661
(0.921) 		0.518
(0.844) 		0.161
(0.59) 		0.622
(0.895)
del 9q34 3 79 (15%) 443 0.704
(0.931) 		0.456
(0.804) 		0.299
(0.693) 		0.858
(0.997) 		0.975
(1.00) 		0.147
(0.574) 		0.89
(1.00) 		0.893
(1.00) 		0.465
(0.809) 		0.0219
(0.274) 		0.327
(0.711) 		0.857
(0.997) 		0.424
(0.784) 		0.563
(0.866)
del 10q23 31 138 (26%) 384 0.634
(0.904) 		0.691
(0.929) 		0.487
(0.831) 		0.285
(0.683) 		0.917
(1.00) 		1
(1.00) 		0.0253
(0.293) 		0.217
(0.63) 		0.609
(0.89) 		0.0581
(0.389) 		0.265
(0.676) 		0.891
(1.00) 		0.466
(0.809) 		0.171
(0.599)
del 11p15 5 163 (31%) 359 0.269
(0.679) 		0.86
(0.998) 		0.0399
(0.343) 		0.546
(0.858) 		0.0277
(0.309) 		1
(1.00) 		0.339
(0.718) 		0.0249
(0.292) 		0.0203
(0.264) 		0.772
(0.967) 		0.891
(1.00) 		0.089
(0.462) 		0.0331
(0.326) 		0.19
(0.618)
del 12q24 33 63 (12%) 459 0.703
(0.931) 		0.587
(0.883) 		0.892
(1.00) 		0.311
(0.704) 		0.525
(0.844) 		1
(1.00) 		0.65
(0.916) 		0.449
(0.801) 		0.423
(0.784) 		0.92
(1.00) 		0.941
(1.00) 		0.601
(0.889) 		0.0428
(0.348) 		0.221
(0.633)
del 13q12 11 233 (45%) 289 0.582
(0.882) 		0.682
(0.929) 		0.0824
(0.457) 		0.11
(0.502) 		0.0832
(0.459) 		0.445
(0.801) 		0.0376
(0.336) 		0.695
(0.929) 		0.734
(0.955) 		0.0825
(0.457) 		0.385
(0.746) 		0.0873
(0.462) 		0.0182
(0.254) 		0.154
(0.579)
del 15q15 1 124 (24%) 398 0.46
(0.807) 		0.682
(0.929) 		0.414
(0.775) 		0.169
(0.599) 		0.554
(0.859) 		1
(1.00) 		0.354
(0.728) 		0.356
(0.728) 		0.042
(0.346) 		0.654
(0.917) 		0.586
(0.883) 		0.645
(0.913) 		0.777
(0.968) 		0.159
(0.589)
del 16q23 1 98 (19%) 424 0.913
(1.00) 		0.224
(0.635) 		0.236
(0.648) 		0.588
(0.883) 		0.0664
(0.42) 		1
(1.00) 		0.207
(0.629) 		0.139
(0.557) 		0.266
(0.676) 		0.472
(0.814) 		0.249
(0.666) 		0.109
(0.502) 		0.497
(0.832) 		1
(1.00)
del 16q23 3 105 (20%) 417 0.618
(0.895) 		0.248
(0.666) 		0.309
(0.704) 		0.226
(0.636) 		0.0779
(0.443) 		1
(1.00) 		0.462
(0.809) 		0.148
(0.574) 		0.298
(0.693) 		0.81
(0.975) 		0.385
(0.746) 		0.0728
(0.436) 		0.413
(0.773) 		0.454
(0.803)
del 19q13 43 97 (19%) 425 0.18
(0.609) 		0.175
(0.603) 		0.0915
(0.462) 		0.0231
(0.28) 		0.7
(0.931) 		1
(1.00) 		0.899
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.63
(0.902) 		0.0217
(0.274) 		0.967
(1.00) 		0.656
(0.917) 		0.124
(0.53)
'amp_2q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00586 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #1: 'amp_2q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 137 100 173
AMP PEAK 1(2Q11.2) MUTATED 5 19 27 44
AMP PEAK 1(2Q11.2) WILD-TYPE 45 118 73 129

Figure S1.  Get High-res Image Gene #1: 'amp_2q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3q26.33' versus 'GENDER'

P value = 0.00541 (Fisher's exact test), Q value = 0.16

Table S2.  Gene #3: 'amp_3q26.33' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
AMP PEAK 3(3Q26.33) MUTATED 89 291
AMP PEAK 3(3Q26.33) WILD-TYPE 51 91

Figure S2.  Get High-res Image Gene #3: 'amp_3q26.33' versus Clinical Feature #7: 'GENDER'

'amp_7p11.2' versus 'Time to Death'

P value = 3.54e-05 (logrank test), Q value = 0.019

Table S3.  Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
AMP PEAK 8(7P11.2) MUTATED 220 112 0.1 - 172.7 (18.3)
AMP PEAK 8(7P11.2) WILD-TYPE 300 107 0.1 - 211.0 (23.0)

Figure S3.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.3' versus 'Time to Death'

P value = 0.00354 (logrank test), Q value = 0.13

Table S4.  Gene #9: 'amp_7q21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
AMP PEAK 9(7Q21.3) MUTATED 169 90 0.1 - 172.7 (19.8)
AMP PEAK 9(7Q21.3) WILD-TYPE 351 129 0.1 - 211.0 (21.2)

Figure S4.  Get High-res Image Gene #9: 'amp_7q21.3' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.3' versus 'RACE'

P value = 0.00055 (Fisher's exact test), Q value = 0.048

Table S5.  Gene #9: 'amp_7q21.3' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
AMP PEAK 9(7Q21.3) MUTATED 1 1 27 138
AMP PEAK 9(7Q21.3) WILD-TYPE 1 10 21 308

Figure S5.  Get High-res Image Gene #9: 'amp_7q21.3' versus Clinical Feature #13: 'RACE'

'amp_8p11.23' versus 'RACE'

P value = 0.00643 (Fisher's exact test), Q value = 0.17

Table S6.  Gene #10: 'amp_8p11.23' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
AMP PEAK 10(8P11.23) MUTATED 0 0 22 134
AMP PEAK 10(8P11.23) WILD-TYPE 2 11 26 312

Figure S6.  Get High-res Image Gene #10: 'amp_8p11.23' versus Clinical Feature #13: 'RACE'

'amp_8q24.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0162 (Wilcoxon-test), Q value = 0.25

Table S7.  Gene #12: 'amp_8q24.21' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
AMP PEAK 12(8Q24.21) MUTATED 315 2.3 (4.0)
AMP PEAK 12(8Q24.21) WILD-TYPE 93 1.9 (5.1)

Figure S7.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'amp_9p24.1' versus 'GENDER'

P value = 0.000125 (Fisher's exact test), Q value = 0.019

Table S8.  Gene #13: 'amp_9p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
AMP PEAK 13(9P24.1) MUTATED 51 75
AMP PEAK 13(9P24.1) WILD-TYPE 89 307

Figure S8.  Get High-res Image Gene #13: 'amp_9p24.1' versus Clinical Feature #7: 'GENDER'

'amp_9p23' versus 'GENDER'

P value = 0.00241 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #14: 'amp_9p23' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
AMP PEAK 14(9P23) MUTATED 47 77
AMP PEAK 14(9P23) WILD-TYPE 93 305

Figure S9.  Get High-res Image Gene #14: 'amp_9p23' versus Clinical Feature #7: 'GENDER'

'amp_9p23' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0102 (Wilcoxon-test), Q value = 0.2

Table S10.  Gene #14: 'amp_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
AMP PEAK 14(9P23) MUTATED 69 37.8 (27.2)
AMP PEAK 14(9P23) WILD-TYPE 224 48.4 (37.2)

Figure S10.  Get High-res Image Gene #14: 'amp_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'amp_9q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00851 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #16: 'amp_9q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 137 100 173
AMP PEAK 16(9Q34.3) MUTATED 11 39 37 75
AMP PEAK 16(9Q34.3) WILD-TYPE 39 98 63 98

Figure S11.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_13q34' versus 'YEARS_TO_BIRTH'

P value = 0.0143 (Wilcoxon-test), Q value = 0.24

Table S12.  Gene #22: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 521 60.9 (11.9)
AMP PEAK 22(13Q34) MUTATED 105 58.4 (12.6)
AMP PEAK 22(13Q34) WILD-TYPE 416 61.5 (11.7)

Figure S12.  Get High-res Image Gene #22: 'amp_13q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_18p11.31' versus 'GENDER'

P value = 0.00023 (Fisher's exact test), Q value = 0.022

Table S13.  Gene #25: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
AMP PEAK 25(18P11.31) MUTATED 25 131
AMP PEAK 25(18P11.31) WILD-TYPE 115 251

Figure S13.  Get High-res Image Gene #25: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

'amp_18q11.2' versus 'GENDER'

P value = 0.00993 (Fisher's exact test), Q value = 0.2

Table S14.  Gene #26: 'amp_18q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
AMP PEAK 26(18Q11.2) MUTATED 18 88
AMP PEAK 26(18Q11.2) WILD-TYPE 122 294

Figure S14.  Get High-res Image Gene #26: 'amp_18q11.2' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.014 (Wilcoxon-test), Q value = 0.24

Table S15.  Gene #28: 'amp_xq28' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
AMP PEAK 28(XQ28) MUTATED 122 2.4 (3.1)
AMP PEAK 28(XQ28) WILD-TYPE 286 2.1 (4.7)

Figure S15.  Get High-res Image Gene #28: 'amp_xq28' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_1p36.21' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00326 (Wilcoxon-test), Q value = 0.13

Table S16.  Gene #29: 'del_1p36.21' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 1(1P36.21) MUTATED 62 58.0 (46.4)
DEL PEAK 1(1P36.21) WILD-TYPE 231 42.6 (31.1)

Figure S16.  Get High-res Image Gene #29: 'del_1p36.21' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_1p13.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00612 (Wilcoxon-test), Q value = 0.17

Table S17.  Gene #30: 'del_1p13.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 2(1P13.2) MUTATED 70 56.0 (43.7)
DEL PEAK 2(1P13.2) WILD-TYPE 223 42.7 (31.7)

Figure S17.  Get High-res Image Gene #30: 'del_1p13.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_2q21.2' versus 'GENDER'

P value = 0.00804 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #32: 'del_2q21.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 4(2Q21.2) MUTATED 31 47
DEL PEAK 4(2Q21.2) WILD-TYPE 109 335

Figure S18.  Get High-res Image Gene #32: 'del_2q21.2' versus Clinical Feature #7: 'GENDER'

'del_2q22.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0127 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #33: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
ALL 27 76 82 252 12 1
DEL PEAK 5(2Q22.1) MUTATED 2 13 20 65 6 1
DEL PEAK 5(2Q22.1) WILD-TYPE 25 63 62 187 6 0

Figure S19.  Get High-res Image Gene #33: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00725 (Fisher's exact test), Q value = 0.18

Table S20.  Gene #33: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 137 100 173
DEL PEAK 5(2Q22.1) MUTATED 5 27 24 54
DEL PEAK 5(2Q22.1) WILD-TYPE 45 110 76 119

Figure S20.  Get High-res Image Gene #33: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q36.2' versus 'PATHOLOGIC_STAGE'

P value = 0.012 (Fisher's exact test), Q value = 0.22

Table S21.  Gene #34: 'del_2q36.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
ALL 27 76 82 252 12 1
DEL PEAK 6(2Q36.2) MUTATED 3 17 33 73 6 0
DEL PEAK 6(2Q36.2) WILD-TYPE 24 59 49 179 6 1

Figure S21.  Get High-res Image Gene #34: 'del_2q36.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q36.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00207 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #34: 'del_2q36.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 137 100 173
DEL PEAK 6(2Q36.2) MUTATED 7 33 41 55
DEL PEAK 6(2Q36.2) WILD-TYPE 43 104 59 118

Figure S22.  Get High-res Image Gene #34: 'del_2q36.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q36.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0113 (Wilcoxon-test), Q value = 0.21

Table S23.  Gene #34: 'del_2q36.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 6(2Q36.2) MUTATED 92 51.8 (33.7)
DEL PEAK 6(2Q36.2) WILD-TYPE 201 43.2 (35.8)

Figure S23.  Get High-res Image Gene #34: 'del_2q36.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_2q36.2' versus 'RACE'

P value = 0.0093 (Fisher's exact test), Q value = 0.2

Table S24.  Gene #34: 'del_2q36.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 6(2Q36.2) MUTATED 1 6 22 125
DEL PEAK 6(2Q36.2) WILD-TYPE 1 5 26 321

Figure S24.  Get High-res Image Gene #34: 'del_2q36.2' versus Clinical Feature #13: 'RACE'

'del_2q36.2' versus 'ETHNICITY'

P value = 0.0141 (Fisher's exact test), Q value = 0.24

Table S25.  Gene #34: 'del_2q36.2' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 459
DEL PEAK 6(2Q36.2) MUTATED 14 134
DEL PEAK 6(2Q36.2) WILD-TYPE 12 325

Figure S25.  Get High-res Image Gene #34: 'del_2q36.2' versus Clinical Feature #14: 'ETHNICITY'

'del_3p26.2' versus 'GENDER'

P value = 0.00331 (Fisher's exact test), Q value = 0.13

Table S26.  Gene #35: 'del_3p26.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 7(3P26.2) MUTATED 79 269
DEL PEAK 7(3P26.2) WILD-TYPE 61 113

Figure S26.  Get High-res Image Gene #35: 'del_3p26.2' versus Clinical Feature #7: 'GENDER'

'del_3p26.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00116 (Wilcoxon-test), Q value = 0.082

Table S27.  Gene #35: 'del_3p26.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 7(3P26.2) MUTATED 204 49.3 (37.2)
DEL PEAK 7(3P26.2) WILD-TYPE 89 38.0 (29.4)

Figure S27.  Get High-res Image Gene #35: 'del_3p26.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p26.2' versus 'RACE'

P value = 9e-05 (Fisher's exact test), Q value = 0.019

Table S28.  Gene #35: 'del_3p26.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 7(3P26.2) MUTATED 2 6 44 285
DEL PEAK 7(3P26.2) WILD-TYPE 0 5 4 161

Figure S28.  Get High-res Image Gene #35: 'del_3p26.2' versus Clinical Feature #13: 'RACE'

'del_3p24.1' versus 'Time to Death'

P value = 0.00893 (logrank test), Q value = 0.2

Table S29.  Gene #36: 'del_3p24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 8(3P24.1) MUTATED 366 168 0.1 - 211.0 (20.6)
DEL PEAK 8(3P24.1) WILD-TYPE 154 51 0.4 - 169.4 (22.1)

Figure S29.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #1: 'Time to Death'

'del_3p24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00534 (Fisher's exact test), Q value = 0.16

Table S30.  Gene #36: 'del_3p24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 137 100 173
DEL PEAK 8(3P24.1) MUTATED 28 90 79 132
DEL PEAK 8(3P24.1) WILD-TYPE 22 47 21 41

Figure S30.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p24.1' versus 'GENDER'

P value = 0.0035 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #36: 'del_3p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 8(3P24.1) MUTATED 85 283
DEL PEAK 8(3P24.1) WILD-TYPE 55 99

Figure S31.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #7: 'GENDER'

'del_3p24.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 7.33e-05 (Wilcoxon-test), Q value = 0.019

Table S32.  Gene #36: 'del_3p24.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 8(3P24.1) MUTATED 216 49.8 (37.2)
DEL PEAK 8(3P24.1) WILD-TYPE 77 34.8 (26.8)

Figure S32.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p24.1' versus 'RACE'

P value = 0.00023 (Fisher's exact test), Q value = 0.022

Table S33.  Gene #36: 'del_3p24.1' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 8(3P24.1) MUTATED 1 7 45 304
DEL PEAK 8(3P24.1) WILD-TYPE 1 4 3 142

Figure S33.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #13: 'RACE'

'del_3p14.2' versus 'Time to Death'

P value = 0.0027 (logrank test), Q value = 0.12

Table S34.  Gene #37: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 9(3P14.2) MUTATED 370 170 0.1 - 211.0 (20.5)
DEL PEAK 9(3P14.2) WILD-TYPE 150 49 0.4 - 172.7 (22.5)

Figure S34.  Get High-res Image Gene #37: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

'del_3p14.2' versus 'GENDER'

P value = 0.00635 (Fisher's exact test), Q value = 0.17

Table S35.  Gene #37: 'del_3p14.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 9(3P14.2) MUTATED 87 285
DEL PEAK 9(3P14.2) WILD-TYPE 53 97

Figure S35.  Get High-res Image Gene #37: 'del_3p14.2' versus Clinical Feature #7: 'GENDER'

'del_3p14.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000107 (Wilcoxon-test), Q value = 0.019

Table S36.  Gene #37: 'del_3p14.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 9(3P14.2) MUTATED 220 49.5 (37.0)
DEL PEAK 9(3P14.2) WILD-TYPE 73 35.0 (27.4)

Figure S36.  Get High-res Image Gene #37: 'del_3p14.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p14.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.014 (Wilcoxon-test), Q value = 0.24

Table S37.  Gene #37: 'del_3p14.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 9(3P14.2) MUTATED 304 2.4 (4.7)
DEL PEAK 9(3P14.2) WILD-TYPE 104 1.5 (2.6)

Figure S37.  Get High-res Image Gene #37: 'del_3p14.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_3p14.2' versus 'RACE'

P value = 0.00173 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #37: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 9(3P14.2) MUTATED 1 7 44 308
DEL PEAK 9(3P14.2) WILD-TYPE 1 4 4 138

Figure S38.  Get High-res Image Gene #37: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

'del_3p12.1' versus 'Time to Death'

P value = 0.00438 (logrank test), Q value = 0.15

Table S39.  Gene #38: 'del_3p12.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 10(3P12.1) MUTATED 341 159 0.1 - 211.0 (21.1)
DEL PEAK 10(3P12.1) WILD-TYPE 179 60 0.4 - 180.2 (21.5)

Figure S39.  Get High-res Image Gene #38: 'del_3p12.1' versus Clinical Feature #1: 'Time to Death'

'del_3p12.1' versus 'GENDER'

P value = 0.0165 (Fisher's exact test), Q value = 0.25

Table S40.  Gene #38: 'del_3p12.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 10(3P12.1) MUTATED 80 263
DEL PEAK 10(3P12.1) WILD-TYPE 60 119

Figure S40.  Get High-res Image Gene #38: 'del_3p12.1' versus Clinical Feature #7: 'GENDER'

'del_3p12.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 8.33e-05 (Wilcoxon-test), Q value = 0.019

Table S41.  Gene #38: 'del_3p12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 10(3P12.1) MUTATED 202 49.2 (33.5)
DEL PEAK 10(3P12.1) WILD-TYPE 91 38.6 (38.4)

Figure S41.  Get High-res Image Gene #38: 'del_3p12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p12.1' versus 'RACE'

P value = 0.00179 (Fisher's exact test), Q value = 0.1

Table S42.  Gene #38: 'del_3p12.1' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 10(3P12.1) MUTATED 1 7 42 281
DEL PEAK 10(3P12.1) WILD-TYPE 1 4 6 165

Figure S42.  Get High-res Image Gene #38: 'del_3p12.1' versus Clinical Feature #13: 'RACE'

'del_4p15.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0152 (Wilcoxon-test), Q value = 0.24

Table S43.  Gene #40: 'del_4p15.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 12(4P15.2) MUTATED 128 48.7 (29.4)
DEL PEAK 12(4P15.2) WILD-TYPE 165 43.7 (39.3)

Figure S43.  Get High-res Image Gene #40: 'del_4p15.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q12.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00626 (Wilcoxon-test), Q value = 0.17

Table S44.  Gene #44: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 16(5Q12.1) MUTATED 125 51.8 (38.4)
DEL PEAK 16(5Q12.1) WILD-TYPE 168 41.5 (32.3)

Figure S44.  Get High-res Image Gene #44: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q12.1' versus 'RACE'

P value = 0.00217 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #44: 'del_5q12.1' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 16(5Q12.1) MUTATED 1 3 31 173
DEL PEAK 16(5Q12.1) WILD-TYPE 1 8 17 273

Figure S45.  Get High-res Image Gene #44: 'del_5q12.1' versus Clinical Feature #13: 'RACE'

'del_5q15' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0111 (Wilcoxon-test), Q value = 0.21

Table S46.  Gene #45: 'del_5q15' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 17(5Q15) MUTATED 131 50.8 (37.7)
DEL PEAK 17(5Q15) WILD-TYPE 162 41.9 (32.9)

Figure S46.  Get High-res Image Gene #45: 'del_5q15' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q15' versus 'RACE'

P value = 0.00968 (Fisher's exact test), Q value = 0.2

Table S47.  Gene #45: 'del_5q15' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 17(5Q15) MUTATED 1 5 31 182
DEL PEAK 17(5Q15) WILD-TYPE 1 6 17 264

Figure S47.  Get High-res Image Gene #45: 'del_5q15' versus Clinical Feature #13: 'RACE'

'del_5q35.3' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0126 (Wilcoxon-test), Q value = 0.23

Table S48.  Gene #46: 'del_5q35.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 18(5Q35.3) MUTATED 114 49.6 (30.1)
DEL PEAK 18(5Q35.3) WILD-TYPE 179 43.5 (38.2)

Figure S48.  Get High-res Image Gene #46: 'del_5q35.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_7q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.25

Table S49.  Gene #48: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 179 68 168 8
DEL PEAK 20(7Q31.1) MUTATED 18 17 29 0
DEL PEAK 20(7Q31.1) WILD-TYPE 161 51 139 8

Figure S49.  Get High-res Image Gene #48: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_8p23.2' versus 'Time to Death'

P value = 0.00729 (logrank test), Q value = 0.18

Table S50.  Gene #50: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 22(8P23.2) MUTATED 304 145 0.1 - 180.2 (19.9)
DEL PEAK 22(8P23.2) WILD-TYPE 216 74 0.4 - 211.0 (22.6)

Figure S50.  Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000175 (Wilcoxon-test), Q value = 0.022

Table S51.  Gene #51: 'del_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 23(9P23) MUTATED 142 50.9 (30.3)
DEL PEAK 23(9P23) WILD-TYPE 151 41.2 (39.0)

Figure S51.  Get High-res Image Gene #51: 'del_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_9p21.3' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00135 (Wilcoxon-test), Q value = 0.085

Table S52.  Gene #52: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 24(9P21.3) MUTATED 179 48.6 (29.5)
DEL PEAK 24(9P21.3) WILD-TYPE 114 41.6 (42.7)

Figure S52.  Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_10p15.3' versus 'Time to Death'

P value = 0.0077 (logrank test), Q value = 0.18

Table S53.  Gene #55: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 27(10P15.3) MUTATED 170 85 0.4 - 172.7 (19.0)
DEL PEAK 27(10P15.3) WILD-TYPE 350 134 0.1 - 211.0 (22.4)

Figure S53.  Get High-res Image Gene #55: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0132 (Wilcoxon-test), Q value = 0.23

Table S54.  Gene #55: 'del_10p15.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 27(10P15.3) MUTATED 140 2.8 (5.8)
DEL PEAK 27(10P15.3) WILD-TYPE 268 1.9 (3.2)

Figure S54.  Get High-res Image Gene #55: 'del_10p15.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_10p11.21' versus 'RACE'

P value = 0.00512 (Fisher's exact test), Q value = 0.16

Table S55.  Gene #56: 'del_10p11.21' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 28(10P11.21) MUTATED 0 5 25 131
DEL PEAK 28(10P11.21) WILD-TYPE 2 6 23 315

Figure S55.  Get High-res Image Gene #56: 'del_10p11.21' versus Clinical Feature #13: 'RACE'

'del_11q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00342 (Wilcoxon-test), Q value = 0.13

Table S56.  Gene #59: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 521 60.9 (11.9)
DEL PEAK 31(11Q23.1) MUTATED 245 59.5 (11.3)
DEL PEAK 31(11Q23.1) WILD-TYPE 276 62.1 (12.4)

Figure S56.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 6e-04 (Fisher's exact test), Q value = 0.048

Table S57.  Gene #59: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 179 68 168 8
DEL PEAK 31(11Q23.1) MUTATED 65 26 96 3
DEL PEAK 31(11Q23.1) WILD-TYPE 114 42 72 5

Figure S57.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.1' versus 'GENDER'

P value = 4.97e-06 (Fisher's exact test), Q value = 0.0053

Table S58.  Gene #59: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
DEL PEAK 31(11Q23.1) MUTATED 43 203
DEL PEAK 31(11Q23.1) WILD-TYPE 97 179

Figure S58.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

'del_11q23.1' versus 'RADIATION_THERAPY'

P value = 0.00124 (Fisher's exact test), Q value = 0.082

Table S59.  Gene #59: 'del_11q23.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 162 301
DEL PEAK 31(11Q23.1) MUTATED 59 158
DEL PEAK 31(11Q23.1) WILD-TYPE 103 143

Figure S59.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_11q23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000219 (Wilcoxon-test), Q value = 0.022

Table S60.  Gene #59: 'del_11q23.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 31(11Q23.1) MUTATED 178 2.9 (5.3)
DEL PEAK 31(11Q23.1) WILD-TYPE 230 1.7 (3.2)

Figure S60.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_13q14.2' versus 'RACE'

P value = 0.0152 (Fisher's exact test), Q value = 0.24

Table S61.  Gene #62: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 34(13Q14.2) MUTATED 2 3 28 178
DEL PEAK 34(13Q14.2) WILD-TYPE 0 8 20 268

Figure S61.  Get High-res Image Gene #62: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

'del_14q11.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0111 (Wilcoxon-test), Q value = 0.21

Table S62.  Gene #63: 'del_14q11.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 35(14Q11.2) MUTATED 46 57.7 (37.0)
DEL PEAK 35(14Q11.2) WILD-TYPE 247 43.7 (34.7)

Figure S62.  Get High-res Image Gene #63: 'del_14q11.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_14q32.32' versus 'RADIATION_THERAPY'

P value = 0.0166 (Fisher's exact test), Q value = 0.25

Table S63.  Gene #64: 'del_14q32.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 162 301
DEL PEAK 36(14Q32.32) MUTATED 14 51
DEL PEAK 36(14Q32.32) WILD-TYPE 148 250

Figure S63.  Get High-res Image Gene #64: 'del_14q32.32' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_17p11.2' versus 'RACE'

P value = 0.00283 (Fisher's exact test), Q value = 0.13

Table S64.  Gene #68: 'del_17p11.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 40(17P11.2) MUTATED 0 2 19 75
DEL PEAK 40(17P11.2) WILD-TYPE 2 9 29 371

Figure S64.  Get High-res Image Gene #68: 'del_17p11.2' versus Clinical Feature #13: 'RACE'

'del_17q25.3' versus 'ETHNICITY'

P value = 0.0145 (Fisher's exact test), Q value = 0.24

Table S65.  Gene #69: 'del_17q25.3' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 459
DEL PEAK 41(17Q25.3) MUTATED 8 57
DEL PEAK 41(17Q25.3) WILD-TYPE 18 402

Figure S65.  Get High-res Image Gene #69: 'del_17q25.3' versus Clinical Feature #14: 'ETHNICITY'

'del_18q23' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.017 (Wilcoxon-test), Q value = 0.25

Table S66.  Gene #70: 'del_18q23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 42(18Q23) MUTATED 166 50.5 (40.3)
DEL PEAK 42(18Q23) WILD-TYPE 127 39.9 (26.6)

Figure S66.  Get High-res Image Gene #70: 'del_18q23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_18q23' versus 'RACE'

P value = 0.00435 (Fisher's exact test), Q value = 0.15

Table S67.  Gene #70: 'del_18q23' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 42(18Q23) MUTATED 2 8 36 233
DEL PEAK 42(18Q23) WILD-TYPE 0 3 12 213

Figure S67.  Get High-res Image Gene #70: 'del_18q23' versus Clinical Feature #13: 'RACE'

'del_19p13.3' versus 'Time to Death'

P value = 0.00756 (logrank test), Q value = 0.18

Table S68.  Gene #71: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
DEL PEAK 43(19P13.3) MUTATED 174 83 0.1 - 153.9 (18.5)
DEL PEAK 43(19P13.3) WILD-TYPE 346 136 0.1 - 211.0 (22.3)

Figure S68.  Get High-res Image Gene #71: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_21q22.3' versus 'RACE'

P value = 0.00694 (Fisher's exact test), Q value = 0.18

Table S69.  Gene #73: 'del_21q22.3' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
DEL PEAK 45(21Q22.3) MUTATED 1 7 28 166
DEL PEAK 45(21Q22.3) WILD-TYPE 1 4 20 280

Figure S69.  Get High-res Image Gene #73: 'del_21q22.3' versus Clinical Feature #13: 'RACE'

'del_xp22.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0157 (Wilcoxon-test), Q value = 0.25

Table S70.  Gene #74: 'del_xp22.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
DEL PEAK 46(XP22.2) MUTATED 96 52.6 (38.5)
DEL PEAK 46(XP22.2) WILD-TYPE 197 42.6 (33.3)

Figure S70.  Get High-res Image Gene #74: 'del_xp22.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_xp22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00063 (Wilcoxon-test), Q value = 0.048

Table S71.  Gene #74: 'del_xp22.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 46(XP22.2) MUTATED 126 3.1 (5.5)
DEL PEAK 46(XP22.2) WILD-TYPE 282 1.8 (3.6)

Figure S71.  Get High-res Image Gene #74: 'del_xp22.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_xp21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0092 (Wilcoxon-test), Q value = 0.2

Table S72.  Gene #75: 'del_xp21.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 47(XP21.3) MUTATED 128 2.8 (5.3)
DEL PEAK 47(XP21.3) WILD-TYPE 280 1.9 (3.8)

Figure S72.  Get High-res Image Gene #75: 'del_xp21.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_xq21.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00524 (Wilcoxon-test), Q value = 0.16

Table S73.  Gene #76: 'del_xq21.33' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
DEL PEAK 48(XQ21.33) MUTATED 57 3.7 (7.2)
DEL PEAK 48(XQ21.33) WILD-TYPE 351 2.0 (3.6)

Figure S73.  Get High-res Image Gene #76: 'del_xq21.33' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

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/HNSC-TP/22508724/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/22506490/HNSC-TP.merged_data.txt

  • Number of patients = 522

  • Number of significantly focal cnvs = 76

  • Number of selected clinical features = 14

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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