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 77 focal events and 14 clinical features across 516 patients, 55 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_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_18p11.31 cnv correlated to 'GENDER'.

  • del_1p36.21 cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION' and '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 'PATHOLOGY_T_STAGE'.

  • del_2q36.2 cnv correlated to 'PATHOLOGY_T_STAGE' and 'NUMBER_PACK_YEARS_SMOKED'.

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

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

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

  • del_3p12.1 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.

  • 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_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'.

  • del_10p11.21 cnv correlated to 'RACE'.

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

  • del_17p11.2 cnv correlated to 'RACE'.

  • del_17q25.3 cnv correlated to 'ETHNICITY'.

  • del_18q21.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED' and 'RACE'.

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

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

  • del_xp22.2 cnv correlated to '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 77 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 55 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		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 3p24 1 363 (70%) 153 0.0193
(0.289) 		0.253
(0.7) 		0.519
(0.873) 		0.00573
(0.172) 		0.157
(0.609) 		1
(1.00) 		0.00335
(0.146) 		0.0726
(0.458) 		0.508
(0.87) 		0.000201
(0.0386) 		0.519
(0.873) 		0.0694
(0.45) 		0.00032
(0.0386) 		0.825
(1.00)
del 3p14 2 367 (71%) 149 0.0107
(0.238) 		0.244
(0.7) 		0.558
(0.884) 		0.139
(0.585) 		0.0612
(0.446) 		1
(1.00) 		0.00612
(0.178) 		0.0473
(0.408) 		0.109
(0.54) 		0.000275
(0.0386) 		0.433
(0.819) 		0.0161
(0.277) 		0.00343
(0.146) 		1
(1.00)
del 11q23 1 243 (47%) 273 0.486
(0.856) 		0.00353
(0.146) 		0.964
(1.00) 		0.893
(1.00) 		0.00122
(0.0939) 		1
(1.00) 		7.33e-06
(0.00791) 		0.434
(0.82) 		0.275
(0.704) 		0.172
(0.629) 		0.234
(0.694) 		0.00048
(0.0517) 		0.0419
(0.399) 		0.218
(0.685)
del 3p26 2 343 (66%) 173 0.0811
(0.483) 		0.909
(1.00) 		0.687
(0.96) 		0.0291
(0.348) 		0.416
(0.802) 		1
(1.00) 		0.00319
(0.146) 		0.123
(0.554) 		0.202
(0.668) 		0.00325
(0.146) 		0.366
(0.779) 		0.116
(0.547) 		0.00013
(0.0386) 		1
(1.00)
amp 7q21 3 166 (32%) 350 0.00951
(0.228) 		0.185
(0.65) 		0.758
(0.991) 		0.0803
(0.483) 		0.323
(0.746) 		1
(1.00) 		0.597
(0.917) 		0.0802
(0.483) 		0.154
(0.602) 		0.0307
(0.351) 		0.756
(0.991) 		0.698
(0.963) 		0.0014
(0.101) 		0.669
(0.947)
amp 9p23 122 (24%) 394 0.163
(0.616) 		0.0601
(0.446) 		0.872
(1.00) 		0.67
(0.949) 		0.0631
(0.446) 		1
(1.00) 		0.00152
(0.103) 		0.592
(0.913) 		0.397
(0.802) 		0.0117
(0.238) 		0.294
(0.717) 		0.055
(0.429) 		0.855
(1.00) 		0.352
(0.766)
del 1p36 21 93 (18%) 423 0.347
(0.766) 		0.0426
(0.4) 		0.547
(0.881) 		0.572
(0.895) 		0.773
(0.991) 		1
(1.00) 		0.519
(0.873) 		0.0325
(0.351) 		0.0115
(0.238) 		0.00351
(0.146) 		0.0833
(0.491) 		0.931
(1.00) 		0.441
(0.825) 		1
(1.00)
del 2q36 2 154 (30%) 362 0.398
(0.802) 		0.678
(0.954) 		0.0241
(0.317) 		0.00232
(0.146) 		0.446
(0.828) 		1
(1.00) 		0.746
(0.988) 		1
(1.00) 		0.6
(0.92) 		0.0112
(0.238) 		0.317
(0.738) 		0.885
(1.00) 		0.0179
(0.285) 		0.0234
(0.313)
del 3p12 1 338 (66%) 178 0.0162
(0.277) 		0.978
(1.00) 		0.336
(0.752) 		0.242
(0.7) 		0.148
(0.598) 		1
(1.00) 		0.0161
(0.277) 		0.56
(0.887) 		0.161
(0.615) 		0.000286
(0.0386) 		0.282
(0.705) 		0.176
(0.643) 		0.00455
(0.157) 		1
(1.00)
del 5q12 1 212 (41%) 304 0.653
(0.935) 		0.548
(0.881) 		0.786
(0.999) 		0.0535
(0.428) 		0.281
(0.705) 		1
(1.00) 		0.0267
(0.333) 		0.607
(0.92) 		0.39
(0.796) 		0.00318
(0.146) 		0.236
(0.696) 		0.265
(0.704) 		0.00366
(0.146) 		0.21
(0.685)
del 5q15 223 (43%) 293 0.999
(1.00) 		0.341
(0.757) 		0.717
(0.973) 		0.0322
(0.351) 		0.718
(0.973) 		1
(1.00) 		0.0457
(0.404) 		0.519
(0.873) 		0.467
(0.84) 		0.00566
(0.172) 		0.525
(0.876) 		0.722
(0.974) 		0.0126
(0.247) 		0.304
(0.723)
del 18q21 2 264 (51%) 252 0.14
(0.585) 		0.638
(0.93) 		0.847
(1.00) 		0.63
(0.93) 		0.627
(0.93) 		1
(1.00) 		0.166
(0.622) 		0.215
(0.685) 		0.4
(0.802) 		0.000868
(0.072) 		0.911
(1.00) 		0.37
(0.784) 		0.00276
(0.146) 		0.099
(0.529)
del 18q23 284 (55%) 232 0.224
(0.691) 		0.179
(0.643) 		0.97
(1.00) 		0.114
(0.542) 		0.88
(1.00) 		1
(1.00) 		0.275
(0.704) 		0.0486
(0.411) 		0.466
(0.84) 		0.00726
(0.197) 		0.409
(0.802) 		0.259
(0.7) 		0.00971
(0.228) 		0.216
(0.685)
amp 2q11 2 106 (21%) 410 0.382
(0.792) 		0.849
(1.00) 		0.218
(0.685) 		0.00909
(0.228) 		0.261
(0.7) 		1
(1.00) 		0.112
(0.54) 		0.757
(0.991) 		0.656
(0.937) 		0.109
(0.54) 		0.313
(0.733) 		0.325
(0.746) 		0.374
(0.785) 		0.612
(0.92)
amp 3q26 33 375 (73%) 141 0.468
(0.84) 		0.0643
(0.446) 		0.118
(0.547) 		0.733
(0.982) 		0.216
(0.685) 		1
(1.00) 		0.00523
(0.166) 		0.377
(0.79) 		0.281
(0.705) 		0.0659
(0.446) 		0.476
(0.85) 		0.0454
(0.404) 		0.603
(0.92) 		0.65
(0.933)
amp 7p11 2 218 (42%) 298 0.000549
(0.0538) 		0.507
(0.87) 		0.766
(0.991) 		0.0368
(0.374) 		0.788
(1) 		0.408
(0.802) 		0.841
(1.00) 		0.146
(0.598) 		0.714
(0.973) 		0.275
(0.704) 		0.563
(0.89) 		0.648
(0.932) 		0.13
(0.574) 		0.54
(0.879)
amp 8p11 23 159 (31%) 357 0.219
(0.685) 		0.707
(0.968) 		0.0269
(0.333) 		0.067
(0.446) 		0.227
(0.693) 		0.293
(0.717) 		0.748
(0.989) 		0.108
(0.54) 		0.602
(0.92) 		0.274
(0.704) 		0.555
(0.883) 		0.186
(0.65) 		0.0114
(0.238) 		0.826
(1.00)
amp 9p24 1 124 (24%) 392 0.357
(0.772) 		0.0667
(0.446) 		0.838
(1.00) 		0.668
(0.947) 		0.212
(0.685) 		1
(1.00) 		7.29e-05
(0.0386) 		0.592
(0.913) 		0.257
(0.7) 		0.0214
(0.301) 		0.189
(0.65) 		0.111
(0.54) 		0.978
(1.00) 		0.234
(0.694)
amp 9q34 3 174 (34%) 342 0.25
(0.7) 		0.112
(0.54) 		0.169
(0.629) 		0.00424
(0.157) 		0.278
(0.704) 		1
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.61
(0.92) 		0.796
(1.00) 		0.877
(1.00) 		0.526
(0.876) 		0.668
(0.947) 		0.133
(0.575)
amp 18p11 31 154 (30%) 362 0.137
(0.585) 		0.531
(0.876) 		0.0404
(0.389) 		0.0299
(0.351) 		0.225
(0.692) 		0.255
(0.7) 		0.000323
(0.0386) 		0.646
(0.93) 		0.431
(0.817) 		0.0479
(0.41) 		0.846
(1.00) 		0.435
(0.821) 		0.262
(0.7) 		0.37
(0.784)
del 1p13 2 130 (25%) 386 0.181
(0.643) 		0.0315
(0.351) 		0.632
(0.93) 		0.276
(0.704) 		0.979
(1.00) 		0.245
(0.7) 		1
(1.00) 		0.463
(0.838) 		0.404
(0.802) 		0.0116
(0.238) 		0.419
(0.802) 		0.542
(0.879) 		0.489
(0.856) 		0.641
(0.93)
del 2q21 2 76 (15%) 440 0.6
(0.92) 		0.18
(0.643) 		0.22
(0.687) 		0.807
(1.00) 		0.257
(0.7) 		1
(1.00) 		0.00484
(0.158) 		0.699
(0.963) 		0.123
(0.554) 		0.398
(0.802) 		0.0663
(0.446) 		0.208
(0.68) 		0.751
(0.991) 		0.244
(0.7)
del 2q22 1 118 (23%) 398 0.864
(1.00) 		0.0664
(0.446) 		0.0162
(0.277) 		0.0073
(0.197) 		0.78
(0.998) 		0.293
(0.717) 		0.0183
(0.285) 		0.772
(0.991) 		0.773
(0.991) 		0.162
(0.616) 		0.583
(0.906) 		0.881
(1.00) 		0.644
(0.93) 		0.465
(0.84)
del 5q35 3 197 (38%) 319 0.55
(0.883) 		0.249
(0.7) 		0.765
(0.991) 		0.0662
(0.446) 		0.613
(0.92) 		1
(1.00) 		0.154
(0.603) 		0.314
(0.735) 		0.457
(0.834) 		0.00973
(0.228) 		0.331
(0.75) 		0.699
(0.963) 		0.112
(0.54) 		0.525
(0.876)
del 8p23 2 299 (58%) 217 0.00751
(0.197) 		0.0185
(0.285) 		0.854
(1.00) 		0.244
(0.7) 		0.406
(0.802) 		1
(1.00) 		0.228
(0.693) 		0.0721
(0.457) 		0.808
(1.00) 		0.502
(0.869) 		0.769
(0.991) 		0.219
(0.685) 		0.412
(0.802) 		0.152
(0.602)
del 9p23 235 (46%) 281 0.609
(0.92) 		0.645
(0.93) 		0.827
(1.00) 		0.298
(0.717) 		0.825
(1.00) 		0.462
(0.838) 		0.0462
(0.405) 		0.871
(1.00) 		0.716
(0.973) 		0.000279
(0.0386) 		0.227
(0.693) 		0.857
(1.00) 		0.142
(0.593) 		0.417
(0.802)
del 9p21 3 297 (58%) 219 0.0627
(0.446) 		0.472
(0.844) 		0.402
(0.802) 		0.0324
(0.351) 		0.691
(0.961) 		1
(1.00) 		1
(1.00) 		0.336
(0.752) 		0.542
(0.879) 		0.00458
(0.157) 		0.161
(0.615) 		0.851
(1.00) 		0.171
(0.629) 		0.837
(1.00)
del 10p15 3 167 (32%) 349 0.0116
(0.238) 		0.567
(0.891) 		0.26
(0.7) 		0.0251
(0.322) 		0.0597
(0.446) 		1
(1.00) 		0.458
(0.834) 		0.0354
(0.374) 		0.0925
(0.509) 		0.868
(1.00) 		0.61
(0.92) 		0.0215
(0.301) 		0.16
(0.615) 		0.826
(1.00)
del 10p11 21 160 (31%) 356 0.0751
(0.468) 		0.737
(0.983) 		0.498
(0.864) 		0.187
(0.65) 		0.414
(0.802) 		1
(1.00) 		0.0869
(0.501) 		0.112
(0.54) 		0.0492
(0.411) 		0.781
(0.998) 		0.812
(1.00) 		0.209
(0.682) 		0.00901
(0.228) 		0.657
(0.937)
del 17p11 2 97 (19%) 419 0.418
(0.802) 		0.729
(0.979) 		0.147
(0.598) 		0.865
(1.00) 		0.336
(0.752) 		0.185
(0.65) 		0.703
(0.965) 		0.52
(0.874) 		0.122
(0.554) 		0.356
(0.771) 		0.954
(1.00) 		0.806
(1.00) 		0.00319
(0.146) 		0.11
(0.54)
del 17q25 3 71 (14%) 445 0.646
(0.93) 		0.329
(0.75) 		0.726
(0.977) 		0.0653
(0.446) 		0.0884
(0.502) 		1
(1.00) 		0.253
(0.7) 		0.17
(0.629) 		0.297
(0.717) 		0.409
(0.802) 		0.42
(0.802) 		0.586
(0.908) 		0.73
(0.979) 		0.0121
(0.242)
del 19p13 3 172 (33%) 344 0.00465
(0.157) 		0.552
(0.883) 		0.136
(0.583) 		0.282
(0.705) 		0.0892
(0.503) 		0.332
(0.75) 		0.528
(0.876) 		0.221
(0.687) 		0.307
(0.726) 		0.413
(0.802) 		0.133
(0.575) 		0.15
(0.598) 		0.85
(1.00) 		0.516
(0.873)
del xp22 2 153 (30%) 363 0.15
(0.598) 		0.85
(1.00) 		0.333
(0.751) 		0.0642
(0.446) 		0.11
(0.54) 		0.255
(0.7) 		0.129
(0.57) 		0.265
(0.704) 		0.188
(0.65) 		0.0169
(0.285) 		0.656
(0.937) 		0.000809
(0.072) 		0.375
(0.786) 		0.823
(1.00)
del xp21 3 156 (30%) 360 0.635
(0.93) 		0.855
(1.00) 		0.274
(0.704) 		0.146
(0.598) 		0.171
(0.629) 		0.283
(0.705) 		0.331
(0.75) 		0.345
(0.764) 		0.149
(0.598) 		0.0682
(0.448) 		0.92
(1.00) 		0.00726
(0.197) 		0.953
(1.00) 		0.507
(0.87)
del xq21 33 80 (16%) 436 0.91
(1.00) 		0.973
(1.00) 		0.0901
(0.503) 		0.68
(0.954) 		0.131
(0.575) 		0.147
(0.598) 		0.784
(0.998) 		0.103
(0.538) 		0.504
(0.87) 		0.51
(0.872) 		0.444
(0.827) 		0.00448
(0.157) 		0.513
(0.872) 		0.567
(0.891)
amp 2q31 2 109 (21%) 407 0.29
(0.715) 		0.641
(0.93) 		0.396
(0.802) 		0.454
(0.832) 		0.135
(0.581) 		1
(1.00) 		0.0884
(0.502) 		0.762
(0.991) 		1
(1.00) 		0.0395
(0.387) 		0.831
(1.00) 		0.124
(0.557) 		0.334
(0.751) 		0.2
(0.668)
amp 5p15 33 237 (46%) 279 0.825
(1.00) 		0.0275
(0.337) 		0.262
(0.7) 		0.553
(0.883) 		0.0263
(0.333) 		0.44
(0.825) 		0.0364
(0.374) 		0.74
(0.983) 		0.182
(0.645) 		0.231
(0.694) 		0.252
(0.7) 		0.0747
(0.468) 		0.0578
(0.445) 		0.216
(0.685)
amp 6p12 1 109 (21%) 407 0.635
(0.93) 		0.155
(0.604) 		0.817
(1.00) 		0.258
(0.7) 		0.567
(0.891) 		1
(1.00) 		0.467
(0.84) 		1
(1.00) 		0.0759
(0.471) 		0.497
(0.864) 		0.99
(1.00) 		0.739
(0.983) 		0.0717
(0.457) 		1
(1.00)
amp 6q12 94 (18%) 422 0.854
(1.00) 		0.265
(0.704) 		0.892
(1.00) 		0.326
(0.746) 		0.817
(1.00) 		1
(1.00) 		0.7
(0.963) 		0.363
(0.777) 		0.0841
(0.492) 		0.82
(1.00) 		0.0319
(0.351) 		0.493
(0.859) 		0.365
(0.779) 		0.193
(0.656)
amp 8q11 21 307 (59%) 209 0.638
(0.93) 		0.882
(1.00) 		0.124
(0.555) 		0.385
(0.792) 		0.489
(0.856) 		0.353
(0.767) 		0.762
(0.991) 		0.722
(0.974) 		0.325
(0.746) 		0.878
(1.00) 		0.233
(0.694) 		0.442
(0.825) 		0.686
(0.959) 		0.407
(0.802)
amp 8q24 21 380 (74%) 136 0.214
(0.685) 		0.538
(0.879) 		0.151
(0.6) 		0.164
(0.618) 		0.0652
(0.446) 		0.223
(0.69) 		0.911
(1.00) 		0.49
(0.856) 		0.891
(1.00) 		0.92
(1.00) 		0.0504
(0.418) 		0.0192
(0.289) 		0.908
(1.00) 		0.252
(0.7)
amp 9p13 3 138 (27%) 378 0.723
(0.974) 		0.297
(0.717) 		0.414
(0.802) 		0.91
(1.00) 		0.404
(0.802) 		1
(1.00) 		0.0925
(0.509) 		0.804
(1.00) 		0.892
(1.00) 		0.372
(0.784) 		0.145
(0.598) 		0.178
(0.643) 		0.91
(1.00) 		0.167
(0.625)
amp 11p13 99 (19%) 417 0.0881
(0.502) 		0.535
(0.879) 		0.186
(0.65) 		0.912
(1.00) 		0.0847
(0.492) 		1
(1.00) 		0.531
(0.876) 		0.756
(0.991) 		0.878
(1.00) 		0.0364
(0.374) 		0.382
(0.792) 		0.799
(1.00) 		0.351
(0.766) 		0.297
(0.717)
amp 11q13 3 225 (44%) 291 0.132
(0.575) 		0.232
(0.694) 		0.489
(0.856) 		0.545
(0.881) 		0.217
(0.685) 		1
(1.00) 		0.37
(0.784) 		0.201
(0.668) 		0.113
(0.542) 		0.0373
(0.375) 		0.765
(0.991) 		0.171
(0.629) 		0.32
(0.743) 		0.837
(1.00)
amp 12p13 33 164 (32%) 352 0.428
(0.813) 		0.985
(1.00) 		0.898
(1.00) 		0.966
(1.00) 		0.484
(0.856) 		1
(1.00) 		0.0553
(0.429) 		1
(1.00) 		0.897
(1.00) 		0.61
(0.92) 		0.797
(1.00) 		0.231
(0.694) 		0.247
(0.7) 		0.51
(0.872)
amp 12q15 101 (20%) 415 0.694
(0.963) 		0.0451
(0.404) 		0.608
(0.92) 		0.689
(0.961) 		0.153
(0.602) 		1
(1.00) 		0.901
(1.00) 		0.756
(0.991) 		0.36
(0.774) 		0.117
(0.547) 		0.218
(0.685) 		0.0656
(0.446) 		0.101
(0.534) 		1
(1.00)
amp 13q22 1 105 (20%) 411 0.0198
(0.289) 		0.0913
(0.507) 		0.874
(1.00) 		0.202
(0.668) 		0.534
(0.878) 		1
(1.00) 		0.461
(0.838) 		0.758
(0.991) 		0.1
(0.533) 		0.714
(0.973) 		0.138
(0.585) 		0.886
(1.00) 		0.267
(0.704) 		0.304
(0.723)
amp 13q34 106 (21%) 410 0.06
(0.446) 		0.0146
(0.267) 		0.238
(0.696) 		0.129
(0.57) 		0.128
(0.57) 		1
(1.00) 		0.326
(0.746) 		1
(1.00) 		0.458
(0.834) 		0.931
(1.00) 		0.11
(0.54) 		0.646
(0.93) 		0.825
(1.00) 		0.202
(0.668)
amp 15q26 3 103 (20%) 413 0.0141
(0.262) 		0.564
(0.89) 		0.754
(0.991) 		0.12
(0.55) 		0.918
(1.00) 		1
(1.00) 		0.804
(1.00) 		0.295
(0.717) 		0.764
(0.991) 		0.806
(1.00) 		0.309
(0.728) 		0.938
(1.00) 		0.639
(0.93) 		0.799
(1.00)
amp 17q12 89 (17%) 427 0.246
(0.7) 		0.0621
(0.446) 		0.12
(0.55) 		0.234
(0.694) 		0.72
(0.974) 		0.19
(0.65) 		0.358
(0.772) 		0.181
(0.643) 		0.632
(0.93) 		0.0319
(0.351) 		0.15
(0.598) 		0.799
(1.00) 		0.742
(0.983) 		0.0547
(0.429)
amp 18q11 2 104 (20%) 412 0.771
(0.991) 		0.103
(0.538) 		0.324
(0.746) 		0.887
(1.00) 		0.852
(1.00) 		0.158
(0.609) 		0.0133
(0.256) 		0.111
(0.54) 		0.548
(0.881) 		0.413
(0.802) 		0.81
(1.00) 		0.821
(1.00) 		0.138
(0.585) 		0.442
(0.825)
amp 19p13 2 58 (11%) 458 0.27
(0.704) 		0.878
(1.00) 		0.529
(0.876) 		0.39
(0.796) 		0.437
(0.821) 		1
(1.00) 		0.0849
(0.492) 		1
(1.00) 		1
(1.00) 		0.446
(0.828) 		0.304
(0.723) 		0.0431
(0.4) 		0.42
(0.802) 		1
(1.00)
amp 20p12 2 190 (37%) 326 0.98
(1.00) 		0.864
(1.00) 		0.627
(0.93) 		0.776
(0.993) 		0.237
(0.696) 		1
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.453
(0.832) 		0.346
(0.765) 		0.801
(1.00) 		0.361
(0.774) 		0.351
(0.766) 		0.0515
(0.424)
amp 20q11 22 225 (44%) 291 0.437
(0.821) 		0.274
(0.704) 		0.448
(0.829) 		0.524
(0.876) 		0.967
(1.00) 		1
(1.00) 		0.485
(0.856) 		0.623
(0.929) 		0.273
(0.704) 		0.783
(0.998) 		0.254
(0.7) 		0.661
(0.94) 		0.677
(0.954) 		0.409
(0.802)
amp xq28 146 (28%) 370 0.371
(0.784) 		0.419
(0.802) 		0.531
(0.876) 		0.116
(0.547) 		0.246
(0.7) 		0.239
(0.699) 		0.379
(0.792) 		0.809
(1.00) 		0.108
(0.54) 		0.955
(1.00) 		0.713
(0.973) 		0.0175
(0.285) 		0.645
(0.93) 		0.654
(0.937)
del 1q44 47 (9%) 469 0.0686
(0.448) 		0.553
(0.883) 		0.815
(1.00) 		0.485
(0.856) 		0.926
(1.00) 		1
(1.00) 		0.49
(0.856) 		0.645
(0.93) 		1
(1.00) 		0.703
(0.965) 		0.104
(0.538) 		0.19
(0.65) 		0.409
(0.802) 		0.279
(0.705)
del 4p15 2 207 (40%) 309 0.501
(0.868) 		0.586
(0.908) 		0.832
(1.00) 		0.39
(0.796) 		0.529
(0.876) 		1
(1.00) 		0.0198
(0.289) 		0.72
(0.974) 		0.269
(0.704) 		0.0179
(0.285) 		0.304
(0.723) 		0.306
(0.724) 		0.138
(0.585) 		1
(1.00)
del 4q21 3 153 (30%) 363 0.839
(1.00) 		0.244
(0.7) 		0.229
(0.693) 		0.0471
(0.408) 		0.845
(1.00) 		1
(1.00) 		1
(1.00) 		0.505
(0.87) 		0.792
(1.00) 		0.0711
(0.456) 		0.0649
(0.446) 		0.48
(0.856) 		0.372
(0.784) 		0.118
(0.547)
del 4q22 1 165 (32%) 351 0.607
(0.92) 		0.531
(0.876) 		0.42
(0.802) 		0.33
(0.75) 		0.896
(1.00) 		1
(1.00) 		0.523
(0.876) 		0.219
(0.685) 		0.605
(0.92) 		0.0524
(0.425) 		0.0801
(0.483) 		0.575
(0.897) 		0.471
(0.844) 		0.194
(0.659)
del 4q35 2 211 (41%) 305 0.549
(0.881) 		0.673
(0.951) 		0.081
(0.483) 		0.0664
(0.446) 		0.38
(0.792) 		0.408
(0.802) 		0.0697
(0.45) 		0.259
(0.7) 		1
(1.00) 		0.497
(0.864) 		0.384
(0.792) 		0.742
(0.983) 		0.62
(0.926) 		1
(1.00)
del 6p25 3 95 (18%) 421 0.381
(0.792) 		0.36
(0.774) 		0.197
(0.662) 		0.0794
(0.483) 		0.593
(0.913) 		1
(1.00) 		0.0973
(0.522) 		1
(1.00) 		0.35
(0.766) 		0.59
(0.913) 		0.296
(0.717) 		0.737
(0.983) 		0.0521
(0.425) 		0.788
(1)
del 7q31 1 75 (15%) 441 0.698
(0.963) 		0.0536
(0.428) 		0.681
(0.954) 		0.77
(0.991) 		0.0231
(0.313) 		1
(1.00) 		1
(1.00) 		0.699
(0.963) 		0.302
(0.723) 		0.018
(0.285) 		0.153
(0.602) 		0.178
(0.643) 		0.569
(0.892) 		1
(1.00)
del 7q36 1 130 (25%) 386 0.095
(0.517) 		0.83
(1.00) 		0.514
(0.872) 		0.642
(0.93) 		0.191
(0.65) 		1
(1.00) 		0.424
(0.807) 		0.79
(1.00) 		0.889
(1.00) 		0.0936
(0.512) 		0.274
(0.704) 		0.416
(0.802) 		0.546
(0.881) 		0.643
(0.93)
del 9q21 11 106 (21%) 410 0.616
(0.922) 		0.261
(0.7) 		0.609
(0.92) 		0.506
(0.87) 		0.761
(0.991) 		0.255
(0.7) 		0.326
(0.746) 		0.384
(0.792) 		0.882
(1.00) 		0.0381
(0.381) 		0.574
(0.896) 		0.64
(0.93) 		0.18
(0.643) 		1
(1.00)
del 9q34 3 78 (15%) 438 0.76
(0.991) 		0.511
(0.872) 		0.332
(0.75) 		0.9
(1.00) 		0.963
(1.00) 		0.147
(0.598) 		0.783
(0.998) 		0.468
(0.84) 		1
(1.00) 		0.0247
(0.321) 		0.236
(0.696) 		0.886
(1.00) 		0.541
(0.879) 		0.385
(0.792)
del 10q23 31 137 (27%) 379 0.408
(0.802) 		0.693
(0.963) 		0.488
(0.856) 		0.273
(0.704) 		0.931
(1.00) 		1
(1.00) 		0.0137
(0.259) 		0.486
(0.856) 		0.682
(0.955) 		0.0386
(0.382) 		0.204
(0.669) 		0.959
(1.00) 		0.311
(0.732) 		0.351
(0.766)
del 11p15 5 162 (31%) 354 0.556
(0.883) 		0.757
(0.991) 		0.0451
(0.404) 		0.541
(0.879) 		0.0303
(0.351) 		1
(1.00) 		0.338
(0.754) 		0.0207
(0.298) 		1
(1.00) 		0.749
(0.989) 		0.842
(1.00) 		0.106
(0.54) 		0.0296
(0.35) 		0.178
(0.643)
del 12q24 33 60 (12%) 456 0.971
(1.00) 		0.741
(0.983) 		0.73
(0.979) 		0.342
(0.757) 		0.448
(0.829) 		1
(1.00) 		0.54
(0.879) 		0.406
(0.802) 		0.85
(1.00) 		0.861
(1.00) 		0.798
(1.00) 		0.583
(0.906) 		0.102
(0.538) 		0.513
(0.872)
del 13q12 11 229 (44%) 287 0.808
(1.00) 		0.698
(0.963) 		0.105
(0.54) 		0.119
(0.55) 		0.0834
(0.491) 		0.451
(0.831) 		0.0361
(0.374) 		0.735
(0.983) 		0.903
(1.00) 		0.117
(0.547) 		0.288
(0.713) 		0.0963
(0.519) 		0.0454
(0.404) 		0.213
(0.685)
del 13q14 2 213 (41%) 303 0.112
(0.54) 		0.0963
(0.519) 		0.388
(0.794) 		0.832
(1.00) 		0.281
(0.705) 		0.391
(0.796) 		0.0437
(0.402) 		0.197
(0.662) 		0.903
(1.00) 		0.539
(0.879) 		0.717
(0.973) 		0.225
(0.692) 		0.0427
(0.4) 		0.295
(0.717)
del 14q11 2 73 (14%) 443 0.897
(1.00) 		0.27
(0.704) 		0.397
(0.802) 		0.578
(0.9) 		0.767
(0.991) 		1
(1.00) 		0.202
(0.668) 		0.275
(0.704) 		1
(1.00) 		0.0278
(0.337) 		0.353
(0.767) 		0.258
(0.7) 		0.451
(0.831) 		0.0605
(0.446)
del 14q32 32 74 (14%) 442 0.299
(0.718) 		0.388
(0.794) 		0.268
(0.704) 		0.554
(0.883) 		0.608
(0.92) 		1
(1.00) 		0.0648
(0.446) 		0.69
(0.961) 		0.232
(0.694) 		0.863
(1.00) 		0.619
(0.925) 		0.84
(1.00) 		0.27
(0.704) 		0.556
(0.883)
del 15q15 1 121 (23%) 395 0.888
(1.00) 		0.659
(0.938) 		0.436
(0.821) 		0.189
(0.65) 		0.615
(0.922) 		1
(1.00) 		0.482
(0.856) 		0.0404
(0.389) 		0.256
(0.7) 		0.635
(0.93) 		0.797
(1.00) 		0.834
(1.00) 		0.976
(1.00) 		0.14
(0.585)
del 16q23 1 95 (18%) 421 0.646
(0.93) 		0.259
(0.7) 		0.341
(0.757) 		0.714
(0.973) 		0.0488
(0.411) 		1
(1.00) 		0.161
(0.615) 		0.259
(0.7) 		0.641
(0.93) 		0.57
(0.892) 		0.189
(0.65) 		0.123
(0.554) 		0.516
(0.873) 		1
(1.00)
del 16q23 3 102 (20%) 414 0.277
(0.704) 		0.285
(0.709) 		0.401
(0.802) 		0.287
(0.713) 		0.0683
(0.448) 		1
(1.00) 		0.455
(0.833) 		0.291
(0.716) 		1
(1.00) 		0.917
(1.00) 		0.316
(0.738) 		0.081
(0.483) 		0.453
(0.832) 		0.612
(0.92)
del 19q13 43 95 (18%) 421 0.25
(0.7) 		0.196
(0.661) 		0.229
(0.693) 		0.0337
(0.36) 		0.64
(0.93) 		1
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.35
(0.766) 		0.678
(0.954) 		0.0548
(0.429) 		0.888
(1.00) 		0.681
(0.954) 		0.289
(0.714)
del 21q22 3 205 (40%) 311 0.796
(1.00) 		0.872
(1.00) 		0.977
(1.00) 		0.0896
(0.503) 		0.42
(0.802) 		1
(1.00) 		0.312
(0.732) 		1
(1.00) 		0.806
(1.00) 		0.0227
(0.313) 		0.77
(0.991) 		0.542
(0.879) 		0.0235
(0.313) 		0.835
(1.00)
'amp_2q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00909 (Fisher's exact test), Q value = 0.23

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

nPatients T0+T1 T2 T3 T4
ALL 50 133 99 172
AMP PEAK 1(2Q11.2) MUTATED 5 19 26 44
AMP PEAK 1(2Q11.2) WILD-TYPE 45 114 73 128

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 = 0.00523 (Fisher's exact test), Q value = 0.17

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

nPatients FEMALE MALE
ALL 139 377
AMP PEAK 3(3Q26.33) MUTATED 88 287
AMP PEAK 3(3Q26.33) WILD-TYPE 51 90

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 = 0.000549 (logrank test), Q value = 0.054

Table S3.  Gene #7: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
AMP PEAK 7(7P11.2) MUTATED 216 98 0.1 - 153.9 (15.9)
AMP PEAK 7(7P11.2) WILD-TYPE 297 102 0.1 - 211.0 (20.4)

Figure S3.  Get High-res Image Gene #7: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.3' versus 'Time to Death'

P value = 0.00951 (logrank test), Q value = 0.23

Table S4.  Gene #8: 'amp_7q21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
AMP PEAK 8(7Q21.3) MUTATED 165 79 0.1 - 153.9 (17.1)
AMP PEAK 8(7Q21.3) WILD-TYPE 348 121 0.1 - 211.0 (19.0)

Figure S4.  Get High-res Image Gene #8: 'amp_7q21.3' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.3' versus 'RACE'

P value = 0.0014 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #8: 'amp_7q21.3' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
AMP PEAK 8(7Q21.3) MUTATED 1 1 25 137
AMP PEAK 8(7Q21.3) WILD-TYPE 1 10 20 304

Figure S5.  Get High-res Image Gene #8: 'amp_7q21.3' versus Clinical Feature #13: 'RACE'

'amp_8p11.23' versus 'RACE'

P value = 0.0114 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #9: 'amp_8p11.23' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
AMP PEAK 9(8P11.23) MUTATED 0 0 20 134
AMP PEAK 9(8P11.23) WILD-TYPE 2 11 25 307

Figure S6.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #13: 'RACE'

'amp_9p24.1' versus 'GENDER'

P value = 7.29e-05 (Fisher's exact test), Q value = 0.039

Table S7.  Gene #12: 'amp_9p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
AMP PEAK 12(9P24.1) MUTATED 51 73
AMP PEAK 12(9P24.1) WILD-TYPE 88 304

Figure S7.  Get High-res Image Gene #12: 'amp_9p24.1' versus Clinical Feature #7: 'GENDER'

'amp_9p23' versus 'GENDER'

P value = 0.00152 (Fisher's exact test), Q value = 0.1

Table S8.  Gene #13: 'amp_9p23' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
AMP PEAK 13(9P23) MUTATED 47 75
AMP PEAK 13(9P23) WILD-TYPE 92 302

Figure S8.  Get High-res Image Gene #13: 'amp_9p23' versus Clinical Feature #7: 'GENDER'

'amp_9p23' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0117 (Wilcoxon-test), Q value = 0.24

Table S9.  Gene #13: 'amp_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
AMP PEAK 13(9P23) MUTATED 67 37.4 (27.5)
AMP PEAK 13(9P23) WILD-TYPE 220 47.6 (37.3)

Figure S9.  Get High-res Image Gene #13: 'amp_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'amp_9q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00424 (Fisher's exact test), Q value = 0.16

Table S10.  Gene #15: 'amp_9q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 133 99 172
AMP PEAK 15(9Q34.3) MUTATED 11 36 37 75
AMP PEAK 15(9Q34.3) WILD-TYPE 39 97 62 97

Figure S10.  Get High-res Image Gene #15: 'amp_9q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_18p11.31' versus 'GENDER'

P value = 0.000323 (Fisher's exact test), Q value = 0.039

Table S11.  Gene #24: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
AMP PEAK 24(18P11.31) MUTATED 25 129
AMP PEAK 24(18P11.31) WILD-TYPE 114 248

Figure S11.  Get High-res Image Gene #24: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

'del_1p36.21' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0115 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #30: 'del_1p36.21' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 81 435
DEL PEAK 1(1P36.21) MUTATED 23 70
DEL PEAK 1(1P36.21) WILD-TYPE 58 365

Figure S12.  Get High-res Image Gene #30: 'del_1p36.21' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_1p36.21' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00351 (Wilcoxon-test), Q value = 0.15

Table S13.  Gene #30: 'del_1p36.21' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 1(1P36.21) MUTATED 61 57.0 (46.0)
DEL PEAK 1(1P36.21) WILD-TYPE 226 42.1 (31.5)

Figure S13.  Get High-res Image Gene #30: 'del_1p36.21' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_1p13.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0116 (Wilcoxon-test), Q value = 0.24

Table S14.  Gene #31: 'del_1p13.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 2(1P13.2) MUTATED 67 55.0 (44.2)
DEL PEAK 2(1P13.2) WILD-TYPE 220 42.3 (31.9)

Figure S14.  Get High-res Image Gene #31: 'del_1p13.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_2q21.2' versus 'GENDER'

P value = 0.00484 (Fisher's exact test), Q value = 0.16

Table S15.  Gene #33: 'del_2q21.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
DEL PEAK 4(2Q21.2) MUTATED 31 45
DEL PEAK 4(2Q21.2) WILD-TYPE 108 332

Figure S15.  Get High-res Image Gene #33: 'del_2q21.2' versus Clinical Feature #7: 'GENDER'

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0073 (Fisher's exact test), Q value = 0.2

Table S16.  Gene #34: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 133 99 172
DEL PEAK 5(2Q22.1) MUTATED 5 25 24 53
DEL PEAK 5(2Q22.1) WILD-TYPE 45 108 75 119

Figure S16.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q36.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00232 (Fisher's exact test), Q value = 0.15

Table S17.  Gene #35: 'del_2q36.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 133 99 172
DEL PEAK 6(2Q36.2) MUTATED 7 31 40 55
DEL PEAK 6(2Q36.2) WILD-TYPE 43 102 59 117

Figure S17.  Get High-res Image Gene #35: 'del_2q36.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q36.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0112 (Wilcoxon-test), Q value = 0.24

Table S18.  Gene #35: 'del_2q36.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 6(2Q36.2) MUTATED 90 51.1 (33.2)
DEL PEAK 6(2Q36.2) WILD-TYPE 197 42.6 (36.3)

Figure S18.  Get High-res Image Gene #35: 'del_2q36.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p26.2' versus 'GENDER'

P value = 0.00319 (Fisher's exact test), Q value = 0.15

Table S19.  Gene #36: 'del_3p26.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
DEL PEAK 7(3P26.2) MUTATED 78 265
DEL PEAK 7(3P26.2) WILD-TYPE 61 112

Figure S19.  Get High-res Image Gene #36: 'del_3p26.2' versus Clinical Feature #7: 'GENDER'

'del_3p26.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00325 (Wilcoxon-test), Q value = 0.15

Table S20.  Gene #36: 'del_3p26.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 7(3P26.2) MUTATED 199 48.4 (37.5)
DEL PEAK 7(3P26.2) WILD-TYPE 88 38.1 (29.5)

Figure S20.  Get High-res Image Gene #36: 'del_3p26.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p26.2' versus 'RACE'

P value = 0.00013 (Fisher's exact test), Q value = 0.039

Table S21.  Gene #36: 'del_3p26.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 7(3P26.2) MUTATED 2 6 41 282
DEL PEAK 7(3P26.2) WILD-TYPE 0 5 4 159

Figure S21.  Get High-res Image Gene #36: 'del_3p26.2' versus Clinical Feature #13: 'RACE'

'del_3p24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00573 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #37: 'del_3p24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 50 133 99 172
DEL PEAK 8(3P24.1) MUTATED 28 87 78 131
DEL PEAK 8(3P24.1) WILD-TYPE 22 46 21 41

Figure S22.  Get High-res Image Gene #37: 'del_3p24.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p24.1' versus 'GENDER'

P value = 0.00335 (Fisher's exact test), Q value = 0.15

Table S23.  Gene #37: 'del_3p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
DEL PEAK 8(3P24.1) MUTATED 84 279
DEL PEAK 8(3P24.1) WILD-TYPE 55 98

Figure S23.  Get High-res Image Gene #37: 'del_3p24.1' versus Clinical Feature #7: 'GENDER'

'del_3p24.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000201 (Wilcoxon-test), Q value = 0.039

Table S24.  Gene #37: 'del_3p24.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 8(3P24.1) MUTATED 210 49.1 (37.5)
DEL PEAK 8(3P24.1) WILD-TYPE 77 34.8 (26.8)

Figure S24.  Get High-res Image Gene #37: 'del_3p24.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p24.1' versus 'RACE'

P value = 0.00032 (Fisher's exact test), Q value = 0.039

Table S25.  Gene #37: 'del_3p24.1' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 8(3P24.1) MUTATED 1 7 42 301
DEL PEAK 8(3P24.1) WILD-TYPE 1 4 3 140

Figure S25.  Get High-res Image Gene #37: 'del_3p24.1' versus Clinical Feature #13: 'RACE'

'del_3p14.2' versus 'Time to Death'

P value = 0.0107 (logrank test), Q value = 0.24

Table S26.  Gene #38: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
DEL PEAK 9(3P14.2) MUTATED 364 153 0.1 - 211.0 (17.9)
DEL PEAK 9(3P14.2) WILD-TYPE 149 47 0.4 - 169.4 (19.9)

Figure S26.  Get High-res Image Gene #38: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

'del_3p14.2' versus 'GENDER'

P value = 0.00612 (Fisher's exact test), Q value = 0.18

Table S27.  Gene #38: 'del_3p14.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
DEL PEAK 9(3P14.2) MUTATED 86 281
DEL PEAK 9(3P14.2) WILD-TYPE 53 96

Figure S27.  Get High-res Image Gene #38: 'del_3p14.2' versus Clinical Feature #7: 'GENDER'

'del_3p14.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000275 (Wilcoxon-test), Q value = 0.039

Table S28.  Gene #38: 'del_3p14.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 9(3P14.2) MUTATED 214 48.7 (37.3)
DEL PEAK 9(3P14.2) WILD-TYPE 73 35.0 (27.4)

Figure S28.  Get High-res Image Gene #38: 'del_3p14.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p14.2' versus 'RACE'

P value = 0.00343 (Fisher's exact test), Q value = 0.15

Table S29.  Gene #38: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 9(3P14.2) MUTATED 1 7 41 305
DEL PEAK 9(3P14.2) WILD-TYPE 1 4 4 136

Figure S29.  Get High-res Image Gene #38: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

'del_3p12.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000286 (Wilcoxon-test), Q value = 0.039

Table S30.  Gene #39: 'del_3p12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 10(3P12.1) MUTATED 197 48.3 (33.7)
DEL PEAK 10(3P12.1) WILD-TYPE 90 38.6 (38.6)

Figure S30.  Get High-res Image Gene #39: 'del_3p12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_3p12.1' versus 'RACE'

P value = 0.00455 (Fisher's exact test), Q value = 0.16

Table S31.  Gene #39: 'del_3p12.1' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 10(3P12.1) MUTATED 1 7 39 278
DEL PEAK 10(3P12.1) WILD-TYPE 1 4 6 163

Figure S31.  Get High-res Image Gene #39: 'del_3p12.1' versus Clinical Feature #13: 'RACE'

'del_5q12.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00318 (Wilcoxon-test), Q value = 0.15

Table S32.  Gene #44: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 15(5Q12.1) MUTATED 122 51.5 (38.2)
DEL PEAK 15(5Q12.1) WILD-TYPE 165 40.6 (32.7)

Figure S32.  Get High-res Image Gene #44: 'del_5q12.1' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q12.1' versus 'RACE'

P value = 0.00366 (Fisher's exact test), Q value = 0.15

Table S33.  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 45 441
DEL PEAK 15(5Q12.1) MUTATED 1 3 29 171
DEL PEAK 15(5Q12.1) WILD-TYPE 1 8 16 270

Figure S33.  Get High-res Image Gene #44: 'del_5q12.1' versus Clinical Feature #13: 'RACE'

'del_5q15' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00566 (Wilcoxon-test), Q value = 0.17

Table S34.  Gene #45: 'del_5q15' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 16(5Q15) MUTATED 128 50.5 (37.6)
DEL PEAK 16(5Q15) WILD-TYPE 159 41.0 (33.3)

Figure S34.  Get High-res Image Gene #45: 'del_5q15' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q15' versus 'RACE'

P value = 0.0126 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #45: 'del_5q15' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 16(5Q15) MUTATED 1 5 29 180
DEL PEAK 16(5Q15) WILD-TYPE 1 6 16 261

Figure S35.  Get High-res Image Gene #45: 'del_5q15' versus Clinical Feature #13: 'RACE'

'del_5q35.3' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00973 (Wilcoxon-test), Q value = 0.23

Table S36.  Gene #46: 'del_5q35.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 17(5Q35.3) MUTATED 111 49.1 (29.7)
DEL PEAK 17(5Q35.3) WILD-TYPE 176 42.8 (38.6)

Figure S36.  Get High-res Image Gene #46: 'del_5q35.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_8p23.2' versus 'Time to Death'

P value = 0.00751 (logrank test), Q value = 0.2

Table S37.  Gene #50: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
DEL PEAK 21(8P23.2) MUTATED 298 133 0.1 - 180.2 (17.9)
DEL PEAK 21(8P23.2) WILD-TYPE 215 67 0.4 - 211.0 (18.7)

Figure S37.  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 = 0.000279 (Wilcoxon-test), Q value = 0.039

Table S38.  Gene #51: 'del_9p23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 22(9P23) MUTATED 138 50.0 (30.2)
DEL PEAK 22(9P23) WILD-TYPE 149 40.9 (39.4)

Figure S38.  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 = 0.00458 (Wilcoxon-test), Q value = 0.16

Table S39.  Gene #52: 'del_9p21.3' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 23(9P21.3) MUTATED 174 47.5 (29.7)
DEL PEAK 23(9P21.3) WILD-TYPE 113 41.7 (42.9)

Figure S39.  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 = 0.0116 (logrank test), Q value = 0.24

Table S40.  Gene #55: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
DEL PEAK 26(10P15.3) MUTATED 166 78 0.4 - 126.2 (17.9)
DEL PEAK 26(10P15.3) WILD-TYPE 347 122 0.1 - 211.0 (18.8)

Figure S40.  Get High-res Image Gene #55: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p11.21' versus 'RACE'

P value = 0.00901 (Fisher's exact test), Q value = 0.23

Table S41.  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 45 441
DEL PEAK 27(10P11.21) MUTATED 0 5 23 129
DEL PEAK 27(10P11.21) WILD-TYPE 2 6 22 312

Figure S41.  Get High-res Image Gene #56: 'del_10p11.21' versus Clinical Feature #13: 'RACE'

'del_11q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00353 (Wilcoxon-test), Q value = 0.15

Table S42.  Gene #59: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 515 60.9 (12.0)
DEL PEAK 30(11Q23.1) MUTATED 242 59.5 (11.3)
DEL PEAK 30(11Q23.1) WILD-TYPE 273 62.1 (12.4)

Figure S42.  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 = 0.00122 (Fisher's exact test), Q value = 0.094

Table S43.  Gene #59: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 178 66 165 8
DEL PEAK 30(11Q23.1) MUTATED 65 26 93 3
DEL PEAK 30(11Q23.1) WILD-TYPE 113 40 72 5

Figure S43.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.1' versus 'GENDER'

P value = 7.33e-06 (Fisher's exact test), Q value = 0.0079

Table S44.  Gene #59: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 139 377
DEL PEAK 30(11Q23.1) MUTATED 43 200
DEL PEAK 30(11Q23.1) WILD-TYPE 96 177

Figure S44.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

'del_11q23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00048 (Wilcoxon-test), Q value = 0.052

Table S45.  Gene #59: 'del_11q23.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 2.2 (4.3)
DEL PEAK 30(11Q23.1) MUTATED 175 2.8 (5.4)
DEL PEAK 30(11Q23.1) WILD-TYPE 227 1.7 (3.2)

Figure S45.  Get High-res Image Gene #59: 'del_11q23.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_17p11.2' versus 'RACE'

P value = 0.00319 (Fisher's exact test), Q value = 0.15

Table S46.  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 45 441
DEL PEAK 39(17P11.2) MUTATED 0 2 18 74
DEL PEAK 39(17P11.2) WILD-TYPE 2 9 27 367

Figure S46.  Get High-res Image Gene #68: 'del_17p11.2' versus Clinical Feature #13: 'RACE'

'del_17q25.3' versus 'ETHNICITY'

P value = 0.0121 (Fisher's exact test), Q value = 0.24

Table S47.  Gene #69: 'del_17q25.3' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 25 454
DEL PEAK 40(17Q25.3) MUTATED 8 57
DEL PEAK 40(17Q25.3) WILD-TYPE 17 397

Figure S47.  Get High-res Image Gene #69: 'del_17q25.3' versus Clinical Feature #14: 'ETHNICITY'

'del_18q21.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000868 (Wilcoxon-test), Q value = 0.072

Table S48.  Gene #70: 'del_18q21.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 41(18Q21.2) MUTATED 150 51.8 (41.5)
DEL PEAK 41(18Q21.2) WILD-TYPE 137 38.0 (25.8)

Figure S48.  Get High-res Image Gene #70: 'del_18q21.2' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_18q21.2' versus 'RACE'

P value = 0.00276 (Fisher's exact test), Q value = 0.15

Table S49.  Gene #70: 'del_18q21.2' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 41(18Q21.2) MUTATED 2 8 32 211
DEL PEAK 41(18Q21.2) WILD-TYPE 0 3 13 230

Figure S49.  Get High-res Image Gene #70: 'del_18q21.2' versus Clinical Feature #13: 'RACE'

'del_18q23' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00726 (Wilcoxon-test), Q value = 0.2

Table S50.  Gene #71: 'del_18q23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 287 45.2 (35.5)
DEL PEAK 42(18Q23) MUTATED 161 50.3 (40.4)
DEL PEAK 42(18Q23) WILD-TYPE 126 38.7 (26.7)

Figure S50.  Get High-res Image Gene #71: 'del_18q23' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_18q23' versus 'RACE'

P value = 0.00971 (Fisher's exact test), Q value = 0.23

Table S51.  Gene #71: 'del_18q23' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 45 441
DEL PEAK 42(18Q23) MUTATED 2 8 33 230
DEL PEAK 42(18Q23) WILD-TYPE 0 3 12 211

Figure S51.  Get High-res Image Gene #71: 'del_18q23' versus Clinical Feature #13: 'RACE'

'del_19p13.3' versus 'Time to Death'

P value = 0.00465 (logrank test), Q value = 0.16

Table S52.  Gene #72: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 513 200 0.1 - 211.0 (18.0)
DEL PEAK 43(19P13.3) MUTATED 171 78 0.1 - 153.9 (17.0)
DEL PEAK 43(19P13.3) WILD-TYPE 342 122 0.1 - 211.0 (18.8)

Figure S52.  Get High-res Image Gene #72: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_xp22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000809 (Wilcoxon-test), Q value = 0.072

Table S53.  Gene #75: 'del_xp22.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 2.2 (4.3)
DEL PEAK 46(XP22.2) MUTATED 122 3.1 (5.6)
DEL PEAK 46(XP22.2) WILD-TYPE 280 1.8 (3.6)

Figure S53.  Get High-res Image Gene #75: 'del_xp22.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_xp21.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00726 (Wilcoxon-test), Q value = 0.2

Table S54.  Gene #76: 'del_xp21.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 2.2 (4.3)
DEL PEAK 47(XP21.3) MUTATED 125 2.8 (5.3)
DEL PEAK 47(XP21.3) WILD-TYPE 277 1.9 (3.8)

Figure S54.  Get High-res Image Gene #76: 'del_xp21.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_xq21.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00448 (Wilcoxon-test), Q value = 0.16

Table S55.  Gene #77: 'del_xq21.33' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 2.2 (4.3)
DEL PEAK 48(XQ21.33) MUTATED 57 3.7 (7.2)
DEL PEAK 48(XQ21.33) WILD-TYPE 345 1.9 (3.6)

Figure S55.  Get High-res Image Gene #77: '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/15085744/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/15078978/HNSC-TP.merged_data.txt

  • Number of patients = 516

  • Number of significantly focal cnvs = 77

  • 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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