Correlation between copy number variation genes (focal events) and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TM79J8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TM79J8
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 75 focal events and 15 clinical features across 516 patients, 25 significant findings detected with Q value < 0.25.

  • amp_5p15.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_5p13.1 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • amp_6p21.1 cnv correlated to 'RACE'.

  • amp_7p21.1 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_7p11.2 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_7q31.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_8q24.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11q13.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_12q14.1 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • amp_13q33.3 cnv correlated to 'PATHOLOGIC_STAGE'.

  • amp_17q12 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_2q22.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_3p21.31 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • del_5q31.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_9p23 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_9p21.3 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_12p13.2 cnv correlated to 'GENDER'.

  • del_13q12.11 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_15q11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_15q15.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_18q23 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_19p13.2 cnv correlated to 'GENDER'.

  • del_21q11.2 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • del_22q13.32 cnv correlated to 'YEARS_TO_BIRTH' and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 25 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 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RESIDUAL
TUMOR 		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 Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
del 22q13 32 250 (48%) 266 0.863
(1.00) 		0.000596
(0.157) 		0.856
(1.00) 		0.988
(1.00) 		0.964
(1.00) 		0.536
(0.899) 		0.0424
(0.426) 		0.333
(0.829) 		0.0109
(0.283) 		0.15
(0.666) 		0.545
(0.901) 		0.00166
(0.181) 		0.852
(1.00) 		0.221
(0.769) 		0.721
(0.957)
amp 5p15 33 333 (65%) 183 0.193
(0.723) 		0.00361
(0.19) 		0.42
(0.862) 		0.301
(0.807) 		0.361
(0.845) 		0.83
(1.00) 		0.31
(0.822) 		0.665
(0.944) 		0.83
(1.00) 		0.152
(0.669) 		0.0407
(0.418) 		0.264
(0.79) 		0.719
(0.957) 		0.64
(0.944) 		1
(1.00)
amp 5p13 1 304 (59%) 212 0.0665
(0.524) 		0.0143
(0.314) 		0.162
(0.69) 		0.195
(0.726) 		0.861
(1.00) 		0.676
(0.944) 		0.37
(0.845) 		0.575
(0.924) 		0.979
(1.00) 		0.0743
(0.533) 		0.00364
(0.19) 		0.376
(0.85) 		0.391
(0.862) 		0.774
(0.987) 		0.251
(0.79)
amp 6p21 1 189 (37%) 327 0.303
(0.807) 		0.922
(1.00) 		0.694
(0.944) 		0.642
(0.944) 		0.458
(0.875) 		0.297
(0.807) 		0.855
(1.00) 		1
(1.00) 		0.181
(0.715) 		0.205
(0.746) 		0.979
(1.00) 		0.342
(0.838) 		0.509
(0.899) 		0.00103
(0.166) 		0.439
(0.87)
amp 7p21 1 284 (55%) 232 0.0572
(0.491) 		0.0918
(0.588) 		0.0996
(0.588) 		0.37
(0.845) 		0.00251
(0.185) 		0.679
(0.944) 		0.479
(0.885) 		0.89
(1.00) 		0.736
(0.966) 		0.205
(0.746) 		0.116
(0.622) 		0.174
(0.705) 		0.432
(0.866) 		0.141
(0.648) 		0.704
(0.953)
amp 7p11 2 274 (53%) 242 0.0111
(0.283) 		0.00818
(0.274) 		0.0721
(0.531) 		0.281
(0.796) 		0.00066
(0.157) 		1
(1.00) 		0.289
(0.802) 		0.782
(0.988) 		0.323
(0.829) 		0.0409
(0.418) 		0.13
(0.625) 		0.0929
(0.588) 		0.886
(1.00) 		0.25
(0.79) 		1
(1.00)
amp 7q31 2 218 (42%) 298 0.492
(0.894) 		0.00178
(0.181) 		0.194
(0.723) 		0.163
(0.69) 		0.0445
(0.435) 		0.528
(0.899) 		0.789
(0.99) 		0.78
(0.988) 		0.651
(0.944) 		0.0903
(0.588) 		0.0708
(0.528) 		0.822
(1.00) 		0.608
(0.935) 		0.926
(1.00) 		0.146
(0.661)
amp 8q24 21 325 (63%) 191 0.029
(0.397) 		0.0149
(0.317) 		0.48
(0.885) 		0.0145
(0.314) 		0.854
(1.00) 		0.519
(0.899) 		0.523
(0.899) 		1
(1.00) 		0.357
(0.842) 		0.00084
(0.157) 		0.255
(0.79) 		0.6
(0.933) 		0.231
(0.782) 		0.134
(0.634) 		0.708
(0.955)
amp 11q13 3 172 (33%) 344 0.279
(0.793) 		0.00356
(0.19) 		0.839
(1.00) 		0.467
(0.875) 		0.66
(0.944) 		0.386
(0.862) 		1
(1.00) 		0.555
(0.914) 		0.908
(1.00) 		0.0206
(0.336) 		0.298
(0.807) 		0.344
(0.838) 		0.929
(1.00) 		0.0939
(0.588) 		0.691
(0.944)
amp 12q14 1 169 (33%) 347 0.0382
(0.409) 		0.0331
(0.397) 		0.327
(0.829) 		0.386
(0.862) 		0.659
(0.944) 		0.272
(0.79) 		0.347
(0.838) 		0.884
(1.00) 		0.415
(0.862) 		0.865
(1.00) 		0.991
(1.00) 		0.00125
(0.176) 		0.329
(0.829) 		0.594
(0.931) 		0.682
(0.944)
amp 13q33 3 76 (15%) 440 0.687
(0.944) 		0.721
(0.957) 		0.0028
(0.185) 		0.153
(0.671) 		0.516
(0.899) 		0.0386
(0.409) 		0.32
(0.829) 		0.0798
(0.551) 		0.993
(1.00) 		0.937
(1.00) 		0.1
(0.588) 		0.576
(0.924) 		0.114
(0.622) 		0.668
(0.944) 		0.257
(0.79)
amp 17q12 227 (44%) 289 0.574
(0.924) 		0.13
(0.625) 		0.322
(0.829) 		0.218
(0.762) 		0.322
(0.829) 		0.537
(0.899) 		0.477
(0.885) 		0.406
(0.862) 		0.0222
(0.345) 		0.104
(0.588) 		0.00401
(0.196) 		0.539
(0.899) 		0.162
(0.69) 		0.166
(0.694) 		1
(1.00)
del 2q22 1 46 (9%) 470 0.412
(0.862) 		0.35
(0.839) 		0.593
(0.931) 		0.466
(0.875) 		0.761
(0.978) 		0.26
(0.79) 		1
(1.00) 		0.633
(0.944) 		0.00518
(0.233) 		0.789
(0.99) 		0.156
(0.676) 		0.418
(0.862) 		0.854
(1.00) 		0.239
(0.789) 		0.463
(0.875)
del 3p21 31 248 (48%) 268 0.598
(0.931) 		0.0227
(0.345) 		0.33
(0.829) 		0.0094
(0.274) 		0.00921
(0.274) 		0.838
(1.00) 		0.428
(0.865) 		0.782
(0.988) 		0.855
(1.00) 		0.162
(0.69) 		0.838
(1.00) 		0.00225
(0.181) 		0.215
(0.76) 		0.557
(0.915) 		1
(1.00)
del 5q31 1 211 (41%) 305 0.0802
(0.551) 		0.00214
(0.181) 		0.956
(1.00) 		0.879
(1.00) 		0.691
(0.944) 		1
(1.00) 		0.243
(0.789) 		0.889
(1.00) 		0.977
(1.00) 		0.0485
(0.456) 		0.02
(0.336) 		0.0803
(0.551) 		0.388
(0.862) 		0.0727
(0.531) 		0.119
(0.622)
del 9p23 287 (56%) 229 0.126
(0.622) 		0.515
(0.899) 		0.62
(0.942) 		0.881
(1.00) 		0.00276
(0.185) 		0.835
(1.00) 		0.33
(0.829) 		0.128
(0.625) 		0.0833
(0.561) 		0.723
(0.957) 		0.591
(0.931) 		0.835
(1.00) 		0.468
(0.875) 		0.851
(1.00) 		1
(1.00)
del 9p21 3 294 (57%) 222 0.0774
(0.548) 		0.253
(0.79) 		0.277
(0.793) 		0.677
(0.944) 		0.00361
(0.19) 		1
(1.00) 		0.0205
(0.336) 		0.33
(0.829) 		0.261
(0.79) 		0.597
(0.931) 		0.899
(1.00) 		0.611
(0.936) 		0.689
(0.944) 		0.807
(0.997) 		1
(1.00)
del 12p13 2 140 (27%) 376 0.356
(0.842) 		0.824
(1.00) 		0.124
(0.622) 		0.526
(0.899) 		0.596
(0.931) 		0.638
(0.944) 		0.000344
(0.157) 		0.757
(0.978) 		0.605
(0.933) 		0.663
(0.944) 		0.0263
(0.376) 		0.263
(0.79) 		0.581
(0.929) 		0.0997
(0.588) 		1
(1.00)
del 13q12 11 293 (57%) 223 0.744
(0.97) 		0.174
(0.705) 		0.992
(1.00) 		0.384
(0.862) 		0.954
(1.00) 		0.683
(0.944) 		0.0616
(0.509) 		0.675
(0.944) 		0.806
(0.997) 		0.129
(0.625) 		0.000645
(0.157) 		0.232
(0.783) 		0.939
(1.00) 		0.697
(0.945) 		0.466
(0.875)
del 15q11 2 263 (51%) 253 0.369
(0.845) 		0.000795
(0.157) 		0.226
(0.777) 		0.539
(0.899) 		0.594
(0.931) 		1
(1.00) 		0.29
(0.802) 		0.333
(0.829) 		0.417
(0.862) 		0.0337
(0.397) 		0.759
(0.978) 		0.268
(0.79) 		0.611
(0.936) 		0.936
(1.00) 		1
(1.00)
del 15q15 1 275 (53%) 241 0.894
(1.00) 		0.0044
(0.206) 		0.262
(0.79) 		0.603
(0.933) 		0.407
(0.862) 		0.679
(0.944) 		0.791
(0.99) 		0.214
(0.758) 		0.138
(0.646) 		0.00934
(0.274) 		0.118
(0.622) 		0.442
(0.871) 		1
(1.00) 		0.743
(0.969) 		0.712
(0.955)
del 18q23 249 (48%) 267 0.255
(0.79) 		0.0367
(0.409) 		0.00371
(0.19) 		0.179
(0.715) 		0.00824
(0.274) 		0.839
(1.00) 		0.185
(0.717) 		0.581
(0.929) 		0.982
(1.00) 		0.0981
(0.588) 		0.52
(0.899) 		0.0458
(0.44) 		0.0752
(0.535) 		0.679
(0.944) 		0.272
(0.79)
del 19p13 2 269 (52%) 247 0.515
(0.899) 		0.0291
(0.397) 		0.125
(0.622) 		0.358
(0.842) 		0.0621
(0.51) 		0.413
(0.862) 		0.00196
(0.181) 		1
(1.00) 		0.522
(0.899) 		0.722
(0.957) 		0.907
(1.00) 		0.237
(0.789) 		0.168
(0.695) 		0.983
(1.00) 		0.449
(0.872)
del 21q11 2 179 (35%) 337 0.957
(1.00) 		0.0134
(0.309) 		0.726
(0.957) 		0.302
(0.807) 		0.843
(1.00) 		0.831
(1.00) 		0.115
(0.622) 		0.193
(0.723) 		0.0393
(0.409) 		0.0313
(0.397) 		0.408
(0.862) 		0.0021
(0.181) 		0.73
(0.962) 		0.0915
(0.588) 		1
(1.00)
amp 1p34 3 137 (27%) 379 0.29
(0.802) 		0.0123
(0.295) 		0.349
(0.839) 		0.468
(0.875) 		0.083
(0.561) 		0.815
(1) 		0.272
(0.79) 		0.537
(0.899) 		0.815
(1) 		0.802
(0.995) 		0.877
(1.00) 		0.242
(0.789) 		0.121
(0.622) 		0.762
(0.978) 		1
(1.00)
amp 1q21 3 377 (73%) 139 0.784
(0.988) 		0.0102
(0.274) 		0.278
(0.793) 		0.558
(0.915) 		0.824
(1.00) 		1
(1.00) 		0.197
(0.729) 		0.641
(0.944) 		0.746
(0.97) 		0.032
(0.397) 		0.295
(0.803) 		0.376
(0.85) 		0.328
(0.829) 		0.781
(0.988) 		1
(1.00)
amp 3q26 2 169 (33%) 347 0.113
(0.622) 		0.357
(0.842) 		0.717
(0.957) 		0.936
(1.00) 		0.187
(0.722) 		0.19
(0.723) 		0.925
(1.00) 		1
(1.00) 		0.432
(0.866) 		0.527
(0.899) 		0.00679
(0.274) 		0.179
(0.715) 		0.317
(0.829) 		0.515
(0.899) 		0.217
(0.762)
amp 4q12 96 (19%) 420 0.528
(0.899) 		0.0102
(0.274) 		0.064
(0.517) 		0.347
(0.838) 		0.197
(0.729) 		0.604
(0.933) 		0.65
(0.944) 		0.483
(0.886) 		0.373
(0.848) 		0.223
(0.774) 		0.306
(0.814) 		0.12
(0.622) 		0.544
(0.901) 		0.0781
(0.549) 		0.116
(0.622)
amp 5q35 1 126 (24%) 390 0.0815
(0.556) 		0.567
(0.922) 		0.155
(0.676) 		0.0703
(0.528) 		0.988
(1.00) 		0.81
(0.999) 		0.124
(0.622) 		0.263
(0.79) 		0.981
(1.00) 		0.643
(0.944) 		0.582
(0.929) 		0.14
(0.648) 		0.645
(0.944) 		0.753
(0.976) 		0.199
(0.734)
amp 8p11 21 175 (34%) 341 0.689
(0.944) 		0.0506
(0.466) 		0.527
(0.899) 		0.263
(0.79) 		0.267
(0.79) 		0.831
(1.00) 		0.0324
(0.397) 		0.0797
(0.551) 		0.671
(0.944) 		0.0264
(0.376) 		0.565
(0.921) 		0.902
(1.00) 		0.857
(1.00) 		0.724
(0.957) 		0.686
(0.944)
amp 10p15 1 142 (28%) 374 0.54
(0.899) 		0.0315
(0.397) 		0.661
(0.944) 		0.259
(0.79) 		0.0571
(0.491) 		0.822
(1.00) 		0.00752
(0.274) 		0.646
(0.944) 		0.449
(0.872) 		0.367
(0.845) 		0.06
(0.509) 		0.609
(0.935) 		0.632
(0.944) 		0.0674
(0.524) 		0.372
(0.847)
amp 12p12 1 178 (34%) 338 0.0168
(0.321) 		0.25
(0.79) 		0.105
(0.588) 		0.291
(0.802) 		0.681
(0.944) 		0.129
(0.625) 		0.711
(0.955) 		0.885
(1.00) 		0.978
(1.00) 		0.507
(0.899) 		0.429
(0.866) 		0.269
(0.79) 		0.0643
(0.517) 		0.499
(0.898) 		1
(1.00)
amp 12q15 169 (33%) 347 0.0183
(0.321) 		0.327
(0.829) 		0.328
(0.829) 		0.467
(0.875) 		0.463
(0.875) 		0.511
(0.899) 		0.259
(0.79) 		0.884
(1.00) 		0.347
(0.838) 		0.873
(1.00) 		0.994
(1.00) 		0.00955
(0.274) 		0.212
(0.756) 		0.877
(1.00) 		0.439
(0.87)
amp 14q13 3 233 (45%) 283 0.539
(0.899) 		0.0613
(0.509) 		0.617
(0.941) 		0.207
(0.746) 		0.965
(1.00) 		1
(1.00) 		0.595
(0.931) 		1
(1.00) 		0.0343
(0.397) 		0.103
(0.588) 		0.231
(0.782) 		0.0304
(0.397) 		0.801
(0.995) 		0.441
(0.871) 		0.457
(0.875)
amp 16p11 2 167 (32%) 349 0.841
(1.00) 		0.135
(0.634) 		0.487
(0.892) 		0.346
(0.838) 		0.779
(0.988) 		0.267
(0.79) 		0.397
(0.862) 		0.769
(0.982) 		0.515
(0.899) 		0.277
(0.793) 		0.3
(0.807) 		0.609
(0.935) 		0.592
(0.931) 		0.547
(0.901) 		1
(1.00)
amp 17q23 1 249 (48%) 267 0.165
(0.692) 		0.0968
(0.588) 		0.269
(0.79) 		0.182
(0.715) 		0.177
(0.711) 		0.542
(0.9) 		0.791
(0.99) 		0.679
(0.944) 		0.0226
(0.345) 		0.0122
(0.295) 		0.0177
(0.321) 		0.488
(0.892) 		0.0189
(0.327) 		0.0615
(0.509) 		0.258
(0.79)
amp 18q11 2 105 (20%) 411 0.857
(1.00) 		0.419
(0.862) 		0.15
(0.666) 		0.71
(0.955) 		0.946
(1.00) 		0.438
(0.87) 		0.126
(0.622) 		0.496
(0.896) 		0.903
(1.00) 		0.0989
(0.588) 		0.407
(0.862) 		0.634
(0.944) 		0.667
(0.944) 		0.332
(0.829) 		1
(1.00)
amp 19q12 139 (27%) 377 0.302
(0.807) 		0.46
(0.875) 		0.483
(0.886) 		0.538
(0.899) 		0.403
(0.862) 		0.353
(0.842) 		0.0733
(0.532) 		1
(1.00) 		0.316
(0.829) 		0.404
(0.862) 		0.0889
(0.585) 		0.16
(0.688) 		0.826
(1.00) 		0.939
(1.00) 		1
(1.00)
amp 20p11 21 201 (39%) 315 0.638
(0.944) 		0.206
(0.746) 		0.053
(0.477) 		0.109
(0.609) 		0.00886
(0.274) 		1
(1.00) 		0.528
(0.899) 		0.778
(0.988) 		0.225
(0.777) 		0.0676
(0.524) 		0.0963
(0.588) 		0.465
(0.875) 		0.618
(0.941) 		0.108
(0.607) 		0.708
(0.955)
amp 20q13 33 251 (49%) 265 0.426
(0.865) 		0.0163
(0.321) 		0.0231
(0.347) 		0.104
(0.588) 		0.043
(0.428) 		0.537
(0.899) 		0.93
(1.00) 		1
(1.00) 		0.3
(0.807) 		0.0279
(0.393) 		0.19
(0.723) 		0.533
(0.899) 		0.665
(0.944) 		0.254
(0.79) 		1
(1.00)
amp 22q11 22 90 (17%) 426 0.283
(0.796) 		0.493
(0.894) 		0.0906
(0.588) 		0.327
(0.829) 		0.764
(0.98) 		0.15
(0.666) 		0.13
(0.625) 		0.717
(0.957) 		0.351
(0.839) 		0.243
(0.789) 		0.772
(0.986) 		0.571
(0.924) 		0.898
(1.00) 		1
(1.00) 		1
(1.00)
amp xq28 159 (31%) 357 0.603
(0.933) 		0.412
(0.862) 		0.996
(1.00) 		0.561
(0.917) 		0.289
(0.802) 		0.509
(0.899) 		0.446
(0.871) 		0.88
(1.00) 		0.46
(0.875) 		0.355
(0.842) 		0.24
(0.789) 		0.892
(1.00) 		0.515
(0.899) 		0.808
(0.998) 		0.678
(0.944)
del 1p36 13 122 (24%) 394 0.311
(0.822) 		0.869
(1.00) 		0.0724
(0.531) 		0.121
(0.622) 		0.0335
(0.397) 		0.812
(1) 		0.0967
(0.588) 		0.748
(0.97) 		0.134
(0.634) 		0.169
(0.696) 		0.758
(0.978) 		0.496
(0.896) 		0.649
(0.944) 		0.687
(0.944) 		1
(1.00)
del 1p13 1 151 (29%) 365 0.587
(0.931) 		0.147
(0.662) 		0.0692
(0.528) 		0.243
(0.789) 		0.182
(0.715) 		0.264
(0.79) 		0.846
(1.00) 		0.291
(0.802) 		0.974
(1.00) 		0.716
(0.957) 		0.911
(1.00) 		0.639
(0.944) 		0.453
(0.875) 		0.445
(0.871) 		0.678
(0.944)
del 3p26 2 233 (45%) 283 0.586
(0.931) 		0.126
(0.622) 		0.124
(0.622) 		0.0198
(0.336) 		0.035
(0.397) 		0.407
(0.862) 		0.791
(0.99) 		0.489
(0.892) 		0.917
(1.00) 		0.173
(0.705) 		0.802
(0.995) 		0.021
(0.338) 		0.209
(0.75) 		0.421
(0.862) 		0.709
(0.955)
del 3q11 1 141 (27%) 375 0.242
(0.789) 		0.0867
(0.574) 		0.742
(0.969) 		0.489
(0.892) 		0.23
(0.782) 		1
(1.00) 		0.49
(0.892) 		0.879
(1.00) 		0.395
(0.862) 		0.785
(0.988) 		0.0566
(0.491) 		0.129
(0.625) 		0.859
(1.00) 		0.589
(0.931) 		0.679
(0.944)
del 3q29 136 (26%) 380 0.663
(0.944) 		0.872
(1.00) 		0.856
(1.00) 		0.731
(0.962) 		0.821
(1.00) 		0.247
(0.79) 		0.92
(1.00) 		1
(1.00) 		0.528
(0.899) 		0.582
(0.929) 		0.165
(0.692) 		0.361
(0.845) 		0.334
(0.829) 		0.327
(0.829) 		0.68
(0.944)
del 4p16 3 130 (25%) 386 0.345
(0.838) 		0.1
(0.588) 		0.963
(1.00) 		0.766
(0.98) 		0.628
(0.944) 		1
(1.00) 		1
(1.00) 		0.637
(0.944) 		0.0101
(0.274) 		0.163
(0.69) 		0.0375
(0.409) 		0.234
(0.787) 		0.497
(0.896) 		0.756
(0.978) 		0.682
(0.944)
del 4q22 1 158 (31%) 358 0.689
(0.944) 		0.456
(0.875) 		0.606
(0.934) 		0.69
(0.944) 		0.0168
(0.321) 		0.824
(1.00) 		1
(1.00) 		0.0521
(0.477) 		0.0322
(0.397) 		0.185
(0.717) 		0.534
(0.899) 		0.154
(0.673) 		0.505
(0.899) 		0.448
(0.872) 		1
(1.00)
del 4q34 3 187 (36%) 329 0.545
(0.901) 		0.0633
(0.516) 		0.411
(0.862) 		0.42
(0.862) 		0.0991
(0.588) 		0.834
(1.00) 		0.2
(0.736) 		0.0323
(0.397) 		0.754
(0.977) 		0.122
(0.622) 		0.459
(0.875) 		0.0682
(0.525) 		0.803
(0.995) 		0.438
(0.87) 		0.104
(0.588)
del 5q12 1 179 (35%) 337 0.172
(0.704) 		0.022
(0.345) 		0.968
(1.00) 		0.658
(0.944) 		0.22
(0.769) 		1
(1.00) 		0.517
(0.899) 		0.885
(1.00) 		0.602
(0.933) 		0.0171
(0.321) 		0.0122
(0.295) 		0.41
(0.862) 		0.414
(0.862) 		0.114
(0.622) 		0.00721
(0.274)
del 6q14 3 253 (49%) 263 0.697
(0.945) 		0.133
(0.634) 		0.314
(0.829) 		0.947
(1.00) 		0.473
(0.881) 		1
(1.00) 		0.48
(0.885) 		0.407
(0.862) 		0.843
(1.00) 		0.816
(1) 		0.226
(0.777) 		0.0173
(0.321) 		0.615
(0.939) 		0.575
(0.924) 		0.279
(0.793)
del 6q26 258 (50%) 258 0.961
(1.00) 		0.501
(0.899) 		0.689
(0.944) 		0.725
(0.957) 		0.532
(0.899) 		0.408
(0.862) 		0.427
(0.865) 		0.784
(0.988) 		0.625
(0.944) 		0.253
(0.79) 		0.466
(0.875) 		0.139
(0.647) 		0.255
(0.79) 		0.743
(0.969) 		0.0675
(0.524)
del 8p23 2 254 (49%) 262 0.615
(0.939) 		0.512
(0.899) 		0.792
(0.99) 		0.461
(0.875) 		0.938
(1.00) 		0.681
(0.944) 		0.0344
(0.397) 		0.679
(0.944) 		0.852
(1.00) 		0.0499
(0.464) 		0.386
(0.862) 		0.856
(1.00) 		0.547
(0.901) 		0.172
(0.704) 		0.45
(0.872)
del 8p11 21 125 (24%) 391 0.879
(1.00) 		0.83
(1.00) 		0.503
(0.899) 		0.302
(0.807) 		0.725
(0.957) 		1
(1.00) 		0.0135
(0.309) 		0.344
(0.838) 		0.264
(0.79) 		0.27
(0.79) 		0.957
(1.00) 		0.251
(0.79) 		0.0864
(0.574) 		0.0672
(0.524) 		1
(1.00)
del 9q21 11 258 (50%) 258 0.894
(1.00) 		0.648
(0.944) 		0.857
(1.00) 		0.436
(0.87) 		0.68
(0.944) 		0.413
(0.862) 		0.659
(0.944) 		0.89
(1.00) 		0.347
(0.838) 		0.205
(0.746) 		0.231
(0.782) 		0.235
(0.788) 		0.918
(1.00) 		0.567
(0.922) 		1
(1.00)
del 10p15 3 131 (25%) 385 0.0569
(0.491) 		0.813
(1) 		0.506
(0.899) 		0.84
(1.00) 		0.328
(0.829) 		0.333
(0.829) 		0.033
(0.397) 		0.641
(0.944) 		0.182
(0.715) 		0.317
(0.829) 		0.397
(0.862) 		0.592
(0.931) 		0.98
(1.00) 		0.712
(0.955) 		0.392
(0.862)
del 10q26 3 148 (29%) 368 0.324
(0.829) 		0.474
(0.882) 		0.86
(1.00) 		0.164
(0.69) 		0.978
(1.00) 		0.366
(0.845) 		0.0972
(0.588) 		0.444
(0.871) 		0.816
(1) 		0.414
(0.862) 		0.102
(0.588) 		0.423
(0.864) 		0.279
(0.793) 		0.157
(0.678) 		0.398
(0.862)
del 11p15 5 143 (28%) 373 0.797
(0.995) 		0.0155
(0.321) 		0.282
(0.796) 		0.416
(0.862) 		0.738
(0.967) 		0.359
(0.843) 		0.0178
(0.321) 		0.0944
(0.588) 		0.78
(0.988) 		0.241
(0.789) 		0.294
(0.803) 		0.0255
(0.373) 		0.444
(0.871) 		0.569
(0.923) 		0.432
(0.866)
del 11q23 1 120 (23%) 396 0.822
(1.00) 		0.747
(0.97) 		0.645
(0.944) 		0.968
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.0604
(0.509) 		1
(1.00) 		0.852
(1.00) 		0.871
(1.00) 		0.908
(1.00) 		0.115
(0.622) 		0.63
(0.944) 		0.803
(0.995) 		1
(1.00)
del 11q25 115 (22%) 401 0.646
(0.944) 		0.828
(1.00) 		0.357
(0.842) 		0.964
(1.00) 		0.19
(0.723) 		1
(1.00) 		0.0448
(0.435) 		0.867
(1.00) 		0.693
(0.944) 		0.696
(0.945) 		0.388
(0.862) 		0.481
(0.885) 		0.747
(0.97) 		0.664
(0.944) 		1
(1.00)
del 12q12 99 (19%) 417 0.285
(0.799) 		0.266
(0.79) 		0.433
(0.868) 		0.851
(1.00) 		0.434
(0.868) 		0.78
(0.988) 		0.0741
(0.533) 		0.603
(0.933) 		0.267
(0.79) 		0.987
(1.00) 		0.0565
(0.491) 		0.591
(0.931) 		0.766
(0.98) 		0.92
(1.00) 		0.654
(0.944)
del 12q24 33 133 (26%) 383 0.956
(1.00) 		0.394
(0.862) 		0.341
(0.838) 		0.362
(0.845) 		0.293
(0.803) 		1
(1.00) 		0.0339
(0.397) 		0.876
(1.00) 		0.8
(0.995) 		0.919
(1.00) 		0.104
(0.588) 		0.423
(0.864) 		0.735
(0.966) 		0.0998
(0.588) 		0.679
(0.944)
del 13q34 241 (47%) 275 0.761
(0.978) 		0.229
(0.782) 		0.962
(1.00) 		0.513
(0.899) 		0.887
(1.00) 		1
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.893
(1.00) 		0.516
(0.899) 		0.143
(0.658) 		0.426
(0.865) 		0.533
(0.899) 		0.0945
(0.588) 		1
(1.00)
del 14q32 33 150 (29%) 366 0.417
(0.862) 		0.249
(0.79) 		0.0393
(0.409) 		0.116
(0.622) 		0.00964
(0.274) 		0.366
(0.845) 		0.56
(0.917) 		0.366
(0.845) 		0.0528
(0.477) 		0.541
(0.9) 		0.215
(0.76) 		0.0541
(0.483) 		0.263
(0.79) 		0.0445
(0.435) 		0.432
(0.866)
del 16p13 3 111 (22%) 405 0.803
(0.995) 		0.125
(0.622) 		0.119
(0.622) 		0.41
(0.862) 		0.631
(0.944) 		0.445
(0.871) 		0.52
(0.899) 		0.739
(0.967) 		0.516
(0.899) 		0.588
(0.931) 		0.664
(0.944) 		0.0696
(0.528) 		0.32
(0.829) 		0.407
(0.862) 		0.168
(0.695)
del 16q23 1 169 (33%) 347 0.574
(0.924) 		0.292
(0.802) 		0.395
(0.862) 		0.39
(0.862) 		0.369
(0.845) 		1
(1.00) 		0.707
(0.955) 		0.884
(1.00) 		0.562
(0.917) 		0.653
(0.944) 		0.574
(0.924) 		0.639
(0.944) 		0.829
(1.00) 		0.255
(0.79) 		0.0391
(0.409)
del 16q24 3 188 (36%) 328 0.716
(0.957) 		0.0348
(0.397) 		0.211
(0.756) 		0.633
(0.944) 		0.278
(0.793) 		0.674
(0.944) 		0.927
(1.00) 		1
(1.00) 		0.123
(0.622) 		0.634
(0.944) 		0.397
(0.862) 		0.597
(0.931) 		0.971
(1.00) 		0.652
(0.944) 		0.104
(0.588)
del 17p13 3 281 (54%) 235 0.404
(0.862) 		0.0386
(0.409) 		0.725
(0.957) 		0.144
(0.659) 		0.837
(1.00) 		0.68
(0.944) 		0.184
(0.717) 		0.212
(0.756) 		0.668
(0.944) 		0.00869
(0.274) 		0.267
(0.79) 		0.00725
(0.274) 		0.247
(0.79) 		0.965
(1.00) 		0.454
(0.875)
del 18q21 32 255 (49%) 261 0.119
(0.622) 		0.0367
(0.409) 		0.0141
(0.314) 		0.291
(0.802) 		0.0181
(0.321) 		0.679
(0.944) 		0.333
(0.829) 		1
(1.00) 		0.778
(0.988) 		0.238
(0.789) 		0.544
(0.901) 		0.0465
(0.443) 		0.0297
(0.397) 		0.658
(0.944) 		0.282
(0.796)
del 19p13 3 276 (53%) 240 0.18
(0.715) 		0.189
(0.723) 		0.126
(0.622) 		0.0947
(0.588) 		0.0487
(0.456) 		0.532
(0.899) 		0.0171
(0.321) 		1
(1.00) 		0.594
(0.931) 		0.513
(0.899) 		0.406
(0.862) 		0.206
(0.746) 		0.408
(0.862) 		0.368
(0.845) 		0.455
(0.875)
del 19q13 33 195 (38%) 321 0.678
(0.944) 		0.452
(0.875) 		0.529
(0.899) 		0.445
(0.871) 		0.471
(0.879) 		0.407
(0.862) 		0.363
(0.845) 		0.569
(0.923) 		0.939
(1.00) 		0.193
(0.723) 		0.843
(1.00) 		0.691
(0.944) 		0.479
(0.885) 		0.531
(0.899) 		1
(1.00)
del 20p13 130 (25%) 386 0.318
(0.829) 		0.889
(1.00) 		0.0862
(0.574) 		0.496
(0.896) 		0.07
(0.528) 		1
(1.00) 		0.0418
(0.424) 		0.528
(0.899) 		0.139
(0.647) 		0.349
(0.839) 		0.295
(0.803) 		0.243
(0.789) 		0.394
(0.862) 		0.693
(0.944) 		0.684
(0.944)
del 20q13 12 82 (16%) 434 0.184
(0.717) 		0.427
(0.865) 		0.147
(0.662) 		0.369
(0.845) 		0.145
(0.659) 		0.192
(0.723) 		0.336
(0.831) 		1
(1.00) 		0.275
(0.793) 		0.237
(0.789) 		0.00703
(0.274) 		0.374
(0.848) 		0.635
(0.944) 		0.354
(0.842) 		0.271
(0.79)
del xp22 2 145 (28%) 371 0.52
(0.899) 		0.339
(0.837) 		0.411
(0.862) 		0.872
(1.00) 		0.15
(0.666) 		1
(1.00) 		0.0243
(0.36) 		0.64
(0.944) 		0.939
(1.00) 		0.334
(0.829) 		0.408
(0.862) 		0.175
(0.708) 		0.981
(1.00) 		0.462
(0.875) 		0.679
(0.944)
'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00361 (Wilcoxon-test), Q value = 0.19

Table S1.  Gene #5: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
AMP PEAK 5(5P15.33) MUTATED 312 64.2 (10.2)
AMP PEAK 5(5P15.33) WILD-TYPE 173 67.1 (9.5)

Figure S1.  Get High-res Image Gene #5: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p13.1' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00364 (Wilcoxon-test), Q value = 0.19

Table S2.  Gene #6: 'amp_5p13.1' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
AMP PEAK 6(5P13.1) MUTATED 209 45.1 (28.3)
AMP PEAK 6(5P13.1) WILD-TYPE 145 37.2 (24.7)

Figure S2.  Get High-res Image Gene #6: 'amp_5p13.1' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'amp_6p21.1' versus 'RACE'

P value = 0.00103 (Fisher's exact test), Q value = 0.17

Table S3.  Gene #8: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 7 52 390
AMP PEAK 8(6P21.1) MUTATED 1 5 10 158
AMP PEAK 8(6P21.1) WILD-TYPE 0 2 42 232

Figure S3.  Get High-res Image Gene #8: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'

'amp_7p21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00251 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #9: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
AMP PEAK 9(7P21.1) MUTATED 169 52 55
AMP PEAK 9(7P21.1) WILD-TYPE 164 44 21

Figure S4.  Get High-res Image Gene #9: 'amp_7p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7p11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00066 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #10: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
AMP PEAK 10(7P11.2) MUTATED 160 51 55
AMP PEAK 10(7P11.2) WILD-TYPE 173 45 21

Figure S5.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 0.00178 (Wilcoxon-test), Q value = 0.18

Table S6.  Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
AMP PEAK 11(7Q31.2) MUTATED 206 63.7 (9.9)
AMP PEAK 11(7Q31.2) WILD-TYPE 279 66.4 (10.0)

Figure S6.  Get High-res Image Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00084 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #13: 'amp_8q24.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA LUNG SIGNET RING ADENOCARCINOMA LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
ALL 18 107 321 5 19 2 3 2 23 1 5 10
AMP PEAK 13(8Q24.21) MUTATED 12 65 213 1 11 1 2 0 15 1 4 0
AMP PEAK 13(8Q24.21) WILD-TYPE 6 42 108 4 8 1 1 2 8 0 1 10

Figure S7.  Get High-res Image Gene #13: 'amp_8q24.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_11q13.3' versus 'YEARS_TO_BIRTH'

P value = 0.00356 (Wilcoxon-test), Q value = 0.19

Table S8.  Gene #15: 'amp_11q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
AMP PEAK 15(11Q13.3) MUTATED 163 63.3 (10.0)
AMP PEAK 15(11Q13.3) WILD-TYPE 322 66.2 (9.9)

Figure S8.  Get High-res Image Gene #15: 'amp_11q13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00125 (Wilcoxon-test), Q value = 0.18

Table S9.  Gene #17: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 277 1965.0 (12.5)
AMP PEAK 17(12Q14.1) MUTATED 92 1968.3 (12.7)
AMP PEAK 17(12Q14.1) WILD-TYPE 185 1963.4 (12.2)

Figure S9.  Get High-res Image Gene #17: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_13q33.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0028 (Fisher's exact test), Q value = 0.19

Table S10.  Gene #19: 'amp_13q33.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
ALL 5 133 139 1 50 72 72 11 25
AMP PEAK 19(13Q33.3) MUTATED 2 12 22 0 13 6 7 3 8
AMP PEAK 19(13Q33.3) WILD-TYPE 3 121 117 1 37 66 65 8 17

Figure S10.  Get High-res Image Gene #19: 'amp_13q33.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q12' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00401 (Wilcoxon-test), Q value = 0.2

Table S11.  Gene #22: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
AMP PEAK 22(17Q12) MUTATED 152 46.7 (29.2)
AMP PEAK 22(17Q12) WILD-TYPE 202 38.2 (25.0)

Figure S11.  Get High-res Image Gene #22: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_2q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00518 (Wilcoxon-test), Q value = 0.23

Table S12.  Gene #32: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 137 78.8 (28.3)
DEL PEAK 3(2Q22.1) MUTATED 15 62.7 (31.7)
DEL PEAK 3(2Q22.1) WILD-TYPE 122 80.8 (27.4)

Figure S12.  Get High-res Image Gene #32: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.31' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00225 (Wilcoxon-test), Q value = 0.18

Table S13.  Gene #34: 'del_3p21.31' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 277 1965.0 (12.5)
DEL PEAK 5(3P21.31) MUTATED 134 1967.5 (12.8)
DEL PEAK 5(3P21.31) WILD-TYPE 143 1962.7 (11.9)

Figure S13.  Get High-res Image Gene #34: 'del_3p21.31' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_5q31.1' versus 'YEARS_TO_BIRTH'

P value = 0.00214 (Wilcoxon-test), Q value = 0.18

Table S14.  Gene #41: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
DEL PEAK 12(5Q31.1) MUTATED 201 63.4 (10.4)
DEL PEAK 12(5Q31.1) WILD-TYPE 284 66.5 (9.5)

Figure S14.  Get High-res Image Gene #41: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00276 (Fisher's exact test), Q value = 0.19

Table S15.  Gene #46: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
DEL PEAK 17(9P23) MUTATED 171 68 43
DEL PEAK 17(9P23) WILD-TYPE 162 28 33

Figure S15.  Get High-res Image Gene #46: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00361 (Fisher's exact test), Q value = 0.19

Table S16.  Gene #47: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
DEL PEAK 18(9P21.3) MUTATED 176 69 45
DEL PEAK 18(9P21.3) WILD-TYPE 157 27 31

Figure S16.  Get High-res Image Gene #47: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_12p13.2' versus 'GENDER'

P value = 0.000344 (Fisher's exact test), Q value = 0.16

Table S17.  Gene #54: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 276 240
DEL PEAK 25(12P13.2) MUTATED 93 47
DEL PEAK 25(12P13.2) WILD-TYPE 183 193

Figure S17.  Get High-res Image Gene #54: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'

'del_13q12.11' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000645 (Wilcoxon-test), Q value = 0.16

Table S18.  Gene #57: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
DEL PEAK 28(13Q12.11) MUTATED 193 46.0 (28.3)
DEL PEAK 28(13Q12.11) WILD-TYPE 161 36.8 (24.9)

Figure S18.  Get High-res Image Gene #57: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_15q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.000795 (Wilcoxon-test), Q value = 0.16

Table S19.  Gene #60: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
DEL PEAK 31(15Q11.2) MUTATED 244 63.7 (10.4)
DEL PEAK 31(15Q11.2) WILD-TYPE 241 66.8 (9.4)

Figure S19.  Get High-res Image Gene #60: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q15.1' versus 'YEARS_TO_BIRTH'

P value = 0.0044 (Wilcoxon-test), Q value = 0.21

Table S20.  Gene #61: 'del_15q15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
DEL PEAK 32(15Q15.1) MUTATED 256 64.1 (10.2)
DEL PEAK 32(15Q15.1) WILD-TYPE 229 66.5 (9.7)

Figure S20.  Get High-res Image Gene #61: 'del_15q15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'PATHOLOGIC_STAGE'

P value = 0.00371 (Fisher's exact test), Q value = 0.19

Table S21.  Gene #67: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
ALL 5 133 139 1 50 72 72 11 25
DEL PEAK 38(18Q23) MUTATED 0 52 66 1 30 47 34 5 12
DEL PEAK 38(18Q23) WILD-TYPE 5 81 73 0 20 25 38 6 13

Figure S21.  Get High-res Image Gene #67: 'del_18q23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19p13.2' versus 'GENDER'

P value = 0.00196 (Fisher's exact test), Q value = 0.18

Table S22.  Gene #69: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 276 240
DEL PEAK 40(19P13.2) MUTATED 126 143
DEL PEAK 40(19P13.2) WILD-TYPE 150 97

Figure S22.  Get High-res Image Gene #69: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'

'del_21q11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0021 (Wilcoxon-test), Q value = 0.18

Table S23.  Gene #73: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 277 1965.0 (12.5)
DEL PEAK 44(21Q11.2) MUTATED 99 1968.2 (13.0)
DEL PEAK 44(21Q11.2) WILD-TYPE 178 1963.3 (12.0)

Figure S23.  Get High-res Image Gene #73: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 0.000596 (Wilcoxon-test), Q value = 0.16

Table S24.  Gene #74: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
DEL PEAK 45(22Q13.32) MUTATED 238 63.7 (9.9)
DEL PEAK 45(22Q13.32) WILD-TYPE 247 66.7 (10.0)

Figure S24.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00166 (Wilcoxon-test), Q value = 0.18

Table S25.  Gene #74: 'del_22q13.32' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 277 1965.0 (12.5)
DEL PEAK 45(22Q13.32) MUTATED 144 1967.3 (12.7)
DEL PEAK 45(22Q13.32) WILD-TYPE 133 1962.6 (11.9)

Figure S25.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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/LUAD-TP/22531212/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/22506767/LUAD-TP.merged_data.txt

  • Number of patients = 516

  • Number of significantly focal cnvs = 75

  • Number of selected clinical features = 15

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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