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 68 focal events and 15 clinical features across 515 patients, 19 significant findings detected with Q value < 0.25.

  • amp_1p22.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_6p21.1 cnv correlated to 'RACE'.

  • 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_12q14.1 cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • amp_17q12 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • del_5q31.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_6q11.1 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 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_14q32.12 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • del_15q11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • 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 68 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		COMPLETENESS
OF
RESECTION 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
del 22q13 32 254 (49%) 261 0.777
(0.976) 		0.000533
(0.0999) 		0.86
(0.991) 		0.98
(1.00) 		0.929
(1.00) 		0.538
(0.902) 		0.0425
(0.477) 		0.0708
(0.543) 		0.156
(0.692) 		1
(1.00) 		0.395
(0.854) 		0.00203
(0.188) 		0.883
(1.00) 		0.12
(0.636) 		0.449
(0.879)
amp 1p22 3 141 (27%) 374 0.786
(0.979) 		0.000371
(0.0999) 		0.54
(0.902) 		0.644
(0.939) 		0.0786
(0.547) 		1
(1.00) 		0.921
(1.00) 		0.32
(0.811) 		0.667
(0.939) 		0.808
(0.982) 		0.86
(0.991) 		0.735
(0.964) 		0.698
(0.945) 		0.132
(0.647) 		0.682
(0.939)
amp 6p21 1 190 (37%) 325 0.289
(0.803) 		0.941
(1.00) 		0.62
(0.939) 		0.632
(0.939) 		0.432
(0.87) 		0.2
(0.745) 		0.855
(0.991) 		0.176
(0.702) 		0.161
(0.695) 		0.82
(0.982) 		0.765
(0.973) 		0.471
(0.879) 		0.4
(0.854) 		0.00121
(0.15) 		0.117
(0.628)
amp 7p11 2 271 (53%) 244 0.0425
(0.477) 		0.00871
(0.322) 		0.0693
(0.543) 		0.238
(0.791) 		0.00036
(0.0999) 		1
(1.00) 		0.289
(0.803) 		0.829
(0.982) 		0.0757
(0.547) 		0.662
(0.939) 		0.227
(0.772) 		0.107
(0.611) 		0.894
(1.00) 		0.27
(0.803) 		1
(1.00)
amp 7q31 2 214 (42%) 301 0.938
(1.00) 		0.00318
(0.217) 		0.143
(0.67) 		0.155
(0.689) 		0.0312
(0.448) 		0.403
(0.854) 		0.72
(0.953) 		0.962
(1.00) 		0.147
(0.679) 		0.367
(0.854) 		0.0679
(0.541) 		0.442
(0.872) 		0.533
(0.902) 		0.745
(0.967) 		0.246
(0.796)
amp 8q24 21 321 (62%) 194 0.0881
(0.572) 		0.0232
(0.376) 		0.619
(0.939) 		0.0374
(0.477) 		0.769
(0.974) 		0.518
(0.902) 		0.274
(0.803) 		0.721
(0.953) 		0.00064
(0.0999) 		0.493
(0.899) 		0.389
(0.854) 		0.634
(0.939) 		0.0778
(0.547) 		0.132
(0.647) 		1
(1.00)
amp 12q14 1 168 (33%) 347 0.0567
(0.532) 		0.0407
(0.477) 		0.32
(0.811) 		0.34
(0.829) 		0.628
(0.939) 		0.269
(0.803) 		0.301
(0.806) 		0.534
(0.902) 		0.855
(0.991) 		0.636
(0.939) 		0.971
(1.00) 		0.00417
(0.229) 		0.289
(0.803) 		0.494
(0.899) 		0.438
(0.87)
amp 17q12 226 (44%) 289 0.842
(0.987) 		0.15
(0.684) 		0.534
(0.902) 		0.343
(0.829) 		0.309
(0.808) 		0.536
(0.902) 		0.534
(0.902) 		0.432
(0.87) 		0.116
(0.628) 		0.263
(0.803) 		0.00331
(0.217) 		0.586
(0.934) 		0.155
(0.689) 		0.182
(0.715) 		1
(1.00)
del 5q31 1 207 (40%) 308 0.196
(0.739) 		0.00341
(0.217) 		0.923
(1.00) 		0.914
(1.00) 		0.631
(0.939) 		1
(1.00) 		0.178
(0.704) 		0.282
(0.803) 		0.0705
(0.543) 		1
(1.00) 		0.00644
(0.273) 		0.204
(0.749) 		0.367
(0.854) 		0.0826
(0.562) 		0.0164
(0.336)
del 6q11 1 134 (26%) 381 0.0891
(0.573) 		0.461
(0.879) 		0.00618
(0.273) 		0.89
(1.00) 		0.00277
(0.217) 		0.639
(0.939) 		0.227
(0.772) 		0.401
(0.854) 		0.923
(1.00) 		0.208
(0.756) 		0.217
(0.758) 		0.474
(0.879) 		0.543
(0.902) 		0.828
(0.982) 		0.686
(0.94)
del 9p23 284 (55%) 231 0.0798
(0.547) 		0.421
(0.87) 		0.591
(0.937) 		0.881
(1.00) 		0.00399
(0.229) 		0.682
(0.939) 		0.33
(0.815) 		0.329
(0.815) 		0.704
(0.948) 		1
(1.00) 		0.65
(0.939) 		0.782
(0.977) 		0.378
(0.854) 		0.881
(1.00) 		1
(1.00)
del 9p21 3 290 (56%) 225 0.0931
(0.576) 		0.159
(0.692) 		0.251
(0.803) 		0.75
(0.967) 		0.00426
(0.229) 		0.836
(0.982) 		0.0259
(0.395) 		0.638
(0.939) 		0.6
(0.939) 		0.823
(0.982) 		0.926
(1.00) 		0.669
(0.939) 		0.568
(0.926) 		0.835
(0.982) 		1
(1.00)
del 12p13 2 138 (27%) 377 0.77
(0.974) 		0.679
(0.939) 		0.139
(0.665) 		0.558
(0.914) 		0.639
(0.939) 		0.639
(0.939) 		0.000314
(0.0999) 		0.0855
(0.572) 		0.614
(0.939) 		1
(1.00) 		0.0393
(0.477) 		0.259
(0.803) 		0.453
(0.879) 		0.0617
(0.536) 		0.679
(0.939)
del 13q12 11 293 (57%) 222 0.454
(0.879) 		0.18
(0.71) 		0.981
(1.00) 		0.326
(0.814) 		0.991
(1.00) 		0.835
(0.982) 		0.0744
(0.547) 		0.0945
(0.58) 		0.135
(0.654) 		0.26
(0.803) 		0.00132
(0.15) 		0.306
(0.808) 		0.811
(0.982) 		0.646
(0.939) 		1
(1.00)
del 14q32 12 144 (28%) 371 0.0741
(0.547) 		0.0637
(0.536) 		0.0115
(0.322) 		0.144
(0.673) 		0.00261
(0.217) 		0.368
(0.854) 		0.623
(0.939) 		0.883
(1.00) 		0.733
(0.963) 		0.322
(0.811) 		0.253
(0.803) 		0.0423
(0.477) 		0.106
(0.61) 		0.0215
(0.369) 		1
(1.00)
del 15q11 2 262 (51%) 253 0.674
(0.939) 		0.000685
(0.0999) 		0.275
(0.803) 		0.709
(0.949) 		0.747
(0.967) 		1
(1.00) 		0.378
(0.854) 		0.227
(0.772) 		0.0579
(0.532) 		1
(1.00) 		0.582
(0.933) 		0.391
(0.854) 		0.778
(0.976) 		0.983
(1.00) 		1
(1.00)
del 19p13 2 269 (52%) 246 0.298
(0.806) 		0.0362
(0.477) 		0.199
(0.742) 		0.303
(0.806) 		0.0662
(0.536) 		0.412
(0.863) 		0.00198
(0.188) 		0.326
(0.814) 		0.691
(0.943) 		0.664
(0.939) 		0.858
(0.991) 		0.308
(0.808) 		0.295
(0.806) 		0.966
(1.00) 		0.122
(0.639)
del 21q11 2 185 (36%) 330 0.816
(0.982) 		0.00672
(0.273) 		0.407
(0.858) 		0.241
(0.794) 		0.736
(0.964) 		0.675
(0.939) 		0.118
(0.628) 		0.436
(0.87) 		0.0321
(0.454) 		0.0603
(0.535) 		0.884
(1.00) 		0.000608
(0.0999) 		0.751
(0.967) 		0.03
(0.437) 		0.702
(0.946)
amp 1q21 3 371 (72%) 144 0.536
(0.902) 		0.034
(0.469) 		0.321
(0.811) 		0.574
(0.927) 		0.797
(0.982) 		0.82
(0.982) 		0.116
(0.628) 		1
(1.00) 		0.0227
(0.374) 		0.461
(0.879) 		0.115
(0.628) 		0.172
(0.702) 		0.323
(0.811) 		0.86
(0.991) 		1
(1.00)
amp 3q26 2 170 (33%) 345 0.234
(0.785) 		0.416
(0.868) 		0.794
(0.982) 		0.926
(1.00) 		0.187
(0.715) 		0.268
(0.803) 		0.851
(0.991) 		0.164
(0.695) 		0.471
(0.879) 		0.814
(0.982) 		0.0115
(0.322) 		0.195
(0.738) 		0.298
(0.806) 		0.471
(0.879) 		0.0387
(0.477)
amp 5p15 33 328 (64%) 187 0.386
(0.854) 		0.0123
(0.322) 		0.305
(0.808) 		0.342
(0.829) 		0.216
(0.758) 		0.832
(0.982) 		0.233
(0.785) 		0.0388
(0.477) 		0.216
(0.758) 		0.256
(0.803) 		0.0145
(0.329) 		0.495
(0.899) 		0.697
(0.945) 		0.561
(0.917) 		1
(1.00)
amp 8p11 21 173 (34%) 342 0.153
(0.689) 		0.0555
(0.532) 		0.533
(0.902) 		0.213
(0.758) 		0.271
(0.803) 		1
(1.00) 		0.0247
(0.394) 		0.541
(0.902) 		0.0205
(0.366) 		0.166
(0.695) 		0.524
(0.902) 		0.717
(0.953) 		0.821
(0.982) 		0.8
(0.982) 		0.684
(0.939)
amp 11q13 3 170 (33%) 345 0.21
(0.758) 		0.00512
(0.261) 		0.7
(0.945) 		0.462
(0.879) 		0.65
(0.939) 		0.188
(0.715) 		0.925
(1.00) 		0.38
(0.854) 		0.0588
(0.532) 		0.639
(0.939) 		0.315
(0.808) 		0.38
(0.854) 		1
(1.00) 		0.0632
(0.536) 		1
(1.00)
amp 12p12 1 178 (35%) 337 0.0473
(0.497) 		0.247
(0.796) 		0.137
(0.657) 		0.237
(0.791) 		0.709
(0.949) 		0.129
(0.647) 		0.579
(0.931) 		0.638
(0.939) 		0.48
(0.884) 		0.815
(0.982) 		0.598
(0.939) 		0.314
(0.808) 		0.0651
(0.536) 		0.547
(0.904) 		1
(1.00)
amp 12q15 171 (33%) 344 0.0253
(0.395) 		0.242
(0.796) 		0.445
(0.875) 		0.516
(0.902) 		0.521
(0.902) 		0.511
(0.902) 		0.261
(0.803) 		0.113
(0.628) 		0.832
(0.982) 		0.35
(0.833) 		0.699
(0.945) 		0.0133
(0.329) 		0.225
(0.772) 		0.761
(0.97) 		0.208
(0.756)
amp 14q13 3 228 (44%) 287 0.846
(0.988) 		0.22
(0.762) 		0.628
(0.939) 		0.406
(0.858) 		0.904
(1.00) 		0.834
(0.982) 		0.594
(0.939) 		0.0848
(0.572) 		0.0871
(0.572) 		0.373
(0.854) 		0.354
(0.837) 		0.164
(0.695) 		0.862
(0.992) 		0.428
(0.87) 		0.464
(0.879)
amp 17q23 1 249 (48%) 266 0.563
(0.918) 		0.0905
(0.573) 		0.416
(0.868) 		0.197
(0.74) 		0.184
(0.715) 		0.543
(0.902) 		0.725
(0.955) 		0.14
(0.666) 		0.0147
(0.329) 		1
(1.00) 		0.0113
(0.322) 		0.464
(0.879) 		0.0153
(0.329) 		0.0758
(0.547) 		0.26
(0.803)
amp 18q11 2 103 (20%) 412 0.711
(0.949) 		0.537
(0.902) 		0.093
(0.576) 		0.668
(0.939) 		0.945
(1.00) 		0.44
(0.872) 		0.124
(0.639) 		0.284
(0.803) 		0.157
(0.692) 		0.277
(0.803) 		0.213
(0.758) 		0.783
(0.977) 		0.623
(0.939) 		0.325
(0.814) 		1
(1.00)
amp 19q12 136 (26%) 379 0.4
(0.854) 		0.585
(0.933) 		0.4
(0.854) 		0.463
(0.879) 		0.366
(0.854) 		0.349
(0.833) 		0.0357
(0.477) 		0.105
(0.606) 		0.287
(0.803) 		0.614
(0.939) 		0.0521
(0.526) 		0.321
(0.811) 		0.742
(0.967) 		0.969
(1.00) 		1
(1.00)
amp 20q13 33 243 (47%) 272 0.553
(0.911) 		0.035
(0.476) 		0.0627
(0.536) 		0.133
(0.647) 		0.095
(0.58) 		0.679
(0.939) 		0.93
(1.00) 		0.643
(0.939) 		0.0857
(0.572) 		0.824
(0.982) 		0.0796
(0.547) 		0.867
(0.997) 		0.808
(0.982) 		0.297
(0.806) 		1
(1.00)
amp 22q11 22 88 (17%) 427 0.534
(0.902) 		0.446
(0.875) 		0.0553
(0.532) 		0.281
(0.803) 		0.726
(0.955) 		0.148
(0.682) 		0.162
(0.695) 		0.886
(1.00) 		0.275
(0.803) 		1
(1.00) 		0.757
(0.967) 		0.37
(0.854) 		0.776
(0.976) 		1
(1.00) 		1
(1.00)
amp xq28 157 (30%) 358 0.78
(0.976) 		0.477
(0.882) 		0.997
(1.00) 		0.473
(0.879) 		0.277
(0.803) 		0.503
(0.902) 		0.388
(0.854) 		0.583
(0.933) 		0.384
(0.854) 		0.471
(0.879) 		0.109
(0.619) 		0.961
(1.00) 		0.71
(0.949) 		0.827
(0.982) 		0.678
(0.939)
del 1p36 11 124 (24%) 391 0.126
(0.643) 		0.813
(0.982) 		0.0221
(0.369) 		0.0466
(0.497) 		0.0188
(0.349) 		0.814
(0.982) 		0.216
(0.758) 		0.541
(0.902) 		0.278
(0.803) 		0.607
(0.939) 		0.601
(0.939) 		0.514
(0.902) 		0.872
(1.00) 		0.531
(0.902) 		0.659
(0.939)
del 1p13 1 148 (29%) 367 0.796
(0.982) 		0.0904
(0.573) 		0.0644
(0.536) 		0.19
(0.719) 		0.163
(0.695) 		0.255
(0.803) 		1
(1.00) 		0.408
(0.858) 		0.721
(0.953) 		0.628
(0.939) 		0.924
(1.00) 		0.496
(0.899) 		0.533
(0.902) 		0.31
(0.808) 		0.679
(0.939)
del 2q22 1 46 (9%) 469 0.755
(0.967) 		0.372
(0.854) 		0.675
(0.939) 		0.679
(0.939) 		0.736
(0.964) 		0.254
(0.803) 		0.757
(0.967) 		0.132
(0.647) 		0.629
(0.939) 		0.421
(0.87) 		0.0736
(0.547) 		0.663
(0.939) 		0.92
(1.00) 		0.28
(0.803) 		0.465
(0.879)
del 3p26 2 236 (46%) 279 0.35
(0.833) 		0.109
(0.619) 		0.168
(0.695) 		0.0145
(0.329) 		0.0489
(0.509) 		0.409
(0.858) 		0.86
(0.991) 		0.894
(1.00) 		0.177
(0.702) 		0.51
(0.902) 		0.723
(0.953) 		0.0419
(0.477) 		0.282
(0.803) 		0.29
(0.803) 		0.0569
(0.532)
del 3p21 31 245 (48%) 270 0.514
(0.902) 		0.0398
(0.477) 		0.302
(0.806) 		0.0122
(0.322) 		0.00695
(0.273) 		0.837
(0.982) 		0.426
(0.87) 		0.719
(0.953) 		0.219
(0.759) 		1
(1.00) 		0.886
(1.00) 		0.0154
(0.329) 		0.293
(0.805) 		0.574
(0.927) 		0.722
(0.953)
del 3q11 1 140 (27%) 375 0.0973
(0.591) 		0.122
(0.639) 		0.642
(0.939) 		0.531
(0.902) 		0.213
(0.758) 		1
(1.00) 		0.552
(0.911) 		0.442
(0.872) 		0.744
(0.967) 		1
(1.00) 		0.066
(0.536) 		0.184
(0.715) 		0.853
(0.991) 		0.616
(0.939) 		0.679
(0.939)
del 3q29 135 (26%) 380 0.383
(0.854) 		0.81
(0.982) 		0.897
(1.00) 		0.788
(0.98) 		0.775
(0.976) 		0.247
(0.796) 		1
(1.00) 		0.553
(0.911) 		0.571
(0.927) 		0.614
(0.939) 		0.17
(0.696) 		0.473
(0.879) 		0.293
(0.805) 		0.346
(0.829) 		0.681
(0.939)
del 4p16 3 130 (25%) 385 0.154
(0.689) 		0.0798
(0.547) 		0.924
(1.00) 		0.819
(0.982) 		0.643
(0.939) 		1
(1.00) 		1
(1.00) 		0.0272
(0.408) 		0.157
(0.692) 		0.798
(0.982) 		0.0414
(0.477) 		0.259
(0.803) 		0.488
(0.894) 		0.706
(0.949) 		0.371
(0.854)
del 4q34 3 187 (36%) 328 0.47
(0.879) 		0.0508
(0.518) 		0.556
(0.913) 		0.387
(0.854) 		0.0989
(0.593) 		0.834
(0.982) 		0.168
(0.695) 		0.746
(0.967) 		0.117
(0.628) 		0.163
(0.695) 		0.323
(0.811) 		0.0537
(0.532) 		0.818
(0.982) 		0.5
(0.902) 		0.104
(0.606)
del 5q12 1 176 (34%) 339 0.315
(0.808) 		0.0184
(0.347) 		0.939
(1.00) 		0.697
(0.945) 		0.201
(0.745) 		1
(1.00) 		0.402
(0.854) 		0.402
(0.854) 		0.0219
(0.369) 		0.647
(0.939) 		0.00694
(0.273) 		0.442
(0.872) 		0.63
(0.939) 		0.125
(0.642) 		0.0443
(0.481)
del 6q22 31 251 (49%) 264 0.699
(0.945) 		0.437
(0.87) 		0.203
(0.748) 		0.423
(0.87) 		0.402
(0.854) 		0.837
(0.982) 		0.218
(0.758) 		0.694
(0.945) 		0.626
(0.939) 		0.507
(0.902) 		0.0622
(0.536) 		0.186
(0.715) 		0.384
(0.854) 		0.753
(0.967) 		0.266
(0.803)
del 6q26 256 (50%) 259 0.934
(1.00) 		0.527
(0.902) 		0.671
(0.939) 		0.758
(0.967) 		0.46
(0.879) 		0.309
(0.808) 		0.427
(0.87) 		0.836
(0.982) 		0.288
(0.803) 		0.274
(0.803) 		0.353
(0.837) 		0.164
(0.695) 		0.206
(0.752) 		0.797
(0.982) 		0.281
(0.803)
del 8p23 2 256 (50%) 259 0.273
(0.803) 		0.238
(0.791) 		0.537
(0.902) 		0.428
(0.87) 		1
(1.00) 		0.408
(0.858) 		0.034
(0.469) 		0.579
(0.931) 		0.0613
(0.536) 		0.827
(0.982) 		0.62
(0.939) 		0.675
(0.939) 		0.603
(0.939) 		0.625
(0.939) 		0.124
(0.639)
del 8p11 21 122 (24%) 393 0.934
(1.00) 		0.955
(1.00) 		0.366
(0.854) 		0.276
(0.803) 		0.591
(0.937) 		0.808
(0.982) 		0.00926
(0.322) 		0.313
(0.808) 		0.3
(0.806) 		0.795
(0.982) 		0.998
(1.00) 		0.502
(0.902) 		0.0592
(0.532) 		0.0591
(0.532) 		1
(1.00)
del 9q21 11 256 (50%) 259 0.457
(0.879) 		0.666
(0.939) 		0.779
(0.976) 		0.419
(0.87) 		0.665
(0.939) 		0.535
(0.902) 		0.537
(0.902) 		0.683
(0.939) 		0.223
(0.768) 		0.373
(0.854) 		0.141
(0.666) 		0.335
(0.819) 		0.903
(1.00) 		0.574
(0.927) 		1
(1.00)
del 10p15 3 126 (24%) 389 0.0366
(0.477) 		0.971
(1.00) 		0.474
(0.879) 		0.57
(0.927) 		0.239
(0.792) 		0.622
(0.939) 		0.0102
(0.322) 		0.38
(0.854) 		0.253
(0.803) 		1
(1.00) 		0.4
(0.854) 		0.743
(0.967) 		0.98
(1.00) 		0.289
(0.803) 		0.0779
(0.547)
del 10q26 3 156 (30%) 359 0.317
(0.81) 		0.174
(0.702) 		0.648
(0.939) 		0.151
(0.684) 		0.897
(1.00) 		0.266
(0.803) 		0.103
(0.605) 		0.772
(0.976) 		0.233
(0.785) 		0.145
(0.673) 		0.184
(0.715) 		0.98
(1.00) 		0.314
(0.808) 		0.187
(0.715) 		0.202
(0.748)
del 11p15 5 143 (28%) 372 0.745
(0.967) 		0.0104
(0.322) 		0.333
(0.819) 		0.43
(0.87) 		0.75
(0.967) 		0.36
(0.85) 		0.0178
(0.343) 		0.784
(0.977) 		0.233
(0.785) 		0.807
(0.982) 		0.333
(0.819) 		0.011
(0.322) 		0.512
(0.902) 		0.533
(0.902) 		0.434
(0.87)
del 11q23 2 119 (23%) 396 0.545
(0.902) 		0.752
(0.967) 		0.484
(0.889) 		0.97
(1.00) 		0.622
(0.939) 		0.639
(0.939) 		0.0472
(0.497) 		0.527
(0.902) 		0.81
(0.982) 		0.434
(0.87) 		0.963
(1.00) 		0.176
(0.702) 		0.777
(0.976) 		0.767
(0.973) 		1
(1.00)
del 11q25 116 (23%) 399 0.957
(1.00) 		0.931
(1.00) 		0.311
(0.808) 		0.88
(1.00) 		0.074
(0.547) 		1
(1.00) 		0.0443
(0.481) 		0.291
(0.803) 		0.648
(0.939) 		0.436
(0.87) 		0.592
(0.937) 		0.462
(0.879) 		0.811
(0.982) 		0.642
(0.939) 		1
(1.00)
del 12q12 98 (19%) 417 0.276
(0.803) 		0.258
(0.803) 		0.511
(0.902) 		0.845
(0.988) 		0.431
(0.87) 		0.78
(0.976) 		0.092
(0.576) 		0.665
(0.939) 		0.992
(1.00) 		0.395
(0.854) 		0.0713
(0.543) 		0.708
(0.949) 		0.616
(0.939) 		0.883
(1.00) 		0.653
(0.939)
del 12q24 33 137 (27%) 378 0.211
(0.758) 		0.174
(0.702) 		0.313
(0.808) 		0.292
(0.804) 		0.37
(0.854) 		1
(1.00) 		0.134
(0.65) 		0.188
(0.715) 		0.889
(1.00) 		0.0798
(0.547) 		0.0528
(0.528) 		0.629
(0.939) 		0.817
(0.982) 		0.058
(0.532) 		1
(1.00)
del 13q12 13 292 (57%) 223 0.615
(0.939) 		0.269
(0.803) 		0.968
(1.00) 		0.544
(0.902) 		1
(1.00) 		0.836
(0.982) 		0.13
(0.647) 		0.103
(0.605) 		0.0987
(0.593) 		0.114
(0.628) 		0.0153
(0.329) 		0.315
(0.808) 		0.813
(0.982) 		0.66
(0.939) 		1
(1.00)
del 13q14 2 281 (55%) 234 0.86
(0.991) 		0.246
(0.796) 		0.967
(1.00) 		0.396
(0.854) 		0.648
(0.939) 		0.68
(0.939) 		0.929
(1.00) 		0.501
(0.902) 		0.493
(0.899) 		1
(1.00) 		0.0709
(0.543) 		0.744
(0.967) 		0.986
(1.00) 		0.766
(0.973) 		0.471
(0.879)
del 13q34 242 (47%) 273 0.9
(1.00) 		0.269
(0.803) 		0.937
(1.00) 		0.401
(0.854) 		0.929
(1.00) 		1
(1.00) 		1
(1.00) 		0.342
(0.829) 		0.48
(0.884) 		0.824
(0.982) 		0.147
(0.679) 		0.606
(0.939) 		0.487
(0.893) 		0.112
(0.628) 		0.715
(0.953)
del 15q15 1 274 (53%) 241 0.951
(1.00) 		0.00552
(0.268) 		0.4
(0.854) 		0.812
(0.982) 		0.643
(0.939) 		0.679
(0.939) 		0.659
(0.939) 		0.14
(0.666) 		0.021
(0.369) 		0.506
(0.902) 		0.151
(0.684) 		0.625
(0.939) 		1
(1.00) 		1
(1.00) 		0.0569
(0.532)
del 16q23 1 169 (33%) 346 0.749
(0.967) 		0.275
(0.803) 		0.289
(0.803) 		0.301
(0.806) 		0.376
(0.854) 		1
(1.00) 		0.573
(0.927) 		0.541
(0.902) 		0.698
(0.945) 		0.346
(0.829) 		0.557
(0.913) 		0.757
(0.967) 		0.618
(0.939) 		0.167
(0.695) 		0.04
(0.477)
del 17p13 3 281 (55%) 234 0.69
(0.943) 		0.0672
(0.54) 		0.675
(0.939) 		0.159
(0.692) 		0.913
(1.00) 		0.835
(0.982) 		0.0918
(0.576) 		0.266
(0.803) 		0.0369
(0.477) 		0.371
(0.854) 		0.169
(0.695) 		0.0126
(0.322) 		0.473
(0.879) 		0.981
(1.00) 		0.454
(0.879)
del 18q21 32 251 (49%) 264 0.0195
(0.355) 		0.0595
(0.532) 		0.0112
(0.322) 		0.328
(0.815) 		0.0122
(0.322) 		0.538
(0.902) 		0.426
(0.87) 		0.457
(0.879) 		0.246
(0.796) 		0.377
(0.854) 		0.835
(0.982) 		0.103
(0.606) 		0.0155
(0.329) 		0.61
(0.939) 		0.717
(0.953)
del 19p13 3 282 (55%) 233 0.0782
(0.547) 		0.0896
(0.573) 		0.346
(0.829) 		0.0653
(0.536) 		0.0996
(0.594) 		0.536
(0.902) 		0.0168
(0.336) 		0.504
(0.902) 		0.422
(0.87) 		0.371
(0.854) 		0.302
(0.806) 		0.13
(0.647) 		0.422
(0.87) 		0.455
(0.879) 		0.0177
(0.343)
del 19p13 2 279 (54%) 236 0.123
(0.639) 		0.0698
(0.543) 		0.244
(0.796) 		0.244
(0.796) 		0.0874
(0.572) 		0.538
(0.902) 		0.0166
(0.336) 		0.616
(0.939) 		0.475
(0.88) 		0.271
(0.803) 		0.847
(0.988) 		0.335
(0.819) 		0.514
(0.902) 		1
(1.00) 		0.129
(0.647)
del 19q11 134 (26%) 381 0.29
(0.803) 		0.0257
(0.395) 		0.453
(0.879) 		0.424
(0.87) 		0.587
(0.934) 		0.645
(0.939) 		0.616
(0.939) 		0.0751
(0.547) 		0.31
(0.808) 		0.614
(0.939) 		0.993
(1.00) 		0.295
(0.806) 		0.961
(1.00) 		0.0499
(0.514) 		1
(1.00)
del 19q13 33 194 (38%) 321 0.395
(0.854) 		0.534
(0.902) 		0.611
(0.939) 		0.584
(0.933) 		0.445
(0.875) 		0.403
(0.854) 		0.525
(0.902) 		0.168
(0.695) 		0.218
(0.758) 		0.819
(0.982) 		0.991
(1.00) 		0.85
(0.991) 		0.528
(0.902) 		0.582
(0.933) 		1
(1.00)
del 20p13 131 (25%) 384 0.344
(0.829) 		0.764
(0.973) 		0.118
(0.628) 		0.496
(0.899) 		0.0865
(0.572) 		0.82
(0.982) 		0.0431
(0.478) 		0.169
(0.695) 		0.341
(0.829) 		1
(1.00) 		0.429
(0.87) 		0.175
(0.702) 		0.52
(0.902) 		0.697
(0.945) 		0.683
(0.939)
del 20q13 12 80 (16%) 435 0.469
(0.879) 		0.431
(0.87) 		0.266
(0.803) 		0.362
(0.853) 		0.11
(0.622) 		0.175
(0.702) 		0.33
(0.815) 		0.395
(0.854) 		0.118
(0.628) 		0.757
(0.967) 		0.00953
(0.322) 		0.654
(0.939) 		0.603
(0.939) 		0.662
(0.939) 		0.259
(0.803)
del xp22 2 143 (28%) 372 0.689
(0.943) 		0.382
(0.854) 		0.534
(0.902) 		0.875
(1.00) 		0.131
(0.647) 		1
(1.00) 		0.0299
(0.437) 		0.97
(1.00) 		0.387
(0.854) 		0.461
(0.879) 		0.663
(0.939) 		0.215
(0.758) 		0.927
(1.00) 		0.388
(0.854) 		0.68
(0.939)
'amp_1p22.3' versus 'YEARS_TO_BIRTH'

P value = 0.000371 (Wilcoxon-test), Q value = 0.1

Table S1.  Gene #1: 'amp_1p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
AMP PEAK 1(1P22.3) MUTATED 134 62.6 (10.2)
AMP PEAK 1(1P22.3) WILD-TYPE 350 66.3 (9.8)

Figure S1.  Get High-res Image Gene #1: 'amp_1p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_6p21.1' versus 'RACE'

P value = 0.00121 (Fisher's exact test), Q value = 0.15

Table S2.  Gene #5: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 7 51 389
AMP PEAK 5(6P21.1) MUTATED 1 5 10 159
AMP PEAK 5(6P21.1) WILD-TYPE 0 2 41 230

Figure S2.  Get High-res Image Gene #5: 'amp_6p21.1' versus Clinical Feature #14: 'RACE'

'amp_7p11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00036 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 332 96 76
AMP PEAK 6(7P11.2) MUTATED 158 51 55
AMP PEAK 6(7P11.2) WILD-TYPE 174 45 21

Figure S3.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 0.00318 (Wilcoxon-test), Q value = 0.22

Table S4.  Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
AMP PEAK 7(7Q31.2) MUTATED 202 63.7 (10.0)
AMP PEAK 7(7Q31.2) WILD-TYPE 282 66.3 (9.9)

Figure S4.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00064 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #9: 'amp_8q24.21' versus Clinical Feature #9: '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 19 107 319 5 19 2 3 2 23 1 5 10
AMP PEAK 9(8Q24.21) MUTATED 13 62 210 1 11 1 2 0 16 1 4 0
AMP PEAK 9(8Q24.21) WILD-TYPE 6 45 109 4 8 1 1 2 7 0 1 10

Figure S5.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12q14.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00417 (Wilcoxon-test), Q value = 0.23

Table S6.  Gene #12: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 276 1965.0 (12.6)
AMP PEAK 12(12Q14.1) MUTATED 91 1967.9 (12.5)
AMP PEAK 12(12Q14.1) WILD-TYPE 185 1963.6 (12.4)

Figure S6.  Get High-res Image Gene #12: 'amp_12q14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q12' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00331 (Wilcoxon-test), Q value = 0.22

Table S7.  Gene #15: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 355 41.6 (27.3)
AMP PEAK 15(17Q12) MUTATED 151 46.6 (29.3)
AMP PEAK 15(17Q12) WILD-TYPE 204 37.9 (25.2)

Figure S7.  Get High-res Image Gene #15: 'amp_17q12' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_5q31.1' versus 'YEARS_TO_BIRTH'

P value = 0.00341 (Wilcoxon-test), Q value = 0.22

Table S8.  Gene #32: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
DEL PEAK 11(5Q31.1) MUTATED 197 63.4 (10.5)
DEL PEAK 11(5Q31.1) WILD-TYPE 287 66.5 (9.5)

Figure S8.  Get High-res Image Gene #32: 'del_5q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q11.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00277 (Fisher's exact test), Q value = 0.22

Table S9.  Gene #33: 'del_6q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 332 96 76
DEL PEAK 12(6Q11.1) MUTATED 75 26 32
DEL PEAK 12(6Q11.1) WILD-TYPE 257 70 44

Figure S9.  Get High-res Image Gene #33: 'del_6q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00399 (Fisher's exact test), Q value = 0.23

Table S10.  Gene #38: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 332 96 76
DEL PEAK 17(9P23) MUTATED 169 67 43
DEL PEAK 17(9P23) WILD-TYPE 163 29 33

Figure S10.  Get High-res Image Gene #38: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00426 (Fisher's exact test), Q value = 0.23

Table S11.  Gene #39: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 332 96 76
DEL PEAK 18(9P21.3) MUTATED 173 68 45
DEL PEAK 18(9P21.3) WILD-TYPE 159 28 31

Figure S11.  Get High-res Image Gene #39: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_12p13.2' versus 'GENDER'

P value = 0.000314 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #46: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 275 240
DEL PEAK 25(12P13.2) MUTATED 92 46
DEL PEAK 25(12P13.2) WILD-TYPE 183 194

Figure S12.  Get High-res Image Gene #46: 'del_12p13.2' versus Clinical Feature #7: 'GENDER'

'del_13q12.11' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00132 (Wilcoxon-test), Q value = 0.15

Table S13.  Gene #49: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 355 41.6 (27.3)
DEL PEAK 28(13Q12.11) MUTATED 195 45.6 (28.5)
DEL PEAK 28(13Q12.11) WILD-TYPE 160 36.8 (25.1)

Figure S13.  Get High-res Image Gene #49: 'del_13q12.11' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_14q32.12' versus 'PATHOLOGY_N_STAGE'

P value = 0.00261 (Fisher's exact test), Q value = 0.22

Table S14.  Gene #53: 'del_14q32.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 332 96 76
DEL PEAK 32(14Q32.12) MUTATED 79 40 24
DEL PEAK 32(14Q32.12) WILD-TYPE 253 56 52

Figure S14.  Get High-res Image Gene #53: 'del_14q32.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.000685 (Wilcoxon-test), Q value = 0.1

Table S15.  Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
DEL PEAK 33(15Q11.2) MUTATED 243 63.7 (10.5)
DEL PEAK 33(15Q11.2) WILD-TYPE 241 66.8 (9.3)

Figure S15.  Get High-res Image Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19p13.2' versus 'GENDER'

P value = 0.00198 (Fisher's exact test), Q value = 0.19

Table S16.  Gene #61: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 275 240
DEL PEAK 40(19P13.2) MUTATED 126 143
DEL PEAK 40(19P13.2) WILD-TYPE 149 97

Figure S16.  Get High-res Image Gene #61: 'del_19p13.2' versus Clinical Feature #7: 'GENDER'

'del_21q11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.000608 (Wilcoxon-test), Q value = 0.1

Table S17.  Gene #66: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 276 1965.0 (12.6)
DEL PEAK 45(21Q11.2) MUTATED 102 1968.5 (13.2)
DEL PEAK 45(21Q11.2) WILD-TYPE 174 1963.0 (11.7)

Figure S17.  Get High-res Image Gene #66: 'del_21q11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 0.000533 (Wilcoxon-test), Q value = 0.1

Table S18.  Gene #67: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
DEL PEAK 46(22Q13.32) MUTATED 242 63.8 (9.8)
DEL PEAK 46(22Q13.32) WILD-TYPE 242 66.7 (10.0)

Figure S18.  Get High-res Image Gene #67: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00203 (Wilcoxon-test), Q value = 0.19

Table S19.  Gene #67: 'del_22q13.32' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 276 1965.0 (12.6)
DEL PEAK 46(22Q13.32) MUTATED 147 1967.2 (12.7)
DEL PEAK 46(22Q13.32) WILD-TYPE 129 1962.6 (12.0)

Figure S19.  Get High-res Image Gene #67: '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/15092520/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/15084450/LUAD-TP.merged_data.txt

  • Number of patients = 515

  • Number of significantly focal cnvs = 68

  • 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.

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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