Correlation between copy number variation genes (focal events) and selected clinical features
Stomach and Esophageal carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C189155B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C189155B
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 99 focal events and 12 clinical features across 625 patients, 65 significant findings detected with Q value < 0.25.

  • amp_1p36.22 cnv correlated to 'GENDER'.

  • amp_1p34.2 cnv correlated to 'RADIATION_THERAPY'.

  • amp_1q42.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_2q12.2 cnv correlated to 'PATHOLOGIC_STAGE'.

  • amp_3q26.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'RACE'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_5p13.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_6q21 cnv correlated to 'Time to Death'.

  • amp_7p22.3 cnv correlated to 'GENDER'.

  • amp_7p11.2 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.

  • amp_7q21.2 cnv correlated to 'GENDER'.

  • amp_8p23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • amp_12p12.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_14q13.3 cnv correlated to 'GENDER'.

  • amp_17q12 cnv correlated to 'PATHOLOGY_M_STAGE',  'GENDER', and 'RACE'.

  • amp_20q13.2 cnv correlated to 'GENDER'.

  • del_4p16.3 cnv correlated to 'GENDER'.

  • del_4q34.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.

  • del_7q31.1 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'GENDER'.

  • del_7q36.3 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_8p23.2 cnv correlated to 'GENDER'.

  • del_9p21.3 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • del_9q21.11 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

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

  • del_10p11.21 cnv correlated to 'PATHOLOGY_T_STAGE' and 'RACE'.

  • del_10q21.1 cnv correlated to 'RACE'.

  • del_10q22.3 cnv correlated to 'RACE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_11p15.5 cnv correlated to 'GENDER' and 'RADIATION_THERAPY'.

  • del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_13q12.11 cnv correlated to 'GENDER'.

  • del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'GENDER',  'RADIATION_THERAPY', and 'RACE'.

  • del_13q21.31 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'RADIATION_THERAPY'.

  • del_14q32.32 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_15q11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_16p13.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_17p12 cnv correlated to 'GENDER'.

  • del_18q12.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_18q21.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_19p13.3 cnv correlated to 'GENDER'.

  • del_22q11.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_xp22.2 cnv correlated to 'GENDER'.

  • del_xp21.1 cnv correlated to 'GENDER'.

  • del_xp11.3 cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 99 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 65 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 		NUMBER
PACK
YEARS
SMOKED 		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 Wilcoxon-test Fisher's exact test Fisher's exact test
del 13q14 2 125 (20%) 500 0.987
(1.00) 		0.00395
(0.144) 		4e-05
(0.0155) 		0.0033
(0.14) 		0.00959
(0.215) 		0.146
(0.575) 		0.00208
(0.11) 		0.0136
(0.249) 		0.0905
(0.495) 		0.305
(0.739) 		0.00933
(0.213) 		1
(1.00)
del 7q31 1 127 (20%) 498 0.248
(0.702) 		0.0412
(0.387) 		0.00092
(0.0729) 		0.00549
(0.166) 		0.00877
(0.209) 		0.304
(0.739) 		0.0015
(0.0992) 		0.898
(1.00) 		1
(1.00) 		0.105
(0.529) 		0.364
(0.781) 		0.699
(0.951)
amp 17q12 222 (36%) 403 0.279
(0.724) 		0.444
(0.821) 		0.0492
(0.433) 		0.716
(0.954) 		0.776
(0.969) 		0.00809
(0.209) 		0.00448
(0.152) 		0.325
(0.748) 		0.691
(0.944) 		0.221
(0.68) 		0.0131
(0.249) 		1
(1.00)
del 9p21 3 334 (53%) 291 0.518
(0.859) 		0.887
(1.00) 		0.0115
(0.24) 		0.00203
(0.11) 		0.105
(0.529) 		0.87
(1.00) 		0.0037
(0.142) 		0.0943
(0.509) 		0.171
(0.611) 		0.25
(0.704) 		0.215
(0.668) 		0.221
(0.68)
del 13q21 31 126 (20%) 499 0.914
(1.00) 		0.0811
(0.465) 		0.0122
(0.245) 		0.0132
(0.249) 		0.318
(0.742) 		0.147
(0.575) 		0.0286
(0.34) 		0.00471
(0.155) 		0.163
(0.6) 		0.57
(0.879) 		0.0519
(0.443) 		0.445
(0.821)
amp 3q26 2 287 (46%) 338 0.986
(1.00) 		0.0146
(0.259) 		0.00664
(0.183) 		0.968
(1.00) 		0.688
(0.944) 		0.739
(0.957) 		0.0647
(0.447) 		0.0158
(0.261) 		0.197
(0.651) 		0.0964
(0.515) 		0.00134
(0.0936) 		0.0655
(0.447)
amp 7p11 2 340 (54%) 285 0.433
(0.818) 		0.0742
(0.455) 		0.2
(0.655) 		0.0113
(0.24) 		0.947
(1.00) 		0.183
(0.631) 		0.00372
(0.142) 		0.347
(0.766) 		0.535
(0.866) 		0.506
(0.852) 		0.0656
(0.447) 		1
(1.00)
amp 8p23 1 229 (37%) 396 0.406
(0.796) 		0.00428
(0.15) 		0.408
(0.796) 		0.38
(0.787) 		0.746
(0.957) 		1
(1.00) 		0.00055
(0.0683) 		0.663
(0.932) 		0.444
(0.821) 		0.279
(0.724) 		0.44
(0.821) 		0.532
(0.864)
del 4q34 3 300 (48%) 325 0.136
(0.565) 		0.0102
(0.221) 		0.00631
(0.178) 		0.179
(0.625) 		0.484
(0.837) 		0.32
(0.742) 		0.54
(0.869) 		0.465
(0.827) 		0.924
(1.00) 		0.881
(1.00) 		0.85
(1.00) 		1
(1.00)
del 10p11 21 102 (16%) 523 0.0841
(0.467) 		0.53
(0.864) 		0.034
(0.372) 		0.00401
(0.144) 		0.911
(1.00) 		1
(1.00) 		0.345
(0.766) 		0.21
(0.663) 		0.407
(0.796) 		0.0561
(0.444) 		0.00067
(0.0683) 		0.396
(0.789)
del 11p15 5 175 (28%) 450 0.876
(1.00) 		0.271
(0.717) 		0.144
(0.575) 		0.0237
(0.303) 		0.616
(0.904) 		0.853
(1.00) 		0.00827
(0.209) 		0.0102
(0.221) 		0.152
(0.581) 		0.447
(0.821) 		0.142
(0.575) 		0.481
(0.837)
amp 1p36 22 101 (16%) 524 0.962
(1.00) 		0.911
(1.00) 		0.334
(0.758) 		0.092
(0.501) 		0.968
(1.00) 		0.82
(0.994) 		0.00079
(0.0722) 		0.117
(0.555) 		0.238
(0.688) 		0.143
(0.575) 		0.215
(0.668) 		0.393
(0.788)
amp 1p34 2 95 (15%) 530 0.892
(1.00) 		0.149
(0.576) 		0.101
(0.518) 		0.178
(0.625) 		0.451
(0.823) 		0.34
(0.763) 		0.145
(0.575) 		0.000689
(0.0683) 		0.884
(1.00) 		0.681
(0.94) 		0.381
(0.787) 		0.673
(0.935)
amp 1q42 3 244 (39%) 381 0.307
(0.739) 		0.00269
(0.128) 		0.459
(0.827) 		0.0533
(0.443) 		0.947
(1.00) 		0.734
(0.957) 		0.0195
(0.29) 		0.0682
(0.447) 		0.522
(0.859) 		0.839
(0.999) 		0.022
(0.297) 		1
(1.00)
amp 2q12 2 155 (25%) 470 0.871
(1.00) 		0.372
(0.787) 		0.00573
(0.166) 		0.0189
(0.285) 		0.501
(0.852) 		0.556
(0.874) 		0.128
(0.563) 		1
(1.00) 		0.777
(0.97) 		0.926
(1.00) 		0.196
(0.651) 		1
(1.00)
amp 5p15 33 228 (36%) 397 0.994
(1.00) 		0.723
(0.956) 		0.215
(0.668) 		1e-05
(0.00594) 		0.88
(1.00) 		1
(1.00) 		0.0232
(0.303) 		0.196
(0.651) 		0.167
(0.608) 		0.602
(0.899) 		0.0232
(0.303) 		0.754
(0.957)
amp 5p13 1 216 (35%) 409 0.812
(0.994) 		0.779
(0.97) 		0.667
(0.934) 		0.00848
(0.209) 		0.443
(0.821) 		0.486
(0.837) 		0.231
(0.684) 		0.827
(0.995) 		0.919
(1.00) 		0.915
(1.00) 		0.286
(0.727) 		1
(1.00)
amp 6q21 111 (18%) 514 0.00568
(0.166) 		0.565
(0.877) 		0.0243
(0.304) 		0.559
(0.874) 		0.415
(0.802) 		0.0149
(0.26) 		0.423
(0.81) 		1
(1.00) 		0.337
(0.763) 		0.57
(0.879) 		0.0566
(0.444) 		1
(1.00)
amp 7p22 3 353 (56%) 272 0.557
(0.874) 		0.285
(0.726) 		0.12
(0.558) 		0.0392
(0.385) 		0.82
(0.994) 		1
(1.00) 		0.000393
(0.0668) 		0.463
(0.827) 		0.851
(1.00) 		0.459
(0.827) 		0.575
(0.883) 		0.23
(0.684)
amp 7q21 2 317 (51%) 308 0.967
(1.00) 		0.942
(1.00) 		0.929
(1.00) 		0.0725
(0.451) 		0.515
(0.859) 		0.741
(0.957) 		0.00213
(0.11) 		0.348
(0.766) 		0.178
(0.625) 		0.262
(0.708) 		0.0979
(0.517) 		0.764
(0.963)
amp 12p12 1 207 (33%) 418 0.209
(0.66) 		0.234
(0.688) 		0.0464
(0.412) 		0.0019
(0.11) 		0.867
(1.00) 		0.723
(0.956) 		0.0405
(0.387) 		0.224
(0.68) 		0.0587
(0.444) 		0.381
(0.787) 		0.141
(0.573) 		1
(1.00)
amp 14q13 3 113 (18%) 512 0.083
(0.465) 		0.101
(0.518) 		0.171
(0.611) 		0.327
(0.748) 		0.747
(0.957) 		1
(1.00) 		0.00881
(0.209) 		0.0612
(0.447) 		0.664
(0.932) 		0.75
(0.957) 		0.303
(0.739) 		0.118
(0.558)
amp 20q13 2 416 (67%) 209 0.105
(0.529) 		0.0374
(0.378) 		0.487
(0.837) 		0.193
(0.651) 		0.0399
(0.387) 		0.863
(1.00) 		0.00301
(0.132) 		0.271
(0.717) 		0.964
(1.00) 		0.208
(0.66) 		0.967
(1.00) 		1
(1.00)
del 4p16 3 271 (43%) 354 0.239
(0.688) 		0.537
(0.867) 		0.401
(0.794) 		0.13
(0.563) 		0.202
(0.655) 		0.131
(0.563) 		0.0133
(0.249) 		0.6
(0.899) 		0.928
(1.00) 		0.375
(0.787) 		0.388
(0.788) 		1
(1.00)
del 7q36 3 163 (26%) 462 0.303
(0.739) 		0.392
(0.788) 		0.00069
(0.0683) 		0.0695
(0.447) 		0.133
(0.563) 		0.455
(0.827) 		0.232
(0.684) 		0.724
(0.956) 		0.669
(0.934) 		0.544
(0.873) 		0.592
(0.896) 		1
(1.00)
del 8p23 2 212 (34%) 413 0.757
(0.957) 		0.26
(0.706) 		0.238
(0.688) 		0.0552
(0.444) 		0.373
(0.787) 		0.382
(0.787) 		0.000291
(0.0668) 		0.189
(0.641) 		0.651
(0.928) 		0.0834
(0.465) 		0.13
(0.563) 		0.328
(0.75)
del 9q21 11 176 (28%) 449 0.269
(0.717) 		0.824
(0.995) 		0.256
(0.706) 		0.259
(0.706) 		0.878
(1.00) 		0.855
(1.00) 		0.0802
(0.462) 		0.909
(1.00) 		1
(1.00) 		0.0121
(0.245) 		0.183
(0.631) 		1
(1.00)
del 10p15 3 131 (21%) 494 0.005
(0.16) 		0.956
(1.00) 		0.245
(0.695) 		0.357
(0.778) 		0.327
(0.748) 		0.838
(0.999) 		0.0406
(0.387) 		0.899
(1.00) 		0.294
(0.729) 		0.514
(0.859) 		0.0311
(0.359) 		0.704
(0.953)
del 10q21 1 112 (18%) 513 0.754
(0.957) 		0.53
(0.864) 		0.65
(0.927) 		0.202
(0.655) 		0.958
(1.00) 		0.385
(0.787) 		0.82
(0.994) 		0.417
(0.803) 		0.293
(0.729) 		0.507
(0.852) 		0.00343
(0.141) 		0.426
(0.812)
del 10q22 3 135 (22%) 490 0.197
(0.651) 		0.117
(0.555) 		0.633
(0.916) 		0.0168
(0.269) 		0.885
(1.00) 		0.842
(0.999) 		0.241
(0.691) 		0.9
(1.00) 		0.122
(0.558) 		0.318
(0.742) 		0.00128
(0.0936) 		0.256
(0.706)
del 10q23 31 183 (29%) 442 0.125
(0.561) 		0.0436
(0.397) 		0.98
(1.00) 		0.0078
(0.206) 		0.896
(1.00) 		0.717
(0.954) 		0.565
(0.877) 		0.567
(0.878) 		0.083
(0.465) 		0.857
(1.00) 		0.0146
(0.259) 		0.506
(0.852)
del 12q23 1 109 (17%) 516 0.982
(1.00) 		0.256
(0.706) 		0.619
(0.904) 		0.00211
(0.11) 		0.88
(1.00) 		0.657
(0.93) 		1
(1.00) 		0.135
(0.565) 		0.329
(0.75) 		0.304
(0.739) 		0.36
(0.779) 		0.653
(0.929)
del 13q12 11 138 (22%) 487 0.742
(0.957) 		0.106
(0.529) 		0.0566
(0.444) 		0.0156
(0.261) 		0.261
(0.706) 		0.689
(0.944) 		5.21e-05
(0.0155) 		0.0831
(0.465) 		0.559
(0.874) 		0.202
(0.655) 		0.268
(0.717) 		0.26
(0.706)
del 14q32 32 190 (30%) 435 0.795
(0.982) 		0.506
(0.852) 		0.148
(0.575) 		0.529
(0.864) 		0.431
(0.818) 		0.00564
(0.166) 		0.447
(0.821) 		0.91
(1.00) 		0.772
(0.965) 		0.639
(0.919) 		0.718
(0.954) 		0.0385
(0.385)
del 15q11 2 183 (29%) 442 0.45
(0.822) 		0.621
(0.904) 		0.461
(0.827) 		0.0134
(0.249) 		0.53
(0.864) 		0.855
(1.00) 		0.443
(0.821) 		0.209
(0.66) 		0.876
(1.00) 		0.423
(0.81) 		0.688
(0.944) 		0.736
(0.957)
del 16p13 3 178 (28%) 447 0.2
(0.655) 		0.109
(0.541) 		0.0366
(0.378) 		0.00921
(0.213) 		0.15
(0.577) 		0.359
(0.779) 		0.0255
(0.316) 		0.908
(1.00) 		0.626
(0.908) 		0.458
(0.827) 		0.853
(1.00) 		1
(1.00)
del 17p12 267 (43%) 358 0.583
(0.89) 		0.171
(0.611) 		0.921
(1.00) 		0.232
(0.684) 		0.761
(0.96) 		0.315
(0.742) 		0.0133
(0.249) 		0.171
(0.611) 		0.163
(0.6) 		0.781
(0.97) 		0.305
(0.739) 		0.344
(0.766)
del 18q12 2 292 (47%) 333 0.188
(0.641) 		0.362
(0.779) 		0.393
(0.788) 		1e-05
(0.00594) 		0.829
(0.997) 		0.868
(1.00) 		0.114
(0.55) 		0.601
(0.899) 		1
(1.00) 		0.125
(0.561) 		0.46
(0.827) 		0.222
(0.68)
del 18q21 2 323 (52%) 302 0.549
(0.874) 		0.548
(0.874) 		0.594
(0.896) 		0.00043
(0.0668) 		0.785
(0.974) 		0.869
(1.00) 		0.0661
(0.447) 		0.347
(0.766) 		0.914
(1.00) 		0.235
(0.688) 		0.319
(0.742) 		0.0342
(0.372)
del 19p13 3 249 (40%) 376 0.0674
(0.447) 		0.942
(1.00) 		0.691
(0.944) 		0.0544
(0.443) 		0.485
(0.837) 		1
(1.00) 		0.000905
(0.0729) 		0.165
(0.606) 		0.268
(0.717) 		0.433
(0.818) 		0.0336
(0.372) 		1
(1.00)
del 22q11 1 230 (37%) 395 0.148
(0.575) 		0.149
(0.575) 		0.0661
(0.447) 		0.00045
(0.0668) 		0.806
(0.991) 		0.734
(0.957) 		0.277
(0.724) 		0.104
(0.529) 		0.684
(0.942) 		0.82
(0.994) 		0.254
(0.706) 		1
(1.00)
del xp22 2 150 (24%) 475 0.489
(0.838) 		0.0781
(0.46) 		0.312
(0.742) 		0.44
(0.821) 		0.361
(0.779) 		0.7
(0.951) 		0.00291
(0.132) 		0.546
(0.873) 		0.542
(0.871) 		0.115
(0.554) 		0.0373
(0.378) 		0.479
(0.835)
del xp21 1 143 (23%) 482 0.558
(0.874) 		0.415
(0.802) 		0.311
(0.742) 		0.742
(0.957) 		0.272
(0.717) 		0.226
(0.68) 		0.00249
(0.123) 		0.711
(0.954) 		0.839
(0.999) 		0.758
(0.957) 		0.611
(0.903) 		0.0716
(0.451)
del xp11 3 146 (23%) 479 0.841
(0.999) 		0.228
(0.681) 		0.0578
(0.444) 		0.252
(0.704) 		0.238
(0.688) 		0.324
(0.748) 		0.00693
(0.187) 		0.175
(0.623) 		0.183
(0.631) 		0.684
(0.942) 		0.155
(0.585) 		0.283
(0.726)
amp 1q21 3 249 (40%) 376 0.393
(0.788) 		0.0704
(0.447) 		0.252
(0.704) 		0.0241
(0.304) 		0.702
(0.952) 		0.61
(0.903) 		0.129
(0.563) 		0.109
(0.541) 		0.892
(1.00) 		0.87
(1.00) 		0.12
(0.558) 		1
(1.00)
amp 6p21 1 192 (31%) 433 0.396
(0.789) 		0.0207
(0.296) 		0.0664
(0.447) 		0.0459
(0.41) 		0.117
(0.555) 		0.468
(0.83) 		0.106
(0.531) 		0.734
(0.957) 		0.135
(0.565) 		0.757
(0.957) 		0.0776
(0.46) 		1
(1.00)
amp 6q12 141 (23%) 484 0.0407
(0.387) 		0.691
(0.944) 		0.0531
(0.443) 		0.474
(0.834) 		0.341
(0.763) 		0.315
(0.742) 		0.464
(0.827) 		0.707
(0.953) 		0.113
(0.549) 		0.661
(0.932) 		0.358
(0.779) 		0.472
(0.833)
amp 8p11 21 272 (44%) 353 0.388
(0.788) 		0.465
(0.827) 		0.067
(0.447) 		0.445
(0.821) 		0.153
(0.581) 		0.506
(0.852) 		0.077
(0.46) 		0.753
(0.957) 		0.412
(0.799) 		0.98
(1.00) 		0.769
(0.965) 		0.765
(0.963)
amp 8q24 21 454 (73%) 171 0.769
(0.965) 		0.386
(0.787) 		0.642
(0.92) 		0.259
(0.706) 		0.241
(0.691) 		0.711
(0.954) 		0.116
(0.554) 		1
(1.00) 		0.128
(0.563) 		0.392
(0.788) 		0.298
(0.733) 		1
(1.00)
amp 9p24 1 91 (15%) 534 0.84
(0.999) 		0.706
(0.953) 		0.882
(1.00) 		0.677
(0.935) 		0.298
(0.733) 		1
(1.00) 		0.385
(0.787) 		0.462
(0.827) 		0.948
(1.00) 		0.603
(0.899) 		0.203
(0.656) 		0.677
(0.935)
amp 9p13 3 132 (21%) 493 0.647
(0.925) 		0.839
(0.999) 		0.133
(0.563) 		0.446
(0.821) 		0.674
(0.935) 		0.838
(0.999) 		0.592
(0.896) 		0.38
(0.787) 		0.796
(0.982) 		0.223
(0.68) 		0.911
(1.00) 		0.237
(0.688)
amp 9q34 3 185 (30%) 440 0.0347
(0.372) 		0.021
(0.297) 		0.755
(0.957) 		0.364
(0.781) 		0.253
(0.706) 		0.717
(0.954) 		0.0438
(0.397) 		0.0292
(0.344) 		0.52
(0.859) 		0.022
(0.297) 		0.588
(0.893) 		0.516
(0.859)
amp 10p11 22 169 (27%) 456 0.853
(1.00) 		0.665
(0.933) 		0.181
(0.631) 		0.0616
(0.447) 		0.983
(1.00) 		0.573
(0.88) 		0.622
(0.904) 		0.56
(0.874) 		0.0454
(0.409) 		0.121
(0.558) 		0.146
(0.575) 		0.735
(0.957)
amp 10q22 2 125 (20%) 500 0.612
(0.903) 		0.524
(0.861) 		0.0761
(0.459) 		0.132
(0.563) 		0.503
(0.852) 		0.675
(0.935) 		0.743
(0.957) 		0.3
(0.735) 		0.0328
(0.372) 		0.0376
(0.378) 		0.138
(0.568) 		0.131
(0.563)
amp 10q26 13 119 (19%) 506 0.383
(0.787) 		0.887
(1.00) 		0.0213
(0.297) 		0.157
(0.587) 		0.877
(1.00) 		0.519
(0.859) 		0.911
(1.00) 		0.791
(0.978) 		0.734
(0.957) 		0.069
(0.447) 		0.243
(0.692) 		0.227
(0.68)
amp 11p13 138 (22%) 487 0.0541
(0.443) 		0.525
(0.861) 		0.251
(0.704) 		0.031
(0.359) 		0.491
(0.839) 		0.0699
(0.447) 		0.0262
(0.321) 		0.38
(0.787) 		0.0968
(0.515) 		0.0992
(0.517) 		0.0726
(0.451) 		1
(1.00)
amp 11q13 3 218 (35%) 407 0.875
(1.00) 		0.56
(0.874) 		0.12
(0.558) 		0.924
(1.00) 		0.17
(0.611) 		0.486
(0.837) 		0.0542
(0.443) 		0.101
(0.518) 		0.81
(0.992) 		0.273
(0.717) 		0.0275
(0.33) 		0.754
(0.957)
amp 12q15 161 (26%) 464 0.0745
(0.455) 		0.228
(0.681) 		0.314
(0.742) 		0.552
(0.874) 		0.393
(0.788) 		0.058
(0.444) 		0.194
(0.651) 		1
(1.00) 		0.346
(0.766) 		0.877
(1.00) 		0.134
(0.565) 		1
(1.00)
amp 13q12 3 216 (35%) 409 0.889
(1.00) 		0.11
(0.544) 		0.405
(0.796) 		0.898
(1.00) 		0.184
(0.632) 		0.382
(0.787) 		0.927
(1.00) 		0.381
(0.787) 		0.42
(0.806) 		0.019
(0.285) 		0.145
(0.575) 		0.755
(0.957)
amp 13q22 1 243 (39%) 382 0.449
(0.822) 		0.801
(0.985) 		0.619
(0.904) 		0.819
(0.994) 		0.198
(0.652) 		1
(1.00) 		0.0589
(0.444) 		0.592
(0.896) 		0.0968
(0.515) 		0.204
(0.656) 		0.306
(0.739) 		0.113
(0.549)
amp 15q26 1 168 (27%) 457 0.56
(0.874) 		0.992
(1.00) 		0.52
(0.859) 		0.169
(0.611) 		0.288
(0.728) 		0.131
(0.563) 		0.0932
(0.505) 		0.291
(0.729) 		0.571
(0.879) 		0.0349
(0.372) 		0.131
(0.563) 		0.292
(0.729)
amp 18p11 32 178 (28%) 447 0.34
(0.763) 		0.634
(0.916) 		0.0586
(0.444) 		0.275
(0.72) 		0.359
(0.779) 		0.459
(0.827) 		0.208
(0.66) 		0.729
(0.957) 		0.414
(0.802) 		0.577
(0.885) 		0.123
(0.561) 		0.308
(0.739)
amp 18q11 2 198 (32%) 427 0.596
(0.896) 		0.127
(0.563) 		0.548
(0.874) 		0.476
(0.834) 		0.716
(0.954) 		0.477
(0.835) 		0.925
(1.00) 		1
(1.00) 		0.379
(0.787) 		0.699
(0.951) 		0.272
(0.717) 		0.746
(0.957)
amp 19p13 2 79 (13%) 546 0.0368
(0.378) 		0.842
(0.999) 		0.157
(0.587) 		0.39
(0.788) 		0.282
(0.726) 		0.446
(0.821) 		0.292
(0.729) 		0.641
(0.919) 		0.237
(0.688) 		0.42
(0.806) 		0.224
(0.68) 		0.373
(0.787)
amp 19q12 185 (30%) 440 0.886
(1.00) 		0.617
(0.904) 		0.919
(1.00) 		0.154
(0.582) 		0.381
(0.787) 		1
(1.00) 		0.292
(0.729) 		0.733
(0.957) 		0.35
(0.768) 		0.468
(0.83) 		0.0792
(0.461) 		1
(1.00)
amp 19q13 43 164 (26%) 461 0.659
(0.93) 		0.849
(1.00) 		0.556
(0.874) 		0.317
(0.742) 		0.378
(0.787) 		0.848
(1.00) 		0.319
(0.742) 		1
(1.00) 		0.809
(0.992) 		0.231
(0.684) 		0.0528
(0.443) 		0.736
(0.957)
amp xq28 154 (25%) 471 0.798
(0.982) 		0.223
(0.68) 		0.447
(0.821) 		0.552
(0.874) 		0.826
(0.995) 		1
(1.00) 		0.0538
(0.443) 		0.717
(0.954) 		0.374
(0.787) 		0.316
(0.742) 		0.0602
(0.447) 		0.158
(0.588)
del 1p36 11 210 (34%) 415 0.26
(0.706) 		0.954
(1.00) 		0.257
(0.706) 		0.278
(0.724) 		0.469
(0.831) 		1
(1.00) 		0.138
(0.569) 		0.438
(0.821) 		0.0202
(0.296) 		0.78
(0.97) 		0.441
(0.821) 		1
(1.00)
del 1p13 2 156 (25%) 469 0.133
(0.563) 		0.82
(0.994) 		0.0902
(0.495) 		0.0662
(0.447) 		0.0973
(0.516) 		1
(1.00) 		0.0429
(0.397) 		0.81
(0.992) 		0.856
(1.00) 		0.401
(0.794) 		0.289
(0.728) 		0.47
(0.831)
del 1q44 46 (7%) 579 0.261
(0.706) 		0.0218
(0.297) 		0.667
(0.934) 		0.538
(0.867) 		0.565
(0.877) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.143
(0.575) 		0.553
(0.874) 		0.271
(0.717) 		1
(1.00)
del 1q44 43 (7%) 582 0.611
(0.903) 		0.744
(0.957) 		0.153
(0.581) 		0.819
(0.994) 		0.453
(0.825) 		0.504
(0.852) 		0.729
(0.957) 		0.838
(0.999) 		0.133
(0.563) 		0.886
(1.00) 		0.65
(0.927) 		1
(1.00)
del 2q22 1 126 (20%) 499 0.521
(0.859) 		0.139
(0.569) 		0.668
(0.934) 		0.613
(0.903) 		0.617
(0.904) 		1
(1.00) 		1
(1.00) 		0.252
(0.704) 		0.0233
(0.303) 		0.603
(0.899) 		0.757
(0.957) 		0.128
(0.563)
del 2q32 1 87 (14%) 538 0.407
(0.796) 		0.571
(0.879) 		0.919
(1.00) 		0.512
(0.858) 		0.162
(0.6) 		0.339
(0.763) 		1
(1.00) 		0.65
(0.927) 		0.294
(0.729) 		0.386
(0.787) 		1
(1.00) 		0.373
(0.787)
del 2q33 3 85 (14%) 540 0.718
(0.954) 		0.459
(0.827) 		0.798
(0.982) 		0.224
(0.68) 		0.788
(0.976) 		0.338
(0.763) 		0.612
(0.903) 		1
(1.00) 		0.592
(0.896) 		0.341
(0.763) 		0.476
(0.834) 		1
(1.00)
del 2q37 2 122 (20%) 503 0.953
(1.00) 		0.136
(0.565) 		0.875
(1.00) 		0.837
(0.999) 		0.708
(0.953) 		0.0591
(0.444) 		0.826
(0.995) 		0.517
(0.859) 		0.895
(1.00) 		0.162
(0.6) 		0.51
(0.856) 		0.227
(0.68)
del 3p26 2 250 (40%) 375 0.818
(0.994) 		0.489
(0.838) 		0.524
(0.861) 		0.489
(0.838) 		0.354
(0.774) 		0.402
(0.795) 		0.0746
(0.455) 		0.596
(0.896) 		0.817
(0.994) 		0.749
(0.957) 		0.406
(0.796) 		0.756
(0.957)
del 3p14 2 282 (45%) 343 0.0816
(0.465) 		0.374
(0.787) 		0.0205
(0.296) 		0.0652
(0.447) 		0.0354
(0.372) 		0.317
(0.742) 		0.481
(0.837) 		1
(1.00) 		0.385
(0.787) 		0.671
(0.935) 		0.0235
(0.303) 		0.545
(0.873)
del 3q11 1 98 (16%) 527 0.294
(0.729) 		0.14
(0.573) 		0.722
(0.956) 		0.284
(0.726) 		0.348
(0.766) 		0.656
(0.93) 		0.399
(0.794) 		0.313
(0.742) 		0.0688
(0.447) 		0.739
(0.957) 		0.951
(1.00) 		1
(1.00)
del 3q26 31 63 (10%) 562 0.635
(0.916) 		0.487
(0.837) 		0.771
(0.965) 		0.303
(0.739) 		0.427
(0.812) 		0.786
(0.975) 		0.771
(0.965) 		0.485
(0.837) 		0.558
(0.874) 		0.264
(0.71) 		0.61
(0.903)
del 4p15 2 269 (43%) 356 0.034
(0.372) 		0.366
(0.783) 		0.254
(0.706) 		0.127
(0.563) 		0.826
(0.995) 		0.243
(0.692) 		0.0271
(0.329) 		0.4
(0.794) 		0.705
(0.953) 		0.201
(0.655) 		0.197
(0.651) 		1
(1.00)
del 4q22 1 298 (48%) 327 0.0997
(0.517) 		0.207
(0.66) 		0.057
(0.444) 		0.0187
(0.285) 		0.327
(0.748) 		1
(1.00) 		0.0796
(0.461) 		0.347
(0.766) 		0.824
(0.995) 		0.505
(0.852) 		0.338
(0.763) 		0.56
(0.874)
del 5q12 1 282 (45%) 343 0.771
(0.965) 		0.609
(0.903) 		0.0567
(0.444) 		0.0668
(0.447) 		0.319
(0.742) 		0.868
(1.00) 		0.0526
(0.443) 		0.531
(0.864) 		0.484
(0.837) 		0.928
(1.00) 		0.384
(0.787) 		1
(1.00)
del 6p25 3 188 (30%) 437 0.269
(0.717) 		0.284
(0.726) 		0.537
(0.867) 		0.121
(0.558) 		0.988
(1.00) 		0.357
(0.778) 		0.634
(0.916) 		0.427
(0.812) 		0.597
(0.897) 		0.989
(1.00) 		1
(1.00) 		0.19
(0.642)
del 6q16 3 147 (24%) 478 0.794
(0.982) 		0.908
(1.00) 		0.581
(0.889) 		0.0695
(0.447) 		0.462
(0.827) 		0.072
(0.451) 		0.0176
(0.276) 		0.214
(0.668) 		0.663
(0.932) 		0.0697
(0.447) 		0.316
(0.742) 		0.72
(0.954)
del 6q26 152 (24%) 473 0.657
(0.93) 		0.596
(0.896) 		0.187
(0.637) 		0.0164
(0.267) 		0.857
(1.00) 		1
(1.00) 		0.0671
(0.447) 		0.46
(0.827) 		0.148
(0.575) 		0.238
(0.688) 		0.479
(0.835) 		0.718
(0.954)
del 9p23 302 (48%) 323 0.836
(0.999) 		0.562
(0.875) 		0.0639
(0.447) 		0.0413
(0.387) 		0.166
(0.606) 		0.408
(0.796) 		0.0352
(0.372) 		0.211
(0.664) 		0.177
(0.625) 		0.616
(0.904) 		0.781
(0.97) 		0.362
(0.779)
del 11q25 178 (28%) 447 0.124
(0.561) 		0.318
(0.742) 		0.0626
(0.447) 		0.0657
(0.447) 		0.365
(0.781) 		0.709
(0.953) 		0.0151
(0.26) 		0.0644
(0.447) 		0.297
(0.733) 		0.207
(0.66) 		0.618
(0.904) 		0.0861
(0.476)
del 12p13 1 113 (18%) 512 0.581
(0.889) 		0.0771
(0.46) 		0.27
(0.717) 		0.0986
(0.517) 		0.961
(1.00) 		0.661
(0.932) 		0.91
(1.00) 		0.42
(0.806) 		0.56
(0.874) 		0.113
(0.549) 		0.378
(0.787) 		0.677
(0.935)
del 14q23 3 187 (30%) 438 0.715
(0.954) 		0.517
(0.859) 		0.289
(0.728) 		0.599
(0.898) 		0.0392
(0.385) 		0.275
(0.72) 		0.444
(0.821) 		0.733
(0.957) 		0.747
(0.957) 		0.904
(1.00) 		0.502
(0.852) 		0.735
(0.957)
del 16p13 3 148 (24%) 477 0.45
(0.822) 		0.206
(0.66) 		0.0329
(0.372) 		0.065
(0.447) 		0.0517
(0.443) 		0.325
(0.748) 		0.122
(0.558) 		1
(1.00) 		0.588
(0.893) 		0.475
(0.834) 		0.439
(0.821) 		0.709
(0.953)
del 16q23 1 265 (42%) 360 0.913
(1.00) 		0.429
(0.816) 		0.0817
(0.465) 		0.617
(0.904) 		0.189
(0.641) 		0.0177
(0.276) 		0.0761
(0.459) 		0.834
(0.999) 		0.967
(1.00) 		0.69
(0.944) 		0.702
(0.952) 		0.353
(0.774)
del 17q24 3 103 (16%) 522 0.654
(0.929) 		0.0541
(0.443) 		0.403
(0.796) 		0.0993
(0.517) 		0.283
(0.726) 		0.658
(0.93) 		0.41
(0.798) 		0.0778
(0.46) 		0.176
(0.625) 		0.745
(0.957) 		0.186
(0.637) 		0.7
(0.951)
del 19q13 11 120 (19%) 505 0.64
(0.919) 		0.834
(0.999) 		0.973
(1.00) 		0.28
(0.726) 		0.534
(0.865) 		0.146
(0.575) 		0.182
(0.631) 		1
(1.00) 		0.677
(0.935) 		0.227
(0.68) 		0.368
(0.784) 		1
(1.00)
del 20p12 1 72 (12%) 553 0.913
(1.00) 		0.935
(1.00) 		0.902
(1.00) 		0.432
(0.818) 		0.94
(1.00) 		1
(1.00) 		0.585
(0.89) 		0.112
(0.549) 		0.471
(0.832) 		0.753
(0.957) 		0.906
(1.00) 		0.287
(0.727)
del 21q11 2 290 (46%) 335 0.583
(0.89) 		0.0735
(0.455) 		0.911
(1.00) 		0.285
(0.726) 		0.308
(0.739) 		0.621
(0.904) 		0.93
(1.00) 		0.464
(0.827) 		0.707
(0.953) 		0.551
(0.874) 		0.623
(0.904) 		0.214
(0.668)
del 21q22 13 305 (49%) 320 0.612
(0.903) 		0.285
(0.726) 		0.865
(1.00) 		0.533
(0.865) 		0.906
(1.00) 		0.409
(0.796) 		0.726
(0.957) 		0.531
(0.864) 		0.0435
(0.397) 		0.145
(0.575) 		0.195
(0.651) 		0.222
(0.68)
del 22q13 31 235 (38%) 390 0.152
(0.581) 		0.521
(0.859) 		0.0158
(0.261) 		0.167
(0.608) 		0.178
(0.625) 		0.394
(0.788) 		0.322
(0.745) 		0.239
(0.688) 		0.507
(0.852) 		0.899
(1.00) 		0.137
(0.568) 		0.754
(0.957)
del xq11 2 103 (16%) 522 0.91
(1.00) 		0.918
(1.00) 		0.965
(1.00) 		0.57
(0.879) 		0.826
(0.995) 		0.25
(0.704) 		0.156
(0.587) 		0.12
(0.558) 		0.346
(0.766) 		0.968
(1.00) 		1
(1.00) 		0.677
(0.935)
del xq21 33 96 (15%) 529 0.439
(0.821) 		0.747
(0.957) 		0.636
(0.916) 		0.551
(0.874) 		0.394
(0.788) 		0.635
(0.916) 		0.331
(0.754) 		0.0796
(0.461) 		0.0704
(0.447) 		0.502
(0.852) 		1
(1.00) 		1
(1.00)
'amp_1p36.22' versus 'GENDER'

P value = 0.00079 (Fisher's exact test), Q value = 0.072

Table S1.  Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 1(1P36.22) MUTATED 16 85
AMP PEAK 1(1P36.22) WILD-TYPE 169 355

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

'amp_1p34.2' versus 'RADIATION_THERAPY'

P value = 0.000689 (Fisher's exact test), Q value = 0.068

Table S2.  Gene #2: 'amp_1p34.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 438 116
AMP PEAK 2(1P34.2) MUTATED 54 30
AMP PEAK 2(1P34.2) WILD-TYPE 384 86

Figure S2.  Get High-res Image Gene #2: 'amp_1p34.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_1q42.3' versus 'YEARS_TO_BIRTH'

P value = 0.00269 (Wilcoxon-test), Q value = 0.13

Table S3.  Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 616 64.8 (11.2)
AMP PEAK 4(1Q42.3) MUTATED 240 63.2 (10.4)
AMP PEAK 4(1Q42.3) WILD-TYPE 376 65.7 (11.6)

Figure S3.  Get High-res Image Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_2q12.2' versus 'PATHOLOGIC_STAGE'

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

Table S4.  Gene #5: 'amp_2q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
AMP PEAK 5(2Q12.2) MUTATED 1 9 10 7 27 30 8 15 12 11 6 2
AMP PEAK 5(2Q12.2) WILD-TYPE 10 11 37 26 60 58 21 82 61 35 45 2

Figure S4.  Get High-res Image Gene #5: 'amp_2q12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3q26.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00664 (Fisher's exact test), Q value = 0.18

Table S5.  Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
AMP PEAK 6(3Q26.2) MUTATED 3 9 18 12 47 43 23 39 29 25 20 3
AMP PEAK 6(3Q26.2) WILD-TYPE 8 11 29 21 40 45 6 58 44 21 31 1

Figure S5.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3q26.2' versus 'RACE'

P value = 0.00134 (Fisher's exact test), Q value = 0.094

Table S6.  Gene #6: 'amp_3q26.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
AMP PEAK 6(3Q26.2) MUTATED 79 10 0 162
AMP PEAK 6(3Q26.2) WILD-TYPE 55 7 1 230

Figure S6.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #11: 'RACE'

'amp_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0059

Table S7.  Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
AMP PEAK 7(5P15.33) MUTATED 12 53 127 26
AMP PEAK 7(5P15.33) WILD-TYPE 43 83 156 98

Figure S7.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_5p13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00848 (Fisher's exact test), Q value = 0.21

Table S8.  Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
AMP PEAK 8(5P13.1) MUTATED 12 50 112 32
AMP PEAK 8(5P13.1) WILD-TYPE 43 86 171 92

Figure S8.  Get High-res Image Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q21' versus 'Time to Death'

P value = 0.00568 (logrank test), Q value = 0.17

Table S9.  Gene #11: 'amp_6q21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 590 235 0.0 - 122.3 (13.5)
AMP PEAK 11(6Q21) MUTATED 103 52 0.7 - 68.0 (12.9)
AMP PEAK 11(6Q21) WILD-TYPE 487 183 0.0 - 122.3 (13.8)

Figure S9.  Get High-res Image Gene #11: 'amp_6q21' versus Clinical Feature #1: 'Time to Death'

'amp_7p22.3' versus 'GENDER'

P value = 0.000393 (Fisher's exact test), Q value = 0.067

Table S10.  Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 12(7P22.3) MUTATED 84 269
AMP PEAK 12(7P22.3) WILD-TYPE 101 171

Figure S10.  Get High-res Image Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'

'amp_7p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0113 (Fisher's exact test), Q value = 0.24

Table S11.  Gene #13: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
AMP PEAK 13(7P11.2) MUTATED 36 61 162 58
AMP PEAK 13(7P11.2) WILD-TYPE 19 75 121 66

Figure S11.  Get High-res Image Gene #13: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7p11.2' versus 'GENDER'

P value = 0.00372 (Fisher's exact test), Q value = 0.14

Table S12.  Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 13(7P11.2) MUTATED 84 256
AMP PEAK 13(7P11.2) WILD-TYPE 101 184

Figure S12.  Get High-res Image Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

'amp_7q21.2' versus 'GENDER'

P value = 0.00213 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 14(7Q21.2) MUTATED 76 241
AMP PEAK 14(7Q21.2) WILD-TYPE 109 199

Figure S13.  Get High-res Image Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'

'amp_8p23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00428 (Wilcoxon-test), Q value = 0.15

Table S14.  Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 616 64.8 (11.2)
AMP PEAK 15(8P23.1) MUTATED 225 66.4 (11.1)
AMP PEAK 15(8P23.1) WILD-TYPE 391 63.9 (11.2)

Figure S14.  Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p23.1' versus 'GENDER'

P value = 0.00055 (Fisher's exact test), Q value = 0.068

Table S15.  Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 15(8P23.1) MUTATED 87 142
AMP PEAK 15(8P23.1) WILD-TYPE 98 298

Figure S15.  Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'

'amp_12p12.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0019 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
AMP PEAK 26(12P12.1) MUTATED 14 40 115 29
AMP PEAK 26(12P12.1) WILD-TYPE 41 96 168 95

Figure S16.  Get High-res Image Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q13.3' versus 'GENDER'

P value = 0.00881 (Fisher's exact test), Q value = 0.21

Table S17.  Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 30(14Q13.3) MUTATED 22 91
AMP PEAK 30(14Q13.3) WILD-TYPE 163 349

Figure S17.  Get High-res Image Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'PATHOLOGY_M_STAGE'

P value = 0.00809 (Fisher's exact test), Q value = 0.21

Table S18.  Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 524 39
AMP PEAK 32(17Q12) MUTATED 169 21
AMP PEAK 32(17Q12) WILD-TYPE 355 18

Figure S18.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_17q12' versus 'GENDER'

P value = 0.00448 (Fisher's exact test), Q value = 0.15

Table S19.  Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 32(17Q12) MUTATED 50 172
AMP PEAK 32(17Q12) WILD-TYPE 135 268

Figure S19.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'RACE'

P value = 0.0131 (Fisher's exact test), Q value = 0.25

Table S20.  Gene #32: 'amp_17q12' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
AMP PEAK 32(17Q12) MUTATED 40 11 1 137
AMP PEAK 32(17Q12) WILD-TYPE 94 6 0 255

Figure S20.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #11: 'RACE'

'amp_20q13.2' versus 'GENDER'

P value = 0.00301 (Fisher's exact test), Q value = 0.13

Table S21.  Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 38(20Q13.2) MUTATED 107 309
AMP PEAK 38(20Q13.2) WILD-TYPE 78 131

Figure S21.  Get High-res Image Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'del_4p16.3' versus 'GENDER'

P value = 0.0133 (Fisher's exact test), Q value = 0.25

Table S22.  Gene #52: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 13(4P16.3) MUTATED 66 205
DEL PEAK 13(4P16.3) WILD-TYPE 119 235

Figure S22.  Get High-res Image Gene #52: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.22

Table S23.  Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 616 64.8 (11.2)
DEL PEAK 16(4Q34.3) MUTATED 295 66.0 (10.5)
DEL PEAK 16(4Q34.3) WILD-TYPE 321 63.6 (11.7)

Figure S23.  Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00631 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 16(4Q34.3) MUTATED 2 6 20 22 39 37 20 46 39 26 17 3
DEL PEAK 16(4Q34.3) WILD-TYPE 9 14 27 11 48 51 9 51 34 20 34 1

Figure S24.  Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_7q31.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00092 (Fisher's exact test), Q value = 0.073

Table S25.  Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 21(7Q31.1) MUTATED 1 5 4 9 19 21 15 22 9 5 8 2
DEL PEAK 21(7Q31.1) WILD-TYPE 10 15 43 24 68 67 14 75 64 41 43 2

Figure S25.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_7q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00549 (Fisher's exact test), Q value = 0.17

Table S26.  Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 21(7Q31.1) MUTATED 14 23 71 14
DEL PEAK 21(7Q31.1) WILD-TYPE 41 113 212 110

Figure S26.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_7q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00877 (Fisher's exact test), Q value = 0.21

Table S27.  Gene #60: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 207 188 98 96
DEL PEAK 21(7Q31.1) MUTATED 36 53 21 12
DEL PEAK 21(7Q31.1) WILD-TYPE 171 135 77 84

Figure S27.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_7q31.1' versus 'GENDER'

P value = 0.0015 (Fisher's exact test), Q value = 0.099

Table S28.  Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 21(7Q31.1) MUTATED 23 104
DEL PEAK 21(7Q31.1) WILD-TYPE 162 336

Figure S28.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'

'del_7q36.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00069 (Fisher's exact test), Q value = 0.068

Table S29.  Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 22(7Q36.3) MUTATED 1 6 5 9 22 33 15 27 12 10 13 3
DEL PEAK 22(7Q36.3) WILD-TYPE 10 14 42 24 65 55 14 70 61 36 38 1

Figure S29.  Get High-res Image Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_8p23.2' versus 'GENDER'

P value = 0.000291 (Fisher's exact test), Q value = 0.067

Table S30.  Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 23(8P23.2) MUTATED 43 169
DEL PEAK 23(8P23.2) WILD-TYPE 142 271

Figure S30.  Get High-res Image Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

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

Table S31.  Gene #64: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 25(9P21.3) MUTATED 3 12 21 18 54 49 23 48 35 18 27 4
DEL PEAK 25(9P21.3) WILD-TYPE 8 8 26 15 33 39 6 49 38 28 24 0

Figure S31.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00203 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 25(9P21.3) MUTATED 31 78 162 47
DEL PEAK 25(9P21.3) WILD-TYPE 24 58 121 77

Figure S32.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.0037 (Fisher's exact test), Q value = 0.14

Table S33.  Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 25(9P21.3) MUTATED 82 252
DEL PEAK 25(9P21.3) WILD-TYPE 103 188

Figure S33.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9q21.11' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0121 (Wilcoxon-test), Q value = 0.25

Table S34.  Gene #65: 'del_9q21.11' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 98 34.5 (21.5)
DEL PEAK 26(9Q21.11) MUTATED 36 42.1 (24.2)
DEL PEAK 26(9Q21.11) WILD-TYPE 62 30.1 (18.6)

Figure S34.  Get High-res Image Gene #65: 'del_9q21.11' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'del_10p15.3' versus 'Time to Death'

P value = 0.005 (logrank test), Q value = 0.16

Table S35.  Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 590 235 0.0 - 122.3 (13.5)
DEL PEAK 27(10P15.3) MUTATED 124 58 0.1 - 115.7 (12.7)
DEL PEAK 27(10P15.3) WILD-TYPE 466 177 0.0 - 122.3 (14.0)

Figure S35.  Get High-res Image Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p11.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00401 (Fisher's exact test), Q value = 0.14

Table S36.  Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 28(10P11.21) MUTATED 6 29 53 9
DEL PEAK 28(10P11.21) WILD-TYPE 49 107 230 115

Figure S36.  Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10p11.21' versus 'RACE'

P value = 0.00067 (Fisher's exact test), Q value = 0.068

Table S37.  Gene #67: 'del_10p11.21' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
DEL PEAK 28(10P11.21) MUTATED 32 7 0 51
DEL PEAK 28(10P11.21) WILD-TYPE 102 10 1 341

Figure S37.  Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #11: 'RACE'

'del_10q21.1' versus 'RACE'

P value = 0.00343 (Fisher's exact test), Q value = 0.14

Table S38.  Gene #68: 'del_10q21.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
DEL PEAK 29(10Q21.1) MUTATED 31 8 0 61
DEL PEAK 29(10Q21.1) WILD-TYPE 103 9 1 331

Figure S38.  Get High-res Image Gene #68: 'del_10q21.1' versus Clinical Feature #11: 'RACE'

'del_10q22.3' versus 'RACE'

P value = 0.00128 (Fisher's exact test), Q value = 0.094

Table S39.  Gene #69: 'del_10q22.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
DEL PEAK 30(10Q22.3) MUTATED 36 9 0 71
DEL PEAK 30(10Q22.3) WILD-TYPE 98 8 1 321

Figure S39.  Get High-res Image Gene #69: 'del_10q22.3' versus Clinical Feature #11: 'RACE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0078 (Fisher's exact test), Q value = 0.21

Table S40.  Gene #70: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 31(10Q23.31) MUTATED 14 51 83 23
DEL PEAK 31(10Q23.31) WILD-TYPE 41 85 200 101

Figure S40.  Get High-res Image Gene #70: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11p15.5' versus 'GENDER'

P value = 0.00827 (Fisher's exact test), Q value = 0.21

Table S41.  Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 32(11P15.5) MUTATED 38 137
DEL PEAK 32(11P15.5) WILD-TYPE 147 303

Figure S41.  Get High-res Image Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.0102 (Fisher's exact test), Q value = 0.22

Table S42.  Gene #71: 'del_11p15.5' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 438 116
DEL PEAK 32(11P15.5) MUTATED 109 43
DEL PEAK 32(11P15.5) WILD-TYPE 329 73

Figure S42.  Get High-res Image Gene #71: 'del_11p15.5' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00211 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 35(12Q23.1) MUTATED 16 17 58 12
DEL PEAK 35(12Q23.1) WILD-TYPE 39 119 225 112

Figure S43.  Get High-res Image Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q12.11' versus 'GENDER'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 36(13Q12.11) MUTATED 22 116
DEL PEAK 36(13Q12.11) WILD-TYPE 163 324

Figure S44.  Get High-res Image Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00395 (Wilcoxon-test), Q value = 0.14

Table S45.  Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 616 64.8 (11.2)
DEL PEAK 37(13Q14.2) MUTATED 123 62.2 (11.3)
DEL PEAK 37(13Q14.2) WILD-TYPE 493 65.4 (11.1)

Figure S45.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.015

Table S46.  Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 37(13Q14.2) MUTATED 4 3 6 5 28 17 15 22 7 5 4 1
DEL PEAK 37(13Q14.2) WILD-TYPE 7 17 41 28 59 71 14 75 66 41 47 3

Figure S46.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0033 (Fisher's exact test), Q value = 0.14

Table S47.  Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 37(13Q14.2) MUTATED 13 32 63 11
DEL PEAK 37(13Q14.2) WILD-TYPE 42 104 220 113

Figure S47.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00959 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #76: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 207 188 98 96
DEL PEAK 37(13Q14.2) MUTATED 50 45 12 12
DEL PEAK 37(13Q14.2) WILD-TYPE 157 143 86 84

Figure S48.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q14.2' versus 'GENDER'

P value = 0.00208 (Fisher's exact test), Q value = 0.11

Table S49.  Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 37(13Q14.2) MUTATED 23 102
DEL PEAK 37(13Q14.2) WILD-TYPE 162 338

Figure S49.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.0136 (Fisher's exact test), Q value = 0.25

Table S50.  Gene #76: 'del_13q14.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 438 116
DEL PEAK 37(13Q14.2) MUTATED 80 34
DEL PEAK 37(13Q14.2) WILD-TYPE 358 82

Figure S50.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_13q14.2' versus 'RACE'

P value = 0.00933 (Fisher's exact test), Q value = 0.21

Table S51.  Gene #76: 'del_13q14.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
DEL PEAK 37(13Q14.2) MUTATED 41 2 0 70
DEL PEAK 37(13Q14.2) WILD-TYPE 93 15 1 322

Figure S51.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #11: 'RACE'

'del_13q21.31' versus 'PATHOLOGIC_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.25

Table S52.  Gene #77: 'del_13q21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 20 47 33 87 88 29 97 73 46 51 4
DEL PEAK 38(13Q21.31) MUTATED 3 5 6 6 24 16 13 23 12 6 4 1
DEL PEAK 38(13Q21.31) WILD-TYPE 8 15 41 27 63 72 16 74 61 40 47 3

Figure S52.  Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q21.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.25

Table S53.  Gene #77: 'del_13q21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 38(13Q21.31) MUTATED 14 33 60 13
DEL PEAK 38(13Q21.31) WILD-TYPE 41 103 223 111

Figure S53.  Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q21.31' versus 'RADIATION_THERAPY'

P value = 0.00471 (Fisher's exact test), Q value = 0.16

Table S54.  Gene #77: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 438 116
DEL PEAK 38(13Q21.31) MUTATED 81 36
DEL PEAK 38(13Q21.31) WILD-TYPE 357 80

Figure S54.  Get High-res Image Gene #77: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_14q32.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00564 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 524 39
DEL PEAK 40(14Q32.32) MUTATED 162 4
DEL PEAK 40(14Q32.32) WILD-TYPE 362 35

Figure S55.  Get High-res Image Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0134 (Fisher's exact test), Q value = 0.25

Table S56.  Gene #80: 'del_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 41(15Q11.2) MUTATED 18 41 93 22
DEL PEAK 41(15Q11.2) WILD-TYPE 37 95 190 102

Figure S56.  Get High-res Image Gene #80: 'del_15q11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00921 (Fisher's exact test), Q value = 0.21

Table S57.  Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 42(16P13.3) MUTATED 20 30 89 23
DEL PEAK 42(16P13.3) WILD-TYPE 35 106 194 101

Figure S57.  Get High-res Image Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p12' versus 'GENDER'

P value = 0.0133 (Fisher's exact test), Q value = 0.25

Table S58.  Gene #84: 'del_17p12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 45(17P12) MUTATED 65 202
DEL PEAK 45(17P12) WILD-TYPE 120 238

Figure S58.  Get High-res Image Gene #84: 'del_17p12' versus Clinical Feature #7: 'GENDER'

'del_18q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0059

Table S59.  Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 47(18Q12.2) MUTATED 22 62 158 36
DEL PEAK 47(18Q12.2) WILD-TYPE 33 74 125 88

Figure S59.  Get High-res Image Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q21.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00043 (Fisher's exact test), Q value = 0.067

Table S60.  Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 48(18Q21.2) MUTATED 27 69 167 45
DEL PEAK 48(18Q21.2) WILD-TYPE 28 67 116 79

Figure S60.  Get High-res Image Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'GENDER'

P value = 0.000905 (Fisher's exact test), Q value = 0.073

Table S61.  Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 49(19P13.3) MUTATED 55 194
DEL PEAK 49(19P13.3) WILD-TYPE 130 246

Figure S61.  Get High-res Image Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

'del_22q11.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.067

Table S62.  Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 54(22Q11.1) MUTATED 28 43 119 30
DEL PEAK 54(22Q11.1) WILD-TYPE 27 93 164 94

Figure S62.  Get High-res Image Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xp22.2' versus 'GENDER'

P value = 0.00291 (Fisher's exact test), Q value = 0.13

Table S63.  Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 56(XP22.2) MUTATED 30 120
DEL PEAK 56(XP22.2) WILD-TYPE 155 320

Figure S63.  Get High-res Image Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

'del_xp21.1' versus 'GENDER'

P value = 0.00249 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 57(XP21.1) MUTATED 28 115
DEL PEAK 57(XP21.1) WILD-TYPE 157 325

Figure S64.  Get High-res Image Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

'del_xp11.3' versus 'GENDER'

P value = 0.00693 (Fisher's exact test), Q value = 0.19

Table S65.  Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 58(XP11.3) MUTATED 30 116
DEL PEAK 58(XP11.3) WILD-TYPE 155 324

Figure S65.  Get High-res Image Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'

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/STES-TP/19785970/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/19775559/STES-TP.merged_data.txt

  • Number of patients = 625

  • Number of significantly focal cnvs = 99

  • Number of selected clinical features = 12

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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