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 94 focal events and 12 clinical features across 625 patients, 47 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_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 'GENDER'.

  • amp_7q21.2 cnv correlated to 'GENDER'.

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

  • amp_9q34.3 cnv correlated to 'Time to Death'.

  • amp_12p12.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_14q13.3 cnv correlated to 'GENDER'.

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

  • amp_20q13.2 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_10p15.3 cnv correlated to 'Time to Death'.

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

  • del_10q22.3 cnv correlated to 'RACE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_11p15.5 cnv correlated to 'GENDER'.

  • del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_13q12.11 cnv correlated to 'GENDER'.

  • del_13q21.31 cnv correlated to 'RADIATION_THERAPY'.

  • 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_22q13.31 cnv correlated to 'PATHOLOGIC_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 94 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 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 7q31 1 127 (20%) 498 0.119
(0.534) 		0.0412
(0.384) 		0.00081
(0.0798) 		0.00556
(0.174) 		0.00744
(0.207) 		0.304
(0.711) 		0.0015
(0.0942) 		0.799
(0.975) 		1
(1.00) 		0.105
(0.508) 		0.364
(0.76) 		0.699
(0.943)
del 9p21 3 334 (53%) 291 0.393
(0.773) 		0.887
(1.00) 		0.00827
(0.207) 		0.002
(0.115) 		0.0954
(0.491) 		0.87
(1.00) 		0.0037
(0.143) 		0.079
(0.47) 		0.171
(0.586) 		0.25
(0.667) 		0.214
(0.626) 		0.221
(0.635)
amp 3q26 2 287 (46%) 338 0.675
(0.931) 		0.0146
(0.267) 		0.00307
(0.128) 		0.968
(1.00) 		0.664
(0.925) 		0.739
(0.949) 		0.0647
(0.448) 		0.0128
(0.264) 		0.197
(0.608) 		0.0964
(0.491) 		0.00104
(0.0838) 		0.0655
(0.448)
amp 8p23 1 229 (37%) 396 0.514
(0.842) 		0.00428
(0.146) 		0.442
(0.812) 		0.382
(0.77) 		0.754
(0.949) 		1
(1.00) 		0.00055
(0.0776) 		0.391
(0.773) 		0.444
(0.812) 		0.279
(0.703) 		0.442
(0.812) 		0.532
(0.851)
amp 17q12 222 (36%) 403 0.294
(0.707) 		0.444
(0.812) 		0.0308
(0.347) 		0.716
(0.948) 		0.768
(0.955) 		0.00809
(0.207) 		0.00448
(0.149) 		0.194
(0.608) 		0.691
(0.941) 		0.221
(0.635) 		0.0125
(0.264) 		1
(1.00)
del 4q34 3 300 (48%) 325 0.148
(0.559) 		0.0102
(0.244) 		0.0038
(0.143) 		0.176
(0.586) 		0.467
(0.815) 		0.32
(0.719) 		0.54
(0.854) 		0.304
(0.711) 		0.924
(1.00) 		0.881
(1.00) 		0.852
(0.996) 		1
(1.00)
del 10p11 21 102 (16%) 523 0.178
(0.586) 		0.53
(0.85) 		0.0297
(0.342) 		0.00428
(0.146) 		0.915
(1.00) 		1
(1.00) 		0.345
(0.747) 		0.0969
(0.491) 		0.407
(0.785) 		0.0561
(0.441) 		0.00075
(0.0798) 		0.396
(0.774)
amp 1p36 22 101 (16%) 524 0.927
(1.00) 		0.911
(1.00) 		0.208
(0.616) 		0.0916
(0.491) 		0.971
(1.00) 		0.82
(0.982) 		0.00079
(0.0798) 		0.0893
(0.491) 		0.238
(0.649) 		0.143
(0.558) 		0.215
(0.627) 		0.393
(0.773)
amp 1p34 2 95 (15%) 530 0.96
(1.00) 		0.149
(0.56) 		0.0659
(0.448) 		0.177
(0.586) 		0.437
(0.812) 		0.34
(0.742) 		0.145
(0.559) 		0.00139
(0.0925) 		0.884
(1.00) 		0.681
(0.935) 		0.384
(0.77) 		0.673
(0.93)
amp 1q42 3 244 (39%) 381 0.329
(0.729) 		0.00269
(0.128) 		0.513
(0.842) 		0.0529
(0.435) 		0.941
(1.00) 		0.734
(0.949) 		0.0195
(0.294) 		0.0569
(0.441) 		0.522
(0.846) 		0.839
(0.992) 		0.0219
(0.296) 		1
(1.00)
amp 5p15 33 228 (36%) 397 0.849
(0.996) 		0.723
(0.949) 		0.291
(0.707) 		1e-05
(0.00564) 		0.876
(1.00) 		1
(1.00) 		0.0232
(0.3) 		0.199
(0.609) 		0.167
(0.583) 		0.602
(0.889) 		0.0234
(0.3) 		0.754
(0.949)
amp 5p13 1 216 (35%) 409 0.948
(1.00) 		0.779
(0.963) 		0.769
(0.955) 		0.00822
(0.207) 		0.428
(0.803) 		0.486
(0.82) 		0.231
(0.642) 		0.914
(1.00) 		0.919
(1.00) 		0.915
(1.00) 		0.288
(0.707) 		1
(1.00)
amp 6q21 111 (18%) 514 0.00134
(0.0925) 		0.565
(0.866) 		0.0288
(0.335) 		0.555
(0.864) 		0.408
(0.785) 		0.0149
(0.267) 		0.423
(0.796) 		0.789
(0.969) 		0.337
(0.742) 		0.57
(0.866) 		0.0585
(0.441) 		1
(1.00)
amp 7p22 3 353 (56%) 272 0.536
(0.851) 		0.285
(0.707) 		0.216
(0.627) 		0.0392
(0.378) 		0.794
(0.973) 		1
(1.00) 		0.000393
(0.0739) 		0.533
(0.851) 		0.851
(0.996) 		0.459
(0.815) 		0.576
(0.872) 		0.23
(0.642)
amp 7p11 2 339 (54%) 286 0.441
(0.812) 		0.0655
(0.448) 		0.304
(0.711) 		0.0118
(0.262) 		0.932
(1.00) 		0.183
(0.599) 		0.00484
(0.156) 		0.409
(0.785) 		0.535
(0.851) 		0.694
(0.942) 		0.0618
(0.448) 		1
(1.00)
amp 7q21 2 317 (51%) 308 0.974
(1.00) 		0.942
(1.00) 		0.942
(1.00) 		0.0753
(0.466) 		0.548
(0.86) 		0.741
(0.949) 		0.00213
(0.115) 		0.303
(0.711) 		0.178
(0.586) 		0.262
(0.686) 		0.0986
(0.492) 		0.764
(0.955)
amp 9q34 3 185 (30%) 440 0.00629
(0.187) 		0.021
(0.296) 		0.727
(0.949) 		0.364
(0.76) 		0.286
(0.707) 		0.717
(0.948) 		0.0438
(0.389) 		0.0311
(0.347) 		0.52
(0.846) 		0.022
(0.296) 		0.589
(0.884) 		0.516
(0.844)
amp 12p12 1 207 (33%) 418 0.239
(0.649) 		0.234
(0.646) 		0.0591
(0.441) 		0.00214
(0.115) 		0.872
(1.00) 		0.723
(0.949) 		0.0405
(0.384) 		0.23
(0.642) 		0.0587
(0.441) 		0.381
(0.77) 		0.141
(0.555) 		1
(1.00)
amp 14q13 3 113 (18%) 512 0.144
(0.558) 		0.101
(0.495) 		0.168
(0.583) 		0.324
(0.723) 		0.746
(0.949) 		1
(1.00) 		0.00881
(0.216) 		0.0253
(0.313) 		0.664
(0.925) 		0.75
(0.949) 		0.306
(0.711) 		0.118
(0.534)
amp 20q13 2 416 (67%) 209 0.101
(0.495) 		0.0374
(0.369) 		0.585
(0.882) 		0.192
(0.608) 		0.0415
(0.384) 		0.863
(1.00) 		0.00301
(0.128) 		0.383
(0.77) 		0.964
(1.00) 		0.208
(0.616) 		0.968
(1.00) 		1
(1.00)
del 7q36 3 165 (26%) 460 0.295
(0.707) 		0.462
(0.815) 		0.00092
(0.0798) 		0.0822
(0.475) 		0.124
(0.543) 		0.571
(0.866) 		0.196
(0.608) 		0.816
(0.982) 		0.669
(0.928) 		0.544
(0.859) 		0.6
(0.889) 		1
(1.00)
del 8p23 2 214 (34%) 411 0.833
(0.992) 		0.279
(0.703) 		0.198
(0.609) 		0.0485
(0.421) 		0.482
(0.819) 		0.384
(0.77) 		0.000315
(0.0739) 		0.0832
(0.476) 		0.651
(0.922) 		0.0657
(0.448) 		0.157
(0.576) 		0.331
(0.733)
del 10p15 3 131 (21%) 494 0.00726
(0.207) 		0.956
(1.00) 		0.209
(0.616) 		0.359
(0.759) 		0.324
(0.723) 		0.838
(0.992) 		0.0406
(0.384) 		0.615
(0.889) 		0.294
(0.707) 		0.514
(0.842) 		0.0319
(0.353) 		0.704
(0.945)
del 10q22 3 135 (22%) 490 0.18
(0.591) 		0.117
(0.53) 		0.639
(0.907) 		0.017
(0.286) 		0.881
(1.00) 		0.842
(0.993) 		0.241
(0.653) 		0.802
(0.977) 		0.122
(0.537) 		0.318
(0.718) 		0.00128
(0.0925) 		0.256
(0.68)
del 10q23 31 183 (29%) 442 0.0984
(0.492) 		0.0436
(0.389) 		0.965
(1.00) 		0.00796
(0.207) 		0.889
(1.00) 		0.717
(0.948) 		0.565
(0.866) 		0.497
(0.832) 		0.083
(0.476) 		0.857
(0.998) 		0.015
(0.267) 		0.506
(0.837)
del 11p15 5 175 (28%) 450 0.696
(0.942) 		0.271
(0.701) 		0.0881
(0.487) 		0.0242
(0.304) 		0.591
(0.886) 		0.853
(0.997) 		0.00827
(0.207) 		0.028
(0.332) 		0.152
(0.565) 		0.447
(0.814) 		0.141
(0.555) 		0.481
(0.819)
del 12q23 1 110 (18%) 515 0.805
(0.978) 		0.31
(0.714) 		0.367
(0.762) 		0.00291
(0.128) 		0.825
(0.986) 		0.657
(0.924) 		1
(1.00) 		0.139
(0.554) 		0.196
(0.608) 		0.356
(0.758) 		0.163
(0.582) 		0.189
(0.608)
del 13q12 11 138 (22%) 487 0.471
(0.815) 		0.106
(0.509) 		0.0567
(0.441) 		0.015
(0.267) 		0.259
(0.683) 		0.689
(0.94) 		5.21e-05
(0.0196) 		0.0867
(0.486) 		0.559
(0.866) 		0.202
(0.609) 		0.269
(0.697) 		0.26
(0.683)
del 13q21 31 126 (20%) 499 0.831
(0.991) 		0.0811
(0.471) 		0.0218
(0.296) 		0.0135
(0.264) 		0.312
(0.717) 		0.147
(0.559) 		0.0286
(0.335) 		0.00231
(0.119) 		0.163
(0.582) 		0.57
(0.866) 		0.0512
(0.431) 		0.445
(0.812)
del 18q12 2 292 (47%) 333 0.137
(0.554) 		0.362
(0.759) 		0.417
(0.788) 		1e-05
(0.00564) 		0.843
(0.994) 		0.868
(1.00) 		0.114
(0.522) 		0.471
(0.815) 		1
(1.00) 		0.125
(0.543) 		0.46
(0.815) 		0.222
(0.635)
del 18q21 2 323 (52%) 302 0.491
(0.826) 		0.548
(0.86) 		0.551
(0.863) 		0.00038
(0.0739) 		0.809
(0.98) 		0.869
(1.00) 		0.0661
(0.448) 		0.302
(0.711) 		0.914
(1.00) 		0.235
(0.646) 		0.315
(0.718) 		0.0342
(0.361)
del 19p13 3 249 (40%) 376 0.0648
(0.448) 		0.942
(1.00) 		0.672
(0.93) 		0.0548
(0.441) 		0.457
(0.815) 		1
(1.00) 		0.000905
(0.0798) 		0.17
(0.586) 		0.268
(0.696) 		0.433
(0.808) 		0.0332
(0.356) 		1
(1.00)
del 22q11 1 230 (37%) 395 0.0937
(0.491) 		0.149
(0.559) 		0.0351
(0.361) 		0.0005
(0.0776) 		0.788
(0.969) 		0.734
(0.949) 		0.277
(0.703) 		0.109
(0.52) 		0.684
(0.937) 		0.82
(0.982) 		0.254
(0.677) 		1
(1.00)
del 22q13 31 235 (38%) 390 0.0957
(0.491) 		0.521
(0.846) 		0.00616
(0.187) 		0.166
(0.583) 		0.176
(0.586) 		0.394
(0.773) 		0.322
(0.721) 		0.396
(0.774) 		0.507
(0.837) 		0.899
(1.00) 		0.139
(0.554) 		0.754
(0.949)
del xp22 2 151 (24%) 474 0.459
(0.815) 		0.059
(0.441) 		0.209
(0.616) 		0.294
(0.707) 		0.214
(0.626) 		0.7
(0.943) 		0.00289
(0.128) 		0.633
(0.906) 		0.741
(0.949) 		0.0991
(0.492) 		0.0652
(0.448) 		0.158
(0.576)
del xp21 1 146 (23%) 479 0.506
(0.837) 		0.365
(0.76) 		0.262
(0.686) 		0.666
(0.925) 		0.238
(0.649) 		0.165
(0.583) 		0.00361
(0.143) 		0.903
(1.00) 		0.63
(0.902) 		0.696
(0.942) 		0.743
(0.949) 		0.021
(0.296)
del xp11 3 148 (24%) 477 0.741
(0.949) 		0.155
(0.571) 		0.0851
(0.482) 		0.205
(0.613) 		0.196
(0.608) 		0.324
(0.723) 		0.00396
(0.144) 		0.227
(0.638) 		0.291
(0.707) 		0.747
(0.949) 		0.173
(0.586) 		0.139
(0.554)
amp 1q21 3 249 (40%) 376 0.414
(0.786) 		0.0704
(0.451) 		0.301
(0.711) 		0.0242
(0.304) 		0.71
(0.946) 		0.61
(0.889) 		0.129
(0.545) 		0.092
(0.491) 		0.892
(1.00) 		0.87
(1.00) 		0.121
(0.535) 		1
(1.00)
amp 2q12 2 155 (25%) 470 0.836
(0.992) 		0.372
(0.767) 		0.0113
(0.257) 		0.0186
(0.294) 		0.499
(0.835) 		0.556
(0.864) 		0.128
(0.545) 		1
(1.00) 		0.777
(0.963) 		0.926
(1.00) 		0.194
(0.608) 		1
(1.00)
amp 6p21 1 192 (31%) 433 0.167
(0.583) 		0.0207
(0.296) 		0.0918
(0.491) 		0.0453
(0.397) 		0.112
(0.522) 		0.468
(0.815) 		0.106
(0.509) 		0.823
(0.985) 		0.135
(0.554) 		0.757
(0.949) 		0.078
(0.469) 		1
(1.00)
amp 6q12 141 (23%) 484 0.0114
(0.257) 		0.691
(0.941) 		0.0943
(0.491) 		0.471
(0.815) 		0.335
(0.739) 		0.315
(0.718) 		0.464
(0.815) 		0.805
(0.978) 		0.113
(0.522) 		0.661
(0.924) 		0.354
(0.757) 		0.472
(0.815)
amp 8p11 21 272 (44%) 353 0.45
(0.815) 		0.465
(0.815) 		0.0873
(0.487) 		0.444
(0.812) 		0.168
(0.583) 		0.506
(0.837) 		0.077
(0.469) 		0.756
(0.949) 		0.412
(0.786) 		0.98
(1.00) 		0.768
(0.955) 		0.765
(0.955)
amp 8q24 21 454 (73%) 171 0.635
(0.906) 		0.386
(0.77) 		0.731
(0.949) 		0.257
(0.68) 		0.249
(0.667) 		0.711
(0.946) 		0.116
(0.528) 		1
(1.00) 		0.128
(0.545) 		0.392
(0.773) 		0.296
(0.71) 		1
(1.00)
amp 9p24 1 91 (15%) 534 0.479
(0.817) 		0.706
(0.945) 		0.897
(1.00) 		0.68
(0.934) 		0.267
(0.696) 		1
(1.00) 		0.385
(0.77) 		0.305
(0.711) 		0.948
(1.00) 		0.603
(0.889) 		0.202
(0.609) 		0.677
(0.931)
amp 9p13 3 132 (21%) 493 0.413
(0.786) 		0.839
(0.992) 		0.113
(0.522) 		0.444
(0.812) 		0.725
(0.949) 		0.838
(0.992) 		0.592
(0.886) 		0.383
(0.77) 		0.796
(0.973) 		0.223
(0.636) 		0.912
(1.00) 		0.237
(0.649)
amp 10p11 22 169 (27%) 456 0.967
(1.00) 		0.665
(0.925) 		0.18
(0.591) 		0.0605
(0.446) 		0.978
(1.00) 		0.573
(0.867) 		0.622
(0.894) 		0.645
(0.916) 		0.0454
(0.397) 		0.121
(0.536) 		0.147
(0.559) 		0.735
(0.949)
amp 10q22 2 125 (20%) 500 0.562
(0.866) 		0.524
(0.848) 		0.0877
(0.487) 		0.13
(0.545) 		0.513
(0.842) 		0.675
(0.931) 		0.743
(0.949) 		0.37
(0.766) 		0.0328
(0.356) 		0.0376
(0.369) 		0.139
(0.554) 		0.131
(0.545)
amp 10q26 13 119 (19%) 506 0.274
(0.702) 		0.887
(1.00) 		0.0148
(0.267) 		0.157
(0.576) 		0.881
(1.00) 		0.519
(0.845) 		0.911
(1.00) 		0.896
(1.00) 		0.734
(0.949) 		0.069
(0.45) 		0.244
(0.656) 		0.227
(0.638)
amp 11p13 138 (22%) 487 0.119
(0.534) 		0.525
(0.848) 		0.251
(0.668) 		0.0308
(0.347) 		0.478
(0.817) 		0.0699
(0.451) 		0.0262
(0.322) 		0.213
(0.626) 		0.0968
(0.491) 		0.0992
(0.492) 		0.0732
(0.461) 		1
(1.00)
amp 11q13 3 218 (35%) 407 0.705
(0.945) 		0.56
(0.866) 		0.13
(0.545) 		0.923
(1.00) 		0.166
(0.583) 		0.486
(0.82) 		0.0542
(0.44) 		0.0511
(0.431) 		0.81
(0.98) 		0.273
(0.701) 		0.0274
(0.329) 		0.754
(0.949)
amp 12q15 161 (26%) 464 0.177
(0.586) 		0.228
(0.64) 		0.284
(0.707) 		0.553
(0.863) 		0.414
(0.786) 		0.058
(0.441) 		0.194
(0.608) 		0.814
(0.982) 		0.346
(0.748) 		0.877
(1.00) 		0.134
(0.55) 		1
(1.00)
amp 13q12 3 216 (35%) 409 0.6
(0.889) 		0.11
(0.521) 		0.422
(0.796) 		0.9
(1.00) 		0.188
(0.608) 		0.382
(0.77) 		0.927
(1.00) 		0.387
(0.77) 		0.42
(0.793) 		0.019
(0.294) 		0.147
(0.559) 		0.755
(0.949)
amp 13q22 1 243 (39%) 382 0.309
(0.714) 		0.801
(0.977) 		0.757
(0.949) 		0.818
(0.982) 		0.194
(0.608) 		1
(1.00) 		0.0589
(0.441) 		0.597
(0.889) 		0.0968
(0.491) 		0.204
(0.611) 		0.307
(0.712) 		0.113
(0.522)
amp 15q26 1 168 (27%) 457 0.545
(0.859) 		0.992
(1.00) 		0.355
(0.757) 		0.169
(0.586) 		0.286
(0.707) 		0.131
(0.545) 		0.0932
(0.491) 		0.2
(0.609) 		0.571
(0.866) 		0.0349
(0.361) 		0.131
(0.545) 		0.292
(0.707)
amp 18p11 32 178 (28%) 447 0.458
(0.815) 		0.634
(0.906) 		0.0493
(0.424) 		0.275
(0.702) 		0.353
(0.757) 		0.459
(0.815) 		0.208
(0.616) 		0.569
(0.866) 		0.414
(0.786) 		0.577
(0.872) 		0.123
(0.539) 		0.308
(0.712)
amp 18q11 2 198 (32%) 427 0.707
(0.946) 		0.127
(0.545) 		0.46
(0.815) 		0.472
(0.815) 		0.718
(0.948) 		0.477
(0.817) 		0.925
(1.00) 		1
(1.00) 		0.379
(0.77) 		0.699
(0.943) 		0.273
(0.701) 		0.746
(0.949)
amp 19q12 185 (30%) 440 0.955
(1.00) 		0.617
(0.889) 		0.931
(1.00) 		0.152
(0.565) 		0.407
(0.785) 		1
(1.00) 		0.292
(0.707) 		0.735
(0.949) 		0.35
(0.752) 		0.468
(0.815) 		0.0806
(0.471) 		1
(1.00)
amp 19q13 43 164 (26%) 461 0.763
(0.955) 		0.849
(0.996) 		0.501
(0.837) 		0.315
(0.718) 		0.372
(0.767) 		0.848
(0.996) 		0.319
(0.719) 		1
(1.00) 		0.809
(0.98) 		0.231
(0.642) 		0.0527
(0.435) 		0.736
(0.949)
amp xq28 155 (25%) 470 0.908
(1.00) 		0.241
(0.653) 		0.46
(0.815) 		0.522
(0.847) 		0.795
(0.973) 		1
(1.00) 		0.0844
(0.481) 		0.905
(1.00) 		0.374
(0.768) 		0.316
(0.718) 		0.0726
(0.46) 		0.161
(0.582)
del 1p36 11 210 (34%) 415 0.22
(0.635) 		0.954
(1.00) 		0.174
(0.586) 		0.276
(0.702) 		0.454
(0.815) 		1
(1.00) 		0.138
(0.554) 		0.443
(0.812) 		0.0202
(0.296) 		0.78
(0.963) 		0.446
(0.812) 		1
(1.00)
del 1p13 2 156 (25%) 469 0.0949
(0.491) 		0.82
(0.982) 		0.0746
(0.465) 		0.0662
(0.448) 		0.0964
(0.491) 		1
(1.00) 		0.0429
(0.389) 		0.552
(0.863) 		0.856
(0.998) 		0.401
(0.78) 		0.289
(0.707) 		0.47
(0.815)
del 1q44 46 (7%) 579 0.199
(0.609) 		0.0218
(0.296) 		0.615
(0.889) 		0.536
(0.851) 		0.57
(0.866) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.143
(0.558) 		0.553
(0.863) 		0.269
(0.697) 		1
(1.00)
del 1q44 43 (7%) 582 0.504
(0.837) 		0.744
(0.949) 		0.163
(0.582) 		0.819
(0.982) 		0.46
(0.815) 		0.504
(0.837) 		0.729
(0.949) 		1
(1.00) 		0.133
(0.549) 		0.886
(1.00) 		0.648
(0.918) 		1
(1.00)
del 2q22 1 126 (20%) 499 0.658
(0.924) 		0.139
(0.554) 		0.605
(0.889) 		0.613
(0.889) 		0.605
(0.889) 		1
(1.00) 		1
(1.00) 		0.164
(0.582) 		0.0233
(0.3) 		0.603
(0.889) 		0.755
(0.949) 		0.128
(0.545)
del 2q32 1 87 (14%) 538 0.567
(0.866) 		0.571
(0.866) 		0.916
(1.00) 		0.513
(0.842) 		0.164
(0.582) 		0.339
(0.742) 		1
(1.00) 		0.766
(0.955) 		0.294
(0.707) 		0.386
(0.77) 		1
(1.00) 		0.373
(0.768)
del 2q33 3 85 (14%) 540 0.897
(1.00) 		0.459
(0.815) 		0.784
(0.966) 		0.225
(0.637) 		0.791
(0.971) 		0.338
(0.742) 		0.612
(0.889) 		0.655
(0.924) 		0.592
(0.886) 		0.341
(0.742) 		0.475
(0.816) 		1
(1.00)
del 2q37 2 122 (20%) 503 0.718
(0.948) 		0.136
(0.554) 		0.793
(0.973) 		0.837
(0.992) 		0.709
(0.946) 		0.0591
(0.441) 		0.826
(0.986) 		0.303
(0.711) 		0.895
(1.00) 		0.162
(0.582) 		0.508
(0.838) 		0.227
(0.638)
del 3p26 2 250 (40%) 375 0.778
(0.963) 		0.489
(0.824) 		0.472
(0.815) 		0.486
(0.82) 		0.34
(0.742) 		0.402
(0.781) 		0.0746
(0.465) 		0.463
(0.815) 		0.817
(0.982) 		0.749
(0.949) 		0.411
(0.786) 		0.756
(0.949)
del 3p14 2 282 (45%) 343 0.0778
(0.469) 		0.374
(0.768) 		0.0154
(0.267) 		0.0636
(0.448) 		0.0335
(0.356) 		0.317
(0.718) 		0.481
(0.819) 		0.836
(0.992) 		0.385
(0.77) 		0.671
(0.93) 		0.0231
(0.3) 		0.545
(0.859)
del 3q11 1 98 (16%) 527 0.217
(0.628) 		0.14
(0.555) 		0.661
(0.924) 		0.283
(0.707) 		0.341
(0.742) 		0.656
(0.924) 		0.399
(0.779) 		0.393
(0.773) 		0.0688
(0.45) 		0.739
(0.949) 		0.952
(1.00) 		1
(1.00)
del 3q26 31 65 (10%) 560 0.932
(1.00) 		0.461
(0.815) 		0.608
(0.889) 		0.4
(0.78) 		0.361
(0.759) 		0.787
(0.969) 		0.569
(0.866) 		0.608
(0.889) 		0.558
(0.866) 		0.326
(0.725) 		0.609
(0.889)
del 4p16 3 271 (43%) 354 0.224
(0.636) 		0.537
(0.851) 		0.295
(0.707) 		0.127
(0.545) 		0.196
(0.608) 		0.131
(0.545) 		0.0133
(0.264) 		0.533
(0.851) 		0.928
(1.00) 		0.375
(0.768) 		0.388
(0.77) 		1
(1.00)
del 4p15 2 269 (43%) 356 0.0368
(0.369) 		0.366
(0.762) 		0.192
(0.608) 		0.127
(0.545) 		0.81
(0.98) 		0.243
(0.656) 		0.0271
(0.329) 		0.348
(0.751) 		0.705
(0.945) 		0.201
(0.609) 		0.195
(0.608) 		1
(1.00)
del 4q22 1 298 (48%) 327 0.0679
(0.45) 		0.139
(0.554) 		0.0411
(0.384) 		0.018
(0.291) 		0.235
(0.646) 		1
(1.00) 		0.0796
(0.47) 		0.301
(0.711) 		0.965
(1.00) 		0.615
(0.889) 		0.34
(0.742) 		0.56
(0.866)
del 5q12 1 282 (45%) 343 0.602
(0.889) 		0.609
(0.889) 		0.0196
(0.294) 		0.0657
(0.448) 		0.298
(0.711) 		0.868
(1.00) 		0.0526
(0.435) 		0.536
(0.851) 		0.484
(0.82) 		0.928
(1.00) 		0.381
(0.77) 		1
(1.00)
del 6p25 3 188 (30%) 437 0.325
(0.723) 		0.284
(0.707) 		0.45
(0.815) 		0.12
(0.534) 		0.987
(1.00) 		0.357
(0.758) 		0.634
(0.906) 		0.26
(0.683) 		0.597
(0.889) 		0.989
(1.00) 		1
(1.00) 		0.19
(0.608)
del 6q16 3 147 (24%) 478 0.746
(0.949) 		0.908
(1.00) 		0.616
(0.889) 		0.0688
(0.45) 		0.449
(0.815) 		0.072
(0.459) 		0.0176
(0.289) 		0.11
(0.521) 		0.663
(0.925) 		0.0697
(0.451) 		0.316
(0.718) 		0.72
(0.948)
del 6q26 152 (24%) 473 0.532
(0.851) 		0.596
(0.889) 		0.203
(0.61) 		0.0158
(0.271) 		0.858
(0.998) 		1
(1.00) 		0.0671
(0.448) 		0.465
(0.815) 		0.148
(0.559) 		0.238
(0.649) 		0.479
(0.817) 		0.718
(0.948)
del 9p23 302 (48%) 323 0.694
(0.942) 		0.562
(0.866) 		0.0595
(0.442) 		0.0421
(0.386) 		0.15
(0.561) 		0.408
(0.785) 		0.0352
(0.361) 		0.216
(0.627) 		0.177
(0.586) 		0.616
(0.889) 		0.778
(0.963) 		0.362
(0.759)
del 9q21 11 175 (28%) 450 0.0959
(0.491) 		0.926
(1.00) 		0.279
(0.703) 		0.301
(0.711) 		0.848
(0.996) 		1
(1.00) 		0.0972
(0.491) 		0.91
(1.00) 		1
(1.00) 		0.0121
(0.262) 		0.16
(0.581) 		1
(1.00)
del 11q25 178 (28%) 447 0.194
(0.608) 		0.318
(0.718) 		0.0497
(0.425) 		0.0643
(0.448) 		0.362
(0.759) 		0.709
(0.946) 		0.0151
(0.267) 		0.0671
(0.448) 		0.297
(0.711) 		0.207
(0.616) 		0.617
(0.889) 		0.0861
(0.486)
del 12p13 1 113 (18%) 512 0.19
(0.608) 		0.0771
(0.469) 		0.188
(0.608) 		0.0969
(0.491) 		0.96
(1.00) 		0.661
(0.924) 		0.91
(1.00) 		0.292
(0.707) 		0.56
(0.866) 		0.113
(0.522) 		0.379
(0.77) 		0.677
(0.931)
del 14q23 3 187 (30%) 438 0.385
(0.77) 		0.517
(0.844) 		0.266
(0.694) 		0.599
(0.889) 		0.0376
(0.369) 		0.275
(0.702) 		0.444
(0.812) 		1
(1.00) 		0.747
(0.949) 		0.904
(1.00) 		0.505
(0.837) 		0.735
(0.949)
del 15q11 2 183 (29%) 442 0.441
(0.812) 		0.621
(0.893) 		0.456
(0.815) 		0.0136
(0.264) 		0.527
(0.849) 		0.855
(0.998) 		0.443
(0.812) 		0.176
(0.586) 		0.876
(1.00) 		0.423
(0.796) 		0.688
(0.94) 		0.736
(0.949)
del 16p13 3 177 (28%) 448 0.202
(0.609) 		0.106
(0.509) 		0.0221
(0.296) 		0.0107
(0.252) 		0.103
(0.5) 		0.197
(0.608) 		0.0194
(0.294) 		1
(1.00) 		0.626
(0.898) 		0.458
(0.815) 		0.851
(0.996) 		1
(1.00)
del 16p13 3 153 (24%) 472 0.317
(0.718) 		0.147
(0.559) 		0.0324
(0.355) 		0.0365
(0.369) 		0.0808
(0.471) 		0.244
(0.656) 		0.0665
(0.448) 		0.813
(0.982) 		0.588
(0.884) 		0.475
(0.816) 		0.492
(0.826) 		0.714
(0.948)
del 16q23 1 265 (42%) 360 0.958
(1.00) 		0.429
(0.804) 		0.0795
(0.47) 		0.615
(0.889) 		0.176
(0.586) 		0.0177
(0.289) 		0.0761
(0.469) 		0.604
(0.889) 		0.967
(1.00) 		0.69
(0.941) 		0.701
(0.944) 		0.353
(0.757)
del 17p12 267 (43%) 358 0.768
(0.955) 		0.171
(0.586) 		0.873
(1.00) 		0.232
(0.642) 		0.752
(0.949) 		0.315
(0.718) 		0.0133
(0.264) 		0.118
(0.534) 		0.163
(0.582) 		0.781
(0.964) 		0.304
(0.711) 		0.344
(0.746)
del 17q24 3 103 (16%) 522 0.617
(0.889) 		0.0541
(0.44) 		0.36
(0.759) 		0.0994
(0.492) 		0.288
(0.707) 		0.658
(0.924) 		0.41
(0.786) 		0.059
(0.441) 		0.176
(0.586) 		0.745
(0.949) 		0.188
(0.608) 		0.7
(0.943)
del 20p12 1 72 (12%) 553 0.683
(0.936) 		0.935
(1.00) 		0.88
(1.00) 		0.432
(0.808) 		0.936
(1.00) 		1
(1.00) 		0.585
(0.882) 		0.0781
(0.469) 		0.471
(0.815) 		0.753
(0.949) 		0.906
(1.00) 		0.287
(0.707)
del 21q11 2 286 (46%) 339 0.638
(0.907) 		0.0383
(0.372) 		0.817
(0.982) 		0.153
(0.565) 		0.357
(0.758) 		0.739
(0.949) 		0.93
(1.00) 		0.408
(0.785) 		0.924
(1.00) 		0.486
(0.82) 		0.569
(0.866) 		0.369
(0.765)
del 21q22 13 305 (49%) 320 0.66
(0.924) 		0.285
(0.707) 		0.711
(0.946) 		0.529
(0.85) 		0.884
(1.00) 		0.409
(0.785) 		0.726
(0.949) 		0.47
(0.815) 		0.0435
(0.389) 		0.145
(0.559) 		0.197
(0.608) 		0.222
(0.635)
del xq11 2 105 (17%) 520 0.997
(1.00) 		0.881
(1.00) 		0.933
(1.00) 		0.526
(0.849) 		0.84
(0.992) 		0.177
(0.586) 		0.102
(0.499) 		0.0943
(0.491) 		0.548
(0.86) 		0.958
(1.00) 		0.932
(1.00) 		0.39
(0.772)
del xq21 33 98 (16%) 527 0.475
(0.816) 		0.954
(1.00) 		0.528
(0.849) 		0.501
(0.837) 		0.35
(0.752) 		0.637
(0.907) 		0.278
(0.703) 		0.113
(0.522) 		0.147
(0.559) 		0.446
(0.812) 		0.86
(1) 		0.66
(0.924)
'amp_1p36.22' versus 'GENDER'

P value = 0.00079 (Fisher's exact test), Q value = 0.08

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 = 0.00139 (Fisher's exact test), Q value = 0.092

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

nPatients NO YES
ALL 445 119
AMP PEAK 2(1P34.2) MUTATED 56 30
AMP PEAK 2(1P34.2) WILD-TYPE 389 89

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_3q26.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00307 (Fisher's exact test), Q value = 0.13

Table S4.  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 10 21 47 33 87 87 28 95 72 46 49 4
AMP PEAK 6(3Q26.2) MUTATED 3 9 18 12 47 43 23 37 29 25 19 3
AMP PEAK 6(3Q26.2) WILD-TYPE 7 12 29 21 40 44 5 58 43 21 30 1

Figure S4.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3q26.2' versus 'RACE'

P value = 0.00104 (Fisher's exact test), Q value = 0.084

Table S5.  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 S5.  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 = 0.0056

Table S6.  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 S6.  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 = 0.00822 (Fisher's exact test), Q value = 0.21

Table S7.  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 S7.  Get High-res Image Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q21' versus 'Time to Death'

P value = 0.00134 (logrank test), Q value = 0.092

Table S8.  Gene #11: 'amp_6q21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 599 245 0.0 - 122.3 (13.9)
AMP PEAK 11(6Q21) MUTATED 107 56 0.7 - 68.0 (12.9)
AMP PEAK 11(6Q21) WILD-TYPE 492 189 0.0 - 122.3 (14.4)

Figure S8.  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 = 0.074

Table S9.  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 S9.  Get High-res Image Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'

'amp_7p11.2' versus 'GENDER'

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

Table S10.  Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 13(7P11.2) MUTATED 84 255
AMP PEAK 13(7P11.2) WILD-TYPE 101 185

Figure S10.  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 S11.  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 S11.  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 S12.  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 S12.  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 = 0.078

Table S13.  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 S13.  Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'

'amp_9q34.3' versus 'Time to Death'

P value = 0.00629 (logrank test), Q value = 0.19

Table S14.  Gene #20: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 599 245 0.0 - 122.3 (13.9)
AMP PEAK 20(9Q34.3) MUTATED 177 58 0.4 - 122.3 (13.4)
AMP PEAK 20(9Q34.3) WILD-TYPE 422 187 0.0 - 116.4 (14.0)

Figure S14.  Get High-res Image Gene #20: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

'amp_12p12.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00214 (Fisher's exact test), Q value = 0.11

Table S15.  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 S15.  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 = 0.22

Table S16.  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 S16.  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 S17.  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 S17.  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 S18.  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 S18.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_20q13.2' versus 'GENDER'

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

Table S19.  Gene #37: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
AMP PEAK 37(20Q13.2) MUTATED 107 309
AMP PEAK 37(20Q13.2) WILD-TYPE 78 131

Figure S19.  Get High-res Image Gene #37: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.24

Table S20.  Gene #54: '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 S20.  Get High-res Image Gene #54: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0038 (Fisher's exact test), Q value = 0.14

Table S21.  Gene #54: '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 10 21 47 33 87 87 28 95 72 46 49 4
DEL PEAK 16(4Q34.3) MUTATED 2 6 20 22 39 37 20 46 39 26 16 3
DEL PEAK 16(4Q34.3) WILD-TYPE 8 15 27 11 48 50 8 49 33 20 33 1

Figure S21.  Get High-res Image Gene #54: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_7q31.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00081 (Fisher's exact test), Q value = 0.08

Table S22.  Gene #59: '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 10 21 47 33 87 87 28 95 72 46 49 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 9 16 43 24 68 66 13 73 63 41 41 2

Figure S22.  Get High-res Image Gene #59: 'del_7q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_7q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00556 (Fisher's exact test), Q value = 0.17

Table S23.  Gene #59: '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 S23.  Get High-res Image Gene #59: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_7q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00744 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #59: 'del_7q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 207 187 98 96
DEL PEAK 21(7Q31.1) MUTATED 36 53 21 12
DEL PEAK 21(7Q31.1) WILD-TYPE 171 134 77 84

Figure S24.  Get High-res Image Gene #59: '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 = 0.094

Table S25.  Gene #59: '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 S25.  Get High-res Image Gene #59: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'

'del_7q36.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00092 (Fisher's exact test), Q value = 0.08

Table S26.  Gene #60: '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 10 21 47 33 87 87 28 95 72 46 49 4
DEL PEAK 22(7Q36.3) MUTATED 1 6 5 9 23 33 14 27 11 10 13 3
DEL PEAK 22(7Q36.3) WILD-TYPE 9 15 42 24 64 54 14 68 61 36 36 1

Figure S26.  Get High-res Image Gene #60: 'del_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_8p23.2' versus 'GENDER'

P value = 0.000315 (Fisher's exact test), Q value = 0.074

Table S27.  Gene #61: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 23(8P23.2) MUTATED 44 170
DEL PEAK 23(8P23.2) WILD-TYPE 141 270

Figure S27.  Get High-res Image Gene #61: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

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

Table S28.  Gene #63: '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 10 21 47 33 87 87 28 95 72 46 49 4
DEL PEAK 25(9P21.3) MUTATED 3 12 21 18 54 48 23 47 34 18 26 4
DEL PEAK 25(9P21.3) WILD-TYPE 7 9 26 15 33 39 5 48 38 28 23 0

Figure S28.  Get High-res Image Gene #63: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.002 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #63: '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 S29.  Get High-res Image Gene #63: '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 S30.  Gene #63: '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 S30.  Get High-res Image Gene #63: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_10p15.3' versus 'Time to Death'

P value = 0.00726 (logrank test), Q value = 0.21

Table S31.  Gene #65: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 599 245 0.0 - 122.3 (13.9)
DEL PEAK 27(10P15.3) MUTATED 127 60 0.1 - 115.7 (12.6)
DEL PEAK 27(10P15.3) WILD-TYPE 472 185 0.0 - 122.3 (14.8)

Figure S31.  Get High-res Image Gene #65: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p11.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00428 (Fisher's exact test), Q value = 0.15

Table S32.  Gene #66: '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 S32.  Get High-res Image Gene #66: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10p11.21' versus 'RACE'

P value = 0.00075 (Fisher's exact test), Q value = 0.08

Table S33.  Gene #66: '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 S33.  Get High-res Image Gene #66: 'del_10p11.21' versus Clinical Feature #11: 'RACE'

'del_10q22.3' versus 'RACE'

P value = 0.00128 (Fisher's exact test), Q value = 0.092

Table S34.  Gene #67: '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 29(10Q22.3) MUTATED 36 9 0 71
DEL PEAK 29(10Q22.3) WILD-TYPE 98 8 1 321

Figure S34.  Get High-res Image Gene #67: 'del_10q22.3' versus Clinical Feature #11: 'RACE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00796 (Fisher's exact test), Q value = 0.21

Table S35.  Gene #68: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 30(10Q23.31) MUTATED 14 51 83 23
DEL PEAK 30(10Q23.31) WILD-TYPE 41 85 200 101

Figure S35.  Get High-res Image Gene #68: '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 S36.  Gene #69: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 31(11P15.5) MUTATED 38 137
DEL PEAK 31(11P15.5) WILD-TYPE 147 303

Figure S36.  Get High-res Image Gene #69: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

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

Table S37.  Gene #72: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 34(12Q23.1) MUTATED 16 18 58 12
DEL PEAK 34(12Q23.1) WILD-TYPE 39 118 225 112

Figure S37.  Get High-res Image Gene #72: '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 = 0.02

Table S38.  Gene #73: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 35(13Q12.11) MUTATED 22 116
DEL PEAK 35(13Q12.11) WILD-TYPE 163 324

Figure S38.  Get High-res Image Gene #73: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

'del_13q21.31' versus 'RADIATION_THERAPY'

P value = 0.00231 (Fisher's exact test), Q value = 0.12

Table S39.  Gene #74: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 445 119
DEL PEAK 36(13Q21.31) MUTATED 82 38
DEL PEAK 36(13Q21.31) WILD-TYPE 363 81

Figure S39.  Get High-res Image Gene #74: 'del_13q21.31' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_18q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0056

Table S40.  Gene #82: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 44(18Q12.2) MUTATED 22 62 158 36
DEL PEAK 44(18Q12.2) WILD-TYPE 33 74 125 88

Figure S40.  Get High-res Image Gene #82: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q21.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.074

Table S41.  Gene #83: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

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

Figure S41.  Get High-res Image Gene #83: '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 = 0.08

Table S42.  Gene #84: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 46(19P13.3) MUTATED 55 194
DEL PEAK 46(19P13.3) WILD-TYPE 130 246

Figure S42.  Get High-res Image Gene #84: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

'del_22q11.1' versus 'PATHOLOGY_T_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.078

Table S43.  Gene #88: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
DEL PEAK 50(22Q11.1) MUTATED 28 43 119 30
DEL PEAK 50(22Q11.1) WILD-TYPE 27 93 164 94

Figure S43.  Get High-res Image Gene #88: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q13.31' versus 'PATHOLOGIC_STAGE'

P value = 0.00616 (Fisher's exact test), Q value = 0.19

Table S44.  Gene #89: 'del_22q13.31' 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 10 21 47 33 87 87 28 95 72 46 49 4
DEL PEAK 51(22Q13.31) MUTATED 6 2 19 12 29 28 18 42 30 14 17 3
DEL PEAK 51(22Q13.31) WILD-TYPE 4 19 28 21 58 59 10 53 42 32 32 1

Figure S44.  Get High-res Image Gene #89: 'del_22q13.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xp22.2' versus 'GENDER'

P value = 0.00289 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #90: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 52(XP22.2) MUTATED 30 121
DEL PEAK 52(XP22.2) WILD-TYPE 155 319

Figure S45.  Get High-res Image Gene #90: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

'del_xp21.1' versus 'GENDER'

P value = 0.00361 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #91: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 53(XP21.1) MUTATED 29 117
DEL PEAK 53(XP21.1) WILD-TYPE 156 323

Figure S46.  Get High-res Image Gene #91: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

'del_xp11.3' versus 'GENDER'

P value = 0.00396 (Fisher's exact test), Q value = 0.14

Table S47.  Gene #92: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
DEL PEAK 54(XP11.3) MUTATED 30 118
DEL PEAK 54(XP11.3) WILD-TYPE 155 322

Figure S47.  Get High-res Image Gene #92: '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/22532764/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/22507048/STES-TP.merged_data.txt

  • Number of patients = 625

  • Number of significantly focal cnvs = 94

  • 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.

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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