Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 68 focal events and 12 clinical features across 439 patients, 42 significant findings detected with Q value < 0.25.

  • amp_7p21.2 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • amp_13q12.13 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_13q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_16p11.2 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • amp_16q12.1 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • amp_20q11.21 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_20q12 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_20q13.12 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_1p36.11 cnv correlated to 'PATHOLOGY.M.STAGE'.

  • del_4p16.2 cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • del_4q22.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_5q21.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_8p23.3 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • del_8p22 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_14q31.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_17p12 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_17q24.3 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_18p11.31 cnv correlated to 'PATHOLOGY.M.STAGE' and 'HISTOLOGICAL.TYPE'.

  • del_18q12.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_18q21.2 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_19p13.3 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • del_22q13.32 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
del 8p22 196 (45%) 243 0.2
(1.00) 		0.0263
(1.00) 		1e-05
(0.00803) 		0.0416
(1.00) 		1e-05
(0.00803) 		0.00014
(0.11) 		0.0543
(1.00) 		0.0108
(1.00) 		0.588
(1.00) 		0.041
(1.00) 		2.68e-07
(0.000217) 		0.395
(1.00)
del 17p12 245 (56%) 194 0.306
(1.00) 		0.0138
(1.00) 		1e-05
(0.00803) 		0.9
(1.00) 		1e-05
(0.00803) 		0.00419
(1.00) 		0.213
(1.00) 		2.35e-06
(0.00189) 		0.258
(1.00) 		0.132
(1.00) 		1.18e-06
(0.000953) 		0.851
(1.00)
del 18q21 2 280 (64%) 159 0.99
(1.00) 		0.0207
(1.00) 		5e-05
(0.0397) 		0.808
(1.00) 		2e-05
(0.016) 		0.00077
(0.586) 		0.0745
(1.00) 		7.32e-09
(5.96e-06) 		0.557
(1.00) 		0.0815
(1.00) 		2.57e-05
(0.0205) 		0.794
(1.00)
amp 7p21 2 249 (57%) 190 0.921
(1.00) 		0.0608
(1.00) 		0.00013
(0.102) 		0.386
(1.00) 		5e-05
(0.0397) 		0.0502
(1.00) 		1
(1.00) 		0.0472
(1.00) 		0.262
(1.00) 		0.264
(1.00) 		0.000153
(0.119) 		0.5
(1.00)
amp 16q12 1 108 (25%) 331 0.146
(1.00) 		0.0546
(1.00) 		0.0002
(0.156) 		0.933
(1.00) 		0.00021
(0.163) 		0.474
(1.00) 		0.507
(1.00) 		0.0144
(1.00) 		0.572
(1.00) 		0.604
(1.00) 		0.000209
(0.162) 		0.203
(1.00)
amp 13q12 13 267 (61%) 172 0.658
(1.00) 		0.603
(1.00) 		8e-05
(0.0633) 		0.885
(1.00) 		0.00078
(0.593) 		0.0009
(0.681) 		0.769
(1.00) 		1.05e-07
(8.55e-05) 		0.283
(1.00) 		0.0226
(1.00) 		0.00317
(1.00) 		0.131
(1.00)
amp 13q22 1 271 (62%) 168 0.474
(1.00) 		0.664
(1.00) 		0.00014
(0.11) 		0.882
(1.00) 		0.00039
(0.301) 		0.00286
(1.00) 		0.28
(1.00) 		1.05e-06
(0.000844) 		0.29
(1.00) 		0.0479
(1.00) 		0.00377
(1.00) 		0.103
(1.00)
amp 16p11 2 122 (28%) 317 0.541
(1.00) 		0.157
(1.00) 		0.0004
(0.309) 		0.567
(1.00) 		0.00015
(0.117) 		0.562
(1.00) 		0.67
(1.00) 		0.00781
(1.00) 		1
(1.00) 		0.641
(1.00) 		7.29e-05
(0.0578) 		0.457
(1.00)
del 4p16 2 130 (30%) 309 0.00719
(1.00) 		0.954
(1.00) 		0.00074
(0.564) 		0.458
(1.00) 		0.00056
(0.429) 		0.00012
(0.0944) 		0.53
(1.00) 		0.0218
(1.00) 		0.0255
(1.00) 		0.0317
(1.00) 		0.000114
(0.0899) 		0.443
(1.00)
del 8p23 3 183 (42%) 256 0.831
(1.00) 		0.0948
(1.00) 		0.00091
(0.688) 		0.132
(1.00) 		8e-05
(0.0633) 		0.00536
(1.00) 		0.0199
(1.00) 		0.0336
(1.00) 		0.573
(1.00) 		0.0896
(1.00) 		2.63e-05
(0.021) 		0.384
(1.00)
del 18p11 31 239 (54%) 200 0.897
(1.00) 		0.00353
(1.00) 		0.00113
(0.847) 		0.902
(1.00) 		0.0293
(1.00) 		0.00014
(0.11) 		0.774
(1.00) 		3.4e-10
(2.78e-07) 		0.254
(1.00) 		0.0264
(1.00) 		0.0197
(1.00) 		0.909
(1.00)
del 19p13 3 61 (14%) 378 0.575
(1.00) 		0.119
(1.00) 		0.00479
(1.00) 		0.923
(1.00) 		0.00012
(0.0944) 		0.0306
(1.00) 		0.335
(1.00) 		0.307
(1.00) 		0.362
(1.00) 		0.078
(1.00) 		2.52e-06
(0.00203) 		1
(1.00)
amp 20q11 21 313 (71%) 126 0.755
(1.00) 		0.442
(1.00) 		0.00266
(1.00) 		0.282
(1.00) 		0.00775
(1.00) 		0.0173
(1.00) 		0.247
(1.00) 		7.13e-07
(0.000577) 		0.561
(1.00) 		0.0931
(1.00) 		0.0126
(1.00) 		0.709
(1.00)
amp 20q12 314 (72%) 125 0.891
(1.00) 		0.442
(1.00) 		0.00114
(0.854) 		0.39
(1.00) 		0.0103
(1.00) 		0.00643
(1.00) 		0.205
(1.00) 		1.11e-07
(9.01e-05) 		0.561
(1.00) 		0.0905
(1.00) 		0.0131
(1.00) 		0.652
(1.00)
amp 20q13 12 317 (72%) 122 0.636
(1.00) 		0.463
(1.00) 		0.00047
(0.361) 		0.495
(1.00) 		0.00664
(1.00) 		0.00215
(1.00) 		0.286
(1.00) 		2.39e-07
(0.000194) 		0.564
(1.00) 		0.0905
(1.00) 		0.00515
(1.00) 		0.606
(1.00)
del 1p36 11 163 (37%) 276 0.0377
(1.00) 		0.0662
(1.00) 		0.00049
(0.376) 		0.789
(1.00) 		0.0151
(1.00) 		3e-05
(0.0239) 		0.198
(1.00) 		0.00136
(1.00) 		1
(1.00) 		0.0922
(1.00) 		0.00244
(1.00) 		0.0885
(1.00)
del 4q22 1 142 (32%) 297 0.0407
(1.00) 		0.318
(1.00) 		0.00364
(1.00) 		0.162
(1.00) 		0.00043
(0.331) 		0.121
(1.00) 		0.358
(1.00) 		0.00674
(1.00) 		0.0334
(1.00) 		0.914
(1.00) 		0.000104
(0.0817) 		0.844
(1.00)
del 5q21 1 121 (28%) 318 0.0962
(1.00) 		0.122
(1.00) 		0.00036
(0.279) 		0.981
(1.00) 		0.00058
(0.444) 		0.00259
(1.00) 		0.201
(1.00) 		0.35
(1.00) 		0.0206
(1.00) 		0.445
(1.00) 		0.000235
(0.182) 		0.326
(1.00)
del 14q31 1 144 (33%) 295 0.465
(1.00) 		0.195
(1.00) 		0.227
(1.00) 		0.304
(1.00) 		0.0388
(1.00) 		0.0232
(1.00) 		0.611
(1.00) 		8.69e-06
(0.00699) 		0.554
(1.00) 		0.312
(1.00) 		0.0124
(1.00) 		0.956
(1.00)
del 17q24 3 68 (15%) 371 0.0751
(1.00) 		0.211
(1.00) 		0.00542
(1.00) 		0.232
(1.00) 		0.00266
(1.00) 		0.00101
(0.762) 		0.294
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.403
(1.00) 		4.67e-05
(0.0372) 		0.292
(1.00)
del 18q12 2 266 (61%) 173 0.884
(1.00) 		0.0102
(1.00) 		0.00064
(0.489) 		0.766
(1.00) 		0.00096
(0.725) 		0.00438
(1.00) 		0.24
(1.00) 		5.78e-09
(4.71e-06) 		0.282
(1.00) 		0.1
(1.00) 		0.00108
(0.813) 		0.891
(1.00)
del 22q13 32 153 (35%) 286 0.118
(1.00) 		0.289
(1.00) 		0.00593
(1.00) 		0.609
(1.00) 		0.00068
(0.519) 		0.0181
(1.00) 		0.689
(1.00) 		0.00184
(1.00) 		1
(1.00) 		0.54
(1.00) 		0.000153
(0.119) 		0.491
(1.00)
amp 2q33 1 88 (20%) 351 0.0321
(1.00) 		0.48
(1.00) 		0.299
(1.00) 		0.83
(1.00) 		0.0219
(1.00) 		0.104
(1.00) 		0.474
(1.00) 		0.384
(1.00) 		0.49
(1.00) 		0.113
(1.00) 		0.0086
(1.00) 		0.388
(1.00)
amp 5p13 2 86 (20%) 353 0.684
(1.00) 		0.0918
(1.00) 		0.237
(1.00) 		0.514
(1.00) 		0.0288
(1.00) 		0.324
(1.00) 		0.47
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.152
(1.00) 		0.0182
(1.00) 		0.268
(1.00)
amp 5q22 3 43 (10%) 396 0.576
(1.00) 		0.697
(1.00) 		0.568
(1.00) 		0.939
(1.00) 		0.305
(1.00) 		0.055
(1.00) 		0.631
(1.00) 		0.243
(1.00) 		0.267
(1.00) 		0.0888
(1.00) 		0.18
(1.00) 		0.594
(1.00)
amp 6p21 1 94 (21%) 345 0.941
(1.00) 		0.749
(1.00) 		0.0367
(1.00) 		0.628
(1.00) 		0.00956
(1.00) 		0.167
(1.00) 		0.244
(1.00) 		0.128
(1.00) 		0.00957
(1.00) 		0.631
(1.00) 		0.00904
(1.00) 		0.155
(1.00)
amp 8p11 23 155 (35%) 284 0.758
(1.00) 		0.367
(1.00) 		0.488
(1.00) 		0.725
(1.00) 		0.714
(1.00) 		0.324
(1.00) 		0.764
(1.00) 		0.188
(1.00) 		0.285
(1.00) 		0.669
(1.00) 		0.561
(1.00) 		0.748
(1.00)
amp 8p11 21 184 (42%) 255 0.985
(1.00) 		0.291
(1.00) 		0.464
(1.00) 		0.607
(1.00) 		0.576
(1.00) 		0.252
(1.00) 		0.208
(1.00) 		0.322
(1.00) 		0.575
(1.00) 		0.26
(1.00) 		0.496
(1.00) 		0.412
(1.00)
amp 8q12 1 230 (52%) 209 0.769
(1.00) 		0.0556
(1.00) 		0.646
(1.00) 		0.683
(1.00) 		0.512
(1.00) 		0.072
(1.00) 		0.566
(1.00) 		0.0255
(1.00) 		0.25
(1.00) 		0.464
(1.00) 		0.401
(1.00) 		0.647
(1.00)
amp 8q24 21 254 (58%) 185 0.641
(1.00) 		0.0606
(1.00) 		0.0964
(1.00) 		0.37
(1.00) 		0.277
(1.00) 		0.0339
(1.00) 		0.287
(1.00) 		0.0897
(1.00) 		0.267
(1.00) 		0.369
(1.00) 		0.28
(1.00) 		0.69
(1.00)
amp 11p15 5 90 (21%) 349 0.992
(1.00) 		0.0199
(1.00) 		0.424
(1.00) 		0.183
(1.00) 		0.0483
(1.00) 		0.215
(1.00) 		0.724
(1.00) 		0.00084
(0.637) 		0.108
(1.00) 		0.437
(1.00) 		0.0451
(1.00) 		0.226
(1.00)
amp 12p13 33 110 (25%) 329 0.211
(1.00) 		0.372
(1.00) 		0.107
(1.00) 		0.128
(1.00) 		0.309
(1.00) 		0.173
(1.00) 		0.826
(1.00) 		0.873
(1.00) 		0.576
(1.00) 		0.443
(1.00) 		0.465
(1.00) 		0.596
(1.00)
amp 17p11 2 43 (10%) 396 0.538
(1.00) 		0.599
(1.00) 		0.675
(1.00) 		0.644
(1.00) 		0.77
(1.00) 		0.51
(1.00) 		0.749
(1.00) 		1
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.693
(1.00) 		0.17
(1.00)
amp 17q12 111 (25%) 328 0.143
(1.00) 		0.313
(1.00) 		0.204
(1.00) 		0.165
(1.00) 		0.145
(1.00) 		0.00986
(1.00) 		0.272
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.16
(1.00) 		0.356
(1.00)
amp 17q24 1 102 (23%) 337 0.0379
(1.00) 		0.518
(1.00) 		0.65
(1.00) 		0.241
(1.00) 		0.497
(1.00) 		0.0551
(1.00) 		0.572
(1.00) 		0.0681
(1.00) 		0.549
(1.00) 		0.28
(1.00) 		0.676
(1.00) 		0.942
(1.00)
amp 19p13 2 73 (17%) 366 0.995
(1.00) 		0.885
(1.00) 		0.723
(1.00) 		0.633
(1.00) 		0.0326
(1.00) 		0.0275
(1.00) 		0.0718
(1.00) 		0.35
(1.00) 		0.421
(1.00) 		0.109
(1.00) 		0.728
(1.00) 		0.929
(1.00)
amp 19q13 11 92 (21%) 347 0.491
(1.00) 		0.913
(1.00) 		0.788
(1.00) 		0.679
(1.00) 		0.118
(1.00) 		0.0897
(1.00) 		0.0999
(1.00) 		0.494
(1.00) 		0.507
(1.00) 		0.767
(1.00) 		0.765
(1.00) 		1
(1.00)
amp 20p12 1 203 (46%) 236 0.0536
(1.00) 		0.749
(1.00) 		0.00081
(0.615) 		0.698
(1.00) 		0.396
(1.00) 		0.00607
(1.00) 		0.213
(1.00) 		0.0247
(1.00) 		0.0981
(1.00) 		0.0208
(1.00) 		0.304
(1.00) 		0.319
(1.00)
amp 20p11 21 244 (56%) 195 0.232
(1.00) 		0.552
(1.00) 		0.00143
(1.00) 		0.769
(1.00) 		0.197
(1.00) 		0.00365
(1.00) 		0.25
(1.00) 		0.00116
(0.867) 		0.258
(1.00) 		0.0184
(1.00) 		0.316
(1.00) 		0.482
(1.00)
del 1p33 119 (27%) 320 0.00859
(1.00) 		0.905
(1.00) 		0.0174
(1.00) 		0.4
(1.00) 		0.0141
(1.00) 		0.00983
(1.00) 		0.52
(1.00) 		0.0601
(1.00) 		0.566
(1.00) 		0.249
(1.00) 		0.00486
(1.00) 		0.367
(1.00)
del 1p13 1 114 (26%) 325 0.141
(1.00) 		0.459
(1.00) 		0.00697
(1.00) 		0.582
(1.00) 		0.00354
(1.00) 		0.00292
(1.00) 		0.327
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.000533
(0.409) 		0.299
(1.00)
del 1q43 52 (12%) 387 0.636
(1.00) 		0.259
(1.00) 		0.0725
(1.00) 		0.112
(1.00) 		0.476
(1.00) 		0.255
(1.00) 		0.768
(1.00) 		0.829
(1.00) 		0.316
(1.00) 		0.436
(1.00) 		0.284
(1.00) 		0.184
(1.00)
del 2p21 16 (4%) 423 0.713
(1.00) 		0.359
(1.00) 		0.156
(1.00) 		0.516
(1.00) 		0.288
(1.00) 		0.218
(1.00) 		0.611
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.339
(1.00) 		0.758
(1.00)
del 2q22 1 24 (5%) 415 0.585
(1.00) 		0.738
(1.00) 		0.241
(1.00) 		0.279
(1.00) 		0.0695
(1.00) 		0.627
(1.00) 		0.676
(1.00) 		1
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.00903
(1.00) 		0.00726
(1.00)
del 3p26 2 69 (16%) 370 0.305
(1.00) 		0.436
(1.00) 		0.0582
(1.00) 		0.151
(1.00) 		0.00825
(1.00) 		0.0204
(1.00) 		0.896
(1.00) 		0.0528
(1.00) 		1
(1.00) 		0.339
(1.00) 		0.00605
(1.00) 		0.906
(1.00)
del 3p14 2 85 (19%) 354 0.62
(1.00) 		0.299
(1.00) 		0.223
(1.00) 		0.12
(1.00) 		0.037
(1.00) 		0.141
(1.00) 		0.545
(1.00) 		0.48
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.0195
(1.00) 		0.719
(1.00)
del 3q26 31 44 (10%) 395 0.643
(1.00) 		0.397
(1.00) 		0.214
(1.00) 		0.19
(1.00) 		0.236
(1.00) 		0.442
(1.00) 		0.751
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.775
(1.00) 		0.422
(1.00) 		0.816
(1.00)
del 4q35 1 150 (34%) 289 0.523
(1.00) 		0.0698
(1.00) 		0.0537
(1.00) 		0.329
(1.00) 		0.00295
(1.00) 		0.056
(1.00) 		0.314
(1.00) 		0.0774
(1.00) 		0.0394
(1.00) 		0.371
(1.00) 		0.000404
(0.312) 		0.357
(1.00)
del 5q12 1 100 (23%) 339 0.0627
(1.00) 		0.0469
(1.00) 		0.00533
(1.00) 		0.9
(1.00) 		0.00244
(1.00) 		0.0117
(1.00) 		0.173
(1.00) 		0.0688
(1.00) 		0.0115
(1.00) 		0.728
(1.00) 		0.00112
(0.842) 		0.477
(1.00)
del 5q22 2 125 (28%) 314 0.0819
(1.00) 		0.163
(1.00) 		0.0179
(1.00) 		0.977
(1.00) 		0.0125
(1.00) 		0.00326
(1.00) 		0.112
(1.00) 		0.163
(1.00) 		0.0227
(1.00) 		0.123
(1.00) 		0.00646
(1.00) 		0.264
(1.00)
del 6p25 3 54 (12%) 385 0.0716
(1.00) 		0.0767
(1.00) 		0.692
(1.00) 		0.416
(1.00) 		0.88
(1.00) 		0.278
(1.00) 		0.08
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.859
(1.00) 		0.0239
(1.00)
del 6q26 61 (14%) 378 0.0148
(1.00) 		0.888
(1.00) 		0.113
(1.00) 		0.452
(1.00) 		0.00616
(1.00) 		0.0688
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00) 		0.152
(1.00) 		0.00102
(0.767) 		0.0619
(1.00)
del 7q31 1 12 (3%) 427 0.917
(1.00) 		0.972
(1.00) 		0.712
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.164
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.48
(1.00)
del 8q11 1 30 (7%) 409 0.801
(1.00) 		0.401
(1.00) 		0.128
(1.00) 		0.618
(1.00) 		0.125
(1.00) 		0.169
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.0996
(1.00) 		0.0418
(1.00)
del 9p21 3 59 (13%) 380 0.714
(1.00) 		0.0339
(1.00) 		0.838
(1.00) 		0.329
(1.00) 		0.296
(1.00) 		0.398
(1.00) 		0.208
(1.00) 		0.041
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.0991
(1.00) 		0.429
(1.00)
del 10p15 3 77 (18%) 362 0.81
(1.00) 		0.429
(1.00) 		0.0017
(1.00) 		0.926
(1.00) 		0.00685
(1.00) 		0.00349
(1.00) 		0.802
(1.00) 		0.464
(1.00) 		0.0809
(1.00) 		0.672
(1.00) 		0.00251
(1.00) 		0.553
(1.00)
del 10q21 1 94 (21%) 345 0.571
(1.00) 		0.04
(1.00) 		0.00534
(1.00) 		0.979
(1.00) 		0.008
(1.00) 		0.0419
(1.00) 		0.908
(1.00) 		0.0605
(1.00) 		0.117
(1.00) 		0.0728
(1.00) 		0.00385
(1.00) 		0.628
(1.00)
del 10q23 31 105 (24%) 334 0.954
(1.00) 		0.00483
(1.00) 		0.00374
(1.00) 		0.918
(1.00) 		0.0319
(1.00) 		0.0141
(1.00) 		0.578
(1.00) 		0.0492
(1.00) 		0.144
(1.00) 		0.186
(1.00) 		0.00903
(1.00) 		0.782
(1.00)
del 10q25 2 106 (24%) 333 0.0754
(1.00) 		0.0629
(1.00) 		0.0338
(1.00) 		0.424
(1.00) 		0.00505
(1.00) 		0.0583
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.146
(1.00) 		0.0801
(1.00) 		0.00369
(1.00) 		0.972
(1.00)
del 12p13 2 57 (13%) 382 0.021
(1.00) 		0.154
(1.00) 		0.127
(1.00) 		0.813
(1.00) 		0.0533
(1.00) 		0.094
(1.00) 		0.777
(1.00) 		0.02
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.0485
(1.00) 		0.867
(1.00)
del 15q11 2 170 (39%) 269 0.916
(1.00) 		0.446
(1.00) 		0.0127
(1.00) 		0.969
(1.00) 		0.00877
(1.00) 		0.00964
(1.00) 		0.695
(1.00) 		0.0307
(1.00) 		0.0574
(1.00) 		0.432
(1.00) 		0.00614
(1.00) 		0.165
(1.00)
del 15q15 2 164 (37%) 275 0.712
(1.00) 		0.172
(1.00) 		0.0176
(1.00) 		0.964
(1.00) 		0.00624
(1.00) 		0.00159
(1.00) 		0.693
(1.00) 		0.029
(1.00) 		0.0515
(1.00) 		0.273
(1.00) 		0.00897
(1.00) 		0.161
(1.00)
del 15q21 1 162 (37%) 277 0.362
(1.00) 		0.422
(1.00) 		0.0757
(1.00) 		0.978
(1.00) 		0.0369
(1.00) 		0.00334
(1.00) 		0.552
(1.00) 		0.0291
(1.00) 		0.0497
(1.00) 		0.176
(1.00) 		0.0421
(1.00) 		0.0669
(1.00)
del 15q22 33 154 (35%) 285 0.929
(1.00) 		0.277
(1.00) 		0.00841
(1.00) 		0.566
(1.00) 		0.00808
(1.00) 		0.00298
(1.00) 		0.618
(1.00) 		0.0278
(1.00) 		0.0426
(1.00) 		0.413
(1.00) 		0.00765
(1.00) 		0.101
(1.00)
del 16p13 3 54 (12%) 385 0.00267
(1.00) 		0.503
(1.00) 		0.0318
(1.00) 		0.0354
(1.00) 		0.118
(1.00) 		0.172
(1.00) 		0.771
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.0727
(1.00) 		0.304
(1.00)
del 16q23 1 58 (13%) 381 0.0127
(1.00) 		0.862
(1.00) 		0.849
(1.00) 		0.539
(1.00) 		0.699
(1.00) 		0.294
(1.00) 		0.325
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.795
(1.00) 		0.49
(1.00) 		0.108
(1.00)
del 20p12 1 83 (19%) 356 0.308
(1.00) 		0.646
(1.00) 		0.487
(1.00) 		0.59
(1.00) 		0.243
(1.00) 		0.979
(1.00) 		0.903
(1.00) 		0.0739
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.18
(1.00) 		0.369
(1.00)
del 21q11 2 136 (31%) 303 0.361
(1.00) 		0.779
(1.00) 		0.262
(1.00) 		0.37
(1.00) 		0.0357
(1.00) 		0.188
(1.00) 		0.837
(1.00) 		0.00213
(1.00) 		0.228
(1.00) 		0.625
(1.00) 		0.0238
(1.00) 		0.506
(1.00)
'amp_7p21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S1.  Gene #5: 'amp_7p21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
AMP PEAK 5(7P21.2) MUTATED 39 1 15 54 2 0 13 11 37 26 30 14 1
AMP PEAK 5(7P21.2) WILD-TYPE 33 0 13 77 6 1 8 1 18 12 13 4 1

Figure S1.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_7p21.2' versus 'PATHOLOGY.N.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S2.  Gene #5: 'amp_7p21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
AMP PEAK 5(7P21.2) MUTATED 122 70 56
AMP PEAK 5(7P21.2) WILD-TYPE 134 33 23

Figure S2.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'amp_7p21.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000153 (Wilcoxon-test), Q value = 0.12

Table S3.  Gene #5: 'amp_7p21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
AMP PEAK 5(7P21.2) MUTATED 241 2.5 (4.8)
AMP PEAK 5(7P21.2) WILD-TYPE 174 1.5 (3.9)

Figure S3.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'amp_13q12.13' versus 'NEOPLASM.DISEASESTAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S4.  Gene #12: 'amp_13q12.13' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
AMP PEAK 12(13Q12.13) MUTATED 42 0 14 68 2 1 11 11 38 24 36 15 0
AMP PEAK 12(13Q12.13) WILD-TYPE 30 1 14 63 6 0 10 1 17 14 7 3 2

Figure S4.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_13q12.13' versus 'HISTOLOGICAL.TYPE'

P value = 1.05e-07 (Fisher's exact test), Q value = 8.6e-05

Table S5.  Gene #12: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
AMP PEAK 12(13Q12.13) MUTATED 249 17
AMP PEAK 12(13Q12.13) WILD-TYPE 129 42

Figure S5.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_13q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S6.  Gene #13: 'amp_13q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
AMP PEAK 13(13Q22.1) MUTATED 44 0 15 66 2 1 12 11 38 26 35 15 0
AMP PEAK 13(13Q22.1) WILD-TYPE 28 1 13 65 6 0 9 1 17 12 8 3 2

Figure S6.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_13q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1.05e-06 (Fisher's exact test), Q value = 0.00084

Table S7.  Gene #13: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
AMP PEAK 13(13Q22.1) MUTATED 251 19
AMP PEAK 13(13Q22.1) WILD-TYPE 127 40

Figure S7.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_16p11.2' versus 'PATHOLOGY.N.STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.12

Table S8.  Gene #14: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
AMP PEAK 14(16P11.2) MUTATED 52 37 33
AMP PEAK 14(16P11.2) WILD-TYPE 204 66 46

Figure S8.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'amp_16p11.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.29e-05 (Wilcoxon-test), Q value = 0.058

Table S9.  Gene #14: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
AMP PEAK 14(16P11.2) MUTATED 117 3.3 (6.2)
AMP PEAK 14(16P11.2) WILD-TYPE 298 1.6 (3.4)

Figure S9.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'amp_16q12.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.16

Table S10.  Gene #15: 'amp_16q12.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
AMP PEAK 15(16Q12.1) MUTATED 13 1 3 22 1 0 5 9 20 14 11 4 1
AMP PEAK 15(16Q12.1) WILD-TYPE 59 0 25 109 7 1 16 3 35 24 32 14 1

Figure S10.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_16q12.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #15: 'amp_16q12.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
AMP PEAK 15(16Q12.1) MUTATED 45 35 28
AMP PEAK 15(16Q12.1) WILD-TYPE 211 68 51

Figure S11.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'amp_16q12.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000209 (Wilcoxon-test), Q value = 0.16

Table S12.  Gene #15: 'amp_16q12.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
AMP PEAK 15(16Q12.1) MUTATED 104 3.2 (6.2)
AMP PEAK 15(16Q12.1) WILD-TYPE 311 1.7 (3.6)

Figure S12.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'amp_20q11.21' versus 'HISTOLOGICAL.TYPE'

P value = 7.13e-07 (Fisher's exact test), Q value = 0.00058

Table S13.  Gene #23: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
AMP PEAK 23(20Q11.21) MUTATED 286 25
AMP PEAK 23(20Q11.21) WILD-TYPE 92 34

Figure S13.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-07 (Fisher's exact test), Q value = 9e-05

Table S14.  Gene #24: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
AMP PEAK 24(20Q12) MUTATED 288 24
AMP PEAK 24(20Q12) WILD-TYPE 90 35

Figure S14.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.12' versus 'HISTOLOGICAL.TYPE'

P value = 2.39e-07 (Fisher's exact test), Q value = 0.00019

Table S15.  Gene #25: 'amp_20q13.12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
AMP PEAK 25(20Q13.12) MUTATED 290 25
AMP PEAK 25(20Q13.12) WILD-TYPE 88 34

Figure S15.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_1p36.11' versus 'PATHOLOGY.M.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.024

Table S16.  Gene #26: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 52 8 2 50
DEL PEAK 1(1P36.11) MUTATED 105 35 4 0 18
DEL PEAK 1(1P36.11) WILD-TYPE 215 17 4 2 32

Figure S16.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_4p16.2' versus 'PATHOLOGY.M.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S17.  Gene #35: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 52 8 2 50
DEL PEAK 10(4P16.2) MUTATED 79 29 4 0 14
DEL PEAK 10(4P16.2) WILD-TYPE 241 23 4 2 36

Figure S17.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_4p16.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000114 (Wilcoxon-test), Q value = 0.09

Table S18.  Gene #35: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 10(4P16.2) MUTATED 126 3.0 (4.7)
DEL PEAK 10(4P16.2) WILD-TYPE 289 1.7 (4.3)

Figure S18.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_4q22.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000104 (Wilcoxon-test), Q value = 0.082

Table S19.  Gene #36: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 11(4Q22.1) MUTATED 136 2.9 (4.5)
DEL PEAK 11(4Q22.1) WILD-TYPE 279 1.7 (4.4)

Figure S19.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_5q21.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000235 (Wilcoxon-test), Q value = 0.18

Table S20.  Gene #39: 'del_5q21.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 14(5Q21.1) MUTATED 116 3.0 (4.9)
DEL PEAK 14(5Q21.1) WILD-TYPE 299 1.7 (4.2)

Figure S20.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_8p23.3' versus 'PATHOLOGY.N.STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.063

Table S21.  Gene #44: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
DEL PEAK 19(8P23.3) MUTATED 84 50 48
DEL PEAK 19(8P23.3) WILD-TYPE 172 53 31

Figure S21.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_8p23.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.63e-05 (Wilcoxon-test), Q value = 0.021

Table S22.  Gene #44: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 19(8P23.3) MUTATED 177 2.9 (5.5)
DEL PEAK 19(8P23.3) WILD-TYPE 238 1.4 (3.3)

Figure S22.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S23.  Gene #45: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
DEL PEAK 20(8P22) MUTATED 23 0 9 42 2 0 10 8 30 25 29 14 1
DEL PEAK 20(8P22) WILD-TYPE 49 1 19 89 6 1 11 4 25 13 14 4 1

Figure S23.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S24.  Gene #45: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
DEL PEAK 20(8P22) MUTATED 87 54 54
DEL PEAK 20(8P22) WILD-TYPE 169 49 25

Figure S24.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'PATHOLOGY.M.STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #45: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 52 8 2 50
DEL PEAK 20(8P22) MUTATED 130 38 5 1 20
DEL PEAK 20(8P22) WILD-TYPE 190 14 3 1 30

Figure S25.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_8p22' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.68e-07 (Wilcoxon-test), Q value = 0.00022

Table S26.  Gene #45: 'del_8p22' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 20(8P22) MUTATED 190 3.0 (5.4)
DEL PEAK 20(8P22) WILD-TYPE 225 1.3 (3.3)

Figure S26.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_14q31.1' versus 'HISTOLOGICAL.TYPE'

P value = 8.69e-06 (Fisher's exact test), Q value = 0.007

Table S27.  Gene #53: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
DEL PEAK 28(14Q31.1) MUTATED 137 5
DEL PEAK 28(14Q31.1) WILD-TYPE 241 54

Figure S27.  Get High-res Image Gene #53: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S28.  Gene #60: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
DEL PEAK 35(17P12) MUTATED 35 0 13 55 1 1 12 11 34 29 33 13 2
DEL PEAK 35(17P12) WILD-TYPE 37 1 15 76 7 0 9 1 21 9 10 5 0

Figure S28.  Get High-res Image Gene #60: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29.  Gene #60: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
DEL PEAK 35(17P12) MUTATED 118 69 57
DEL PEAK 35(17P12) WILD-TYPE 138 34 22

Figure S29.  Get High-res Image Gene #60: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 2.35e-06 (Fisher's exact test), Q value = 0.0019

Table S30.  Gene #60: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
DEL PEAK 35(17P12) MUTATED 227 16
DEL PEAK 35(17P12) WILD-TYPE 151 43

Figure S30.  Get High-res Image Gene #60: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.18e-06 (Wilcoxon-test), Q value = 0.00095

Table S31.  Gene #60: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 35(17P12) MUTATED 232 2.8 (5.4)
DEL PEAK 35(17P12) WILD-TYPE 183 1.2 (2.6)

Figure S31.  Get High-res Image Gene #60: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_17q24.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.67e-05 (Wilcoxon-test), Q value = 0.037

Table S32.  Gene #61: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 36(17Q24.3) MUTATED 64 3.0 (3.9)
DEL PEAK 36(17Q24.3) WILD-TYPE 351 1.9 (4.5)

Figure S32.  Get High-res Image Gene #61: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_18p11.31' versus 'PATHOLOGY.M.STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #62: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 52 8 2 50
DEL PEAK 37(18P11.31) MUTATED 160 40 8 1 27
DEL PEAK 37(18P11.31) WILD-TYPE 160 12 0 1 23

Figure S33.  Get High-res Image Gene #62: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_18p11.31' versus 'HISTOLOGICAL.TYPE'

P value = 3.4e-10 (Fisher's exact test), Q value = 2.8e-07

Table S34.  Gene #62: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
DEL PEAK 37(18P11.31) MUTATED 227 10
DEL PEAK 37(18P11.31) WILD-TYPE 151 49

Figure S34.  Get High-res Image Gene #62: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 5.78e-09 (Fisher's exact test), Q value = 4.7e-06

Table S35.  Gene #63: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
DEL PEAK 38(18Q12.2) MUTATED 250 15
DEL PEAK 38(18Q12.2) WILD-TYPE 128 44

Figure S35.  Get High-res Image Gene #63: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.04

Table S36.  Gene #64: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
DEL PEAK 39(18Q21.2) MUTATED 39 0 16 71 2 1 11 11 39 30 37 15 2
DEL PEAK 39(18Q21.2) WILD-TYPE 33 1 12 60 6 0 10 1 16 8 6 3 0

Figure S36.  Get High-res Image Gene #64: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_18q21.2' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.016

Table S37.  Gene #64: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
DEL PEAK 39(18Q21.2) MUTATED 141 76 62
DEL PEAK 39(18Q21.2) WILD-TYPE 115 27 17

Figure S37.  Get High-res Image Gene #64: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_18q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 7.32e-09 (Fisher's exact test), Q value = 6e-06

Table S38.  Gene #64: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
DEL PEAK 39(18Q21.2) MUTATED 262 17
DEL PEAK 39(18Q21.2) WILD-TYPE 116 42

Figure S38.  Get High-res Image Gene #64: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.57e-05 (Wilcoxon-test), Q value = 0.02

Table S39.  Gene #64: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 39(18Q21.2) MUTATED 267 2.4 (4.6)
DEL PEAK 39(18Q21.2) WILD-TYPE 148 1.5 (4.1)

Figure S39.  Get High-res Image Gene #64: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_19p13.3' versus 'PATHOLOGY.N.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.094

Table S40.  Gene #65: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
DEL PEAK 40(19P13.3) MUTATED 23 15 23
DEL PEAK 40(19P13.3) WILD-TYPE 233 88 56

Figure S40.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_19p13.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.52e-06 (Wilcoxon-test), Q value = 0.002

Table S41.  Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 40(19P13.3) MUTATED 59 4.3 (6.0)
DEL PEAK 40(19P13.3) WILD-TYPE 356 1.7 (4.0)

Figure S41.  Get High-res Image Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_22q13.32' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000153 (Wilcoxon-test), Q value = 0.12

Table S42.  Gene #68: 'del_22q13.32' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
DEL PEAK 43(22Q13.32) MUTATED 145 2.8 (4.9)
DEL PEAK 43(22Q13.32) WILD-TYPE 270 1.7 (4.2)

Figure S42.  Get High-res Image Gene #68: 'del_22q13.32' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = COAD-TP.merged_data.txt

  • Number of patients = 439

  • Number of significantly focal cnvs = 68

  • 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)
Made with Nozzle