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 69 focal events and 12 clinical features across 430 patients, 43 significant findings detected with Q value < 0.25.

  • amp_13q12.13 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_13q22.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • amp_20p11.23 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.M.STAGE'.

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

  • amp_20q12 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_20q13.32 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_5q21.3 cnv correlated to 'PATHOLOGY.N.STAGE' and '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_8p11.21 cnv correlated to '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_18q22.1 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 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 43 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 192 (45%) 238 0.257
(1.00) 		0.0341
(1.00) 		4e-05
(0.0324) 		0.155
(1.00) 		1e-05
(0.00815) 		0.00022
(0.174) 		0.0993
(1.00) 		0.0136
(1.00) 		0.588
(1.00) 		0.0534
(1.00) 		1.56e-06
(0.00128) 		0.404
(1.00)
del 17p12 239 (56%) 191 0.473
(1.00) 		0.0111
(1.00) 		1e-05
(0.00815) 		0.882
(1.00) 		1e-05
(0.00815) 		0.00388
(1.00) 		0.285
(1.00) 		1.99e-06
(0.00163) 		0.258
(1.00) 		0.184
(1.00) 		1.93e-06
(0.00159) 		0.869
(1.00)
del 18q21 2 271 (63%) 159 0.827
(1.00) 		0.0363
(1.00) 		4e-05
(0.0324) 		0.858
(1.00) 		0.00014
(0.112) 		0.00113
(0.864) 		0.0888
(1.00) 		2.13e-09
(1.76e-06) 		0.299
(1.00) 		0.138
(1.00) 		6.76e-05
(0.0545) 		0.686
(1.00)
del 18q22 1 271 (63%) 159 0.914
(1.00) 		0.0727
(1.00) 		0.00016
(0.127) 		0.857
(1.00) 		0.00026
(0.205) 		0.00149
(1.00) 		0.0888
(1.00) 		2.35e-10
(1.94e-07) 		0.299
(1.00) 		0.23
(1.00) 		0.000177
(0.14) 		0.727
(1.00)
amp 16p11 2 120 (28%) 310 0.645
(1.00) 		0.154
(1.00) 		0.00077
(0.595) 		0.499
(1.00) 		0.00018
(0.143) 		0.541
(1.00) 		0.667
(1.00) 		0.00611
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.000119
(0.0956) 		0.495
(1.00)
amp 20p11 23 211 (49%) 219 0.163
(1.00) 		0.875
(1.00) 		6e-05
(0.0485) 		0.963
(1.00) 		0.0686
(1.00) 		0.00012
(0.0961) 		0.386
(1.00) 		0.0135
(1.00) 		0.117
(1.00) 		0.0094
(1.00) 		0.0874
(1.00) 		0.41
(1.00)
amp 20q12 308 (72%) 122 0.93
(1.00) 		0.341
(1.00) 		0.00029
(0.228) 		0.394
(1.00) 		0.0237
(1.00) 		0.00187
(1.00) 		0.284
(1.00) 		7.62e-07
(0.000628) 		0.562
(1.00) 		0.129
(1.00) 		0.0325
(1.00) 		0.659
(1.00)
del 4p16 2 128 (30%) 302 0.0163
(1.00) 		0.932
(1.00) 		0.00083
(0.64) 		0.593
(1.00) 		0.00036
(0.282) 		0.00019
(0.151) 		0.673
(1.00) 		0.0259
(1.00) 		0.0259
(1.00) 		0.0361
(1.00) 		8.83e-05
(0.071) 		0.441
(1.00)
del 5q21 3 121 (28%) 309 0.179
(1.00) 		0.071
(1.00) 		0.00123
(0.94) 		0.932
(1.00) 		0.00012
(0.0961) 		0.0179
(1.00) 		0.521
(1.00) 		0.199
(1.00) 		0.0219
(1.00) 		0.25
(1.00) 		5.41e-05
(0.0437) 		0.0657
(1.00)
del 8p23 3 178 (41%) 252 0.951
(1.00) 		0.0982
(1.00) 		0.00273
(1.00) 		0.132
(1.00) 		8e-05
(0.0644) 		0.00943
(1.00) 		0.0507
(1.00) 		0.0564
(1.00) 		0.572
(1.00) 		0.105
(1.00) 		8.95e-05
(0.0719) 		0.431
(1.00)
del 18p11 31 231 (54%) 199 0.677
(1.00) 		0.00705
(1.00) 		0.00193
(1.00) 		0.943
(1.00) 		0.0405
(1.00) 		0.00026
(0.205) 		0.847
(1.00) 		2.31e-11
(1.91e-08) 		0.252
(1.00) 		0.028
(1.00) 		0.034
(1.00) 		1
(1.00)
del 19p13 3 59 (14%) 371 0.898
(1.00) 		0.188
(1.00) 		0.00094
(0.721) 		0.966
(1.00) 		0.00013
(0.104) 		0.026
(1.00) 		0.483
(1.00) 		0.204
(1.00) 		0.358
(1.00) 		0.0741
(1.00) 		1.67e-06
(0.00137) 		1
(1.00)
amp 13q12 13 261 (61%) 169 0.548
(1.00) 		0.567
(1.00) 		0.00044
(0.344) 		0.962
(1.00) 		0.00084
(0.647) 		0.00065
(0.504) 		0.843
(1.00) 		4.9e-07
(0.000404) 		0.283
(1.00) 		0.0334
(1.00) 		0.00515
(1.00) 		0.134
(1.00)
amp 13q22 1 265 (62%) 165 0.379
(1.00) 		0.633
(1.00) 		0.00057
(0.444) 		0.925
(1.00) 		0.00041
(0.321) 		0.00244
(1.00) 		0.322
(1.00) 		4.77e-06
(0.0039) 		0.289
(1.00) 		0.0727
(1.00) 		0.00602
(1.00) 		0.106
(1.00)
amp 20q11 21 307 (71%) 123 0.791
(1.00) 		0.343
(1.00) 		0.00092
(0.707) 		0.279
(1.00) 		0.0192
(1.00) 		0.00523
(1.00) 		0.336
(1.00) 		4.36e-06
(0.00356) 		0.561
(1.00) 		0.135
(1.00) 		0.0313
(1.00) 		0.723
(1.00)
amp 20q13 32 311 (72%) 119 0.847
(1.00) 		0.389
(1.00) 		0.00062
(0.482) 		0.337
(1.00) 		0.0172
(1.00) 		0.00273
(1.00) 		0.332
(1.00) 		2.84e-06
(0.00233) 		0.564
(1.00) 		0.132
(1.00) 		0.014
(1.00) 		0.658
(1.00)
del 1p36 11 161 (37%) 269 0.0679
(1.00) 		0.0413
(1.00) 		0.00107
(0.82) 		0.805
(1.00) 		0.0119
(1.00) 		6e-05
(0.0485) 		0.233
(1.00) 		0.00155
(1.00) 		1
(1.00) 		0.0832
(1.00) 		0.00194
(1.00) 		0.126
(1.00)
del 4q22 1 138 (32%) 292 0.0639
(1.00) 		0.379
(1.00) 		0.00175
(1.00) 		0.202
(1.00) 		0.0009
(0.692) 		0.137
(1.00) 		0.536
(1.00) 		0.00805
(1.00) 		0.0326
(1.00) 		0.924
(1.00) 		0.000257
(0.203) 		0.909
(1.00)
del 8p11 21 45 (10%) 385 0.515
(1.00) 		0.291
(1.00) 		0.00319
(1.00) 		0.109
(1.00) 		0.00196
(1.00) 		0.0404
(1.00) 		0.875
(1.00) 		0.488
(1.00) 		0.283
(1.00) 		0.109
(1.00) 		0.000229
(0.181) 		0.192
(1.00)
del 14q31 1 141 (33%) 289 0.483
(1.00) 		0.195
(1.00) 		0.168
(1.00) 		0.298
(1.00) 		0.0445
(1.00) 		0.0237
(1.00) 		0.609
(1.00) 		2.35e-05
(0.0191) 		0.554
(1.00) 		0.302
(1.00) 		0.0179
(1.00) 		0.906
(1.00)
del 17q24 3 64 (15%) 366 0.118
(1.00) 		0.358
(1.00) 		0.0118
(1.00) 		0.544
(1.00) 		0.00532
(1.00) 		0.0385
(1.00) 		0.279
(1.00) 		1
(1.00) 		1
(1.00) 		0.334
(1.00) 		0.000225
(0.178) 		0.221
(1.00)
del 18q12 2 257 (60%) 173 0.75
(1.00) 		0.0183
(1.00) 		0.00067
(0.519) 		0.721
(1.00) 		0.00232
(1.00) 		0.00348
(1.00) 		0.325
(1.00) 		1.74e-10
(1.44e-07) 		0.277
(1.00) 		0.149
(1.00) 		0.00316
(1.00) 		0.648
(1.00)
del 22q13 32 150 (35%) 280 0.15
(1.00) 		0.395
(1.00) 		0.00297
(1.00) 		0.596
(1.00) 		0.00064
(0.497) 		0.0105
(1.00) 		0.761
(1.00) 		0.00142
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.000127
(0.101) 		0.51
(1.00)
amp 2q33 1 84 (20%) 346 0.0343
(1.00) 		0.274
(1.00) 		0.282
(1.00) 		0.815
(1.00) 		0.0413
(1.00) 		0.228
(1.00) 		0.396
(1.00) 		0.367
(1.00) 		0.48
(1.00) 		0.0749
(1.00) 		0.0173
(1.00) 		0.441
(1.00)
amp 5p13 2 82 (19%) 348 0.736
(1.00) 		0.125
(1.00) 		0.16
(1.00) 		0.435
(1.00) 		0.0626
(1.00) 		0.597
(1.00) 		0.326
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.0623
(1.00) 		0.287
(1.00)
amp 5q22 3 43 (10%) 387 0.612
(1.00) 		0.622
(1.00) 		0.486
(1.00) 		0.928
(1.00) 		0.255
(1.00) 		0.0272
(1.00) 		0.631
(1.00) 		0.335
(1.00) 		0.272
(1.00) 		0.1
(1.00) 		0.159
(1.00) 		0.381
(1.00)
amp 6p21 1 91 (21%) 339 0.996
(1.00) 		0.594
(1.00) 		0.0947
(1.00) 		0.439
(1.00) 		0.00964
(1.00) 		0.461
(1.00) 		0.287
(1.00) 		0.0516
(1.00) 		0.00923
(1.00) 		0.669
(1.00) 		0.0109
(1.00) 		0.102
(1.00)
amp 8p11 23 151 (35%) 279 0.839
(1.00) 		0.382
(1.00) 		0.419
(1.00) 		0.688
(1.00) 		0.713
(1.00) 		0.519
(1.00) 		0.762
(1.00) 		0.13
(1.00) 		0.283
(1.00) 		0.822
(1.00) 		0.583
(1.00) 		0.603
(1.00)
amp 8p11 21 179 (42%) 251 0.934
(1.00) 		0.358
(1.00) 		0.43
(1.00) 		0.617
(1.00) 		0.613
(1.00) 		0.461
(1.00) 		0.205
(1.00) 		0.187
(1.00) 		0.573
(1.00) 		0.301
(1.00) 		0.586
(1.00) 		0.236
(1.00)
amp 8q12 1 224 (52%) 206 0.761
(1.00) 		0.0887
(1.00) 		0.793
(1.00) 		0.74
(1.00) 		0.516
(1.00) 		0.17
(1.00) 		0.629
(1.00) 		0.0136
(1.00) 		0.25
(1.00) 		0.469
(1.00) 		0.379
(1.00) 		0.616
(1.00)
amp 8q24 21 247 (57%) 183 0.613
(1.00) 		0.0731
(1.00) 		0.276
(1.00) 		0.356
(1.00) 		0.395
(1.00) 		0.106
(1.00) 		0.381
(1.00) 		0.0585
(1.00) 		0.265
(1.00) 		0.384
(1.00) 		0.34
(1.00) 		0.49
(1.00)
amp 11p15 5 88 (20%) 342 0.864
(1.00) 		0.0293
(1.00) 		0.545
(1.00) 		0.272
(1.00) 		0.0773
(1.00) 		0.185
(1.00) 		0.632
(1.00) 		0.00202
(1.00) 		0.108
(1.00) 		0.434
(1.00) 		0.0773
(1.00) 		0.163
(1.00)
amp 12p13 33 107 (25%) 323 0.238
(1.00) 		0.207
(1.00) 		0.172
(1.00) 		0.135
(1.00) 		0.401
(1.00) 		0.303
(1.00) 		0.823
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.527
(1.00) 		0.522
(1.00)
amp 16q12 1 106 (25%) 324 0.187
(1.00) 		0.0552
(1.00) 		0.0006
(0.467) 		0.908
(1.00) 		0.00047
(0.367) 		0.364
(1.00) 		0.575
(1.00) 		0.0113
(1.00) 		0.573
(1.00) 		0.701
(1.00) 		0.000357
(0.28) 		0.2
(1.00)
amp 17p11 2 42 (10%) 388 0.585
(1.00) 		0.486
(1.00) 		0.633
(1.00) 		0.647
(1.00) 		0.686
(1.00) 		0.406
(1.00) 		0.627
(1.00) 		1
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.551
(1.00) 		0.176
(1.00)
amp 17q12 107 (25%) 323 0.206
(1.00) 		0.563
(1.00) 		0.132
(1.00) 		0.213
(1.00) 		0.16
(1.00) 		0.00599
(1.00) 		0.222
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.133
(1.00) 		0.164
(1.00) 		0.451
(1.00)
amp 17q24 1 99 (23%) 331 0.0551
(1.00) 		0.721
(1.00) 		0.475
(1.00) 		0.346
(1.00) 		0.399
(1.00) 		0.0298
(1.00) 		0.647
(1.00) 		0.0591
(1.00) 		0.545
(1.00) 		0.329
(1.00) 		0.769
(1.00) 		1
(1.00)
amp 19p13 2 70 (16%) 360 0.88
(1.00) 		0.779
(1.00) 		0.718
(1.00) 		0.704
(1.00) 		0.0169
(1.00) 		0.0307
(1.00) 		0.0371
(1.00) 		0.328
(1.00) 		0.414
(1.00) 		0.0935
(1.00) 		0.643
(1.00) 		1
(1.00)
amp 19q13 11 89 (21%) 341 0.588
(1.00) 		0.808
(1.00) 		0.811
(1.00) 		0.815
(1.00) 		0.0718
(1.00) 		0.0681
(1.00) 		0.0577
(1.00) 		0.478
(1.00) 		0.502
(1.00) 		0.758
(1.00) 		0.675
(1.00) 		0.968
(1.00)
del 1p33 117 (27%) 313 0.0104
(1.00) 		0.806
(1.00) 		0.0242
(1.00) 		0.426
(1.00) 		0.0124
(1.00) 		0.00515
(1.00) 		0.665
(1.00) 		0.0528
(1.00) 		0.566
(1.00) 		0.227
(1.00) 		0.00441
(1.00) 		0.338
(1.00)
del 1p13 1 112 (26%) 318 0.167
(1.00) 		0.383
(1.00) 		0.0097
(1.00) 		0.544
(1.00) 		0.00341
(1.00) 		0.00124
(0.946) 		0.441
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.000468
(0.365) 		0.286
(1.00)
del 1q43 51 (12%) 379 0.84
(1.00) 		0.309
(1.00) 		0.0621
(1.00) 		0.13
(1.00) 		0.406
(1.00) 		0.136
(1.00) 		0.767
(1.00) 		0.656
(1.00) 		0.316
(1.00) 		0.442
(1.00) 		0.2
(1.00) 		0.209
(1.00)
del 2p21 16 (4%) 414 0.751
(1.00) 		0.33
(1.00) 		0.185
(1.00) 		0.517
(1.00) 		0.263
(1.00) 		0.244
(1.00) 		0.611
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.316
(1.00) 		0.737
(1.00)
del 2q32 1 14 (3%) 416 0.559
(1.00) 		0.924
(1.00) 		0.337
(1.00) 		0.882
(1.00) 		0.698
(1.00) 		0.254
(1.00) 		0.427
(1.00) 		1
(1.00) 		1
(1.00) 		0.824
(1.00) 		0.497
(1.00) 		0.185
(1.00)
del 3p26 1 66 (15%) 364 0.206
(1.00) 		0.35
(1.00) 		0.0531
(1.00) 		0.145
(1.00) 		0.011
(1.00) 		0.00619
(1.00) 		1
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.0141
(1.00) 		0.949
(1.00)
del 3p14 2 81 (19%) 349 0.375
(1.00) 		0.325
(1.00) 		0.134
(1.00) 		0.13
(1.00) 		0.0429
(1.00) 		0.0841
(1.00) 		0.538
(1.00) 		0.269
(1.00) 		1
(1.00) 		0.491
(1.00) 		0.0227
(1.00) 		0.958
(1.00)
del 3q26 31 44 (10%) 386 0.55
(1.00) 		0.734
(1.00) 		0.0515
(1.00) 		0.132
(1.00) 		0.927
(1.00) 		0.475
(1.00) 		0.874
(1.00) 		0.0965
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.936
(1.00) 		0.203
(1.00)
del 4q35 1 146 (34%) 284 0.676
(1.00) 		0.0635
(1.00) 		0.06
(1.00) 		0.451
(1.00) 		0.00417
(1.00) 		0.102
(1.00) 		0.223
(1.00) 		0.0474
(1.00) 		0.0386
(1.00) 		0.367
(1.00) 		0.000776
(0.599) 		0.462
(1.00)
del 5q11 2 96 (22%) 334 0.115
(1.00) 		0.0607
(1.00) 		0.0167
(1.00) 		0.957
(1.00) 		0.00369
(1.00) 		0.0441
(1.00) 		0.246
(1.00) 		0.0362
(1.00) 		0.0109
(1.00) 		0.726
(1.00) 		0.00192
(1.00) 		0.345
(1.00)
del 5q23 1 112 (26%) 318 0.237
(1.00) 		0.199
(1.00) 		0.0304
(1.00) 		0.95
(1.00) 		0.00637
(1.00) 		0.0103
(1.00) 		0.226
(1.00) 		0.0993
(1.00) 		0.0173
(1.00) 		0.294
(1.00) 		0.00468
(1.00) 		0.111
(1.00)
del 6p25 3 54 (13%) 376 0.123
(1.00) 		0.0955
(1.00) 		0.632
(1.00) 		0.346
(1.00) 		0.88
(1.00) 		0.174
(1.00) 		0.0795
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.91
(1.00) 		0.0604
(1.00)
del 6q26 60 (14%) 370 0.0256
(1.00) 		0.962
(1.00) 		0.1
(1.00) 		0.395
(1.00) 		0.0101
(1.00) 		0.0238
(1.00) 		0.781
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.00148
(1.00) 		0.0587
(1.00)
del 7q31 1 12 (3%) 418 0.877
(1.00) 		0.934
(1.00) 		0.71
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.136
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.584
(1.00)
del 9p21 3 59 (14%) 371 0.761
(1.00) 		0.0243
(1.00) 		0.73
(1.00) 		0.32
(1.00) 		0.254
(1.00) 		0.192
(1.00) 		0.207
(1.00) 		0.0593
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.082
(1.00) 		0.394
(1.00)
del 10p15 3 75 (17%) 355 0.69
(1.00) 		0.457
(1.00) 		0.00348
(1.00) 		0.946
(1.00) 		0.0124
(1.00) 		0.00336
(1.00) 		0.799
(1.00) 		0.446
(1.00) 		0.08
(1.00) 		0.612
(1.00) 		0.00456
(1.00) 		0.514
(1.00)
del 10q21 1 90 (21%) 340 0.435
(1.00) 		0.0803
(1.00) 		0.00764
(1.00) 		0.994
(1.00) 		0.0162
(1.00) 		0.0678
(1.00) 		0.906
(1.00) 		0.0516
(1.00) 		0.112
(1.00) 		0.053
(1.00) 		0.00767
(1.00) 		0.593
(1.00)
del 10q23 31 102 (24%) 328 0.898
(1.00) 		0.0064
(1.00) 		0.0084
(1.00) 		0.93
(1.00) 		0.036
(1.00) 		0.0182
(1.00) 		0.734
(1.00) 		0.0421
(1.00) 		0.141
(1.00) 		0.176
(1.00) 		0.01
(1.00) 		0.785
(1.00)
del 10q25 2 103 (24%) 327 0.0474
(1.00) 		0.0789
(1.00) 		0.0336
(1.00) 		0.453
(1.00) 		0.00618
(1.00) 		0.0317
(1.00) 		0.91
(1.00) 		0.091
(1.00) 		0.144
(1.00) 		0.0728
(1.00) 		0.00409
(1.00) 		1
(1.00)
del 12p13 2 54 (13%) 376 0.0248
(1.00) 		0.316
(1.00) 		0.0922
(1.00) 		0.797
(1.00) 		0.0342
(1.00) 		0.167
(1.00) 		0.665
(1.00) 		0.00752
(1.00) 		1
(1.00) 		0.392
(1.00) 		0.032
(1.00) 		0.805
(1.00)
del 13q14 13 18 (4%) 412 0.83
(1.00) 		0.265
(1.00) 		0.0931
(1.00) 		0.647
(1.00) 		0.0695
(1.00) 		0.0863
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.87
(1.00) 		0.236
(1.00) 		0.0362
(1.00)
del 15q11 2 166 (39%) 264 0.936
(1.00) 		0.574
(1.00) 		0.056
(1.00) 		0.965
(1.00) 		0.0136
(1.00) 		0.0346
(1.00) 		0.843
(1.00) 		0.0174
(1.00) 		0.0569
(1.00) 		0.474
(1.00) 		0.00902
(1.00) 		0.112
(1.00)
del 15q15 2 160 (37%) 270 0.722
(1.00) 		0.244
(1.00) 		0.0547
(1.00) 		0.946
(1.00) 		0.00779
(1.00) 		0.00543
(1.00) 		0.765
(1.00) 		0.016
(1.00) 		0.0509
(1.00) 		0.328
(1.00) 		0.0132
(1.00) 		0.126
(1.00)
del 15q21 1 158 (37%) 272 0.364
(1.00) 		0.555
(1.00) 		0.187
(1.00) 		0.993
(1.00) 		0.0516
(1.00) 		0.0109
(1.00) 		0.618
(1.00) 		0.0161
(1.00) 		0.049
(1.00) 		0.202
(1.00) 		0.0597
(1.00) 		0.0341
(1.00)
del 15q22 33 152 (35%) 278 0.507
(1.00) 		0.371
(1.00) 		0.0293
(1.00) 		0.498
(1.00) 		0.0212
(1.00) 		0.00372
(1.00) 		0.614
(1.00) 		0.00597
(1.00) 		0.0436
(1.00) 		0.62
(1.00) 		0.0234
(1.00) 		0.0258
(1.00)
del 16p13 3 52 (12%) 378 0.00346
(1.00) 		0.701
(1.00) 		0.0449
(1.00) 		0.0391
(1.00) 		0.12
(1.00) 		0.356
(1.00) 		0.884
(1.00) 		1
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.0695
(1.00) 		0.346
(1.00)
del 16q23 1 56 (13%) 374 0.0161
(1.00) 		0.64
(1.00) 		0.871
(1.00) 		0.603
(1.00) 		0.583
(1.00) 		0.546
(1.00) 		0.2
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.473
(1.00) 		0.168
(1.00)
del 20p12 1 121 (28%) 309 0.4
(1.00) 		0.899
(1.00) 		0.265
(1.00) 		0.398
(1.00) 		0.21
(1.00) 		0.822
(1.00) 		0.747
(1.00) 		0.521
(1.00) 		0.562
(1.00) 		0.214
(1.00) 		0.527
(1.00) 		0.0256
(1.00)
del 20p12 1 121 (28%) 309 0.4
(1.00) 		0.899
(1.00) 		0.263
(1.00) 		0.4
(1.00) 		0.214
(1.00) 		0.822
(1.00) 		0.747
(1.00) 		0.521
(1.00) 		0.562
(1.00) 		0.213
(1.00) 		0.527
(1.00) 		0.0266
(1.00)
del 21q11 2 135 (31%) 295 0.41
(1.00) 		0.838
(1.00) 		0.206
(1.00) 		0.332
(1.00) 		0.0189
(1.00) 		0.0884
(1.00) 		0.755
(1.00) 		0.00457
(1.00) 		0.233
(1.00) 		0.672
(1.00) 		0.0127
(1.00) 		0.568
(1.00)
'amp_13q12.13' versus 'HISTOLOGICAL.TYPE'

P value = 4.9e-07 (Fisher's exact test), Q value = 4e-04

Table S1.  Gene #11: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
AMP PEAK 11(13Q12.13) MUTATED 244 16
AMP PEAK 11(13Q12.13) WILD-TYPE 129 39

Figure S1.  Get High-res Image Gene #11: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_13q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 4.77e-06 (Fisher's exact test), Q value = 0.0039

Table S2.  Gene #12: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
AMP PEAK 12(13Q22.1) MUTATED 246 18
AMP PEAK 12(13Q22.1) WILD-TYPE 127 37

Figure S2.  Get High-res Image Gene #12: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.00018 (Fisher's exact test), Q value = 0.14

Table S3.  Gene #13: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
AMP PEAK 13(16P11.2) MUTATED 52 36 32
AMP PEAK 13(16P11.2) WILD-TYPE 200 65 44

Figure S3.  Get High-res Image Gene #13: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 0.000119 (Wilcoxon-test), Q value = 0.096

Table S4.  Gene #13: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
AMP PEAK 13(16P11.2) MUTATED 115 3.3 (6.3)
AMP PEAK 13(16P11.2) WILD-TYPE 291 1.6 (3.3)

Figure S4.  Get High-res Image Gene #13: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'amp_20p11.23' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S5.  Gene #20: 'amp_20p11.23' 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 28 127 8 1 21 13 53 38 42 16 1
AMP PEAK 20(20P11.23) MUTATED 34 1 11 54 3 0 9 12 20 17 33 10 0
AMP PEAK 20(20P11.23) WILD-TYPE 38 0 17 73 5 1 12 1 33 21 9 6 1

Figure S5.  Get High-res Image Gene #20: 'amp_20p11.23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_20p11.23' versus 'PATHOLOGY.M.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.096

Table S6.  Gene #20: 'amp_20p11.23' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
AMP PEAK 20(20P11.23) MUTATED 142 35 7 0 25
AMP PEAK 20(20P11.23) WILD-TYPE 178 15 0 1 20

Figure S6.  Get High-res Image Gene #20: 'amp_20p11.23' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'amp_20q11.21' versus 'HISTOLOGICAL.TYPE'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0036

Table S7.  Gene #21: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
AMP PEAK 21(20Q11.21) MUTATED 281 24
AMP PEAK 21(20Q11.21) WILD-TYPE 92 31

Figure S7.  Get High-res Image Gene #21: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q12' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00029 (Fisher's exact test), Q value = 0.23

Table S8.  Gene #22: 'amp_20q12' 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 28 127 8 1 21 13 53 38 42 16 1
AMP PEAK 22(20Q12) MUTATED 51 1 16 83 3 1 13 13 37 30 37 16 0
AMP PEAK 22(20Q12) WILD-TYPE 21 0 12 44 5 0 8 0 16 8 5 0 1

Figure S8.  Get High-res Image Gene #22: 'amp_20q12' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 7.62e-07 (Fisher's exact test), Q value = 0.00063

Table S9.  Gene #22: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
AMP PEAK 22(20Q12) MUTATED 283 23
AMP PEAK 22(20Q12) WILD-TYPE 90 32

Figure S9.  Get High-res Image Gene #22: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.32' versus 'HISTOLOGICAL.TYPE'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023

Table S10.  Gene #23: 'amp_20q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
AMP PEAK 23(20Q13.32) MUTATED 285 24
AMP PEAK 23(20Q13.32) WILD-TYPE 88 31

Figure S10.  Get High-res Image Gene #23: 'amp_20q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 6e-05 (Fisher's exact test), Q value = 0.048

Table S11.  Gene #24: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
DEL PEAK 1(1P36.11) MUTATED 105 34 3 0 18
DEL PEAK 1(1P36.11) WILD-TYPE 215 16 4 1 27

Figure S11.  Get High-res Image Gene #24: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #33: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
DEL PEAK 10(4P16.2) MUTATED 79 28 3 0 14
DEL PEAK 10(4P16.2) WILD-TYPE 241 22 4 1 31

Figure S12.  Get High-res Image Gene #33: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 8.83e-05 (Wilcoxon-test), Q value = 0.071

Table S13.  Gene #33: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 10(4P16.2) MUTATED 124 2.9 (4.6)
DEL PEAK 10(4P16.2) WILD-TYPE 282 1.7 (4.3)

Figure S13.  Get High-res Image Gene #33: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 0.000257 (Wilcoxon-test), Q value = 0.2

Table S14.  Gene #34: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 11(4Q22.1) MUTATED 132 2.8 (4.5)
DEL PEAK 11(4Q22.1) WILD-TYPE 274 1.7 (4.4)

Figure S14.  Get High-res Image Gene #34: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_5q21.3' versus 'PATHOLOGY.N.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.096

Table S15.  Gene #37: 'del_5q21.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 14(5Q21.3) MUTATED 52 36 33
DEL PEAK 14(5Q21.3) WILD-TYPE 200 65 43

Figure S15.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_5q21.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.41e-05 (Wilcoxon-test), Q value = 0.044

Table S16.  Gene #37: 'del_5q21.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 14(5Q21.3) MUTATED 116 3.0 (4.9)
DEL PEAK 14(5Q21.3) WILD-TYPE 290 1.6 (4.2)

Figure S16.  Get High-res Image Gene #37: 'del_5q21.3' 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 = 0.064

Table S17.  Gene #42: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 19(8P23.3) MUTATED 83 49 45
DEL PEAK 19(8P23.3) WILD-TYPE 169 52 31

Figure S17.  Get High-res Image Gene #42: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 8.95e-05 (Wilcoxon-test), Q value = 0.072

Table S18.  Gene #42: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 19(8P23.3) MUTATED 172 2.8 (5.5)
DEL PEAK 19(8P23.3) WILD-TYPE 234 1.5 (3.3)

Figure S18.  Get High-res Image Gene #42: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S19.  Gene #43: '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 28 127 8 1 21 13 53 38 42 16 1
DEL PEAK 20(8P22) MUTATED 24 0 9 42 2 0 10 8 28 25 28 12 1
DEL PEAK 20(8P22) WILD-TYPE 48 1 19 85 6 1 11 5 25 13 14 4 0

Figure S19.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S20.  Gene #43: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 20(8P22) MUTATED 87 53 51
DEL PEAK 20(8P22) WILD-TYPE 165 48 25

Figure S20.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'PATHOLOGY.M.STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #43: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
DEL PEAK 20(8P22) MUTATED 131 36 4 1 18
DEL PEAK 20(8P22) WILD-TYPE 189 14 3 0 27

Figure S21.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.56e-06 (Wilcoxon-test), Q value = 0.0013

Table S22.  Gene #43: 'del_8p22' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 20(8P22) MUTATED 186 2.9 (5.4)
DEL PEAK 20(8P22) WILD-TYPE 220 1.3 (3.3)

Figure S22.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_8p11.21' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000229 (Wilcoxon-test), Q value = 0.18

Table S23.  Gene #44: 'del_8p11.21' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 21(8P11.21) MUTATED 44 4.7 (8.4)
DEL PEAK 21(8P11.21) WILD-TYPE 362 1.7 (3.6)

Figure S23.  Get High-res Image Gene #44: 'del_8p11.21' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_14q31.1' versus 'HISTOLOGICAL.TYPE'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.019

Table S24.  Gene #52: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 29(14Q31.1) MUTATED 134 5
DEL PEAK 29(14Q31.1) WILD-TYPE 239 50

Figure S24.  Get High-res Image Gene #52: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S25.  Gene #59: '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 28 127 8 1 21 13 53 38 42 16 1
DEL PEAK 36(17P12) MUTATED 35 0 13 53 1 1 12 12 32 29 32 12 1
DEL PEAK 36(17P12) WILD-TYPE 37 1 15 74 7 0 9 1 21 9 10 4 0

Figure S25.  Get High-res Image Gene #59: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0081

Table S26.  Gene #59: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 36(17P12) MUTATED 116 67 55
DEL PEAK 36(17P12) WILD-TYPE 136 34 21

Figure S26.  Get High-res Image Gene #59: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 1.99e-06 (Fisher's exact test), Q value = 0.0016

Table S27.  Gene #59: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 36(17P12) MUTATED 223 14
DEL PEAK 36(17P12) WILD-TYPE 150 41

Figure S27.  Get High-res Image Gene #59: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 1.93e-06 (Wilcoxon-test), Q value = 0.0016

Table S28.  Gene #59: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 36(17P12) MUTATED 226 2.7 (5.4)
DEL PEAK 36(17P12) WILD-TYPE 180 1.1 (2.5)

Figure S28.  Get High-res Image Gene #59: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 0.000225 (Wilcoxon-test), Q value = 0.18

Table S29.  Gene #60: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 37(17Q24.3) MUTATED 60 3.0 (4.1)
DEL PEAK 37(17Q24.3) WILD-TYPE 346 1.9 (4.5)

Figure S29.  Get High-res Image Gene #60: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 0.00026 (Fisher's exact test), Q value = 0.2

Table S30.  Gene #61: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
DEL PEAK 38(18P11.31) MUTATED 160 38 7 0 23
DEL PEAK 38(18P11.31) WILD-TYPE 160 12 0 1 22

Figure S30.  Get High-res Image Gene #61: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_18p11.31' versus 'HISTOLOGICAL.TYPE'

P value = 2.31e-11 (Fisher's exact test), Q value = 1.9e-08

Table S31.  Gene #61: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 38(18P11.31) MUTATED 222 7
DEL PEAK 38(18P11.31) WILD-TYPE 151 48

Figure S31.  Get High-res Image Gene #61: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.74e-10 (Fisher's exact test), Q value = 1.4e-07

Table S32.  Gene #62: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 39(18Q12.2) MUTATED 245 11
DEL PEAK 39(18Q12.2) WILD-TYPE 128 44

Figure S32.  Get High-res Image Gene #62: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.032

Table S33.  Gene #63: '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 28 127 8 1 21 13 53 38 42 16 1
DEL PEAK 40(18Q21.2) MUTATED 39 0 16 68 2 1 11 12 36 30 36 13 1
DEL PEAK 40(18Q21.2) WILD-TYPE 33 1 12 59 6 0 10 1 17 8 6 3 0

Figure S33.  Get High-res Image Gene #63: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

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

Table S34.  Gene #63: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 40(18Q21.2) MUTATED 138 73 59
DEL PEAK 40(18Q21.2) WILD-TYPE 114 28 17

Figure S34.  Get High-res Image Gene #63: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_18q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 2.13e-09 (Fisher's exact test), Q value = 1.8e-06

Table S35.  Gene #63: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 40(18Q21.2) MUTATED 256 14
DEL PEAK 40(18Q21.2) WILD-TYPE 117 41

Figure S35.  Get High-res Image Gene #63: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 6.76e-05 (Wilcoxon-test), Q value = 0.054

Table S36.  Gene #63: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 40(18Q21.2) MUTATED 258 2.4 (4.6)
DEL PEAK 40(18Q21.2) WILD-TYPE 148 1.5 (4.1)

Figure S36.  Get High-res Image Gene #63: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_18q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.13

Table S37.  Gene #64: 'del_18q22.1' 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 28 127 8 1 21 13 53 38 42 16 1
DEL PEAK 41(18Q22.1) MUTATED 39 0 17 68 2 1 11 11 36 30 36 13 1
DEL PEAK 41(18Q22.1) WILD-TYPE 33 1 11 59 6 0 10 2 17 8 6 3 0

Figure S37.  Get High-res Image Gene #64: 'del_18q22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_18q22.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.2

Table S38.  Gene #64: 'del_18q22.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 41(18Q22.1) MUTATED 139 72 59
DEL PEAK 41(18Q22.1) WILD-TYPE 113 29 17

Figure S38.  Get High-res Image Gene #64: 'del_18q22.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_18q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 2.35e-10 (Fisher's exact test), Q value = 1.9e-07

Table S39.  Gene #64: 'del_18q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
DEL PEAK 41(18Q22.1) MUTATED 257 13
DEL PEAK 41(18Q22.1) WILD-TYPE 116 42

Figure S39.  Get High-res Image Gene #64: 'del_18q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q22.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000177 (Wilcoxon-test), Q value = 0.14

Table S40.  Gene #64: 'del_18q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 41(18Q22.1) MUTATED 258 2.4 (4.6)
DEL PEAK 41(18Q22.1) WILD-TYPE 148 1.5 (4.1)

Figure S40.  Get High-res Image Gene #64: 'del_18q22.1' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

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

Table S41.  Gene #65: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
DEL PEAK 42(19P13.3) MUTATED 22 15 22
DEL PEAK 42(19P13.3) WILD-TYPE 230 86 54

Figure S41.  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 = 1.67e-06 (Wilcoxon-test), Q value = 0.0014

Table S42.  Gene #65: 'del_19p13.3' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 42(19P13.3) MUTATED 57 4.3 (6.0)
DEL PEAK 42(19P13.3) WILD-TYPE 349 1.7 (4.0)

Figure S42.  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 = 0.000127 (Wilcoxon-test), Q value = 0.1

Table S43.  Gene #69: 'del_22q13.32' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
DEL PEAK 46(22Q13.32) MUTATED 142 2.8 (4.9)
DEL PEAK 46(22Q13.32) WILD-TYPE 264 1.6 (4.1)

Figure S43.  Get High-res Image Gene #69: '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 = 430

  • Number of significantly focal cnvs = 69

  • 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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