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 67 focal events and 11 clinical features across 424 patients, 27 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'.

  • amp_20p11.23 cnv correlated to 'PATHOLOGY.M.STAGE'.

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

  • amp_20q12 cnv correlated to '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.N.STAGE' and 'PATHOLOGY.M.STAGE'.

  • del_5q21.3 cnv correlated to 'PATHOLOGY.N.STAGE'.

  • del_8p23.3 cnv correlated to 'PATHOLOGY.N.STAGE'.

  • del_8p22 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • del_13q14.13 cnv correlated to 'PATHOLOGY.M.STAGE'.

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

  • del_18p11.31 cnv correlated to 'HISTOLOGICAL.TYPE'.

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

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

  • del_18q22.1 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • del_19p13.3 cnv correlated to 'PATHOLOGY.N.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 67 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 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
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test
del 17p12 235 (55%) 189 0.3
(1.00) 		0.034
(1.00) 		1.91e-05
(0.0139) 		0.828
(1.00) 		1.73e-05
(0.0125) 		0.00915
(1.00) 		0.282
(1.00) 		2.08e-06
(0.00152) 		0.257
(1.00) 		0.18
(1.00) 		0.000144
(0.103)
del 18q21 2 268 (63%) 156 0.665
(1.00) 		0.149
(1.00) 		0.00019
(0.136) 		0.773
(1.00) 		8.82e-05
(0.0636) 		0.00524
(1.00) 		0.107
(1.00) 		1.07e-09
(7.86e-07) 		0.301
(1.00) 		0.133
(1.00) 		0.0352
(1.00)
del 4p16 2 127 (30%) 297 0.0142
(1.00) 		0.676
(1.00) 		0.000863
(0.602) 		0.579
(1.00) 		0.000223
(0.159) 		0.000191
(0.136) 		0.671
(1.00) 		0.0181
(1.00) 		0.0264
(1.00) 		0.0366
(1.00) 		0.0116
(1.00)
del 8p22 189 (45%) 235 0.297
(1.00) 		0.117
(1.00) 		0.000107
(0.0771) 		0.177
(1.00) 		1.71e-06
(0.00125) 		0.000735
(0.517) 		0.117
(1.00) 		0.0137
(1.00) 		0.588
(1.00) 		0.0529
(1.00) 		0.00111
(0.767)
del 18q22 1 268 (63%) 156 0.482
(1.00) 		0.249
(1.00) 		0.000531
(0.376) 		0.773
(1.00) 		0.000185
(0.132) 		0.00524
(1.00) 		0.107
(1.00) 		1.98e-10
(1.46e-07) 		0.301
(1.00) 		0.229
(1.00) 		0.0445
(1.00)
amp 13q12 13 259 (61%) 165 0.511
(1.00) 		0.508
(1.00) 		0.00182
(1.00) 		0.939
(1.00) 		0.00127
(0.88) 		0.00215
(1.00) 		0.921
(1.00) 		4.19e-07
(0.000307) 		0.285
(1.00) 		0.0339
(1.00) 		0.0883
(1.00)
amp 13q22 1 262 (62%) 162 0.26
(1.00) 		0.46
(1.00) 		0.00391
(1.00) 		0.978
(1.00) 		0.000897
(0.625) 		0.00583
(1.00) 		0.317
(1.00) 		4.5e-06
(0.00327) 		0.29
(1.00) 		0.0699
(1.00) 		0.124
(1.00)
amp 16p11 2 119 (28%) 305 0.764
(1.00) 		0.168
(1.00) 		0.00147
(1.00) 		0.553
(1.00) 		0.000335
(0.238) 		0.576
(1.00) 		0.665
(1.00) 		0.00596
(1.00) 		1
(1.00) 		0.694
(1.00) 		0.00876
(1.00)
amp 20p11 23 208 (49%) 216 0.714
(1.00) 		0.746
(1.00) 		0.000364
(0.258) 		0.986
(1.00) 		0.0651
(1.00) 		0.000232
(0.165) 		0.332
(1.00) 		0.0134
(1.00) 		0.117
(1.00) 		0.00943
(1.00) 		0.258
(1.00)
amp 20q11 21 304 (72%) 120 0.637
(1.00) 		0.642
(1.00) 		0.00323
(1.00) 		0.351
(1.00) 		0.0194
(1.00) 		0.00809
(1.00) 		0.331
(1.00) 		3.54e-06
(0.00257) 		0.562
(1.00) 		0.13
(1.00) 		0.13
(1.00)
amp 20q12 305 (72%) 119 0.585
(1.00) 		0.682
(1.00) 		0.00128
(0.884) 		0.487
(1.00) 		0.0241
(1.00) 		0.00373
(1.00) 		0.279
(1.00) 		5.77e-07
(0.000422) 		0.563
(1.00) 		0.13
(1.00) 		0.167
(1.00)
amp 20q13 32 308 (73%) 116 0.593
(1.00) 		0.717
(1.00) 		0.00195
(1.00) 		0.413
(1.00) 		0.0165
(1.00) 		0.00534
(1.00) 		0.326
(1.00) 		1.24e-06
(0.000905) 		0.565
(1.00) 		0.127
(1.00) 		0.0562
(1.00)
del 1p36 11 159 (38%) 265 0.023
(1.00) 		0.144
(1.00) 		0.00368
(1.00) 		0.841
(1.00) 		0.0147
(1.00) 		8.75e-05
(0.0632) 		0.315
(1.00) 		0.00153
(1.00) 		1
(1.00) 		0.083
(1.00) 		0.0107
(1.00)
del 5q21 3 121 (29%) 303 0.28
(1.00) 		0.149
(1.00) 		0.0013
(0.9) 		0.929
(1.00) 		9.45e-05
(0.068) 		0.0206
(1.00) 		0.666
(1.00) 		0.151
(1.00) 		0.0228
(1.00) 		0.273
(1.00) 		0.00901
(1.00)
del 8p23 3 175 (41%) 249 0.796
(1.00) 		0.267
(1.00) 		0.00663
(1.00) 		0.132
(1.00) 		0.000144
(0.103) 		0.0142
(1.00) 		0.0606
(1.00) 		0.0564
(1.00) 		0.572
(1.00) 		0.103
(1.00) 		0.00534
(1.00)
del 13q14 13 18 (4%) 406 0.221
(1.00) 		0.301
(1.00) 		0.000721
(0.508) 		0.67
(1.00) 		0.0643
(1.00) 		3.28e-05
(0.0237) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.868
(1.00) 		0.226
(1.00)
del 18p11 31 229 (54%) 195 0.82
(1.00) 		0.0379
(1.00) 		0.00462
(1.00) 		0.921
(1.00) 		0.0348
(1.00) 		0.000674
(0.475) 		0.922
(1.00) 		1.72e-11
(1.26e-08) 		0.253
(1.00) 		0.0292
(1.00) 		0.481
(1.00)
del 18q12 2 255 (60%) 169 0.902
(1.00) 		0.0829
(1.00) 		0.00177
(1.00) 		0.708
(1.00) 		0.00148
(1.00) 		0.0121
(1.00) 		0.322
(1.00) 		1.42e-10
(1.04e-07) 		0.279
(1.00) 		0.146
(1.00) 		0.128
(1.00)
del 19p13 3 59 (14%) 365 0.676
(1.00) 		0.185
(1.00) 		0.000461
(0.326) 		0.966
(1.00) 		8.43e-05
(0.0609) 		0.0181
(1.00) 		0.486
(1.00) 		0.205
(1.00) 		0.363
(1.00) 		0.074
(1.00) 		0.00198
(1.00)
amp 2q33 1 83 (20%) 341 0.0307
(1.00) 		0.319
(1.00) 		0.24
(1.00) 		0.786
(1.00) 		0.0278
(1.00) 		0.142
(1.00) 		0.392
(1.00) 		0.366
(1.00) 		0.481
(1.00) 		0.0846
(1.00) 		0.0865
(1.00)
amp 5p13 2 81 (19%) 343 0.989
(1.00) 		0.178
(1.00) 		0.159
(1.00) 		0.539
(1.00) 		0.0458
(1.00) 		0.681
(1.00) 		0.323
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.0491
(1.00)
amp 5q22 3 41 (10%) 383 0.549
(1.00) 		0.693
(1.00) 		0.438
(1.00) 		0.831
(1.00) 		0.309
(1.00) 		0.0112
(1.00) 		0.87
(1.00) 		0.333
(1.00) 		0.264
(1.00) 		0.0935
(1.00) 		0.31
(1.00)
amp 6p21 1 91 (21%) 333 0.34
(1.00) 		0.535
(1.00) 		0.0967
(1.00) 		0.444
(1.00) 		0.00792
(1.00) 		0.569
(1.00) 		0.343
(1.00) 		0.0511
(1.00) 		0.00963
(1.00) 		0.675
(1.00) 		0.0204
(1.00)
amp 8p11 23 149 (35%) 275 0.874
(1.00) 		0.405
(1.00) 		0.474
(1.00) 		0.767
(1.00) 		0.686
(1.00) 		0.459
(1.00) 		0.838
(1.00) 		0.13
(1.00) 		0.283
(1.00) 		0.821
(1.00) 		0.651
(1.00)
amp 8p11 21 179 (42%) 245 0.585
(1.00) 		0.558
(1.00) 		0.63
(1.00) 		0.677
(1.00) 		0.6
(1.00) 		0.427
(1.00) 		0.202
(1.00) 		0.144
(1.00) 		0.576
(1.00) 		0.32
(1.00) 		0.944
(1.00)
amp 8q12 1 221 (52%) 203 0.794
(1.00) 		0.226
(1.00) 		0.815
(1.00) 		0.705
(1.00) 		0.675
(1.00) 		0.188
(1.00) 		0.697
(1.00) 		0.0135
(1.00) 		0.25
(1.00) 		0.491
(1.00) 		0.12
(1.00)
amp 8q24 21 245 (58%) 179 0.741
(1.00) 		0.144
(1.00) 		0.359
(1.00) 		0.404
(1.00) 		0.39
(1.00) 		0.116
(1.00) 		0.431
(1.00) 		0.0567
(1.00) 		0.266
(1.00) 		0.413
(1.00) 		0.0934
(1.00)
amp 11p15 5 88 (21%) 336 0.733
(1.00) 		0.0325
(1.00) 		0.631
(1.00) 		0.283
(1.00) 		0.0864
(1.00) 		0.281
(1.00) 		0.549
(1.00) 		0.00196
(1.00) 		0.111
(1.00) 		0.462
(1.00) 		0.275
(1.00)
amp 12p13 33 105 (25%) 319 0.118
(1.00) 		0.137
(1.00) 		0.185
(1.00) 		0.102
(1.00) 		0.408
(1.00) 		0.293
(1.00) 		0.91
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.75
(1.00)
amp 16q12 1 105 (25%) 319 0.389
(1.00) 		0.0512
(1.00) 		0.000453
(0.321) 		0.933
(1.00) 		0.000743
(0.521) 		0.393
(1.00) 		0.573
(1.00) 		0.0112
(1.00) 		0.575
(1.00) 		0.683
(1.00) 		0.0242
(1.00)
amp 17q12 105 (25%) 319 0.482
(1.00) 		0.571
(1.00) 		0.134
(1.00) 		0.162
(1.00) 		0.179
(1.00) 		0.00712
(1.00) 		0.178
(1.00) 		0.314
(1.00) 		0.575
(1.00) 		0.132
(1.00) 		0.183
(1.00)
amp 17q24 1 97 (23%) 327 0.0916
(1.00) 		0.61
(1.00) 		0.452
(1.00) 		0.36
(1.00) 		0.354
(1.00) 		0.0293
(1.00) 		0.729
(1.00) 		0.0592
(1.00) 		0.542
(1.00) 		0.327
(1.00) 		0.999
(1.00)
amp 19p13 2 69 (16%) 355 0.871
(1.00) 		0.76
(1.00) 		0.784
(1.00) 		0.519
(1.00) 		0.0165
(1.00) 		0.0149
(1.00) 		0.0348
(1.00) 		0.328
(1.00) 		0.414
(1.00) 		0.0948
(1.00) 		0.362
(1.00)
amp 19q13 11 87 (21%) 337 0.28
(1.00) 		0.705
(1.00) 		0.751
(1.00) 		0.764
(1.00) 		0.0658
(1.00) 		0.0372
(1.00) 		0.0409
(1.00) 		0.477
(1.00) 		0.499
(1.00) 		0.757
(1.00) 		0.903
(1.00)
del 1p33 115 (27%) 309 0.00432
(1.00) 		0.906
(1.00) 		0.0409
(1.00) 		0.475
(1.00) 		0.0145
(1.00) 		0.00531
(1.00) 		0.743
(1.00) 		0.0528
(1.00) 		0.566
(1.00) 		0.227
(1.00) 		0.0237
(1.00)
del 1p13 1 110 (26%) 314 0.261
(1.00) 		0.677
(1.00) 		0.0107
(1.00) 		0.543
(1.00) 		0.00393
(1.00) 		0.001
(0.696) 		0.506
(1.00) 		0.0988
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.02
(1.00)
del 1q43 51 (12%) 373 0.718
(1.00) 		0.339
(1.00) 		0.0454
(1.00) 		0.134
(1.00) 		0.378
(1.00) 		0.0767
(1.00) 		0.881
(1.00) 		0.657
(1.00) 		0.32
(1.00) 		0.455
(1.00) 		0.481
(1.00)
del 2p21 16 (4%) 408 0.713
(1.00) 		0.33
(1.00) 		0.315
(1.00) 		0.518
(1.00) 		0.282
(1.00) 		0.269
(1.00) 		0.456
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.644
(1.00) 		0.772
(1.00)
del 2q22 1 20 (5%) 404 0.648
(1.00) 		0.288
(1.00) 		0.35
(1.00) 		0.402
(1.00) 		0.187
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.735
(1.00) 		1
(1.00) 		1
(1.00) 		0.335
(1.00)
del 2q37 2 21 (5%) 403 0.295
(1.00) 		0.409
(1.00) 		0.82
(1.00) 		0.435
(1.00) 		0.82
(1.00) 		0.33
(1.00) 		0.374
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.213
(1.00) 		0.161
(1.00)
del 3p26 1 65 (15%) 359 0.0066
(1.00) 		0.495
(1.00) 		0.0902
(1.00) 		0.194
(1.00) 		0.0203
(1.00) 		0.00609
(1.00) 		0.893
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.13
(1.00)
del 3p14 2 80 (19%) 344 0.929
(1.00) 		0.432
(1.00) 		0.172
(1.00) 		0.199
(1.00) 		0.0658
(1.00) 		0.0815
(1.00) 		0.386
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.0441
(1.00)
del 3q26 31 44 (10%) 380 0.271
(1.00) 		0.917
(1.00) 		0.141
(1.00) 		0.128
(1.00) 		0.926
(1.00) 		0.63
(1.00) 		0.875
(1.00) 		0.0963
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.117
(1.00)
del 4q22 1 136 (32%) 288 0.117
(1.00) 		0.673
(1.00) 		0.00286
(1.00) 		0.248
(1.00) 		0.000852
(0.596) 		0.159
(1.00) 		0.677
(1.00) 		0.00799
(1.00) 		0.0325
(1.00) 		0.946
(1.00) 		0.0247
(1.00)
del 4q35 1 144 (34%) 280 0.334
(1.00) 		0.199
(1.00) 		0.0912
(1.00) 		0.524
(1.00) 		0.00499
(1.00) 		0.125
(1.00) 		0.182
(1.00) 		0.0472
(1.00) 		0.0386
(1.00) 		0.376
(1.00) 		0.0726
(1.00)
del 5q11 2 96 (23%) 328 0.199
(1.00) 		0.104
(1.00) 		0.0163
(1.00) 		0.967
(1.00) 		0.00339
(1.00) 		0.0417
(1.00) 		0.296
(1.00) 		0.0247
(1.00) 		0.0113
(1.00) 		0.754
(1.00) 		0.0253
(1.00)
del 5q23 1 112 (26%) 312 0.556
(1.00) 		0.331
(1.00) 		0.0306
(1.00) 		0.949
(1.00) 		0.00644
(1.00) 		0.00823
(1.00) 		0.27
(1.00) 		0.0727
(1.00) 		0.0181
(1.00) 		0.328
(1.00) 		0.0447
(1.00)
del 6p25 3 54 (13%) 370 0.516
(1.00) 		0.135
(1.00) 		0.64
(1.00) 		0.347
(1.00) 		0.843
(1.00) 		0.139
(1.00) 		0.0801
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.362
(1.00) 		0.751
(1.00)
del 6q26 59 (14%) 365 0.0773
(1.00) 		0.931
(1.00) 		0.0702
(1.00) 		0.515
(1.00) 		0.0186
(1.00) 		0.022
(1.00) 		0.889
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.0167
(1.00)
del 7q31 1 12 (3%) 412 0.642
(1.00) 		0.825
(1.00) 		0.944
(1.00) 		0.647
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.56
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.584
(1.00)
del 8p11 21 44 (10%) 380 0.722
(1.00) 		0.445
(1.00) 		0.00331
(1.00) 		0.129
(1.00) 		0.000996
(0.693) 		0.0094
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.281
(1.00) 		0.11
(1.00) 		0.0209
(1.00)
del 9p21 3 57 (13%) 367 0.076
(1.00) 		0.054
(1.00) 		0.542
(1.00) 		0.363
(1.00) 		0.293
(1.00) 		0.1
(1.00) 		0.202
(1.00) 		0.0874
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.428
(1.00)
del 10p15 3 75 (18%) 349 0.986
(1.00) 		0.348
(1.00) 		0.00331
(1.00) 		0.94
(1.00) 		0.0109
(1.00) 		0.0027
(1.00) 		0.8
(1.00) 		0.348
(1.00) 		0.0821
(1.00) 		0.667
(1.00) 		0.114
(1.00)
del 10q21 1 90 (21%) 334 0.99
(1.00) 		0.0688
(1.00) 		0.00396
(1.00) 		0.995
(1.00) 		0.0142
(1.00) 		0.0971
(1.00) 		0.905
(1.00) 		0.0511
(1.00) 		0.115
(1.00) 		0.0575
(1.00) 		0.116
(1.00)
del 10q23 31 101 (24%) 323 0.987
(1.00) 		0.00874
(1.00) 		0.00458
(1.00) 		0.927
(1.00) 		0.0287
(1.00) 		0.0232
(1.00) 		0.732
(1.00) 		0.0417
(1.00) 		0.143
(1.00) 		0.177
(1.00) 		0.287
(1.00)
del 10q25 2 101 (24%) 323 0.304
(1.00) 		0.111
(1.00) 		0.026
(1.00) 		0.332
(1.00) 		0.00316
(1.00) 		0.0445
(1.00) 		0.82
(1.00) 		0.0909
(1.00) 		0.143
(1.00) 		0.0672
(1.00) 		0.124
(1.00)
del 12p13 2 54 (13%) 370 0.0103
(1.00) 		0.286
(1.00) 		0.109
(1.00) 		0.808
(1.00) 		0.0358
(1.00) 		0.205
(1.00) 		0.662
(1.00) 		0.00462
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.521
(1.00)
del 14q32 11 140 (33%) 284 0.185
(1.00) 		0.407
(1.00) 		0.137
(1.00) 		0.321
(1.00) 		0.0665
(1.00) 		0.0364
(1.00) 		0.836
(1.00) 		0.000577
(0.407) 		0.554
(1.00) 		0.317
(1.00) 		0.149
(1.00)
del 15q11 2 165 (39%) 259 0.836
(1.00) 		0.88
(1.00) 		0.0474
(1.00) 		0.973
(1.00) 		0.0109
(1.00) 		0.0488
(1.00) 		0.842
(1.00) 		0.017
(1.00) 		0.0583
(1.00) 		0.486
(1.00) 		0.277
(1.00)
del 15q21 1 157 (37%) 267 0.29
(1.00) 		0.861
(1.00) 		0.167
(1.00) 		0.99
(1.00) 		0.0474
(1.00) 		0.0133
(1.00) 		0.687
(1.00) 		0.0159
(1.00) 		0.0502
(1.00) 		0.212
(1.00) 		0.501
(1.00)
del 15q22 33 151 (36%) 273 0.577
(1.00) 		0.595
(1.00) 		0.0258
(1.00) 		0.528
(1.00) 		0.0165
(1.00) 		0.00496
(1.00) 		0.613
(1.00) 		0.00393
(1.00) 		0.0446
(1.00) 		0.629
(1.00) 		0.359
(1.00)
del 16p13 3 51 (12%) 373 0.000791
(0.555) 		0.798
(1.00) 		0.0699
(1.00) 		0.0445
(1.00) 		0.0847
(1.00) 		0.472
(1.00) 		0.881
(1.00) 		1
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.132
(1.00)
del 16q23 1 55 (13%) 369 0.00362
(1.00) 		0.545
(1.00) 		0.943
(1.00) 		0.592
(1.00) 		0.67
(1.00) 		0.662
(1.00) 		0.247
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.352
(1.00)
del 17q24 3 62 (15%) 362 0.618
(1.00) 		0.79
(1.00) 		0.0225
(1.00) 		0.653
(1.00) 		0.00619
(1.00) 		0.049
(1.00) 		0.335
(1.00) 		1
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.0572
(1.00)
del 20p12 1 80 (19%) 344 0.983
(1.00) 		0.537
(1.00) 		0.495
(1.00) 		0.619
(1.00) 		0.452
(1.00) 		0.973
(1.00) 		0.536
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.56
(1.00)
del 21q11 2 132 (31%) 292 0.739
(1.00) 		0.752
(1.00) 		0.17
(1.00) 		0.368
(1.00) 		0.0188
(1.00) 		0.145
(1.00) 		0.753
(1.00) 		0.00457
(1.00) 		0.23
(1.00) 		0.625
(1.00) 		0.0113
(1.00)
del 22q13 32 148 (35%) 276 0.223
(1.00) 		0.765
(1.00) 		0.00553
(1.00) 		0.69
(1.00) 		0.000851
(0.596) 		0.0157
(1.00) 		0.839
(1.00) 		0.0014
(0.968) 		1
(1.00) 		0.46
(1.00) 		0.0133
(1.00)
'amp_13q12.13' versus 'HISTOLOGICAL.TYPE'

P value = 4.19e-07 (Fisher's exact test), Q value = 0.00031

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
AMP PEAK 11(13Q12.13) MUTATED 242 16
AMP PEAK 11(13Q12.13) WILD-TYPE 125 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 = 4.5e-06 (Fisher's exact test), Q value = 0.0033

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
AMP PEAK 12(13Q22.1) MUTATED 243 18
AMP PEAK 12(13Q22.1) WILD-TYPE 124 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 = 0.000335 (Fisher's exact test), Q value = 0.24

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

nPatients N0 N1 N2
ALL 248 101 74
AMP PEAK 13(16P11.2) MUTATED 52 36 31
AMP PEAK 13(16P11.2) WILD-TYPE 196 65 43

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

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

P value = 0.000232 (Chi-square test), Q value = 0.17

Table S4.  Gene #19: 'amp_20p11.23' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 318 50 7 1 41
AMP PEAK 19(20P11.23) MUTATED 140 35 7 0 24
AMP PEAK 19(20P11.23) WILD-TYPE 178 15 0 1 17

Figure S4.  Get High-res Image Gene #19: 'amp_20p11.23' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'amp_20q11.21' versus 'HISTOLOGICAL.TYPE'

P value = 3.54e-06 (Fisher's exact test), Q value = 0.0026

Table S5.  Gene #20: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
AMP PEAK 20(20Q11.21) MUTATED 278 24
AMP PEAK 20(20Q11.21) WILD-TYPE 89 31

Figure S5.  Get High-res Image Gene #20: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 5.77e-07 (Fisher's exact test), Q value = 0.00042

Table S6.  Gene #21: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
AMP PEAK 21(20Q12) MUTATED 280 23
AMP PEAK 21(20Q12) WILD-TYPE 87 32

Figure S6.  Get High-res Image Gene #21: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'amp_20q13.32' versus 'HISTOLOGICAL.TYPE'

P value = 1.24e-06 (Fisher's exact test), Q value = 9e-04

Table S7.  Gene #22: 'amp_20q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
AMP PEAK 22(20Q13.32) MUTATED 282 24
AMP PEAK 22(20Q13.32) WILD-TYPE 85 31

Figure S7.  Get High-res Image Gene #22: 'amp_20q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 8.75e-05 (Chi-square test), Q value = 0.063

Table S8.  Gene #23: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 318 50 7 1 41
DEL PEAK 1(1P36.11) MUTATED 104 34 3 0 17
DEL PEAK 1(1P36.11) WILD-TYPE 214 16 4 1 24

Figure S8.  Get High-res Image Gene #23: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_4p16.2' versus 'PATHOLOGY.N.STAGE'

P value = 0.000223 (Fisher's exact test), Q value = 0.16

Table S9.  Gene #33: 'del_4p16.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 11(4P16.2) MUTATED 56 38 33
DEL PEAK 11(4P16.2) WILD-TYPE 192 63 41

Figure S9.  Get High-res Image Gene #33: 'del_4p16.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 0.000191 (Chi-square test), Q value = 0.14

Table S10.  Gene #33: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 318 50 7 1 41
DEL PEAK 11(4P16.2) MUTATED 78 28 3 0 14
DEL PEAK 11(4P16.2) WILD-TYPE 240 22 4 1 27

Figure S10.  Get High-res Image Gene #33: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 9.45e-05 (Fisher's exact test), Q value = 0.068

Table S11.  Gene #37: 'del_5q21.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 15(5Q21.3) MUTATED 52 36 33
DEL PEAK 15(5Q21.3) WILD-TYPE 196 65 41

Figure S11.  Get High-res Image Gene #37: 'del_5q21.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 0.000144 (Fisher's exact test), Q value = 0.1

Table S12.  Gene #42: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 20(8P23.3) MUTATED 82 49 43
DEL PEAK 20(8P23.3) WILD-TYPE 166 52 31

Figure S12.  Get High-res Image Gene #42: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000107 (Chi-square test), Q value = 0.077

Table S13.  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 71 1 33 119 8 1 22 13 52 36 42 16 1
DEL PEAK 21(8P22) MUTATED 24 0 9 41 2 0 11 8 27 23 28 12 1
DEL PEAK 21(8P22) WILD-TYPE 47 1 24 78 6 1 11 5 25 13 14 4 0

Figure S13.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 1.71e-06 (Fisher's exact test), Q value = 0.0012

Table S14.  Gene #43: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 21(8P22) MUTATED 86 53 49
DEL PEAK 21(8P22) WILD-TYPE 162 48 25

Figure S14.  Get High-res Image Gene #43: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_13q14.13' versus 'PATHOLOGY.M.STAGE'

P value = 3.28e-05 (Chi-square test), Q value = 0.024

Table S15.  Gene #51: 'del_13q14.13' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 318 50 7 1 41
DEL PEAK 29(13Q14.13) MUTATED 12 1 0 1 2
DEL PEAK 29(13Q14.13) WILD-TYPE 306 49 7 0 39

Figure S15.  Get High-res Image Gene #51: 'del_13q14.13' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_17p12' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.91e-05 (Chi-square test), Q value = 0.014

Table S16.  Gene #58: '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 71 1 33 119 8 1 22 13 52 36 42 16 1
DEL PEAK 36(17P12) MUTATED 34 0 15 50 1 1 13 12 31 27 32 12 1
DEL PEAK 36(17P12) WILD-TYPE 37 1 18 69 7 0 9 1 21 9 10 4 0

Figure S16.  Get High-res Image Gene #58: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 1.73e-05 (Fisher's exact test), Q value = 0.013

Table S17.  Gene #58: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 36(17P12) MUTATED 114 67 53
DEL PEAK 36(17P12) WILD-TYPE 134 34 21

Figure S17.  Get High-res Image Gene #58: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0015

Table S18.  Gene #58: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
DEL PEAK 36(17P12) MUTATED 219 14
DEL PEAK 36(17P12) WILD-TYPE 148 41

Figure S18.  Get High-res Image Gene #58: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000144 (t-test), Q value = 0.1

Table S19.  Gene #58: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 400 2.0 (4.5)
DEL PEAK 36(17P12) MUTATED 222 2.7 (5.4)
DEL PEAK 36(17P12) WILD-TYPE 178 1.2 (2.6)

Figure S19.  Get High-res Image Gene #58: 'del_17p12' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'del_18p11.31' versus 'HISTOLOGICAL.TYPE'

P value = 1.72e-11 (Fisher's exact test), Q value = 1.3e-08

Table S20.  Gene #60: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
DEL PEAK 38(18P11.31) MUTATED 220 7
DEL PEAK 38(18P11.31) WILD-TYPE 147 48

Figure S20.  Get High-res Image Gene #60: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.42e-10 (Fisher's exact test), Q value = 1e-07

Table S21.  Gene #61: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
DEL PEAK 39(18Q12.2) MUTATED 243 11
DEL PEAK 39(18Q12.2) WILD-TYPE 124 44

Figure S21.  Get High-res Image Gene #61: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00019 (Chi-square test), Q value = 0.14

Table S22.  Gene #62: '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 71 1 33 119 8 1 22 13 52 36 42 16 1
DEL PEAK 40(18Q21.2) MUTATED 38 0 18 65 2 1 12 12 35 29 36 13 1
DEL PEAK 40(18Q21.2) WILD-TYPE 33 1 15 54 6 0 10 1 17 7 6 3 0

Figure S22.  Get High-res Image Gene #62: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 8.82e-05 (Fisher's exact test), Q value = 0.064

Table S23.  Gene #62: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 40(18Q21.2) MUTATED 136 73 58
DEL PEAK 40(18Q21.2) WILD-TYPE 112 28 16

Figure S23.  Get High-res Image Gene #62: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_18q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.07e-09 (Fisher's exact test), Q value = 7.9e-07

Table S24.  Gene #62: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
DEL PEAK 40(18Q21.2) MUTATED 253 14
DEL PEAK 40(18Q21.2) WILD-TYPE 114 41

Figure S24.  Get High-res Image Gene #62: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000185 (Fisher's exact test), Q value = 0.13

Table S25.  Gene #63: 'del_18q22.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 41(18Q22.1) MUTATED 137 72 58
DEL PEAK 41(18Q22.1) WILD-TYPE 111 29 16

Figure S25.  Get High-res Image Gene #63: 'del_18q22.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_18q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1.98e-10 (Fisher's exact test), Q value = 1.5e-07

Table S26.  Gene #63: 'del_18q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
DEL PEAK 41(18Q22.1) MUTATED 254 13
DEL PEAK 41(18Q22.1) WILD-TYPE 113 42

Figure S26.  Get High-res Image Gene #63: 'del_18q22.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 8.43e-05 (Fisher's exact test), Q value = 0.061

Table S27.  Gene #64: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
DEL PEAK 42(19P13.3) MUTATED 22 15 22
DEL PEAK 42(19P13.3) WILD-TYPE 226 86 52

Figure S27.  Get High-res Image Gene #64: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 424

  • Number of significantly focal cnvs = 67

  • Number of selected clinical features = 11

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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