Correlation between copy number variation genes (focal events) and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1JM2826
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JM2826
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 72 focal events and 12 clinical features across 586 patients, 47 significant findings detected with Q value < 0.25.

  • amp_6p21.1 cnv correlated to 'PATHOLOGY.N.STAGE'.

  • amp_7p21.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • amp_13q12.13 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • amp_13q12.2 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_13q22.1 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_16p11.2 cnv correlated to 'PATHOLOGY.N.STAGE'.

  • amp_20q11.21 cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • amp_20q12 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE', and 'HISTOLOGICAL.TYPE'.

  • amp_20q13.31 cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • del_4p16.1 cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • del_5q11.2 cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • del_8p23.3 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • del_8p23.2 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • del_8p22 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_14q21.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_16p13.3 cnv correlated to 'Time to Death'.

  • del_17p12 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • del_18p11.31 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.M.STAGE', and 'HISTOLOGICAL.TYPE'.

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

  • del_18q22.1 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  '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 72 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		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 Fisher's exact 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 8p22 289 (49%) 297 0.318
(1.00) 		0.348
(1.00) 		0.000283
(0.232) 		0.000148
(0.122) 		0.0741
(1.00) 		5.86e-07
(0.000498) 		0.0026
(1.00) 		0.186
(1.00) 		0.00016
(0.131) 		0.0191
(1.00) 		0.0114
(1.00) 		0.000124
(0.102)
del 18q21 2 411 (70%) 175 0.745
(1.00) 		0.13
(1.00) 		1.25e-09
(1.07e-06) 		4.27e-05
(0.0356) 		0.283
(1.00) 		1.94e-06
(0.00165) 		0.00126
(0.995) 		0.124
(1.00) 		1.03e-16
(8.85e-14) 		0.0638
(1.00) 		0.0498
(1.00) 		0.00239
(1.00)
del 18q22 1 406 (69%) 180 0.551
(1.00) 		0.311
(1.00) 		2.19e-07
(0.000187) 		9.58e-05
(0.0794) 		0.423
(1.00) 		2.3e-05
(0.0194) 		0.00193
(1.00) 		0.209
(1.00) 		5.81e-16
(5.01e-13) 		0.0632
(1.00) 		0.0934
(1.00) 		0.00418
(1.00)
amp 13q12 13 382 (65%) 204 0.236
(1.00) 		0.325
(1.00) 		0.00125
(0.99) 		0.000181
(0.148) 		0.674
(1.00) 		1.51e-05
(0.0128) 		0.00547
(1.00) 		0.728
(1.00) 		1.19e-10
(1.02e-07) 		0.507
(1.00) 		0.0477
(1.00) 		0.0454
(1.00)
amp 20q12 449 (77%) 137 0.416
(1.00) 		0.91
(1.00) 		5.15e-06
(0.00436) 		0.000209
(0.171) 		0.463
(1.00) 		0.00102
(0.813) 		0.00105
(0.837) 		0.328
(1.00) 		1.57e-13
(1.35e-10) 		0.693
(1.00) 		0.0512
(1.00) 		0.488
(1.00)
del 8p23 3 275 (47%) 311 0.804
(1.00) 		0.292
(1.00) 		1.65e-05
(0.0139) 		0.00266
(1.00) 		0.093
(1.00) 		4.91e-05
(0.0409) 		0.0137
(1.00) 		0.159
(1.00) 		2.97e-05
(0.025) 		0.0907
(1.00) 		0.0206
(1.00) 		0.000625
(0.505)
del 8p23 2 275 (47%) 311 0.658
(1.00) 		0.249
(1.00) 		3.81e-05
(0.0318) 		0.000801
(0.643) 		0.083
(1.00) 		2.79e-05
(0.0234) 		0.00638
(1.00) 		0.0818
(1.00) 		3.29e-05
(0.0276) 		0.0907
(1.00) 		0.00797
(1.00) 		0.000624
(0.505)
del 18p11 31 350 (60%) 236 0.846
(1.00) 		0.102
(1.00) 		4.65e-06
(0.00395) 		0.000679
(0.547) 		0.908
(1.00) 		0.0088
(1.00) 		0.000131
(0.108) 		0.866
(1.00) 		5.18e-17
(4.48e-14) 		0.325
(1.00) 		0.0199
(1.00) 		0.588
(1.00)
amp 7p21 3 345 (59%) 241 0.539
(1.00) 		0.142
(1.00) 		0.0232
(1.00) 		0.000178
(0.146) 		0.924
(1.00) 		3.34e-06
(0.00284) 		0.0251
(1.00) 		1
(1.00) 		0.000468
(0.38) 		0.089
(1.00) 		0.181
(1.00) 		0.0196
(1.00)
amp 13q12 2 377 (64%) 209 0.193
(1.00) 		0.25
(1.00) 		0.00095
(0.76) 		0.000549
(0.445) 		0.704
(1.00) 		3.39e-05
(0.0284) 		0.0135
(1.00) 		0.545
(1.00) 		2.8e-10
(2.4e-07) 		0.502
(1.00) 		0.0886
(1.00) 		0.0469
(1.00)
amp 13q22 1 379 (65%) 207 0.137
(1.00) 		0.363
(1.00) 		0.0257
(1.00) 		0.00585
(1.00) 		0.687
(1.00) 		9.1e-05
(0.0755) 		0.0187
(1.00) 		0.26
(1.00) 		1.43e-08
(1.22e-05) 		0.504
(1.00) 		0.268
(1.00) 		0.226
(1.00)
amp 20q11 21 447 (76%) 139 0.449
(1.00) 		0.993
(1.00) 		9.85e-06
(0.00832) 		0.000775
(0.623) 		0.366
(1.00) 		0.00133
(1.00) 		0.00443
(1.00) 		0.33
(1.00) 		2.55e-12
(2.19e-09) 		0.693
(1.00) 		0.0513
(1.00) 		0.434
(1.00)
amp 20q13 31 452 (77%) 134 0.436
(1.00) 		0.912
(1.00) 		7.94e-06
(0.00671) 		0.000409
(0.333) 		0.304
(1.00) 		0.00128
(1.00) 		0.00209
(1.00) 		0.49
(1.00) 		7.26e-13
(6.24e-10) 		0.692
(1.00) 		0.0517
(1.00) 		0.428
(1.00)
del 17p12 349 (60%) 237 0.508
(1.00) 		0.248
(1.00) 		0.00174
(1.00) 		0.00102
(0.813) 		0.46
(1.00) 		8.77e-05
(0.0729) 		0.0317
(1.00) 		0.555
(1.00) 		3.31e-08
(2.83e-05) 		0.324
(1.00) 		0.159
(1.00) 		0.00421
(1.00)
amp 6p21 1 148 (25%) 438 0.768
(1.00) 		0.483
(1.00) 		0.0313
(1.00) 		0.0469
(1.00) 		0.201
(1.00) 		0.000232
(0.19) 		0.144
(1.00) 		0.153
(1.00) 		0.0019
(1.00) 		0.00131
(1.00) 		0.091
(1.00) 		0.00384
(1.00)
amp 16p11 2 164 (28%) 422 0.914
(1.00) 		0.402
(1.00) 		0.918
(1.00) 		0.00159
(1.00) 		0.745
(1.00) 		6.84e-05
(0.0569) 		0.199
(1.00) 		0.927
(1.00) 		0.00198
(1.00) 		0.275
(1.00) 		0.245
(1.00) 		0.0231
(1.00)
del 4p16 1 189 (32%) 397 0.153
(1.00) 		0.975
(1.00) 		0.0582
(1.00) 		0.00368
(1.00) 		0.979
(1.00) 		0.000767
(0.617) 		0.0118
(1.00) 		0.132
(1.00) 		0.0178
(1.00) 		3.31e-05
(0.0277) 		0.0718
(1.00) 		0.00266
(1.00)
del 5q11 2 147 (25%) 439 0.163
(1.00) 		0.242
(1.00) 		0.0244
(1.00) 		0.0331
(1.00) 		1
(1.00) 		0.00672
(1.00) 		0.0239
(1.00) 		0.849
(1.00) 		0.00596
(1.00) 		9.59e-05
(0.0794) 		0.707
(1.00) 		0.0162
(1.00)
del 14q21 2 195 (33%) 391 0.242
(1.00) 		0.259
(1.00) 		0.0297
(1.00) 		0.447
(1.00) 		0.432
(1.00) 		0.0136
(1.00) 		0.0972
(1.00) 		0.335
(1.00) 		4.49e-07
(0.000382) 		0.725
(1.00) 		0.924
(1.00) 		0.755
(1.00)
del 16p13 3 64 (11%) 522 4.32e-05
(0.036) 		0.513
(1.00) 		0.234
(1.00) 		0.0278
(1.00) 		0.0683
(1.00) 		0.167
(1.00) 		0.643
(1.00) 		0.895
(1.00) 		0.285
(1.00) 		0.607
(1.00) 		0.481
(1.00) 		0.0707
(1.00)
del 19p13 3 93 (16%) 493 0.803
(1.00) 		0.251
(1.00) 		0.0553
(1.00) 		0.00173
(1.00) 		0.376
(1.00) 		0.000107
(0.0882) 		0.0133
(1.00) 		0.498
(1.00) 		0.0574
(1.00) 		0.64
(1.00) 		0.145
(1.00) 		0.00289
(1.00)
amp 1q31 1 139 (24%) 447 0.712
(1.00) 		0.47
(1.00) 		0.0379
(1.00) 		0.319
(1.00) 		0.309
(1.00) 		0.06
(1.00) 		0.144
(1.00) 		0.208
(1.00) 		0.104
(1.00) 		0.0384
(1.00) 		0.731
(1.00) 		0.0179
(1.00)
amp 2q33 1 130 (22%) 456 0.0922
(1.00) 		0.421
(1.00) 		0.0138
(1.00) 		0.0409
(1.00) 		0.907
(1.00) 		0.00284
(1.00) 		0.203
(1.00) 		0.921
(1.00) 		0.00147
(1.00) 		0.116
(1.00) 		0.407
(1.00) 		0.0361
(1.00)
amp 5p12 109 (19%) 477 0.0936
(1.00) 		0.326
(1.00) 		0.0565
(1.00) 		0.338
(1.00) 		0.5
(1.00) 		0.096
(1.00) 		0.376
(1.00) 		0.751
(1.00) 		0.0207
(1.00) 		0.379
(1.00) 		0.0297
(1.00) 		0.086
(1.00)
amp 5q22 3 61 (10%) 525 0.337
(1.00) 		0.859
(1.00) 		0.362
(1.00) 		0.597
(1.00) 		0.911
(1.00) 		0.321
(1.00) 		0.0456
(1.00) 		1
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.0705
(1.00) 		0.584
(1.00)
amp 8p11 23 201 (34%) 385 0.277
(1.00) 		0.899
(1.00) 		0.625
(1.00) 		0.264
(1.00) 		0.463
(1.00) 		0.577
(1.00) 		0.348
(1.00) 		0.486
(1.00) 		0.191
(1.00) 		0.501
(1.00) 		0.166
(1.00) 		0.797
(1.00)
amp 8p11 21 244 (42%) 342 0.822
(1.00) 		0.704
(1.00) 		0.706
(1.00) 		0.0999
(1.00) 		0.516
(1.00) 		0.387
(1.00) 		0.249
(1.00) 		0.179
(1.00) 		0.0971
(1.00) 		0.742
(1.00) 		0.0482
(1.00) 		0.552
(1.00)
amp 8q12 1 315 (54%) 271 0.79
(1.00) 		0.325
(1.00) 		0.305
(1.00) 		0.144
(1.00) 		0.318
(1.00) 		0.198
(1.00) 		0.0358
(1.00) 		0.507
(1.00) 		0.00694
(1.00) 		0.0424
(1.00) 		0.112
(1.00) 		0.0541
(1.00)
amp 8q24 21 351 (60%) 235 0.489
(1.00) 		0.365
(1.00) 		0.0872
(1.00) 		0.207
(1.00) 		0.295
(1.00) 		0.234
(1.00) 		0.077
(1.00) 		0.353
(1.00) 		0.00815
(1.00) 		0.0927
(1.00) 		0.225
(1.00) 		0.106
(1.00)
amp 10q22 3 36 (6%) 550 0.86
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.58
(1.00) 		0.269
(1.00) 		0.0161
(1.00) 		0.892
(1.00) 		0.608
(1.00) 		0.953
(1.00) 		0.437
(1.00) 		0.923
(1.00) 		0.096
(1.00)
amp 11p15 5 132 (23%) 454 0.774
(1.00) 		0.0603
(1.00) 		0.118
(1.00) 		0.949
(1.00) 		0.382
(1.00) 		0.598
(1.00) 		0.419
(1.00) 		0.621
(1.00) 		0.000817
(0.654) 		0.121
(1.00) 		0.901
(1.00) 		0.464
(1.00)
amp 12p13 32 144 (25%) 442 0.249
(1.00) 		0.0501
(1.00) 		0.914
(1.00) 		0.15
(1.00) 		0.375
(1.00) 		0.123
(1.00) 		0.161
(1.00) 		0.773
(1.00) 		0.474
(1.00) 		0.465
(1.00) 		0.791
(1.00) 		0.388
(1.00)
amp 15q26 1 41 (7%) 545 0.294
(1.00) 		0.691
(1.00) 		0.585
(1.00) 		0.028
(1.00) 		0.154
(1.00) 		0.00111
(0.883) 		0.839
(1.00) 		0.256
(1.00) 		0.491
(1.00) 		0.126
(1.00) 		0.487
(1.00) 		0.0472
(1.00)
amp 17q12 148 (25%) 438 0.557
(1.00) 		0.462
(1.00) 		0.594
(1.00) 		0.176
(1.00) 		0.28
(1.00) 		0.235
(1.00) 		0.00652
(1.00) 		0.0704
(1.00) 		0.431
(1.00) 		0.461
(1.00) 		0.0303
(1.00) 		0.418
(1.00)
amp 17q24 1 133 (23%) 453 0.078
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.929
(1.00) 		0.9
(1.00) 		0.0413
(1.00) 		0.693
(1.00) 		0.0729
(1.00) 		0.692
(1.00) 		0.122
(1.00) 		0.673
(1.00)
amp 19p13 2 103 (18%) 483 0.4
(1.00) 		0.661
(1.00) 		0.18
(1.00) 		0.71
(1.00) 		0.321
(1.00) 		0.0453
(1.00) 		0.271
(1.00) 		0.157
(1.00) 		0.0443
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.906
(1.00)
amp 19q12 129 (22%) 457 0.582
(1.00) 		0.968
(1.00) 		0.145
(1.00) 		0.415
(1.00) 		0.732
(1.00) 		0.0529
(1.00) 		0.0399
(1.00) 		0.134
(1.00) 		0.0175
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.448
(1.00)
amp 20p11 23 306 (52%) 280 0.993
(1.00) 		0.765
(1.00) 		0.0198
(1.00) 		0.00222
(1.00) 		0.978
(1.00) 		0.0642
(1.00) 		0.000477
(0.387) 		0.0472
(1.00) 		0.000516
(0.419) 		0.18
(1.00) 		0.185
(1.00) 		0.471
(1.00)
amp xq28 118 (20%) 468 0.184
(1.00) 		0.398
(1.00) 		0.485
(1.00) 		0.157
(1.00) 		0.517
(1.00) 		0.0501
(1.00) 		0.207
(1.00) 		0.606
(1.00) 		0.0372
(1.00) 		0.695
(1.00) 		0.294
(1.00) 		0.334
(1.00)
del 1p36 11 232 (40%) 354 0.0449
(1.00) 		0.144
(1.00) 		0.182
(1.00) 		0.0225
(1.00) 		0.426
(1.00) 		0.00332
(1.00) 		0.000335
(0.274) 		0.272
(1.00) 		0.00343
(1.00) 		0.745
(1.00) 		0.084
(1.00) 		0.00108
(0.859)
del 1p33 165 (28%) 421 0.027
(1.00) 		0.963
(1.00) 		0.47
(1.00) 		0.0545
(1.00) 		0.377
(1.00) 		0.0192
(1.00) 		0.0138
(1.00) 		0.783
(1.00) 		0.0499
(1.00) 		0.716
(1.00) 		0.278
(1.00) 		0.0257
(1.00)
del 1p13 2 165 (28%) 421 0.238
(1.00) 		0.901
(1.00) 		0.257
(1.00) 		0.0109
(1.00) 		0.24
(1.00) 		0.00808
(1.00) 		0.00273
(1.00) 		0.646
(1.00) 		0.0963
(1.00) 		0.278
(1.00) 		0.374
(1.00) 		0.00601
(1.00)
del 2p12 21 (4%) 565 0.707
(1.00) 		0.0945
(1.00) 		0.000754
(0.607) 		0.516
(1.00) 		1
(1.00) 		0.399
(1.00) 		0.517
(1.00) 		0.658
(1.00) 		0.00737
(1.00) 		0.282
(1.00) 		0.889
(1.00) 		0.348
(1.00)
del 2q22 1 34 (6%) 552 0.907
(1.00) 		0.637
(1.00) 		0.843
(1.00) 		0.553
(1.00) 		0.628
(1.00) 		0.714
(1.00) 		0.626
(1.00) 		0.597
(1.00) 		0.982
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00)
del 2q37 2 31 (5%) 555 0.735
(1.00) 		0.0764
(1.00) 		0.537
(1.00) 		0.25
(1.00) 		0.446
(1.00) 		0.139
(1.00) 		0.105
(1.00) 		0.359
(1.00) 		0.885
(1.00) 		1
(1.00) 		0.395
(1.00) 		0.808
(1.00)
del 3p26 3 88 (15%) 498 0.0038
(1.00) 		0.616
(1.00) 		0.432
(1.00) 		0.0285
(1.00) 		0.0903
(1.00) 		0.0177
(1.00) 		0.00258
(1.00) 		0.908
(1.00) 		0.0919
(1.00) 		0.63
(1.00) 		0.0576
(1.00) 		0.0379
(1.00)
del 3p14 2 109 (19%) 477 0.417
(1.00) 		0.435
(1.00) 		0.633
(1.00) 		0.164
(1.00) 		0.144
(1.00) 		0.212
(1.00) 		0.049
(1.00) 		0.596
(1.00) 		0.483
(1.00) 		0.676
(1.00) 		0.234
(1.00) 		0.0332
(1.00)
del 3q26 31 60 (10%) 526 0.834
(1.00) 		0.98
(1.00) 		0.878
(1.00) 		0.0105
(1.00) 		0.018
(1.00) 		0.734
(1.00) 		0.612
(1.00) 		0.133
(1.00) 		0.0233
(1.00) 		1
(1.00) 		0.44
(1.00) 		0.674
(1.00)
del 4q22 1 208 (35%) 378 0.438
(1.00) 		0.355
(1.00) 		0.0112
(1.00) 		0.026
(1.00) 		0.187
(1.00) 		0.00114
(0.901) 		0.429
(1.00) 		0.196
(1.00) 		0.00155
(1.00) 		0.00144
(1.00) 		0.751
(1.00) 		0.00408
(1.00)
del 4q35 1 217 (37%) 369 0.613
(1.00) 		0.247
(1.00) 		0.0665
(1.00) 		0.108
(1.00) 		0.424
(1.00) 		0.00165
(1.00) 		0.306
(1.00) 		0.732
(1.00) 		0.0279
(1.00) 		0.00199
(1.00) 		0.717
(1.00) 		0.0236
(1.00)
del 5q22 2 178 (30%) 408 0.108
(1.00) 		0.692
(1.00) 		0.106
(1.00) 		0.0844
(1.00) 		0.744
(1.00) 		0.0188
(1.00) 		0.0297
(1.00) 		0.53
(1.00) 		0.031
(1.00) 		0.000431
(0.351) 		0.239
(1.00) 		0.096
(1.00)
del 6p25 3 78 (13%) 508 0.293
(1.00) 		0.0953
(1.00) 		0.89
(1.00) 		0.611
(1.00) 		0.398
(1.00) 		0.455
(1.00) 		0.272
(1.00) 		0.0882
(1.00) 		0.537
(1.00) 		0.342
(1.00) 		0.406
(1.00) 		0.741
(1.00)
del 6q26 89 (15%) 497 0.0524
(1.00) 		0.774
(1.00) 		0.297
(1.00) 		0.09
(1.00) 		0.179
(1.00) 		0.00694
(1.00) 		0.0388
(1.00) 		0.357
(1.00) 		0.0364
(1.00) 		0.632
(1.00) 		0.159
(1.00) 		0.01
(1.00)
del 7q31 1 16 (3%) 570 0.636
(1.00) 		0.519
(1.00) 		1
(1.00) 		0.904
(1.00) 		0.514
(1.00) 		0.885
(1.00) 		0.159
(1.00) 		0.456
(1.00) 		0.489
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.634
(1.00)
del 8q11 1 45 (8%) 541 0.796
(1.00) 		0.433
(1.00) 		0.163
(1.00) 		0.0417
(1.00) 		0.722
(1.00) 		0.0499
(1.00) 		0.00192
(1.00) 		0.276
(1.00) 		0.429
(1.00) 		0.515
(1.00) 		0.344
(1.00) 		0.341
(1.00)
del 9p24 2 80 (14%) 506 0.015
(1.00) 		0.162
(1.00) 		0.345
(1.00) 		0.518
(1.00) 		0.495
(1.00) 		0.223
(1.00) 		0.0241
(1.00) 		0.054
(1.00) 		0.183
(1.00) 		0.354
(1.00) 		0.112
(1.00) 		0.323
(1.00)
del 10p15 3 109 (19%) 477 0.441
(1.00) 		0.032
(1.00) 		0.404
(1.00) 		0.112
(1.00) 		0.614
(1.00) 		0.0448
(1.00) 		0.181
(1.00) 		0.751
(1.00) 		0.41
(1.00) 		0.0137
(1.00) 		0.921
(1.00) 		0.0766
(1.00)
del 10q21 1 126 (22%) 460 0.992
(1.00) 		0.0299
(1.00) 		0.734
(1.00) 		0.303
(1.00) 		0.703
(1.00) 		0.251
(1.00) 		0.726
(1.00) 		0.92
(1.00) 		0.0888
(1.00) 		0.0255
(1.00) 		0.487
(1.00) 		0.236
(1.00)
del 10q23 31 152 (26%) 434 0.646
(1.00) 		0.00724
(1.00) 		0.0713
(1.00) 		0.102
(1.00) 		0.617
(1.00) 		0.0714
(1.00) 		0.116
(1.00) 		0.925
(1.00) 		0.0113
(1.00) 		0.0115
(1.00) 		0.631
(1.00) 		0.429
(1.00)
del 10q25 2 148 (25%) 438 0.807
(1.00) 		0.067
(1.00) 		0.239
(1.00) 		0.208
(1.00) 		0.274
(1.00) 		0.0198
(1.00) 		0.343
(1.00) 		0.924
(1.00) 		0.0308
(1.00) 		0.00999
(1.00) 		0.59
(1.00) 		0.24
(1.00)
del 11q22 3 108 (18%) 478 0.276
(1.00) 		0.659
(1.00) 		0.0695
(1.00) 		0.771
(1.00) 		0.77
(1.00) 		0.233
(1.00) 		0.566
(1.00) 		0.594
(1.00) 		0.0505
(1.00) 		0.22
(1.00) 		0.653
(1.00) 		0.0762
(1.00)
del 12p13 1 86 (15%) 500 0.0451
(1.00) 		0.325
(1.00) 		0.11
(1.00) 		0.369
(1.00) 		0.485
(1.00) 		0.0203
(1.00) 		0.107
(1.00) 		0.641
(1.00) 		0.00536
(1.00) 		0.627
(1.00) 		0.867
(1.00) 		0.977
(1.00)
del 12q21 33 85 (15%) 501 0.204
(1.00) 		0.674
(1.00) 		0.291
(1.00) 		0.0124
(1.00) 		0.514
(1.00) 		0.154
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.041
(1.00) 		0.625
(1.00) 		0.607
(1.00) 		0.273
(1.00)
del 15q11 2 239 (41%) 347 0.733
(1.00) 		0.742
(1.00) 		0.157
(1.00) 		0.126
(1.00) 		0.771
(1.00) 		0.0173
(1.00) 		0.237
(1.00) 		0.448
(1.00) 		0.0356
(1.00) 		0.0357
(1.00) 		0.746
(1.00) 		0.0736
(1.00)
del 15q21 1 234 (40%) 352 0.633
(1.00) 		0.884
(1.00) 		0.0292
(1.00) 		0.167
(1.00) 		0.827
(1.00) 		0.0218
(1.00) 		0.095
(1.00) 		0.206
(1.00) 		0.00814
(1.00) 		0.0337
(1.00) 		0.39
(1.00) 		0.0677
(1.00)
del 15q22 33 224 (38%) 362 0.775
(1.00) 		0.545
(1.00) 		0.00979
(1.00) 		0.0123
(1.00) 		0.0793
(1.00) 		0.00417
(1.00) 		0.0725
(1.00) 		0.551
(1.00) 		0.00357
(1.00) 		0.00253
(1.00) 		0.504
(1.00) 		0.0355
(1.00)
del 16q23 1 78 (13%) 508 0.00571
(1.00) 		0.44
(1.00) 		0.682
(1.00) 		0.325
(1.00) 		0.212
(1.00) 		0.589
(1.00) 		0.801
(1.00) 		0.273
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.254
(1.00)
del 17q24 3 87 (15%) 499 0.459
(1.00) 		0.624
(1.00) 		0.896
(1.00) 		0.0456
(1.00) 		0.211
(1.00) 		0.00548
(1.00) 		0.0619
(1.00) 		0.162
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.397
(1.00) 		0.0589
(1.00)
del 20p12 1 181 (31%) 405 0.0543
(1.00) 		0.563
(1.00) 		0.0355
(1.00) 		0.252
(1.00) 		0.415
(1.00) 		0.247
(1.00) 		0.682
(1.00) 		0.324
(1.00) 		0.116
(1.00) 		0.0632
(1.00) 		0.317
(1.00) 		0.82
(1.00)
del 20p12 1 181 (31%) 405 0.0543
(1.00) 		0.563
(1.00) 		0.0355
(1.00) 		0.252
(1.00) 		0.415
(1.00) 		0.247
(1.00) 		0.682
(1.00) 		0.324
(1.00) 		0.116
(1.00) 		0.0632
(1.00) 		0.317
(1.00) 		0.82
(1.00)
del 21q11 2 203 (35%) 383 0.615
(1.00) 		0.824
(1.00) 		0.00604
(1.00) 		0.229
(1.00) 		0.899
(1.00) 		0.031
(1.00) 		0.403
(1.00) 		0.602
(1.00) 		0.000364
(0.297) 		0.288
(1.00) 		0.737
(1.00) 		0.00501
(1.00)
del 22q13 32 216 (37%) 370 0.0484
(1.00) 		0.507
(1.00) 		0.21
(1.00) 		0.0192
(1.00) 		0.391
(1.00) 		0.000555
(0.449) 		0.0189
(1.00) 		0.493
(1.00) 		0.00387
(1.00) 		0.732
(1.00) 		0.451
(1.00) 		0.0182
(1.00)
'amp_6p21.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.000232 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #5: 'amp_6p21.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 5(6P21.1) MUTATED 65 40 42
AMP PEAK 5(6P21.1) WILD-TYPE 266 106 64

Figure S1.  Get High-res Image Gene #5: 'amp_6p21.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_7p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000178 (Chi-square test), Q value = 0.15

Table S2.  Gene #6: 'amp_7p21.3' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
AMP PEAK 6(7P21.3) MUTATED 55 1 20 72 3 2 15 15 56 35 41 20 0
AMP PEAK 6(7P21.3) WILD-TYPE 46 0 21 85 7 1 12 7 19 15 18 5 1

Figure S2.  Get High-res Image Gene #6: 'amp_7p21.3' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_7p21.3' versus 'PATHOLOGY.N.STAGE'

P value = 3.34e-06 (Fisher's exact test), Q value = 0.0028

Table S3.  Gene #6: 'amp_7p21.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 6(7P21.3) MUTATED 165 105 72
AMP PEAK 6(7P21.3) WILD-TYPE 166 41 34

Figure S3.  Get High-res Image Gene #6: 'amp_7p21.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q12.13' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000181 (Chi-square test), Q value = 0.15

Table S4.  Gene #14: 'amp_13q12.13' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
AMP PEAK 14(13Q12.13) MUTATED 62 0 18 92 4 3 16 17 55 36 48 22 0
AMP PEAK 14(13Q12.13) WILD-TYPE 39 1 23 65 6 0 11 5 20 14 11 3 1

Figure S4.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_13q12.13' versus 'PATHOLOGY.N.STAGE'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.013

Table S5.  Gene #14: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 14(13Q12.13) MUTATED 189 111 80
AMP PEAK 14(13Q12.13) WILD-TYPE 142 35 26

Figure S5.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q12.13' versus 'HISTOLOGICAL.TYPE'

P value = 1.19e-10 (Fisher's exact test), Q value = 1e-07

Table S6.  Gene #14: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 14(13Q12.13) MUTATED 242 16 114 5
AMP PEAK 14(13Q12.13) WILD-TYPE 125 39 29 8

Figure S6.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_13q12.2' versus 'PATHOLOGY.N.STAGE'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.028

Table S7.  Gene #15: 'amp_13q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 15(13Q12.2) MUTATED 187 109 79
AMP PEAK 15(13Q12.2) WILD-TYPE 144 37 27

Figure S7.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 2.8e-10 (Fisher's exact test), Q value = 2.4e-07

Table S8.  Gene #15: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 15(13Q12.2) MUTATED 238 16 113 5
AMP PEAK 15(13Q12.2) WILD-TYPE 129 39 30 8

Figure S8.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_13q22.1' versus 'PATHOLOGY.N.STAGE'

P value = 9.1e-05 (Fisher's exact test), Q value = 0.075

Table S9.  Gene #16: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 16(13Q22.1) MUTATED 189 110 77
AMP PEAK 16(13Q22.1) WILD-TYPE 142 36 29

Figure S9.  Get High-res Image Gene #16: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1.43e-08 (Fisher's exact test), Q value = 1.2e-05

Table S10.  Gene #16: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 16(13Q22.1) MUTATED 243 18 109 4
AMP PEAK 16(13Q22.1) WILD-TYPE 124 37 34 9

Figure S10.  Get High-res Image Gene #16: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 6.84e-05 (Fisher's exact test), Q value = 0.057

Table S11.  Gene #18: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
AMP PEAK 18(16P11.2) MUTATED 69 54 40
AMP PEAK 18(16P11.2) WILD-TYPE 262 92 66

Figure S11.  Get High-res Image Gene #18: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_20q11.21' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.85e-06 (Fisher's exact test), Q value = 0.0083

Table S12.  Gene #24: 'amp_20q11.21' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
AMP PEAK 24(20Q11.21) MUTATED 303 141
AMP PEAK 24(20Q11.21) WILD-TYPE 120 18

Figure S12.  Get High-res Image Gene #24: 'amp_20q11.21' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q11.21' versus 'HISTOLOGICAL.TYPE'

P value = 2.55e-12 (Fisher's exact test), Q value = 2.2e-09

Table S13.  Gene #24: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 24(20Q11.21) MUTATED 278 24 132 7
AMP PEAK 24(20Q11.21) WILD-TYPE 89 31 11 6

Figure S13.  Get High-res Image Gene #24: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_20q12' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.15e-06 (Fisher's exact test), Q value = 0.0044

Table S14.  Gene #25: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
AMP PEAK 25(20Q12) MUTATED 304 142
AMP PEAK 25(20Q12) WILD-TYPE 119 17

Figure S14.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q12' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000209 (Chi-square test), Q value = 0.17

Table S15.  Gene #25: 'amp_20q12' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
AMP PEAK 25(20Q12) MUTATED 76 1 24 110 5 3 19 21 59 42 53 24 0
AMP PEAK 25(20Q12) WILD-TYPE 25 0 17 47 5 0 8 1 16 8 6 1 1

Figure S15.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 1.57e-13 (Fisher's exact test), Q value = 1.3e-10

Table S16.  Gene #25: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 25(20Q12) MUTATED 280 23 133 7
AMP PEAK 25(20Q12) WILD-TYPE 87 32 10 6

Figure S16.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_20q13.31' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.94e-06 (Fisher's exact test), Q value = 0.0067

Table S17.  Gene #26: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
AMP PEAK 26(20Q13.31) MUTATED 306 142
AMP PEAK 26(20Q13.31) WILD-TYPE 117 17

Figure S17.  Get High-res Image Gene #26: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q13.31' versus 'HISTOLOGICAL.TYPE'

P value = 7.26e-13 (Fisher's exact test), Q value = 6.2e-10

Table S18.  Gene #26: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
AMP PEAK 26(20Q13.31) MUTATED 281 24 133 7
AMP PEAK 26(20Q13.31) WILD-TYPE 86 31 10 6

Figure S18.  Get High-res Image Gene #26: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_4p16.1' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.028

Table S19.  Gene #37: 'del_4p16.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 577
DEL PEAK 10(4P16.1) MUTATED 9 180
DEL PEAK 10(4P16.1) WILD-TYPE 0 397

Figure S19.  Get High-res Image Gene #37: 'del_4p16.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'del_5q11.2' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.59e-05 (Fisher's exact test), Q value = 0.079

Table S20.  Gene #40: 'del_5q11.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 577
DEL PEAK 13(5Q11.2) MUTATED 8 139
DEL PEAK 13(5Q11.2) WILD-TYPE 1 438

Figure S20.  Get High-res Image Gene #40: 'del_5q11.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'del_8p23.3' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.65e-05 (Fisher's exact test), Q value = 0.014

Table S21.  Gene #45: 'del_8p23.3' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 18(8P23.3) MUTATED 175 98
DEL PEAK 18(8P23.3) WILD-TYPE 248 61

Figure S21.  Get High-res Image Gene #45: 'del_8p23.3' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 4.91e-05 (Fisher's exact test), Q value = 0.041

Table S22.  Gene #45: 'del_8p23.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 18(8P23.3) MUTATED 130 77 66
DEL PEAK 18(8P23.3) WILD-TYPE 201 69 40

Figure S22.  Get High-res Image Gene #45: 'del_8p23.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p23.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.97e-05 (Fisher's exact test), Q value = 0.025

Table S23.  Gene #45: 'del_8p23.3' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 18(8P23.3) MUTATED 158 16 89 7
DEL PEAK 18(8P23.3) WILD-TYPE 209 39 54 6

Figure S23.  Get High-res Image Gene #45: 'del_8p23.3' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_8p23.2' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.032

Table S24.  Gene #46: 'del_8p23.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 19(8P23.2) MUTATED 176 97
DEL PEAK 19(8P23.2) WILD-TYPE 247 62

Figure S24.  Get High-res Image Gene #46: 'del_8p23.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_8p23.2' versus 'PATHOLOGY.N.STAGE'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.023

Table S25.  Gene #46: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 19(8P23.2) MUTATED 129 78 66
DEL PEAK 19(8P23.2) WILD-TYPE 202 68 40

Figure S25.  Get High-res Image Gene #46: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.028

Table S26.  Gene #46: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 19(8P23.2) MUTATED 160 15 88 7
DEL PEAK 19(8P23.2) WILD-TYPE 207 40 55 6

Figure S26.  Get High-res Image Gene #46: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_8p22' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.000283 (Fisher's exact test), Q value = 0.23

Table S27.  Gene #47: 'del_8p22' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 20(8P22) MUTATED 189 98
DEL PEAK 20(8P22) WILD-TYPE 234 61

Figure S27.  Get High-res Image Gene #47: 'del_8p22' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000148 (Chi-square test), Q value = 0.12

Table S28.  Gene #47: 'del_8p22' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
DEL PEAK 20(8P22) MUTATED 39 0 13 65 3 2 15 13 42 33 42 15 1
DEL PEAK 20(8P22) WILD-TYPE 62 1 28 92 7 1 12 9 33 17 17 10 0

Figure S28.  Get High-res Image Gene #47: 'del_8p22' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 5.86e-07 (Fisher's exact test), Q value = 5e-04

Table S29.  Gene #47: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 20(8P22) MUTATED 133 82 72
DEL PEAK 20(8P22) WILD-TYPE 198 64 34

Figure S29.  Get High-res Image Gene #47: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'HISTOLOGICAL.TYPE'

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

Table S30.  Gene #47: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 20(8P22) MUTATED 172 16 89 7
DEL PEAK 20(8P22) WILD-TYPE 195 39 54 6

Figure S30.  Get High-res Image Gene #47: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 0.000124 (t-test), Q value = 0.1

Table S31.  Gene #47: 'del_8p22' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 552 2.2 (4.7)
DEL PEAK 20(8P22) MUTATED 277 3.0 (5.7)
DEL PEAK 20(8P22) WILD-TYPE 275 1.4 (3.3)

Figure S31.  Get High-res Image Gene #47: 'del_8p22' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_14q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 4.49e-07 (Fisher's exact test), Q value = 0.00038

Table S32.  Gene #57: 'del_14q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 30(14Q21.2) MUTATED 124 4 63 1
DEL PEAK 30(14Q21.2) WILD-TYPE 243 51 80 12

Figure S32.  Get High-res Image Gene #57: 'del_14q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_16p13.3' versus 'Time to Death'

P value = 4.32e-05 (logrank test), Q value = 0.036

Table S33.  Gene #61: 'del_16p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 76 0.1 - 140.4 (12.4)
DEL PEAK 34(16P13.3) MUTATED 50 17 0.2 - 61.8 (13.0)
DEL PEAK 34(16P13.3) WILD-TYPE 420 59 0.1 - 140.4 (12.2)

Figure S33.  Get High-res Image Gene #61: 'del_16p13.3' versus Clinical Feature #1: 'Time to Death'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 8.77e-05 (Fisher's exact test), Q value = 0.073

Table S34.  Gene #63: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 36(17P12) MUTATED 172 99 76
DEL PEAK 36(17P12) WILD-TYPE 159 47 30

Figure S34.  Get High-res Image Gene #63: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 3.31e-08 (Fisher's exact test), Q value = 2.8e-05

Table S35.  Gene #63: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 36(17P12) MUTATED 219 14 103 6
DEL PEAK 36(17P12) WILD-TYPE 148 41 40 7

Figure S35.  Get High-res Image Gene #63: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18p11.31' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.65e-06 (Fisher's exact test), Q value = 0.0039

Table S36.  Gene #65: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 38(18P11.31) MUTATED 228 119
DEL PEAK 38(18P11.31) WILD-TYPE 195 40

Figure S36.  Get High-res Image Gene #65: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 0.000131 (Chi-square test), Q value = 0.11

Table S37.  Gene #65: 'del_18p11.31' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 441 72 9 1 54
DEL PEAK 38(18P11.31) MUTATED 248 58 9 0 31
DEL PEAK 38(18P11.31) WILD-TYPE 193 14 0 1 23

Figure S37.  Get High-res Image Gene #65: 'del_18p11.31' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_18p11.31' versus 'HISTOLOGICAL.TYPE'

P value = 5.18e-17 (Fisher's exact test), Q value = 4.5e-14

Table S38.  Gene #65: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 38(18P11.31) MUTATED 220 7 113 6
DEL PEAK 38(18P11.31) WILD-TYPE 147 48 30 7

Figure S38.  Get High-res Image Gene #65: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.25e-09 (Fisher's exact test), Q value = 1.1e-06

Table S39.  Gene #66: 'del_18q21.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 39(18Q21.2) MUTATED 268 140
DEL PEAK 39(18Q21.2) WILD-TYPE 155 19

Figure S39.  Get High-res Image Gene #66: 'del_18q21.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.27e-05 (Chi-square test), Q value = 0.036

Table S40.  Gene #66: 'del_18q21.2' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
DEL PEAK 39(18Q21.2) MUTATED 60 0 25 99 4 3 17 18 58 41 53 22 1
DEL PEAK 39(18Q21.2) WILD-TYPE 41 1 16 58 6 0 10 4 17 9 6 3 0

Figure S40.  Get High-res Image Gene #66: 'del_18q21.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.94e-06 (Fisher's exact test), Q value = 0.0017

Table S41.  Gene #66: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 39(18Q21.2) MUTATED 204 116 88
DEL PEAK 39(18Q21.2) WILD-TYPE 127 30 18

Figure S41.  Get High-res Image Gene #66: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-16 (Fisher's exact test), Q value = 8.9e-14

Table S42.  Gene #66: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 39(18Q21.2) MUTATED 253 14 126 12
DEL PEAK 39(18Q21.2) WILD-TYPE 114 41 17 1

Figure S42.  Get High-res Image Gene #66: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q22.1' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.19e-07 (Fisher's exact test), Q value = 0.00019

Table S43.  Gene #67: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
DEL PEAK 40(18Q22.1) MUTATED 268 135
DEL PEAK 40(18Q22.1) WILD-TYPE 155 24

Figure S43.  Get High-res Image Gene #67: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.58e-05 (Chi-square test), Q value = 0.079

Table S44.  Gene #67: 'del_18q22.1' versus Clinical Feature #4: '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 101 1 41 157 10 3 27 22 75 50 59 25 1
DEL PEAK 40(18Q22.1) MUTATED 60 0 25 99 4 3 15 17 57 41 52 22 1
DEL PEAK 40(18Q22.1) WILD-TYPE 41 1 16 58 6 0 12 5 18 9 7 3 0

Figure S44.  Get High-res Image Gene #67: 'del_18q22.1' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 2.3e-05 (Fisher's exact test), Q value = 0.019

Table S45.  Gene #67: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 40(18Q22.1) MUTATED 204 112 87
DEL PEAK 40(18Q22.1) WILD-TYPE 127 34 19

Figure S45.  Get High-res Image Gene #67: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 5.81e-16 (Fisher's exact test), Q value = 5e-13

Table S46.  Gene #67: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
DEL PEAK 40(18Q22.1) MUTATED 254 13 124 10
DEL PEAK 40(18Q22.1) WILD-TYPE 113 42 19 3

Figure S46.  Get High-res Image Gene #67: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 0.000107 (Fisher's exact test), Q value = 0.088

Table S47.  Gene #68: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
DEL PEAK 41(19P13.3) MUTATED 36 27 30
DEL PEAK 41(19P13.3) WILD-TYPE 295 119 76

Figure S47.  Get High-res Image Gene #68: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 586

  • Number of significantly focal cnvs = 72

  • 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

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

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

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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