Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1T152GV
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 78 arm-level events and 12 clinical features across 439 patients, 20 significant findings detected with Q value < 0.25.

  • 7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 4p loss cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 5q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 17p loss cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • 18p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18q loss cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • 19p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 22q loss 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 78 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 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
17p loss 230 (52%) 209 0.099
(1.00)
0.0534
(1.00)
7e-05
(0.0647)
0.645
(1.00)
0.0001
(0.092)
0.00419
(1.00)
0.0555
(1.00)
9.99e-06
(0.00926)
0.25
(1.00)
0.0372
(1.00)
8.56e-06
(0.00794)
0.833
(1.00)
18q loss 264 (60%) 175 0.871
(1.00)
0.0108
(1.00)
7e-05
(0.0647)
0.851
(1.00)
0.00013
(0.119)
0.0015
(1.00)
0.329
(1.00)
7.48e-09
(6.97e-06)
0.279
(1.00)
0.107
(1.00)
0.000114
(0.105)
0.908
(1.00)
7p gain 242 (55%) 197 0.985
(1.00)
0.0835
(1.00)
6e-05
(0.0556)
0.333
(1.00)
9e-05
(0.0829)
0.0608
(1.00)
1
(1.00)
0.0358
(1.00)
0.256
(1.00)
0.286
(1.00)
0.000331
(0.302)
0.413
(1.00)
20p gain 236 (54%) 203 0.267
(1.00)
0.396
(1.00)
0.0001
(0.092)
0.756
(1.00)
0.196
(1.00)
0.00198
(1.00)
0.125
(1.00)
0.000215
(0.197)
0.253
(1.00)
0.0626
(1.00)
0.0871
(1.00)
0.797
(1.00)
13q gain 250 (57%) 189 0.91
(1.00)
0.603
(1.00)
0.00049
(0.443)
0.989
(1.00)
0.00331
(1.00)
0.0017
(1.00)
0.385
(1.00)
8.48e-07
(0.000789)
0.263
(1.00)
0.03
(1.00)
0.0124
(1.00)
0.178
(1.00)
20q gain 311 (71%) 128 0.699
(1.00)
0.212
(1.00)
0.00205
(1.00)
0.305
(1.00)
0.0162
(1.00)
0.0136
(1.00)
0.248
(1.00)
9.99e-07
(0.000929)
0.559
(1.00)
0.091
(1.00)
0.0172
(1.00)
0.467
(1.00)
4p loss 129 (29%) 310 0.028
(1.00)
0.786
(1.00)
0.00192
(1.00)
0.314
(1.00)
0.00304
(1.00)
0.00026
(0.238)
1
(1.00)
0.0131
(1.00)
0.025
(1.00)
0.0267
(1.00)
0.000573
(0.518)
0.881
(1.00)
5q loss 74 (17%) 365 0.0224
(1.00)
0.163
(1.00)
0.0189
(1.00)
0.555
(1.00)
0.0003
(0.274)
0.0217
(1.00)
0.251
(1.00)
0.351
(1.00)
0.075
(1.00)
0.646
(1.00)
6.4e-05
(0.0592)
0.33
(1.00)
14q loss 133 (30%) 306 0.596
(1.00)
0.343
(1.00)
0.207
(1.00)
0.331
(1.00)
0.144
(1.00)
0.019
(1.00)
1
(1.00)
6.05e-06
(0.00562)
0.557
(1.00)
0.638
(1.00)
0.173
(1.00)
0.927
(1.00)
18p loss 247 (56%) 192 0.937
(1.00)
0.0163
(1.00)
0.00044
(0.399)
0.937
(1.00)
0.00451
(1.00)
0.00037
(0.336)
0.441
(1.00)
2.29e-09
(2.14e-06)
0.26
(1.00)
0.027
(1.00)
0.00127
(1.00)
0.951
(1.00)
19p loss 39 (9%) 400 0.0479
(1.00)
0.222
(1.00)
0.018
(1.00)
1
(1.00)
0.00294
(1.00)
0.00386
(1.00)
0.868
(1.00)
0.327
(1.00)
0.244
(1.00)
0.286
(1.00)
7.31e-05
(0.0674)
0.74
(1.00)
22q loss 139 (32%) 300 0.0671
(1.00)
0.581
(1.00)
0.0017
(1.00)
0.443
(1.00)
0.00032
(0.292)
0.00726
(1.00)
0.919
(1.00)
0.00261
(1.00)
1
(1.00)
0.414
(1.00)
0.000191
(0.175)
0.522
(1.00)
1p gain 32 (7%) 407 0.705
(1.00)
0.295
(1.00)
0.787
(1.00)
0.948
(1.00)
0.485
(1.00)
0.22
(1.00)
0.717
(1.00)
0.6
(1.00)
0.204
(1.00)
0.18
(1.00)
0.127
(1.00)
0.48
(1.00)
1q gain 78 (18%) 361 0.514
(1.00)
0.51
(1.00)
0.184
(1.00)
0.461
(1.00)
0.0938
(1.00)
0.0171
(1.00)
0.169
(1.00)
0.272
(1.00)
0.445
(1.00)
0.232
(1.00)
0.0195
(1.00)
1
(1.00)
2p gain 78 (18%) 361 0.285
(1.00)
0.883
(1.00)
0.46
(1.00)
0.595
(1.00)
0.239
(1.00)
0.22
(1.00)
0.708
(1.00)
0.0446
(1.00)
0.445
(1.00)
0.074
(1.00)
0.108
(1.00)
0.841
(1.00)
2q gain 74 (17%) 365 0.156
(1.00)
0.401
(1.00)
0.238
(1.00)
0.508
(1.00)
0.0797
(1.00)
0.13
(1.00)
0.899
(1.00)
0.0639
(1.00)
0.426
(1.00)
0.14
(1.00)
0.0354
(1.00)
0.598
(1.00)
3p gain 45 (10%) 394 0.159
(1.00)
0.0688
(1.00)
0.00235
(1.00)
0.826
(1.00)
0.191
(1.00)
0.00074
(0.667)
0.637
(1.00)
0.818
(1.00)
1
(1.00)
0.946
(1.00)
0.126
(1.00)
0.181
(1.00)
3q gain 64 (15%) 375 0.168
(1.00)
0.209
(1.00)
0.0166
(1.00)
0.622
(1.00)
0.0701
(1.00)
0.00308
(1.00)
0.499
(1.00)
0.425
(1.00)
1
(1.00)
0.875
(1.00)
0.123
(1.00)
0.267
(1.00)
4p gain 12 (3%) 427 0.668
(1.00)
0.254
(1.00)
0.2
(1.00)
0.691
(1.00)
0.027
(1.00)
0.0918
(1.00)
0.391
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.0153
(1.00)
0.00144
(1.00)
4q gain 17 (4%) 422 0.282
(1.00)
0.805
(1.00)
0.422
(1.00)
0.952
(1.00)
0.00644
(1.00)
0.146
(1.00)
0.458
(1.00)
0.49
(1.00)
1
(1.00)
0.337
(1.00)
0.00618
(1.00)
0.0286
(1.00)
5p gain 68 (15%) 371 0.559
(1.00)
0.0598
(1.00)
0.276
(1.00)
0.986
(1.00)
0.0248
(1.00)
0.377
(1.00)
0.355
(1.00)
0.847
(1.00)
1
(1.00)
0.294
(1.00)
0.0162
(1.00)
0.151
(1.00)
5q gain 42 (10%) 397 0.34
(1.00)
0.906
(1.00)
0.429
(1.00)
0.836
(1.00)
0.307
(1.00)
0.347
(1.00)
0.518
(1.00)
0.634
(1.00)
1
(1.00)
0.341
(1.00)
0.972
(1.00)
0.173
(1.00)
6p gain 82 (19%) 357 0.906
(1.00)
0.749
(1.00)
0.131
(1.00)
0.904
(1.00)
0.0395
(1.00)
0.229
(1.00)
0.271
(1.00)
0.368
(1.00)
0.00632
(1.00)
0.661
(1.00)
0.0454
(1.00)
0.294
(1.00)
6q gain 74 (17%) 365 0.563
(1.00)
0.513
(1.00)
0.0549
(1.00)
0.911
(1.00)
0.0497
(1.00)
0.134
(1.00)
0.702
(1.00)
0.35
(1.00)
0.00463
(1.00)
0.841
(1.00)
0.0715
(1.00)
0.819
(1.00)
7q gain 221 (50%) 218 0.824
(1.00)
0.0564
(1.00)
0.0191
(1.00)
0.181
(1.00)
0.0103
(1.00)
0.0386
(1.00)
0.924
(1.00)
0.0691
(1.00)
1
(1.00)
0.462
(1.00)
0.0108
(1.00)
0.25
(1.00)
8p gain 129 (29%) 310 0.329
(1.00)
0.223
(1.00)
0.637
(1.00)
0.776
(1.00)
0.551
(1.00)
0.937
(1.00)
0.917
(1.00)
0.358
(1.00)
0.208
(1.00)
0.47
(1.00)
0.359
(1.00)
0.979
(1.00)
8q gain 222 (51%) 217 0.891
(1.00)
0.0202
(1.00)
0.583
(1.00)
0.236
(1.00)
0.6
(1.00)
0.32
(1.00)
0.504
(1.00)
0.0353
(1.00)
0.248
(1.00)
0.557
(1.00)
0.494
(1.00)
0.886
(1.00)
9p gain 78 (18%) 361 0.0118
(1.00)
0.287
(1.00)
0.0175
(1.00)
0.358
(1.00)
0.141
(1.00)
0.0374
(1.00)
0.803
(1.00)
0.00992
(1.00)
1
(1.00)
0.904
(1.00)
0.143
(1.00)
0.0308
(1.00)
9q gain 69 (16%) 370 0.0121
(1.00)
0.398
(1.00)
0.139
(1.00)
0.309
(1.00)
0.451
(1.00)
0.172
(1.00)
0.896
(1.00)
0.0195
(1.00)
1
(1.00)
0.943
(1.00)
0.39
(1.00)
0.0831
(1.00)
10p gain 34 (8%) 405 0.0206
(1.00)
0.266
(1.00)
0.365
(1.00)
0.236
(1.00)
0.037
(1.00)
0.302
(1.00)
0.725
(1.00)
1
(1.00)
1
(1.00)
0.315
(1.00)
0.0341
(1.00)
0.165
(1.00)
10q gain 20 (5%) 419 0.607
(1.00)
0.0119
(1.00)
0.389
(1.00)
0.833
(1.00)
0.0527
(1.00)
0.281
(1.00)
0.648
(1.00)
0.329
(1.00)
1
(1.00)
0.68
(1.00)
0.0133
(1.00)
0.0465
(1.00)
11p gain 52 (12%) 387 0.862
(1.00)
0.0133
(1.00)
0.0129
(1.00)
0.096
(1.00)
0.0228
(1.00)
0.0563
(1.00)
1
(1.00)
0.00749
(1.00)
0.0382
(1.00)
0.217
(1.00)
0.0199
(1.00)
0.486
(1.00)
11q gain 49 (11%) 390 0.749
(1.00)
0.00035
(0.319)
0.00789
(1.00)
0.328
(1.00)
0.0111
(1.00)
0.154
(1.00)
1
(1.00)
0.000703
(0.634)
0.0341
(1.00)
0.373
(1.00)
0.0177
(1.00)
0.686
(1.00)
12p gain 92 (21%) 347 0.429
(1.00)
0.316
(1.00)
0.0833
(1.00)
0.375
(1.00)
0.242
(1.00)
0.0493
(1.00)
0.907
(1.00)
0.607
(1.00)
1
(1.00)
0.502
(1.00)
0.117
(1.00)
0.925
(1.00)
12q gain 85 (19%) 354 0.814
(1.00)
0.154
(1.00)
0.00796
(1.00)
0.455
(1.00)
0.0727
(1.00)
0.0077
(1.00)
0.904
(1.00)
0.218
(1.00)
1
(1.00)
0.34
(1.00)
0.0282
(1.00)
0.61
(1.00)
14q gain 34 (8%) 405 0.697
(1.00)
0.923
(1.00)
0.618
(1.00)
0.799
(1.00)
0.663
(1.00)
0.0161
(1.00)
0.481
(1.00)
0.111
(1.00)
1
(1.00)
0.717
(1.00)
0.461
(1.00)
0.0146
(1.00)
15q gain 12 (3%) 427 0.62
(1.00)
0.289
(1.00)
0.758
(1.00)
0.506
(1.00)
0.722
(1.00)
0.121
(1.00)
0.0757
(1.00)
1
(1.00)
1
(1.00)
0.0504
(1.00)
0.32
(1.00)
0.293
(1.00)
16p gain 105 (24%) 334 0.352
(1.00)
0.104
(1.00)
0.00371
(1.00)
0.933
(1.00)
0.00177
(1.00)
0.384
(1.00)
0.911
(1.00)
0.00795
(1.00)
0.561
(1.00)
0.862
(1.00)
0.00166
(1.00)
0.425
(1.00)
16q gain 103 (23%) 336 0.313
(1.00)
0.0737
(1.00)
0.00107
(0.961)
0.949
(1.00)
0.00111
(0.993)
0.496
(1.00)
0.822
(1.00)
0.00812
(1.00)
0.553
(1.00)
0.713
(1.00)
0.0016
(1.00)
0.441
(1.00)
17p gain 26 (6%) 413 0.121
(1.00)
0.704
(1.00)
0.665
(1.00)
0.769
(1.00)
0.347
(1.00)
0.113
(1.00)
0.546
(1.00)
0.767
(1.00)
1
(1.00)
0.901
(1.00)
0.666
(1.00)
0.0892
(1.00)
17q gain 79 (18%) 360 0.216
(1.00)
0.295
(1.00)
0.155
(1.00)
0.378
(1.00)
0.156
(1.00)
0.024
(1.00)
1
(1.00)
0.272
(1.00)
0.449
(1.00)
0.293
(1.00)
0.859
(1.00)
0.707
(1.00)
18p gain 22 (5%) 417 0.471
(1.00)
0.51
(1.00)
0.0908
(1.00)
0.967
(1.00)
0.0296
(1.00)
0.27
(1.00)
0.382
(1.00)
0.0189
(1.00)
1
(1.00)
0.53
(1.00)
0.0538
(1.00)
0.878
(1.00)
18q gain 13 (3%) 426 0.754
(1.00)
0.0874
(1.00)
0.451
(1.00)
0.718
(1.00)
0.298
(1.00)
1
(1.00)
0.584
(1.00)
0.0207
(1.00)
1
(1.00)
1
(1.00)
0.881
(1.00)
0.479
(1.00)
19p gain 71 (16%) 368 0.662
(1.00)
0.964
(1.00)
0.541
(1.00)
0.643
(1.00)
0.119
(1.00)
0.0279
(1.00)
0.0686
(1.00)
0.253
(1.00)
0.412
(1.00)
0.293
(1.00)
0.747
(1.00)
1
(1.00)
19q gain 79 (18%) 360 0.626
(1.00)
0.783
(1.00)
0.89
(1.00)
0.908
(1.00)
0.29
(1.00)
0.0355
(1.00)
0.214
(1.00)
1
(1.00)
0.449
(1.00)
0.339
(1.00)
0.951
(1.00)
0.967
(1.00)
21q gain 22 (5%) 417 0.482
(1.00)
0.000765
(0.688)
0.503
(1.00)
0.145
(1.00)
0.328
(1.00)
0.5
(1.00)
0.829
(1.00)
0.507
(1.00)
1
(1.00)
0.469
(1.00)
0.18
(1.00)
0.799
(1.00)
22q gain 12 (3%) 427 0.827
(1.00)
0.535
(1.00)
0.508
(1.00)
0.272
(1.00)
1
(1.00)
0.512
(1.00)
0.776
(1.00)
0.383
(1.00)
1
(1.00)
0.306
(1.00)
0.826
(1.00)
1
(1.00)
xq gain 73 (17%) 366 0.439
(1.00)
0.691
(1.00)
0.156
(1.00)
0.0143
(1.00)
0.706
(1.00)
0.528
(1.00)
0.523
(1.00)
0.576
(1.00)
0.421
(1.00)
0.895
(1.00)
0.609
(1.00)
0.641
(1.00)
1p loss 94 (21%) 345 0.0568
(1.00)
0.961
(1.00)
0.0416
(1.00)
0.627
(1.00)
0.00197
(1.00)
0.0109
(1.00)
0.352
(1.00)
0.237
(1.00)
1
(1.00)
0.47
(1.00)
0.000877
(0.788)
0.447
(1.00)
1q loss 54 (12%) 385 0.134
(1.00)
0.581
(1.00)
0.173
(1.00)
0.881
(1.00)
0.0638
(1.00)
0.193
(1.00)
0.244
(1.00)
0.676
(1.00)
1
(1.00)
0.49
(1.00)
0.0567
(1.00)
0.222
(1.00)
2p loss 6 (1%) 433 0.75
(1.00)
0.684
(1.00)
0.229
(1.00)
0.843
(1.00)
0.851
(1.00)
1
(1.00)
0.22
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.519
(1.00)
2q loss 7 (2%) 432 0.997
(1.00)
0.657
(1.00)
0.286
(1.00)
1
(1.00)
1
(1.00)
0.593
(1.00)
0.126
(1.00)
0.601
(1.00)
1
(1.00)
1
(1.00)
0.801
(1.00)
3p loss 52 (12%) 387 0.493
(1.00)
0.412
(1.00)
0.26
(1.00)
0.142
(1.00)
0.0805
(1.00)
0.127
(1.00)
0.884
(1.00)
0.278
(1.00)
1
(1.00)
0.823
(1.00)
0.0971
(1.00)
0.779
(1.00)
3q loss 32 (7%) 407 0.494
(1.00)
0.615
(1.00)
0.692
(1.00)
0.501
(1.00)
0.846
(1.00)
0.28
(1.00)
0.468
(1.00)
0.6
(1.00)
1
(1.00)
0.865
(1.00)
0.844
(1.00)
0.475
(1.00)
4q loss 117 (27%) 322 0.0529
(1.00)
0.768
(1.00)
0.0274
(1.00)
0.297
(1.00)
0.00313
(1.00)
0.0368
(1.00)
0.746
(1.00)
0.0817
(1.00)
0.0186
(1.00)
0.551
(1.00)
0.00108
(0.965)
0.829
(1.00)
5p loss 53 (12%) 386 0.13
(1.00)
0.292
(1.00)
0.00442
(1.00)
0.329
(1.00)
0.0107
(1.00)
0.0455
(1.00)
0.883
(1.00)
0.519
(1.00)
0.0397
(1.00)
0.386
(1.00)
0.012
(1.00)
0.545
(1.00)
6p loss 33 (8%) 406 0.00562
(1.00)
0.192
(1.00)
0.75
(1.00)
0.116
(1.00)
0.72
(1.00)
0.305
(1.00)
0.371
(1.00)
0.79
(1.00)
1
(1.00)
0.114
(1.00)
0.947
(1.00)
0.048
(1.00)
6q loss 45 (10%) 394 0.0112
(1.00)
0.81
(1.00)
0.674
(1.00)
0.228
(1.00)
0.112
(1.00)
0.068
(1.00)
0.531
(1.00)
0.647
(1.00)
1
(1.00)
0.174
(1.00)
0.00686
(1.00)
0.0192
(1.00)
8p loss 137 (31%) 302 0.781
(1.00)
0.423
(1.00)
0.0135
(1.00)
0.214
(1.00)
0.00107
(0.961)
0.00376
(1.00)
0.258
(1.00)
0.0689
(1.00)
1
(1.00)
0.0581
(1.00)
0.000436
(0.395)
0.348
(1.00)
8q loss 23 (5%) 416 0.963
(1.00)
0.957
(1.00)
0.0168
(1.00)
0.0586
(1.00)
0.0167
(1.00)
0.0325
(1.00)
0.522
(1.00)
0.533
(1.00)
1
(1.00)
0.788
(1.00)
0.608
(1.00)
0.0367
(1.00)
9p loss 51 (12%) 388 0.831
(1.00)
0.229
(1.00)
0.945
(1.00)
0.077
(1.00)
0.262
(1.00)
0.508
(1.00)
0.237
(1.00)
0.0295
(1.00)
1
(1.00)
0.493
(1.00)
0.0954
(1.00)
0.75
(1.00)
9q loss 51 (12%) 388 0.855
(1.00)
0.0398
(1.00)
0.642
(1.00)
0.13
(1.00)
0.103
(1.00)
0.176
(1.00)
0.768
(1.00)
0.0449
(1.00)
1
(1.00)
0.495
(1.00)
0.0729
(1.00)
0.718
(1.00)
10p loss 67 (15%) 372 0.974
(1.00)
0.191
(1.00)
0.0358
(1.00)
0.947
(1.00)
0.0717
(1.00)
0.0611
(1.00)
0.791
(1.00)
0.33
(1.00)
0.0622
(1.00)
0.553
(1.00)
0.0311
(1.00)
0.582
(1.00)
10q loss 71 (16%) 368 0.698
(1.00)
0.127
(1.00)
0.146
(1.00)
0.908
(1.00)
0.187
(1.00)
0.15
(1.00)
0.699
(1.00)
0.253
(1.00)
0.0694
(1.00)
0.249
(1.00)
0.122
(1.00)
0.693
(1.00)
11p loss 50 (11%) 389 0.294
(1.00)
0.471
(1.00)
0.419
(1.00)
0.776
(1.00)
0.0656
(1.00)
0.0444
(1.00)
0.882
(1.00)
0.829
(1.00)
1
(1.00)
0.448
(1.00)
0.00936
(1.00)
0.586
(1.00)
11q loss 61 (14%) 378 0.242
(1.00)
0.489
(1.00)
0.224
(1.00)
0.184
(1.00)
0.0608
(1.00)
0.0336
(1.00)
0.582
(1.00)
1
(1.00)
1
(1.00)
0.417
(1.00)
0.0311
(1.00)
0.404
(1.00)
12p loss 46 (10%) 393 0.232
(1.00)
0.329
(1.00)
0.395
(1.00)
0.454
(1.00)
0.0837
(1.00)
0.261
(1.00)
1
(1.00)
0.0117
(1.00)
0.283
(1.00)
0.904
(1.00)
0.0382
(1.00)
0.938
(1.00)
12q loss 48 (11%) 391 0.381
(1.00)
0.453
(1.00)
0.152
(1.00)
0.486
(1.00)
0.034
(1.00)
0.281
(1.00)
0.76
(1.00)
0.0442
(1.00)
1
(1.00)
0.87
(1.00)
0.0134
(1.00)
0.5
(1.00)
13q loss 12 (3%) 427 0.269
(1.00)
0.995
(1.00)
0.776
(1.00)
0.478
(1.00)
0.0902
(1.00)
0.279
(1.00)
0.776
(1.00)
0.175
(1.00)
1
(1.00)
0.82
(1.00)
0.0131
(1.00)
0.0185
(1.00)
15q loss 150 (34%) 289 0.384
(1.00)
0.406
(1.00)
0.0314
(1.00)
0.616
(1.00)
0.0335
(1.00)
0.00453
(1.00)
0.763
(1.00)
0.0181
(1.00)
0.0394
(1.00)
0.382
(1.00)
0.024
(1.00)
0.0528
(1.00)
16p loss 30 (7%) 409 0.0968
(1.00)
0.0743
(1.00)
0.392
(1.00)
0.54
(1.00)
0.543
(1.00)
0.163
(1.00)
0.571
(1.00)
0.271
(1.00)
1
(1.00)
0.181
(1.00)
0.44
(1.00)
0.251
(1.00)
16q loss 27 (6%) 412 0.175
(1.00)
0.0232
(1.00)
0.563
(1.00)
0.751
(1.00)
0.702
(1.00)
0.11
(1.00)
0.692
(1.00)
0.39
(1.00)
1
(1.00)
0.266
(1.00)
0.613
(1.00)
0.23
(1.00)
17q loss 65 (15%) 374 0.083
(1.00)
0.823
(1.00)
0.149
(1.00)
0.374
(1.00)
0.0213
(1.00)
0.0215
(1.00)
0.894
(1.00)
1
(1.00)
1
(1.00)
0.726
(1.00)
0.000527
(0.477)
0.135
(1.00)
19q loss 36 (8%) 403 0.0836
(1.00)
0.492
(1.00)
0.045
(1.00)
1
(1.00)
0.00677
(1.00)
0.00435
(1.00)
0.731
(1.00)
0.449
(1.00)
0.227
(1.00)
0.269
(1.00)
0.000396
(0.36)
0.0892
(1.00)
20p loss 43 (10%) 396 0.665
(1.00)
0.59
(1.00)
0.553
(1.00)
0.928
(1.00)
0.449
(1.00)
0.762
(1.00)
0.631
(1.00)
0.818
(1.00)
1
(1.00)
1
(1.00)
0.709
(1.00)
0.802
(1.00)
20q loss 4 (1%) 435 0.243
(1.00)
0.247
(1.00)
0.464
(1.00)
0.776
(1.00)
0.127
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.16
(1.00)
21q loss 120 (27%) 319 0.826
(1.00)
0.966
(1.00)
0.544
(1.00)
0.488
(1.00)
0.0305
(1.00)
0.147
(1.00)
0.83
(1.00)
0.0114
(1.00)
1
(1.00)
0.784
(1.00)
0.0195
(1.00)
0.404
(1.00)
xq loss 50 (11%) 389 0.536
(1.00)
0.739
(1.00)
0.156
(1.00)
0.258
(1.00)
0.0228
(1.00)
0.0392
(1.00)
0.456
(1.00)
1
(1.00)
1
(1.00)
0.467
(1.00)
0.00375
(1.00)
0.816
(1.00)
'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S1.  Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
7P GAIN MUTATED 39 1 14 52 2 0 12 12 36 25 29 13 1
7P GAIN WILD-TYPE 33 0 14 79 6 1 9 0 19 13 14 5 1

Figure S1.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7p gain' versus 'PATHOLOGY.N.STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.083

Table S2.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
7P GAIN MUTATED 119 70 52
7P GAIN WILD-TYPE 137 33 27

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.48e-07 (Fisher's exact test), Q value = 0.00079

Table S3.  Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
13Q GAIN MUTATED 233 16
13Q GAIN WILD-TYPE 145 43

Figure S3.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.092

Table S4.  Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
20P GAIN MUTATED 40 1 13 60 3 0 9 12 24 20 33 14 1
20P GAIN WILD-TYPE 32 0 15 71 5 1 12 0 31 18 10 4 1

Figure S4.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000215 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
20P GAIN MUTATED 216 18
20P GAIN WILD-TYPE 162 41

Figure S5.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.99e-07 (Fisher's exact test), Q value = 0.00093

Table S6.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
20Q GAIN MUTATED 284 25
20Q GAIN WILD-TYPE 94 34

Figure S6.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'4p loss' versus 'PATHOLOGY.M.STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.24

Table S7.  Gene #47: '4p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 320 52 8 2 50
4P LOSS MUTATED 78 28 4 1 14
4P LOSS WILD-TYPE 242 24 4 1 36

Figure S7.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'5q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.4e-05 (Wilcoxon-test), Q value = 0.059

Table S8.  Gene #50: '5q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
5Q LOSS MUTATED 70 3.8 (5.8)
5Q LOSS WILD-TYPE 345 1.7 (4.1)

Figure S8.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.05e-06 (Fisher's exact test), Q value = 0.0056

Table S9.  Gene #64: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
14Q LOSS MUTATED 127 4
14Q LOSS WILD-TYPE 251 55

Figure S9.  Get High-res Image Gene #64: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.065

Table S10.  Gene #68: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
17P LOSS MUTATED 31 0 13 54 1 1 11 10 30 27 32 12 2
17P LOSS WILD-TYPE 41 1 15 77 7 0 10 2 25 11 11 6 0

Figure S10.  Get High-res Image Gene #68: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p loss' versus 'PATHOLOGY.N.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.092

Table S11.  Gene #68: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
17P LOSS MUTATED 112 63 54
17P LOSS WILD-TYPE 144 40 25

Figure S11.  Get High-res Image Gene #68: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.99e-06 (Fisher's exact test), Q value = 0.0093

Table S12.  Gene #68: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
17P LOSS MUTATED 213 15
17P LOSS WILD-TYPE 165 44

Figure S12.  Get High-res Image Gene #68: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 8.56e-06 (Wilcoxon-test), Q value = 0.0079

Table S13.  Gene #68: '17p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
17P LOSS MUTATED 218 2.8 (5.5)
17P LOSS WILD-TYPE 197 1.2 (2.6)

Figure S13.  Get High-res Image Gene #68: '17p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-09 (Fisher's exact test), Q value = 2.1e-06

Table S14.  Gene #70: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
18P LOSS MUTATED 233 12
18P LOSS WILD-TYPE 145 47

Figure S14.  Get High-res Image Gene #70: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.065

Table S15.  Gene #71: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 72 1 28 131 8 1 21 12 55 38 43 18 2
18Q LOSS MUTATED 36 0 14 68 2 1 10 11 36 29 35 15 1
18Q LOSS WILD-TYPE 36 1 14 63 6 0 11 1 19 9 8 3 1

Figure S15.  Get High-res Image Gene #71: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.N.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.12

Table S16.  Gene #71: '18q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 256 103 79
18Q LOSS MUTATED 133 72 58
18Q LOSS WILD-TYPE 123 31 21

Figure S16.  Get High-res Image Gene #71: '18q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.48e-09 (Fisher's exact test), Q value = 7e-06

Table S17.  Gene #71: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 378 59
18Q LOSS MUTATED 248 15
18Q LOSS WILD-TYPE 130 44

Figure S17.  Get High-res Image Gene #71: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000114 (Wilcoxon-test), Q value = 0.1

Table S18.  Gene #71: '18q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
18Q LOSS MUTATED 251 2.4 (4.7)
18Q LOSS WILD-TYPE 164 1.6 (4.1)

Figure S18.  Get High-res Image Gene #71: '18q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.31e-05 (Wilcoxon-test), Q value = 0.067

Table S19.  Gene #72: '19p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
19P LOSS MUTATED 37 4.5 (5.3)
19P LOSS WILD-TYPE 378 1.8 (4.3)

Figure S19.  Get High-res Image Gene #72: '19p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'22q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000191 (Wilcoxon-test), Q value = 0.17

Table S20.  Gene #77: '22q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 415 2.1 (4.4)
22Q LOSS MUTATED 132 2.9 (5.0)
22Q LOSS WILD-TYPE 283 1.7 (4.1)

Figure S20.  Get High-res Image Gene #77: '22q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 439

  • Number of significantly arm-level cnvs = 78

  • Number of selected clinical features = 12

  • Exclude regions 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.

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] 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)