Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1K07307
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/C1K07307
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 79 arm-level events and 12 clinical features across 430 patients, 21 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'.

  • 17q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

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

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

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

  • 22q loss cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 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 224 (52%) 206 0.18
(1.00) 		0.0474
(1.00) 		7e-05
(0.0654) 		0.725
(1.00) 		0.00016
(0.148) 		0.00455
(1.00) 		0.0664
(1.00) 		9.15e-06
(0.00862) 		0.25
(1.00) 		0.0504
(1.00) 		1.46e-05
(0.0137) 		0.863
(1.00)
18q loss 256 (60%) 174 0.914
(1.00) 		0.0189
(1.00) 		3e-05
(0.0281) 		0.883
(1.00) 		0.0005
(0.459) 		0.00171
(1.00) 		0.376
(1.00) 		1.71e-09
(1.61e-06) 		0.276
(1.00) 		0.145
(1.00) 		0.000233
(0.216) 		0.868
(1.00)
7p gain 235 (55%) 195 0.806
(1.00) 		0.122
(1.00) 		7e-05
(0.0654) 		0.334
(1.00) 		0.00016
(0.148) 		0.0136
(1.00) 		0.923
(1.00) 		0.0207
(1.00) 		0.255
(1.00) 		0.206
(1.00) 		0.00033
(0.304) 		0.626
(1.00)
20p gain 233 (54%) 197 0.255
(1.00) 		0.544
(1.00) 		9e-05
(0.0838) 		0.761
(1.00) 		0.262
(1.00) 		0.00074
(0.676) 		0.146
(1.00) 		0.000263
(0.243) 		0.254
(1.00) 		0.0869
(1.00) 		0.135
(1.00) 		0.983
(1.00)
22q loss 138 (32%) 292 0.125
(1.00) 		0.544
(1.00) 		0.00091
(0.829) 		0.433
(1.00) 		7e-05
(0.0654) 		0.00541
(1.00) 		1
(1.00) 		0.00195
(1.00) 		1
(1.00) 		0.387
(1.00) 		6.56e-05
(0.0614) 		0.302
(1.00)
13q gain 246 (57%) 184 0.865
(1.00) 		0.465
(1.00) 		0.00183
(1.00) 		0.976
(1.00) 		0.00382
(1.00) 		0.00133
(1.00) 		0.33
(1.00) 		1.85e-06
(0.00174) 		0.264
(1.00) 		0.0426
(1.00) 		0.0182
(1.00) 		0.186
(1.00)
20q gain 305 (71%) 125 0.737
(1.00) 		0.153
(1.00) 		0.00069
(0.631) 		0.296
(1.00) 		0.0371
(1.00) 		0.00435
(1.00) 		0.338
(1.00) 		9.73e-06
(0.00916) 		0.56
(1.00) 		0.131
(1.00) 		0.0419
(1.00) 		0.461
(1.00)
4p loss 127 (30%) 303 0.057
(1.00) 		0.678
(1.00) 		0.00166
(1.00) 		0.456
(1.00) 		0.00237
(1.00) 		0.00013
(0.121) 		0.833
(1.00) 		0.0106
(1.00) 		0.0253
(1.00) 		0.0316
(1.00) 		0.000471
(0.433) 		0.873
(1.00)
5q loss 72 (17%) 358 0.0279
(1.00) 		0.233
(1.00) 		0.0322
(1.00) 		0.586
(1.00) 		0.00047
(0.432) 		0.0394
(1.00) 		0.365
(1.00) 		0.25
(1.00) 		0.0741
(1.00) 		0.604
(1.00) 		4.77e-05
(0.0447) 		0.295
(1.00)
14q loss 130 (30%) 300 0.628
(1.00) 		0.368
(1.00) 		0.251
(1.00) 		0.328
(1.00) 		0.116
(1.00) 		0.0414
(1.00) 		0.917
(1.00) 		2.73e-05
(0.0256) 		0.557
(1.00) 		0.608
(1.00) 		0.319
(1.00) 		0.897
(1.00)
17q loss 61 (14%) 369 0.175
(1.00) 		0.996
(1.00) 		0.0945
(1.00) 		0.424
(1.00) 		0.00724
(1.00) 		0.0775
(1.00) 		0.679
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.000112
(0.104) 		0.19
(1.00)
18p loss 239 (56%) 191 0.843
(1.00) 		0.0292
(1.00) 		0.00058
(0.532) 		0.946
(1.00) 		0.00758
(1.00) 		0.00044
(0.405) 		0.496
(1.00) 		3.65e-10
(3.45e-07) 		0.258
(1.00) 		0.0312
(1.00) 		0.00248
(1.00) 		0.946
(1.00)
19p loss 38 (9%) 392 0.15
(1.00) 		0.339
(1.00) 		0.00375
(1.00) 		1
(1.00) 		0.0016
(1.00) 		0.00401
(1.00) 		0.737
(1.00) 		0.605
(1.00) 		0.243
(1.00) 		0.268
(1.00) 		1.82e-05
(0.017) 		0.718
(1.00)
1p gain 31 (7%) 399 0.605
(1.00) 		0.354
(1.00) 		0.728
(1.00) 		0.981
(1.00) 		0.63
(1.00) 		0.209
(1.00) 		0.854
(1.00) 		0.783
(1.00) 		0.201
(1.00) 		0.119
(1.00) 		0.183
(1.00) 		0.449
(1.00)
1q gain 78 (18%) 352 0.302
(1.00) 		0.642
(1.00) 		0.134
(1.00) 		0.353
(1.00) 		0.0847
(1.00) 		0.00839
(1.00) 		0.168
(1.00) 		0.349
(1.00) 		0.452
(1.00) 		0.261
(1.00) 		0.0133
(1.00) 		0.959
(1.00)
2p gain 74 (17%) 356 0.317
(1.00) 		0.576
(1.00) 		0.508
(1.00) 		0.562
(1.00) 		0.383
(1.00) 		0.485
(1.00) 		0.701
(1.00) 		0.0355
(1.00) 		0.433
(1.00) 		0.0499
(1.00) 		0.189
(1.00) 		0.763
(1.00)
2q gain 70 (16%) 360 0.176
(1.00) 		0.198
(1.00) 		0.212
(1.00) 		0.418
(1.00) 		0.155
(1.00) 		0.384
(1.00) 		0.795
(1.00) 		0.0519
(1.00) 		0.414
(1.00) 		0.109
(1.00) 		0.0688
(1.00) 		0.917
(1.00)
3p gain 43 (10%) 387 0.122
(1.00) 		0.0972
(1.00) 		0.0119
(1.00) 		0.844
(1.00) 		0.181
(1.00) 		0.00532
(1.00) 		0.873
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.112
(1.00) 		0.194
(1.00)
3q gain 62 (14%) 368 0.129
(1.00) 		0.254
(1.00) 		0.0538
(1.00) 		0.612
(1.00) 		0.0658
(1.00) 		0.0102
(1.00) 		0.681
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.105
(1.00) 		0.228
(1.00)
4p gain 10 (2%) 420 0.475
(1.00) 		0.686
(1.00) 		0.44
(1.00) 		0.821
(1.00) 		0.114
(1.00) 		0.125
(1.00) 		0.755
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0793
(1.00) 		0.0082
(1.00)
4q gain 15 (3%) 415 0.166
(1.00) 		0.346
(1.00) 		0.478
(1.00) 		0.896
(1.00) 		0.0453
(1.00) 		0.263
(1.00) 		0.61
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.0286
(1.00) 		0.0505
(1.00)
5p gain 64 (15%) 366 0.624
(1.00) 		0.0912
(1.00) 		0.307
(1.00) 		0.977
(1.00) 		0.0906
(1.00) 		0.684
(1.00) 		0.222
(1.00) 		0.839
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.0635
(1.00) 		0.278
(1.00)
5q gain 40 (9%) 390 0.491
(1.00) 		0.828
(1.00) 		0.533
(1.00) 		0.825
(1.00) 		0.573
(1.00) 		0.787
(1.00) 		0.509
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.792
(1.00) 		0.247
(1.00)
6p gain 79 (18%) 351 0.83
(1.00) 		0.933
(1.00) 		0.299
(1.00) 		0.799
(1.00) 		0.0381
(1.00) 		0.576
(1.00) 		0.319
(1.00) 		0.189
(1.00) 		0.00601
(1.00) 		0.713
(1.00) 		0.0561
(1.00) 		0.226
(1.00)
6q gain 71 (17%) 359 0.482
(1.00) 		0.689
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.0494
(1.00) 		0.418
(1.00) 		0.699
(1.00) 		0.17
(1.00) 		0.00434
(1.00) 		0.855
(1.00) 		0.0899
(1.00) 		0.595
(1.00)
7q gain 213 (50%) 217 0.995
(1.00) 		0.0701
(1.00) 		0.00712
(1.00) 		0.177
(1.00) 		0.00925
(1.00) 		0.00897
(1.00) 		0.923
(1.00) 		0.043
(1.00) 		0.621
(1.00) 		0.348
(1.00) 		0.00942
(1.00) 		0.416
(1.00)
8p gain 124 (29%) 306 0.42
(1.00) 		0.18
(1.00) 		0.614
(1.00) 		0.705
(1.00) 		0.5
(1.00) 		0.996
(1.00) 		0.831
(1.00) 		0.151
(1.00) 		0.201
(1.00) 		0.584
(1.00) 		0.291
(1.00) 		0.883
(1.00)
8q gain 213 (50%) 217 0.839
(1.00) 		0.0321
(1.00) 		0.8
(1.00) 		0.228
(1.00) 		0.713
(1.00) 		0.528
(1.00) 		0.63
(1.00) 		0.0205
(1.00) 		0.121
(1.00) 		0.529
(1.00) 		0.616
(1.00) 		0.967
(1.00)
9p gain 74 (17%) 356 0.00882
(1.00) 		0.403
(1.00) 		0.0292
(1.00) 		0.52
(1.00) 		0.073
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.0539
(1.00) 		1
(1.00) 		0.775
(1.00) 		0.0771
(1.00) 		0.0771
(1.00)
9q gain 65 (15%) 365 0.00938
(1.00) 		0.56
(1.00) 		0.235
(1.00) 		0.424
(1.00) 		0.267
(1.00) 		0.584
(1.00) 		0.687
(1.00) 		0.0705
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.25
(1.00) 		0.31
(1.00)
10p gain 32 (7%) 398 0.0125
(1.00) 		0.511
(1.00) 		0.45
(1.00) 		0.258
(1.00) 		0.044
(1.00) 		0.249
(1.00) 		0.717
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.0353
(1.00) 		0.157
(1.00)
10q gain 18 (4%) 412 0.506
(1.00) 		0.0495
(1.00) 		0.438
(1.00) 		0.88
(1.00) 		0.0535
(1.00) 		0.272
(1.00) 		0.631
(1.00) 		0.715
(1.00) 		1
(1.00) 		0.541
(1.00) 		0.0129
(1.00) 		0.0486
(1.00)
11p gain 50 (12%) 380 0.727
(1.00) 		0.0265
(1.00) 		0.0311
(1.00) 		0.126
(1.00) 		0.0514
(1.00) 		0.0463
(1.00) 		1
(1.00) 		0.0116
(1.00) 		0.0369
(1.00) 		0.224
(1.00) 		0.0448
(1.00) 		0.4
(1.00)
11q gain 47 (11%) 383 0.878
(1.00) 		0.00087
(0.794) 		0.0219
(1.00) 		0.43
(1.00) 		0.0203
(1.00) 		0.126
(1.00) 		0.877
(1.00) 		0.0019
(1.00) 		0.0327
(1.00) 		0.449
(1.00) 		0.0417
(1.00) 		0.492
(1.00)
12p gain 89 (21%) 341 0.498
(1.00) 		0.151
(1.00) 		0.161
(1.00) 		0.39
(1.00) 		0.289
(1.00) 		0.0806
(1.00) 		0.905
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.136
(1.00) 		1
(1.00)
12q gain 82 (19%) 348 0.713
(1.00) 		0.0585
(1.00) 		0.0224
(1.00) 		0.484
(1.00) 		0.0693
(1.00) 		0.0082
(1.00) 		0.806
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.0329
(1.00) 		0.789
(1.00)
14q gain 33 (8%) 397 0.736
(1.00) 		0.897
(1.00) 		0.879
(1.00) 		0.903
(1.00) 		0.534
(1.00) 		0.0373
(1.00) 		0.37
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.553
(1.00) 		0.00473
(1.00)
15q gain 12 (3%) 418 0.596
(1.00) 		0.269
(1.00) 		0.702
(1.00) 		0.472
(1.00) 		0.718
(1.00) 		0.0983
(1.00) 		0.0757
(1.00) 		1
(1.00) 		1
(1.00) 		0.0513
(1.00) 		0.302
(1.00) 		0.275
(1.00)
16p gain 103 (24%) 327 0.425
(1.00) 		0.107
(1.00) 		0.00888
(1.00) 		0.914
(1.00) 		0.003
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.00601
(1.00) 		0.561
(1.00) 		0.938
(1.00) 		0.00274
(1.00) 		0.409
(1.00)
16q gain 101 (23%) 329 0.382
(1.00) 		0.0758
(1.00) 		0.00264
(1.00) 		0.936
(1.00) 		0.00168
(1.00) 		0.457
(1.00) 		0.82
(1.00) 		0.00597
(1.00) 		0.553
(1.00) 		0.752
(1.00) 		0.00266
(1.00) 		0.456
(1.00)
17p gain 25 (6%) 405 0.132
(1.00) 		0.894
(1.00) 		0.564
(1.00) 		0.837
(1.00) 		0.303
(1.00) 		0.109
(1.00) 		0.682
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.823
(1.00) 		0.0891
(1.00)
17q gain 78 (18%) 352 0.244
(1.00) 		0.433
(1.00) 		0.0952
(1.00) 		0.428
(1.00) 		0.135
(1.00) 		0.00994
(1.00) 		1
(1.00) 		0.187
(1.00) 		0.452
(1.00) 		0.323
(1.00) 		0.923
(1.00) 		0.712
(1.00)
18p gain 22 (5%) 408 0.453
(1.00) 		0.552
(1.00) 		0.0646
(1.00) 		0.935
(1.00) 		0.0244
(1.00) 		0.14
(1.00) 		0.382
(1.00) 		0.0144
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.048
(1.00) 		1
(1.00)
18q gain 13 (3%) 417 0.762
(1.00) 		0.0958
(1.00) 		0.472
(1.00) 		0.763
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.0168
(1.00) 		1
(1.00) 		1
(1.00) 		0.858
(1.00) 		0.583
(1.00)
19p gain 67 (16%) 363 0.768
(1.00) 		0.636
(1.00) 		0.567
(1.00) 		0.668
(1.00) 		0.0472
(1.00) 		0.0549
(1.00) 		0.0462
(1.00) 		0.169
(1.00) 		0.399
(1.00) 		0.265
(1.00) 		0.634
(1.00) 		0.959
(1.00)
19q gain 76 (18%) 354 0.733
(1.00) 		0.904
(1.00) 		0.893
(1.00) 		0.976
(1.00) 		0.201
(1.00) 		0.0356
(1.00) 		0.164
(1.00) 		0.852
(1.00) 		0.443
(1.00) 		0.325
(1.00) 		0.97
(1.00) 		1
(1.00)
21q gain 20 (5%) 410 0.353
(1.00) 		0.00301
(1.00) 		0.338
(1.00) 		0.119
(1.00) 		0.406
(1.00) 		0.393
(1.00) 		0.822
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.188
(1.00) 		0.425
(1.00)
22q gain 11 (3%) 419 0.966
(1.00) 		0.744
(1.00) 		0.493
(1.00) 		0.298
(1.00) 		0.833
(1.00) 		0.348
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.33
(1.00) 		0.865
(1.00) 		0.712
(1.00)
xq gain 71 (17%) 359 0.302
(1.00) 		0.406
(1.00) 		0.0817
(1.00) 		0.0232
(1.00) 		0.477
(1.00) 		0.227
(1.00) 		0.603
(1.00) 		0.33
(1.00) 		0.419
(1.00) 		0.917
(1.00) 		0.494
(1.00) 		0.834
(1.00)
1p loss 92 (21%) 338 0.0728
(1.00) 		0.885
(1.00) 		0.0754
(1.00) 		0.708
(1.00) 		0.00151
(1.00) 		0.00986
(1.00) 		0.48
(1.00) 		0.219
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.000832
(0.76) 		0.44
(1.00)
1q loss 51 (12%) 379 0.341
(1.00) 		0.407
(1.00) 		0.322
(1.00) 		0.708
(1.00) 		0.134
(1.00) 		0.164
(1.00) 		0.374
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.108
(1.00) 		0.233
(1.00)
2p loss 6 (1%) 424 0.731
(1.00) 		0.653
(1.00) 		0.244
(1.00) 		0.838
(1.00) 		0.848
(1.00) 		1
(1.00) 		0.22
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.499
(1.00)
2q loss 7 (2%) 423 0.978
(1.00) 		0.624
(1.00) 		0.297
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.126
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00) 		0.777
(1.00)
3p loss 51 (12%) 379 0.386
(1.00) 		0.444
(1.00) 		0.214
(1.00) 		0.125
(1.00) 		0.0938
(1.00) 		0.0646
(1.00) 		0.881
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.853
(1.00) 		0.123
(1.00) 		0.722
(1.00)
3q loss 31 (7%) 399 0.379
(1.00) 		0.512
(1.00) 		0.583
(1.00) 		0.507
(1.00) 		0.964
(1.00) 		0.187
(1.00) 		0.58
(1.00) 		0.783
(1.00) 		1
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.554
(1.00)
4q loss 115 (27%) 315 0.106
(1.00) 		0.672
(1.00) 		0.0259
(1.00) 		0.45
(1.00) 		0.00249
(1.00) 		0.0472
(1.00) 		0.586
(1.00) 		0.0727
(1.00) 		0.0188
(1.00) 		0.563
(1.00) 		0.000927
(0.843) 		0.751
(1.00)
5p loss 53 (12%) 377 0.241
(1.00) 		0.384
(1.00) 		0.0123
(1.00) 		0.52
(1.00) 		0.00922
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.276
(1.00) 		0.0413
(1.00) 		0.363
(1.00) 		0.00933
(1.00) 		0.576
(1.00)
6p loss 33 (8%) 397 0.0177
(1.00) 		0.22
(1.00) 		0.75
(1.00) 		0.104
(1.00) 		0.747
(1.00) 		0.205
(1.00) 		0.37
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.115
(1.00) 		0.901
(1.00) 		0.0705
(1.00)
6q loss 45 (10%) 385 0.0272
(1.00) 		0.888
(1.00) 		0.536
(1.00) 		0.206
(1.00) 		0.0949
(1.00) 		0.0172
(1.00) 		0.53
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.171
(1.00) 		0.0054
(1.00) 		0.022
(1.00)
7q loss 3 (1%) 427 0.498
(1.00) 		0.147
(1.00) 		0.401
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00) 		0.604
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.515
(1.00) 		1
(1.00)
8p loss 134 (31%) 296 0.992
(1.00) 		0.525
(1.00) 		0.00868
(1.00) 		0.153
(1.00) 		0.00059
(0.54) 		0.00372
(1.00) 		0.211
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.0727
(1.00) 		0.000282
(0.26) 		0.334
(1.00)
8q loss 24 (6%) 406 0.973
(1.00) 		0.775
(1.00) 		0.0446
(1.00) 		0.0465
(1.00) 		0.0589
(1.00) 		0.0277
(1.00) 		0.676
(1.00) 		0.531
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.441
(1.00) 		0.053
(1.00)
9p loss 50 (12%) 380 0.896
(1.00) 		0.137
(1.00) 		0.956
(1.00) 		0.123
(1.00) 		0.352
(1.00) 		0.435
(1.00) 		0.295
(1.00) 		0.0443
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.14
(1.00) 		0.772
(1.00)
9q loss 50 (12%) 380 0.786
(1.00) 		0.0187
(1.00) 		0.728
(1.00) 		0.174
(1.00) 		0.133
(1.00) 		0.194
(1.00) 		0.881
(1.00) 		0.0663
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.109
(1.00) 		0.698
(1.00)
10p loss 64 (15%) 366 0.889
(1.00) 		0.272
(1.00) 		0.0453
(1.00) 		0.896
(1.00) 		0.0897
(1.00) 		0.0944
(1.00) 		0.892
(1.00) 		0.228
(1.00) 		0.0592
(1.00) 		0.476
(1.00) 		0.0396
(1.00) 		0.409
(1.00)
10q loss 68 (16%) 362 0.828
(1.00) 		0.182
(1.00) 		0.175
(1.00) 		0.926
(1.00) 		0.221
(1.00) 		0.197
(1.00) 		0.895
(1.00) 		0.168
(1.00) 		0.0665
(1.00) 		0.213
(1.00) 		0.15
(1.00) 		0.556
(1.00)
11p loss 49 (11%) 381 0.455
(1.00) 		0.42
(1.00) 		0.653
(1.00) 		0.893
(1.00) 		0.0946
(1.00) 		0.0646
(1.00) 		0.763
(1.00) 		1
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.0111
(1.00) 		0.556
(1.00)
11q loss 60 (14%) 370 0.356
(1.00) 		0.428
(1.00) 		0.4
(1.00) 		0.227
(1.00) 		0.0865
(1.00) 		0.0448
(1.00) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		0.411
(1.00) 		0.0347
(1.00) 		0.441
(1.00)
12p loss 44 (10%) 386 0.162
(1.00) 		0.467
(1.00) 		0.288
(1.00) 		0.547
(1.00) 		0.0746
(1.00) 		0.313
(1.00) 		1
(1.00) 		0.0291
(1.00) 		0.277
(1.00) 		0.947
(1.00) 		0.0359
(1.00) 		0.813
(1.00)
12q loss 47 (11%) 383 0.293
(1.00) 		0.497
(1.00) 		0.152
(1.00) 		0.551
(1.00) 		0.0478
(1.00) 		0.254
(1.00) 		0.643
(1.00) 		0.0657
(1.00) 		1
(1.00) 		0.866
(1.00) 		0.0188
(1.00) 		0.445
(1.00)
13q loss 11 (3%) 419 0.686
(1.00) 		0.892
(1.00) 		0.568
(1.00) 		0.463
(1.00) 		0.0209
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.125
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.0235
(1.00) 		0.0143
(1.00)
15q loss 145 (34%) 285 0.395
(1.00) 		0.604
(1.00) 		0.0618
(1.00) 		0.482
(1.00) 		0.0403
(1.00) 		0.00935
(1.00) 		1
(1.00) 		0.00937
(1.00) 		0.0378
(1.00) 		0.386
(1.00) 		0.0289
(1.00) 		0.0182
(1.00)
16p loss 28 (7%) 402 0.146
(1.00) 		0.167
(1.00) 		0.578
(1.00) 		0.666
(1.00) 		0.584
(1.00) 		0.407
(1.00) 		0.329
(1.00) 		0.385
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.459
(1.00) 		0.356
(1.00)
16q loss 25 (6%) 405 0.269
(1.00) 		0.0628
(1.00) 		0.76
(1.00) 		0.897
(1.00) 		0.744
(1.00) 		0.356
(1.00) 		0.413
(1.00) 		0.546
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.649
(1.00) 		0.393
(1.00)
19q loss 34 (8%) 396 0.252
(1.00) 		0.771
(1.00) 		0.00986
(1.00) 		0.984
(1.00) 		0.00832
(1.00) 		0.00733
(1.00) 		0.592
(1.00) 		0.596
(1.00) 		0.219
(1.00) 		0.2
(1.00) 		0.000323
(0.298) 		0.0529
(1.00)
20p loss 41 (10%) 389 0.797
(1.00) 		0.8
(1.00) 		0.572
(1.00) 		0.914
(1.00) 		0.419
(1.00) 		0.964
(1.00) 		0.624
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.724
(1.00)
20q loss 4 (1%) 426 0.197
(1.00) 		0.256
(1.00) 		0.469
(1.00) 		0.773
(1.00) 		0.123
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.153
(1.00)
21q loss 119 (28%) 311 0.918
(1.00) 		0.989
(1.00) 		0.494
(1.00) 		0.478
(1.00) 		0.0174
(1.00) 		0.0681
(1.00) 		0.914
(1.00) 		0.023
(1.00) 		1
(1.00) 		0.842
(1.00) 		0.0104
(1.00) 		0.43
(1.00)
xq loss 47 (11%) 383 0.905
(1.00) 		0.889
(1.00) 		0.277
(1.00) 		0.467
(1.00) 		0.0306
(1.00) 		0.104
(1.00) 		0.538
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.0048
(1.00) 		0.855
(1.00)
'7p gain' versus 'NEOPLASM.DISEASESTAGE'

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

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 28 127 8 1 21 13 53 38 42 16 1
7P GAIN MUTATED 39 1 14 49 2 0 12 12 34 25 29 12 0
7P GAIN WILD-TYPE 33 0 14 78 6 1 9 1 19 13 13 4 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 = 0.00016 (Fisher's exact test), Q value = 0.15

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

nPatients N0 N1 N2
ALL 252 101 76
7P GAIN MUTATED 116 68 50
7P GAIN WILD-TYPE 136 33 26

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

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.85e-06 (Fisher's exact test), Q value = 0.0017

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
13Q GAIN MUTATED 230 15
13Q GAIN WILD-TYPE 143 40

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

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.084

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 28 127 8 1 21 13 53 38 42 16 1
20P GAIN MUTATED 40 1 13 59 3 0 9 13 24 20 32 13 0
20P GAIN WILD-TYPE 32 0 15 68 5 1 12 0 29 18 10 3 1

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

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000263 (Fisher's exact test), Q value = 0.24

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
20P GAIN MUTATED 214 17
20P GAIN WILD-TYPE 159 38

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

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.73e-06 (Fisher's exact test), Q value = 0.0092

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
20Q GAIN MUTATED 279 24
20Q GAIN WILD-TYPE 94 31

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

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

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

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

nPatients M0 M1 M1A M1B MX
ALL 320 50 7 1 45
4P LOSS MUTATED 78 27 3 1 14
4P LOSS WILD-TYPE 242 23 4 0 31

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 = 4.77e-05 (Wilcoxon-test), Q value = 0.045

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

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
5Q LOSS MUTATED 68 3.9 (5.8)
5Q LOSS WILD-TYPE 338 1.7 (4.0)

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 = 2.73e-05 (Fisher's exact test), Q value = 0.026

Table S9.  Gene #65: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
14Q LOSS MUTATED 124 4
14Q LOSS WILD-TYPE 249 51

Figure S9.  Get High-res Image Gene #65: '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 #69: '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 28 127 8 1 21 13 53 38 42 16 1
17P LOSS MUTATED 31 0 13 52 1 1 11 11 28 27 31 11 1
17P LOSS WILD-TYPE 41 1 15 75 7 0 10 2 25 11 11 5 0

Figure S10.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.00016 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #69: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
17P LOSS MUTATED 110 61 52
17P LOSS WILD-TYPE 142 40 24

Figure S11.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.15e-06 (Fisher's exact test), Q value = 0.0086

Table S12.  Gene #69: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
17P LOSS MUTATED 209 13
17P LOSS WILD-TYPE 164 42

Figure S12.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 1.46e-05 (Wilcoxon-test), Q value = 0.014

Table S13.  Gene #69: '17p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
17P LOSS MUTATED 212 2.8 (5.5)
17P LOSS WILD-TYPE 194 1.2 (2.6)

Figure S13.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 0.000112 (Wilcoxon-test), Q value = 0.1

Table S14.  Gene #70: '17q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
17Q LOSS MUTATED 57 3.9 (7.4)
17Q LOSS WILD-TYPE 349 1.7 (3.7)

Figure S14.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.65e-10 (Fisher's exact test), Q value = 3.4e-07

Table S15.  Gene #71: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
18P LOSS MUTATED 228 9
18P LOSS WILD-TYPE 145 46

Figure S15.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S16.  Gene #72: '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 28 127 8 1 21 13 53 38 42 16 1
18Q LOSS MUTATED 36 0 14 65 2 1 10 12 34 29 34 13 0
18Q LOSS WILD-TYPE 36 1 14 62 6 0 11 1 19 9 8 3 1

Figure S16.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.71e-09 (Fisher's exact test), Q value = 1.6e-06

Table S17.  Gene #72: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 373 55
18Q LOSS MUTATED 243 12
18Q LOSS WILD-TYPE 130 43

Figure S17.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000233 (Wilcoxon-test), Q value = 0.22

Table S18.  Gene #72: '18q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
18Q LOSS MUTATED 243 2.4 (4.7)
18Q LOSS WILD-TYPE 163 1.6 (4.1)

Figure S18.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.82e-05 (Wilcoxon-test), Q value = 0.017

Table S19.  Gene #73: '19p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
19P LOSS MUTATED 36 4.8 (5.4)
19P LOSS WILD-TYPE 370 1.8 (4.2)

Figure S19.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'22q loss' versus 'PATHOLOGY.N.STAGE'

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

Table S20.  Gene #78: '22q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 252 101 76
22Q LOSS MUTATED 61 42 35
22Q LOSS WILD-TYPE 191 59 41

Figure S20.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 6.56e-05 (Wilcoxon-test), Q value = 0.061

Table S21.  Gene #78: '22q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 406 2.0 (4.4)
22Q LOSS MUTATED 131 2.9 (5.0)
22Q LOSS WILD-TYPE 275 1.6 (4.1)

Figure S21.  Get High-res Image Gene #78: '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 = 430

  • Number of significantly arm-level cnvs = 79

  • 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)
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