Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1PC30SH
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/C1PC30SH
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 586 patients, 19 significant findings detected with Q value < 0.25.

  • 6q gain cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

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

  • 11p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

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

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

  • 20q gain cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • 7q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

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

  • 17p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18p loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE', and 'HISTOLOGICAL.TYPE'.

  • 18q loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • 19p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 22q loss 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 79 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 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
18q loss 387 (66%) 199 0.764
(1.00) 		0.117
(1.00) 		1.51e-08
(1.43e-05) 		5.39e-05
(0.0504) 		0.314
(1.00) 		0.000124
(0.115) 		0.000317
(0.294) 		0.663
(1.00) 		4.44e-16
(4.2e-13) 		0.285
(1.00) 		0.0245
(1.00) 		0.107
(1.00)
18p loss 361 (62%) 225 0.594
(1.00) 		0.2
(1.00) 		9.73e-07
(0.000916) 		0.000167
(0.156) 		0.762
(1.00) 		0.00164
(1.00) 		0.000311
(0.289) 		0.552
(1.00) 		3.79e-16
(3.59e-13) 		0.164
(1.00) 		0.0248
(1.00) 		0.112
(1.00)
20q gain 444 (76%) 142 0.368
(1.00) 		0.521
(1.00) 		4.11e-06
(0.00387) 		0.000513
(0.472) 		0.386
(1.00) 		0.00168
(1.00) 		0.00203
(1.00) 		0.335
(1.00) 		2.29e-12
(2.17e-09) 		0.695
(1.00) 		0.0229
(1.00) 		0.354
(1.00)
6q gain 105 (18%) 481 0.405
(1.00) 		0.669
(1.00) 		0.272
(1.00) 		0.0725
(1.00) 		0.773
(1.00) 		0.0037
(1.00) 		0.16
(1.00) 		0.451
(1.00) 		0.0367
(1.00) 		0.000131
(0.122) 		0.287
(1.00) 		0.0718
(1.00)
7p gain 333 (57%) 253 0.447
(1.00) 		0.407
(1.00) 		0.0751
(1.00) 		0.000558
(0.512) 		0.899
(1.00) 		4.69e-05
(0.044) 		0.0442
(1.00) 		0.677
(1.00) 		0.000303
(0.281) 		0.312
(1.00) 		0.256
(1.00) 		0.0155
(1.00)
11p gain 79 (13%) 507 0.966
(1.00) 		0.01
(1.00) 		0.0205
(1.00) 		0.396
(1.00) 		0.226
(1.00) 		0.388
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.000109
(0.102) 		0.108
(1.00) 		0.328
(1.00) 		0.377
(1.00)
13q gain 353 (60%) 233 0.189
(1.00) 		0.274
(1.00) 		0.0291
(1.00) 		0.0093
(1.00) 		0.779
(1.00) 		0.000356
(0.329) 		0.0642
(1.00) 		0.271
(1.00) 		4.77e-09
(4.51e-06) 		0.329
(1.00) 		0.0901
(1.00) 		0.647
(1.00)
20p gain 337 (58%) 249 0.197
(1.00) 		0.493
(1.00) 		0.00645
(1.00) 		0.000871
(0.794) 		0.6
(1.00) 		0.0637
(1.00) 		0.0106
(1.00) 		0.131
(1.00) 		2.16e-05
(0.0203) 		0.314
(1.00) 		0.0779
(1.00) 		0.371
(1.00)
7q loss 4 (1%) 582 0.608
(1.00) 		0.97
(1.00) 		0.301
(1.00) 		0.815
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.342
(1.00) 		0.141
(1.00) 		1
(1.00) 		1
(1.00) 		0.000264
(0.246)
14q loss 193 (33%) 393 0.155
(1.00) 		0.378
(1.00) 		0.0226
(1.00) 		0.419
(1.00) 		0.441
(1.00) 		0.0218
(1.00) 		0.161
(1.00) 		0.539
(1.00) 		7.65e-07
(0.000722) 		1
(1.00) 		0.944
(1.00) 		0.77
(1.00)
17p loss 322 (55%) 264 0.199
(1.00) 		0.398
(1.00) 		0.0251
(1.00) 		0.00913
(1.00) 		0.589
(1.00) 		0.0023
(1.00) 		0.0303
(1.00) 		0.318
(1.00) 		2.85e-06
(0.00268) 		0.196
(1.00) 		0.0733
(1.00) 		0.0104
(1.00)
19p loss 61 (10%) 525 0.399
(1.00) 		0.409
(1.00) 		0.0934
(1.00) 		0.000221
(0.206) 		0.838
(1.00) 		0.00058
(0.53) 		0.00298
(1.00) 		0.685
(1.00) 		0.141
(1.00) 		0.239
(1.00) 		0.429
(1.00) 		0.0022
(1.00)
22q loss 192 (33%) 394 0.0411
(1.00) 		0.524
(1.00) 		0.692
(1.00) 		0.00867
(1.00) 		0.333
(1.00) 		2.28e-05
(0.0214) 		0.0123
(1.00) 		0.86
(1.00) 		0.0163
(1.00) 		0.484
(1.00) 		0.489
(1.00) 		0.0279
(1.00)
1p gain 46 (8%) 540 0.792
(1.00) 		0.977
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.367
(1.00) 		0.291
(1.00) 		0.329
(1.00) 		0.539
(1.00) 		0.126
(1.00) 		0.523
(1.00) 		0.115
(1.00) 		0.123
(1.00)
1q gain 113 (19%) 473 0.793
(1.00) 		0.608
(1.00) 		0.287
(1.00) 		0.0743
(1.00) 		0.0382
(1.00) 		0.0268
(1.00) 		0.0356
(1.00) 		0.529
(1.00) 		0.245
(1.00) 		0.385
(1.00) 		0.317
(1.00) 		0.00553
(1.00)
2p gain 113 (19%) 473 0.784
(1.00) 		0.368
(1.00) 		0.0605
(1.00) 		0.335
(1.00) 		0.501
(1.00) 		0.154
(1.00) 		0.328
(1.00) 		0.347
(1.00) 		0.00515
(1.00) 		0.385
(1.00) 		0.0294
(1.00) 		0.888
(1.00)
2q gain 111 (19%) 475 0.381
(1.00) 		0.118
(1.00) 		0.0131
(1.00) 		0.273
(1.00) 		0.573
(1.00) 		0.0736
(1.00) 		0.291
(1.00) 		0.291
(1.00) 		0.00149
(1.00) 		0.0708
(1.00) 		0.364
(1.00) 		0.743
(1.00)
3p gain 68 (12%) 518 0.611
(1.00) 		0.15
(1.00) 		0.029
(1.00) 		0.0188
(1.00) 		0.969
(1.00) 		0.158
(1.00) 		0.00293
(1.00) 		0.438
(1.00) 		0.0648
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.207
(1.00)
3q gain 94 (16%) 492 0.179
(1.00) 		0.29
(1.00) 		0.0316
(1.00) 		0.052
(1.00) 		0.886
(1.00) 		0.0438
(1.00) 		0.000401
(0.369) 		0.499
(1.00) 		0.0277
(1.00) 		0.642
(1.00) 		0.56
(1.00) 		0.201
(1.00)
4p gain 17 (3%) 569 0.748
(1.00) 		0.86
(1.00) 		0.0247
(1.00) 		0.689
(1.00) 		0.507
(1.00) 		0.589
(1.00) 		0.443
(1.00) 		0.217
(1.00) 		0.0657
(1.00) 		1
(1.00) 		0.727
(1.00) 		0.0301
(1.00)
4q gain 19 (3%) 567 0.721
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.864
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.424
(1.00) 		0.244
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.459
(1.00)
5p gain 97 (17%) 489 0.892
(1.00) 		0.23
(1.00) 		0.0799
(1.00) 		0.373
(1.00) 		0.74
(1.00) 		0.0537
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.0354
(1.00) 		0.174
(1.00) 		0.116
(1.00) 		0.258
(1.00)
5q gain 61 (10%) 525 0.925
(1.00) 		0.949
(1.00) 		0.0676
(1.00) 		0.76
(1.00) 		0.76
(1.00) 		0.49
(1.00) 		0.954
(1.00) 		0.588
(1.00) 		0.0633
(1.00) 		1
(1.00) 		0.15
(1.00) 		0.918
(1.00)
6p gain 118 (20%) 468 0.159
(1.00) 		0.724
(1.00) 		0.162
(1.00) 		0.206
(1.00) 		0.507
(1.00) 		0.000866
(0.79) 		0.445
(1.00) 		0.256
(1.00) 		0.121
(1.00) 		0.00029
(0.269) 		0.223
(1.00) 		0.0195
(1.00)
7q gain 297 (51%) 289 0.471
(1.00) 		0.333
(1.00) 		0.577
(1.00) 		0.000466
(0.429) 		0.606
(1.00) 		0.00119
(1.00) 		0.0187
(1.00) 		0.679
(1.00) 		0.00357
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.318
(1.00)
8p gain 161 (27%) 425 0.339
(1.00) 		0.65
(1.00) 		0.467
(1.00) 		0.452
(1.00) 		0.746
(1.00) 		0.285
(1.00) 		0.892
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.712
(1.00) 		0.162
(1.00) 		0.284
(1.00)
8q gain 301 (51%) 285 0.264
(1.00) 		0.272
(1.00) 		0.354
(1.00) 		0.0649
(1.00) 		0.193
(1.00) 		0.109
(1.00) 		0.119
(1.00) 		0.804
(1.00) 		0.0304
(1.00) 		0.0383
(1.00) 		0.0962
(1.00) 		0.0522
(1.00)
9p gain 116 (20%) 470 0.165
(1.00) 		0.858
(1.00) 		0.0198
(1.00) 		0.0101
(1.00) 		0.569
(1.00) 		0.116
(1.00) 		0.791
(1.00) 		0.836
(1.00) 		0.0114
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.156
(1.00)
9q gain 98 (17%) 488 0.28
(1.00) 		0.95
(1.00) 		0.214
(1.00) 		0.0361
(1.00) 		0.485
(1.00) 		0.306
(1.00) 		0.971
(1.00) 		0.657
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.325
(1.00)
10p gain 44 (8%) 542 0.171
(1.00) 		0.787
(1.00) 		0.861
(1.00) 		0.745
(1.00) 		0.177
(1.00) 		0.0268
(1.00) 		0.54
(1.00) 		0.876
(1.00) 		0.864
(1.00) 		0.507
(1.00) 		0.58
(1.00) 		0.219
(1.00)
10q gain 24 (4%) 562 0.974
(1.00) 		0.0772
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.514
(1.00) 		0.0395
(1.00) 		0.727
(1.00) 		0.835
(1.00) 		0.914
(1.00) 		0.315
(1.00) 		0.675
(1.00) 		0.107
(1.00)
11q gain 72 (12%) 514 0.74
(1.00) 		0.000353
(0.326) 		0.157
(1.00) 		0.526
(1.00) 		0.608
(1.00) 		0.444
(1.00) 		0.0357
(1.00) 		0.9
(1.00) 		0.000995
(0.905) 		0.305
(1.00) 		0.462
(1.00) 		0.657
(1.00)
12p gain 123 (21%) 463 0.3
(1.00) 		0.0875
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.332
(1.00) 		0.208
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.406
(1.00) 		0.784
(1.00) 		0.83
(1.00)
12q gain 107 (18%) 479 0.608
(1.00) 		0.0255
(1.00) 		0.231
(1.00) 		0.0333
(1.00) 		0.489
(1.00) 		0.0299
(1.00) 		0.0787
(1.00) 		0.668
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.00442
(1.00)
14q gain 41 (7%) 545 0.356
(1.00) 		0.968
(1.00) 		0.28
(1.00) 		0.921
(1.00) 		0.964
(1.00) 		0.794
(1.00) 		0.0223
(1.00) 		0.749
(1.00) 		0.307
(1.00) 		0.482
(1.00) 		0.612
(1.00) 		0.378
(1.00)
15q gain 14 (2%) 572 0.785
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.0418
(1.00) 		0.573
(1.00) 		0.267
(1.00) 		0.1
(1.00) 		0.0764
(1.00) 		0.197
(1.00) 		0.542
(1.00) 		0.362
(1.00)
16p gain 141 (24%) 445 0.67
(1.00) 		0.198
(1.00) 		0.913
(1.00) 		0.0231
(1.00) 		0.995
(1.00) 		0.00276
(1.00) 		0.374
(1.00) 		0.923
(1.00) 		0.00271
(1.00) 		0.229
(1.00) 		0.733
(1.00) 		0.239
(1.00)
16q gain 138 (24%) 448 0.927
(1.00) 		0.142
(1.00) 		0.743
(1.00) 		0.0093
(1.00) 		0.982
(1.00) 		0.000853
(0.779) 		0.297
(1.00) 		0.922
(1.00) 		0.00355
(1.00) 		0.226
(1.00) 		0.686
(1.00) 		0.489
(1.00)
17p gain 34 (6%) 552 0.104
(1.00) 		0.971
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.346
(1.00) 		0.784
(1.00) 		0.209
(1.00) 		0.86
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.627
(1.00)
17q gain 105 (18%) 481 0.466
(1.00) 		0.453
(1.00) 		0.904
(1.00) 		0.114
(1.00) 		0.739
(1.00) 		0.402
(1.00) 		0.00403
(1.00) 		0.914
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.214
(1.00)
18p gain 30 (5%) 556 0.974
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.000391
(0.361) 		0.769
(1.00) 		0.0403
(1.00) 		0.000622
(0.568) 		0.348
(1.00) 		0.0188
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.0593
(1.00)
18q gain 19 (3%) 567 0.402
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.365
(1.00) 		0.0793
(1.00) 		0.717
(1.00) 		0.244
(1.00) 		0.0504
(1.00) 		0.258
(1.00) 		0.61
(1.00) 		0.178
(1.00)
19p gain 98 (17%) 488 0.294
(1.00) 		0.909
(1.00) 		0.32
(1.00) 		0.807
(1.00) 		0.933
(1.00) 		0.154
(1.00) 		0.348
(1.00) 		0.183
(1.00) 		0.0637
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.678
(1.00)
19q gain 106 (18%) 480 0.377
(1.00) 		0.866
(1.00) 		0.631
(1.00) 		0.719
(1.00) 		0.947
(1.00) 		0.115
(1.00) 		0.0943
(1.00) 		0.283
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.485
(1.00) 		0.71
(1.00)
21q gain 30 (5%) 556 0.173
(1.00) 		0.0362
(1.00) 		0.395
(1.00) 		0.894
(1.00) 		0.212
(1.00) 		0.588
(1.00) 		0.814
(1.00) 		0.711
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.674
(1.00)
22q gain 22 (4%) 564 0.976
(1.00) 		0.419
(1.00) 		0.0837
(1.00) 		0.818
(1.00) 		0.135
(1.00) 		0.377
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.293
(1.00) 		0.312
(1.00) 		0.261
(1.00)
xq gain 101 (17%) 485 0.948
(1.00) 		0.424
(1.00) 		0.712
(1.00) 		0.133
(1.00) 		0.701
(1.00) 		0.316
(1.00) 		0.154
(1.00) 		0.274
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.781
(1.00)
1p loss 130 (22%) 456 0.242
(1.00) 		0.649
(1.00) 		0.148
(1.00) 		0.265
(1.00) 		0.793
(1.00) 		0.0095
(1.00) 		0.0714
(1.00) 		0.55
(1.00) 		0.0252
(1.00) 		0.423
(1.00) 		0.791
(1.00) 		0.0167
(1.00)
1q loss 73 (12%) 513 0.235
(1.00) 		0.346
(1.00) 		0.401
(1.00) 		0.623
(1.00) 		0.718
(1.00) 		0.175
(1.00) 		0.0806
(1.00) 		0.103
(1.00) 		0.315
(1.00) 		0.311
(1.00) 		0.482
(1.00) 		0.384
(1.00)
2p loss 17 (3%) 569 0.801
(1.00) 		0.102
(1.00) 		0.00119
(1.00) 		0.766
(1.00) 		0.85
(1.00) 		0.892
(1.00) 		0.834
(1.00) 		0.806
(1.00) 		0.013
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.963
(1.00)
2q loss 13 (2%) 573 0.193
(1.00) 		0.502
(1.00) 		0.203
(1.00) 		0.336
(1.00) 		0.832
(1.00) 		0.799
(1.00) 		0.392
(1.00) 		0.59
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00)
3p loss 65 (11%) 521 0.0346
(1.00) 		0.894
(1.00) 		0.372
(1.00) 		0.0858
(1.00) 		0.0417
(1.00) 		0.0551
(1.00) 		0.00754
(1.00) 		0.6
(1.00) 		0.0961
(1.00) 		0.263
(1.00) 		0.145
(1.00) 		0.114
(1.00)
3q loss 42 (7%) 544 0.0785
(1.00) 		0.402
(1.00) 		0.473
(1.00) 		0.198
(1.00) 		0.122
(1.00) 		0.506
(1.00) 		0.104
(1.00) 		0.335
(1.00) 		0.0087
(1.00) 		0.131
(1.00) 		0.461
(1.00) 		0.478
(1.00)
4p loss 184 (31%) 402 0.255
(1.00) 		0.85
(1.00) 		0.16
(1.00) 		0.00666
(1.00) 		0.819
(1.00) 		0.00174
(1.00) 		0.00648
(1.00) 		0.858
(1.00) 		0.0145
(1.00) 		0.000558
(0.512) 		0.119
(1.00) 		0.0125
(1.00)
4q loss 177 (30%) 409 0.571
(1.00) 		0.782
(1.00) 		0.00602
(1.00) 		0.0827
(1.00) 		0.8
(1.00) 		0.00612
(1.00) 		0.245
(1.00) 		0.857
(1.00) 		0.00568
(1.00) 		0.000412
(0.38) 		0.846
(1.00) 		0.0324
(1.00)
5p loss 80 (14%) 506 0.95
(1.00) 		0.382
(1.00) 		0.177
(1.00) 		0.021
(1.00) 		0.879
(1.00) 		0.00963
(1.00) 		0.364
(1.00) 		0.399
(1.00) 		0.208
(1.00) 		0.0237
(1.00) 		0.751
(1.00) 		0.025
(1.00)
5q loss 113 (19%) 473 0.136
(1.00) 		0.642
(1.00) 		0.0347
(1.00) 		0.0823
(1.00) 		0.576
(1.00) 		0.00278
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.039
(1.00) 		0.00231
(1.00) 		0.521
(1.00) 		0.0138
(1.00)
6p loss 45 (8%) 541 0.0929
(1.00) 		0.467
(1.00) 		0.861
(1.00) 		0.746
(1.00) 		0.495
(1.00) 		0.264
(1.00) 		0.5
(1.00) 		0.641
(1.00) 		0.147
(1.00) 		0.515
(1.00) 		0.0467
(1.00) 		0.199
(1.00)
6q loss 67 (11%) 519 0.1
(1.00) 		0.76
(1.00) 		0.376
(1.00) 		0.0792
(1.00) 		0.362
(1.00) 		0.136
(1.00) 		0.0315
(1.00) 		0.301
(1.00) 		0.0382
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.0629
(1.00)
8p loss 206 (35%) 380 0.972
(1.00) 		0.797
(1.00) 		0.00344
(1.00) 		0.0495
(1.00) 		0.215
(1.00) 		0.000567
(0.519) 		0.0616
(1.00) 		0.194
(1.00) 		0.00384
(1.00) 		0.29
(1.00) 		0.169
(1.00) 		0.00125
(1.00)
8q loss 31 (5%) 555 0.394
(1.00) 		0.964
(1.00) 		0.537
(1.00) 		0.54
(1.00) 		0.538
(1.00) 		0.466
(1.00) 		0.798
(1.00) 		0.0629
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.626
(1.00) 		0.757
(1.00)
9p loss 71 (12%) 515 0.0243
(1.00) 		0.26
(1.00) 		0.571
(1.00) 		0.894
(1.00) 		0.148
(1.00) 		0.671
(1.00) 		0.267
(1.00) 		0.253
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.0363
(1.00) 		0.423
(1.00)
9q loss 70 (12%) 516 0.0155
(1.00) 		0.07
(1.00) 		0.472
(1.00) 		0.629
(1.00) 		0.153
(1.00) 		0.528
(1.00) 		0.111
(1.00) 		0.61
(1.00) 		0.183
(1.00) 		1
(1.00) 		0.0363
(1.00) 		0.768
(1.00)
10p loss 96 (16%) 490 0.178
(1.00) 		0.00987
(1.00) 		0.132
(1.00) 		0.645
(1.00) 		0.782
(1.00) 		0.144
(1.00) 		0.65
(1.00) 		0.739
(1.00) 		0.0205
(1.00) 		0.0078
(1.00) 		0.984
(1.00) 		0.34
(1.00)
10q loss 104 (18%) 482 0.384
(1.00) 		0.0147
(1.00) 		0.0671
(1.00) 		0.778
(1.00) 		0.968
(1.00) 		0.302
(1.00) 		0.891
(1.00) 		0.665
(1.00) 		0.015
(1.00) 		0.0111
(1.00) 		0.958
(1.00) 		0.532
(1.00)
11p loss 73 (12%) 513 0.387
(1.00) 		0.537
(1.00) 		0.396
(1.00) 		0.341
(1.00) 		0.51
(1.00) 		0.0244
(1.00) 		0.0264
(1.00) 		0.707
(1.00) 		0.235
(1.00) 		0.311
(1.00) 		0.888
(1.00) 		0.0183
(1.00)
11q loss 89 (15%) 497 0.259
(1.00) 		0.645
(1.00) 		0.356
(1.00) 		0.646
(1.00) 		0.776
(1.00) 		0.107
(1.00) 		0.329
(1.00) 		0.73
(1.00) 		0.135
(1.00) 		0.143
(1.00) 		0.964
(1.00) 		0.15
(1.00)
12p loss 68 (12%) 518 0.138
(1.00) 		0.636
(1.00) 		0.19
(1.00) 		0.459
(1.00) 		0.336
(1.00) 		0.0391
(1.00) 		0.502
(1.00) 		0.796
(1.00) 		0.015
(1.00) 		0.0752
(1.00) 		0.926
(1.00) 		0.565
(1.00)
12q loss 68 (12%) 518 0.222
(1.00) 		0.901
(1.00) 		0.662
(1.00) 		0.249
(1.00) 		0.531
(1.00) 		0.0391
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.429
(1.00)
13q loss 19 (3%) 567 0.36
(1.00) 		0.891
(1.00) 		0.187
(1.00) 		0.519
(1.00) 		0.567
(1.00) 		0.0252
(1.00) 		0.019
(1.00) 		1
(1.00) 		0.0237
(1.00) 		1
(1.00) 		1
(1.00) 		0.0703
(1.00)
15q loss 216 (37%) 370 0.917
(1.00) 		0.788
(1.00) 		0.0425
(1.00) 		0.0471
(1.00) 		0.249
(1.00) 		0.0155
(1.00) 		0.121
(1.00) 		0.493
(1.00) 		0.00259
(1.00) 		0.0147
(1.00) 		0.795
(1.00) 		0.0526
(1.00)
16p loss 36 (6%) 550 0.00577
(1.00) 		0.705
(1.00) 		0.848
(1.00) 		0.179
(1.00) 		0.535
(1.00) 		0.56
(1.00) 		0.931
(1.00) 		0.302
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.65
(1.00)
16q loss 39 (7%) 547 0.0105
(1.00) 		0.335
(1.00) 		0.263
(1.00) 		0.314
(1.00) 		0.868
(1.00) 		0.223
(1.00) 		0.884
(1.00) 		0.619
(1.00) 		0.579
(1.00) 		0.464
(1.00) 		0.38
(1.00) 		0.165
(1.00)
17q loss 85 (15%) 501 0.701
(1.00) 		0.661
(1.00) 		0.598
(1.00) 		0.0687
(1.00) 		0.16
(1.00) 		0.0273
(1.00) 		0.323
(1.00) 		0.239
(1.00) 		0.905
(1.00) 		0.625
(1.00) 		0.507
(1.00) 		0.0475
(1.00)
19q loss 53 (9%) 533 0.919
(1.00) 		0.832
(1.00) 		0.141
(1.00) 		0.00191
(1.00) 		0.775
(1.00) 		0.0047
(1.00) 		0.0243
(1.00) 		0.248
(1.00) 		0.222
(1.00) 		0.192
(1.00) 		0.792
(1.00) 		0.00811
(1.00)
20p loss 61 (10%) 525 0.82
(1.00) 		0.962
(1.00) 		0.285
(1.00) 		0.702
(1.00) 		0.436
(1.00) 		0.333
(1.00) 		0.874
(1.00) 		0.685
(1.00) 		0.562
(1.00) 		0.608
(1.00) 		0.584
(1.00) 		0.988
(1.00)
20q loss 5 (1%) 581 0.303
(1.00) 		0.0404
(1.00) 		0.33
(1.00) 		0.915
(1.00) 		0.806
(1.00) 		0.382
(1.00) 		0.817
(1.00) 		1
(1.00) 		0.52
(1.00) 		1
(1.00) 		1
(1.00) 		0.87
(1.00)
21q loss 183 (31%) 403 0.837
(1.00) 		0.599
(1.00) 		0.00261
(1.00) 		0.277
(1.00) 		0.954
(1.00) 		0.00442
(1.00) 		0.635
(1.00) 		0.593
(1.00) 		0.00106
(0.96) 		0.471
(1.00) 		0.769
(1.00) 		0.00115
(1.00)
xq loss 71 (12%) 515 0.589
(1.00) 		0.45
(1.00) 		0.0622
(1.00) 		0.276
(1.00) 		0.815
(1.00) 		0.202
(1.00) 		0.0885
(1.00) 		0.801
(1.00) 		0.0797
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.214
(1.00)
'6q gain' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000131 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 577
6Q GAIN MUTATED 7 98
6Q GAIN WILD-TYPE 2 479

Figure S1.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 4.69e-05 (Fisher's exact test), Q value = 0.044

Table S2.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
7P GAIN MUTATED 161 99 70
7P GAIN WILD-TYPE 170 47 36

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'11p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000109 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
11P GAIN MUTATED 48 0 30 0
11P GAIN WILD-TYPE 319 55 113 13

Figure S3.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.77e-09 (Fisher's exact test), Q value = 4.5e-06

Table S4.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
13Q GAIN MUTATED 227 15 103 3
13Q GAIN WILD-TYPE 140 40 40 10

Figure S4.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.02

Table S5.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
20P GAIN MUTATED 210 18 99 5
20P GAIN WILD-TYPE 157 37 44 8

Figure S5.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.11e-06 (Fisher's exact test), Q value = 0.0039

Table S6.  Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
20Q GAIN MUTATED 300 141
20Q GAIN WILD-TYPE 123 18

Figure S6.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-12 (Fisher's exact test), Q value = 2.2e-09

Table S7.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
20Q GAIN MUTATED 275 24 132 7
20Q GAIN WILD-TYPE 92 31 11 6

Figure S7.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'7q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000264 (t-test), Q value = 0.25

Table S8.  Gene #53: '7q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 552 2.2 (4.7)
7Q LOSS MUTATED 4 0.2 (0.5)
7Q LOSS WILD-TYPE 548 2.2 (4.7)

Figure S8.  Get High-res Image Gene #53: '7q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.65e-07 (Fisher's exact test), Q value = 0.00072

Table S9.  Gene #65: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
14Q LOSS MUTATED 122 4 62 1
14Q LOSS WILD-TYPE 245 51 81 12

Figure S9.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.85e-06 (Fisher's exact test), Q value = 0.0027

Table S10.  Gene #69: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
17P LOSS MUTATED 205 13 92 6
17P LOSS WILD-TYPE 162 42 51 7

Figure S10.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.73e-07 (Fisher's exact test), Q value = 0.00092

Table S11.  Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
18P LOSS MUTATED 235 123
18P LOSS WILD-TYPE 188 36

Figure S11.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000167 (Chi-square test), Q value = 0.16

Table S12.  Gene #71: '18p loss' 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
18P LOSS MUTATED 55 0 18 89 4 3 12 16 51 36 47 21 0
18P LOSS WILD-TYPE 46 1 23 68 6 0 15 6 24 14 12 4 1

Figure S12.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.79e-16 (Fisher's exact test), Q value = 3.6e-13

Table S13.  Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
18P LOSS MUTATED 225 9 116 7
18P LOSS WILD-TYPE 142 46 27 6

Figure S13.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.51e-08 (Fisher's exact test), Q value = 1.4e-05

Table S14.  Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 423 159
18Q LOSS MUTATED 251 133
18Q LOSS WILD-TYPE 172 26

Figure S14.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.39e-05 (Chi-square test), Q value = 0.05

Table S15.  Gene #72: '18q loss' 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
18Q LOSS MUTATED 56 0 22 96 4 3 14 18 54 38 50 22 0
18Q LOSS WILD-TYPE 45 1 19 61 6 0 13 4 21 12 9 3 1

Figure S15.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.000124 (Fisher's exact test), Q value = 0.12

Table S16.  Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
18Q LOSS MUTATED 194 110 80
18Q LOSS WILD-TYPE 137 36 26

Figure S16.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.44e-16 (Fisher's exact test), Q value = 4.2e-13

Table S17.  Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 367 55 143 13
18Q LOSS MUTATED 238 12 122 10
18Q LOSS WILD-TYPE 129 43 21 3

Figure S17.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'19p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000221 (Chi-square test), Q value = 0.21

Table S18.  Gene #73: '19p loss' 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
19P LOSS MUTATED 8 0 2 9 1 2 4 3 5 9 10 6 1
19P LOSS WILD-TYPE 93 1 39 148 9 1 23 19 70 41 49 19 0

Figure S18.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 2.28e-05 (Fisher's exact test), Q value = 0.021

Table S19.  Gene #78: '22q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 331 146 106
22Q LOSS MUTATED 83 66 42
22Q LOSS WILD-TYPE 248 80 64

Figure S19.  Get High-res Image Gene #78: '22q loss' 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 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

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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