Colon/Rectal Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 76 arm-level results and 10 clinical features across 574 patients, 20 significant findings detected with Q value < 0.25.

  • 3p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • 7p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.

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

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

  • 3p loss cnv correlated to 'Time to Death' and 'PATHOLOGICSPREAD(M)'.

  • 6p loss cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • 8q loss cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • 12q loss cnv correlated to 'PATHOLOGICSPREAD(M)'.

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

  • 15q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

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

  • 18q loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • 22q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 arm-level results and 10 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 PRIMARY
SITE
OF
DISEASE 		GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) RADIATIONS
RADIATION
REGIMENINDICATION 		NEOADJUVANT
THERAPY
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test
13q gain 324 (56%) 250 0.423
(1.00) 		0.927
(1.00) 		0.0144
(1.00) 		0.354
(1.00) 		7.03e-08
(5.3e-05) 		0.571
(1.00) 		0.000172
(0.127) 		0.0283
(1.00) 		0.738
(1.00) 		0.28
(1.00)
20q gain 401 (70%) 173 0.335
(1.00) 		0.809
(1.00) 		0.000104
(0.0778) 		0.122
(1.00) 		7.84e-14
(5.93e-11) 		0.517
(1.00) 		0.0254
(1.00) 		0.0396
(1.00) 		1
(1.00) 		0.603
(1.00)
3p loss 41 (7%) 533 7.53e-08
(5.68e-05) 		0.961
(1.00) 		0.471
(1.00) 		0.335
(1.00) 		0.0614
(1.00) 		0.0197
(1.00) 		0.0327
(1.00) 		0.000168
(0.125) 		0.489
(1.00) 		0.82
(1.00)
18p loss 326 (57%) 248 0.541
(1.00) 		0.404
(1.00) 		0.000106
(0.0789) 		0.933
(1.00) 		3.29e-14
(2.5e-11) 		0.583
(1.00) 		0.00241
(1.00) 		0.00119
(0.866) 		1
(1.00) 		0.719
(1.00)
18q loss 353 (61%) 221 0.832
(1.00) 		0.215
(1.00) 		1.3e-06
(0.000978) 		0.606
(1.00) 		1.77e-14
(1.35e-11) 		0.337
(1.00) 		0.00075
(0.552) 		0.0133
(1.00) 		0.494
(1.00) 		0.624
(1.00)
3p gain 37 (6%) 537 0.132
(1.00) 		0.217
(1.00) 		0.0113
(1.00) 		1
(1.00) 		0.0475
(1.00) 		0.542
(1.00) 		0.109
(1.00) 		5.8e-05
(0.0434) 		0.109
(1.00) 		0.0865
(1.00)
7p gain 286 (50%) 288 0.258
(1.00) 		0.654
(1.00) 		0.262
(1.00) 		0.802
(1.00) 		6.24e-05
(0.0466) 		0.839
(1.00) 		0.00203
(1.00) 		0.0551
(1.00) 		0.339
(1.00) 		0.476
(1.00)
20p gain 289 (50%) 285 0.299
(1.00) 		0.508
(1.00) 		0.0611
(1.00) 		0.0941
(1.00) 		4.56e-06
(0.00342) 		0.285
(1.00) 		0.572
(1.00) 		0.0369
(1.00) 		1
(1.00) 		0.634
(1.00)
6p loss 28 (5%) 546 0.361
(1.00) 		0.927
(1.00) 		0.261
(1.00) 		0.252
(1.00) 		0.175
(1.00) 		0.59
(1.00) 		0.367
(1.00) 		4.25e-05
(0.0319) 		1
(1.00) 		0.16
(1.00)
8q loss 21 (4%) 553 0.901
(1.00) 		0.799
(1.00) 		0.802
(1.00) 		0.0435
(1.00) 		0.861
(1.00) 		0.569
(1.00) 		0.4
(1.00) 		7.96e-06
(0.00597) 		0.287
(1.00) 		0.754
(1.00)
12q loss 28 (5%) 546 0.233
(1.00) 		0.634
(1.00) 		0.193
(1.00) 		0.173
(1.00) 		0.126
(1.00) 		0.192
(1.00) 		0.0325
(1.00) 		0.000134
(0.0998) 		0.364
(1.00) 		1
(1.00)
14q loss 154 (27%) 420 0.802
(1.00) 		0.455
(1.00) 		0.00808
(1.00) 		0.778
(1.00) 		7.66e-07
(0.000577) 		0.394
(1.00) 		0.036
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.893
(1.00)
15q loss 156 (27%) 418 0.508
(1.00) 		0.636
(1.00) 		0.00589
(1.00) 		0.925
(1.00) 		0.000295
(0.218) 		0.389
(1.00) 		0.155
(1.00) 		0.286
(1.00) 		0.263
(1.00) 		0.688
(1.00)
17p loss 264 (46%) 310 0.278
(1.00) 		0.28
(1.00) 		0.000509
(0.376) 		0.867
(1.00) 		6.6e-08
(4.99e-05) 		0.394
(1.00) 		0.00996
(1.00) 		0.0299
(1.00) 		0.314
(1.00) 		0.283
(1.00)
22q loss 122 (21%) 452 0.0744
(1.00) 		0.0955
(1.00) 		0.109
(1.00) 		0.475
(1.00) 		9.94e-05
(0.0741) 		0.5
(1.00) 		0.00773
(1.00) 		0.229
(1.00) 		0.409
(1.00) 		0.243
(1.00)
1p gain 17 (3%) 557 0.622
(1.00) 		0.887
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.663
(1.00) 		0.153
(1.00) 		0.935
(1.00) 		1
(1.00) 		0.722
(1.00)
1q gain 79 (14%) 495 0.462
(1.00) 		0.939
(1.00) 		0.5
(1.00) 		0.182
(1.00) 		0.371
(1.00) 		0.224
(1.00) 		0.0609
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.862
(1.00)
2p gain 58 (10%) 516 0.178
(1.00) 		0.73
(1.00) 		0.539
(1.00) 		0.0533
(1.00) 		0.0112
(1.00) 		0.7
(1.00) 		0.16
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.32
(1.00)
2q gain 60 (10%) 514 0.188
(1.00) 		0.612
(1.00) 		0.451
(1.00) 		0.0564
(1.00) 		0.0535
(1.00) 		0.892
(1.00) 		0.14
(1.00) 		0.99
(1.00) 		1
(1.00) 		0.176
(1.00)
3q gain 57 (10%) 517 0.0269
(1.00) 		0.408
(1.00) 		0.00158
(1.00) 		0.161
(1.00) 		0.00186
(1.00) 		0.949
(1.00) 		0.118
(1.00) 		0.00385
(1.00) 		0.222
(1.00) 		0.429
(1.00)
4p gain 7 (1%) 567 0.364
(1.00) 		0.798
(1.00) 		0.0197
(1.00) 		0.458
(1.00) 		0.0708
(1.00) 		0.873
(1.00) 		0.137
(1.00) 		0.0992
(1.00) 		1
(1.00) 		1
(1.00)
4q gain 6 (1%) 568 0.975
(1.00) 		0.915
(1.00) 		0.0529
(1.00) 		0.69
(1.00) 		0.198
(1.00) 		0.513
(1.00) 		0.0762
(1.00) 		0.593
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 64 (11%) 510 0.934
(1.00) 		0.24
(1.00) 		0.553
(1.00) 		0.289
(1.00) 		0.264
(1.00) 		0.847
(1.00) 		0.364
(1.00) 		0.84
(1.00) 		0.265
(1.00) 		0.453
(1.00)
5q gain 34 (6%) 540 0.654
(1.00) 		0.251
(1.00) 		0.0774
(1.00) 		0.481
(1.00) 		0.135
(1.00) 		0.879
(1.00) 		0.512
(1.00) 		0.796
(1.00) 		0.0944
(1.00) 		0.0445
(1.00)
6p gain 80 (14%) 494 0.944
(1.00) 		0.64
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.889
(1.00) 		0.000582
(0.429) 		0.799
(1.00) 		0.117
(1.00) 		0.39
(1.00)
6q gain 72 (13%) 502 0.954
(1.00) 		0.348
(1.00) 		0.257
(1.00) 		0.707
(1.00) 		0.211
(1.00) 		0.571
(1.00) 		0.012
(1.00) 		0.453
(1.00) 		0.314
(1.00) 		0.367
(1.00)
7q gain 251 (44%) 323 0.156
(1.00) 		0.903
(1.00) 		0.573
(1.00) 		0.866
(1.00) 		0.000523
(0.386) 		0.885
(1.00) 		0.0251
(1.00) 		0.119
(1.00) 		1
(1.00) 		0.719
(1.00)
8p gain 112 (20%) 462 0.122
(1.00) 		0.53
(1.00) 		0.101
(1.00) 		0.833
(1.00) 		0.428
(1.00) 		0.6
(1.00) 		0.595
(1.00) 		0.946
(1.00) 		1
(1.00) 		0.549
(1.00)
8q gain 246 (43%) 328 0.409
(1.00) 		0.166
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.108
(1.00) 		0.104
(1.00) 		0.0254
(1.00) 		0.0187
(1.00) 		0.313
(1.00) 		1
(1.00)
9p gain 82 (14%) 492 0.133
(1.00) 		0.294
(1.00) 		0.00197
(1.00) 		1
(1.00) 		0.011
(1.00) 		0.767
(1.00) 		0.363
(1.00) 		0.959
(1.00) 		0.371
(1.00) 		0.0597
(1.00)
9q gain 65 (11%) 509 0.325
(1.00) 		0.289
(1.00) 		0.0118
(1.00) 		0.43
(1.00) 		0.0866
(1.00) 		0.714
(1.00) 		0.448
(1.00) 		0.773
(1.00) 		0.607
(1.00) 		0.0141
(1.00)
10p gain 20 (3%) 554 0.0564
(1.00) 		0.232
(1.00) 		0.453
(1.00) 		0.822
(1.00) 		0.711
(1.00) 		0.29
(1.00) 		0.00281
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.186
(1.00)
10q gain 10 (2%) 564 0.519
(1.00) 		0.0118
(1.00) 		0.475
(1.00) 		0.526
(1.00) 		0.272
(1.00) 		0.323
(1.00) 		0.038
(1.00) 		0.854
(1.00) 		1
(1.00) 		0.0412
(1.00)
11p gain 43 (7%) 531 0.44
(1.00) 		0.0187
(1.00) 		0.00408
(1.00) 		0.427
(1.00) 		0.00192
(1.00) 		0.177
(1.00) 		0.0291
(1.00) 		0.829
(1.00) 		0.506
(1.00) 		0.653
(1.00)
11q gain 41 (7%) 533 0.92
(1.00) 		0.000939
(0.69) 		0.0472
(1.00) 		0.748
(1.00) 		0.015
(1.00) 		0.263
(1.00) 		0.042
(1.00) 		0.00731
(1.00) 		1
(1.00) 		0.163
(1.00)
12p gain 95 (17%) 479 0.529
(1.00) 		0.013
(1.00) 		0.8
(1.00) 		0.822
(1.00) 		0.943
(1.00) 		0.496
(1.00) 		0.0211
(1.00) 		0.405
(1.00) 		0.648
(1.00) 		0.335
(1.00)
12q gain 80 (14%) 494 0.713
(1.00) 		0.00557
(1.00) 		0.499
(1.00) 		0.904
(1.00) 		0.81
(1.00) 		0.57
(1.00) 		0.0467
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.302
(1.00)
14q gain 20 (3%) 554 0.322
(1.00) 		0.899
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.29
(1.00) 		0.279
(1.00) 		0.79
(1.00) 		0.275
(1.00) 		0.0519
(1.00)
15q gain 10 (2%) 564 0.986
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.457
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.16
(1.00)
16p gain 99 (17%) 475 0.574
(1.00) 		0.532
(1.00) 		0.804
(1.00) 		0.74
(1.00) 		0.0215
(1.00) 		0.943
(1.00) 		0.00272
(1.00) 		0.116
(1.00) 		0.191
(1.00) 		0.0812
(1.00)
16q gain 99 (17%) 475 0.835
(1.00) 		0.146
(1.00) 		0.456
(1.00) 		0.74
(1.00) 		0.016
(1.00) 		0.959
(1.00) 		0.00215
(1.00) 		0.263
(1.00) 		0.191
(1.00) 		0.0812
(1.00)
17p gain 16 (3%) 558 0.0993
(1.00) 		0.667
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.538
(1.00) 		0.743
(1.00) 		0.884
(1.00) 		0.0137
(1.00) 		1
(1.00) 		0.265
(1.00)
17q gain 59 (10%) 515 0.052
(1.00) 		0.94
(1.00) 		0.76
(1.00) 		0.053
(1.00) 		0.238
(1.00) 		0.747
(1.00) 		0.945
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.00547
(1.00)
18p gain 22 (4%) 552 0.0871
(1.00) 		0.696
(1.00) 		1
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.435
(1.00) 		0.00746
(1.00) 		0.978
(1.00) 		0.298
(1.00) 		1
(1.00)
18q gain 12 (2%) 562 0.803
(1.00) 		0.175
(1.00) 		0.525
(1.00) 		0.779
(1.00) 		0.337
(1.00) 		0.375
(1.00) 		0.122
(1.00) 		0.987
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 51 (9%) 523 0.736
(1.00) 		0.716
(1.00) 		0.139
(1.00) 		0.661
(1.00) 		0.0503
(1.00) 		0.842
(1.00) 		0.775
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.833
(1.00)
19q gain 67 (12%) 507 0.364
(1.00) 		0.439
(1.00) 		0.195
(1.00) 		0.696
(1.00) 		0.23
(1.00) 		0.963
(1.00) 		0.626
(1.00) 		0.987
(1.00) 		0.608
(1.00) 		1
(1.00)
21q gain 17 (3%) 557 0.307
(1.00) 		0.966
(1.00) 		0.779
(1.00) 		0.629
(1.00) 		0.773
(1.00) 		0.12
(1.00) 		0.536
(1.00) 		0.985
(1.00) 		1
(1.00) 		0.489
(1.00)
22q gain 9 (2%) 565 0.828
(1.00) 		0.5
(1.00) 		0.0409
(1.00) 		0.74
(1.00) 		0.131
(1.00) 		0.821
(1.00) 		0.233
(1.00) 		0.0649
(1.00) 		1
(1.00) 		0.371
(1.00)
1p loss 79 (14%) 495 0.491
(1.00) 		0.837
(1.00) 		0.685
(1.00) 		0.275
(1.00) 		0.494
(1.00) 		0.488
(1.00) 		0.0287
(1.00) 		0.034
(1.00) 		1
(1.00) 		0.167
(1.00)
1q loss 23 (4%) 551 0.607
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.29
(1.00) 		0.886
(1.00) 		0.75
(1.00) 		0.325
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.759
(1.00)
2p loss 9 (2%) 565 0.419
(1.00) 		0.141
(1.00) 		0.00241
(1.00) 		1
(1.00) 		0.0196
(1.00) 		0.742
(1.00) 		0.807
(1.00) 		0.993
(1.00) 		0.133
(1.00) 		0.371
(1.00)
2q loss 5 (1%) 569 0.00109
(0.796) 		0.58
(1.00) 		0.621
(1.00) 		1
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.698
(1.00) 		0.831
(1.00) 		0.0762
(1.00) 		1
(1.00)
3q loss 17 (3%) 557 0.0623
(1.00) 		0.598
(1.00) 		0.791
(1.00) 		0.0815
(1.00) 		0.00193
(1.00) 		0.462
(1.00) 		0.892
(1.00) 		0.442
(1.00) 		0.239
(1.00) 		1
(1.00)
4p loss 133 (23%) 441 0.077
(1.00) 		0.7
(1.00) 		0.267
(1.00) 		0.766
(1.00) 		0.0446
(1.00) 		0.904
(1.00) 		0.00129
(0.939) 		0.00414
(1.00) 		0.223
(1.00) 		0.0486
(1.00)
4q loss 120 (21%) 454 0.6
(1.00) 		0.707
(1.00) 		0.00363
(1.00) 		1
(1.00) 		0.000942
(0.692) 		0.973
(1.00) 		0.00807
(1.00) 		0.285
(1.00) 		0.0964
(1.00) 		0.0788
(1.00)
5p loss 40 (7%) 534 0.824
(1.00) 		0.804
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.189
(1.00) 		0.454
(1.00) 		0.915
(1.00) 		0.125
(1.00) 		0.489
(1.00)
5q loss 67 (12%) 507 0.233
(1.00) 		0.507
(1.00) 		0.195
(1.00) 		0.194
(1.00) 		0.0497
(1.00) 		0.779
(1.00) 		0.201
(1.00) 		0.467
(1.00) 		0.0763
(1.00) 		0.457
(1.00)
6q loss 35 (6%) 539 0.0258
(1.00) 		0.549
(1.00) 		0.315
(1.00) 		0.862
(1.00) 		0.0972
(1.00) 		0.298
(1.00) 		0.00504
(1.00) 		0.00248
(1.00) 		1
(1.00) 		0.455
(1.00)
7q loss 3 (1%) 571 0.191
(1.00) 		0.021
(1.00) 		0.6
(1.00) 		0.0106
(1.00) 		0.68
(1.00) 		0.757
(1.00) 		0.924
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 150 (26%) 424 0.678
(1.00) 		0.273
(1.00) 		0.0247
(1.00) 		0.775
(1.00) 		0.00285
(1.00) 		0.765
(1.00) 		0.446
(1.00) 		0.495
(1.00) 		0.25
(1.00) 		0.498
(1.00)
9p loss 43 (7%) 531 0.00272
(1.00) 		0.177
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.612
(1.00) 		0.188
(1.00) 		0.00448
(1.00) 		1
(1.00) 		0.495
(1.00)
9q loss 38 (7%) 536 0.403
(1.00) 		0.00894
(1.00) 		0.342
(1.00) 		0.313
(1.00) 		0.344
(1.00) 		0.0382
(1.00) 		0.802
(1.00) 		0.713
(1.00) 		1
(1.00) 		1
(1.00)
10p loss 46 (8%) 528 0.295
(1.00) 		0.0626
(1.00) 		0.0853
(1.00) 		0.646
(1.00) 		0.0332
(1.00) 		0.262
(1.00) 		0.261
(1.00) 		0.39
(1.00) 		0.531
(1.00) 		0.512
(1.00)
10q loss 54 (9%) 520 0.256
(1.00) 		0.138
(1.00) 		0.00221
(1.00) 		0.886
(1.00) 		0.002
(1.00) 		0.401
(1.00) 		0.364
(1.00) 		0.895
(1.00) 		0.592
(1.00) 		0.84
(1.00)
11p loss 39 (7%) 535 0.692
(1.00) 		0.596
(1.00) 		0.0146
(1.00) 		1
(1.00) 		0.00169
(1.00) 		0.95
(1.00) 		0.163
(1.00) 		0.965
(1.00) 		0.472
(1.00) 		0.1
(1.00)
11q loss 49 (9%) 525 0.739
(1.00) 		0.562
(1.00) 		0.0101
(1.00) 		0.371
(1.00) 		0.0025
(1.00) 		0.431
(1.00) 		0.131
(1.00) 		0.967
(1.00) 		0.175
(1.00) 		0.523
(1.00)
12p loss 34 (6%) 540 0.0407
(1.00) 		0.855
(1.00) 		0.169
(1.00) 		0.0768
(1.00) 		0.0776
(1.00) 		0.114
(1.00) 		0.0129
(1.00) 		0.514
(1.00) 		0.0944
(1.00) 		0.805
(1.00)
13q loss 8 (1%) 566 0.886
(1.00) 		0.435
(1.00) 		0.0409
(1.00) 		1
(1.00) 		0.014
(1.00) 		0.103
(1.00) 		0.131
(1.00) 		0.915
(1.00) 		1
(1.00) 		1
(1.00)
16p loss 16 (3%) 558 0.0178
(1.00) 		0.491
(1.00) 		0.0513
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.497
(1.00) 		0.273
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.146
(1.00)
16q loss 19 (3%) 555 0.391
(1.00) 		0.462
(1.00) 		0.0011
(0.805) 		1
(1.00) 		0.0132
(1.00) 		0.707
(1.00) 		0.454
(1.00) 		0.785
(1.00) 		0.263
(1.00) 		0.744
(1.00)
17q loss 67 (12%) 507 0.593
(1.00) 		0.609
(1.00) 		0.0411
(1.00) 		0.436
(1.00) 		0.192
(1.00) 		0.374
(1.00) 		0.0775
(1.00) 		0.0808
(1.00) 		0.0763
(1.00) 		0.71
(1.00)
19p loss 22 (4%) 552 0.799
(1.00) 		0.553
(1.00) 		0.633
(1.00) 		0.829
(1.00) 		0.506
(1.00) 		0.473
(1.00) 		0.413
(1.00) 		0.0786
(1.00) 		1
(1.00) 		0.755
(1.00)
19q loss 20 (3%) 554 0.688
(1.00) 		0.0316
(1.00) 		0.212
(1.00) 		0.498
(1.00) 		0.408
(1.00) 		0.835
(1.00) 		1
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.336
(1.00)
20p loss 54 (9%) 520 0.312
(1.00) 		0.469
(1.00) 		0.106
(1.00) 		0.316
(1.00) 		0.0661
(1.00) 		0.541
(1.00) 		0.941
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.84
(1.00)
21q loss 119 (21%) 455 0.358
(1.00) 		0.993
(1.00) 		0.00558
(1.00) 		0.354
(1.00) 		0.0115
(1.00) 		0.769
(1.00) 		0.116
(1.00) 		0.635
(1.00) 		0.402
(1.00) 		0.659
(1.00)
'3p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 5.8e-05 (Chi-square test), Q value = 0.043

Table S1.  Gene #5: '3p gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 434 71 9 1 49
3P GAIN MUTATED 22 5 0 1 8
3P GAIN WILD-TYPE 412 66 9 0 41

Figure S1.  Get High-res Image Gene #5: '3p gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'7p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.24e-05 (Fisher's exact test), Q value = 0.047

Table S2.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
7P GAIN MUTATED 184 15 83 2
7P GAIN WILD-TYPE 172 39 59 11

Figure S2.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'13q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.03e-08 (Fisher's exact test), Q value = 5.3e-05

Table S3.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
13Q GAIN MUTATED 206 13 97 4
13Q GAIN WILD-TYPE 150 41 45 9

Figure S3.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'13q gain mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000172 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 327 140 103
13Q GAIN MUTATED 160 96 64
13Q GAIN WILD-TYPE 167 44 39

Figure S4.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'20p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.56e-06 (Fisher's exact test), Q value = 0.0034

Table S5.  Gene #36: '20p gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
20P GAIN MUTATED 183 12 85 3
20P GAIN WILD-TYPE 173 42 57 10

Figure S5.  Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 0.000104 (Fisher's exact test), Q value = 0.078

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

nPatients COLON RECTUM
ALL 412 158
20Q GAIN MUTATED 269 129
20Q GAIN WILD-TYPE 143 29

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

'20q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.84e-14 (Fisher's exact test), Q value = 5.9e-11

Table S7.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
20Q GAIN MUTATED 251 16 122 5
20Q GAIN WILD-TYPE 105 38 20 8

Figure S7.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'3p loss mutation analysis' versus 'Time to Death'

P value = 7.53e-08 (logrank test), Q value = 5.7e-05

Table S8.  Gene #44: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 443 60 0.1 - 135.5 (7.0)
3P LOSS MUTATED 25 7 0.3 - 15.5 (5.0)
3P LOSS WILD-TYPE 418 53 0.1 - 135.5 (7.2)

Figure S8.  Get High-res Image Gene #44: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'3p loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000168 (Chi-square test), Q value = 0.12

Table S9.  Gene #44: '3p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 434 71 9 1 49
3P LOSS MUTATED 25 14 1 0 0
3P LOSS WILD-TYPE 409 57 8 1 49

Figure S9.  Get High-res Image Gene #44: '3p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'6p loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 4.25e-05 (Chi-square test), Q value = 0.032

Table S10.  Gene #50: '6p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 434 71 9 1 49
6P LOSS MUTATED 19 3 2 1 3
6P LOSS WILD-TYPE 415 68 7 0 46

Figure S10.  Get High-res Image Gene #50: '6p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'8q loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 7.96e-06 (Chi-square test), Q value = 0.006

Table S11.  Gene #54: '8q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 434 71 9 1 49
8Q LOSS MUTATED 13 3 0 1 3
8Q LOSS WILD-TYPE 421 68 9 0 46

Figure S11.  Get High-res Image Gene #54: '8q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'12q loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000134 (Chi-square test), Q value = 0.1

Table S12.  Gene #62: '12q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 434 71 9 1 49
12Q LOSS MUTATED 19 5 0 1 1
12Q LOSS WILD-TYPE 415 66 9 0 48

Figure S12.  Get High-res Image Gene #62: '12q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'14q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.66e-07 (Fisher's exact test), Q value = 0.00058

Table S13.  Gene #64: '14q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
14Q LOSS MUTATED 94 3 55 0
14Q LOSS WILD-TYPE 262 51 87 13

Figure S13.  Get High-res Image Gene #64: '14q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000295 (Fisher's exact test), Q value = 0.22

Table S14.  Gene #65: '15q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
15Q LOSS MUTATED 93 4 51 4
15Q LOSS WILD-TYPE 263 50 91 9

Figure S14.  Get High-res Image Gene #65: '15q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.6e-08 (Fisher's exact test), Q value = 5e-05

Table S15.  Gene #68: '17p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
17P LOSS MUTATED 163 7 83 6
17P LOSS WILD-TYPE 193 47 59 7

Figure S15.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 0.000106 (Fisher's exact test), Q value = 0.079

Table S16.  Gene #70: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 158
18P LOSS MUTATED 213 110
18P LOSS WILD-TYPE 199 48

Figure S16.  Get High-res Image Gene #70: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.29e-14 (Fisher's exact test), Q value = 2.5e-11

Table S17.  Gene #70: '18p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
18P LOSS MUTATED 205 7 105 5
18P LOSS WILD-TYPE 151 47 37 8

Figure S17.  Get High-res Image Gene #70: '18p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00098

Table S18.  Gene #71: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 158
18Q LOSS MUTATED 228 122
18Q LOSS WILD-TYPE 184 36

Figure S18.  Get High-res Image Gene #71: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.77e-14 (Fisher's exact test), Q value = 1.3e-11

Table S19.  Gene #71: '18q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
18Q LOSS MUTATED 218 9 112 9
18Q LOSS WILD-TYPE 138 45 30 4

Figure S19.  Get High-res Image Gene #71: '18q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.074

Table S20.  Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 142 13
22Q LOSS MUTATED 79 1 36 5
22Q LOSS WILD-TYPE 277 53 106 8

Figure S20.  Get High-res Image Gene #76: '22q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = COADREAD.clin.merged.picked.txt

  • Number of patients = 574

  • Number of significantly arm-level cnvs = 76

  • Number of selected clinical features = 10

  • 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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