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 78 arm-level results and 11 clinical features across 575 patients, 22 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'Time to Death' and 'PATHOLOGICSPREAD(M)'.

  • 7p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.

  • 7q gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.

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

  • 18p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.

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

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

  • Xq gain cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • 2q loss cnv correlated to 'Time to Death'.

  • 3p loss cnv correlated to 'Time to Death'.

  • 14q 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',  'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

  • 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 78 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		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 Fisher's exact test
18q loss 352 (61%) 223 0.422
(1.00) 		0.32
(1.00) 		1.89e-07
(0.000161) 		0.731
(1.00) 		3.75e-14
(3.2e-11) 		0.231
(1.00) 		0.000363
(0.303) 		0.0028
(1.00) 		0.000242
(0.202) 		0.494
(1.00) 		0.714
(1.00)
3q gain 53 (9%) 522 0.000218
(0.182) 		0.644
(1.00) 		0.00881
(1.00) 		0.148
(1.00) 		0.0154
(1.00) 		0.952
(1.00) 		0.0296
(1.00) 		0.000283
(0.236) 		0.025
(1.00) 		0.198
(1.00) 		0.837
(1.00)
7p gain 290 (50%) 285 0.157
(1.00) 		0.631
(1.00) 		0.113
(1.00) 		1
(1.00) 		1.76e-05
(0.0149) 		0.923
(1.00) 		0.000378
(0.315) 		0.0472
(1.00) 		1.12e-05
(0.00946) 		0.505
(1.00) 		0.285
(1.00)
7q gain 255 (44%) 320 0.216
(1.00) 		0.615
(1.00) 		0.16
(1.00) 		0.866
(1.00) 		0.000112
(0.0942) 		0.898
(1.00) 		0.00972
(1.00) 		0.0213
(1.00) 		5.3e-05
(0.0446) 		0.519
(1.00) 		1
(1.00)
20q gain 403 (70%) 172 0.431
(1.00) 		0.88
(1.00) 		4.38e-05
(0.0369) 		0.362
(1.00) 		1.96e-15
(1.68e-12) 		0.221
(1.00) 		0.0403
(1.00) 		0.0328
(1.00) 		0.00152
(1.00) 		0.731
(1.00) 		0.244
(1.00)
18p loss 324 (56%) 251 0.607
(1.00) 		0.351
(1.00) 		2.12e-05
(0.0179) 		0.933
(1.00) 		1.18e-14
(1.01e-11) 		0.671
(1.00) 		0.00134
(1.00) 		0.00874
(1.00) 		0.00147
(1.00) 		0.738
(1.00) 		0.81
(1.00)
13q gain 314 (55%) 261 0.29
(1.00) 		0.874
(1.00) 		0.0192
(1.00) 		0.45
(1.00) 		3.94e-09
(3.36e-06) 		0.788
(1.00) 		0.00123
(1.00) 		0.188
(1.00) 		0.00258
(1.00) 		0.521
(1.00) 		0.474
(1.00)
18p gain 21 (4%) 554 0.696
(1.00) 		0.931
(1.00) 		1
(1.00) 		1
(1.00) 		0.0799
(1.00) 		0.528
(1.00) 		0.00317
(1.00) 		1.41e-05
(0.0119) 		0.719
(1.00) 		0.286
(1.00) 		1
(1.00)
20p gain 288 (50%) 287 0.34
(1.00) 		0.564
(1.00) 		0.00146
(1.00) 		0.024
(1.00) 		8.79e-09
(7.49e-06) 		0.354
(1.00) 		0.366
(1.00) 		0.0171
(1.00) 		0.035
(1.00) 		1
(1.00) 		0.635
(1.00)
Xq gain 17 (3%) 558 0.0508
(1.00) 		0.469
(1.00) 		0.583
(1.00) 		0.628
(1.00) 		0.723
(1.00) 		0.232
(1.00) 		0.159
(1.00) 		1.67e-07
(0.000142) 		0.132
(1.00) 		1
(1.00) 		0.489
(1.00)
2q loss 8 (1%) 567 3.78e-07
(0.000322) 		0.809
(1.00) 		1
(1.00) 		0.73
(1.00) 		0.868
(1.00) 		0.893
(1.00) 		0.885
(1.00) 		0.658
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.609
(1.00)
3p loss 35 (6%) 540 3.17e-05
(0.0267) 		0.909
(1.00) 		0.335
(1.00) 		0.163
(1.00) 		0.0365
(1.00) 		0.0472
(1.00) 		0.0698
(1.00) 		0.00361
(1.00) 		0.0391
(1.00) 		0.434
(1.00) 		0.455
(1.00)
14q loss 143 (25%) 432 0.382
(1.00) 		0.696
(1.00) 		0.0658
(1.00) 		1
(1.00) 		2.34e-05
(0.0197) 		0.506
(1.00) 		0.0125
(1.00) 		0.219
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.582
(1.00)
17p loss 252 (44%) 323 0.429
(1.00) 		0.587
(1.00) 		0.0019
(1.00) 		0.614
(1.00) 		5.69e-07
(0.000483) 		0.648
(1.00) 		0.0436
(1.00) 		0.000879
(0.728) 		0.0196
(1.00) 		0.19
(1.00) 		1
(1.00)
22q loss 122 (21%) 453 0.143
(1.00) 		0.0712
(1.00) 		0.17
(1.00) 		0.262
(1.00) 		0.000204
(0.171) 		0.573
(1.00) 		0.013
(1.00) 		0.243
(1.00) 		0.0543
(1.00) 		0.101
(1.00) 		0.382
(1.00)
1p gain 15 (3%) 560 0.85
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.503
(1.00) 		0.903
(1.00) 		0.0439
(1.00) 		0.813
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.707
(1.00)
1q gain 80 (14%) 495 0.656
(1.00) 		0.838
(1.00) 		0.174
(1.00) 		0.148
(1.00) 		0.0623
(1.00) 		0.202
(1.00) 		0.176
(1.00) 		0.33
(1.00) 		0.0305
(1.00) 		1
(1.00) 		1
(1.00)
2p gain 60 (10%) 515 0.328
(1.00) 		0.924
(1.00) 		0.361
(1.00) 		0.173
(1.00) 		0.0437
(1.00) 		0.666
(1.00) 		0.3
(1.00) 		0.976
(1.00) 		0.155
(1.00) 		1
(1.00) 		0.846
(1.00)
2q gain 59 (10%) 516 0.384
(1.00) 		0.448
(1.00) 		0.169
(1.00) 		0.217
(1.00) 		0.0315
(1.00) 		0.871
(1.00) 		0.365
(1.00) 		0.9
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.844
(1.00)
3p gain 36 (6%) 539 0.0324
(1.00) 		0.31
(1.00) 		0.0194
(1.00) 		0.301
(1.00) 		0.0545
(1.00) 		0.919
(1.00) 		0.608
(1.00) 		0.00172
(1.00) 		0.42
(1.00) 		0.444
(1.00) 		0.625
(1.00)
4p gain 6 (1%) 569 0.421
(1.00) 		0.885
(1.00) 		0.0537
(1.00) 		0.691
(1.00) 		0.199
(1.00) 		0.718
(1.00) 		0.323
(1.00) 		0.0446
(1.00) 		0.129
(1.00) 		1
(1.00) 		1
(1.00)
4q gain 7 (1%) 568 0.983
(1.00) 		0.758
(1.00) 		0.404
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.581
(1.00) 		0.113
(1.00) 		0.179
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 60 (10%) 515 0.953
(1.00) 		0.356
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.904
(1.00) 		0.213
(1.00) 		0.777
(1.00) 		0.518
(1.00) 		0.24
(1.00) 		0.56
(1.00)
5q gain 33 (6%) 542 0.903
(1.00) 		0.867
(1.00) 		0.316
(1.00) 		0.592
(1.00) 		0.327
(1.00) 		0.817
(1.00) 		0.219
(1.00) 		0.416
(1.00) 		0.254
(1.00) 		1
(1.00) 		0.45
(1.00)
6p gain 77 (13%) 498 0.624
(1.00) 		0.48
(1.00) 		0.0769
(1.00) 		1
(1.00) 		0.0568
(1.00) 		0.628
(1.00) 		0.00301
(1.00) 		0.752
(1.00) 		0.0536
(1.00) 		0.107
(1.00) 		1
(1.00)
6q gain 71 (12%) 504 0.875
(1.00) 		0.874
(1.00) 		0.0866
(1.00) 		0.899
(1.00) 		0.0795
(1.00) 		0.892
(1.00) 		0.00864
(1.00) 		0.631
(1.00) 		0.0294
(1.00) 		0.307
(1.00) 		0.472
(1.00)
8p gain 108 (19%) 467 0.64
(1.00) 		0.516
(1.00) 		0.551
(1.00) 		0.831
(1.00) 		0.945
(1.00) 		0.468
(1.00) 		0.316
(1.00) 		0.832
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.543
(1.00)
8q gain 235 (41%) 340 0.232
(1.00) 		0.125
(1.00) 		0.395
(1.00) 		0.396
(1.00) 		0.041
(1.00) 		0.207
(1.00) 		0.253
(1.00) 		0.29
(1.00) 		0.37
(1.00) 		0.744
(1.00) 		0.808
(1.00)
9p gain 79 (14%) 496 0.239
(1.00) 		0.339
(1.00) 		0.00178
(1.00) 		0.717
(1.00) 		0.0107
(1.00) 		0.87
(1.00) 		0.311
(1.00) 		0.674
(1.00) 		0.306
(1.00) 		0.619
(1.00) 		0.036
(1.00)
9q gain 64 (11%) 511 0.106
(1.00) 		0.197
(1.00) 		0.0386
(1.00) 		0.233
(1.00) 		0.194
(1.00) 		0.379
(1.00) 		0.321
(1.00) 		0.7
(1.00) 		0.205
(1.00) 		0.607
(1.00) 		0.0212
(1.00)
10p gain 28 (5%) 547 0.0421
(1.00) 		0.165
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.768
(1.00) 		0.103
(1.00) 		0.00549
(1.00) 		0.14
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.1
(1.00)
10q gain 13 (2%) 562 0.431
(1.00) 		0.0098
(1.00) 		0.762
(1.00) 		0.4
(1.00) 		0.603
(1.00) 		0.292
(1.00) 		0.0309
(1.00) 		0.494
(1.00) 		0.137
(1.00) 		1
(1.00) 		0.00527
(1.00)
11p gain 39 (7%) 536 0.458
(1.00) 		0.031
(1.00) 		0.000607
(0.503) 		0.187
(1.00) 		0.000327
(0.273) 		0.0993
(1.00) 		0.377
(1.00) 		0.479
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.636
(1.00)
11q gain 39 (7%) 536 0.414
(1.00) 		0.00274
(1.00) 		0.0272
(1.00) 		1
(1.00) 		0.0125
(1.00) 		0.191
(1.00) 		0.478
(1.00) 		0.751
(1.00) 		0.0946
(1.00) 		1
(1.00) 		0.478
(1.00)
12p gain 93 (16%) 482 0.659
(1.00) 		0.0189
(1.00) 		0.801
(1.00) 		0.91
(1.00) 		0.951
(1.00) 		0.528
(1.00) 		0.00985
(1.00) 		0.409
(1.00) 		0.081
(1.00) 		0.644
(1.00) 		0.196
(1.00)
12q gain 78 (14%) 497 0.834
(1.00) 		0.00427
(1.00) 		0.344
(1.00) 		0.393
(1.00) 		0.729
(1.00) 		0.676
(1.00) 		0.0409
(1.00) 		0.443
(1.00) 		0.036
(1.00) 		0.617
(1.00) 		0.167
(1.00)
14q gain 19 (3%) 556 0.313
(1.00) 		0.908
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.366
(1.00) 		0.469
(1.00) 		0.0266
(1.00) 		0.446
(1.00) 		0.263
(1.00) 		0.0406
(1.00)
15q gain 7 (1%) 568 0.91
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.71
(1.00) 		0.208
(1.00) 		0.872
(1.00) 		0.875
(1.00) 		0.714
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.262
(1.00)
16p gain 96 (17%) 479 0.689
(1.00) 		0.342
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.0208
(1.00) 		0.842
(1.00) 		0.00671
(1.00) 		0.371
(1.00) 		0.00407
(1.00) 		0.178
(1.00) 		0.522
(1.00)
16q gain 96 (17%) 479 0.853
(1.00) 		0.215
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.0172
(1.00) 		0.809
(1.00) 		0.000484
(0.402) 		0.312
(1.00) 		0.000404
(0.336) 		0.178
(1.00) 		0.336
(1.00)
17p gain 13 (2%) 562 0.163
(1.00) 		0.669
(1.00) 		0.531
(1.00) 		0.78
(1.00) 		0.533
(1.00) 		0.55
(1.00) 		0.862
(1.00) 		0.00171
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.0997
(1.00)
17q gain 67 (12%) 508 0.0443
(1.00) 		0.51
(1.00) 		0.772
(1.00) 		0.3
(1.00) 		0.121
(1.00) 		0.877
(1.00) 		0.983
(1.00) 		0.0163
(1.00) 		0.387
(1.00) 		1
(1.00) 		0.00892
(1.00)
18q gain 12 (2%) 563 0.639
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.398
(1.00) 		0.32
(1.00) 		0.105
(1.00) 		0.0996
(1.00) 		0.826
(1.00) 		0.976
(1.00) 		0.174
(1.00) 		0.684
(1.00)
19p gain 52 (9%) 523 0.575
(1.00) 		0.37
(1.00) 		0.259
(1.00) 		0.884
(1.00) 		0.0798
(1.00) 		0.936
(1.00) 		0.882
(1.00) 		0.724
(1.00) 		0.985
(1.00) 		1
(1.00) 		0.146
(1.00)
19q gain 61 (11%) 514 0.279
(1.00) 		0.351
(1.00) 		0.367
(1.00) 		0.499
(1.00) 		0.363
(1.00) 		0.848
(1.00) 		0.982
(1.00) 		0.992
(1.00) 		0.883
(1.00) 		0.608
(1.00) 		0.566
(1.00)
21q gain 19 (3%) 556 0.262
(1.00) 		0.607
(1.00) 		0.292
(1.00) 		0.644
(1.00) 		0.669
(1.00) 		0.146
(1.00) 		0.145
(1.00) 		0.741
(1.00) 		0.227
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 7 (1%) 568 0.487
(1.00) 		0.542
(1.00) 		0.0201
(1.00) 		0.71
(1.00) 		0.071
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.179
(1.00) 		0.0359
(1.00) 		1
(1.00) 		0.601
(1.00)
1p loss 68 (12%) 507 0.054
(1.00) 		0.932
(1.00) 		0.774
(1.00) 		0.52
(1.00) 		0.281
(1.00) 		0.716
(1.00) 		0.0533
(1.00) 		0.185
(1.00) 		0.0962
(1.00) 		1
(1.00) 		0.0964
(1.00)
1q loss 25 (4%) 550 0.717
(1.00) 		0.179
(1.00) 		0.651
(1.00) 		0.312
(1.00) 		0.876
(1.00) 		0.758
(1.00) 		0.164
(1.00) 		0.631
(1.00) 		0.346
(1.00) 		0.332
(1.00) 		1
(1.00)
2p loss 10 (2%) 565 0.311
(1.00) 		0.324
(1.00) 		0.151
(1.00) 		0.758
(1.00) 		0.247
(1.00) 		0.836
(1.00) 		0.748
(1.00) 		0.855
(1.00) 		0.968
(1.00) 		1
(1.00) 		0.371
(1.00)
3q loss 17 (3%) 558 0.0355
(1.00) 		0.121
(1.00) 		0.791
(1.00) 		0.0815
(1.00) 		0.00183
(1.00) 		0.598
(1.00) 		0.746
(1.00) 		0.169
(1.00) 		0.164
(1.00) 		0.238
(1.00) 		0.489
(1.00)
4p loss 122 (21%) 453 0.028
(1.00) 		0.29
(1.00) 		0.304
(1.00) 		0.475
(1.00) 		0.0198
(1.00) 		0.81
(1.00) 		0.00971
(1.00) 		0.0151
(1.00) 		0.00857
(1.00) 		0.101
(1.00) 		0.0293
(1.00)
4q loss 113 (20%) 462 0.417
(1.00) 		0.288
(1.00) 		0.00866
(1.00) 		0.674
(1.00) 		0.00132
(1.00) 		0.743
(1.00) 		0.0763
(1.00) 		0.518
(1.00) 		0.149
(1.00) 		0.0795
(1.00) 		0.0722
(1.00)
5p loss 34 (6%) 541 0.508
(1.00) 		0.66
(1.00) 		0.845
(1.00) 		0.481
(1.00) 		0.177
(1.00) 		0.804
(1.00) 		0.0599
(1.00) 		0.974
(1.00) 		0.114
(1.00) 		0.0941
(1.00) 		0.0189
(1.00)
5q loss 60 (10%) 515 0.533
(1.00) 		0.659
(1.00) 		0.0672
(1.00) 		0.891
(1.00) 		0.046
(1.00) 		0.461
(1.00) 		0.045
(1.00) 		0.769
(1.00) 		0.439
(1.00) 		0.00908
(1.00) 		1
(1.00)
6p loss 18 (3%) 557 0.401
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.605
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.492
(1.00)
6q loss 33 (6%) 542 0.0672
(1.00) 		0.211
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.0943
(1.00) 		0.683
(1.00) 		0.0842
(1.00) 		0.000881
(0.729) 		0.471
(1.00) 		1
(1.00) 		0.606
(1.00)
7q loss 3 (1%) 572 0.191
(1.00) 		0.0213
(1.00) 		0.6
(1.00) 		0.0106
(1.00) 		0.679
(1.00) 		0.757
(1.00) 		0.924
(1.00) 		0.55
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 145 (25%) 430 0.948
(1.00) 		0.996
(1.00) 		0.00687
(1.00) 		0.0831
(1.00) 		0.00148
(1.00) 		0.812
(1.00) 		0.0373
(1.00) 		0.19
(1.00) 		0.269
(1.00) 		0.0493
(1.00) 		0.169
(1.00)
8q loss 12 (2%) 563 0.765
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.154
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.2
(1.00) 		0.0709
(1.00) 		1
(1.00) 		0.232
(1.00)
9p loss 39 (7%) 536 0.0253
(1.00) 		0.271
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.748
(1.00) 		0.204
(1.00) 		0.758
(1.00) 		0.83
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.34
(1.00)
9q loss 37 (6%) 538 0.287
(1.00) 		0.00981
(1.00) 		1
(1.00) 		0.395
(1.00) 		0.53
(1.00) 		0.111
(1.00) 		0.634
(1.00) 		0.925
(1.00) 		0.343
(1.00) 		1
(1.00) 		1
(1.00)
10p loss 40 (7%) 535 0.566
(1.00) 		0.0105
(1.00) 		0.043
(1.00) 		0.511
(1.00) 		0.0111
(1.00) 		0.722
(1.00) 		0.353
(1.00) 		0.595
(1.00) 		0.185
(1.00) 		0.48
(1.00) 		0.489
(1.00)
10q loss 46 (8%) 529 0.346
(1.00) 		0.0151
(1.00) 		0.00307
(1.00) 		1
(1.00) 		0.00268
(1.00) 		0.841
(1.00) 		0.73
(1.00) 		0.829
(1.00) 		0.532
(1.00) 		0.53
(1.00) 		0.826
(1.00)
11p loss 40 (7%) 535 0.377
(1.00) 		0.969
(1.00) 		0.00589
(1.00) 		0.743
(1.00) 		0.00128
(1.00) 		0.94
(1.00) 		0.216
(1.00) 		0.962
(1.00) 		0.0417
(1.00) 		0.48
(1.00) 		0.248
(1.00)
11q loss 51 (9%) 524 0.74
(1.00) 		0.821
(1.00) 		0.00745
(1.00) 		0.378
(1.00) 		0.00239
(1.00) 		0.702
(1.00) 		0.152
(1.00) 		0.981
(1.00) 		0.469
(1.00) 		0.0377
(1.00) 		1
(1.00)
12p loss 33 (6%) 542 0.0704
(1.00) 		0.986
(1.00) 		0.316
(1.00) 		0.0481
(1.00) 		0.12
(1.00) 		0.0526
(1.00) 		0.0182
(1.00) 		0.511
(1.00) 		0.19
(1.00) 		0.415
(1.00) 		0.8
(1.00)
12q loss 28 (5%) 547 0.103
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.303
(1.00) 		0.259
(1.00) 		0.0259
(1.00) 		0.29
(1.00) 		0.096
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 12 (2%) 563 0.874
(1.00) 		0.864
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.394
(1.00) 		0.0251
(1.00) 		0.426
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.232
(1.00)
15q loss 156 (27%) 419 0.531
(1.00) 		0.64
(1.00) 		0.0113
(1.00) 		0.851
(1.00) 		0.000516
(0.428) 		0.393
(1.00) 		0.289
(1.00) 		0.365
(1.00) 		0.208
(1.00) 		0.263
(1.00) 		0.893
(1.00)
16p loss 15 (3%) 560 0.993
(1.00) 		0.548
(1.00) 		0.379
(1.00) 		0.123
(1.00) 		0.26
(1.00) 		0.951
(1.00) 		0.673
(1.00) 		0.985
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00)
16q loss 17 (3%) 558 0.455
(1.00) 		0.852
(1.00) 		0.00999
(1.00) 		0.628
(1.00) 		0.0229
(1.00) 		0.885
(1.00) 		0.179
(1.00) 		0.972
(1.00) 		0.652
(1.00) 		0.238
(1.00) 		1
(1.00)
17q loss 45 (8%) 530 0.52
(1.00) 		0.854
(1.00) 		0.39
(1.00) 		0.877
(1.00) 		0.278
(1.00) 		0.602
(1.00) 		0.112
(1.00) 		0.922
(1.00) 		0.459
(1.00) 		0.152
(1.00) 		0.376
(1.00)
19p loss 20 (3%) 555 0.758
(1.00) 		0.538
(1.00) 		0.454
(1.00) 		0.111
(1.00) 		0.519
(1.00) 		0.577
(1.00) 		0.775
(1.00) 		0.56
(1.00) 		0.619
(1.00) 		1
(1.00) 		1
(1.00)
19q loss 18 (3%) 557 0.957
(1.00) 		0.166
(1.00) 		0.598
(1.00) 		0.235
(1.00) 		0.698
(1.00) 		0.62
(1.00) 		0.76
(1.00) 		0.404
(1.00) 		0.945
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 47 (8%) 528 0.39
(1.00) 		0.814
(1.00) 		0.304
(1.00) 		0.761
(1.00) 		0.327
(1.00) 		0.418
(1.00) 		0.777
(1.00) 		0.731
(1.00) 		0.596
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 114 (20%) 461 0.35
(1.00) 		0.956
(1.00) 		0.00967
(1.00) 		0.403
(1.00) 		0.00996
(1.00) 		0.651
(1.00) 		0.0763
(1.00) 		0.843
(1.00) 		0.214
(1.00) 		0.695
(1.00) 		0.767
(1.00)
Xq loss 11 (2%) 564 0.386
(1.00) 		0.251
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.291
(1.00) 		0.744
(1.00) 		0.337
(1.00) 		0.402
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00)
'3q gain mutation analysis' versus 'Time to Death'

P value = 0.000218 (logrank test), Q value = 0.18

Table S1.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 444 60 0.1 - 135.5 (7.0)
3Q GAIN MUTATED 38 10 0.2 - 60.0 (5.7)
3Q GAIN WILD-TYPE 406 50 0.1 - 135.5 (7.6)

Figure S1.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'3q gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000283 (Chi-square test), Q value = 0.24

Table S2.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 435 71 9 1 49
3Q GAIN MUTATED 32 8 3 1 8
3Q GAIN WILD-TYPE 403 63 6 0 41

Figure S2.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

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

P value = 1.76e-05 (Fisher's exact test), Q value = 0.015

Table S3.  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 54 143 13
7P GAIN MUTATED 184 15 87 2
7P GAIN WILD-TYPE 172 39 56 11

Figure S3.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'7p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0095

Table S4.  Gene #13: '7p gain mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
7P GAIN MUTATED 46 78 99 52
7P GAIN WILD-TYPE 51 129 67 29

Figure S4.  Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 0.000112 (Fisher's exact test), Q value = 0.094

Table S5.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
7Q GAIN MUTATED 161 14 77 1
7Q GAIN WILD-TYPE 195 40 66 12

Figure S5.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'7q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 5.3e-05 (Fisher's exact test), Q value = 0.045

Table S6.  Gene #14: '7q gain mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
7Q GAIN MUTATED 42 67 88 46
7Q GAIN WILD-TYPE 55 140 78 35

Figure S6.  Get High-res Image Gene #14: '7q gain mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 3.94e-09 (Fisher's exact test), Q value = 3.4e-06

Table S7.  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 54 143 13
13Q GAIN MUTATED 199 12 96 2
13Q GAIN WILD-TYPE 157 42 47 11

Figure S7.  Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'18p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.41e-05 (Chi-square test), Q value = 0.012

Table S8.  Gene #32: '18p gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 435 71 9 1 49
18P GAIN MUTATED 15 2 0 1 2
18P GAIN WILD-TYPE 420 69 9 0 47

Figure S8.  Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

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

P value = 8.79e-09 (Fisher's exact test), Q value = 7.5e-06

Table S9.  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 54 143 13
20P GAIN MUTATED 176 11 93 2
20P GAIN WILD-TYPE 180 43 50 11

Figure S9.  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 = 4.38e-05 (Fisher's exact test), Q value = 0.037

Table S10.  Gene #37: '20q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
20Q GAIN MUTATED 269 131
20Q GAIN WILD-TYPE 143 28

Figure S10.  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 = 1.96e-15 (Fisher's exact test), Q value = 1.7e-12

Table S11.  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 54 143 13
20Q GAIN MUTATED 251 16 125 4
20Q GAIN WILD-TYPE 105 38 18 9

Figure S11.  Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Xq gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.67e-07 (Chi-square test), Q value = 0.00014

Table S12.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 435 71 9 1 49
XQ GAIN MUTATED 10 4 0 1 1
XQ GAIN WILD-TYPE 425 67 9 0 48

Figure S12.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGICSPREAD(M)'

'2q loss mutation analysis' versus 'Time to Death'

P value = 3.78e-07 (logrank test), Q value = 0.00032

Table S13.  Gene #44: '2q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 444 60 0.1 - 135.5 (7.0)
2Q LOSS MUTATED 5 1 0.3 - 1.0 (1.0)
2Q LOSS WILD-TYPE 439 59 0.1 - 135.5 (7.3)

Figure S13.  Get High-res Image Gene #44: '2q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

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

P value = 3.17e-05 (logrank test), Q value = 0.027

Table S14.  Gene #45: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 444 60 0.1 - 135.5 (7.0)
3P LOSS MUTATED 21 5 0.3 - 14.5 (4.0)
3P LOSS WILD-TYPE 423 55 0.1 - 135.5 (7.3)

Figure S14.  Get High-res Image Gene #45: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

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

P value = 2.34e-05 (Fisher's exact test), Q value = 0.02

Table S15.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
14Q LOSS MUTATED 90 3 48 0
14Q LOSS WILD-TYPE 266 51 95 13

Figure S15.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 5.69e-07 (Fisher's exact test), Q value = 0.00048

Table S16.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
17P LOSS MUTATED 156 7 79 6
17P LOSS WILD-TYPE 200 47 64 7

Figure S16.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 2.12e-05 (Fisher's exact test), Q value = 0.018

Table S17.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
18P LOSS MUTATED 209 112
18P LOSS WILD-TYPE 203 47

Figure S17.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 1.18e-14 (Fisher's exact test), Q value = 1e-11

Table S18.  Gene #71: '18p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
18P LOSS MUTATED 201 7 107 5
18P LOSS WILD-TYPE 155 47 36 8

Figure S18.  Get High-res Image Gene #71: '18p loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 1.89e-07 (Fisher's exact test), Q value = 0.00016

Table S19.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
18Q LOSS MUTATED 225 124
18Q LOSS WILD-TYPE 187 35

Figure S19.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 3.75e-14 (Fisher's exact test), Q value = 3.2e-11

Table S20.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
18Q LOSS MUTATED 214 10 114 9
18Q LOSS WILD-TYPE 142 44 29 4

Figure S20.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'18q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000242 (Fisher's exact test), Q value = 0.2

Table S21.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
18Q LOSS MUTATED 50 112 112 62
18Q LOSS WILD-TYPE 47 95 54 19

Figure S21.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 0.000204 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #77: '22q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
22Q LOSS MUTATED 80 1 36 4
22Q LOSS WILD-TYPE 276 53 107 9

Figure S22.  Get High-res Image Gene #77: '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 = 575

  • Number of significantly arm-level cnvs = 78

  • Number of selected clinical features = 11

  • 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)
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