Correlation between copy number variations of arm-level result and selected clinical features
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1959FK0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1959FK0
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 12 clinical features across 575 patients, 23 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'LYMPH.NODE.METASTASIS'.

  • 3q gain cnv correlated to 'Time to Death' and 'DISTANT.METASTASIS'.

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

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

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

  • 18p gain cnv correlated to 'DISTANT.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.

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

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

  • Xq gain cnv correlated to 'DISTANT.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.

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

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

  • 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' 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 78 arm-level results and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Chi-square test Fisher's exact test t-test t-test Chi-square test
3q gain 0 (0%) 522 0.000266
(0.222) 		0.644
(1.00) 		0.00881
(1.00) 		0.148
(1.00) 		0.0152
(1.00) 		0.198
(1.00) 		0.000274
(0.228) 		0.00202
(1.00) 		0.487
(1.00) 		0.145
(1.00) 		0.0419
(1.00)
18p gain 0 (0%) 554 0.695
(1.00) 		0.931
(1.00) 		1
(1.00) 		1
(1.00) 		0.0795
(1.00) 		0.286
(1.00) 		1.38e-05
(0.0116) 		0.0122
(1.00) 		0.736
(1.00) 		0.0429
(1.00) 		8.93e-06
(0.00755)
20q gain 0 (0%) 172 0.425
(1.00) 		0.88
(1.00) 		4.38e-05
(0.0369) 		0.361
(1.00) 		1.97e-15
(1.69e-12) 		0.731
(1.00) 		0.0336
(1.00) 		0.286
(1.00) 		0.0133
(1.00) 		0.466
(1.00) 		0.00521
(1.00)
Xq gain 0 (0%) 558 0.0426
(1.00) 		0.469
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.723
(1.00) 		1
(1.00) 		1.61e-07
(0.000137) 		0.437
(1.00) 		0.411
(1.00) 		0.201
(1.00) 		7e-05
(0.0588)
18p loss 0 (0%) 251 0.626
(1.00) 		0.351
(1.00) 		2.12e-05
(0.0179) 		1
(1.00) 		1.2e-14
(1.02e-11) 		0.738
(1.00) 		0.00844
(1.00) 		0.0212
(1.00) 		0.0844
(1.00) 		0.207
(1.00) 		0.0103
(1.00)
18q loss 0 (0%) 223 0.438
(1.00) 		0.32
(1.00) 		1.89e-07
(0.000161) 		0.668
(1.00) 		3.62e-14
(3.09e-11) 		0.494
(1.00) 		0.00269
(1.00) 		0.00952
(1.00) 		0.0419
(1.00) 		0.132
(1.00) 		0.00468
(1.00)
1p gain 0 (0%) 560 0.858
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.814
(1.00) 		2.08e-06
(0.00176) 		1
(1.00) 		0.243
(1.00) 		0.304
(1.00)
7p gain 0 (0%) 285 0.152
(1.00) 		0.631
(1.00) 		0.113
(1.00) 		1
(1.00) 		1.81e-05
(0.0153) 		0.505
(1.00) 		0.0453
(1.00) 		0.00454
(1.00) 		0.176
(1.00) 		0.0219
(1.00) 		0.0022
(1.00)
7q gain 0 (0%) 320 0.202
(1.00) 		0.615
(1.00) 		0.16
(1.00) 		0.801
(1.00) 		0.000112
(0.0942) 		0.519
(1.00) 		0.0205
(1.00) 		0.0336
(1.00) 		0.12
(1.00) 		0.131
(1.00) 		0.00562
(1.00)
13q gain 0 (0%) 261 0.271
(1.00) 		0.874
(1.00) 		0.0192
(1.00) 		0.401
(1.00) 		4.12e-09
(3.51e-06) 		0.521
(1.00) 		0.193
(1.00) 		0.00875
(1.00) 		0.09
(1.00) 		0.856
(1.00) 		0.024
(1.00)
20p gain 0 (0%) 287 0.319
(1.00) 		0.564
(1.00) 		0.00146
(1.00) 		0.0297
(1.00) 		8.85e-09
(7.54e-06) 		1
(1.00) 		0.0177
(1.00) 		0.65
(1.00) 		0.0222
(1.00) 		0.47
(1.00) 		0.00996
(1.00)
2q loss 0 (0%) 567 8.15e-07
(0.000691) 		0.809
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.986
(1.00) 		1
(1.00) 		0.497
(1.00) 		0.527
(1.00)
3p loss 0 (0%) 540 0.00013
(0.109) 		0.909
(1.00) 		0.335
(1.00) 		0.164
(1.00) 		0.037
(1.00) 		0.434
(1.00) 		0.00354
(1.00) 		0.242
(1.00) 		0.0341
(1.00) 		0.149
(1.00) 		0.308
(1.00)
7q loss 0 (0%) 572 0.191
(1.00) 		0.0213
(1.00) 		0.598
(1.00) 		0.0106
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.972
(1.00) 		1
(1.00) 		1.54e-24
(1.32e-21) 		0.988
(1.00)
14q loss 0 (0%) 432 0.396
(1.00) 		0.696
(1.00) 		0.0658
(1.00) 		1
(1.00) 		2.36e-05
(0.0199) 		1
(1.00) 		0.218
(1.00) 		0.0178
(1.00) 		0.798
(1.00) 		0.516
(1.00) 		0.371
(1.00)
17p loss 0 (0%) 323 0.442
(1.00) 		0.587
(1.00) 		0.0019
(1.00) 		0.674
(1.00) 		5.66e-07
(0.000481) 		0.19
(1.00) 		0.000859
(0.712) 		0.0669
(1.00) 		0.0444
(1.00) 		0.0206
(1.00) 		0.0802
(1.00)
22q loss 0 (0%) 453 0.165
(1.00) 		0.0712
(1.00) 		0.17
(1.00) 		0.306
(1.00) 		0.000207
(0.174) 		0.101
(1.00) 		0.24
(1.00) 		0.0113
(1.00) 		0.177
(1.00) 		0.279
(1.00) 		0.403
(1.00)
1q gain 0 (0%) 495 0.644
(1.00) 		0.838
(1.00) 		0.174
(1.00) 		0.15
(1.00) 		0.0624
(1.00) 		1
(1.00) 		0.325
(1.00) 		0.00229
(1.00) 		0.344
(1.00) 		0.0412
(1.00) 		0.331
(1.00)
2p gain 0 (0%) 515 0.335
(1.00) 		0.924
(1.00) 		0.361
(1.00) 		0.172
(1.00) 		0.0434
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.0481
(1.00) 		0.115
(1.00) 		0.301
(1.00) 		0.365
(1.00)
2q gain 0 (0%) 516 0.392
(1.00) 		0.448
(1.00) 		0.169
(1.00) 		0.216
(1.00) 		0.0316
(1.00) 		1
(1.00) 		0.899
(1.00) 		0.129
(1.00) 		0.451
(1.00) 		0.136
(1.00) 		0.573
(1.00)
3p gain 0 (0%) 539 0.0374
(1.00) 		0.31
(1.00) 		0.0194
(1.00) 		0.301
(1.00) 		0.0531
(1.00) 		0.444
(1.00) 		0.00169
(1.00) 		0.251
(1.00) 		0.762
(1.00) 		0.264
(1.00) 		0.0415
(1.00)
4p gain 0 (0%) 569 0.421
(1.00) 		0.885
(1.00) 		0.0537
(1.00) 		0.691
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.0442
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.0161
(1.00) 		0.0023
(1.00)
4q gain 0 (0%) 568 0.983
(1.00) 		0.758
(1.00) 		0.404
(1.00) 		1
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.463
(1.00) 		0.16
(1.00) 		0.301
(1.00) 		0.597
(1.00)
5p gain 0 (0%) 515 0.938
(1.00) 		0.356
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.243
(1.00) 		0.24
(1.00) 		0.775
(1.00) 		0.149
(1.00) 		0.241
(1.00) 		0.882
(1.00) 		0.532
(1.00)
5q gain 0 (0%) 542 0.893
(1.00) 		0.867
(1.00) 		0.316
(1.00) 		0.592
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.0253
(1.00) 		0.306
(1.00) 		0.142
(1.00) 		0.262
(1.00)
6p gain 0 (0%) 498 0.633
(1.00) 		0.48
(1.00) 		0.0769
(1.00) 		1
(1.00) 		0.0553
(1.00) 		0.107
(1.00) 		0.748
(1.00) 		0.0151
(1.00) 		0.233
(1.00) 		0.131
(1.00) 		0.52
(1.00)
6q gain 0 (0%) 504 0.865
(1.00) 		0.874
(1.00) 		0.0866
(1.00) 		0.899
(1.00) 		0.0783
(1.00) 		0.307
(1.00) 		0.627
(1.00) 		0.0255
(1.00) 		0.184
(1.00) 		0.154
(1.00) 		0.39
(1.00)
8p gain 0 (0%) 467 0.642
(1.00) 		0.516
(1.00) 		0.551
(1.00) 		0.748
(1.00) 		0.945
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.302
(1.00) 		0.0717
(1.00) 		0.124
(1.00) 		0.324
(1.00)
8q gain 0 (0%) 340 0.228
(1.00) 		0.125
(1.00) 		0.395
(1.00) 		0.35
(1.00) 		0.0417
(1.00) 		0.744
(1.00) 		0.3
(1.00) 		0.103
(1.00) 		0.0308
(1.00) 		0.639
(1.00) 		0.388
(1.00)
9p gain 0 (0%) 496 0.246
(1.00) 		0.339
(1.00) 		0.00178
(1.00) 		0.718
(1.00) 		0.0103
(1.00) 		0.619
(1.00) 		0.649
(1.00) 		0.413
(1.00) 		0.516
(1.00) 		0.384
(1.00) 		0.0724
(1.00)
9q gain 0 (0%) 511 0.105
(1.00) 		0.197
(1.00) 		0.0386
(1.00) 		0.234
(1.00) 		0.19
(1.00) 		0.607
(1.00) 		0.672
(1.00) 		0.236
(1.00) 		0.639
(1.00) 		0.747
(1.00) 		0.045
(1.00)
10p gain 0 (0%) 547 0.0425
(1.00) 		0.165
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.000625
(0.519) 		0.351
(1.00) 		0.183
(1.00) 		0.194
(1.00)
10q gain 0 (0%) 562 0.433
(1.00) 		0.0098
(1.00) 		0.762
(1.00) 		0.278
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.493
(1.00) 		0.000688
(0.571) 		0.66
(1.00) 		0.167
(1.00) 		0.316
(1.00)
11p gain 0 (0%) 536 0.478
(1.00) 		0.031
(1.00) 		0.000607
(0.505) 		0.188
(1.00) 		0.000318
(0.265) 		1
(1.00) 		0.478
(1.00) 		0.218
(1.00) 		0.419
(1.00) 		0.217
(1.00) 		0.375
(1.00)
11q gain 0 (0%) 536 0.435
(1.00) 		0.00274
(1.00) 		0.0272
(1.00) 		1
(1.00) 		0.0122
(1.00) 		1
(1.00) 		0.749
(1.00) 		0.199
(1.00) 		0.243
(1.00) 		0.518
(1.00) 		0.557
(1.00)
12p gain 0 (0%) 482 0.664
(1.00) 		0.0189
(1.00) 		0.801
(1.00) 		0.822
(1.00) 		0.947
(1.00) 		0.644
(1.00) 		0.41
(1.00) 		0.162
(1.00) 		0.743
(1.00) 		0.854
(1.00) 		0.034
(1.00)
12q gain 0 (0%) 497 0.823
(1.00) 		0.00427
(1.00) 		0.344
(1.00) 		0.393
(1.00) 		0.704
(1.00) 		0.617
(1.00) 		0.445
(1.00) 		0.35
(1.00) 		0.532
(1.00) 		0.0317
(1.00) 		0.0128
(1.00)
14q gain 0 (0%) 556 0.316
(1.00) 		0.908
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.263
(1.00) 		0.0265
(1.00) 		0.00268
(1.00) 		0.736
(1.00) 		0.861
(1.00) 		0.564
(1.00)
15q gain 0 (0%) 568 0.912
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.965
(1.00)
16p gain 0 (0%) 479 0.682
(1.00) 		0.342
(1.00) 		0.618
(1.00) 		0.911
(1.00) 		0.0209
(1.00) 		0.178
(1.00) 		0.367
(1.00) 		0.0248
(1.00) 		0.574
(1.00) 		0.984
(1.00) 		0.129
(1.00)
16q gain 0 (0%) 479 0.865
(1.00) 		0.215
(1.00) 		0.454
(1.00) 		0.911
(1.00) 		0.0173
(1.00) 		0.178
(1.00) 		0.308
(1.00) 		0.00452
(1.00) 		0.837
(1.00) 		0.739
(1.00) 		0.0142
(1.00)
17p gain 0 (0%) 562 0.164
(1.00) 		0.669
(1.00) 		0.531
(1.00) 		0.589
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.00169
(1.00) 		0.00219
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.0832
(1.00)
17q gain 0 (0%) 508 0.0437
(1.00) 		0.51
(1.00) 		0.772
(1.00) 		0.362
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.016
(1.00) 		0.173
(1.00) 		0.712
(1.00) 		0.0612
(1.00) 		0.288
(1.00)
18q gain 0 (0%) 563 0.641
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.399
(1.00) 		0.319
(1.00) 		0.174
(1.00) 		0.825
(1.00) 		0.0381
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.645
(1.00)
19p gain 0 (0%) 523 0.581
(1.00) 		0.37
(1.00) 		0.259
(1.00) 		0.884
(1.00) 		0.0803
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.927
(1.00) 		0.192
(1.00) 		0.525
(1.00) 		0.873
(1.00)
19q gain 0 (0%) 514 0.287
(1.00) 		0.351
(1.00) 		0.367
(1.00) 		0.498
(1.00) 		0.363
(1.00) 		0.608
(1.00) 		0.992
(1.00) 		0.933
(1.00) 		0.251
(1.00) 		0.554
(1.00) 		0.963
(1.00)
21q gain 0 (0%) 556 0.265
(1.00) 		0.607
(1.00) 		0.292
(1.00) 		0.643
(1.00) 		0.669
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.0175
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.666
(1.00)
22q gain 0 (0%) 568 0.468
(1.00) 		0.542
(1.00) 		0.0201
(1.00) 		0.709
(1.00) 		0.0706
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.611
(1.00) 		0.16
(1.00) 		0.377
(1.00) 		0.274
(1.00)
1p loss 0 (0%) 507 0.0605
(1.00) 		0.932
(1.00) 		0.774
(1.00) 		0.605
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.157
(1.00) 		0.408
(1.00) 		0.0781
(1.00) 		0.218
(1.00)
1q loss 0 (0%) 550 0.71
(1.00) 		0.179
(1.00) 		0.651
(1.00) 		0.314
(1.00) 		0.876
(1.00) 		0.332
(1.00) 		0.628
(1.00) 		0.653
(1.00) 		0.326
(1.00) 		0.366
(1.00) 		0.721
(1.00)
2p loss 0 (0%) 565 0.305
(1.00) 		0.324
(1.00) 		0.151
(1.00) 		0.759
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.974
(1.00) 		0.7
(1.00) 		0.605
(1.00) 		0.873
(1.00)
3q loss 0 (0%) 558 0.0354
(1.00) 		0.121
(1.00) 		0.791
(1.00) 		0.0817
(1.00) 		0.00181
(1.00) 		0.238
(1.00) 		0.168
(1.00) 		0.915
(1.00) 		0.0802
(1.00) 		0.592
(1.00) 		0.36
(1.00)
4p loss 0 (0%) 453 0.0308
(1.00) 		0.29
(1.00) 		0.304
(1.00) 		0.54
(1.00) 		0.0199
(1.00) 		0.101
(1.00) 		0.0146
(1.00) 		0.0201
(1.00) 		0.263
(1.00) 		0.00455
(1.00) 		0.0869
(1.00)
4q loss 0 (0%) 462 0.436
(1.00) 		0.288
(1.00) 		0.00866
(1.00) 		0.674
(1.00) 		0.00131
(1.00) 		0.0795
(1.00) 		0.513
(1.00) 		0.129
(1.00) 		0.502
(1.00) 		0.0228
(1.00) 		0.588
(1.00)
5p loss 0 (0%) 541 0.511
(1.00) 		0.66
(1.00) 		0.845
(1.00) 		0.48
(1.00) 		0.178
(1.00) 		0.0941
(1.00) 		0.974
(1.00) 		0.143
(1.00) 		0.924
(1.00) 		0.0672
(1.00) 		0.0356
(1.00)
5q loss 0 (0%) 515 0.529
(1.00) 		0.659
(1.00) 		0.0672
(1.00) 		0.892
(1.00) 		0.046
(1.00) 		0.00908
(1.00) 		0.766
(1.00) 		0.275
(1.00) 		0.662
(1.00) 		0.0664
(1.00) 		0.186
(1.00)
6p loss 0 (0%) 557 0.389
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.92
(1.00) 		0.00319
(1.00) 		0.479
(1.00) 		0.987
(1.00)
6q loss 0 (0%) 542 0.0895
(1.00) 		0.211
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.0938
(1.00) 		1
(1.00) 		0.000861
(0.713) 		0.49
(1.00) 		0.0672
(1.00) 		0.0469
(1.00) 		0.029
(1.00)
8p loss 0 (0%) 430 0.961
(1.00) 		0.996
(1.00) 		0.00687
(1.00) 		0.0838
(1.00) 		0.00145
(1.00) 		0.0493
(1.00) 		0.19
(1.00) 		0.166
(1.00) 		0.368
(1.00) 		0.00537
(1.00) 		0.229
(1.00)
8q loss 0 (0%) 563 0.764
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.155
(1.00) 		1
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.948
(1.00) 		0.101
(1.00) 		0.845
(1.00) 		0.398
(1.00)
9p loss 0 (0%) 536 0.0238
(1.00) 		0.271
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.433
(1.00) 		0.166
(1.00) 		0.396
(1.00) 		0.932
(1.00)
9q loss 0 (0%) 538 0.317
(1.00) 		0.00981
(1.00) 		1
(1.00) 		0.395
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.82
(1.00) 		0.166
(1.00) 		0.326
(1.00) 		0.879
(1.00)
10p loss 0 (0%) 535 0.568
(1.00) 		0.0105
(1.00) 		0.043
(1.00) 		0.417
(1.00) 		0.011
(1.00) 		0.48
(1.00) 		0.591
(1.00) 		0.854
(1.00) 		0.65
(1.00) 		0.2
(1.00) 		0.713
(1.00)
10q loss 0 (0%) 529 0.347
(1.00) 		0.0151
(1.00) 		0.00307
(1.00) 		1
(1.00) 		0.00262
(1.00) 		0.53
(1.00) 		0.826
(1.00) 		0.97
(1.00) 		0.642
(1.00) 		0.34
(1.00) 		0.852
(1.00)
11p loss 0 (0%) 535 0.432
(1.00) 		0.969
(1.00) 		0.00589
(1.00) 		0.627
(1.00) 		0.00129
(1.00) 		0.48
(1.00) 		0.962
(1.00) 		0.397
(1.00) 		0.331
(1.00) 		0.134
(1.00) 		0.545
(1.00)
11q loss 0 (0%) 524 0.791
(1.00) 		0.821
(1.00) 		0.00745
(1.00) 		0.378
(1.00) 		0.00237
(1.00) 		0.0377
(1.00) 		0.98
(1.00) 		0.316
(1.00) 		0.411
(1.00) 		0.677
(1.00) 		0.943
(1.00)
12p loss 0 (0%) 542 0.0732
(1.00) 		0.986
(1.00) 		0.316
(1.00) 		0.0476
(1.00) 		0.12
(1.00) 		0.415
(1.00) 		0.509
(1.00) 		0.0808
(1.00) 		0.816
(1.00) 		0.673
(1.00) 		0.718
(1.00)
12q loss 0 (0%) 547 0.13
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.224
(1.00) 		0.592
(1.00) 		0.505
(1.00) 		0.678
(1.00)
13q loss 0 (0%) 563 0.804
(1.00) 		0.864
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.46
(1.00) 		0.534
(1.00) 		0.148
(1.00) 		0.883
(1.00)
15q loss 0 (0%) 419 0.545
(1.00) 		0.64
(1.00) 		0.0113
(1.00) 		0.851
(1.00) 		0.000506
(0.422) 		0.263
(1.00) 		0.36
(1.00) 		0.313
(1.00) 		0.416
(1.00) 		0.0579
(1.00) 		0.192
(1.00)
16p loss 0 (0%) 560 0.933
(1.00) 		0.548
(1.00) 		0.379
(1.00) 		0.122
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.888
(1.00) 		0.66
(1.00) 		0.207
(1.00) 		0.848
(1.00)
16q loss 0 (0%) 558 0.455
(1.00) 		0.852
(1.00) 		0.00999
(1.00) 		0.627
(1.00) 		0.0228
(1.00) 		0.238
(1.00) 		0.972
(1.00) 		0.844
(1.00) 		0.696
(1.00) 		0.418
(1.00) 		0.831
(1.00)
17q loss 0 (0%) 530 0.558
(1.00) 		0.854
(1.00) 		0.39
(1.00) 		0.877
(1.00) 		0.278
(1.00) 		0.152
(1.00) 		0.921
(1.00) 		0.0922
(1.00) 		0.328
(1.00) 		0.745
(1.00) 		0.576
(1.00)
19p loss 0 (0%) 555 0.761
(1.00) 		0.538
(1.00) 		0.454
(1.00) 		0.11
(1.00) 		0.519
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.13
(1.00) 		0.112
(1.00) 		0.448
(1.00) 		0.446
(1.00)
19q loss 0 (0%) 557 0.955
(1.00) 		0.166
(1.00) 		0.598
(1.00) 		0.234
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.95
(1.00) 		0.0829
(1.00) 		0.789
(1.00) 		0.235
(1.00)
20p loss 0 (0%) 528 0.386
(1.00) 		0.814
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.326
(1.00) 		1
(1.00) 		0.73
(1.00) 		0.961
(1.00) 		0.505
(1.00) 		0.632
(1.00) 		0.703
(1.00)
21q loss 0 (0%) 461 0.341
(1.00) 		0.956
(1.00) 		0.00967
(1.00) 		0.402
(1.00) 		0.00983
(1.00) 		0.695
(1.00) 		0.844
(1.00) 		0.195
(1.00) 		0.834
(1.00) 		0.0153
(1.00) 		0.355
(1.00)
Xq loss 0 (0%) 564 0.383
(1.00) 		0.251
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.399
(1.00) 		0.681
(1.00) 		0.244
(1.00) 		0.381
(1.00) 		0.988
(1.00)
'1p gain' versus 'LYMPH.NODE.METASTASIS'

P value = 2.08e-06 (Chi-square test), Q value = 0.0018

Table S1.  Gene #1: '1p gain' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
1P GAIN CNV 7 1 0 0 0 2 1 3 1
1P GAIN WILD-TYPE 320 103 17 17 3 79 5 13 1

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'3q gain' versus 'Time to Death'

P value = 0.000266 (logrank test), Q value = 0.22

Table S2.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 451 60 0.1 - 135.5 (7.0)
3Q GAIN CNV 39 10 0.2 - 60.0 (5.7)
3Q GAIN WILD-TYPE 412 50 0.1 - 135.5 (7.6)

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'DISTANT.METASTASIS'

P value = 0.000274 (Chi-square test), Q value = 0.23

Table S3.  Gene #6: '3q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 436 71 9 1 49
3Q GAIN CNV 32 8 3 1 8
3Q GAIN WILD-TYPE 404 63 6 0 41

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

'7p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.015

Table S4.  Gene #13: '7p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
7P GAIN CNV 184 15 87 2
7P GAIN WILD-TYPE 173 39 56 11

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'7q gain' versus 'HISTOLOGICAL.TYPE'

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

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
7Q GAIN CNV 161 14 77 1
7Q GAIN WILD-TYPE 196 40 66 12

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

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.12e-09 (Fisher's exact test), Q value = 3.5e-06

Table S6.  Gene #25: '13q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
13Q GAIN CNV 199 12 96 2
13Q GAIN WILD-TYPE 158 42 47 11

Figure S6.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'18p gain' versus 'DISTANT.METASTASIS'

P value = 1.38e-05 (Chi-square test), Q value = 0.012

Table S7.  Gene #32: '18p gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 436 71 9 1 49
18P GAIN CNV 15 2 0 1 2
18P GAIN WILD-TYPE 421 69 9 0 47

Figure S7.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

'18p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.93e-06 (Chi-square test), Q value = 0.0076

Table S8.  Gene #32: '18p gain' versus Clinical Feature #12: '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 98 1 41 154 10 3 27 22 70 47 57 25 1
18P GAIN CNV 3 0 3 3 0 0 2 0 0 6 3 0 1
18P GAIN WILD-TYPE 95 1 38 151 10 3 25 22 70 41 54 25 0

Figure S8.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.85e-09 (Fisher's exact test), Q value = 7.5e-06

Table S9.  Gene #36: '20p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
20P GAIN CNV 177 11 93 2
20P GAIN WILD-TYPE 180 43 50 11

Figure S9.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

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

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

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

Figure S10.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.97e-15 (Fisher's exact test), Q value = 1.7e-12

Table S11.  Gene #37: '20q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
20Q GAIN CNV 252 16 125 4
20Q GAIN WILD-TYPE 105 38 18 9

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

'Xq gain' versus 'DISTANT.METASTASIS'

P value = 1.61e-07 (Chi-square test), Q value = 0.00014

Table S12.  Gene #40: 'Xq gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 436 71 9 1 49
XQ GAIN CNV 10 4 0 1 1
XQ GAIN WILD-TYPE 426 67 9 0 48

Figure S12.  Get High-res Image Gene #40: 'Xq gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

'Xq gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 7e-05 (Chi-square test), Q value = 0.059

Table S13.  Gene #40: 'Xq gain' versus Clinical Feature #12: '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 98 1 41 154 10 3 27 22 70 47 57 25 1
XQ GAIN CNV 3 0 1 4 0 0 2 0 0 1 3 2 1
XQ GAIN WILD-TYPE 95 1 40 150 10 3 25 22 70 46 54 23 0

Figure S13.  Get High-res Image Gene #40: 'Xq gain' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

'2q loss' versus 'Time to Death'

P value = 8.15e-07 (logrank test), Q value = 0.00069

Table S14.  Gene #44: '2q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 451 60 0.1 - 135.5 (7.0)
2Q LOSS CNV 5 1 0.3 - 2.0 (1.0)
2Q LOSS WILD-TYPE 446 59 0.1 - 135.5 (7.2)

Figure S14.  Get High-res Image Gene #44: '2q loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'Time to Death'

P value = 0.00013 (logrank test), Q value = 0.11

Table S15.  Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 451 60 0.1 - 135.5 (7.0)
3P LOSS CNV 22 5 0.3 - 14.5 (5.0)
3P LOSS WILD-TYPE 429 55 0.1 - 135.5 (7.1)

Figure S15.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

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

P value = 1.54e-24 (t-test), Q value = 1.3e-21

Table S16.  Gene #53: '7q loss' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 541 2.2 (4.7)
7Q LOSS CNV 3 0.0 (0.0)
7Q LOSS WILD-TYPE 538 2.2 (4.8)

Figure S16.  Get High-res Image Gene #53: '7q loss' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.02

Table S17.  Gene #65: '14q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
14Q LOSS CNV 90 3 48 0
14Q LOSS WILD-TYPE 267 51 95 13

Figure S17.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.66e-07 (Fisher's exact test), Q value = 0.00048

Table S18.  Gene #69: '17p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
17P LOSS CNV 156 7 79 6
17P LOSS WILD-TYPE 201 47 64 7

Figure S18.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

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

Table S19.  Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

Figure S19.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.2e-14 (Fisher's exact test), Q value = 1e-11

Table S20.  Gene #71: '18p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
18P LOSS CNV 201 7 107 5
18P LOSS WILD-TYPE 156 47 36 8

Figure S20.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

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

Table S21.  Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

Figure S21.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.62e-14 (Fisher's exact test), Q value = 3.1e-11

Table S22.  Gene #72: '18q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
18Q LOSS CNV 214 10 114 9
18Q LOSS WILD-TYPE 143 44 29 4

Figure S22.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000207 (Fisher's exact test), Q value = 0.17

Table S23.  Gene #77: '22q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
22Q LOSS CNV 80 1 36 4
22Q LOSS WILD-TYPE 277 53 107 9

Figure S23.  Get High-res Image Gene #77: '22q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

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

  • Number of patients = 575

  • Number of significantly arm-level cnvs = 78

  • Number of selected clinical features = 12

  • 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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