Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1QF8R8S
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/C1QF8R8S
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 11 clinical features across 424 patients, 12 significant findings detected with Q value < 0.25.

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

  • 12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

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

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

  • 4p loss cnv correlated to 'PATHOLOGY.M.STAGE'.

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

  • 17p loss cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

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

  • 18q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

  • 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 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-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
17p loss 221 (52%) 203 0.111
(1.00) 		0.106
(1.00) 		0.000339
(0.289) 		0.784
(1.00) 		0.000241
(0.207) 		0.0099
(1.00) 		0.0799
(1.00) 		8.94e-06
(0.00775) 		0.25
(1.00) 		0.0531
(1.00) 		0.00051
(0.434)
18q loss 251 (59%) 173 0.681
(1.00) 		0.0614
(1.00) 		0.000188
(0.162) 		0.637
(1.00) 		0.000392
(0.335) 		0.00369
(1.00) 		0.553
(1.00) 		1.98e-09
(1.72e-06) 		0.274
(1.00) 		0.149
(1.00) 		0.0713
(1.00)
7p gain 232 (55%) 192 0.693
(1.00) 		0.233
(1.00) 		0.000598
(0.508) 		0.325
(1.00) 		0.000258
(0.221) 		0.0257
(1.00) 		1
(1.00) 		0.0204
(1.00) 		0.255
(1.00) 		0.206
(1.00) 		0.0554
(1.00)
12q gain 80 (19%) 344 0.931
(1.00) 		0.0409
(1.00) 		0.0199
(1.00) 		0.474
(1.00) 		0.0435
(1.00) 		0.0132
(1.00) 		0.901
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.000231
(0.198)
13q gain 244 (58%) 180 0.454
(1.00) 		0.39
(1.00) 		0.00678
(1.00) 		0.98
(1.00) 		0.00545
(1.00) 		0.00471
(1.00) 		0.376
(1.00) 		1.56e-06
(0.00135) 		0.265
(1.00) 		0.0418
(1.00) 		0.685
(1.00)
20q gain 300 (71%) 124 0.76
(1.00) 		0.262
(1.00) 		0.00211
(1.00) 		0.273
(1.00) 		0.0481
(1.00) 		0.00672
(1.00) 		0.394
(1.00) 		9.98e-06
(0.00863) 		0.559
(1.00) 		0.132
(1.00) 		0.0864
(1.00)
4p loss 126 (30%) 298 0.0561
(1.00) 		0.987
(1.00) 		0.0013
(1.00) 		0.434
(1.00) 		0.00157
(1.00) 		0.000182
(0.157) 		0.832
(1.00) 		0.00722
(1.00) 		0.0258
(1.00) 		0.0315
(1.00) 		0.0122
(1.00)
14q loss 128 (30%) 296 0.201
(1.00) 		0.487
(1.00) 		0.178
(1.00) 		0.352
(1.00) 		0.123
(1.00) 		0.0522
(1.00) 		1
(1.00) 		2.69e-05
(0.0233) 		0.557
(1.00) 		0.609
(1.00) 		0.886
(1.00)
18p loss 236 (56%) 188 0.465
(1.00) 		0.0969
(1.00) 		0.000813
(0.686) 		0.853
(1.00) 		0.00392
(1.00) 		0.00124
(1.00) 		0.557
(1.00) 		3.43e-10
(2.98e-07) 		0.258
(1.00) 		0.0315
(1.00) 		0.027
(1.00)
22q loss 137 (32%) 287 0.235
(1.00) 		0.888
(1.00) 		0.00191
(1.00) 		0.544
(1.00) 		0.000206
(0.178) 		0.00861
(1.00) 		1
(1.00) 		0.00187
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.0137
(1.00)
1p gain 30 (7%) 394 0.389
(1.00) 		0.589
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.532
(1.00) 		0.173
(1.00) 		0.85
(1.00) 		0.782
(1.00) 		0.198
(1.00) 		0.111
(1.00) 		0.287
(1.00)
1q gain 75 (18%) 349 0.971
(1.00) 		0.856
(1.00) 		0.123
(1.00) 		0.508
(1.00) 		0.142
(1.00) 		0.0053
(1.00) 		0.205
(1.00) 		0.348
(1.00) 		0.443
(1.00) 		0.224
(1.00) 		0.136
(1.00)
2p gain 73 (17%) 351 0.399
(1.00) 		0.648
(1.00) 		0.334
(1.00) 		0.512
(1.00) 		0.333
(1.00) 		0.426
(1.00) 		0.608
(1.00) 		0.0353
(1.00) 		0.434
(1.00) 		0.055
(1.00) 		0.671
(1.00)
2q gain 69 (16%) 355 0.205
(1.00) 		0.234
(1.00) 		0.173
(1.00) 		0.4
(1.00) 		0.122
(1.00) 		0.237
(1.00) 		0.793
(1.00) 		0.0517
(1.00) 		0.414
(1.00) 		0.112
(1.00) 		0.494
(1.00)
3p gain 42 (10%) 382 0.327
(1.00) 		0.121
(1.00) 		0.000614
(0.521) 		0.803
(1.00) 		0.133
(1.00) 		0.000316
(0.271) 		1
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.173
(1.00)
3q gain 61 (14%) 363 0.161
(1.00) 		0.23
(1.00) 		0.0171
(1.00) 		0.595
(1.00) 		0.0591
(1.00) 		0.00239
(1.00) 		0.68
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.198
(1.00)
4p gain 9 (2%) 415 0.653
(1.00) 		0.76
(1.00) 		0.675
(1.00) 		0.724
(1.00) 		0.0385
(1.00) 		0.144
(1.00) 		0.512
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.352
(1.00)
4q gain 15 (4%) 409 0.97
(1.00) 		0.48
(1.00) 		0.503
(1.00) 		0.894
(1.00) 		0.05
(1.00) 		0.43
(1.00) 		0.793
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.287
(1.00)
5p gain 62 (15%) 362 0.903
(1.00) 		0.179
(1.00) 		0.277
(1.00) 		0.873
(1.00) 		0.107
(1.00) 		0.845
(1.00) 		0.171
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.308
(1.00)
5q gain 38 (9%) 386 0.55
(1.00) 		0.906
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.958
(1.00) 		0.734
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.987
(1.00)
6p gain 78 (18%) 346 0.233
(1.00) 		0.919
(1.00) 		0.255
(1.00) 		0.846
(1.00) 		0.0281
(1.00) 		0.766
(1.00) 		0.451
(1.00) 		0.188
(1.00) 		0.00603
(1.00) 		0.715
(1.00) 		0.0613
(1.00)
6q gain 71 (17%) 353 0.299
(1.00) 		0.684
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.0456
(1.00) 		0.6
(1.00) 		0.795
(1.00) 		0.123
(1.00) 		0.00453
(1.00) 		0.88
(1.00) 		0.106
(1.00)
7q gain 210 (50%) 214 0.591
(1.00) 		0.151
(1.00) 		0.0258
(1.00) 		0.167
(1.00) 		0.0161
(1.00) 		0.0176
(1.00) 		1
(1.00) 		0.0428
(1.00) 		0.621
(1.00) 		0.346
(1.00) 		0.168
(1.00)
8p gain 121 (29%) 303 0.523
(1.00) 		0.271
(1.00) 		0.678
(1.00) 		0.79
(1.00) 		0.435
(1.00) 		0.978
(1.00) 		0.748
(1.00) 		0.151
(1.00) 		0.197
(1.00) 		0.582
(1.00) 		0.479
(1.00)
8q gain 210 (50%) 214 0.815
(1.00) 		0.101
(1.00) 		0.772
(1.00) 		0.207
(1.00) 		0.842
(1.00) 		0.513
(1.00) 		0.698
(1.00) 		0.0204
(1.00) 		0.121
(1.00) 		0.528
(1.00) 		0.692
(1.00)
9p gain 74 (17%) 350 0.101
(1.00) 		0.451
(1.00) 		0.0302
(1.00) 		0.526
(1.00) 		0.071
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0557
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.146
(1.00)
9q gain 65 (15%) 359 0.171
(1.00) 		0.593
(1.00) 		0.164
(1.00) 		0.426
(1.00) 		0.251
(1.00) 		0.785
(1.00) 		0.787
(1.00) 		0.0742
(1.00) 		1
(1.00) 		0.835
(1.00) 		0.21
(1.00)
10p gain 32 (8%) 392 0.139
(1.00) 		0.595
(1.00) 		0.796
(1.00) 		0.259
(1.00) 		0.042
(1.00) 		0.266
(1.00) 		0.854
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.0983
(1.00)
10q gain 18 (4%) 406 0.617
(1.00) 		0.0511
(1.00) 		0.748
(1.00) 		0.878
(1.00) 		0.049
(1.00) 		0.458
(1.00) 		0.631
(1.00) 		0.717
(1.00) 		1
(1.00) 		0.556
(1.00) 		0.109
(1.00)
11p gain 49 (12%) 375 0.864
(1.00) 		0.0136
(1.00) 		0.0441
(1.00) 		0.139
(1.00) 		0.0368
(1.00) 		0.033
(1.00) 		0.762
(1.00) 		0.00113
(0.951) 		0.0364
(1.00) 		0.231
(1.00) 		0.213
(1.00)
11q gain 47 (11%) 377 0.78
(1.00) 		0.00113
(0.95) 		0.0509
(1.00) 		0.437
(1.00) 		0.0232
(1.00) 		0.0874
(1.00) 		0.759
(1.00) 		0.00193
(1.00) 		0.0336
(1.00) 		0.402
(1.00) 		0.279
(1.00)
12p gain 87 (21%) 337 0.438
(1.00) 		0.0924
(1.00) 		0.138
(1.00) 		0.367
(1.00) 		0.252
(1.00) 		0.0799
(1.00) 		1
(1.00) 		0.858
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.0682
(1.00)
14q gain 33 (8%) 391 0.599
(1.00) 		0.936
(1.00) 		0.926
(1.00) 		0.904
(1.00) 		0.516
(1.00) 		0.00896
(1.00) 		0.468
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.37
(1.00)
15q gain 11 (3%) 413 0.369
(1.00) 		0.336
(1.00) 		0.741
(1.00) 		0.387
(1.00) 		0.479
(1.00) 		0.122
(1.00) 		0.123
(1.00) 		1
(1.00) 		1
(1.00) 		0.0473
(1.00) 		0.517
(1.00)
16p gain 102 (24%) 322 0.694
(1.00) 		0.132
(1.00) 		0.0121
(1.00) 		0.935
(1.00) 		0.00549
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.00393
(1.00) 		0.563
(1.00) 		0.94
(1.00) 		0.153
(1.00)
16q gain 99 (23%) 325 0.579
(1.00) 		0.0793
(1.00) 		0.00288
(1.00) 		0.968
(1.00) 		0.00459
(1.00) 		0.465
(1.00) 		0.73
(1.00) 		0.00599
(1.00) 		0.551
(1.00) 		0.754
(1.00) 		0.221
(1.00)
17p gain 24 (6%) 400 0.126
(1.00) 		0.985
(1.00) 		0.761
(1.00) 		0.716
(1.00) 		0.299
(1.00) 		0.0711
(1.00) 		0.834
(1.00) 		1
(1.00) 		1
(1.00) 		0.892
(1.00) 		0.656
(1.00)
17q gain 74 (17%) 350 0.359
(1.00) 		0.346
(1.00) 		0.169
(1.00) 		0.332
(1.00) 		0.149
(1.00) 		0.00382
(1.00) 		0.798
(1.00) 		0.25
(1.00) 		0.438
(1.00) 		0.303
(1.00) 		0.425
(1.00)
18p gain 22 (5%) 402 0.995
(1.00) 		0.362
(1.00) 		0.00898
(1.00) 		0.879
(1.00) 		0.0778
(1.00) 		0.000503
(0.429) 		0.383
(1.00) 		0.0155
(1.00) 		1
(1.00) 		0.668
(1.00) 		0.137
(1.00)
18q gain 14 (3%) 410 0.417
(1.00) 		0.0298
(1.00) 		0.771
(1.00) 		0.575
(1.00) 		0.24
(1.00) 		0.957
(1.00) 		0.431
(1.00) 		0.0249
(1.00) 		1
(1.00) 		1
(1.00) 		0.813
(1.00)
19p gain 66 (16%) 358 0.268
(1.00) 		0.642
(1.00) 		0.591
(1.00) 		0.496
(1.00) 		0.0491
(1.00) 		0.0307
(1.00) 		0.0437
(1.00) 		0.169
(1.00) 		0.399
(1.00) 		0.276
(1.00) 		0.217
(1.00)
19q gain 75 (18%) 349 0.31
(1.00) 		0.813
(1.00) 		0.851
(1.00) 		0.887
(1.00) 		0.121
(1.00) 		0.0151
(1.00) 		0.128
(1.00) 		0.852
(1.00) 		0.443
(1.00) 		0.47
(1.00) 		0.847
(1.00)
20p gain 228 (54%) 196 0.34
(1.00) 		0.417
(1.00) 		0.000625
(0.529) 		0.905
(1.00) 		0.194
(1.00) 		0.00145
(1.00) 		0.118
(1.00) 		0.000424
(0.362) 		0.253
(1.00) 		0.0768
(1.00) 		0.275
(1.00)
21q gain 20 (5%) 404 0.125
(1.00) 		0.000953
(0.802) 		0.57
(1.00) 		0.121
(1.00) 		0.406
(1.00) 		0.69
(1.00) 		0.821
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.807
(1.00)
22q gain 10 (2%) 414 0.611
(1.00) 		0.989
(1.00) 		0.617
(1.00) 		0.32
(1.00) 		0.822
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.443
(1.00)
xq gain 68 (16%) 356 0.972
(1.00) 		0.583
(1.00) 		0.148
(1.00) 		0.0327
(1.00) 		0.456
(1.00) 		0.148
(1.00) 		0.597
(1.00) 		0.327
(1.00) 		0.409
(1.00) 		0.913
(1.00) 		0.995
(1.00)
1p loss 91 (21%) 333 0.0351
(1.00) 		0.929
(1.00) 		0.0841
(1.00) 		0.743
(1.00) 		0.00294
(1.00) 		0.0123
(1.00) 		0.636
(1.00) 		0.219
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.0145
(1.00)
1q loss 52 (12%) 372 0.161
(1.00) 		0.587
(1.00) 		0.298
(1.00) 		0.734
(1.00) 		0.0757
(1.00) 		0.163
(1.00) 		0.375
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.163
(1.00)
2p loss 6 (1%) 418 0.00089
(0.75) 		0.761
(1.00) 		0.708
(1.00) 		0.839
(1.00) 		0.85
(1.00) 		0.755
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.806
(1.00)
2q loss 7 (2%) 417 0.00089
(0.75) 		0.752
(1.00) 		0.759
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.128
(1.00) 		0.602
(1.00) 		1
(1.00) 		1
(1.00) 		0.536
(1.00)
3p loss 50 (12%) 374 0.0962
(1.00) 		0.657
(1.00) 		0.49
(1.00) 		0.166
(1.00) 		0.14
(1.00) 		0.0464
(1.00) 		0.653
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.846
(1.00) 		0.682
(1.00)
3q loss 31 (7%) 393 0.149
(1.00) 		0.315
(1.00) 		0.84
(1.00) 		0.488
(1.00) 		0.933
(1.00) 		0.203
(1.00) 		0.709
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.933
(1.00) 		0.258
(1.00)
4q loss 114 (27%) 310 0.0281
(1.00) 		0.894
(1.00) 		0.016
(1.00) 		0.593
(1.00) 		0.00191
(1.00) 		0.0356
(1.00) 		0.443
(1.00) 		0.0722
(1.00) 		0.0191
(1.00) 		0.348
(1.00) 		0.0266
(1.00)
5p loss 54 (13%) 370 0.908
(1.00) 		0.288
(1.00) 		0.00949
(1.00) 		0.312
(1.00) 		0.00623
(1.00) 		0.0892
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.0439
(1.00) 		0.529
(1.00) 		0.0612
(1.00)
5q loss 74 (17%) 350 0.244
(1.00) 		0.26
(1.00) 		0.0465
(1.00) 		0.828
(1.00) 		0.000587
(0.499) 		0.0639
(1.00) 		0.525
(1.00) 		0.446
(1.00) 		0.0801
(1.00) 		0.669
(1.00) 		0.00558
(1.00)
6p loss 33 (8%) 391 0.323
(1.00) 		0.368
(1.00) 		0.962
(1.00) 		0.103
(1.00) 		0.744
(1.00) 		0.227
(1.00) 		0.468
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.779
(1.00)
6q loss 44 (10%) 380 0.171
(1.00) 		0.946
(1.00) 		0.406
(1.00) 		0.321
(1.00) 		0.167
(1.00) 		0.00771
(1.00) 		0.636
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.171
(1.00) 		0.0917
(1.00)
7q loss 3 (1%) 421 0.571
(1.00) 		0.13
(1.00) 		0.416
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.919
(1.00) 		0.601
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0114
(1.00)
8p loss 133 (31%) 291 0.802
(1.00) 		0.771
(1.00) 		0.0131
(1.00) 		0.151
(1.00) 		0.000334
(0.286) 		0.00677
(1.00) 		0.21
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.0737
(1.00) 		0.00569
(1.00)
8q loss 23 (5%) 401 0.676
(1.00) 		0.898
(1.00) 		0.104
(1.00) 		0.0504
(1.00) 		0.0478
(1.00) 		0.0307
(1.00) 		0.523
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.88
(1.00) 		0.194
(1.00)
9p loss 49 (12%) 375 0.13
(1.00) 		0.207
(1.00) 		0.982
(1.00) 		0.2
(1.00) 		0.49
(1.00) 		0.651
(1.00) 		0.447
(1.00) 		0.0672
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.53
(1.00)
9q loss 49 (12%) 375 0.0671
(1.00) 		0.0302
(1.00) 		0.824
(1.00) 		0.252
(1.00) 		0.198
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.0657
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.62
(1.00)
10p loss 64 (15%) 360 0.669
(1.00) 		0.227
(1.00) 		0.0379
(1.00) 		0.896
(1.00) 		0.0848
(1.00) 		0.109
(1.00) 		0.787
(1.00) 		0.227
(1.00) 		0.0608
(1.00) 		0.478
(1.00) 		0.393
(1.00)
10q loss 68 (16%) 356 0.508
(1.00) 		0.149
(1.00) 		0.15
(1.00) 		0.927
(1.00) 		0.225
(1.00) 		0.284
(1.00) 		0.791
(1.00) 		0.168
(1.00) 		0.0683
(1.00) 		0.231
(1.00) 		0.651
(1.00)
11p loss 49 (12%) 375 0.295
(1.00) 		0.904
(1.00) 		0.815
(1.00) 		0.892
(1.00) 		0.107
(1.00) 		0.0518
(1.00) 		0.649
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.458
(1.00) 		0.146
(1.00)
11q loss 59 (14%) 365 0.34
(1.00) 		0.737
(1.00) 		0.448
(1.00) 		0.222
(1.00) 		0.074
(1.00) 		0.0397
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.302
(1.00)
12p loss 44 (10%) 380 0.291
(1.00) 		0.464
(1.00) 		0.394
(1.00) 		0.559
(1.00) 		0.0782
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.0184
(1.00) 		0.281
(1.00) 		0.949
(1.00) 		0.396
(1.00)
12q loss 47 (11%) 377 0.482
(1.00) 		0.44
(1.00) 		0.196
(1.00) 		0.576
(1.00) 		0.0471
(1.00) 		0.347
(1.00) 		0.539
(1.00) 		0.0652
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.312
(1.00)
13q loss 11 (3%) 413 0.816
(1.00) 		0.893
(1.00) 		0.623
(1.00) 		0.466
(1.00) 		0.0206
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.764
(1.00) 		0.144
(1.00)
15q loss 144 (34%) 280 0.48
(1.00) 		0.864
(1.00) 		0.054
(1.00) 		0.525
(1.00) 		0.0342
(1.00) 		0.0129
(1.00) 		1
(1.00) 		0.00908
(1.00) 		0.0386
(1.00) 		0.398
(1.00) 		0.375
(1.00)
16p loss 27 (6%) 397 0.0311
(1.00) 		0.34
(1.00) 		0.536
(1.00) 		0.692
(1.00) 		0.453
(1.00) 		0.661
(1.00) 		0.426
(1.00) 		0.375
(1.00) 		1
(1.00) 		0.19
(1.00) 		0.94
(1.00)
16q loss 25 (6%) 399 0.048
(1.00) 		0.16
(1.00) 		0.589
(1.00) 		0.898
(1.00) 		0.426
(1.00) 		0.641
(1.00) 		0.681
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.675
(1.00)
17q loss 61 (14%) 363 0.963
(1.00) 		0.447
(1.00) 		0.0245
(1.00) 		0.341
(1.00) 		0.00851
(1.00) 		0.0928
(1.00) 		0.406
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.0429
(1.00)
19p loss 38 (9%) 386 0.501
(1.00) 		0.351
(1.00) 		0.00275
(1.00) 		1
(1.00) 		0.00141
(1.00) 		0.000669
(0.566) 		0.734
(1.00) 		0.607
(1.00) 		0.246
(1.00) 		0.24
(1.00) 		0.00281
(1.00)
19q loss 32 (8%) 392 0.521
(1.00) 		0.778
(1.00) 		0.00334
(1.00) 		0.965
(1.00) 		0.00428
(1.00) 		0.000714
(0.603) 		0.467
(1.00) 		0.58
(1.00) 		0.21
(1.00) 		0.432
(1.00) 		0.00869
(1.00)
20p loss 43 (10%) 381 0.818
(1.00) 		0.88
(1.00) 		0.267
(1.00) 		0.804
(1.00) 		0.609
(1.00) 		0.897
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.207
(1.00)
20q loss 6 (1%) 418 0.107
(1.00) 		0.0247
(1.00) 		0.87
(1.00) 		0.5
(1.00) 		0.312
(1.00) 		0.882
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.905
(1.00)
21q loss 116 (27%) 308 0.75
(1.00) 		0.923
(1.00) 		0.428
(1.00) 		0.508
(1.00) 		0.0167
(1.00) 		0.128
(1.00) 		0.913
(1.00) 		0.0228
(1.00) 		1
(1.00) 		0.78
(1.00) 		0.0131
(1.00)
xq loss 46 (11%) 378 0.824
(1.00) 		0.373
(1.00) 		0.296
(1.00) 		0.604
(1.00) 		0.0515
(1.00) 		0.125
(1.00) 		0.532
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.189
(1.00)
'7p gain' versus 'PATHOLOGY.N.STAGE'

P value = 0.000258 (Fisher's exact test), Q value = 0.22

Table S1.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
7P GAIN MUTATED 115 68 48
7P GAIN WILD-TYPE 133 33 26

Figure S1.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'12q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000231 (t-test), Q value = 0.2

Table S2.  Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 400 2.0 (4.5)
12Q GAIN MUTATED 76 1.0 (1.9)
12Q GAIN WILD-TYPE 324 2.3 (4.8)

Figure S2.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.56e-06 (Fisher's exact test), Q value = 0.0014

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
13Q GAIN MUTATED 228 15
13Q GAIN WILD-TYPE 139 40

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

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 9.98e-06 (Fisher's exact test), Q value = 0.0086

Table S4.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
20Q GAIN MUTATED 274 24
20Q GAIN WILD-TYPE 93 31

Figure S4.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000182 (Chi-square test), Q value = 0.16

Table S5.  Gene #47: '4p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 318 50 7 1 41
4P LOSS MUTATED 77 27 3 1 14
4P LOSS WILD-TYPE 241 23 4 0 27

Figure S5.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.023

Table S6.  Gene #65: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
14Q LOSS MUTATED 122 4
14Q LOSS WILD-TYPE 245 51

Figure S6.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000241 (Fisher's exact test), Q value = 0.21

Table S7.  Gene #69: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
17P LOSS MUTATED 109 61 50
17P LOSS WILD-TYPE 139 40 24

Figure S7.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.94e-06 (Fisher's exact test), Q value = 0.0077

Table S8.  Gene #69: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
17P LOSS MUTATED 206 13
17P LOSS WILD-TYPE 161 42

Figure S8.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.43e-10 (Fisher's exact test), Q value = 3e-07

Table S9.  Gene #71: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
18P LOSS MUTATED 225 9
18P LOSS WILD-TYPE 142 46

Figure S9.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000188 (Chi-square test), Q value = 0.16

Table S10.  Gene #72: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 71 1 33 119 8 1 22 13 52 36 42 16 1
18Q LOSS MUTATED 34 0 16 62 2 1 11 12 33 27 34 13 0
18Q LOSS WILD-TYPE 37 1 17 57 6 0 11 1 19 9 8 3 1

Figure S10.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.98e-09 (Fisher's exact test), Q value = 1.7e-06

Table S11.  Gene #72: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 367 55
18Q LOSS MUTATED 238 12
18Q LOSS WILD-TYPE 129 43

Figure S11.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

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

P value = 0.000206 (Fisher's exact test), Q value = 0.18

Table S12.  Gene #78: '22q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 248 101 74
22Q LOSS MUTATED 61 42 34
22Q LOSS WILD-TYPE 187 59 40

Figure S12.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = COAD-TP.merged_data.txt

  • Number of patients = 424

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 11

  • 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

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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