Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1B8565J
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/C1B8565J
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 11 clinical features across 413 patients, 20 significant findings detected with Q value < 0.25.

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

  • 3p gain cnv correlated to 'DISTANT.METASTASIS'.

  • 3q gain cnv correlated to 'Time to Death'.

  • 11p gain cnv correlated to 'LYMPH.NODE.METASTASIS'.

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

  • 17p gain cnv correlated to 'DISTANT.METASTASIS' and 'LYMPH.NODE.METASTASIS'.

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

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

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

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

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

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

  • 6q loss cnv correlated to 'DISTANT.METASTASIS'.

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

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

  • 18q loss cnv correlated to '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 11 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 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 Chi-square test Chi-square test Fisher's exact test t-test t-test Chi-square test
17p gain 0 (0%) 404 0.209
(1.00) 		0.863
(1.00) 		0.739
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.000123
(0.0914) 		3.74e-05
(0.028) 		1
(1.00) 		0.324
(1.00) 		0.00752
(1.00)
18p gain 0 (0%) 398 0.32
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.0347
(1.00) 		1
(1.00) 		5.91e-06
(0.00444) 		0.0497
(1.00) 		1
(1.00) 		0.0804
(1.00) 		0.00021
(0.155)
Xq gain 0 (0%) 401 0.0126
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.663
(1.00) 		1
(1.00) 		1.43e-07
(0.000108) 		0.00922
(1.00) 		0.621
(1.00) 		0.0911
(1.00) 		0.000207
(0.154)
1p gain 0 (0%) 402 0.443
(1.00) 		0.664
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.775
(1.00) 		2.42e-08
(1.83e-05) 		0.76
(1.00) 		0.573
(1.00) 		0.725
(1.00)
3p gain 0 (0%) 393 0.00107
(0.786) 		0.152
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		0.000104
(0.0773) 		0.248
(1.00) 		0.513
(1.00) 		0.291
(1.00) 		0.00329
(1.00)
3q gain 0 (0%) 383 4e-05
(0.03) 		0.588
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00) 		0.000351
(0.26) 		0.00246
(1.00) 		0.839
(1.00) 		0.215
(1.00) 		0.00551
(1.00)
11p gain 0 (0%) 395 0.401
(1.00) 		0.198
(1.00) 		0.631
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.929
(1.00) 		0.000122
(0.0912) 		0.48
(1.00) 		0.223
(1.00) 		0.33
(1.00)
13q gain 0 (0%) 202 0.742
(1.00) 		0.942
(1.00) 		0.325
(1.00) 		4.23e-06
(0.00318) 		0.249
(1.00) 		0.13
(1.00) 		0.0767
(1.00) 		0.0374
(1.00) 		0.818
(1.00) 		0.0521
(1.00)
20p gain 0 (0%) 225 0.273
(1.00) 		0.283
(1.00) 		0.0745
(1.00) 		6.17e-05
(0.0461) 		0.594
(1.00) 		0.0401
(1.00) 		0.842
(1.00) 		0.0301
(1.00) 		0.369
(1.00) 		0.00357
(1.00)
20q gain 0 (0%) 146 0.617
(1.00) 		0.625
(1.00) 		0.217
(1.00) 		2.71e-08
(2.05e-05) 		1
(1.00) 		0.174
(1.00) 		0.405
(1.00) 		0.201
(1.00) 		0.306
(1.00) 		0.00973
(1.00)
2p loss 0 (0%) 409 2.2e-07
(0.000166) 		0.693
(1.00) 		0.627
(1.00) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.998
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.857
(1.00)
2q loss 0 (0%) 407 2.52e-06
(0.0019) 		0.81
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.988
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.666
(1.00)
6q loss 0 (0%) 392 0.0106
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.000176
(0.13) 		0.184
(1.00) 		0.102
(1.00) 		0.0243
(1.00) 		0.0167
(1.00)
17p loss 0 (0%) 249 0.171
(1.00) 		0.339
(1.00) 		0.227
(1.00) 		5.55e-06
(0.00418) 		0.566
(1.00) 		0.000854
(0.628) 		0.0311
(1.00) 		0.0105
(1.00) 		0.00374
(1.00) 		0.00548
(1.00)
18p loss 0 (0%) 204 0.372
(1.00) 		0.108
(1.00) 		1
(1.00) 		1.11e-09
(8.41e-07) 		1
(1.00) 		0.0279
(1.00) 		0.0454
(1.00) 		0.0597
(1.00) 		0.0435
(1.00) 		0.00696
(1.00)
18q loss 0 (0%) 188 0.272
(1.00) 		0.119
(1.00) 		0.374
(1.00) 		8.37e-09
(6.36e-06) 		0.254
(1.00) 		0.0135
(1.00) 		0.062
(1.00) 		0.12
(1.00) 		0.0477
(1.00) 		0.00489
(1.00)
22q loss 0 (0%) 332 0.571
(1.00) 		0.105
(1.00) 		0.536
(1.00) 		7.3e-05
(0.0545) 		0.481
(1.00) 		0.145
(1.00) 		0.0621
(1.00) 		0.0495
(1.00) 		0.095
(1.00) 		0.346
(1.00)
1q gain 0 (0%) 366 0.897
(1.00) 		0.466
(1.00) 		0.087
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.152
(1.00) 		0.625
(1.00) 		0.663
(1.00) 		0.337
(1.00)
2p gain 0 (0%) 373 0.614
(1.00) 		0.61
(1.00) 		0.869
(1.00) 		0.0446
(1.00) 		0.264
(1.00) 		0.895
(1.00) 		0.00703
(1.00) 		0.152
(1.00) 		0.616
(1.00) 		0.0121
(1.00)
2q gain 0 (0%) 374 0.916
(1.00) 		0.781
(1.00) 		0.738
(1.00) 		0.0436
(1.00) 		0.258
(1.00) 		0.786
(1.00) 		0.00183
(1.00) 		0.288
(1.00) 		0.304
(1.00) 		0.00398
(1.00)
4p gain 0 (0%) 410 0.449
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.000367
(0.271) 		0.00156
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.431
(1.00)
4q gain 0 (0%) 408 0.448
(1.00) 		0.856
(1.00) 		0.667
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.212
(1.00) 		0.119
(1.00) 		0.393
(1.00) 		0.514
(1.00)
5p gain 0 (0%) 374 0.802
(1.00) 		0.0805
(1.00) 		0.238
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.346
(1.00) 		0.251
(1.00) 		0.744
(1.00) 		0.861
(1.00) 		0.332
(1.00)
5q gain 0 (0%) 392 0.609
(1.00) 		0.285
(1.00) 		0.372
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.0724
(1.00) 		0.868
(1.00) 		0.234
(1.00) 		0.133
(1.00)
6p gain 0 (0%) 363 0.754
(1.00) 		0.574
(1.00) 		0.763
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.113
(1.00) 		0.852
(1.00) 		0.128
(1.00) 		0.162
(1.00)
6q gain 0 (0%) 368 0.681
(1.00) 		0.9
(1.00) 		0.874
(1.00) 		1
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.0225
(1.00) 		0.702
(1.00) 		0.157
(1.00) 		0.104
(1.00)
7p gain 0 (0%) 213 0.253
(1.00) 		0.362
(1.00) 		0.921
(1.00) 		0.00121
(0.888) 		0.113
(1.00) 		0.0308
(1.00) 		0.0623
(1.00) 		0.0927
(1.00) 		0.142
(1.00) 		0.00231
(1.00)
7q gain 0 (0%) 238 0.3
(1.00) 		0.448
(1.00) 		0.842
(1.00) 		0.0115
(1.00) 		0.577
(1.00) 		0.0177
(1.00) 		0.418
(1.00) 		0.0879
(1.00) 		0.347
(1.00) 		0.151
(1.00)
8p gain 0 (0%) 333 0.832
(1.00) 		0.199
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.936
(1.00) 		0.21
(1.00) 		0.321
(1.00) 		0.371
(1.00) 		0.469
(1.00)
8q gain 0 (0%) 251 0.605
(1.00) 		0.0678
(1.00) 		0.226
(1.00) 		0.00677
(1.00) 		0.564
(1.00) 		0.305
(1.00) 		0.255
(1.00) 		0.421
(1.00) 		0.993
(1.00) 		0.4
(1.00)
9p gain 0 (0%) 367 0.0763
(1.00) 		0.544
(1.00) 		0.347
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.93
(1.00) 		0.769
(1.00) 		0.949
(1.00) 		0.357
(1.00)
9q gain 0 (0%) 374 0.0608
(1.00) 		0.608
(1.00) 		0.18
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.773
(1.00) 		0.678
(1.00) 		0.759
(1.00) 		0.926
(1.00) 		0.681
(1.00)
10p gain 0 (0%) 395 0.0108
(1.00) 		0.098
(1.00) 		0.812
(1.00) 		0.489
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.0515
(1.00) 		0.19
(1.00) 		0.118
(1.00) 		0.247
(1.00)
10q gain 0 (0%) 406 0.786
(1.00) 		0.0299
(1.00) 		1
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.188
(1.00) 		0.416
(1.00) 		0.115
(1.00) 		0.127
(1.00)
11q gain 0 (0%) 391 0.194
(1.00) 		0.0508
(1.00) 		0.827
(1.00) 		0.0955
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.175
(1.00) 		0.198
(1.00) 		0.302
(1.00) 		0.0979
(1.00)
12p gain 0 (0%) 347 0.642
(1.00) 		0.0837
(1.00) 		1
(1.00) 		0.69
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.108
(1.00) 		0.544
(1.00) 		0.0639
(1.00) 		0.0364
(1.00)
12q gain 0 (0%) 353 0.861
(1.00) 		0.0503
(1.00) 		0.781
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.189
(1.00) 		0.35
(1.00) 		0.449
(1.00) 		0.000723
(0.532) 		0.0112
(1.00)
14q gain 0 (0%) 398 0.512
(1.00) 		0.922
(1.00) 		0.43
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.00351
(1.00) 		0.485
(1.00) 		0.847
(1.00) 		0.81
(1.00) 		0.649
(1.00)
15q gain 0 (0%) 408 0.489
(1.00) 		0.709
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.00881
(1.00) 		0.981
(1.00)
16p gain 0 (0%) 346 0.929
(1.00) 		0.205
(1.00) 		0.79
(1.00) 		0.018
(1.00) 		0.413
(1.00) 		0.657
(1.00) 		0.0767
(1.00) 		0.816
(1.00) 		0.539
(1.00) 		0.0366
(1.00)
16q gain 0 (0%) 347 0.747
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.0269
(1.00) 		0.408
(1.00) 		0.63
(1.00) 		0.00873
(1.00) 		0.872
(1.00) 		0.543
(1.00) 		0.00174
(1.00)
17q gain 0 (0%) 365 0.0555
(1.00) 		0.335
(1.00) 		0.539
(1.00) 		0.0648
(1.00) 		0.31
(1.00) 		0.00593
(1.00) 		0.0168
(1.00) 		0.955
(1.00) 		0.117
(1.00) 		0.192
(1.00)
18q gain 0 (0%) 404 0.7
(1.00) 		0.331
(1.00) 		0.513
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.855
(1.00)
19p gain 0 (0%) 379 0.604
(1.00) 		0.445
(1.00) 		0.858
(1.00) 		0.0671
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.695
(1.00) 		0.158
(1.00) 		0.0304
(1.00) 		0.808
(1.00)
19q gain 0 (0%) 372 0.29
(1.00) 		0.403
(1.00) 		0.869
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.588
(1.00) 		0.937
(1.00) 		0.144
(1.00) 		0.994
(1.00) 		0.983
(1.00)
21q gain 0 (0%) 402 0.155
(1.00) 		0.00583
(1.00) 		0.761
(1.00) 		1
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.177
(1.00)
1p loss 0 (0%) 362 0.0134
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.0296
(1.00) 		0.0825
(1.00) 		0.14
(1.00) 		0.0719
(1.00) 		0.184
(1.00)
1q loss 0 (0%) 395 0.548
(1.00) 		0.256
(1.00) 		0.631
(1.00) 		1
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.804
(1.00) 		0.256
(1.00) 		0.53
(1.00) 		0.922
(1.00)
3p loss 0 (0%) 386 0.00037
(0.273) 		0.754
(1.00) 		0.327
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.0256
(1.00) 		0.399
(1.00) 		0.211
(1.00) 		0.204
(1.00) 		0.446
(1.00)
3q loss 0 (0%) 401 0.0356
(1.00) 		0.0171
(1.00) 		0.0414
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.971
(1.00) 		0.219
(1.00) 		0.475
(1.00) 		0.524
(1.00)
4p loss 0 (0%) 329 0.00181
(1.00) 		0.764
(1.00) 		0.808
(1.00) 		0.0104
(1.00) 		0.495
(1.00) 		0.0021
(1.00) 		0.114
(1.00) 		0.0621
(1.00) 		0.0143
(1.00) 		0.0457
(1.00)
4q loss 0 (0%) 345 0.0268
(1.00) 		0.478
(1.00) 		0.595
(1.00) 		0.018
(1.00) 		0.418
(1.00) 		0.123
(1.00) 		0.29
(1.00) 		0.172
(1.00) 		0.0607
(1.00) 		0.401
(1.00)
5p loss 0 (0%) 388 0.764
(1.00) 		0.819
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.171
(1.00) 		0.821
(1.00) 		0.355
(1.00) 		0.651
(1.00) 		0.22
(1.00) 		0.00114
(0.832)
5q loss 0 (0%) 375 0.34
(1.00) 		0.867
(1.00) 		0.0609
(1.00) 		0.0434
(1.00) 		0.252
(1.00) 		0.724
(1.00) 		0.0543
(1.00) 		0.521
(1.00) 		0.0202
(1.00) 		0.189
(1.00)
6p loss 0 (0%) 401 0.736
(1.00) 		0.625
(1.00) 		0.778
(1.00) 		1
(1.00) 		1
(1.00) 		0.363
(1.00) 		0.961
(1.00) 		0.0139
(1.00) 		0.927
(1.00) 		0.98
(1.00)
8p loss 0 (0%) 320 0.601
(1.00) 		0.641
(1.00) 		0.239
(1.00) 		0.0813
(1.00) 		0.536
(1.00) 		0.117
(1.00) 		0.124
(1.00) 		0.187
(1.00) 		0.0337
(1.00) 		0.336
(1.00)
8q loss 0 (0%) 405 0.881
(1.00) 		0.21
(1.00) 		0.294
(1.00) 		1
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.569
(1.00) 		0.612
(1.00) 		0.811
(1.00) 		0.341
(1.00)
9p loss 0 (0%) 386 0.203
(1.00) 		0.0653
(1.00) 		1
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.917
(1.00) 		0.0125
(1.00) 		0.816
(1.00) 		0.702
(1.00) 		0.949
(1.00)
9q loss 0 (0%) 387 0.802
(1.00) 		0.0045
(1.00) 		0.31
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.489
(1.00) 		0.816
(1.00) 		0.736
(1.00) 		0.947
(1.00)
10p loss 0 (0%) 391 0.812
(1.00) 		0.321
(1.00) 		0.512
(1.00) 		1
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.876
(1.00) 		0.0603
(1.00) 		0.526
(1.00) 		0.546
(1.00)
10q loss 0 (0%) 389 0.28
(1.00) 		0.178
(1.00) 		0.528
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.812
(1.00) 		0.0384
(1.00) 		0.772
(1.00) 		0.839
(1.00)
11p loss 0 (0%) 391 0.297
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.857
(1.00) 		0.147
(1.00) 		0.348
(1.00) 		0.966
(1.00)
11q loss 0 (0%) 386 0.799
(1.00) 		0.285
(1.00) 		0.425
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.726
(1.00) 		0.109
(1.00) 		0.485
(1.00) 		0.905
(1.00)
12p loss 0 (0%) 392 0.29
(1.00) 		0.775
(1.00) 		0.372
(1.00) 		0.0918
(1.00) 		0.145
(1.00) 		0.795
(1.00) 		0.287
(1.00) 		0.886
(1.00) 		0.396
(1.00) 		0.764
(1.00)
12q loss 0 (0%) 393 0.474
(1.00) 		0.941
(1.00) 		0.254
(1.00) 		0.0904
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.428
(1.00) 		0.793
(1.00) 		0.484
(1.00) 		0.858
(1.00)
13q loss 0 (0%) 407 0.232
(1.00) 		0.627
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		0.493
(1.00) 		0.505
(1.00) 		0.288
(1.00) 		0.282
(1.00) 		0.842
(1.00)
14q loss 0 (0%) 319 0.373
(1.00) 		0.939
(1.00) 		0.638
(1.00) 		0.000718
(0.529) 		1
(1.00) 		0.264
(1.00) 		0.194
(1.00) 		0.489
(1.00) 		0.739
(1.00) 		0.327
(1.00)
15q loss 0 (0%) 314 0.371
(1.00) 		0.424
(1.00) 		0.908
(1.00) 		0.00172
(1.00) 		0.562
(1.00) 		0.211
(1.00) 		0.856
(1.00) 		0.428
(1.00) 		0.524
(1.00) 		0.54
(1.00)
16p loss 0 (0%) 404 0.88
(1.00) 		0.999
(1.00) 		0.314
(1.00) 		0.336
(1.00) 		1
(1.00) 		0.993
(1.00) 		0.928
(1.00) 		0.527
(1.00) 		0.486
(1.00) 		0.957
(1.00)
16q loss 0 (0%) 406 0.478
(1.00) 		0.612
(1.00) 		0.709
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.999
(1.00) 		0.235
(1.00) 		0.351
(1.00) 		0.997
(1.00)
17q loss 0 (0%) 381 0.763
(1.00) 		0.544
(1.00) 		0.715
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.366
(1.00) 		0.167
(1.00) 		0.0531
(1.00) 		0.204
(1.00) 		0.238
(1.00)
19p loss 0 (0%) 399 0.289
(1.00) 		0.5
(1.00) 		0.187
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.943
(1.00) 		0.0642
(1.00) 		0.261
(1.00) 		0.27
(1.00)
19q loss 0 (0%) 400 0.289
(1.00) 		0.73
(1.00) 		0.155
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.966
(1.00) 		0.049
(1.00) 		0.543
(1.00) 		0.366
(1.00)
20p loss 0 (0%) 380 0.562
(1.00) 		0.806
(1.00) 		0.857
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.908
(1.00) 		0.678
(1.00) 		0.509
(1.00) 		0.224
(1.00)
21q loss 0 (0%) 342 0.666
(1.00) 		0.675
(1.00) 		0.795
(1.00) 		0.0513
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.713
(1.00) 		0.947
(1.00) 		0.144
(1.00) 		0.761
(1.00)
Xq loss 0 (0%) 408 0.718
(1.00) 		0.78
(1.00) 		0.667
(1.00) 		0.507
(1.00) 		1
(1.00) 		0.868
(1.00) 		0.0925
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.764
(1.00)
'1p gain' versus 'LYMPH.NODE.METASTASIS'

P value = 2.42e-08 (Chi-square test), Q value = 1.8e-05

Table S1.  Gene #1: '1p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 244 69 13 12 2 58 4 9 1
1P GAIN CNV 6 1 0 0 0 1 0 2 1
1P GAIN WILD-TYPE 238 68 13 12 2 57 4 7 0

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'3p gain' versus 'DISTANT.METASTASIS'

P value = 0.000104 (Chi-square test), Q value = 0.077

Table S2.  Gene #5: '3p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
3P GAIN CNV 12 2 1 1 3
3P GAIN WILD-TYPE 301 47 6 0 33

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'3q gain' versus 'Time to Death'

P value = 4e-05 (logrank test), Q value = 0.03

Table S3.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 321 49 0.1 - 135.5 (7.7)
3Q GAIN CNV 23 8 0.2 - 46.8 (5.0)
3Q GAIN WILD-TYPE 298 41 0.1 - 135.5 (8.0)

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000122 (Chi-square test), Q value = 0.091

Table S4.  Gene #21: '11p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 244 69 13 12 2 58 4 9 1
11P GAIN CNV 7 3 0 1 0 5 1 0 1
11P GAIN WILD-TYPE 237 66 13 11 2 53 3 9 0

Figure S4.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 4.23e-06 (Fisher's exact test), Q value = 0.0032

Table S5.  Gene #25: '13q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
13Q GAIN CNV 198 12
13Q GAIN WILD-TYPE 159 42

Figure S5.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'17p gain' versus 'DISTANT.METASTASIS'

P value = 0.000123 (Chi-square test), Q value = 0.091

Table S6.  Gene #30: '17p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
17P GAIN CNV 5 1 2 0 1
17P GAIN WILD-TYPE 308 48 5 1 35

Figure S6.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'17p gain' versus 'LYMPH.NODE.METASTASIS'

P value = 3.74e-05 (Chi-square test), Q value = 0.028

Table S7.  Gene #30: '17p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 244 69 13 12 2 58 4 9 1
17P GAIN CNV 5 0 2 0 1 1 0 0 0
17P GAIN WILD-TYPE 239 69 11 12 1 57 4 9 1

Figure S7.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'18p gain' versus 'DISTANT.METASTASIS'

P value = 5.91e-06 (Chi-square test), Q value = 0.0044

Table S8.  Gene #32: '18p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
18P GAIN CNV 11 2 0 1 0
18P GAIN WILD-TYPE 302 47 7 0 36

Figure S8.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'18p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00021 (Chi-square test), Q value = 0.16

Table S9.  Gene #32: '18p gain' versus Clinical Feature #11: '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 68 1 33 116 8 1 22 13 47 34 40 16 1
18P GAIN CNV 3 0 2 2 0 0 1 0 0 4 2 0 1
18P GAIN WILD-TYPE 65 1 31 114 8 1 21 13 47 30 38 16 0

Figure S9.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.17e-05 (Fisher's exact test), Q value = 0.046

Table S10.  Gene #36: '20p gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
20P GAIN CNV 175 11
20P GAIN WILD-TYPE 182 43

Figure S10.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.71e-08 (Fisher's exact test), Q value = 2.1e-05

Table S11.  Gene #37: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
20Q GAIN CNV 249 16
20Q GAIN WILD-TYPE 108 38

Figure S11.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Xq gain' versus 'DISTANT.METASTASIS'

P value = 1.43e-07 (Chi-square test), Q value = 0.00011

Table S12.  Gene #39: 'Xq gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
XQ GAIN CNV 8 2 0 1 0
XQ GAIN WILD-TYPE 305 47 7 0 36

Figure S12.  Get High-res Image Gene #39: 'Xq gain' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'Xq gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000207 (Chi-square test), Q value = 0.15

Table S13.  Gene #39: 'Xq gain' versus Clinical Feature #11: '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 68 1 33 116 8 1 22 13 47 34 40 16 1
XQ GAIN CNV 1 0 1 3 0 0 2 0 1 1 1 1 1
XQ GAIN WILD-TYPE 67 1 32 113 8 1 20 13 46 33 39 15 0

Figure S13.  Get High-res Image Gene #39: 'Xq gain' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'2p loss' versus 'Time to Death'

P value = 2.2e-07 (logrank test), Q value = 0.00017

Table S14.  Gene #42: '2p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 321 49 0.1 - 135.5 (7.7)
2P LOSS CNV 3 1 0.3 - 2.0 (1.0)
2P LOSS WILD-TYPE 318 48 0.1 - 135.5 (7.9)

Figure S14.  Get High-res Image Gene #42: '2p loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'Time to Death'

P value = 2.52e-06 (logrank test), Q value = 0.0019

Table S15.  Gene #43: '2q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 321 49 0.1 - 135.5 (7.7)
2Q LOSS CNV 4 1 0.3 - 2.0 (1.0)
2Q LOSS WILD-TYPE 317 48 0.1 - 135.5 (8.0)

Figure S15.  Get High-res Image Gene #43: '2q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'DISTANT.METASTASIS'

P value = 0.000176 (Chi-square test), Q value = 0.13

Table S16.  Gene #51: '6q loss' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
6Q LOSS CNV 12 4 1 1 3
6Q LOSS WILD-TYPE 301 45 6 0 33

Figure S16.  Get High-res Image Gene #51: '6q loss' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.55e-06 (Fisher's exact test), Q value = 0.0042

Table S17.  Gene #67: '17p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
17P LOSS CNV 157 7
17P LOSS WILD-TYPE 200 47

Figure S17.  Get High-res Image Gene #67: '17p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-09 (Fisher's exact test), Q value = 8.4e-07

Table S18.  Gene #69: '18p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
18P LOSS CNV 200 7
18P LOSS WILD-TYPE 157 47

Figure S18.  Get High-res Image Gene #69: '18p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.37e-09 (Fisher's exact test), Q value = 6.4e-06

Table S19.  Gene #70: '18q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
18Q LOSS CNV 214 10
18Q LOSS WILD-TYPE 143 44

Figure S19.  Get High-res Image Gene #70: '18q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.054

Table S20.  Gene #75: '22q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
22Q LOSS CNV 80 1
22Q LOSS WILD-TYPE 277 53

Figure S20.  Get High-res Image Gene #75: '22q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

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

  • Number of patients = 413

  • Number of significantly arm-level cnvs = 76

  • 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)
[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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