Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C14M938R
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/C14M938R
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 13 clinical features across 592 patients, 27 significant findings detected with Q value < 0.25.

  • 6q gain cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • 7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 7q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

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

  • 20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.

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

  • 8p 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',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'HISTOLOGICAL.TYPE'.

  • 18q loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'PATHOLOGY.M.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • 19p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 22q loss cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

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 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
18q loss 390 (66%) 202 0.912
(1.00) 		0.021
(1.00) 		1.01e-08
(1.03e-05) 		1e-05
(0.0102) 		0.458
(1.00) 		0.00019
(0.19) 		0.0001
(0.1) 		0.602
(1.00) 		1e-05
(0.0102) 		0.177
(1.00) 		0.0228
(1.00) 		0.000136
(0.137) 		0.385
(1.00)
18p loss 361 (61%) 231 0.718
(1.00) 		0.0334
(1.00) 		4.02e-07
(0.000412) 		6e-05
(0.0606) 		0.861
(1.00) 		0.00504
(1.00) 		5e-05
(0.0505) 		0.673
(1.00) 		1e-05
(0.0102) 		0.098
(1.00) 		0.0236
(1.00) 		0.00232
(1.00) 		0.466
(1.00)
7p gain 336 (57%) 256 0.457
(1.00) 		0.199
(1.00) 		0.0753
(1.00) 		0.00016
(0.16) 		0.878
(1.00) 		2e-05
(0.0203) 		0.0332
(1.00) 		0.618
(1.00) 		0.00026
(0.259) 		0.312
(1.00) 		0.256
(1.00) 		6.23e-05
(0.0628) 		0.683
(1.00)
20q gain 447 (76%) 145 0.479
(1.00) 		0.165
(1.00) 		2.77e-06
(0.00283) 		0.00017
(0.17) 		0.304
(1.00) 		0.0013
(1.00) 		0.00104
(1.00) 		0.339
(1.00) 		1e-05
(0.0102) 		0.696
(1.00) 		0.0248
(1.00) 		0.00705
(1.00) 		0.0956
(1.00)
20p gain 340 (57%) 252 0.138
(1.00) 		0.598
(1.00) 		0.00647
(1.00) 		0.00013
(0.13) 		0.524
(1.00) 		0.0665
(1.00) 		0.00633
(1.00) 		0.135
(1.00) 		3e-05
(0.0304) 		0.314
(1.00) 		0.0801
(1.00) 		0.0362
(1.00) 		0.819
(1.00)
22q loss 194 (33%) 398 0.0355
(1.00) 		0.8
(1.00) 		0.693
(1.00) 		0.00623
(1.00) 		0.274
(1.00) 		4e-05
(0.0405) 		0.00915
(1.00) 		0.793
(1.00) 		0.0152
(1.00) 		0.484
(1.00) 		0.476
(1.00) 		8.35e-05
(0.0841) 		0.358
(1.00)
6q gain 105 (18%) 487 0.509
(1.00) 		0.633
(1.00) 		0.223
(1.00) 		0.057
(1.00) 		0.787
(1.00) 		0.00409
(1.00) 		0.111
(1.00) 		0.39
(1.00) 		0.0359
(1.00) 		0.000122
(0.123) 		0.277
(1.00) 		0.00658
(1.00) 		0.829
(1.00)
7q gain 300 (51%) 292 0.663
(1.00) 		0.171
(1.00) 		0.578
(1.00) 		9e-05
(0.0905) 		0.567
(1.00) 		0.00061
(0.601) 		0.0121
(1.00) 		0.621
(1.00) 		0.0036
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.0019
(1.00) 		0.441
(1.00)
13q gain 355 (60%) 237 0.504
(1.00) 		0.404
(1.00) 		0.0233
(1.00) 		0.00282
(1.00) 		0.809
(1.00) 		0.00037
(0.367) 		0.039
(1.00) 		0.24
(1.00) 		1e-05
(0.0102) 		0.327
(1.00) 		0.0896
(1.00) 		0.00197
(1.00) 		0.0444
(1.00)
8p loss 209 (35%) 383 0.745
(1.00) 		0.74
(1.00) 		0.00472
(1.00) 		0.0222
(1.00) 		0.231
(1.00) 		0.00035
(0.348) 		0.027
(1.00) 		0.196
(1.00) 		0.00419
(1.00) 		0.291
(1.00) 		0.107
(1.00) 		6.9e-05
(0.0696) 		0.469
(1.00)
14q loss 195 (33%) 397 0.663
(1.00) 		0.326
(1.00) 		0.0229
(1.00) 		0.412
(1.00) 		0.39
(1.00) 		0.0217
(1.00) 		0.142
(1.00) 		0.6
(1.00) 		1e-05
(0.0102) 		1
(1.00) 		0.942
(1.00) 		0.304
(1.00) 		0.956
(1.00)
17p loss 325 (55%) 267 0.221
(1.00) 		0.301
(1.00) 		0.0253
(1.00) 		0.00394
(1.00) 		0.528
(1.00) 		0.00127
(1.00) 		0.0157
(1.00) 		0.248
(1.00) 		1e-05
(0.0102) 		0.195
(1.00) 		0.0745
(1.00) 		0.000289
(0.287) 		0.334
(1.00)
19p loss 61 (10%) 531 0.127
(1.00) 		0.36
(1.00) 		0.091
(1.00) 		0.0011
(1.00) 		0.861
(1.00) 		0.0006
(0.592) 		0.0101
(1.00) 		0.787
(1.00) 		0.129
(1.00) 		0.235
(1.00) 		0.431
(1.00) 		2.74e-06
(0.0028) 		0.861
(1.00)
1p gain 47 (8%) 545 0.164
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.38
(1.00) 		0.345
(1.00) 		0.231
(1.00) 		0.648
(1.00) 		0.12
(1.00) 		0.528
(1.00) 		0.137
(1.00) 		0.0732
(1.00) 		0.636
(1.00)
1q gain 115 (19%) 477 0.373
(1.00) 		0.409
(1.00) 		0.292
(1.00) 		0.0936
(1.00) 		0.0214
(1.00) 		0.0224
(1.00) 		0.0298
(1.00) 		0.467
(1.00) 		0.246
(1.00) 		0.387
(1.00) 		0.333
(1.00) 		0.0014
(1.00) 		1
(1.00)
2p gain 114 (19%) 478 0.288
(1.00) 		0.456
(1.00) 		0.0606
(1.00) 		0.441
(1.00) 		0.539
(1.00) 		0.186
(1.00) 		0.387
(1.00) 		0.348
(1.00) 		0.00507
(1.00) 		0.385
(1.00) 		0.0286
(1.00) 		0.289
(1.00) 		0.939
(1.00)
2q gain 112 (19%) 480 0.149
(1.00) 		0.185
(1.00) 		0.0132
(1.00) 		0.307
(1.00) 		0.603
(1.00) 		0.0913
(1.00) 		0.402
(1.00) 		0.249
(1.00) 		0.0015
(1.00) 		0.0705
(1.00) 		0.347
(1.00) 		0.149
(1.00) 		0.608
(1.00)
3p gain 69 (12%) 523 0.359
(1.00) 		0.11
(1.00) 		0.0302
(1.00) 		0.0832
(1.00) 		0.971
(1.00) 		0.201
(1.00) 		0.0154
(1.00) 		0.37
(1.00) 		0.0661
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.109
(1.00) 		0.24
(1.00)
3q gain 95 (16%) 497 0.205
(1.00) 		0.256
(1.00) 		0.042
(1.00) 		0.0916
(1.00) 		0.885
(1.00) 		0.0559
(1.00) 		0.00178
(1.00) 		0.434
(1.00) 		0.0278
(1.00) 		0.642
(1.00) 		0.575
(1.00) 		0.0497
(1.00) 		0.27
(1.00)
4p gain 18 (3%) 574 0.754
(1.00) 		0.73
(1.00) 		0.0328
(1.00) 		0.636
(1.00) 		0.357
(1.00) 		0.605
(1.00) 		0.254
(1.00) 		0.338
(1.00) 		0.0919
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.665
(1.00) 		0.396
(1.00)
4q gain 19 (3%) 573 0.259
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.403
(1.00) 		0.321
(1.00) 		0.243
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.269
(1.00) 		0.763
(1.00)
5p gain 98 (17%) 494 0.43
(1.00) 		0.178
(1.00) 		0.0805
(1.00) 		0.437
(1.00) 		0.681
(1.00) 		0.0658
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.0352
(1.00) 		0.174
(1.00) 		0.117
(1.00) 		0.0605
(1.00) 		0.258
(1.00)
5q gain 62 (10%) 530 0.5
(1.00) 		0.908
(1.00) 		0.0695
(1.00) 		0.682
(1.00) 		0.662
(1.00) 		0.535
(1.00) 		0.846
(1.00) 		0.687
(1.00) 		0.0669
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.711
(1.00) 		0.372
(1.00)
6p gain 118 (20%) 474 0.47
(1.00) 		0.582
(1.00) 		0.13
(1.00) 		0.118
(1.00) 		0.503
(1.00) 		0.00094
(0.923) 		0.357
(1.00) 		0.217
(1.00) 		0.112
(1.00) 		0.000271
(0.27) 		0.223
(1.00) 		0.0019
(1.00) 		0.283
(1.00)
8p gain 162 (27%) 430 0.355
(1.00) 		0.371
(1.00) 		0.468
(1.00) 		0.461
(1.00) 		0.797
(1.00) 		0.28
(1.00) 		0.921
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.711
(1.00) 		0.231
(1.00) 		0.165
(1.00) 		1
(1.00)
8q gain 302 (51%) 290 0.473
(1.00) 		0.117
(1.00) 		0.405
(1.00) 		0.145
(1.00) 		0.21
(1.00) 		0.148
(1.00) 		0.156
(1.00) 		0.869
(1.00) 		0.0392
(1.00) 		0.038
(1.00) 		0.173
(1.00) 		0.246
(1.00) 		0.846
(1.00)
9p gain 116 (20%) 476 0.00788
(1.00) 		0.773
(1.00) 		0.0192
(1.00) 		0.017
(1.00) 		0.585
(1.00) 		0.12
(1.00) 		0.745
(1.00) 		0.918
(1.00) 		0.00846
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.143
(1.00) 		0.108
(1.00)
9q gain 98 (17%) 494 0.0093
(1.00) 		0.903
(1.00) 		0.173
(1.00) 		0.088
(1.00) 		0.483
(1.00) 		0.326
(1.00) 		0.899
(1.00) 		0.58
(1.00) 		0.0912
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.319
(1.00) 		0.361
(1.00)
10p gain 44 (7%) 548 0.0279
(1.00) 		0.727
(1.00) 		0.861
(1.00) 		0.6
(1.00) 		0.176
(1.00) 		0.0325
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.503
(1.00) 		0.575
(1.00) 		0.105
(1.00) 		0.153
(1.00)
10q gain 24 (4%) 568 0.586
(1.00) 		0.0741
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.513
(1.00) 		0.0401
(1.00) 		0.409
(1.00) 		0.836
(1.00) 		0.912
(1.00) 		0.313
(1.00) 		0.672
(1.00) 		0.0226
(1.00) 		0.0441
(1.00)
11p gain 80 (14%) 512 0.991
(1.00) 		0.0169
(1.00) 		0.0211
(1.00) 		0.225
(1.00) 		0.222
(1.00) 		0.462
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.00094
(0.923) 		0.109
(1.00) 		0.338
(1.00) 		0.357
(1.00) 		0.481
(1.00)
11q gain 72 (12%) 520 0.596
(1.00) 		0.000256
(0.256) 		0.121
(1.00) 		0.36
(1.00) 		0.604
(1.00) 		0.424
(1.00) 		0.0549
(1.00) 		1
(1.00) 		0.00109
(1.00) 		0.301
(1.00) 		0.474
(1.00) 		0.386
(1.00) 		0.639
(1.00)
12p gain 125 (21%) 467 0.261
(1.00) 		0.119
(1.00) 		0.91
(1.00) 		0.232
(1.00) 		0.312
(1.00) 		0.21
(1.00) 		0.266
(1.00) 		0.92
(1.00) 		0.775
(1.00) 		0.407
(1.00) 		0.784
(1.00) 		0.211
(1.00) 		0.895
(1.00)
12q gain 109 (18%) 483 0.536
(1.00) 		0.0334
(1.00) 		0.232
(1.00) 		0.051
(1.00) 		0.467
(1.00) 		0.0451
(1.00) 		0.0593
(1.00) 		0.526
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.616
(1.00) 		0.0207
(1.00) 		0.957
(1.00)
14q gain 41 (7%) 551 0.4
(1.00) 		0.914
(1.00) 		0.361
(1.00) 		0.914
(1.00) 		0.964
(1.00) 		0.816
(1.00) 		0.0539
(1.00) 		0.748
(1.00) 		0.302
(1.00) 		0.478
(1.00) 		0.606
(1.00) 		0.453
(1.00) 		0.0065
(1.00)
15q gain 15 (3%) 577 0.967
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.0719
(1.00) 		0.718
(1.00) 		0.167
(1.00) 		0.0631
(1.00) 		0.0808
(1.00) 		0.208
(1.00) 		0.698
(1.00) 		0.401
(1.00) 		0.452
(1.00)
16p gain 141 (24%) 451 0.459
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.0197
(1.00) 		0.99
(1.00) 		0.00225
(1.00) 		0.321
(1.00) 		0.847
(1.00) 		0.00326
(1.00) 		0.227
(1.00) 		0.737
(1.00) 		0.00445
(1.00) 		0.439
(1.00)
16q gain 139 (23%) 453 0.726
(1.00) 		0.111
(1.00) 		0.743
(1.00) 		0.00663
(1.00) 		0.977
(1.00) 		0.00047
(0.466) 		0.268
(1.00) 		0.923
(1.00) 		0.0038
(1.00) 		0.225
(1.00) 		0.685
(1.00) 		0.00285
(1.00) 		0.409
(1.00)
17p gain 35 (6%) 557 0.0578
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.299
(1.00) 		0.862
(1.00) 		0.197
(1.00) 		1
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.835
(1.00) 		0.0745
(1.00)
17q gain 105 (18%) 487 0.175
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.135
(1.00) 		0.761
(1.00) 		0.381
(1.00) 		0.00545
(1.00) 		1
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.169
(1.00) 		0.815
(1.00) 		0.629
(1.00)
18p gain 33 (6%) 559 0.455
(1.00) 		0.573
(1.00) 		0.841
(1.00) 		0.012
(1.00) 		0.664
(1.00) 		0.0121
(1.00) 		0.129
(1.00) 		0.15
(1.00) 		0.0356
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.0118
(1.00) 		0.805
(1.00)
18q gain 20 (3%) 572 0.965
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.088
(1.00) 		0.476
(1.00) 		0.154
(1.00) 		0.671
(1.00) 		0.171
(1.00) 		0.0611
(1.00) 		0.268
(1.00) 		0.634
(1.00) 		0.241
(1.00) 		0.22
(1.00)
19p gain 99 (17%) 493 0.744
(1.00) 		0.998
(1.00) 		0.321
(1.00) 		0.864
(1.00) 		0.946
(1.00) 		0.134
(1.00) 		0.361
(1.00) 		0.186
(1.00) 		0.0638
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.689
(1.00) 		1
(1.00)
19q gain 109 (18%) 483 0.502
(1.00) 		0.833
(1.00) 		0.552
(1.00) 		0.71
(1.00) 		0.946
(1.00) 		0.085
(1.00) 		0.143
(1.00) 		0.457
(1.00) 		0.209
(1.00) 		1
(1.00) 		0.497
(1.00) 		0.912
(1.00) 		0.933
(1.00)
21q gain 30 (5%) 562 0.643
(1.00) 		0.0299
(1.00) 		0.392
(1.00) 		0.591
(1.00) 		0.205
(1.00) 		0.589
(1.00) 		0.466
(1.00) 		0.851
(1.00) 		0.539
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.298
(1.00) 		0.44
(1.00)
22q gain 22 (4%) 570 0.608
(1.00) 		0.397
(1.00) 		0.0828
(1.00) 		0.62
(1.00) 		0.134
(1.00) 		0.397
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.0997
(1.00) 		0.291
(1.00) 		0.336
(1.00) 		0.177
(1.00) 		0.61
(1.00)
xq gain 101 (17%) 491 0.561
(1.00) 		0.354
(1.00) 		0.623
(1.00) 		0.133
(1.00) 		0.703
(1.00) 		0.232
(1.00) 		0.206
(1.00) 		0.229
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.367
(1.00) 		0.786
(1.00)
1p loss 131 (22%) 461 0.218
(1.00) 		0.472
(1.00) 		0.148
(1.00) 		0.295
(1.00) 		0.835
(1.00) 		0.00552
(1.00) 		0.0651
(1.00) 		0.428
(1.00) 		0.024
(1.00) 		0.422
(1.00) 		0.781
(1.00) 		0.00136
(1.00) 		0.395
(1.00)
1q loss 73 (12%) 519 0.19
(1.00) 		0.272
(1.00) 		0.398
(1.00) 		0.653
(1.00) 		0.712
(1.00) 		0.179
(1.00) 		0.0964
(1.00) 		0.08
(1.00) 		0.295
(1.00) 		0.307
(1.00) 		0.462
(1.00) 		0.121
(1.00) 		0.159
(1.00)
2p loss 17 (3%) 575 0.879
(1.00) 		0.232
(1.00) 		0.00108
(1.00) 		0.635
(1.00) 		0.85
(1.00) 		0.893
(1.00) 		0.87
(1.00) 		0.806
(1.00) 		0.0119
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.215
(1.00)
2q loss 13 (2%) 579 0.551
(1.00) 		0.719
(1.00) 		0.124
(1.00) 		0.143
(1.00) 		0.833
(1.00) 		0.798
(1.00) 		0.36
(1.00) 		0.587
(1.00) 		0.463
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.589
(1.00)
3p loss 66 (11%) 526 0.0731
(1.00) 		0.682
(1.00) 		0.374
(1.00) 		0.0445
(1.00) 		0.0335
(1.00) 		0.0357
(1.00) 		0.0101
(1.00) 		0.513
(1.00) 		0.0944
(1.00) 		0.265
(1.00) 		0.165
(1.00) 		0.0295
(1.00) 		0.354
(1.00)
3q loss 42 (7%) 550 0.163
(1.00) 		0.475
(1.00) 		0.585
(1.00) 		0.13
(1.00) 		0.126
(1.00) 		0.523
(1.00) 		0.0818
(1.00) 		0.265
(1.00) 		0.00888
(1.00) 		0.129
(1.00) 		0.453
(1.00) 		0.652
(1.00) 		0.293
(1.00)
4p loss 185 (31%) 407 0.346
(1.00) 		0.853
(1.00) 		0.134
(1.00) 		0.0129
(1.00) 		0.815
(1.00) 		0.002
(1.00) 		0.00486
(1.00) 		0.791
(1.00) 		0.0144
(1.00) 		0.000538
(0.531) 		0.121
(1.00) 		0.000657
(0.646) 		0.746
(1.00)
4q loss 179 (30%) 413 0.776
(1.00) 		0.428
(1.00) 		0.00619
(1.00) 		0.118
(1.00) 		0.724
(1.00) 		0.00568
(1.00) 		0.229
(1.00) 		0.788
(1.00) 		0.00574
(1.00) 		0.000416
(0.413) 		0.846
(1.00) 		0.00285
(1.00) 		0.677
(1.00)
5p loss 80 (14%) 512 0.578
(1.00) 		0.399
(1.00) 		0.175
(1.00) 		0.0253
(1.00) 		0.898
(1.00) 		0.00965
(1.00) 		0.338
(1.00) 		0.402
(1.00) 		0.2
(1.00) 		0.0229
(1.00) 		0.747
(1.00) 		0.00681
(1.00) 		0.48
(1.00)
5q loss 113 (19%) 479 0.0627
(1.00) 		0.581
(1.00) 		0.0335
(1.00) 		0.0818
(1.00) 		0.589
(1.00) 		0.00319
(1.00) 		0.106
(1.00) 		0.917
(1.00) 		0.0373
(1.00) 		0.00219
(1.00) 		0.519
(1.00) 		0.00135
(1.00) 		0.398
(1.00)
6p loss 45 (8%) 547 0.0137
(1.00) 		0.384
(1.00) 		0.861
(1.00) 		0.492
(1.00) 		0.499
(1.00) 		0.27
(1.00) 		0.377
(1.00) 		0.539
(1.00) 		0.142
(1.00) 		0.512
(1.00) 		0.0432
(1.00) 		0.374
(1.00) 		0.0163
(1.00)
6q loss 68 (11%) 524 0.0569
(1.00) 		0.646
(1.00) 		0.378
(1.00) 		0.269
(1.00) 		0.329
(1.00) 		0.0907
(1.00) 		0.0594
(1.00) 		0.245
(1.00) 		0.0405
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.0462
(1.00) 		0.00791
(1.00)
7q loss 4 (1%) 588 0.516
(1.00) 		0.989
(1.00) 		0.296
(1.00) 		0.665
(1.00) 		0.315
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00) 		0.302
(1.00)
8q loss 33 (6%) 559 0.678
(1.00) 		0.694
(1.00) 		0.422
(1.00) 		0.341
(1.00) 		0.53
(1.00) 		0.354
(1.00) 		0.342
(1.00) 		0.0298
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.853
(1.00) 		0.116
(1.00)
9p loss 72 (12%) 520 0.491
(1.00) 		0.159
(1.00) 		0.669
(1.00) 		0.879
(1.00) 		0.095
(1.00) 		0.542
(1.00) 		0.223
(1.00) 		0.167
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.0429
(1.00) 		0.164
(1.00) 		0.702
(1.00)
9q loss 71 (12%) 521 0.275
(1.00) 		0.0406
(1.00) 		0.564
(1.00) 		0.651
(1.00) 		0.106
(1.00) 		0.487
(1.00) 		0.0915
(1.00) 		0.448
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.0431
(1.00) 		0.379
(1.00) 		0.707
(1.00)
10p loss 96 (16%) 496 0.411
(1.00) 		0.00925
(1.00) 		0.13
(1.00) 		0.53
(1.00) 		0.792
(1.00) 		0.143
(1.00) 		0.514
(1.00) 		0.738
(1.00) 		0.0193
(1.00) 		0.00745
(1.00) 		0.984
(1.00) 		0.037
(1.00) 		0.499
(1.00)
10q loss 104 (18%) 488 0.483
(1.00) 		0.0153
(1.00) 		0.0511
(1.00) 		0.737
(1.00) 		0.967
(1.00) 		0.304
(1.00) 		0.77
(1.00) 		0.59
(1.00) 		0.0136
(1.00) 		0.0106
(1.00) 		0.958
(1.00) 		0.149
(1.00) 		0.618
(1.00)
11p loss 73 (12%) 519 0.827
(1.00) 		0.271
(1.00) 		0.323
(1.00) 		0.28
(1.00) 		0.522
(1.00) 		0.0239
(1.00) 		0.0494
(1.00) 		0.803
(1.00) 		0.24
(1.00) 		0.307
(1.00) 		0.889
(1.00) 		0.000474
(0.47) 		0.266
(1.00)
11q loss 90 (15%) 502 0.336
(1.00) 		0.484
(1.00) 		0.358
(1.00) 		0.621
(1.00) 		0.8
(1.00) 		0.124
(1.00) 		0.325
(1.00) 		0.731
(1.00) 		0.138
(1.00) 		0.144
(1.00) 		0.963
(1.00) 		0.0471
(1.00) 		0.221
(1.00)
12p loss 68 (11%) 524 0.114
(1.00) 		0.676
(1.00) 		0.188
(1.00) 		0.437
(1.00) 		0.33
(1.00) 		0.0364
(1.00) 		0.384
(1.00) 		0.797
(1.00) 		0.0149
(1.00) 		0.0734
(1.00) 		0.924
(1.00) 		0.0441
(1.00) 		0.758
(1.00)
12q loss 68 (11%) 524 0.202
(1.00) 		0.952
(1.00) 		0.562
(1.00) 		0.196
(1.00) 		0.521
(1.00) 		0.0353
(1.00) 		0.226
(1.00) 		1
(1.00) 		0.114
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.0274
(1.00) 		0.37
(1.00)
13q loss 19 (3%) 573 0.933
(1.00) 		0.962
(1.00) 		0.186
(1.00) 		0.342
(1.00) 		0.568
(1.00) 		0.0283
(1.00) 		0.0598
(1.00) 		1
(1.00) 		0.0215
(1.00) 		1
(1.00) 		1
(1.00) 		0.0112
(1.00) 		0.011
(1.00)
15q loss 217 (37%) 375 0.771
(1.00) 		0.514
(1.00) 		0.0341
(1.00) 		0.0598
(1.00) 		0.227
(1.00) 		0.0181
(1.00) 		0.0955
(1.00) 		0.443
(1.00) 		0.0026
(1.00) 		0.0142
(1.00) 		0.786
(1.00) 		0.00758
(1.00) 		0.0512
(1.00)
16p loss 38 (6%) 554 0.136
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.462
(1.00) 		0.448
(1.00) 		0.71
(1.00) 		0.315
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.446
(1.00) 		0.283
(1.00)
16q loss 40 (7%) 552 0.42
(1.00) 		0.2
(1.00) 		0.269
(1.00) 		0.38
(1.00) 		0.854
(1.00) 		0.233
(1.00) 		0.671
(1.00) 		0.513
(1.00) 		0.613
(1.00) 		0.47
(1.00) 		0.407
(1.00) 		0.499
(1.00) 		0.251
(1.00)
17q loss 88 (15%) 504 0.134
(1.00) 		0.994
(1.00) 		0.515
(1.00) 		0.223
(1.00) 		0.158
(1.00) 		0.0183
(1.00) 		0.254
(1.00) 		0.356
(1.00) 		0.872
(1.00) 		0.629
(1.00) 		0.673
(1.00) 		0.000495
(0.489) 		0.148
(1.00)
19q loss 52 (9%) 540 0.427
(1.00) 		0.958
(1.00) 		0.187
(1.00) 		0.0107
(1.00) 		0.808
(1.00) 		0.00382
(1.00) 		0.107
(1.00) 		0.31
(1.00) 		0.294
(1.00) 		0.183
(1.00) 		0.761
(1.00) 		0.000617
(0.608) 		0.0994
(1.00)
20p loss 62 (10%) 530 0.947
(1.00) 		0.808
(1.00) 		0.173
(1.00) 		0.513
(1.00) 		0.434
(1.00) 		0.369
(1.00) 		0.961
(1.00) 		0.594
(1.00) 		0.429
(1.00) 		0.608
(1.00) 		0.584
(1.00) 		0.8
(1.00) 		0.722
(1.00)
20q loss 5 (1%) 587 0.332
(1.00) 		0.0851
(1.00) 		0.331
(1.00) 		0.604
(1.00) 		0.807
(1.00) 		0.385
(1.00) 		1
(1.00) 		1
(1.00) 		0.517
(1.00) 		1
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.0751
(1.00)
21q loss 186 (31%) 406 0.932
(1.00) 		0.486
(1.00) 		0.00366
(1.00) 		0.308
(1.00) 		0.986
(1.00) 		0.00482
(1.00) 		0.567
(1.00) 		0.657
(1.00) 		0.00105
(1.00) 		0.472
(1.00) 		0.77
(1.00) 		0.000866
(0.852) 		0.505
(1.00)
xq loss 74 (12%) 518 0.893
(1.00) 		0.758
(1.00) 		0.0908
(1.00) 		0.341
(1.00) 		0.849
(1.00) 		0.21
(1.00) 		0.124
(1.00) 		1
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.0924
(1.00) 		0.721
(1.00)
'6q gain' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000122 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 583
6Q GAIN MUTATED 7 98
6Q GAIN WILD-TYPE 2 485

Figure S1.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.16

Table S2.  Gene #13: '7p gain' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
7P GAIN MUTATED 56 1 18 70 3 2 13 15 54 36 41 18 0
7P GAIN WILD-TYPE 46 0 18 95 7 1 13 7 22 16 19 7 1

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'7p gain' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.02

Table S3.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
7P GAIN MUTATED 162 99 72
7P GAIN WILD-TYPE 173 47 36

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'7p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.23e-05 (Wilcoxon-test), Q value = 0.063

Table S4.  Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
7P GAIN MUTATED 320 2.6 (5.2)
7P GAIN WILD-TYPE 238 1.6 (3.8)

Figure S4.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.091

Table S5.  Gene #14: '7q gain' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
7Q GAIN MUTATED 53 1 16 59 3 1 12 10 52 31 37 17 0
7Q GAIN WILD-TYPE 49 0 20 106 7 2 14 12 24 21 23 8 1

Figure S5.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S6.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
13Q GAIN MUTATED 229 15 103 3
13Q GAIN WILD-TYPE 144 40 40 10

Figure S6.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.13

Table S7.  Gene #36: '20p gain' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
20P GAIN MUTATED 61 1 13 84 4 2 13 20 40 30 46 16 0
20P GAIN WILD-TYPE 41 0 23 81 6 1 13 2 36 22 14 9 1

Figure S7.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.03

Table S8.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
20P GAIN MUTATED 213 18 99 5
20P GAIN WILD-TYPE 160 37 44 8

Figure S8.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 2.77e-06 (Fisher's exact test), Q value = 0.0028

Table S9.  Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
20Q GAIN MUTATED 303 141
20Q GAIN WILD-TYPE 126 18

Figure S9.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.17

Table S10.  Gene #37: '20q gain' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
20Q GAIN MUTATED 77 1 21 112 5 3 18 21 59 42 54 23 0
20Q GAIN WILD-TYPE 25 0 15 53 5 0 8 1 17 10 6 2 1

Figure S10.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S11.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
20Q GAIN MUTATED 278 24 132 7
20Q GAIN WILD-TYPE 95 31 11 6

Figure S11.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'8p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.9e-05 (Wilcoxon-test), Q value = 0.07

Table S12.  Gene #54: '8p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
8P LOSS MUTATED 202 3.2 (6.2)
8P LOSS WILD-TYPE 356 1.6 (3.5)

Figure S12.  Get High-res Image Gene #54: '8p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S13.  Gene #65: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
14Q LOSS MUTATED 124 4 62 1
14Q LOSS WILD-TYPE 249 51 81 12

Figure S13.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S14.  Gene #69: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
17P LOSS MUTATED 208 13 92 6
17P LOSS WILD-TYPE 165 42 51 7

Figure S14.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 4.02e-07 (Fisher's exact test), Q value = 0.00041

Table S15.  Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
18P LOSS MUTATED 235 123
18P LOSS WILD-TYPE 194 36

Figure S15.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.061

Table S16.  Gene #71: '18p loss' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
18P LOSS MUTATED 56 0 16 92 4 3 11 15 51 36 48 21 0
18P LOSS WILD-TYPE 46 1 20 73 6 0 15 7 25 16 12 4 1

Figure S16.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'PATHOLOGY.M.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.051

Table S17.  Gene #71: '18p loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
18P LOSS MUTATED 257 60 8 0 32
18P LOSS WILD-TYPE 186 12 1 1 26

Figure S17.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'18p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S18.  Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
18P LOSS MUTATED 225 9 116 7
18P LOSS WILD-TYPE 148 46 27 6

Figure S18.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 1.01e-08 (Fisher's exact test), Q value = 1e-05

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

nPatients COLON RECTUM
ALL 429 159
18Q LOSS MUTATED 254 133
18Q LOSS WILD-TYPE 175 26

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

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S20.  Gene #72: '18q loss' versus Clinical Feature #4: '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 102 1 36 165 10 3 26 22 76 52 60 25 1
18Q LOSS MUTATED 57 0 20 99 4 3 13 17 55 40 51 22 0
18Q LOSS WILD-TYPE 45 1 16 66 6 0 13 5 21 12 9 3 1

Figure S20.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.N.STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.19

Table S21.  Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
18Q LOSS MUTATED 196 109 82
18Q LOSS WILD-TYPE 139 37 26

Figure S21.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'18q loss' versus 'PATHOLOGY.M.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.1

Table S22.  Gene #72: '18q loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
18Q LOSS MUTATED 280 63 8 0 35
18Q LOSS WILD-TYPE 163 9 1 1 23

Figure S22.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S23.  Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
18Q LOSS MUTATED 241 12 122 10
18Q LOSS WILD-TYPE 132 43 21 3

Figure S23.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000136 (Wilcoxon-test), Q value = 0.14

Table S24.  Gene #72: '18q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
18Q LOSS MUTATED 369 2.4 (4.8)
18Q LOSS WILD-TYPE 189 1.7 (4.5)

Figure S24.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'19p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.74e-06 (Wilcoxon-test), Q value = 0.0028

Table S25.  Gene #73: '19p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
19P LOSS MUTATED 57 4.5 (6.0)
19P LOSS WILD-TYPE 501 1.9 (4.5)

Figure S25.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 4e-05 (Fisher's exact test), Q value = 0.04

Table S26.  Gene #78: '22q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
22Q LOSS MUTATED 84 66 43
22Q LOSS WILD-TYPE 251 80 65

Figure S26.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'22q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 8.35e-05 (Wilcoxon-test), Q value = 0.084

Table S27.  Gene #78: '22q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
22Q LOSS MUTATED 183 2.8 (5.1)
22Q LOSS WILD-TYPE 375 1.9 (4.5)

Figure S27.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 592

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 13

  • 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

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] 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)
[3] 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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