Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1445KB3
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/C1445KB3
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 604 patients, 28 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'.

  • 11q gain cnv correlated to 'AGE'.

  • 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' 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' and 'NUMBER.OF.LYMPH.NODES'.

  • 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, 28 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 401 (66%) 203 0.976
(1.00) 		0.0109
(1.00) 		1.14e-08
(1.17e-05) 		3e-05
(0.0304) 		0.421
(1.00) 		8e-05
(0.0806) 		9e-05
(0.0905) 		0.546
(1.00) 		1e-05
(0.0102) 		0.285
(1.00) 		0.0224
(1.00) 		7.95e-05
(0.0802) 		0.566
(1.00)
18p loss 372 (62%) 232 0.82
(1.00) 		0.0167
(1.00) 		4.54e-07
(0.000465) 		0.00014
(0.14) 		0.828
(1.00) 		0.00319
(1.00) 		0.00012
(0.12) 		0.615
(1.00) 		1e-05
(0.0102) 		0.164
(1.00) 		0.0237
(1.00) 		0.00141
(1.00) 		0.773
(1.00)
7p gain 345 (57%) 259 0.665
(1.00) 		0.15
(1.00) 		0.0943
(1.00) 		0.00022
(0.22) 		0.92
(1.00) 		2e-05
(0.0203) 		0.0879
(1.00) 		0.681
(1.00) 		0.00078
(0.762) 		0.313
(1.00) 		0.377
(1.00) 		4.94e-05
(0.05) 		0.504
(1.00)
20p gain 347 (57%) 257 0.184
(1.00) 		0.563
(1.00) 		0.00689
(1.00) 		0.00022
(0.22) 		0.55
(1.00) 		0.057
(1.00) 		0.00394
(1.00) 		0.118
(1.00) 		2e-05
(0.0203) 		0.314
(1.00) 		0.0834
(1.00) 		0.0283
(1.00) 		0.579
(1.00)
20q gain 455 (75%) 149 0.509
(1.00) 		0.224
(1.00) 		1.21e-06
(0.00124) 		0.00031
(0.308) 		0.295
(1.00) 		0.00051
(0.502) 		0.00428
(1.00) 		0.257
(1.00) 		1e-05
(0.0102) 		0.464
(1.00) 		0.018
(1.00) 		0.00226
(1.00) 		0.14
(1.00)
17p loss 334 (55%) 270 0.168
(1.00) 		0.264
(1.00) 		0.0207
(1.00) 		0.00356
(1.00) 		0.443
(1.00) 		0.00087
(0.849) 		0.0199
(1.00) 		0.251
(1.00) 		1e-05
(0.0102) 		0.311
(1.00) 		0.0777
(1.00) 		0.0002
(0.2) 		0.654
(1.00)
22q loss 196 (32%) 408 0.0218
(1.00) 		0.782
(1.00) 		0.624
(1.00) 		0.00797
(1.00) 		0.289
(1.00) 		4e-05
(0.0405) 		0.0168
(1.00) 		0.794
(1.00) 		0.0196
(1.00) 		0.481
(1.00) 		0.398
(1.00) 		0.000114
(0.115) 		0.537
(1.00)
6q gain 109 (18%) 495 0.52
(1.00) 		0.455
(1.00) 		0.231
(1.00) 		0.0147
(1.00) 		0.599
(1.00) 		0.00214
(1.00) 		0.0397
(1.00) 		0.399
(1.00) 		0.0693
(1.00) 		0.000138
(0.139) 		0.384
(1.00) 		0.00317
(1.00) 		0.698
(1.00)
7q gain 309 (51%) 295 0.899
(1.00) 		0.116
(1.00) 		0.582
(1.00) 		0.00018
(0.18) 		0.648
(1.00) 		0.00054
(0.53) 		0.0274
(1.00) 		0.684
(1.00) 		0.00678
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.00145
(1.00) 		0.202
(1.00)
11q gain 75 (12%) 529 0.438
(1.00) 		8.33e-05
(0.0839) 		0.126
(1.00) 		0.211
(1.00) 		0.551
(1.00) 		0.215
(1.00) 		0.0855
(1.00) 		1
(1.00) 		0.00047
(0.463) 		0.31
(1.00) 		0.703
(1.00) 		0.171
(1.00) 		0.498
(1.00)
13q gain 362 (60%) 242 0.779
(1.00) 		0.596
(1.00) 		0.0147
(1.00) 		0.00123
(1.00) 		0.769
(1.00) 		0.00027
(0.269) 		0.0141
(1.00) 		0.28
(1.00) 		1e-05
(0.0102) 		0.327
(1.00) 		0.0878
(1.00) 		0.00139
(1.00) 		0.0503
(1.00)
8p loss 213 (35%) 391 0.684
(1.00) 		0.787
(1.00) 		0.00276
(1.00) 		0.0335
(1.00) 		0.167
(1.00) 		0.00027
(0.269) 		0.0617
(1.00) 		0.105
(1.00) 		0.00293
(1.00) 		0.291
(1.00) 		0.11
(1.00) 		7.63e-05
(0.0771) 		0.489
(1.00)
14q loss 201 (33%) 403 0.724
(1.00) 		0.241
(1.00) 		0.0191
(1.00) 		0.422
(1.00) 		0.366
(1.00) 		0.0451
(1.00) 		0.0859
(1.00) 		0.604
(1.00) 		1e-05
(0.0102) 		1
(1.00) 		0.946
(1.00) 		0.186
(1.00) 		0.98
(1.00)
19p loss 63 (10%) 541 0.0415
(1.00) 		0.255
(1.00) 		0.13
(1.00) 		0.00272
(1.00) 		0.797
(1.00) 		0.00054
(0.53) 		0.0112
(1.00) 		0.895
(1.00) 		0.143
(1.00) 		0.24
(1.00) 		0.477
(1.00) 		3.72e-06
(0.0038) 		1
(1.00)
1p gain 49 (8%) 555 0.104
(1.00) 		0.836
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.5
(1.00) 		0.253
(1.00) 		0.112
(1.00) 		0.456
(1.00) 		0.0937
(1.00) 		0.535
(1.00) 		0.187
(1.00) 		0.0468
(1.00) 		0.668
(1.00)
1q gain 116 (19%) 488 0.401
(1.00) 		0.461
(1.00) 		0.349
(1.00) 		0.119
(1.00) 		0.0353
(1.00) 		0.0176
(1.00) 		0.0528
(1.00) 		0.408
(1.00) 		0.183
(1.00) 		0.385
(1.00) 		0.295
(1.00) 		0.00118
(1.00) 		0.857
(1.00)
2p gain 119 (20%) 485 0.407
(1.00) 		0.934
(1.00) 		0.0496
(1.00) 		0.263
(1.00) 		0.52
(1.00) 		0.0771
(1.00) 		0.197
(1.00) 		0.413
(1.00) 		0.00208
(1.00) 		0.39
(1.00) 		0.0257
(1.00) 		0.142
(1.00) 		0.845
(1.00)
2q gain 117 (19%) 487 0.233
(1.00) 		0.518
(1.00) 		0.0105
(1.00) 		0.197
(1.00) 		0.579
(1.00) 		0.0352
(1.00) 		0.176
(1.00) 		0.303
(1.00) 		0.00062
(0.607) 		0.076
(1.00) 		0.339
(1.00) 		0.0652
(1.00) 		0.327
(1.00)
3p gain 72 (12%) 532 0.425
(1.00) 		0.0875
(1.00) 		0.0323
(1.00) 		0.0181
(1.00) 		0.982
(1.00) 		0.166
(1.00) 		0.00109
(1.00) 		0.315
(1.00) 		0.0963
(1.00) 		1
(1.00) 		0.973
(1.00) 		0.0815
(1.00) 		0.228
(1.00)
3q gain 97 (16%) 507 0.235
(1.00) 		0.253
(1.00) 		0.0456
(1.00) 		0.0397
(1.00) 		0.893
(1.00) 		0.0574
(1.00) 		0.00063
(0.616) 		0.32
(1.00) 		0.079
(1.00) 		0.642
(1.00) 		0.574
(1.00) 		0.0584
(1.00) 		0.273
(1.00)
4p gain 20 (3%) 584 0.889
(1.00) 		0.378
(1.00) 		0.075
(1.00) 		0.371
(1.00) 		0.372
(1.00) 		0.778
(1.00) 		0.199
(1.00) 		0.171
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.819
(1.00) 		0.155
(1.00)
4q gain 21 (3%) 583 0.355
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.674
(1.00) 		0.969
(1.00) 		0.116
(1.00) 		0.228
(1.00) 		0.118
(1.00) 		0.437
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.0986
(1.00) 		0.365
(1.00)
5p gain 103 (17%) 501 0.559
(1.00) 		0.0808
(1.00) 		0.0513
(1.00) 		0.208
(1.00) 		0.447
(1.00) 		0.0167
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.0266
(1.00) 		0.186
(1.00) 		0.232
(1.00) 		0.0126
(1.00) 		0.0772
(1.00)
5q gain 65 (11%) 539 0.48
(1.00) 		0.718
(1.00) 		0.0747
(1.00) 		0.421
(1.00) 		0.258
(1.00) 		0.298
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.075
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.42
(1.00) 		0.213
(1.00)
6p gain 122 (20%) 482 0.479
(1.00) 		0.434
(1.00) 		0.136
(1.00) 		0.0393
(1.00) 		0.472
(1.00) 		0.00044
(0.435) 		0.145
(1.00) 		0.224
(1.00) 		0.165
(1.00) 		0.000297
(0.295) 		0.294
(1.00) 		0.000906
(0.883) 		0.255
(1.00)
8p gain 167 (28%) 437 0.421
(1.00) 		0.35
(1.00) 		0.307
(1.00) 		0.58
(1.00) 		0.951
(1.00) 		0.317
(1.00) 		0.772
(1.00) 		0.927
(1.00) 		0.575
(1.00) 		0.713
(1.00) 		0.0511
(1.00) 		0.304
(1.00) 		1
(1.00)
8q gain 310 (51%) 294 0.443
(1.00) 		0.108
(1.00) 		0.521
(1.00) 		0.0604
(1.00) 		0.242
(1.00) 		0.0826
(1.00) 		0.0359
(1.00) 		0.871
(1.00) 		0.0434
(1.00) 		0.0383
(1.00) 		0.0277
(1.00) 		0.122
(1.00) 		0.871
(1.00)
9p gain 120 (20%) 484 0.00812
(1.00) 		0.697
(1.00) 		0.0295
(1.00) 		0.0096
(1.00) 		0.458
(1.00) 		0.217
(1.00) 		0.268
(1.00) 		0.759
(1.00) 		0.00402
(1.00) 		1
(1.00) 		0.384
(1.00) 		0.223
(1.00) 		0.0678
(1.00)
9q gain 101 (17%) 503 0.00804
(1.00) 		0.931
(1.00) 		0.269
(1.00) 		0.0398
(1.00) 		0.408
(1.00) 		0.462
(1.00) 		0.42
(1.00) 		0.663
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.729
(1.00) 		0.523
(1.00) 		0.171
(1.00)
10p gain 46 (8%) 558 0.0351
(1.00) 		0.478
(1.00) 		0.731
(1.00) 		0.581
(1.00) 		0.139
(1.00) 		0.0234
(1.00) 		0.462
(1.00) 		1
(1.00) 		0.927
(1.00) 		0.512
(1.00) 		0.575
(1.00) 		0.1
(1.00) 		0.166
(1.00)
10q gain 26 (4%) 578 0.643
(1.00) 		0.0237
(1.00) 		0.822
(1.00) 		0.607
(1.00) 		0.405
(1.00) 		0.0368
(1.00) 		0.386
(1.00) 		0.842
(1.00) 		0.768
(1.00) 		0.329
(1.00) 		0.824
(1.00) 		0.022
(1.00) 		0.0414
(1.00)
11p gain 83 (14%) 521 0.807
(1.00) 		0.00763
(1.00) 		0.0225
(1.00) 		0.145
(1.00) 		0.174
(1.00) 		0.221
(1.00) 		0.133
(1.00) 		0.906
(1.00) 		0.0004
(0.396) 		0.114
(1.00) 		0.535
(1.00) 		0.162
(1.00) 		0.519
(1.00)
12p gain 127 (21%) 477 0.295
(1.00) 		0.151
(1.00) 		0.822
(1.00) 		0.186
(1.00) 		0.337
(1.00) 		0.163
(1.00) 		0.127
(1.00) 		0.921
(1.00) 		0.665
(1.00) 		0.406
(1.00) 		0.783
(1.00) 		0.143
(1.00) 		0.904
(1.00)
12q gain 111 (18%) 493 0.587
(1.00) 		0.0499
(1.00) 		0.192
(1.00) 		0.023
(1.00) 		0.485
(1.00) 		0.0276
(1.00) 		0.0261
(1.00) 		0.53
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.0116
(1.00) 		0.826
(1.00)
14q gain 42 (7%) 562 0.395
(1.00) 		0.977
(1.00) 		0.281
(1.00) 		0.639
(1.00) 		0.942
(1.00) 		0.78
(1.00) 		0.0187
(1.00) 		0.874
(1.00) 		0.211
(1.00) 		0.48
(1.00) 		0.671
(1.00) 		0.382
(1.00) 		0.012
(1.00)
15q gain 15 (2%) 589 0.959
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.603
(1.00) 		0.0782
(1.00) 		0.72
(1.00) 		0.181
(1.00) 		0.0632
(1.00) 		0.0785
(1.00) 		0.204
(1.00) 		0.704
(1.00) 		0.417
(1.00) 		0.393
(1.00)
16p gain 145 (24%) 459 0.277
(1.00) 		0.123
(1.00) 		0.83
(1.00) 		0.0123
(1.00) 		0.985
(1.00) 		0.00144
(1.00) 		0.35
(1.00) 		0.849
(1.00) 		0.00426
(1.00) 		0.229
(1.00) 		0.745
(1.00) 		0.00236
(1.00) 		0.429
(1.00)
16q gain 143 (24%) 461 0.476
(1.00) 		0.0831
(1.00) 		0.589
(1.00) 		0.00415
(1.00) 		0.965
(1.00) 		0.00033
(0.327) 		0.298
(1.00) 		0.849
(1.00) 		0.00377
(1.00) 		0.227
(1.00) 		0.747
(1.00) 		0.00148
(1.00) 		0.429
(1.00)
17p gain 36 (6%) 568 0.0559
(1.00) 		0.766
(1.00) 		0.849
(1.00) 		0.574
(1.00) 		0.311
(1.00) 		0.891
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.699
(1.00) 		0.0678
(1.00)
17q gain 110 (18%) 494 0.1
(1.00) 		0.258
(1.00) 		1
(1.00) 		0.409
(1.00) 		0.65
(1.00) 		0.55
(1.00) 		0.0233
(1.00) 		0.916
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.958
(1.00) 		0.774
(1.00)
18p gain 33 (5%) 571 0.455
(1.00) 		0.515
(1.00) 		0.841
(1.00) 		0.0169
(1.00) 		0.697
(1.00) 		0.0143
(1.00) 		0.243
(1.00) 		0.15
(1.00) 		0.0438
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.0133
(1.00) 		0.812
(1.00)
18q gain 20 (3%) 584 0.98
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.0776
(1.00) 		0.475
(1.00) 		0.154
(1.00) 		0.698
(1.00) 		0.171
(1.00) 		0.0792
(1.00) 		0.263
(1.00) 		0.74
(1.00) 		0.25
(1.00) 		0.177
(1.00)
19p gain 102 (17%) 502 0.548
(1.00) 		0.724
(1.00) 		0.273
(1.00) 		0.883
(1.00) 		0.876
(1.00) 		0.268
(1.00) 		0.296
(1.00) 		0.232
(1.00) 		0.0723
(1.00) 		1
(1.00) 		0.29
(1.00) 		0.499
(1.00) 		0.794
(1.00)
19q gain 111 (18%) 493 0.362
(1.00) 		0.697
(1.00) 		0.637
(1.00) 		0.824
(1.00) 		0.997
(1.00) 		0.24
(1.00) 		0.12
(1.00) 		0.461
(1.00) 		0.25
(1.00) 		1
(1.00) 		0.418
(1.00) 		0.661
(1.00) 		0.595
(1.00)
21q gain 32 (5%) 572 0.749
(1.00) 		0.0122
(1.00) 		0.534
(1.00) 		0.681
(1.00) 		0.233
(1.00) 		0.607
(1.00) 		0.513
(1.00) 		0.72
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.285
(1.00) 		0.804
(1.00)
22q gain 23 (4%) 581 0.701
(1.00) 		0.314
(1.00) 		0.0912
(1.00) 		0.605
(1.00) 		0.117
(1.00) 		0.25
(1.00) 		0.513
(1.00) 		0.833
(1.00) 		0.113
(1.00) 		0.297
(1.00) 		0.328
(1.00) 		0.113
(1.00) 		0.816
(1.00)
xq gain 104 (17%) 500 0.843
(1.00) 		0.478
(1.00) 		0.626
(1.00) 		0.204
(1.00) 		0.597
(1.00) 		0.283
(1.00) 		0.412
(1.00) 		0.281
(1.00) 		0.284
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.424
(1.00) 		0.556
(1.00)
1p loss 134 (22%) 470 0.319
(1.00) 		0.353
(1.00) 		0.0975
(1.00) 		0.192
(1.00) 		0.847
(1.00) 		0.00603
(1.00) 		0.0656
(1.00) 		0.493
(1.00) 		0.0171
(1.00) 		0.423
(1.00) 		0.879
(1.00) 		0.00126
(1.00) 		0.332
(1.00)
1q loss 77 (13%) 527 0.206
(1.00) 		0.19
(1.00) 		0.272
(1.00) 		0.549
(1.00) 		0.931
(1.00) 		0.165
(1.00) 		0.133
(1.00) 		0.0882
(1.00) 		0.23
(1.00) 		0.322
(1.00) 		0.567
(1.00) 		0.0915
(1.00) 		0.0643
(1.00)
2p loss 17 (3%) 587 0.862
(1.00) 		0.206
(1.00) 		0.00107
(1.00) 		0.648
(1.00) 		0.881
(1.00) 		0.797
(1.00) 		0.832
(1.00) 		0.806
(1.00) 		0.0107
(1.00) 		0.228
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.15
(1.00)
2q loss 14 (2%) 590 0.437
(1.00) 		0.505
(1.00) 		0.0657
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.327
(1.00) 		0.432
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.845
(1.00) 		0.44
(1.00)
3p loss 67 (11%) 537 0.101
(1.00) 		0.678
(1.00) 		0.305
(1.00) 		0.0597
(1.00) 		0.037
(1.00) 		0.0272
(1.00) 		0.021
(1.00) 		0.436
(1.00) 		0.0672
(1.00) 		0.263
(1.00) 		0.18
(1.00) 		0.0224
(1.00) 		0.351
(1.00)
3q loss 43 (7%) 561 0.216
(1.00) 		0.537
(1.00) 		0.474
(1.00) 		0.17
(1.00) 		0.13
(1.00) 		0.386
(1.00) 		0.111
(1.00) 		0.207
(1.00) 		0.00737
(1.00) 		0.13
(1.00) 		0.483
(1.00) 		0.527
(1.00) 		0.333
(1.00)
4p loss 188 (31%) 416 0.251
(1.00) 		0.947
(1.00) 		0.136
(1.00) 		0.0143
(1.00) 		0.752
(1.00) 		0.00198
(1.00) 		0.00545
(1.00) 		0.725
(1.00) 		0.0162
(1.00) 		0.000523
(0.514) 		0.15
(1.00) 		0.000449
(0.443) 		0.809
(1.00)
4q loss 182 (30%) 422 0.609
(1.00) 		0.503
(1.00) 		0.00646
(1.00) 		0.0929
(1.00) 		0.643
(1.00) 		0.00455
(1.00) 		0.195
(1.00) 		0.723
(1.00) 		0.00572
(1.00) 		0.000406
(0.402) 		0.942
(1.00) 		0.00196
(1.00) 		0.729
(1.00)
5p loss 82 (14%) 522 0.448
(1.00) 		0.43
(1.00) 		0.228
(1.00) 		0.0151
(1.00) 		0.818
(1.00) 		0.0202
(1.00) 		0.191
(1.00) 		0.554
(1.00) 		0.315
(1.00) 		0.0233
(1.00) 		0.713
(1.00) 		0.0162
(1.00) 		0.428
(1.00)
5q loss 116 (19%) 488 0.0678
(1.00) 		0.572
(1.00) 		0.0272
(1.00) 		0.0724
(1.00) 		0.65
(1.00) 		0.00421
(1.00) 		0.066
(1.00) 		0.535
(1.00) 		0.0397
(1.00) 		0.00227
(1.00) 		0.494
(1.00) 		0.00225
(1.00) 		0.398
(1.00)
6p loss 45 (7%) 559 0.00453
(1.00) 		0.329
(1.00) 		0.861
(1.00) 		0.362
(1.00) 		0.536
(1.00) 		0.265
(1.00) 		0.472
(1.00) 		0.539
(1.00) 		0.148
(1.00) 		0.504
(1.00) 		0.0527
(1.00) 		0.352
(1.00) 		0.00852
(1.00)
6q loss 68 (11%) 536 0.0279
(1.00) 		0.756
(1.00) 		0.378
(1.00) 		0.337
(1.00) 		0.341
(1.00) 		0.111
(1.00) 		0.162
(1.00) 		0.246
(1.00) 		0.0396
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.053
(1.00) 		0.00465
(1.00)
7q loss 4 (1%) 600 0.512
(1.00) 		0.963
(1.00) 		0.296
(1.00) 		0.637
(1.00) 		0.311
(1.00) 		1
(1.00) 		1
(1.00) 		0.345
(1.00) 		0.142
(1.00) 		1
(1.00) 		1
(1.00) 		0.298
(1.00)
8q loss 35 (6%) 569 0.792
(1.00) 		0.902
(1.00) 		0.329
(1.00) 		0.359
(1.00) 		0.56
(1.00) 		0.259
(1.00) 		0.305
(1.00) 		0.0135
(1.00) 		0.48
(1.00) 		1
(1.00) 		0.618
(1.00) 		0.782
(1.00) 		0.0713
(1.00)
9p loss 74 (12%) 530 0.659
(1.00) 		0.209
(1.00) 		0.574
(1.00) 		0.769
(1.00) 		0.0718
(1.00) 		0.329
(1.00) 		0.183
(1.00) 		0.173
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.0466
(1.00) 		0.0778
(1.00) 		0.809
(1.00)
9q loss 74 (12%) 530 0.432
(1.00) 		0.0379
(1.00) 		0.481
(1.00) 		0.517
(1.00) 		0.103
(1.00) 		0.297
(1.00) 		0.0853
(1.00) 		0.536
(1.00) 		0.115
(1.00) 		1
(1.00) 		0.0538
(1.00) 		0.165
(1.00) 		0.778
(1.00)
10p loss 100 (17%) 504 0.293
(1.00) 		0.00501
(1.00) 		0.137
(1.00) 		0.369
(1.00) 		0.818
(1.00) 		0.0967
(1.00) 		0.368
(1.00) 		0.913
(1.00) 		0.0242
(1.00) 		0.00819
(1.00) 		0.985
(1.00) 		0.0192
(1.00) 		0.762
(1.00)
10q loss 109 (18%) 495 0.27
(1.00) 		0.0124
(1.00) 		0.0723
(1.00) 		0.577
(1.00) 		0.986
(1.00) 		0.242
(1.00) 		0.647
(1.00) 		0.833
(1.00) 		0.0197
(1.00) 		0.012
(1.00) 		1
(1.00) 		0.109
(1.00) 		0.876
(1.00)
11p loss 74 (12%) 530 0.612
(1.00) 		0.34
(1.00) 		0.399
(1.00) 		0.203
(1.00) 		0.398
(1.00) 		0.0199
(1.00) 		0.0326
(1.00) 		0.902
(1.00) 		0.226
(1.00) 		0.304
(1.00) 		0.93
(1.00) 		0.00041
(0.406) 		0.27
(1.00)
11q loss 91 (15%) 513 0.225
(1.00) 		0.591
(1.00) 		0.363
(1.00) 		0.505
(1.00) 		0.717
(1.00) 		0.0895
(1.00) 		0.208
(1.00) 		0.649
(1.00) 		0.136
(1.00) 		0.141
(1.00) 		0.981
(1.00) 		0.0432
(1.00) 		0.187
(1.00)
12p loss 70 (12%) 534 0.145
(1.00) 		0.572
(1.00) 		0.248
(1.00) 		0.528
(1.00) 		0.257
(1.00) 		0.0409
(1.00) 		0.344
(1.00) 		0.8
(1.00) 		0.0122
(1.00) 		0.075
(1.00) 		0.905
(1.00) 		0.0465
(1.00) 		0.863
(1.00)
12q loss 69 (11%) 535 0.248
(1.00) 		0.964
(1.00) 		0.664
(1.00) 		0.21
(1.00) 		0.465
(1.00) 		0.0283
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.0881
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.0211
(1.00) 		0.339
(1.00)
13q loss 20 (3%) 584 0.517
(1.00) 		0.912
(1.00) 		0.202
(1.00) 		0.628
(1.00) 		0.592
(1.00) 		0.068
(1.00) 		0.0599
(1.00) 		1
(1.00) 		0.0337
(1.00) 		1
(1.00) 		1
(1.00) 		0.007
(1.00) 		0.0149
(1.00)
15q loss 222 (37%) 382 0.746
(1.00) 		0.407
(1.00) 		0.0448
(1.00) 		0.0385
(1.00) 		0.265
(1.00) 		0.00919
(1.00) 		0.0585
(1.00) 		0.399
(1.00) 		0.00628
(1.00) 		0.0144
(1.00) 		0.832
(1.00) 		0.00332
(1.00) 		0.107
(1.00)
16p loss 40 (7%) 564 0.0845
(1.00) 		0.216
(1.00) 		0.855
(1.00) 		0.123
(1.00) 		0.417
(1.00) 		0.333
(1.00) 		0.368
(1.00) 		0.513
(1.00) 		0.534
(1.00) 		1
(1.00) 		0.149
(1.00) 		0.428
(1.00) 		0.24
(1.00)
16q loss 42 (7%) 562 0.287
(1.00) 		0.113
(1.00) 		0.368
(1.00) 		0.38
(1.00) 		0.769
(1.00) 		0.173
(1.00) 		0.337
(1.00) 		0.749
(1.00) 		0.635
(1.00) 		0.48
(1.00) 		0.39
(1.00) 		0.476
(1.00) 		0.185
(1.00)
17q loss 93 (15%) 511 0.0435
(1.00) 		0.899
(1.00) 		0.444
(1.00) 		0.0447
(1.00) 		0.0635
(1.00) 		0.0129
(1.00) 		0.0651
(1.00) 		0.432
(1.00) 		0.792
(1.00) 		0.635
(1.00) 		0.601
(1.00) 		0.000475
(0.468) 		0.151
(1.00)
19q loss 55 (9%) 549 0.19
(1.00) 		0.606
(1.00) 		0.198
(1.00) 		0.0327
(1.00) 		0.777
(1.00) 		0.00426
(1.00) 		0.128
(1.00) 		0.397
(1.00) 		0.231
(1.00) 		0.194
(1.00) 		0.832
(1.00) 		0.000614
(0.601) 		0.142
(1.00)
20p loss 65 (11%) 539 0.734
(1.00) 		0.511
(1.00) 		0.18
(1.00) 		0.538
(1.00) 		0.442
(1.00) 		0.489
(1.00) 		0.86
(1.00) 		0.514
(1.00) 		0.372
(1.00) 		0.607
(1.00) 		0.579
(1.00) 		0.877
(1.00) 		0.592
(1.00)
20q loss 6 (1%) 598 0.399
(1.00) 		0.168
(1.00) 		0.198
(1.00) 		0.653
(1.00) 		0.717
(1.00) 		0.729
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.354
(1.00) 		1
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.244
(1.00)
21q loss 190 (31%) 414 0.953
(1.00) 		0.463
(1.00) 		0.0021
(1.00) 		0.499
(1.00) 		0.921
(1.00) 		0.0186
(1.00) 		0.707
(1.00) 		0.661
(1.00) 		0.00027
(0.269) 		0.473
(1.00) 		0.668
(1.00) 		0.00389
(1.00) 		0.431
(1.00)
xq loss 77 (13%) 527 0.725
(1.00) 		0.82
(1.00) 		0.0962
(1.00) 		0.307
(1.00) 		0.838
(1.00) 		0.204
(1.00) 		0.0661
(1.00) 		1
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.108
(1.00) 		0.537
(1.00)
'6q gain' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000138 (Fisher's exact test), Q value = 0.14

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

nPatients NO YES
ALL 9 595
6Q GAIN MUTATED 7 102
6Q GAIN WILD-TYPE 2 493

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

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.22

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 36 171 10 3 26 21 78 53 61 27 2
7P GAIN MUTATED 56 1 18 74 3 2 13 15 56 37 41 19 1
7P GAIN WILD-TYPE 46 0 18 97 7 1 13 6 22 16 20 8 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 341 148 112
7P GAIN MUTATED 166 101 75
7P GAIN WILD-TYPE 175 47 37

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 = 4.94e-05 (Wilcoxon-test), Q value = 0.05

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

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
7P GAIN MUTATED 329 2.6 (5.2)
7P GAIN WILD-TYPE 241 1.7 (3.9)

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 = 0.00018 (Fisher's exact test), Q value = 0.18

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 36 171 10 3 26 21 78 53 61 27 2
7Q GAIN MUTATED 53 1 16 63 3 1 12 10 54 32 37 18 1
7Q GAIN WILD-TYPE 49 0 20 108 7 2 14 11 24 21 24 9 1

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

'11q gain' versus 'AGE'

P value = 8.33e-05 (Wilcoxon-test), Q value = 0.084

Table S6.  Gene #22: '11q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 602 66.3 (12.7)
11Q GAIN MUTATED 75 60.9 (12.3)
11Q GAIN WILD-TYPE 527 67.0 (12.6)

Figure S6.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'AGE'

'13q gain' versus 'HISTOLOGICAL.TYPE'

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

Table S7.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
13Q GAIN MUTATED 232 16 106 3
13Q GAIN WILD-TYPE 146 43 40 10

Figure S7.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.22

Table S8.  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 36 171 10 3 26 21 78 53 61 27 2
20P GAIN MUTATED 61 1 13 87 4 2 13 19 40 31 47 18 1
20P GAIN WILD-TYPE 41 0 23 84 6 1 13 2 38 22 14 9 1

Figure S8.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

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

Table S9.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
20P GAIN MUTATED 217 19 101 5
20P GAIN WILD-TYPE 161 40 45 8

Figure S9.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 1.21e-06 (Fisher's exact test), Q value = 0.0012

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

nPatients COLON RECTUM
ALL 438 162
20Q GAIN MUTATED 308 144
20Q GAIN WILD-TYPE 130 18

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 = 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 378 59 146 13
20Q GAIN MUTATED 283 24 135 7
20Q GAIN WILD-TYPE 95 35 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 = 7.63e-05 (Wilcoxon-test), Q value = 0.077

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

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
8P LOSS MUTATED 205 3.2 (6.2)
8P LOSS WILD-TYPE 365 1.7 (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 378 59 146 13
14Q LOSS MUTATED 128 4 64 1
14Q LOSS WILD-TYPE 250 55 82 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 378 59 146 13
17P LOSS MUTATED 212 15 95 6
17P LOSS WILD-TYPE 166 44 51 7

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

'17p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2e-04 (Wilcoxon-test), Q value = 0.2

Table S15.  Gene #69: '17p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
17P LOSS MUTATED 315 2.7 (5.3)
17P LOSS WILD-TYPE 255 1.6 (3.7)

Figure S15.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 4.54e-07 (Fisher's exact test), Q value = 0.00047

Table S16.  Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
18P LOSS MUTATED 243 126
18P LOSS WILD-TYPE 195 36

Figure S16.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.14

Table S17.  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 36 171 10 3 26 21 78 53 61 27 2
18P LOSS MUTATED 56 0 16 97 4 3 11 14 53 37 49 23 1
18P LOSS WILD-TYPE 46 1 20 74 6 0 15 7 25 16 12 4 1

Figure S17.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.00012 (Fisher's exact test), Q value = 0.12

Table S18.  Gene #71: '18p loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
18P LOSS MUTATED 260 62 9 1 36
18P LOSS WILD-TYPE 186 12 1 1 27

Figure S18.  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 S19.  Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
18P LOSS MUTATED 230 12 119 7
18P LOSS WILD-TYPE 148 47 27 6

Figure S19.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 1.14e-08 (Fisher's exact test), Q value = 1.2e-05

Table S20.  Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
18Q LOSS MUTATED 262 136
18Q LOSS WILD-TYPE 176 26

Figure S20.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

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

Table S21.  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 36 171 10 3 26 21 78 53 61 27 2
18Q LOSS MUTATED 57 0 20 104 4 3 13 16 57 41 52 24 1
18Q LOSS WILD-TYPE 45 1 16 67 6 0 13 5 21 12 9 3 1

Figure S21.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 8e-05 (Fisher's exact test), Q value = 0.081

Table S22.  Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
18Q LOSS MUTATED 201 111 86
18Q LOSS WILD-TYPE 140 37 26

Figure S22.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

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

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

Table S23.  Gene #72: '18q loss' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
18Q LOSS MUTATED 283 65 9 1 39
18Q LOSS WILD-TYPE 163 9 1 1 24

Figure S23.  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 S24.  Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
18Q LOSS MUTATED 246 15 125 10
18Q LOSS WILD-TYPE 132 44 21 3

Figure S24.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 7.95e-05 (Wilcoxon-test), Q value = 0.08

Table S25.  Gene #72: '18q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
18Q LOSS MUTATED 380 2.5 (4.8)
18Q LOSS WILD-TYPE 190 1.7 (4.5)

Figure S25.  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 = 3.72e-06 (Wilcoxon-test), Q value = 0.0038

Table S26.  Gene #73: '19p loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
19P LOSS MUTATED 59 4.5 (5.9)
19P LOSS WILD-TYPE 511 2.0 (4.5)

Figure S26.  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 S27.  Gene #78: '22q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
22Q LOSS MUTATED 85 66 44
22Q LOSS WILD-TYPE 256 82 68

Figure S27.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

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

P value = 0.000114 (Wilcoxon-test), Q value = 0.11

Table S28.  Gene #78: '22q loss' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
22Q LOSS MUTATED 185 2.9 (5.1)
22Q LOSS WILD-TYPE 385 1.9 (4.5)

Figure S28.  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 = 604

  • 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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