Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1WD3ZQD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WD3ZQD
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 81 arm-level events and 13 clinical features across 447 patients, 182 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'PATHOLOGY_M_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 2q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 3p gain cnv correlated to 'PATHOLOGIC_STAGE'.

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

  • 4p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 4q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 5p gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 6p gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 6q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 7p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 7q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 8q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 9p gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 9q gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 10p gain cnv correlated to 'Time to Death'.

  • 10q gain cnv correlated to 'RACE' and 'ETHNICITY'.

  • 11p gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 12q gain cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 13q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.

  • 14q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 16p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 16q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17q gain cnv correlated to 'ETHNICITY'.

  • 18p gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 18q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 20q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xp gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • xq gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 1p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 1q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 4p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 4q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 5p loss cnv correlated to 'PATHOLOGIC_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'ETHNICITY'.

  • 5q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'ETHNICITY'.

  • 6p loss cnv correlated to 'Time to Death' and 'RACE'.

  • 6q loss cnv correlated to 'Time to Death',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 8p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.

  • 8q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'PATHOLOGY_M_STAGE'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 9q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 10p loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 10q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 11p loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 11q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 12p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 12q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 13q loss cnv correlated to 'NUMBER_OF_LYMPH_NODES' and 'RACE'.

  • 14q loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 15q loss cnv correlated to 'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17q loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 18p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 18q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 19p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 19q loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 21q loss cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 22q loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • xp loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • xq loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_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 81 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 182 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
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 Wilcoxon-test Fisher's exact test Fisher's exact test
11p gain 53 (12%) 394 0.528
(0.892) 		0.0057
(0.0793) 		0.0115
(0.124) 		0.071
(0.34) 		0.0125
(0.129) 		0.00805
(0.0998) 		1
(1.00) 		1
(1.00) 		0.00471
(0.0709) 		0.28
(0.729) 		0.0106
(0.118) 		0.625
(0.949) 		0.429
(0.835)
13q gain 255 (57%) 192 0.554
(0.91) 		0.657
(0.97) 		0.00057
(0.0188) 		0.98
(1.00) 		0.00356
(0.0595) 		0.00233
(0.0472) 		0.444
(0.845) 		0.746
(1.00) 		2.06e-06
(0.000434) 		0.0236
(0.176) 		0.0082
(0.1) 		0.188
(0.599) 		0.641
(0.96)
5q loss 78 (17%) 369 0.0319
(0.209) 		0.344
(0.763) 		0.0415
(0.244) 		0.812
(1.00) 		0.00199
(0.0419) 		0.0258
(0.189) 		0.262
(0.701) 		1
(1.00) 		0.273
(0.722) 		0.748
(1.00) 		0.000516
(0.0181) 		0.351
(0.769) 		0.0212
(0.164)
18q loss 269 (60%) 178 0.952
(1.00) 		0.0318
(0.209) 		8e-05
(0.00702) 		0.779
(1.00) 		0.00039
(0.0152) 		0.000234
(0.013) 		0.208
(0.629) 		0.739
(1.00) 		5.53e-10
(2.91e-07) 		0.162
(0.555) 		0.000373
(0.0152) 		0.929
(1.00) 		1
(1.00)
7p gain 245 (55%) 202 0.823
(1.00) 		0.123
(0.493) 		0.00012
(0.00972) 		0.326
(0.75) 		0.0002
(0.0129) 		0.0201
(0.16) 		0.924
(1.00) 		0.737
(1.00) 		0.0171
(0.15) 		0.368
(0.781) 		0.000717
(0.0229) 		0.65
(0.967) 		1
(1.00)
7q gain 222 (50%) 225 0.941
(1.00) 		0.0706
(0.34) 		0.0161
(0.145) 		0.16
(0.549) 		0.0151
(0.14) 		0.0195
(0.158) 		1
(1.00) 		0.747
(1.00) 		0.0371
(0.229) 		0.554
(0.91) 		0.0148
(0.14) 		0.448
(0.846) 		1
(1.00)
11q gain 51 (11%) 396 0.757
(1.00) 		0.00034
(0.0152) 		0.015
(0.14) 		0.26
(0.698) 		0.0135
(0.135) 		0.0802
(0.366) 		1
(1.00) 		1
(1.00) 		0.00759
(0.0963) 		0.354
(0.771) 		0.014
(0.137) 		0.708
(0.999) 		0.409
(0.812)
20q gain 318 (71%) 129 0.957
(1.00) 		0.288
(0.729) 		0.0119
(0.126) 		0.24
(0.676) 		0.0186
(0.153) 		0.00399
(0.0627) 		0.211
(0.633) 		1
(1.00) 		3.68e-07
(0.000129) 		0.16
(0.549) 		0.0289
(0.204) 		0.658
(0.97) 		1
(1.00)
1p loss 94 (21%) 353 0.00558
(0.0793) 		0.945
(1.00) 		0.0101
(0.116) 		0.43
(0.835) 		0.00158
(0.0362) 		0.00119
(0.0299) 		0.245
(0.683) 		0.214
(0.634) 		0.237
(0.673) 		0.498
(0.879) 		0.000411
(0.0155) 		0.44
(0.841) 		0.198
(0.616)
1q loss 55 (12%) 392 0.00897
(0.106) 		0.916
(1.00) 		0.0403
(0.238) 		0.862
(1.00) 		0.0418
(0.244) 		0.0325
(0.209) 		0.194
(0.612) 		0.61
(0.941) 		1
(1.00) 		0.523
(0.89) 		0.0216
(0.166) 		0.222
(0.646) 		0.0749
(0.353)
4p loss 135 (30%) 312 0.0557
(0.289) 		0.983
(1.00) 		0.00217
(0.0448) 		0.352
(0.769) 		0.00328
(0.0586) 		1.86e-05
(0.00245) 		0.918
(1.00) 		0.465
(0.857) 		0.015
(0.14) 		0.0489
(0.266) 		0.000909
(0.0252) 		0.705
(0.998) 		0.0748
(0.353)
4q loss 124 (28%) 323 0.0206
(0.162) 		0.947
(1.00) 		0.0138
(0.136) 		0.33
(0.75) 		0.00242
(0.0481) 		0.00514
(0.0752) 		0.832
(1.00) 		0.285
(0.729) 		0.0887
(0.394) 		0.486
(0.875) 		0.000981
(0.0254) 		0.401
(0.805) 		0.0622
(0.308)
8p loss 140 (31%) 307 0.702
(0.997) 		0.41
(0.812) 		0.0111
(0.122) 		0.234
(0.669) 		0.00099
(0.0254) 		0.000385
(0.0152) 		0.309
(0.739) 		1
(1.00) 		0.051
(0.271) 		0.0388
(0.232) 		0.000359
(0.0152) 		0.322
(0.75) 		0.595
(0.94)
17p loss 233 (52%) 214 0.132
(0.498) 		0.117
(0.478) 		1e-05
(0.0015) 		0.659
(0.97) 		0.00037
(0.0152) 		0.000325
(0.0152) 		0.0463
(0.255) 		1
(1.00) 		2.68e-06
(0.00047) 		0.0562
(0.29) 		6.64e-05
(0.00699) 		0.832
(1.00) 		1
(1.00)
18p loss 252 (56%) 195 0.785
(1.00) 		0.0449
(0.252) 		0.00018
(0.0129) 		0.91
(1.00) 		0.00572
(0.0793) 		4.93e-05
(0.00577) 		0.293
(0.729) 		1
(1.00) 		1.55e-10
(1.64e-07) 		0.048
(0.263) 		0.00333
(0.0586) 		0.936
(1.00) 		0.638
(0.957)
22q loss 144 (32%) 303 0.0997
(0.43) 		0.692
(0.989) 		0.00022
(0.0129) 		0.467
(0.857) 		0.00021
(0.0129) 		0.00123
(0.0302) 		0.919
(1.00) 		1
(1.00) 		0.00459
(0.0709) 		0.509
(0.884) 		0.000317
(0.0152) 		0.302
(0.736) 		0.591
(0.938)
9p gain 80 (18%) 367 0.00339
(0.0586) 		0.423
(0.827) 		0.0106
(0.118) 		0.541
(0.895) 		0.252
(0.687) 		0.138
(0.507) 		0.805
(1.00) 		0.655
(0.97) 		0.0176
(0.153) 		0.928
(1.00) 		0.214
(0.634) 		0.0272
(0.195) 		0.153
(0.534)
16p gain 107 (24%) 340 0.316
(0.744) 		0.173
(0.574) 		0.00321
(0.0586) 		0.924
(1.00) 		0.00531
(0.0766) 		0.329
(0.75) 		0.912
(1.00) 		1
(1.00) 		0.00172
(0.0377) 		0.888
(1.00) 		0.00351
(0.0595) 		0.436
(0.838) 		1
(1.00)
16q gain 105 (23%) 342 0.306
(0.737) 		0.128
(0.496) 		0.00056
(0.0188) 		0.941
(1.00) 		0.00273
(0.0523) 		0.623
(0.948) 		0.823
(1.00) 		1
(1.00) 		0.00271
(0.0523) 		0.761
(1.00) 		0.00339
(0.0586) 		0.444
(0.845) 		1
(1.00)
19p loss 39 (9%) 408 0.0791
(0.365) 		0.223
(0.648) 		0.00932
(0.109) 		1
(1.00) 		0.0008
(0.0241) 		0.00505
(0.0749) 		0.868
(1.00) 		0.557
(0.911) 		0.33
(0.75) 		0.311
(0.743) 		7.82e-05
(0.00702) 		0.909
(1.00) 		1
(1.00)
4p gain 12 (3%) 435 0.911
(1.00) 		0.255
(0.691) 		0.205
(0.627) 		0.689
(0.987) 		0.027
(0.195) 		0.172
(0.574) 		0.39
(0.799) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0159
(0.144) 		0.0029
(0.0545) 		1
(1.00)
4q gain 17 (4%) 430 0.491
(0.875) 		0.808
(1.00) 		0.461
(0.857) 		0.952
(1.00) 		0.0084
(0.101) 		0.0629
(0.309) 		0.336
(0.75) 		1
(1.00) 		0.489
(0.875) 		0.403
(0.808) 		0.00652
(0.088) 		0.0314
(0.209) 		1
(1.00)
6q gain 77 (17%) 370 0.532
(0.892) 		0.442
(0.842) 		0.0293
(0.205) 		0.97
(1.00) 		0.0246
(0.182) 		0.282
(0.729) 		0.802
(1.00) 		0.187
(0.599) 		0.716
(1.00) 		0.868
(1.00) 		0.0367
(0.227) 		0.83
(1.00) 		1
(1.00)
20p gain 241 (54%) 206 0.321
(0.75) 		0.335
(0.75) 		0.0039
(0.0627) 		0.805
(1.00) 		0.147
(0.524) 		0.000933
(0.0252) 		0.217
(0.639) 		0.514
(0.888) 		0.00075
(0.0232) 		0.102
(0.439) 		0.106
(0.451) 		0.931
(1.00) 		0.35
(0.769)
5p loss 59 (13%) 388 0.153
(0.535) 		0.489
(0.875) 		0.0163
(0.146) 		0.366
(0.781) 		0.0579
(0.294) 		0.151
(0.532) 		0.889
(1.00) 		1
(1.00) 		0.306
(0.737) 		0.491
(0.875) 		0.038
(0.232) 		0.499
(0.879) 		0.00948
(0.11)
6q loss 45 (10%) 402 0.0186
(0.153) 		0.811
(1.00) 		0.714
(1.00) 		0.248
(0.687) 		0.0504
(0.27) 		0.241
(0.676) 		0.531
(0.892) 		0.213
(0.634) 		0.643
(0.96) 		0.176
(0.577) 		0.00714
(0.094) 		0.0133
(0.135) 		1
(1.00)
15q loss 156 (35%) 291 0.309
(0.739) 		0.59
(0.938) 		0.0544
(0.286) 		0.648
(0.967) 		0.0601
(0.299) 		0.00141
(0.0331) 		0.62
(0.947) 		0.727
(1.00) 		0.028
(0.199) 		0.467
(0.857) 		0.0318
(0.209) 		0.279
(0.729) 		0.618
(0.947)
17q loss 66 (15%) 381 0.127
(0.496) 		0.88
(1.00) 		0.13
(0.496) 		0.407
(0.812) 		0.0158
(0.144) 		0.0427
(0.247) 		0.791
(1.00) 		0.634
(0.956) 		1
(1.00) 		0.748
(1.00) 		0.000913
(0.0252) 		0.139
(0.507) 		1
(1.00)
19q loss 35 (8%) 412 0.249
(0.687) 		0.369
(0.781) 		0.0446
(0.252) 		0.984
(1.00) 		0.00172
(0.0377) 		0.018
(0.153) 		0.603
(0.941) 		0.506
(0.884) 		0.439
(0.841) 		0.264
(0.703) 		0.000486
(0.0176) 		0.0751
(0.353) 		1
(1.00)
21q loss 122 (27%) 325 0.669
(0.973) 		0.863
(1.00) 		0.534
(0.892) 		0.47
(0.861) 		0.0304
(0.209) 		0.121
(0.487) 		1
(1.00) 		0.712
(1.00) 		0.00781
(0.0979) 		0.869
(1.00) 		0.0332
(0.211) 		0.387
(0.799) 		0.0646
(0.317)
xp loss 64 (14%) 383 0.096
(0.419) 		0.699
(0.997) 		0.137
(0.507) 		0.173
(0.574) 		0.00132
(0.0316) 		0.032
(0.209) 		0.177
(0.578) 		0.367
(0.781) 		0.331
(0.75) 		0.901
(1.00) 		0.000213
(0.0129) 		0.619
(0.947) 		1
(1.00)
xq loss 52 (12%) 395 0.399
(0.805) 		0.618
(0.947) 		0.249
(0.687) 		0.181
(0.586) 		0.0122
(0.128) 		0.0106
(0.118) 		0.306
(0.737) 		0.606
(0.941) 		0.83
(1.00) 		0.558
(0.911) 		0.00396
(0.0627) 		0.557
(0.911) 		1
(1.00)
1q gain 80 (18%) 367 0.294
(0.729) 		0.541
(0.895) 		0.333
(0.75) 		0.486
(0.875) 		0.144
(0.518) 		0.00711
(0.094) 		0.108
(0.458) 		0.667
(0.973) 		0.103
(0.44) 		0.29
(0.729) 		0.0363
(0.226) 		1
(1.00) 		1
(1.00)
3q gain 65 (15%) 382 0.0345
(0.217) 		0.296
(0.729) 		0.00381
(0.0627) 		0.62
(0.947) 		0.0675
(0.328) 		0.0651
(0.318) 		0.592
(0.938) 		0.365
(0.781) 		0.331
(0.75) 		0.871
(1.00) 		0.156
(0.544) 		0.25
(0.687) 		0.486
(0.875)
6p gain 85 (19%) 362 0.827
(1.00) 		0.666
(0.973) 		0.0771
(0.358) 		0.937
(1.00) 		0.0181
(0.153) 		0.601
(0.941) 		0.336
(0.75) 		0.381
(0.795) 		0.725
(1.00) 		0.67
(0.973) 		0.0229
(0.173) 		0.302
(0.736) 		1
(1.00)
8q gain 226 (51%) 221 0.489
(0.875) 		0.015
(0.14) 		0.487
(0.875) 		0.268
(0.712) 		0.542
(0.896) 		0.173
(0.574) 		0.508
(0.884) 		1
(1.00) 		0.0257
(0.189) 		0.502
(0.88) 		0.397
(0.804) 		0.891
(1.00) 		0.627
(0.95)
9q gain 71 (16%) 376 0.00842
(0.101) 		0.391
(0.799) 		0.181
(0.585) 		0.475
(0.868) 		0.538
(0.894) 		0.252
(0.687) 		0.898
(1.00) 		0.628
(0.95) 		0.0225
(0.172) 		0.971
(1.00) 		0.377
(0.792) 		0.17
(0.57) 		0.486
(0.875)
10q gain 23 (5%) 424 0.677
(0.979) 		0.0798
(0.365) 		0.527
(0.892) 		0.911
(1.00) 		0.237
(0.673) 		0.499
(0.879) 		0.522
(0.89) 		0.371
(0.781) 		0.535
(0.893) 		0.881
(1.00) 		0.0818
(0.369) 		0.0185
(0.153) 		0.0186
(0.153)
12q gain 87 (19%) 360 0.893
(1.00) 		0.123
(0.493) 		0.0301
(0.209) 		0.456
(0.857) 		0.0574
(0.294) 		0.3
(0.734) 		0.72
(1.00) 		0.683
(0.984) 		0.294
(0.729) 		0.335
(0.75) 		0.0268
(0.195) 		0.759
(1.00) 		1
(1.00)
14q gain 35 (8%) 412 0.654
(0.97) 		0.777
(1.00) 		0.516
(0.889) 		0.832
(1.00) 		0.479
(0.871) 		0.294
(0.729) 		0.725
(1.00) 		1
(1.00) 		0.0387
(0.232) 		0.727
(1.00) 		0.296
(0.729) 		0.023
(0.173) 		1
(1.00)
18p gain 22 (5%) 425 0.282
(0.729) 		0.514
(0.888) 		0.0973
(0.422) 		0.966
(1.00) 		0.0321
(0.209) 		1
(1.00) 		0.382
(0.796) 		1
(1.00) 		0.0195
(0.158) 		0.531
(0.892) 		0.0547
(0.287) 		0.774
(1.00) 		1
(1.00)
6p loss 33 (7%) 414 0.0356
(0.223) 		0.195
(0.612) 		0.706
(0.998) 		0.128
(0.496) 		0.939
(1.00) 		0.434
(0.837) 		0.371
(0.781) 		0.148
(0.525) 		0.788
(1.00) 		0.112
(0.463) 		0.95
(1.00) 		0.0315
(0.209) 		1
(1.00)
8q loss 24 (5%) 423 0.88
(1.00) 		0.791
(1.00) 		0.0454
(0.252) 		0.27
(0.716) 		0.0198
(0.159) 		0.0329
(0.21) 		0.676
(0.979) 		1
(1.00) 		0.552
(0.909) 		0.877
(1.00) 		0.742
(1.00) 		0.07
(0.338) 		1
(1.00)
10p loss 67 (15%) 380 0.886
(1.00) 		0.19
(0.604) 		0.0455
(0.252) 		0.927
(1.00) 		0.0814
(0.369) 		0.0203
(0.16) 		0.791
(1.00) 		0.187
(0.599) 		0.332
(0.75) 		0.582
(0.932) 		0.0324
(0.209) 		0.493
(0.875) 		0.521
(0.89)
12p loss 46 (10%) 401 0.147
(0.524) 		0.325
(0.75) 		0.42
(0.824) 		0.436
(0.838) 		0.0933
(0.411) 		0.241
(0.676) 		1
(1.00) 		1
(1.00) 		0.0117
(0.125) 		0.952
(1.00) 		0.0392
(0.233) 		0.831
(1.00) 		1
(1.00)
12q loss 48 (11%) 399 0.253
(0.687) 		0.447
(0.846) 		0.145
(0.52) 		0.474
(0.867) 		0.0387
(0.232) 		0.113
(0.466) 		0.76
(1.00) 		0.606
(0.941) 		0.0443
(0.252) 		0.87
(1.00) 		0.0138
(0.136) 		0.314
(0.743) 		1
(1.00)
13q loss 12 (3%) 435 0.398
(0.804) 		0.996
(1.00) 		0.791
(1.00) 		0.454
(0.854) 		0.11
(0.462) 		0.624
(0.948) 		0.776
(1.00) 		1
(1.00) 		0.177
(0.578) 		0.82
(1.00) 		0.0131
(0.134) 		0.0179
(0.153) 		1
(1.00)
14q loss 136 (30%) 311 0.788
(1.00) 		0.458
(0.857) 		0.152
(0.533) 		0.333
(0.75) 		0.129
(0.496) 		0.0115
(0.124) 		0.837
(1.00) 		0.724
(1.00) 		6.07e-07
(0.00016) 		0.737
(1.00) 		0.208
(0.629) 		0.891
(1.00) 		1
(1.00)
2q gain 77 (17%) 370 0.307
(0.737) 		0.397
(0.804) 		0.252
(0.687) 		0.288
(0.729) 		0.0437
(0.251) 		0.575
(0.929) 		0.802
(1.00) 		0.671
(0.973) 		0.141
(0.513) 		0.159
(0.548) 		0.0387
(0.232) 		0.522
(0.89) 		0.175
(0.577)
3p gain 45 (10%) 402 0.219
(0.642) 		0.0958
(0.419) 		0.00091
(0.0252) 		0.834
(1.00) 		0.234
(0.669) 		0.21
(0.633) 		0.638
(0.957) 		0.606
(0.941) 		0.818
(1.00) 		0.945
(1.00) 		0.127
(0.496) 		0.195
(0.612) 		1
(1.00)
5p gain 67 (15%) 380 0.755
(1.00) 		0.0915
(0.405) 		0.17
(0.57) 		0.88
(1.00) 		0.0494
(0.267) 		0.559
(0.911) 		0.289
(0.729) 		1
(1.00) 		0.847
(1.00) 		0.422
(0.825) 		0.0315
(0.209) 		0.216
(0.637) 		1
(1.00)
10p gain 37 (8%) 410 0.0325
(0.209) 		0.555
(0.911) 		0.417
(0.824) 		0.409
(0.812) 		0.0886
(0.394) 		0.306
(0.737) 		0.731
(1.00) 		1
(1.00) 		0.803
(1.00) 		0.396
(0.804) 		0.112
(0.463) 		0.112
(0.463) 		0.055
(0.287)
17q gain 81 (18%) 366 0.206
(0.627) 		0.418
(0.824) 		0.135
(0.507) 		0.325
(0.75) 		0.131
(0.498) 		0.0449
(0.252) 		0.902
(1.00) 		0.671
(0.973) 		0.207
(0.628) 		0.328
(0.75) 		0.772
(1.00) 		0.795
(1.00) 		0.0294
(0.205)
18q gain 13 (3%) 434 0.706
(0.998) 		0.0885
(0.394) 		0.431
(0.836) 		0.719
(1.00) 		0.3
(0.734) 		1
(1.00) 		0.583
(0.932) 		1
(1.00) 		0.0212
(0.164) 		1
(1.00) 		0.884
(1.00) 		0.313
(0.743) 		1
(1.00)
21q gain 24 (5%) 423 0.757
(1.00) 		0.00175
(0.0377) 		0.387
(0.799) 		0.111
(0.463) 		0.287
(0.729) 		0.514
(0.888) 		0.533
(0.892) 		0.355
(0.771) 		0.221
(0.643) 		0.43
(0.835) 		0.139
(0.507) 		0.602
(0.941) 		1
(1.00)
xp gain 66 (15%) 381 0.887
(1.00) 		0.679
(0.979) 		0.277
(0.728) 		0.00586
(0.0801) 		0.494
(0.875) 		0.847
(1.00) 		0.23
(0.662) 		0.369
(0.781) 		0.846
(1.00) 		0.968
(1.00) 		0.668
(0.973) 		0.831
(1.00) 		1
(1.00)
xq gain 76 (17%) 371 0.517
(0.89) 		0.737
(1.00) 		0.0829
(0.373) 		0.0075
(0.0963) 		0.79
(1.00) 		1
(1.00) 		0.315
(0.744) 		0.651
(0.969) 		0.465
(0.857) 		0.834
(1.00) 		0.85
(1.00) 		0.73
(1.00) 		1
(1.00)
9p loss 53 (12%) 394 0.669
(0.973) 		0.381
(0.795) 		0.949
(1.00) 		0.139
(0.507) 		0.391
(0.799) 		0.4
(0.805) 		0.146
(0.524) 		0.61
(0.941) 		0.00471
(0.0709) 		0.514
(0.888) 		0.129
(0.496) 		0.804
(1.00) 		0.419
(0.824)
9q loss 52 (12%) 395 0.532
(0.892) 		0.138
(0.507) 		0.769
(1.00) 		0.158
(0.547) 		0.243
(0.681) 		0.0567
(0.291) 		0.465
(0.857) 		0.61
(0.941) 		0.00743
(0.0963) 		0.55
(0.908) 		0.136
(0.507) 		0.809
(1.00) 		0.439
(0.841)
10q loss 71 (16%) 376 0.576
(0.929) 		0.126
(0.496) 		0.163
(0.555) 		0.915
(1.00) 		0.202
(0.623) 		0.0427
(0.247) 		0.7
(0.997) 		0.214
(0.634) 		0.19
(0.604) 		0.264
(0.703) 		0.126
(0.496) 		0.579
(0.931) 		0.538
(0.894)
11p loss 51 (11%) 396 0.537
(0.894) 		0.636
(0.957) 		0.524
(0.89) 		0.847
(1.00) 		0.0599
(0.299) 		0.124
(0.494) 		0.768
(1.00) 		1
(1.00) 		0.664
(0.973) 		0.479
(0.871) 		0.0148
(0.14) 		0.459
(0.857) 		1
(1.00)
11q loss 62 (14%) 385 0.434
(0.837) 		0.401
(0.805) 		0.296
(0.729) 		0.255
(0.691) 		0.058
(0.294) 		0.0171
(0.15) 		0.494
(0.875) 		1
(1.00) 		1
(1.00) 		0.458
(0.857) 		0.0439
(0.251) 		0.407
(0.812) 		1
(1.00)
1p gain 35 (8%) 412 0.691
(0.989) 		0.379
(0.794) 		0.902
(1.00) 		0.781
(1.00) 		0.759
(1.00) 		0.196
(0.612) 		0.725
(1.00) 		0.52
(0.89) 		0.202
(0.623) 		0.312
(0.743) 		0.316
(0.744) 		0.361
(0.781) 		0.347
(0.766)
2p gain 81 (18%) 366 0.362
(0.781) 		0.868
(1.00) 		0.463
(0.857) 		0.344
(0.763) 		0.143
(0.518) 		0.467
(0.857) 		0.624
(0.948) 		0.679
(0.979) 		0.0752
(0.353) 		0.0756
(0.353) 		0.113
(0.466) 		0.732
(1.00) 		0.198
(0.616)
5q gain 42 (9%) 405 0.654
(0.97) 		0.906
(1.00) 		0.256
(0.691) 		0.824
(1.00) 		0.293
(0.729) 		0.632
(0.954) 		0.519
(0.89) 		1
(1.00) 		0.635
(0.956) 		0.366
(0.781) 		0.975
(1.00) 		0.274
(0.722) 		1
(1.00)
8p gain 132 (30%) 315 0.664
(0.973) 		0.239
(0.676) 		0.793
(1.00) 		0.702
(0.997) 		0.448
(0.846) 		1
(1.00) 		0.836
(1.00) 		0.718
(1.00) 		0.289
(0.729) 		0.531
(0.892) 		0.37
(0.781) 		0.98
(1.00) 		0.599
(0.941)
12p gain 93 (21%) 354 0.392
(0.799) 		0.34
(0.757) 		0.167
(0.565) 		0.389
(0.799) 		0.291
(0.729) 		0.739
(1.00) 		0.816
(1.00) 		0.687
(0.986) 		0.613
(0.944) 		0.504
(0.882) 		0.133
(0.501) 		1
(1.00) 		1
(1.00)
15q gain 12 (3%) 435 0.744
(1.00) 		0.29
(0.729) 		0.719
(1.00) 		0.508
(0.884) 		0.721
(1.00) 		0.118
(0.481) 		0.0759
(0.353) 		1
(1.00) 		1
(1.00) 		0.0503
(0.27) 		0.326
(0.75) 		0.392
(0.799) 		1
(1.00)
17p gain 29 (6%) 418 0.0795
(0.365) 		0.607
(0.941) 		0.585
(0.933) 		0.85
(1.00) 		0.329
(0.75) 		0.56
(0.911) 		0.702
(0.997) 		1
(1.00) 		0.573
(0.927) 		0.913
(1.00) 		0.782
(1.00) 		0.052
(0.275) 		0.279
(0.729)
19p gain 74 (17%) 373 0.291
(0.729) 		0.882
(1.00) 		0.579
(0.931) 		0.813
(1.00) 		0.121
(0.487) 		0.563
(0.914) 		0.0971
(0.422) 		0.194
(0.612) 		0.352
(0.769) 		0.302
(0.736) 		0.934
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 84 (19%) 363 0.491
(0.875) 		0.892
(1.00) 		0.739
(1.00) 		0.918
(1.00) 		0.2
(0.619) 		0.463
(0.857) 		0.184
(0.591) 		0.39
(0.799) 		1
(1.00) 		0.331
(0.75) 		0.905
(1.00) 		0.861
(1.00) 		1
(1.00)
22q gain 13 (3%) 434 0.572
(0.926) 		0.334
(0.75) 		0.58
(0.931) 		0.29
(0.729) 		0.924
(1.00) 		0.118
(0.481) 		0.583
(0.932) 		1
(1.00) 		0.231
(0.663) 		0.371
(0.781) 		0.492
(0.875) 		0.791
(1.00) 		1
(1.00)
2p loss 6 (1%) 441 0.75
(1.00) 		0.685
(0.985) 		0.178
(0.578) 		0.844
(1.00) 		0.849
(1.00) 		0.595
(0.94) 		0.22
(0.643) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.522
(0.89) 		1
(1.00)
2q loss 7 (2%) 440 0.994
(1.00) 		0.658
(0.97) 		0.225
(0.65) 		1
(1.00) 		1
(1.00) 		0.605
(0.941) 		0.126
(0.496) 		1
(1.00) 		0.601
(0.941) 		1
(1.00) 		0.804
(1.00) 		1
(1.00)
3p loss 54 (12%) 393 0.165
(0.559) 		0.595
(0.94) 		0.205
(0.627) 		0.138
(0.507) 		0.15
(0.529) 		0.0586
(0.294) 		1
(1.00) 		0.609
(0.941) 		0.204
(0.626) 		0.896
(1.00) 		0.13
(0.496) 		0.642
(0.96) 		0.419
(0.824)
3q loss 33 (7%) 414 0.814
(1.00) 		0.463
(0.857) 		0.662
(0.973) 		0.501
(0.879) 		0.909
(1.00) 		0.294
(0.729) 		0.371
(0.781) 		1
(1.00) 		0.6
(0.941) 		0.933
(1.00) 		0.842
(1.00) 		0.5
(0.879) 		1
(1.00)
7q loss 4 (1%) 443 0.363
(0.781) 		0.1
(0.432) 		0.314
(0.743) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.325
(0.75) 		1
(1.00) 		0.0585
(0.294)
16p loss 31 (7%) 416 0.212
(0.634) 		0.132
(0.498) 		0.391
(0.799) 		0.526
(0.892) 		0.687
(0.986) 		0.274
(0.722) 		0.71
(1) 		1
(1.00) 		0.41
(0.812) 		0.176
(0.577) 		0.445
(0.845) 		0.257
(0.691) 		0.325
(0.75)
16q loss 28 (6%) 419 0.35
(0.769) 		0.0489
(0.266) 		0.601
(0.941) 		0.732
(1.00) 		0.83
(1.00) 		0.383
(0.796) 		0.846
(1.00) 		1
(1.00) 		0.565
(0.917) 		0.284
(0.729) 		0.618
(0.947) 		0.231
(0.663) 		0.291
(0.729)
20p loss 43 (10%) 404 0.36
(0.781) 		0.432
(0.836) 		0.588
(0.936) 		0.91
(1.00) 		0.489
(0.875) 		0.815
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.244
(0.681) 		1
(1.00) 		0.716
(1.00) 		0.709
(0.999) 		0.357
(0.776)
20q loss 4 (1%) 443 0.347
(0.766) 		0.247
(0.685) 		0.467
(0.857) 		0.779
(1.00) 		0.13
(0.496) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.163
(0.555) 		1
(1.00)
'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00711 (Fisher's exact test), Q value = 0.094

Table S1.  Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
1Q GAIN MUTATED 51 20
1Q GAIN WILD-TYPE 273 44

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0363 (Wilcoxon-test), Q value = 0.23

Table S2.  Gene #2: '1q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
1Q GAIN MUTATED 76 2.7 (4.4)
1Q GAIN WILD-TYPE 345 2.0 (4.5)

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'2q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0387 (Wilcoxon-test), Q value = 0.23

Table S3.  Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
2Q GAIN MUTATED 74 2.4 (3.6)
2Q GAIN WILD-TYPE 347 2.0 (4.6)

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00091 (Fisher's exact test), Q value = 0.025

Table S4.  Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
3P GAIN MUTATED 6 1 2 9 1 0 3 4 2 6 5 1 2
3P GAIN WILD-TYPE 68 0 26 124 7 1 18 5 57 34 40 16 0

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q gain' versus 'Time to Death'

P value = 0.0345 (logrank test), Q value = 0.22

Table S5.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
3Q GAIN MUTATED 62 18 0.2 - 78.1 (18.9)
3Q GAIN WILD-TYPE 371 81 0.0 - 148.0 (22.1)

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00381 (Fisher's exact test), Q value = 0.063

Table S6.  Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
3Q GAIN MUTATED 8 1 4 13 1 0 4 5 6 7 8 3 2
3Q GAIN WILD-TYPE 66 0 24 120 7 1 17 4 53 33 37 14 0

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.027 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
4P GAIN MUTATED 3 4 5
4P GAIN WILD-TYPE 257 101 77

Figure S7.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0159 (Wilcoxon-test), Q value = 0.14

Table S8.  Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
4P GAIN MUTATED 12 3.4 (3.7)
4P GAIN WILD-TYPE 409 2.1 (4.5)

Figure S8.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4p gain' versus 'RACE'

P value = 0.0029 (Fisher's exact test), Q value = 0.055

Table S9.  Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
4P GAIN MUTATED 1 0 5 4
4P GAIN WILD-TYPE 0 11 53 207

Figure S9.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

'4q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0084 (Fisher's exact test), Q value = 0.1

Table S10.  Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
4Q GAIN MUTATED 5 4 8
4Q GAIN WILD-TYPE 255 101 74

Figure S10.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00652 (Wilcoxon-test), Q value = 0.088

Table S11.  Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
4Q GAIN MUTATED 17 3.3 (3.3)
4Q GAIN WILD-TYPE 404 2.0 (4.5)

Figure S11.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q gain' versus 'RACE'

P value = 0.0314 (Fisher's exact test), Q value = 0.21

Table S12.  Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
4Q GAIN MUTATED 1 0 4 7
4Q GAIN WILD-TYPE 0 11 54 204

Figure S12.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0315 (Wilcoxon-test), Q value = 0.21

Table S13.  Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
5P GAIN MUTATED 65 2.6 (3.8)
5P GAIN WILD-TYPE 356 2.0 (4.6)

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0181 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
6P GAIN MUTATED 42 18 25
6P GAIN WILD-TYPE 218 87 57

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0229 (Wilcoxon-test), Q value = 0.17

Table S15.  Gene #11: '6p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
6P GAIN MUTATED 83 3.1 (4.9)
6P GAIN WILD-TYPE 338 1.9 (4.3)

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0293 (Fisher's exact test), Q value = 0.21

Table S16.  Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
6Q GAIN MUTATED 11 0 2 17 2 0 4 5 10 11 7 6 1
6Q GAIN WILD-TYPE 63 1 26 116 6 1 17 4 49 29 38 11 1

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0246 (Fisher's exact test), Q value = 0.18

Table S17.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
6Q GAIN MUTATED 38 16 23
6Q GAIN WILD-TYPE 222 89 59

Figure S17.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0367 (Wilcoxon-test), Q value = 0.23

Table S18.  Gene #12: '6q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
6Q GAIN MUTATED 75 3.1 (4.9)
6Q GAIN WILD-TYPE 346 1.9 (4.3)

Figure S18.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0097

Table S19.  Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
7P GAIN MUTATED 40 1 14 52 2 0 13 9 40 25 30 12 1
7P GAIN WILD-TYPE 34 0 14 81 6 1 8 0 19 15 15 5 1

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.013

Table S20.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
7P GAIN MUTATED 121 72 52
7P GAIN WILD-TYPE 139 33 30

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
7P GAIN MUTATED 166 43
7P GAIN WILD-TYPE 158 21

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0171 (Fisher's exact test), Q value = 0.15

Table S22.  Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
7P GAIN MUTATED 219 24
7P GAIN WILD-TYPE 163 36

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000717 (Wilcoxon-test), Q value = 0.023

Table S23.  Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
7P GAIN MUTATED 236 2.4 (4.8)
7P GAIN WILD-TYPE 185 1.7 (4.0)

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0161 (Fisher's exact test), Q value = 0.15

Table S24.  Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
7Q GAIN MUTATED 38 1 13 48 2 0 12 6 35 22 27 12 1
7Q GAIN WILD-TYPE 36 0 15 85 6 1 9 3 24 18 18 5 1

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0151 (Fisher's exact test), Q value = 0.14

Table S25.  Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
7Q GAIN MUTATED 114 61 47
7Q GAIN WILD-TYPE 146 44 35

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0195 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
7Q GAIN MUTATED 148 40
7Q GAIN WILD-TYPE 176 24

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0371 (Fisher's exact test), Q value = 0.23

Table S27.  Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
7Q GAIN MUTATED 197 22
7Q GAIN WILD-TYPE 185 38

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0148 (Wilcoxon-test), Q value = 0.14

Table S28.  Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
7Q GAIN MUTATED 215 2.3 (4.8)
7Q GAIN WILD-TYPE 206 1.8 (4.0)

Figure S28.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.015 (Wilcoxon-test), Q value = 0.14

Table S29.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 445 67.0 (13.0)
8Q GAIN MUTATED 225 65.7 (12.6)
8Q GAIN WILD-TYPE 220 68.3 (13.4)

Figure S29.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0257 (Fisher's exact test), Q value = 0.19

Table S30.  Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
8Q GAIN MUTATED 202 22
8Q GAIN WILD-TYPE 180 38

Figure S30.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'Time to Death'

P value = 0.00339 (logrank test), Q value = 0.059

Table S31.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
9P GAIN MUTATED 77 27 0.0 - 98.2 (17.8)
9P GAIN WILD-TYPE 356 72 0.0 - 148.0 (22.1)

Figure S31.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0106 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
9P GAIN MUTATED 9 1 6 18 2 0 1 4 8 13 9 5 1
9P GAIN WILD-TYPE 65 0 22 115 6 1 20 5 51 27 36 12 1

Figure S32.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0176 (Fisher's exact test), Q value = 0.15

Table S33.  Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
9P GAIN MUTATED 62 18
9P GAIN WILD-TYPE 320 42

Figure S33.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'RACE'

P value = 0.0272 (Fisher's exact test), Q value = 0.19

Table S34.  Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
9P GAIN MUTATED 1 1 17 35
9P GAIN WILD-TYPE 0 10 41 176

Figure S34.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

'9q gain' versus 'Time to Death'

P value = 0.00842 (logrank test), Q value = 0.1

Table S35.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
9Q GAIN MUTATED 68 24 0.0 - 98.2 (16.7)
9Q GAIN WILD-TYPE 365 75 0.0 - 148.0 (22.1)

Figure S35.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0225 (Fisher's exact test), Q value = 0.17

Table S36.  Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
9Q GAIN MUTATED 55 16
9Q GAIN WILD-TYPE 327 44

Figure S36.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 0.0325 (logrank test), Q value = 0.21

Table S37.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
10P GAIN MUTATED 34 12 0.0 - 91.8 (19.2)
10P GAIN WILD-TYPE 399 87 0.0 - 148.0 (22.0)

Figure S37.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'RACE'

P value = 0.0185 (Fisher's exact test), Q value = 0.15

Table S38.  Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
10Q GAIN MUTATED 1 1 6 10
10Q GAIN WILD-TYPE 0 10 52 201

Figure S38.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

'10q gain' versus 'ETHNICITY'

P value = 0.0186 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 265
10Q GAIN MUTATED 2 14
10Q GAIN WILD-TYPE 2 251

Figure S39.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0057 (Wilcoxon-test), Q value = 0.079

Table S40.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 445 67.0 (13.0)
11P GAIN MUTATED 53 62.2 (13.2)
11P GAIN WILD-TYPE 392 67.6 (12.9)

Figure S40.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
11P GAIN MUTATED 6 0 2 7 1 0 1 3 10 7 9 5 0
11P GAIN WILD-TYPE 68 1 26 126 7 1 20 6 49 33 36 12 2

Figure S41.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0125 (Fisher's exact test), Q value = 0.13

Table S42.  Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
11P GAIN MUTATED 21 17 15
11P GAIN WILD-TYPE 239 88 67

Figure S42.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00805 (Fisher's exact test), Q value = 0.1

Table S43.  Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
11P GAIN MUTATED 30 14
11P GAIN WILD-TYPE 294 50

Figure S43.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00471 (Fisher's exact test), Q value = 0.071

Table S44.  Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
11P GAIN MUTATED 51 1
11P GAIN WILD-TYPE 331 59

Figure S44.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0106 (Wilcoxon-test), Q value = 0.12

Table S45.  Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
11P GAIN MUTATED 52 3.5 (7.5)
11P GAIN WILD-TYPE 369 1.9 (3.8)

Figure S45.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00034 (Wilcoxon-test), Q value = 0.015

Table S46.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 445 67.0 (13.0)
11Q GAIN MUTATED 51 60.5 (13.2)
11Q GAIN WILD-TYPE 394 67.8 (12.8)

Figure S46.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.015 (Fisher's exact test), Q value = 0.14

Table S47.  Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
11Q GAIN MUTATED 5 0 3 7 1 0 1 3 10 8 6 5 0
11Q GAIN WILD-TYPE 69 1 25 126 7 1 20 6 49 32 39 12 2

Figure S47.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
11Q GAIN MUTATED 20 17 14
11Q GAIN WILD-TYPE 240 88 68

Figure S48.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00759 (Fisher's exact test), Q value = 0.096

Table S49.  Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
11Q GAIN MUTATED 50 1
11Q GAIN WILD-TYPE 332 59

Figure S49.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.014 (Wilcoxon-test), Q value = 0.14

Table S50.  Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
11Q GAIN MUTATED 50 3.3 (7.4)
11Q GAIN WILD-TYPE 371 1.9 (3.9)

Figure S50.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0301 (Fisher's exact test), Q value = 0.21

Table S51.  Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
12Q GAIN MUTATED 12 1 7 36 1 0 3 3 7 8 3 6 0
12Q GAIN WILD-TYPE 62 0 21 97 7 1 18 6 52 32 42 11 2

Figure S51.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0268 (Wilcoxon-test), Q value = 0.19

Table S52.  Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
12Q GAIN MUTATED 83 1.1 (2.0)
12Q GAIN WILD-TYPE 338 2.3 (4.8)

Figure S52.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00057 (Fisher's exact test), Q value = 0.019

Table S53.  Gene #25: '13q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
13Q GAIN MUTATED 41 0 14 63 2 1 12 9 36 24 35 13 0
13Q GAIN WILD-TYPE 33 1 14 70 6 0 9 0 23 16 10 4 2

Figure S53.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00356 (Fisher's exact test), Q value = 0.06

Table S54.  Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
13Q GAIN MUTATED 131 70 54
13Q GAIN WILD-TYPE 129 35 28

Figure S54.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00233 (Fisher's exact test), Q value = 0.047

Table S55.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
13Q GAIN MUTATED 177 48
13Q GAIN WILD-TYPE 147 16

Figure S55.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.06e-06 (Fisher's exact test), Q value = 0.00043

Table S56.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
13Q GAIN MUTATED 236 17
13Q GAIN WILD-TYPE 146 43

Figure S56.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0236 (Fisher's exact test), Q value = 0.18

Table S57.  Gene #25: '13q gain' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 319 3 25 25
13Q GAIN MUTATED 177 1 19 9
13Q GAIN WILD-TYPE 142 2 6 16

Figure S57.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0082 (Wilcoxon-test), Q value = 0.1

Table S58.  Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
13Q GAIN MUTATED 247 2.3 (3.9)
13Q GAIN WILD-TYPE 174 1.9 (5.2)

Figure S58.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0387 (Fisher's exact test), Q value = 0.23

Table S59.  Gene #26: '14q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
14Q GAIN MUTATED 26 9
14Q GAIN WILD-TYPE 356 51

Figure S59.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'RACE'

P value = 0.023 (Fisher's exact test), Q value = 0.17

Table S60.  Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
14Q GAIN MUTATED 1 2 2 19
14Q GAIN WILD-TYPE 0 9 56 192

Figure S60.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

'16p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00321 (Fisher's exact test), Q value = 0.059

Table S61.  Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
16P GAIN MUTATED 12 1 3 26 1 0 7 7 14 14 13 4 1
16P GAIN WILD-TYPE 62 0 25 107 7 1 14 2 45 26 32 13 1

Figure S61.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00531 (Fisher's exact test), Q value = 0.077

Table S62.  Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
16P GAIN MUTATED 48 32 27
16P GAIN WILD-TYPE 212 73 55

Figure S62.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00172 (Fisher's exact test), Q value = 0.038

Table S63.  Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
16P GAIN MUTATED 100 5
16P GAIN WILD-TYPE 282 55

Figure S63.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00351 (Wilcoxon-test), Q value = 0.06

Table S64.  Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
16P GAIN MUTATED 102 2.6 (4.0)
16P GAIN WILD-TYPE 319 1.9 (4.6)

Figure S64.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.019

Table S65.  Gene #29: '16q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
16Q GAIN MUTATED 12 1 3 24 1 0 7 8 17 12 11 4 1
16Q GAIN WILD-TYPE 62 0 25 109 7 1 14 1 42 28 34 13 1

Figure S65.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00273 (Fisher's exact test), Q value = 0.052

Table S66.  Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
16Q GAIN MUTATED 46 33 26
16Q GAIN WILD-TYPE 214 72 56

Figure S66.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00271 (Fisher's exact test), Q value = 0.052

Table S67.  Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
16Q GAIN MUTATED 98 5
16Q GAIN WILD-TYPE 284 55

Figure S67.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00339 (Wilcoxon-test), Q value = 0.059

Table S68.  Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
16Q GAIN MUTATED 101 2.6 (4.1)
16Q GAIN WILD-TYPE 320 1.9 (4.6)

Figure S68.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'ETHNICITY'

P value = 0.0294 (Fisher's exact test), Q value = 0.21

Table S69.  Gene #31: '17q gain' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 265
17Q GAIN MUTATED 3 53
17Q GAIN WILD-TYPE 1 212

Figure S69.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #13: 'ETHNICITY'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0321 (Fisher's exact test), Q value = 0.21

Table S70.  Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
18P GAIN MUTATED 10 3 9
18P GAIN WILD-TYPE 250 102 73

Figure S70.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0195 (Fisher's exact test), Q value = 0.16

Table S71.  Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
18P GAIN MUTATED 15 7
18P GAIN WILD-TYPE 367 53

Figure S71.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0212 (Fisher's exact test), Q value = 0.16

Table S72.  Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
18Q GAIN MUTATED 8 5
18Q GAIN WILD-TYPE 374 55

Figure S72.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0039 (Fisher's exact test), Q value = 0.063

Table S73.  Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
20P GAIN MUTATED 41 1 13 62 3 0 10 9 28 21 33 13 1
20P GAIN WILD-TYPE 33 0 15 71 5 1 11 0 31 19 12 4 1

Figure S73.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000933 (Fisher's exact test), Q value = 0.025

Table S74.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
20P GAIN MUTATED 165 47
20P GAIN WILD-TYPE 159 17

Figure S74.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00075 (Fisher's exact test), Q value = 0.023

Table S75.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
20P GAIN MUTATED 218 20
20P GAIN WILD-TYPE 164 40

Figure S75.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0119 (Fisher's exact test), Q value = 0.13

Table S76.  Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
20Q GAIN MUTATED 53 1 16 86 3 1 14 9 42 31 39 15 1
20Q GAIN WILD-TYPE 21 0 12 47 5 0 7 0 17 9 6 2 1

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0186 (Fisher's exact test), Q value = 0.15

Table S77.  Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
20Q GAIN MUTATED 172 84 62
20Q GAIN WILD-TYPE 88 21 20

Figure S77.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00399 (Fisher's exact test), Q value = 0.063

Table S78.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
20Q GAIN MUTATED 222 55
20Q GAIN WILD-TYPE 102 9

Figure S78.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3.68e-07 (Fisher's exact test), Q value = 0.00013

Table S79.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
20Q GAIN MUTATED 289 25
20Q GAIN WILD-TYPE 93 35

Figure S79.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0289 (Wilcoxon-test), Q value = 0.2

Table S80.  Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
20Q GAIN MUTATED 302 2.3 (4.8)
20Q GAIN WILD-TYPE 119 1.6 (3.4)

Figure S80.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00175 (Wilcoxon-test), Q value = 0.038

Table S81.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 445 67.0 (13.0)
21Q GAIN MUTATED 24 59.8 (10.0)
21Q GAIN WILD-TYPE 421 67.4 (13.1)

Figure S81.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00586 (Fisher's exact test), Q value = 0.08

Table S82.  Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 77 305 53
XP GAIN MUTATED 0 13 52 1
XP GAIN WILD-TYPE 11 64 253 52

Figure S82.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0075 (Fisher's exact test), Q value = 0.096

Table S83.  Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 77 305 53
XQ GAIN MUTATED 0 14 60 2
XQ GAIN WILD-TYPE 11 63 245 51

Figure S83.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'Time to Death'

P value = 0.00558 (logrank test), Q value = 0.079

Table S84.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
1P LOSS MUTATED 90 28 0.2 - 92.8 (17.4)
1P LOSS WILD-TYPE 343 71 0.0 - 148.0 (22.1)

Figure S84.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.12

Table S85.  Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
1P LOSS MUTATED 9 0 3 24 0 0 5 3 11 11 20 4 0
1P LOSS WILD-TYPE 65 1 25 109 8 1 16 6 48 29 25 13 2

Figure S85.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00158 (Fisher's exact test), Q value = 0.036

Table S86.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
1P LOSS MUTATED 41 25 28
1P LOSS WILD-TYPE 219 80 54

Figure S86.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00119 (Fisher's exact test), Q value = 0.03

Table S87.  Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
1P LOSS MUTATED 58 24
1P LOSS WILD-TYPE 266 40

Figure S87.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000411 (Wilcoxon-test), Q value = 0.015

Table S88.  Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
1P LOSS MUTATED 88 3.7 (6.8)
1P LOSS WILD-TYPE 333 1.7 (3.5)

Figure S88.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'Time to Death'

P value = 0.00897 (logrank test), Q value = 0.11

Table S89.  Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
1Q LOSS MUTATED 53 16 0.2 - 91.8 (13.0)
1Q LOSS WILD-TYPE 380 83 0.0 - 148.0 (22.2)

Figure S89.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

'1q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0403 (Fisher's exact test), Q value = 0.24

Table S90.  Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
1Q LOSS MUTATED 6 0 2 14 0 0 3 3 2 8 11 2 0
1Q LOSS WILD-TYPE 68 1 26 119 8 1 18 6 57 32 34 15 2

Figure S90.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0418 (Fisher's exact test), Q value = 0.24

Table S91.  Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
1Q LOSS MUTATED 26 12 17
1Q LOSS WILD-TYPE 234 93 65

Figure S91.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0325 (Fisher's exact test), Q value = 0.21

Table S92.  Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
1Q LOSS MUTATED 33 13
1Q LOSS WILD-TYPE 291 51

Figure S92.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0216 (Wilcoxon-test), Q value = 0.17

Table S93.  Gene #43: '1q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
1Q LOSS MUTATED 51 3.3 (4.6)
1Q LOSS WILD-TYPE 370 1.9 (4.4)

Figure S93.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00217 (Fisher's exact test), Q value = 0.045

Table S94.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
4P LOSS MUTATED 16 0 4 35 2 0 6 5 15 14 26 7 1
4P LOSS WILD-TYPE 58 1 24 98 6 1 15 4 44 26 19 10 1

Figure S94.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00328 (Fisher's exact test), Q value = 0.059

Table S95.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
4P LOSS MUTATED 63 37 35
4P LOSS WILD-TYPE 197 68 47

Figure S95.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 1.86e-05 (Fisher's exact test), Q value = 0.0024

Table S96.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
4P LOSS MUTATED 81 34
4P LOSS WILD-TYPE 243 30

Figure S96.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.015 (Fisher's exact test), Q value = 0.14

Table S97.  Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
4P LOSS MUTATED 124 10
4P LOSS WILD-TYPE 258 50

Figure S97.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000909 (Wilcoxon-test), Q value = 0.025

Table S98.  Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
4P LOSS MUTATED 129 3.0 (4.7)
4P LOSS WILD-TYPE 292 1.7 (4.3)

Figure S98.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'Time to Death'

P value = 0.0206 (logrank test), Q value = 0.16

Table S99.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
4Q LOSS MUTATED 120 35 0.2 - 140.4 (21.4)
4Q LOSS WILD-TYPE 313 64 0.0 - 148.0 (22.0)

Figure S99.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.14

Table S100.  Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
4Q LOSS MUTATED 13 0 4 33 1 0 5 5 17 16 21 6 0
4Q LOSS WILD-TYPE 61 1 24 100 7 1 16 4 42 24 24 11 2

Figure S100.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00242 (Fisher's exact test), Q value = 0.048

Table S101.  Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
4Q LOSS MUTATED 56 37 31
4Q LOSS WILD-TYPE 204 68 51

Figure S101.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00514 (Fisher's exact test), Q value = 0.075

Table S102.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
4Q LOSS MUTATED 78 27
4Q LOSS WILD-TYPE 246 37

Figure S102.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000981 (Wilcoxon-test), Q value = 0.025

Table S103.  Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
4Q LOSS MUTATED 118 2.9 (4.7)
4Q LOSS WILD-TYPE 303 1.8 (4.3)

Figure S103.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0163 (Fisher's exact test), Q value = 0.15

Table S104.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
5P LOSS MUTATED 9 0 3 9 0 1 2 3 10 8 6 6 0
5P LOSS WILD-TYPE 65 1 25 124 8 0 19 6 49 32 39 11 2

Figure S104.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.038 (Wilcoxon-test), Q value = 0.23

Table S105.  Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
5P LOSS MUTATED 57 3.2 (5.9)
5P LOSS WILD-TYPE 364 1.9 (4.2)

Figure S105.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'ETHNICITY'

P value = 0.00948 (Fisher's exact test), Q value = 0.11

Table S106.  Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 265
5P LOSS MUTATED 3 35
5P LOSS WILD-TYPE 1 230

Figure S106.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

'5q loss' versus 'Time to Death'

P value = 0.0319 (logrank test), Q value = 0.21

Table S107.  Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
5Q LOSS MUTATED 75 23 0.2 - 91.8 (21.9)
5Q LOSS WILD-TYPE 358 76 0.0 - 148.0 (21.7)

Figure S107.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0415 (Fisher's exact test), Q value = 0.24

Table S108.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
5Q LOSS MUTATED 10 0 3 15 0 0 3 3 11 13 11 6 0
5Q LOSS WILD-TYPE 64 1 25 118 8 1 18 6 48 27 34 11 2

Figure S108.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00199 (Fisher's exact test), Q value = 0.042

Table S109.  Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
5Q LOSS MUTATED 34 19 25
5Q LOSS WILD-TYPE 226 86 57

Figure S109.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0258 (Fisher's exact test), Q value = 0.19

Table S110.  Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
5Q LOSS MUTATED 47 17
5Q LOSS WILD-TYPE 277 47

Figure S110.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000516 (Wilcoxon-test), Q value = 0.018

Table S111.  Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
5Q LOSS MUTATED 74 3.6 (5.7)
5Q LOSS WILD-TYPE 347 1.8 (4.1)

Figure S111.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'ETHNICITY'

P value = 0.0212 (Fisher's exact test), Q value = 0.16

Table S112.  Gene #51: '5q loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 265
5Q LOSS MUTATED 3 47
5Q LOSS WILD-TYPE 1 218

Figure S112.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #13: 'ETHNICITY'

'6p loss' versus 'Time to Death'

P value = 0.0356 (logrank test), Q value = 0.22

Table S113.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
6P LOSS MUTATED 32 10 1.5 - 45.4 (17.9)
6P LOSS WILD-TYPE 401 89 0.0 - 148.0 (22.0)

Figure S113.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'RACE'

P value = 0.0315 (Fisher's exact test), Q value = 0.21

Table S114.  Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
6P LOSS MUTATED 0 3 1 17
6P LOSS WILD-TYPE 1 8 57 194

Figure S114.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

'6q loss' versus 'Time to Death'

P value = 0.0186 (logrank test), Q value = 0.15

Table S115.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 433 99 0.0 - 148.0 (21.9)
6Q LOSS MUTATED 44 13 0.5 - 61.0 (14.5)
6Q LOSS WILD-TYPE 389 86 0.0 - 148.0 (22.1)

Figure S115.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00714 (Wilcoxon-test), Q value = 0.094

Table S116.  Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
6Q LOSS MUTATED 40 3.2 (4.3)
6Q LOSS WILD-TYPE 381 2.0 (4.5)

Figure S116.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'RACE'

P value = 0.0133 (Fisher's exact test), Q value = 0.13

Table S117.  Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
6Q LOSS MUTATED 1 3 3 19
6Q LOSS WILD-TYPE 0 8 55 192

Figure S117.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0111 (Fisher's exact test), Q value = 0.12

Table S118.  Gene #55: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
8P LOSS MUTATED 16 0 6 34 2 0 8 5 17 16 23 9 1
8P LOSS WILD-TYPE 58 1 22 99 6 1 13 4 42 24 22 8 1

Figure S118.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00099 (Fisher's exact test), Q value = 0.025

Table S119.  Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
8P LOSS MUTATED 65 37 38
8P LOSS WILD-TYPE 195 68 44

Figure S119.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000385 (Fisher's exact test), Q value = 0.015

Table S120.  Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
8P LOSS MUTATED 91 33
8P LOSS WILD-TYPE 233 31

Figure S120.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0388 (Fisher's exact test), Q value = 0.23

Table S121.  Gene #55: '8p loss' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 319 3 25 25
8P LOSS MUTATED 96 1 12 3
8P LOSS WILD-TYPE 223 2 13 22

Figure S121.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000359 (Wilcoxon-test), Q value = 0.015

Table S122.  Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
8P LOSS MUTATED 135 3.1 (5.8)
8P LOSS WILD-TYPE 286 1.6 (3.6)

Figure S122.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0198 (Fisher's exact test), Q value = 0.16

Table S123.  Gene #56: '8q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
8Q LOSS MUTATED 15 1 8
8Q LOSS WILD-TYPE 245 104 74

Figure S123.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0329 (Fisher's exact test), Q value = 0.21

Table S124.  Gene #56: '8q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
8Q LOSS MUTATED 10 6
8Q LOSS WILD-TYPE 314 58

Figure S124.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00471 (Fisher's exact test), Q value = 0.071

Table S125.  Gene #57: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
9P LOSS MUTATED 51 1
9P LOSS WILD-TYPE 331 59

Figure S125.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00743 (Fisher's exact test), Q value = 0.096

Table S126.  Gene #58: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
9Q LOSS MUTATED 49 1
9Q LOSS WILD-TYPE 333 59

Figure S126.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0203 (Fisher's exact test), Q value = 0.16

Table S127.  Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
10P LOSS MUTATED 42 16
10P LOSS WILD-TYPE 282 48

Figure S127.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0324 (Wilcoxon-test), Q value = 0.21

Table S128.  Gene #59: '10p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
10P LOSS MUTATED 64 2.4 (3.4)
10P LOSS WILD-TYPE 357 2.0 (4.6)

Figure S128.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0427 (Fisher's exact test), Q value = 0.25

Table S129.  Gene #60: '10q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
10Q LOSS MUTATED 47 16
10Q LOSS WILD-TYPE 277 48

Figure S129.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0148 (Wilcoxon-test), Q value = 0.14

Table S130.  Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
11P LOSS MUTATED 48 2.9 (4.6)
11P LOSS WILD-TYPE 373 2.0 (4.4)

Figure S130.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'11q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0171 (Fisher's exact test), Q value = 0.15

Table S131.  Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
11Q LOSS MUTATED 38 15
11Q LOSS WILD-TYPE 286 49

Figure S131.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.12

Table S132.  Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
12P LOSS MUTATED 45 1
12P LOSS WILD-TYPE 337 59

Figure S132.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0392 (Wilcoxon-test), Q value = 0.23

Table S133.  Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
12P LOSS MUTATED 44 2.5 (3.7)
12P LOSS WILD-TYPE 377 2.0 (4.5)

Figure S133.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0387 (Fisher's exact test), Q value = 0.23

Table S134.  Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
12Q LOSS MUTATED 20 15 13
12Q LOSS WILD-TYPE 240 90 69

Figure S134.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0138 (Wilcoxon-test), Q value = 0.14

Table S135.  Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
12Q LOSS MUTATED 45 2.7 (3.8)
12Q LOSS WILD-TYPE 376 2.0 (4.5)

Figure S135.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0131 (Wilcoxon-test), Q value = 0.13

Table S136.  Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
13Q LOSS MUTATED 9 10.6 (15.8)
13Q LOSS WILD-TYPE 412 1.9 (3.7)

Figure S136.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'RACE'

P value = 0.0179 (Fisher's exact test), Q value = 0.15

Table S137.  Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 58 211
13Q LOSS MUTATED 1 1 1 6
13Q LOSS WILD-TYPE 0 10 57 205

Figure S137.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.12

Table S138.  Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
14Q LOSS MUTATED 92 29
14Q LOSS WILD-TYPE 232 35

Figure S138.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 6.07e-07 (Fisher's exact test), Q value = 0.00016

Table S139.  Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
14Q LOSS MUTATED 129 3
14Q LOSS WILD-TYPE 253 57

Figure S139.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00141 (Fisher's exact test), Q value = 0.033

Table S140.  Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
15Q LOSS MUTATED 101 34
15Q LOSS WILD-TYPE 223 30

Figure S140.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.028 (Fisher's exact test), Q value = 0.2

Table S141.  Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
15Q LOSS MUTATED 140 13
15Q LOSS WILD-TYPE 242 47

Figure S141.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0318 (Wilcoxon-test), Q value = 0.21

Table S142.  Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
15Q LOSS MUTATED 147 2.3 (3.8)
15Q LOSS WILD-TYPE 274 2.0 (4.8)

Figure S142.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S143.  Gene #70: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
17P LOSS MUTATED 32 0 13 56 1 1 11 9 31 26 33 12 2
17P LOSS WILD-TYPE 42 1 15 77 7 0 10 0 28 14 12 5 0

Figure S143.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.015

Table S144.  Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
17P LOSS MUTATED 115 64 54
17P LOSS WILD-TYPE 145 41 28

Figure S144.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000325 (Fisher's exact test), Q value = 0.015

Table S145.  Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
17P LOSS MUTATED 158 47
17P LOSS WILD-TYPE 166 17

Figure S145.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2.68e-06 (Fisher's exact test), Q value = 0.00047

Table S146.  Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
17P LOSS MUTATED 215 14
17P LOSS WILD-TYPE 167 46

Figure S146.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.64e-05 (Wilcoxon-test), Q value = 0.007

Table S147.  Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
17P LOSS MUTATED 220 2.7 (5.5)
17P LOSS WILD-TYPE 201 1.4 (2.8)

Figure S147.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.14

Table S148.  Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
17Q LOSS MUTATED 28 20 18
17Q LOSS WILD-TYPE 232 85 64

Figure S148.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0427 (Fisher's exact test), Q value = 0.25

Table S149.  Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
17Q LOSS MUTATED 38 14
17Q LOSS WILD-TYPE 286 50

Figure S149.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000913 (Wilcoxon-test), Q value = 0.025

Table S150.  Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
17Q LOSS MUTATED 62 3.6 (7.2)
17Q LOSS WILD-TYPE 359 1.8 (3.7)

Figure S150.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.013

Table S151.  Gene #72: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
18P LOSS MUTATED 37 0 11 66 2 1 9 8 36 25 35 15 1
18P LOSS WILD-TYPE 37 1 17 67 6 0 12 1 23 15 10 2 1

Figure S151.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00572 (Fisher's exact test), Q value = 0.079

Table S152.  Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
18P LOSS MUTATED 130 69 53
18P LOSS WILD-TYPE 130 36 29

Figure S152.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 4.93e-05 (Fisher's exact test), Q value = 0.0058

Table S153.  Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
18P LOSS MUTATED 170 51
18P LOSS WILD-TYPE 154 13

Figure S153.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1.55e-10 (Fisher's exact test), Q value = 1.6e-07

Table S154.  Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
18P LOSS MUTATED 237 11
18P LOSS WILD-TYPE 145 49

Figure S154.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00333 (Wilcoxon-test), Q value = 0.059

Table S155.  Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
18P LOSS MUTATED 237 2.5 (5.1)
18P LOSS WILD-TYPE 184 1.6 (3.5)

Figure S155.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0318 (Wilcoxon-test), Q value = 0.21

Table S156.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 445 67.0 (13.0)
18Q LOSS MUTATED 269 66.1 (12.3)
18Q LOSS WILD-TYPE 176 68.3 (14.0)

Figure S156.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.007

Table S157.  Gene #73: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
18Q LOSS MUTATED 37 0 14 70 2 1 11 9 38 29 36 15 1
18Q LOSS WILD-TYPE 37 1 14 63 6 0 10 0 21 11 9 2 1

Figure S157.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.015

Table S158.  Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
18Q LOSS MUTATED 136 74 59
18Q LOSS WILD-TYPE 124 31 23

Figure S158.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000234 (Fisher's exact test), Q value = 0.013

Table S159.  Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
18Q LOSS MUTATED 185 52
18Q LOSS WILD-TYPE 139 12

Figure S159.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 5.53e-10 (Fisher's exact test), Q value = 2.9e-07

Table S160.  Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
18Q LOSS MUTATED 252 14
18Q LOSS WILD-TYPE 130 46

Figure S160.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000373 (Wilcoxon-test), Q value = 0.015

Table S161.  Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
18Q LOSS MUTATED 254 2.4 (4.6)
18Q LOSS WILD-TYPE 167 1.7 (4.1)

Figure S161.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00932 (Fisher's exact test), Q value = 0.11

Table S162.  Gene #74: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
19P LOSS MUTATED 7 0 1 5 0 0 4 0 3 7 7 4 1
19P LOSS WILD-TYPE 67 1 27 128 8 1 17 9 56 33 38 13 1

Figure S162.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.024

Table S163.  Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
19P LOSS MUTATED 14 9 16
19P LOSS WILD-TYPE 246 96 66

Figure S163.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00505 (Fisher's exact test), Q value = 0.075

Table S164.  Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
19P LOSS MUTATED 21 12
19P LOSS WILD-TYPE 303 52

Figure S164.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.82e-05 (Wilcoxon-test), Q value = 0.007

Table S165.  Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
19P LOSS MUTATED 37 4.5 (5.3)
19P LOSS WILD-TYPE 384 1.9 (4.3)

Figure S165.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00172 (Fisher's exact test), Q value = 0.038

Table S166.  Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
19Q LOSS MUTATED 14 6 15
19Q LOSS WILD-TYPE 246 99 67

Figure S166.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.018 (Fisher's exact test), Q value = 0.15

Table S167.  Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
19Q LOSS MUTATED 20 10
19Q LOSS WILD-TYPE 304 54

Figure S167.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000486 (Wilcoxon-test), Q value = 0.018

Table S168.  Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
19Q LOSS MUTATED 33 4.6 (5.5)
19Q LOSS WILD-TYPE 388 1.9 (4.3)

Figure S168.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0304 (Fisher's exact test), Q value = 0.21

Table S169.  Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
21Q LOSS MUTATED 62 28 32
21Q LOSS WILD-TYPE 198 77 50

Figure S169.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00781 (Fisher's exact test), Q value = 0.098

Table S170.  Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
21Q LOSS MUTATED 114 8
21Q LOSS WILD-TYPE 268 52

Figure S170.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0332 (Wilcoxon-test), Q value = 0.21

Table S171.  Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
21Q LOSS MUTATED 116 3.1 (6.6)
21Q LOSS WILD-TYPE 305 1.7 (3.3)

Figure S171.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.013

Table S172.  Gene #79: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 74 1 28 133 8 1 21 9 59 40 45 17 2
22Q LOSS MUTATED 17 0 7 33 1 0 6 7 17 20 24 8 0
22Q LOSS WILD-TYPE 57 1 21 100 7 1 15 2 42 20 21 9 2

Figure S172.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.013

Table S173.  Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
22Q LOSS MUTATED 64 43 37
22Q LOSS WILD-TYPE 196 62 45

Figure S173.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00123 (Fisher's exact test), Q value = 0.03

Table S174.  Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
22Q LOSS MUTATED 93 32
22Q LOSS WILD-TYPE 231 32

Figure S174.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00459 (Fisher's exact test), Q value = 0.071

Table S175.  Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 60
22Q LOSS MUTATED 134 10
22Q LOSS WILD-TYPE 248 50

Figure S175.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000317 (Wilcoxon-test), Q value = 0.015

Table S176.  Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
22Q LOSS MUTATED 136 2.9 (5.0)
22Q LOSS WILD-TYPE 285 1.7 (4.1)

Figure S176.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00132 (Fisher's exact test), Q value = 0.032

Table S177.  Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
XP LOSS MUTATED 25 18 21
XP LOSS WILD-TYPE 235 87 61

Figure S177.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.032 (Fisher's exact test), Q value = 0.21

Table S178.  Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
XP LOSS MUTATED 41 15
XP LOSS WILD-TYPE 283 49

Figure S178.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000213 (Wilcoxon-test), Q value = 0.013

Table S179.  Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
XP LOSS MUTATED 60 3.3 (4.5)
XP LOSS WILD-TYPE 361 1.9 (4.4)

Figure S179.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.13

Table S180.  Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 260 105 82
XQ LOSS MUTATED 21 15 16
XQ LOSS WILD-TYPE 239 90 66

Figure S180.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0106 (Fisher's exact test), Q value = 0.12

Table S181.  Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 324 64
XQ LOSS MUTATED 32 14
XQ LOSS WILD-TYPE 292 50

Figure S181.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xq loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00396 (Wilcoxon-test), Q value = 0.063

Table S182.  Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 421 2.1 (4.5)
XQ LOSS MUTATED 47 3.0 (4.5)
XQ LOSS WILD-TYPE 374 2.0 (4.5)

Figure S182.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/19780706/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COAD-TP/19775087/COAD-TP.merged_data.txt

  • Number of patients = 447

  • Number of significantly arm-level cnvs = 81

  • 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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