Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12V2F9G
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/C12V2F9G
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 82 arm-level events and 14 clinical features across 612 patients, 200 significant findings detected with Q value < 0.25.

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

  • 2p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

  • 2q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 3p gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'PATHOLOGIC_STAGE'.

  • 3q gain cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_M_STAGE'.

  • 5p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 6q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_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 'PATHOLOGIC_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'RESIDUAL_TUMOR'.

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

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

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

  • 11p gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 14q gain cnv correlated to '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 'PATHOLOGY_M_STAGE'.

  • 18p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

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

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

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 1p loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 1q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 2p loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 3q loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'HISTOLOGICAL_TYPE'.

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

  • 4q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 5q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

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

  • 6q loss cnv correlated to 'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 7p loss cnv correlated to 'ETHNICITY'.

  • 7q loss cnv correlated to 'ETHNICITY'.

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

  • 8q loss cnv correlated to 'GENDER'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 9q loss cnv correlated to 'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 11p loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 12p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

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

  • 14q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

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

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

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

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

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

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

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

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

  • xq loss cnv correlated to 'PATHOLOGY_M_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 200 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		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 Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
18q loss 407 (67%) 205 0.683
(0.902) 		0.0258
(0.184) 		3.73e-09
(4.28e-06) 		2e-05
(0.00153) 		0.33
(0.688) 		7e-05
(0.00423) 		1.83e-05
(0.00153) 		0.345
(0.694) 		0.413
(0.749) 		1e-05
(0.000957) 		0.0393
(0.233) 		0.000116
(0.00603) 		0.543
(0.834) 		1
(1.00)
20q gain 462 (75%) 150 0.944
(1.00) 		0.297
(0.671) 		1.33e-06
(0.000509) 		0.00147
(0.0338) 		0.241
(0.606) 		0.00059
(0.0199) 		0.00162
(0.0358) 		0.222
(0.581) 		0.186
(0.534) 		1e-05
(0.000957) 		0.0324
(0.207) 		0.00409
(0.0602) 		0.237
(0.599) 		1
(1.00)
18p loss 377 (62%) 235 0.455
(0.779) 		0.0415
(0.242) 		4.85e-07
(0.000278) 		6e-05
(0.00401) 		0.76
(0.949) 		0.00383
(0.0586) 		7.06e-06
(0.000957) 		0.454
(0.779) 		0.323
(0.688) 		1e-05
(0.000957) 		0.0444
(0.253) 		0.00321
(0.0533) 		0.781
(0.961) 		0.653
(0.884)
13q gain 367 (60%) 245 0.676
(0.9) 		0.644
(0.883) 		0.0149
(0.138) 		0.00126
(0.0301) 		0.785
(0.964) 		0.00026
(0.0107) 		0.0327
(0.207) 		0.322
(0.688) 		0.162
(0.496) 		1e-05
(0.000957) 		0.0738
(0.324) 		0.000904
(0.0253) 		0.0545
(0.273) 		0.654
(0.884)
4p loss 195 (32%) 417 0.59
(0.857) 		0.83
(0.985) 		0.201
(0.552) 		0.0222
(0.171) 		0.761
(0.949) 		0.00263
(0.0487) 		0.000642
(0.0205) 		0.602
(0.858) 		0.0202
(0.163) 		0.0272
(0.19) 		0.175
(0.514) 		0.000882
(0.0253) 		0.594
(0.857) 		0.166
(0.504)
8p loss 216 (35%) 396 0.454
(0.779) 		0.763
(0.95) 		0.00284
(0.0492) 		0.0355
(0.216) 		0.192
(0.538) 		0.00025
(0.0106) 		0.00506
(0.0668) 		0.127
(0.44) 		0.231
(0.591) 		0.00225
(0.0445) 		0.0858
(0.354) 		6.28e-05
(0.00401) 		0.487
(0.794) 		0.347
(0.697)
17p loss 338 (55%) 274 0.252
(0.618) 		0.44
(0.766) 		0.0168
(0.148) 		0.00452
(0.0633) 		0.438
(0.766) 		0.00194
(0.0405) 		0.0023
(0.0448) 		0.167
(0.506) 		0.848
(0.987) 		1e-05
(0.000957) 		0.116
(0.421) 		0.000503
(0.018) 		0.61
(0.861) 		1
(1.00)
22q loss 201 (33%) 411 0.0403
(0.236) 		0.679
(0.901) 		0.697
(0.91) 		0.00294
(0.0496) 		0.294
(0.667) 		3e-05
(0.00215) 		0.00276
(0.0492) 		0.73
(0.927) 		0.84
(0.987) 		0.0311
(0.205) 		0.513
(0.815) 		0.000177
(0.00845) 		0.352
(0.698) 		0.332
(0.688)
7p gain 348 (57%) 264 0.768
(0.951) 		0.201
(0.552) 		0.0784
(0.334) 		0.00017
(0.00845) 		0.915
(1.00) 		2e-05
(0.00153) 		0.0255
(0.184) 		0.624
(0.867) 		0.44
(0.766) 		0.00023
(0.0106) 		0.442
(0.766) 		0.000103
(0.00563) 		0.79
(0.966) 		0.395
(0.735)
7q gain 310 (51%) 302 0.949
(1.00) 		0.205
(0.555) 		0.521
(0.819) 		0.00038
(0.0145) 		0.63
(0.871) 		0.00116
(0.0296) 		0.01
(0.111) 		0.746
(0.939) 		1
(1.00) 		0.00287
(0.0492) 		0.544
(0.834) 		0.00366
(0.0575) 		0.473
(0.791) 		0.671
(0.896)
20p gain 350 (57%) 262 0.227
(0.588) 		0.542
(0.834) 		0.0158
(0.142) 		0.00406
(0.0602) 		0.581
(0.857) 		0.0449
(0.253) 		0.00206
(0.0423) 		0.191
(0.538) 		0.243
(0.607) 		1e-05
(0.000957) 		0.11
(0.403) 		0.0326
(0.207) 		0.679
(0.901) 		0.656
(0.885)
3p loss 69 (11%) 543 0.0205
(0.163) 		0.878
(1.00) 		0.248
(0.612) 		0.0426
(0.244) 		0.0302
(0.205) 		0.0554
(0.275) 		0.00263
(0.0487) 		0.306
(0.682) 		1
(1.00) 		0.0538
(0.271) 		0.227
(0.588) 		0.0314
(0.205) 		0.332
(0.688) 		0.471
(0.791)
4q loss 188 (31%) 424 0.727
(0.925) 		0.697
(0.91) 		0.0124
(0.122) 		0.0717
(0.32) 		0.649
(0.884) 		0.00446
(0.0633) 		0.0746
(0.324) 		0.599
(0.858) 		0.0349
(0.215) 		0.0124
(0.122) 		0.894
(1.00) 		0.00276
(0.0492) 		0.473
(0.791) 		0.17
(0.508)
21q loss 192 (31%) 420 0.812
(0.974) 		0.544
(0.834) 		0.00212
(0.0426) 		0.397
(0.736) 		0.869
(0.999) 		0.0186
(0.157) 		0.706
(0.915) 		0.793
(0.966) 		0.205
(0.555) 		0.00025
(0.0106) 		0.681
(0.901) 		0.00657
(0.0833) 		0.403
(0.741) 		0.0367
(0.221)
1q gain 117 (19%) 495 0.402
(0.74) 		0.554
(0.842) 		0.482
(0.792) 		0.233
(0.595) 		0.0339
(0.211) 		0.0343
(0.212) 		0.0253
(0.184) 		0.354
(0.7) 		0.0904
(0.364) 		0.176
(0.516) 		0.573
(0.852) 		0.0033
(0.0542) 		0.813
(0.974) 		1
(1.00)
5p gain 103 (17%) 509 0.995
(1.00) 		0.0799
(0.337) 		0.0498
(0.263) 		0.172
(0.512) 		0.468
(0.789) 		0.0178
(0.155) 		0.271
(0.643) 		1
(1.00) 		0.0306
(0.205) 		0.0224
(0.171) 		0.244
(0.607) 		0.0131
(0.127) 		0.151
(0.476) 		0.593
(0.857)
6q gain 111 (18%) 501 0.479
(0.792) 		0.482
(0.792) 		0.234
(0.595) 		0.0101
(0.111) 		0.716
(0.922) 		0.00187
(0.0405) 		0.0148
(0.138) 		0.53
(0.824) 		0.0686
(0.315) 		0.0945
(0.372) 		0.408
(0.743) 		0.00261
(0.0487) 		0.692
(0.909) 		0.588
(0.857)
8q gain 314 (51%) 298 0.278
(0.649) 		0.0881
(0.359) 		0.522
(0.819) 		0.0328
(0.207) 		0.21
(0.564) 		0.0717
(0.32) 		0.00721
(0.0871) 		0.871
(0.999) 		0.332
(0.688) 		0.0317
(0.206) 		0.0207
(0.163) 		0.0935
(0.37) 		0.9
(1.00) 		1
(1.00)
9p gain 122 (20%) 490 0.0109
(0.113) 		0.861
(0.995) 		0.0388
(0.232) 		0.0105
(0.112) 		0.589
(0.857) 		0.316
(0.686) 		0.557
(0.844) 		0.761
(0.949) 		0.803
(0.97) 		0.0066
(0.0833) 		0.363
(0.706) 		0.299
(0.671) 		0.0655
(0.304) 		0.247
(0.611)
11p gain 85 (14%) 527 0.828
(0.985) 		0.00718
(0.0871) 		0.0327
(0.207) 		0.262
(0.63) 		0.164
(0.502) 		0.19
(0.538) 		0.0288
(0.197) 		0.907
(1.00) 		0.571
(0.852) 		0.00194
(0.0405) 		0.56
(0.846) 		0.138
(0.458) 		0.487
(0.794) 		0.574
(0.852)
16p gain 147 (24%) 465 0.142
(0.459) 		0.187
(0.535) 		0.83
(0.985) 		0.0226
(0.171) 		1
(1.00) 		0.00353
(0.0563) 		0.333
(0.688) 		0.85
(0.987) 		0.658
(0.887) 		0.00116
(0.0296) 		0.768
(0.951) 		0.00438
(0.0633) 		0.443
(0.766) 		1
(1.00)
16q gain 145 (24%) 467 0.275
(0.648) 		0.132
(0.447) 		0.59
(0.857) 		0.00674
(0.0841) 		0.98
(1.00) 		0.00079
(0.0239) 		0.267
(0.638) 		0.85
(0.987) 		0.652
(0.884) 		0.00121
(0.0296) 		0.77
(0.951) 		0.00282
(0.0492) 		0.438
(0.766) 		1
(1.00)
1p loss 137 (22%) 475 0.138
(0.458) 		0.423
(0.756) 		0.0786
(0.334) 		0.0946
(0.372) 		0.794
(0.966) 		0.00732
(0.0875) 		0.0122
(0.122) 		0.332
(0.688) 		0.48
(0.792) 		0.0118
(0.12) 		0.747
(0.939) 		0.000942
(0.0253) 		0.279
(0.649) 		0.312
(0.684)
10p loss 100 (16%) 512 0.167
(0.506) 		0.00496
(0.0664) 		0.107
(0.4) 		0.404
(0.742) 		0.815
(0.974) 		0.102
(0.391) 		0.161
(0.496) 		0.913
(1.00) 		0.00835
(0.0978) 		0.0221
(0.171) 		0.985
(1.00) 		0.0197
(0.162) 		0.578
(0.856) 		1
(1.00)
15q loss 228 (37%) 384 0.459
(0.781) 		0.573
(0.852) 		0.0582
(0.284) 		0.0529
(0.271) 		0.278
(0.649) 		0.0168
(0.148) 		0.00819
(0.097) 		0.357
(0.703) 		0.108
(0.401) 		0.0122
(0.122) 		0.884
(1.00) 		0.0045
(0.0633) 		0.319
(0.688) 		1
(1.00)
19p loss 63 (10%) 549 0.129
(0.441) 		0.254
(0.62) 		0.128
(0.44) 		0.00119
(0.0296) 		0.813
(0.974) 		0.00027
(0.0107) 		0.00597
(0.0779) 		1
(1.00) 		1
(1.00) 		0.139
(0.458) 		0.499
(0.802) 		3.95e-06
(0.000957) 		0.879
(1.00) 		1
(1.00)
2q gain 120 (20%) 492 0.432
(0.763) 		0.497
(0.8) 		0.0152
(0.139) 		0.174
(0.514) 		0.406
(0.742) 		0.0209
(0.163) 		0.452
(0.778) 		0.359
(0.705) 		0.0516
(0.267) 		0.00136
(0.0319) 		0.34
(0.69) 		0.0688
(0.315) 		0.243
(0.607) 		0.324
(0.688)
6p gain 124 (20%) 488 0.471
(0.791) 		0.461
(0.783) 		0.138
(0.458) 		0.0272
(0.19) 		0.556
(0.844) 		0.00056
(0.0195) 		0.0786
(0.334) 		0.315
(0.686) 		0.0467
(0.254) 		0.199
(0.548) 		0.324
(0.688) 		0.000745
(0.0231) 		0.245
(0.608) 		0.589
(0.857)
12q gain 111 (18%) 501 0.626
(0.87) 		0.042
(0.242) 		0.124
(0.431) 		0.0498
(0.263) 		0.439
(0.766) 		0.0091
(0.104) 		0.29
(0.663) 		0.462
(0.783) 		0.801
(0.97) 		0.235
(0.595) 		0.562
(0.846) 		0.00494
(0.0664) 		0.829
(0.985) 		0.593
(0.857)
18p gain 33 (5%) 579 0.248
(0.612) 		0.521
(0.819) 		0.842
(0.987) 		0.0156
(0.141) 		0.726
(0.925) 		0.0144
(0.137) 		1
(1.00) 		0.15
(0.475) 		0.645
(0.883) 		0.0447
(0.253) 		1
(1.00) 		0.0134
(0.129) 		0.664
(0.893) 		1
(1.00)
6q loss 68 (11%) 544 0.0533
(0.271) 		0.75
(0.941) 		0.306
(0.682) 		0.336
(0.688) 		0.345
(0.694) 		0.0702
(0.318) 		0.349
(0.698) 		0.246
(0.61) 		0.0356
(0.216) 		0.0333
(0.209) 		0.19
(0.538) 		0.0537
(0.271) 		0.0034
(0.055) 		1
(1.00)
9q loss 77 (13%) 535 0.436
(0.766) 		0.0608
(0.29) 		0.578
(0.856) 		0.742
(0.936) 		0.197
(0.546) 		0.493
(0.797) 		0.0359
(0.217) 		0.331
(0.688) 		0.563
(0.846) 		0.0249
(0.184) 		0.077
(0.331) 		0.249
(0.613) 		0.871
(0.999) 		0.0206
(0.163)
10q loss 110 (18%) 502 0.202
(0.553) 		0.0203
(0.163) 		0.0723
(0.32) 		0.724
(0.925) 		0.986
(1.00) 		0.308
(0.683) 		0.652
(0.884) 		0.753
(0.943) 		0.00498
(0.0664) 		0.0186
(0.157) 		1
(1.00) 		0.134
(0.452) 		0.652
(0.884) 		1
(1.00)
13q loss 20 (3%) 592 0.338
(0.688) 		0.911
(1.00) 		0.198
(0.546) 		0.612
(0.861) 		0.59
(0.857) 		0.072
(0.32) 		0.158
(0.489) 		1
(1.00) 		0.22
(0.579) 		0.0343
(0.212) 		1
(1.00) 		0.00705
(0.087) 		0.0145
(0.137) 		1
(1.00)
14q loss 204 (33%) 408 0.978
(1.00) 		0.322
(0.688) 		0.0196
(0.162) 		0.296
(0.67) 		0.375
(0.718) 		0.0402
(0.236) 		0.05
(0.263) 		0.44
(0.766) 		0.104
(0.394) 		1e-05
(0.000957) 		0.97
(1.00) 		0.216
(0.574) 		0.981
(1.00) 		0.665
(0.893)
19q loss 55 (9%) 557 0.503
(0.806) 		0.601
(0.858) 		0.148
(0.47) 		0.0108
(0.113) 		0.788
(0.965) 		0.00153
(0.0344) 		0.109
(0.401) 		0.397
(0.736) 		0.728
(0.926) 		0.216
(0.574) 		0.862
(0.995) 		0.000635
(0.0205) 		0.134
(0.452) 		1
(1.00)
2p gain 122 (20%) 490 0.545
(0.834) 		0.904
(1.00) 		0.0664
(0.307) 		0.219
(0.578) 		0.336
(0.688) 		0.0473
(0.255) 		0.299
(0.671) 		0.478
(0.792) 		0.147
(0.469) 		0.00398
(0.0601) 		0.0256
(0.184) 		0.147
(0.469) 		0.725
(0.925) 		0.342
(0.691)
3p gain 72 (12%) 540 0.839
(0.987) 		0.108
(0.401) 		0.0312
(0.205) 		0.00925
(0.105) 		0.982
(1.00) 		0.179
(0.522) 		0.0879
(0.359) 		0.316
(0.686) 		1
(1.00) 		0.0891
(0.36) 		0.972
(1.00) 		0.0821
(0.344) 		0.226
(0.588) 		1
(1.00)
3q gain 98 (16%) 514 0.258
(0.624) 		0.329
(0.688) 		0.0454
(0.253) 		0.0174
(0.153) 		0.771
(0.952) 		0.0606
(0.29) 		0.0309
(0.205) 		0.379
(0.718) 		0.794
(0.966) 		0.0741
(0.324) 		0.565
(0.847) 		0.0742
(0.324) 		0.272
(0.644) 		1
(1.00)
9q gain 101 (17%) 511 0.00883
(0.102) 		0.873
(1) 		0.219
(0.578) 		0.0557
(0.275) 		0.585
(0.857) 		0.503
(0.806) 		0.635
(0.875) 		0.827
(0.985) 		0.786
(0.965) 		0.0272
(0.19) 		0.765
(0.95) 		0.522
(0.819) 		0.378
(0.718) 		1
(1.00)
10q gain 29 (5%) 583 0.695
(0.91) 		0.117
(0.423) 		0.526
(0.822) 		0.801
(0.97) 		0.55
(0.84) 		0.139
(0.458) 		0.382
(0.719) 		1
(1.00) 		0.378
(0.718) 		0.842
(0.987) 		0.837
(0.987) 		0.096
(0.376) 		0.0183
(0.157) 		0.0249
(0.184)
11q gain 77 (13%) 535 0.437
(0.766) 		8.36e-05
(0.0048) 		0.132
(0.447) 		0.333
(0.688) 		0.511
(0.814) 		0.209
(0.564) 		0.0522
(0.269) 		1
(1.00) 		1
(1.00) 		0.0038
(0.0586) 		0.667
(0.895) 		0.145
(0.467) 		0.406
(0.742) 		0.528
(0.822)
2p loss 17 (3%) 595 0.653
(0.884) 		0.21
(0.564) 		0.000949
(0.0253) 		0.592
(0.857) 		0.881
(1.00) 		0.794
(0.966) 		0.49
(0.795) 		0.806
(0.971) 		0.198
(0.546) 		0.00992
(0.111) 		1
(1.00) 		0.689
(0.906) 		0.15
(0.473) 		1
(1.00)
3q loss 44 (7%) 568 0.158
(0.489) 		0.414
(0.749) 		0.475
(0.792) 		0.174
(0.514) 		0.12
(0.424) 		0.485
(0.794) 		0.0393
(0.233) 		0.16
(0.495) 		1
(1.00) 		0.0066
(0.0833) 		0.526
(0.822) 		0.528
(0.822) 		0.31
(0.683) 		1
(1.00)
5p loss 86 (14%) 526 0.29
(0.663) 		0.729
(0.926) 		0.294
(0.667) 		0.0276
(0.191) 		0.891
(1.00) 		0.0719
(0.32) 		0.399
(0.738) 		0.561
(0.846) 		1
(1.00) 		0.335
(0.688) 		0.696
(0.91) 		0.0509
(0.265) 		0.479
(0.792) 		0.0271
(0.19)
5q loss 121 (20%) 491 0.0934
(0.37) 		0.77
(0.951) 		0.0508
(0.265) 		0.118
(0.423) 		0.864
(0.996) 		0.0195
(0.162) 		0.0539
(0.271) 		0.612
(0.861) 		0.814
(0.974) 		0.0488
(0.262) 		0.52
(0.819) 		0.0105
(0.112) 		0.364
(0.706) 		0.0597
(0.288)
6p loss 45 (7%) 567 0.0309
(0.205) 		0.335
(0.688) 		0.861
(0.995) 		0.341
(0.69) 		0.563
(0.846) 		0.421
(0.753) 		1
(1.00) 		0.539
(0.831) 		0.0632
(0.295) 		0.14
(0.459) 		0.05
(0.263) 		0.352
(0.698) 		0.00482
(0.0664) 		1
(1.00)
11p loss 74 (12%) 538 0.932
(1.00) 		0.337
(0.688) 		0.325
(0.688) 		0.203
(0.553) 		0.424
(0.756) 		0.011
(0.113) 		0.364
(0.706) 		0.902
(1.00) 		0.374
(0.718) 		0.225
(0.587) 		0.929
(1.00) 		0.000426
(0.0158) 		0.214
(0.572) 		1
(1.00)
12q loss 70 (11%) 542 0.112
(0.408) 		0.908
(1.00) 		0.47
(0.791) 		0.103
(0.393) 		0.41
(0.745) 		0.0233
(0.175) 		0.0933
(0.37) 		0.899
(1.00) 		1
(1.00) 		0.068
(0.314) 		1
(1.00) 		0.0114
(0.117) 		0.205
(0.555) 		1
(1.00)
17q loss 96 (16%) 516 0.189
(0.538) 		0.877
(1.00) 		0.528
(0.822) 		0.0599
(0.288) 		0.0874
(0.358) 		0.0102
(0.112) 		0.181
(0.525) 		0.507
(0.809) 		0.431
(0.763) 		0.848
(0.987) 		0.632
(0.874) 		0.000855
(0.0252) 		0.166
(0.504) 		1
(1.00)
xp loss 90 (15%) 522 0.156
(0.486) 		0.654
(0.884) 		0.604
(0.858) 		0.516
(0.818) 		0.432
(0.764) 		0.0314
(0.205) 		0.0724
(0.32) 		0.494
(0.797) 		0.597
(0.857) 		0.286
(0.66) 		0.98
(1.00) 		0.0194
(0.162) 		0.395
(0.735) 		1
(1.00)
14q gain 43 (7%) 569 0.417
(0.752) 		0.842
(0.987) 		0.283
(0.656) 		0.594
(0.857) 		0.955
(1.00) 		0.648
(0.884) 		0.349
(0.698) 		1
(1.00) 		1
(1.00) 		0.107
(0.4) 		0.597
(0.857) 		0.251
(0.615) 		0.0226
(0.171) 		1
(1.00)
17q gain 110 (18%) 502 0.143
(0.461) 		0.254
(0.62) 		0.905
(1.00) 		0.333
(0.688) 		0.604
(0.858) 		0.531
(0.824) 		0.0133
(0.128) 		0.916
(1.00) 		1
(1.00) 		0.615
(0.861) 		0.168
(0.507) 		0.963
(1.00) 		0.696
(0.91) 		0.0553
(0.275)
21q gain 34 (6%) 578 0.722
(0.925) 		0.0185
(0.157) 		0.686
(0.904) 		0.706
(0.915) 		0.196
(0.544) 		0.519
(0.819) 		0.421
(0.753) 		0.485
(0.794) 		0.645
(0.883) 		0.466
(0.789) 		0.834
(0.985) 		0.23
(0.591) 		0.604
(0.858) 		1
(1.00)
1q loss 78 (13%) 534 0.12
(0.424) 		0.264
(0.632) 		0.273
(0.644) 		0.406
(0.742) 		0.965
(1.00) 		0.211
(0.564) 		0.0204
(0.163) 		0.0694
(0.316) 		0.386
(0.723) 		0.234
(0.595) 		0.597
(0.857) 		0.0927
(0.37) 		0.0461
(0.253) 		0.124
(0.43)
7p loss 3 (0%) 609 0.469
(0.791) 		0.881
(1.00) 		1
(1.00) 		1
(1.00) 		0.68
(0.901) 		0.581
(0.857) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.121
(0.426) 		1
(1.00) 		0.147
(0.469) 		0.0282
(0.194)
7q loss 5 (1%) 607 0.325
(0.688) 		0.671
(0.896) 		0.613
(0.861) 		0.568
(0.85) 		0.417
(0.752) 		0.832
(0.985) 		1
(1.00) 		0.669
(0.896) 		0.263
(0.631) 		0.18
(0.522) 		1
(1.00) 		0.192
(0.538) 		0.505
(0.808) 		0.042
(0.242)
8q loss 36 (6%) 576 0.704
(0.915) 		0.894
(1.00) 		0.337
(0.688) 		0.382
(0.719) 		0.734
(0.928) 		0.257
(0.624) 		0.421
(0.753) 		0.0241
(0.18) 		1
(1.00) 		0.535
(0.826) 		0.615
(0.861) 		0.897
(1.00) 		0.0856
(0.354) 		1
(1.00)
9p loss 76 (12%) 536 0.196
(0.544) 		0.331
(0.688) 		0.578
(0.856) 		0.85
(0.987) 		0.18
(0.522) 		0.452
(0.778) 		0.0812
(0.341) 		0.111
(0.407) 		1
(1.00) 		0.0254
(0.184) 		0.0625
(0.295) 		0.102
(0.391) 		0.861
(0.995) 		0.124
(0.43)
12p loss 70 (11%) 542 0.101
(0.39) 		0.562
(0.846) 		0.194
(0.542) 		0.49
(0.795) 		0.242
(0.607) 		0.0458
(0.253) 		0.19
(0.538) 		0.8
(0.97) 		0.368
(0.712) 		0.0104
(0.112) 		0.906
(1.00) 		0.0472
(0.255) 		0.711
(0.918) 		1
(1.00)
xq loss 78 (13%) 534 0.38
(0.718) 		0.747
(0.939) 		0.132
(0.447) 		0.379
(0.718) 		0.788
(0.965) 		0.135
(0.454) 		0.0155
(0.141) 		0.717
(0.922) 		0.769
(0.951) 		0.158
(0.489) 		0.477
(0.792) 		0.0861
(0.354) 		0.456
(0.779) 		1
(1.00)
1p gain 50 (8%) 562 0.221
(0.581) 		0.995
(1.00) 		0.613
(0.861) 		0.289
(0.663) 		0.461
(0.783) 		0.37
(0.714) 		0.184
(0.529) 		0.375
(0.718) 		0.725
(0.925) 		0.0595
(0.288) 		0.279
(0.649) 		0.12
(0.424) 		0.609
(0.861) 		0.418
(0.752)
4p gain 20 (3%) 592 0.847
(0.987) 		0.378
(0.718) 		0.0718
(0.32) 		0.352
(0.698) 		0.361
(0.706) 		0.779
(0.96) 		0.312
(0.684) 		0.171
(0.511) 		1
(1.00) 		0.128
(0.44) 		0.601
(0.858) 		0.822
(0.981) 		0.271
(0.643) 		1
(1.00)
4q gain 21 (3%) 591 0.491
(0.795) 		0.636
(0.875) 		1
(1.00) 		0.701
(0.913) 		0.969
(1.00) 		0.119
(0.424) 		0.104
(0.394) 		0.118
(0.423) 		0.615
(0.861) 		0.436
(0.766) 		0.621
(0.865) 		0.1
(0.39) 		0.456
(0.779) 		1
(1.00)
5q gain 64 (10%) 548 0.867
(0.999) 		0.819
(0.978) 		0.0509
(0.265) 		0.298
(0.671) 		0.332
(0.688) 		0.277
(0.649) 		0.443
(0.766) 		0.895
(1.00) 		0.102
(0.391) 		0.0577
(0.283) 		0.397
(0.736) 		0.359
(0.705) 		0.309
(0.683) 		1
(1.00)
8p gain 170 (28%) 442 0.645
(0.883) 		0.373
(0.718) 		0.307
(0.683) 		0.602
(0.858) 		0.891
(1.00) 		0.256
(0.622) 		0.361
(0.706) 		1
(1.00) 		1
(1.00) 		0.521
(0.819) 		0.0624
(0.295) 		0.31
(0.684) 		1
(1.00) 		0.641
(0.881)
10p gain 49 (8%) 563 0.0464
(0.254) 		0.81
(0.974) 		0.613
(0.861) 		0.656
(0.885) 		0.217
(0.576) 		0.045
(0.253) 		0.377
(0.718) 		1
(1.00) 		0.711
(0.918) 		0.85
(0.987) 		0.612
(0.861) 		0.227
(0.588) 		0.101
(0.391) 		0.0749
(0.324)
12p gain 127 (21%) 485 0.231
(0.591) 		0.155
(0.485) 		0.91
(1.00) 		0.177
(0.518) 		0.345
(0.694) 		0.155
(0.486) 		0.665
(0.893) 		1
(1.00) 		0.232
(0.593) 		0.686
(0.904) 		0.763
(0.95) 		0.144
(0.463) 		0.829
(0.985) 		0.587
(0.857)
15q gain 15 (2%) 597 0.932
(1.00) 		0.355
(0.701) 		1
(1.00) 		0.564
(0.846) 		0.083
(0.347) 		0.72
(0.923) 		0.285
(0.659) 		0.0633
(0.295) 		0.523
(0.819) 		0.0792
(0.335) 		0.703
(0.915) 		0.419
(0.753) 		0.481
(0.792) 		1
(1.00)
17p gain 38 (6%) 574 0.046
(0.253) 		0.628
(0.87) 		0.85
(0.987) 		0.682
(0.901) 		0.363
(0.706) 		0.803
(0.97) 		0.619
(0.863) 		1
(1.00) 		1
(1.00) 		0.747
(0.939) 		0.94
(1.00) 		0.937
(1.00) 		0.0453
(0.253) 		0.309
(0.683)
18q gain 19 (3%) 593 0.975
(1.00) 		0.0966
(0.377) 		0.793
(0.966) 		0.0923
(0.37) 		0.401
(0.74) 		0.33
(0.688) 		0.485
(0.794) 		0.243
(0.607) 		0.552
(0.84) 		0.06
(0.288) 		0.607
(0.861) 		0.476
(0.792) 		0.141
(0.459) 		1
(1.00)
19p gain 104 (17%) 508 0.262
(0.63) 		0.759
(0.949) 		0.33
(0.688) 		0.919
(1.00) 		0.87
(0.999) 		0.34
(0.69) 		0.428
(0.762) 		0.332
(0.688) 		0.297
(0.67) 		0.108
(0.401) 		0.29
(0.663) 		0.57
(0.852) 		0.735
(0.929) 		0.588
(0.857)
19q gain 114 (19%) 498 0.262
(0.63) 		0.803
(0.97) 		0.725
(0.925) 		0.85
(0.987) 		0.975
(1.00) 		0.312
(0.684) 		0.172
(0.512) 		0.533
(0.824) 		1
(1.00) 		0.268
(0.639) 		0.406
(0.742) 		0.67
(0.896) 		0.473
(0.791) 		0.288
(0.663)
22q gain 23 (4%) 589 0.832
(0.985) 		0.314
(0.686) 		0.0889
(0.36) 		0.674
(0.898) 		0.111
(0.407) 		0.288
(0.663) 		0.382
(0.719) 		0.833
(0.985) 		0.618
(0.863) 		0.103
(0.393) 		0.332
(0.688) 		0.113
(0.412) 		0.676
(0.9) 		1
(1.00)
xp gain 98 (16%) 514 0.475
(0.792) 		0.583
(0.857) 		0.211
(0.564) 		0.118
(0.423) 		0.327
(0.688) 		0.12
(0.424) 		0.335
(0.688) 		0.124
(0.43) 		1
(1.00) 		0.128
(0.44) 		0.596
(0.857) 		0.787
(0.965) 		0.805
(0.97) 		0.595
(0.857)
xq gain 107 (17%) 505 0.843
(0.987) 		0.513
(0.815) 		0.717
(0.922) 		0.136
(0.454) 		0.491
(0.795) 		0.292
(0.665) 		0.758
(0.949) 		0.166
(0.504) 		0.801
(0.97) 		0.277
(0.649) 		0.972
(1.00) 		0.441
(0.766) 		0.634
(0.875) 		0.589
(0.857)
2q loss 14 (2%) 598 0.368
(0.712) 		0.508
(0.81) 		0.0631
(0.295) 		0.276
(0.649) 		1
(1.00) 		0.706
(0.915) 		0.141
(0.459) 		0.431
(0.763) 		0.523
(0.819) 		0.303
(0.677) 		0.844
(0.987) 		0.441
(0.766) 		1
(1.00)
11q loss 92 (15%) 520 0.467
(0.789) 		0.503
(0.806) 		0.363
(0.706) 		0.496
(0.8) 		0.741
(0.936) 		0.0847
(0.352) 		0.32
(0.688) 		0.571
(0.852) 		0.192
(0.538) 		0.14
(0.459) 		0.981
(1.00) 		0.0562
(0.277) 		0.174
(0.514) 		0.551
(0.84)
16p loss 41 (7%) 571 0.224
(0.587) 		0.316
(0.686) 		0.856
(0.991) 		0.107
(0.4) 		0.381
(0.719) 		0.383
(0.719) 		0.487
(0.794) 		0.628
(0.87) 		1
(1.00) 		0.564
(0.846) 		0.149
(0.472) 		0.431
(0.763) 		0.228
(0.589) 		0.35
(0.698)
16q loss 43 (7%) 569 0.545
(0.834) 		0.176
(0.516) 		0.373
(0.718) 		0.389
(0.727) 		0.808
(0.972) 		0.183
(0.529) 		1
(1.00) 		0.874
(1.00) 		0.451
(0.778) 		0.717
(0.922) 		0.385
(0.721) 		0.478
(0.792) 		0.188
(0.537) 		0.34
(0.69)
20p loss 67 (11%) 545 0.237
(0.599) 		0.457
(0.78) 		0.0758
(0.327) 		0.551
(0.84) 		0.854
(0.991) 		0.413
(0.749) 		0.708
(0.916) 		0.699
(0.912) 		0.533
(0.824) 		0.136
(0.454) 		0.622
(0.865) 		0.922
(1.00) 		0.776
(0.957) 		0.418
(0.752)
20q loss 6 (1%) 606 0.609
(0.861) 		0.169
(0.507) 		0.35
(0.698) 		0.647
(0.884) 		0.718
(0.922) 		0.732
(0.927) 		0.596
(0.857) 		1
(1.00) 		1
(1.00) 		0.353
(0.699) 		1
(1.00) 		0.688
(0.906) 		0.261
(0.63) 		1
(1.00)
'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0339 (Fisher's exact test), Q value = 0.21

Table S1.  Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 20 106 417 67
1Q GAIN MUTATED 4 14 78 21
1Q GAIN WILD-TYPE 16 92 339 46

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0343 (Fisher's exact test), Q value = 0.21

Table S2.  Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
1Q GAIN MUTATED 55 30 31
1Q GAIN WILD-TYPE 290 120 84

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0253 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #2: '1q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
1Q GAIN MUTATED 78 25
1Q GAIN WILD-TYPE 372 63

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0033 (Wilcoxon-test), Q value = 0.054

Table S4.  Gene #2: '1q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
1Q GAIN MUTATED 112 3.5 (6.1)
1Q GAIN WILD-TYPE 464 1.9 (4.3)

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00398 (Fisher's exact test), Q value = 0.06

Table S5.  Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
2P GAIN MUTATED 75 6 41 0
2P GAIN WILD-TYPE 307 54 105 13

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0256 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #3: '2p gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 442 5 37 29
2P GAIN MUTATED 86 3 5 10
2P GAIN WILD-TYPE 356 2 32 19

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'2q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0152 (Fisher's exact test), Q value = 0.14

Table S7.  Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
2Q GAIN MUTATED 77 43
2Q GAIN WILD-TYPE 369 119

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0209 (Fisher's exact test), Q value = 0.16

Table S8.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
2Q GAIN MUTATED 57 29 33
2Q GAIN WILD-TYPE 288 121 82

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00136 (Fisher's exact test), Q value = 0.032

Table S9.  Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
2Q GAIN MUTATED 71 6 43 0
2Q GAIN WILD-TYPE 311 54 103 13

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0312 (Fisher's exact test), Q value = 0.2

Table S10.  Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
3P GAIN MUTATED 44 27
3P GAIN WILD-TYPE 402 135

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00925 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #5: '3p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
3P GAIN MUTATED 9 1 2 18 1 0 5 5 6 6 9 5 2
3P GAIN WILD-TYPE 95 0 34 155 9 3 21 13 77 48 54 21 0

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #6: '3q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
3Q GAIN MUTATED 11 1 4 24 1 0 6 6 11 9 13 7 2
3Q GAIN WILD-TYPE 93 0 32 149 9 3 20 12 72 45 50 19 0

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0309 (Fisher's exact test), Q value = 0.2

Table S13.  Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
3Q GAIN MUTATED 59 20
3Q GAIN WILD-TYPE 391 68

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0178 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #9: '5p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
5P GAIN MUTATED 45 31 26
5P GAIN WILD-TYPE 300 119 89

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'RADIATION_THERAPY'

P value = 0.0306 (Fisher's exact test), Q value = 0.2

Table S15.  Gene #9: '5p gain' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
5P GAIN MUTATED 68 9
5P GAIN WILD-TYPE 378 19

Figure S15.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #9: 'RADIATION_THERAPY'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0224 (Fisher's exact test), Q value = 0.17

Table S16.  Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
5P GAIN MUTATED 59 8 36 0
5P GAIN WILD-TYPE 323 52 110 13

Figure S16.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

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

Table S17.  Gene #9: '5p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
5P GAIN MUTATED 100 2.8 (4.3)
5P GAIN WILD-TYPE 476 2.1 (4.8)

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'PATHOLOGIC_STAGE'

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

Table S18.  Gene #11: '6p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
6P GAIN MUTATED 18 0 3 24 2 1 5 6 22 16 15 9 1
6P GAIN WILD-TYPE 86 1 33 149 8 2 21 12 61 38 48 17 1

Figure S18.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

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

Table S19.  Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
6P GAIN MUTATED 54 31 38
6P GAIN WILD-TYPE 291 119 77

Figure S19.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000745 (Wilcoxon-test), Q value = 0.023

Table S20.  Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
6P GAIN MUTATED 120 3.3 (5.2)
6P GAIN WILD-TYPE 456 2.0 (4.6)

Figure S20.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.11

Table S21.  Gene #12: '6q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
6Q GAIN MUTATED 16 0 3 20 2 0 5 5 19 14 13 11 1
6Q GAIN WILD-TYPE 88 1 33 153 8 3 21 13 64 40 50 15 1

Figure S21.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00187 (Fisher's exact test), Q value = 0.04

Table S22.  Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
6Q GAIN MUTATED 48 29 33
6Q GAIN WILD-TYPE 297 121 82

Figure S22.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0148 (Fisher's exact test), Q value = 0.14

Table S23.  Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
6Q GAIN MUTATED 72 24
6Q GAIN WILD-TYPE 378 64

Figure S23.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00261 (Wilcoxon-test), Q value = 0.049

Table S24.  Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
6Q GAIN MUTATED 107 3.1 (4.8)
6Q GAIN WILD-TYPE 469 2.0 (4.7)

Figure S24.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0085

Table S25.  Gene #13: '7p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
7P GAIN MUTATED 57 1 18 74 3 2 14 12 61 36 42 18 1
7P GAIN WILD-TYPE 47 0 18 99 7 1 12 6 22 18 21 8 1

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0015

Table S26.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
7P GAIN MUTATED 168 103 75
7P GAIN WILD-TYPE 177 47 40

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0255 (Fisher's exact test), Q value = 0.18

Table S27.  Gene #13: '7p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
7P GAIN MUTATED 242 59
7P GAIN WILD-TYPE 208 29

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00023 (Fisher's exact test), Q value = 0.011

Table S28.  Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
7P GAIN MUTATED 219 24 98 3
7P GAIN WILD-TYPE 163 36 48 10

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000103 (Wilcoxon-test), Q value = 0.0056

Table S29.  Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
7P GAIN MUTATED 331 2.6 (5.2)
7P GAIN WILD-TYPE 245 1.7 (4.0)

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.015

Table S30.  Gene #14: '7q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
7Q GAIN MUTATED 54 1 16 63 3 1 13 8 56 31 38 17 1
7Q GAIN WILD-TYPE 50 0 20 110 7 2 13 10 27 23 25 9 1

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.03

Table S31.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
7Q GAIN MUTATED 152 90 66
7Q GAIN WILD-TYPE 193 60 49

Figure S31.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.01 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #14: '7q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
7Q GAIN MUTATED 211 55
7Q GAIN WILD-TYPE 239 33

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00287 (Fisher's exact test), Q value = 0.049

Table S33.  Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
7Q GAIN MUTATED 198 22 83 2
7Q GAIN WILD-TYPE 184 38 63 11

Figure S33.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00366 (Wilcoxon-test), Q value = 0.058

Table S34.  Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
7Q GAIN MUTATED 297 2.4 (4.7)
7Q GAIN WILD-TYPE 279 2.1 (4.7)

Figure S34.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0328 (Fisher's exact test), Q value = 0.21

Table S35.  Gene #16: '8q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
8Q GAIN MUTATED 45 0 21 85 3 2 11 11 41 33 44 13 0
8Q GAIN WILD-TYPE 59 1 15 88 7 1 15 7 42 21 19 13 2

Figure S35.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00721 (Fisher's exact test), Q value = 0.087

Table S36.  Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
8Q GAIN MUTATED 220 57
8Q GAIN WILD-TYPE 230 31

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0317 (Fisher's exact test), Q value = 0.21

Table S37.  Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
8Q GAIN MUTATED 202 22 81 4
8Q GAIN WILD-TYPE 180 38 65 9

Figure S37.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0207 (Fisher's exact test), Q value = 0.16

Table S38.  Gene #16: '8q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 442 5 37 29
8Q GAIN MUTATED 214 3 27 17
8Q GAIN WILD-TYPE 228 2 10 12

Figure S38.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'9p gain' versus 'Time to Death'

P value = 0.0109 (logrank test), Q value = 0.11

Table S39.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 593 121 0.0 - 148.0 (20.0)
9P GAIN MUTATED 118 33 0.0 - 129.3 (17.8)
9P GAIN WILD-TYPE 475 88 0.0 - 148.0 (20.2)

Figure S39.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'TUMOR_TISSUE_SITE'

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

Table S40.  Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
9P GAIN MUTATED 80 42
9P GAIN WILD-TYPE 366 120

Figure S40.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0105 (Fisher's exact test), Q value = 0.11

Table S41.  Gene #17: '9p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
9P GAIN MUTATED 15 1 7 31 2 2 3 8 12 17 12 7 1
9P GAIN WILD-TYPE 89 0 29 142 8 1 23 10 71 37 51 19 1

Figure S41.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0066 (Fisher's exact test), Q value = 0.083

Table S42.  Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
9P GAIN MUTATED 62 18 36 5
9P GAIN WILD-TYPE 320 42 110 8

Figure S42.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'Time to Death'

P value = 0.00883 (logrank test), Q value = 0.1

Table S43.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 593 121 0.0 - 148.0 (20.0)
9Q GAIN MUTATED 98 29 0.0 - 129.3 (17.0)
9Q GAIN WILD-TYPE 495 92 0.0 - 148.0 (20.3)

Figure S43.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'HISTOLOGICAL_TYPE'

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

Table S44.  Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
9Q GAIN MUTATED 53 16 27 4
9Q GAIN WILD-TYPE 329 44 119 9

Figure S44.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'RACE'

P value = 0.0183 (Fisher's exact test), Q value = 0.16

Table S45.  Gene #20: '10q gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 64 292
10Q GAIN MUTATED 1 1 6 13
10Q GAIN WILD-TYPE 0 11 58 279

Figure S45.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #13: 'RACE'

'10q gain' versus 'ETHNICITY'

P value = 0.0249 (Fisher's exact test), Q value = 0.18

Table S46.  Gene #20: '10q gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
10Q GAIN MUTATED 2 17
10Q GAIN WILD-TYPE 3 331

Figure S46.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #14: 'ETHNICITY'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00718 (Wilcoxon-test), Q value = 0.087

Table S47.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
11P GAIN MUTATED 85 62.9 (12.3)
11P GAIN WILD-TYPE 525 66.8 (12.8)

Figure S47.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0327 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
11P GAIN MUTATED 53 31
11P GAIN WILD-TYPE 393 131

Figure S48.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0288 (Fisher's exact test), Q value = 0.2

Table S49.  Gene #21: '11p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
11P GAIN MUTATED 56 19
11P GAIN WILD-TYPE 394 69

Figure S49.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00194 (Fisher's exact test), Q value = 0.04

Table S50.  Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
11P GAIN MUTATED 51 2 31 0
11P GAIN WILD-TYPE 331 58 115 13

Figure S50.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 8.36e-05 (Wilcoxon-test), Q value = 0.0048

Table S51.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
11Q GAIN MUTATED 77 61.0 (12.3)
11Q GAIN WILD-TYPE 533 67.0 (12.7)

Figure S51.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0038 (Fisher's exact test), Q value = 0.059

Table S52.  Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
11Q GAIN MUTATED 50 1 26 0
11Q GAIN WILD-TYPE 332 59 120 13

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 0.042 (Wilcoxon-test), Q value = 0.24

Table S53.  Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
12Q GAIN MUTATED 111 68.5 (12.3)
12Q GAIN WILD-TYPE 499 65.8 (12.8)

Figure S53.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0091 (Fisher's exact test), Q value = 0.1

Table S54.  Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
12Q GAIN MUTATED 75 25 11
12Q GAIN WILD-TYPE 270 125 104

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00494 (Wilcoxon-test), Q value = 0.066

Table S55.  Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
12Q GAIN MUTATED 107 1.1 (2.0)
12Q GAIN WILD-TYPE 469 2.5 (5.1)

Figure S55.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0149 (Fisher's exact test), Q value = 0.14

Table S56.  Gene #25: '13q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
13Q GAIN MUTATED 253 110
13Q GAIN WILD-TYPE 193 52

Figure S56.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'13q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00126 (Fisher's exact test), Q value = 0.03

Table S57.  Gene #25: '13q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
13Q GAIN MUTATED 60 0 18 87 4 3 16 15 55 37 48 16 0
13Q GAIN WILD-TYPE 44 1 18 86 6 0 10 3 28 17 15 10 2

Figure S57.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.011

Table S58.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
13Q GAIN MUTATED 182 103 80
13Q GAIN WILD-TYPE 163 47 35

Figure S58.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0327 (Fisher's exact test), Q value = 0.21

Table S59.  Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
13Q GAIN MUTATED 262 62
13Q GAIN WILD-TYPE 188 26

Figure S59.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S60.  Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
13Q GAIN MUTATED 235 17 106 3
13Q GAIN WILD-TYPE 147 43 40 10

Figure S60.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000904 (Wilcoxon-test), Q value = 0.025

Table S61.  Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
13Q GAIN MUTATED 352 2.4 (4.1)
13Q GAIN WILD-TYPE 224 2.0 (5.5)

Figure S61.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'RACE'

P value = 0.0226 (Fisher's exact test), Q value = 0.17

Table S62.  Gene #26: '14q gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 64 292
14Q GAIN MUTATED 1 2 2 22
14Q GAIN WILD-TYPE 0 10 62 270

Figure S62.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #13: 'RACE'

'16p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0226 (Fisher's exact test), Q value = 0.17

Table S63.  Gene #28: '16p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
16P GAIN MUTATED 18 1 4 33 3 0 8 8 25 18 17 6 1
16P GAIN WILD-TYPE 86 0 32 140 7 3 18 10 58 36 46 20 1

Figure S63.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00353 (Fisher's exact test), Q value = 0.056

Table S64.  Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
16P GAIN MUTATED 65 46 35
16P GAIN WILD-TYPE 280 104 80

Figure S64.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00116 (Fisher's exact test), Q value = 0.03

Table S65.  Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
16P GAIN MUTATED 100 5 40 0
16P GAIN WILD-TYPE 282 55 106 13

Figure S65.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00438 (Wilcoxon-test), Q value = 0.063

Table S66.  Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
16P GAIN MUTATED 139 2.5 (3.7)
16P GAIN WILD-TYPE 437 2.2 (5.0)

Figure S66.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00674 (Fisher's exact test), Q value = 0.084

Table S67.  Gene #29: '16q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
16Q GAIN MUTATED 17 1 4 32 2 0 8 9 27 16 16 7 1
16Q GAIN WILD-TYPE 87 0 32 141 8 3 18 9 56 38 47 19 1

Figure S67.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00079 (Fisher's exact test), Q value = 0.024

Table S68.  Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
16Q GAIN MUTATED 62 48 34
16Q GAIN WILD-TYPE 283 102 81

Figure S68.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00121 (Fisher's exact test), Q value = 0.03

Table S69.  Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
16Q GAIN MUTATED 97 5 41 0
16Q GAIN WILD-TYPE 285 55 105 13

Figure S69.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00282 (Wilcoxon-test), Q value = 0.049

Table S70.  Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
16Q GAIN MUTATED 138 2.5 (3.8)
16Q GAIN WILD-TYPE 438 2.2 (5.0)

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'PATHOLOGY_M_STAGE'

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

Table S71.  Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
17Q GAIN MUTATED 70 24
17Q GAIN WILD-TYPE 380 64

Figure S71.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0156 (Fisher's exact test), Q value = 0.14

Table S72.  Gene #32: '18p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
18P GAIN MUTATED 5 0 5 4 0 0 3 1 3 7 4 0 1
18P GAIN WILD-TYPE 99 1 31 169 10 3 23 17 80 47 59 26 1

Figure S72.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0144 (Fisher's exact test), Q value = 0.14

Table S73.  Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
18P GAIN MUTATED 14 6 13
18P GAIN WILD-TYPE 331 144 102

Figure S73.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0134 (Wilcoxon-test), Q value = 0.13

Table S74.  Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
18P GAIN MUTATED 31 4.6 (6.8)
18P GAIN WILD-TYPE 545 2.1 (4.5)

Figure S74.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'TUMOR_TISSUE_SITE'

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

Table S75.  Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
20P GAIN MUTATED 242 106
20P GAIN WILD-TYPE 204 56

Figure S75.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00406 (Fisher's exact test), Q value = 0.06

Table S76.  Gene #36: '20p gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
20P GAIN MUTATED 63 1 13 87 4 2 14 15 44 32 47 17 1
20P GAIN WILD-TYPE 41 0 23 86 6 1 12 3 39 22 16 9 1

Figure S76.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00206 (Fisher's exact test), Q value = 0.042

Table S77.  Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
20P GAIN MUTATED 247 64
20P GAIN WILD-TYPE 203 24

Figure S77.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S78.  Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
20P GAIN MUTATED 220 19 100 4
20P GAIN WILD-TYPE 162 41 46 9

Figure S78.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0326 (Wilcoxon-test), Q value = 0.21

Table S79.  Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
20P GAIN MUTATED 334 2.4 (4.8)
20P GAIN WILD-TYPE 242 2.0 (4.6)

Figure S79.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00051

Table S80.  Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
20Q GAIN MUTATED 315 144
20Q GAIN WILD-TYPE 131 18

Figure S80.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00147 (Fisher's exact test), Q value = 0.034

Table S81.  Gene #37: '20q gain' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
20Q GAIN MUTATED 79 1 21 117 5 3 19 17 66 43 56 23 1
20Q GAIN WILD-TYPE 25 0 15 56 5 0 7 1 17 11 7 3 1

Figure S81.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00059 (Fisher's exact test), Q value = 0.02

Table S82.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
20Q GAIN MUTATED 241 128 91
20Q GAIN WILD-TYPE 104 22 24

Figure S82.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00162 (Fisher's exact test), Q value = 0.036

Table S83.  Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
20Q GAIN MUTATED 329 78
20Q GAIN WILD-TYPE 121 10

Figure S83.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S84.  Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
20Q GAIN MUTATED 288 24 135 7
20Q GAIN WILD-TYPE 94 36 11 6

Figure S84.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0324 (Fisher's exact test), Q value = 0.21

Table S85.  Gene #37: '20q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 442 5 37 29
20Q GAIN MUTATED 333 4 32 16
20Q GAIN WILD-TYPE 109 1 5 13

Figure S85.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00409 (Wilcoxon-test), Q value = 0.06

Table S86.  Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
20Q GAIN MUTATED 438 2.4 (4.7)
20Q GAIN WILD-TYPE 138 1.8 (4.8)

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0185 (Wilcoxon-test), Q value = 0.16

Table S87.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
21Q GAIN MUTATED 34 61.9 (11.3)
21Q GAIN WILD-TYPE 576 66.5 (12.8)

Figure S87.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00732 (Fisher's exact test), Q value = 0.088

Table S88.  Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
1P LOSS MUTATED 62 38 36
1P LOSS WILD-TYPE 283 112 79

Figure S88.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.12

Table S89.  Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
1P LOSS MUTATED 92 29
1P LOSS WILD-TYPE 358 59

Figure S89.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0118 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
1P LOSS MUTATED 83 9 44 0
1P LOSS WILD-TYPE 299 51 102 13

Figure S90.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000942 (Wilcoxon-test), Q value = 0.025

Table S91.  Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
1P LOSS MUTATED 127 3.4 (6.3)
1P LOSS WILD-TYPE 449 1.9 (4.1)

Figure S91.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0204 (Fisher's exact test), Q value = 0.16

Table S92.  Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
1Q LOSS MUTATED 49 18
1Q LOSS WILD-TYPE 401 70

Figure S92.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'2p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000949 (Fisher's exact test), Q value = 0.025

Table S93.  Gene #44: '2p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
2P LOSS MUTATED 6 11
2P LOSS WILD-TYPE 440 151

Figure S93.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00992 (Fisher's exact test), Q value = 0.11

Table S94.  Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
2P LOSS MUTATED 6 0 9 1
2P LOSS WILD-TYPE 376 60 137 12

Figure S94.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.0205 (logrank test), Q value = 0.16

Table S95.  Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 593 121 0.0 - 148.0 (20.0)
3P LOSS MUTATED 67 16 0.4 - 85.0 (14.5)
3P LOSS WILD-TYPE 526 105 0.0 - 148.0 (20.9)

Figure S95.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0426 (Fisher's exact test), Q value = 0.24

Table S96.  Gene #46: '3p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
3P LOSS MUTATED 5 0 1 21 0 1 4 1 10 6 14 5 0
3P LOSS WILD-TYPE 99 1 35 152 10 2 22 17 73 48 49 21 2

Figure S96.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.2

Table S97.  Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 20 106 417 67
3P LOSS MUTATED 2 4 54 9
3P LOSS WILD-TYPE 18 102 363 58

Figure S97.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00263 (Fisher's exact test), Q value = 0.049

Table S98.  Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
3P LOSS MUTATED 42 19
3P LOSS WILD-TYPE 408 69

Figure S98.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0314 (Wilcoxon-test), Q value = 0.2

Table S99.  Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
3P LOSS MUTATED 63 3.3 (5.6)
3P LOSS WILD-TYPE 513 2.1 (4.6)

Figure S99.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'3q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0393 (Fisher's exact test), Q value = 0.23

Table S100.  Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
3Q LOSS MUTATED 27 11
3Q LOSS WILD-TYPE 423 77

Figure S100.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0066 (Fisher's exact test), Q value = 0.083

Table S101.  Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
3Q LOSS MUTATED 31 3 5 4
3Q LOSS WILD-TYPE 351 57 141 9

Figure S101.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0222 (Fisher's exact test), Q value = 0.17

Table S102.  Gene #48: '4p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
4P LOSS MUTATED 26 0 6 51 2 0 7 8 26 22 31 11 1
4P LOSS WILD-TYPE 78 1 30 122 8 3 19 10 57 32 32 15 1

Figure S102.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00263 (Fisher's exact test), Q value = 0.049

Table S103.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
4P LOSS MUTATED 91 56 48
4P LOSS WILD-TYPE 254 94 67

Figure S103.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000642 (Fisher's exact test), Q value = 0.02

Table S104.  Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
4P LOSS MUTATED 128 42
4P LOSS WILD-TYPE 322 46

Figure S104.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'RADIATION_THERAPY'

P value = 0.0202 (Fisher's exact test), Q value = 0.16

Table S105.  Gene #48: '4p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
4P LOSS MUTATED 138 15
4P LOSS WILD-TYPE 308 13

Figure S105.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'4p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S106.  Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
4P LOSS MUTATED 125 10 54 3
4P LOSS WILD-TYPE 257 50 92 10

Figure S106.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000882 (Wilcoxon-test), Q value = 0.025

Table S107.  Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
4P LOSS MUTATED 185 3.0 (5.1)
4P LOSS WILD-TYPE 391 1.9 (4.5)

Figure S107.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0124 (Fisher's exact test), Q value = 0.12

Table S108.  Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
4Q LOSS MUTATED 122 62
4Q LOSS WILD-TYPE 324 100

Figure S108.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00446 (Fisher's exact test), Q value = 0.063

Table S109.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
4Q LOSS MUTATED 88 56 44
4Q LOSS WILD-TYPE 257 94 71

Figure S109.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.0349 (Fisher's exact test), Q value = 0.21

Table S110.  Gene #49: '4q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
4Q LOSS MUTATED 134 14
4Q LOSS WILD-TYPE 312 14

Figure S110.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0124 (Fisher's exact test), Q value = 0.12

Table S111.  Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
4Q LOSS MUTATED 111 11 58 3
4Q LOSS WILD-TYPE 271 49 88 10

Figure S111.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00276 (Wilcoxon-test), Q value = 0.049

Table S112.  Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
4Q LOSS MUTATED 177 3.0 (5.1)
4Q LOSS WILD-TYPE 399 1.9 (4.5)

Figure S112.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0276 (Fisher's exact test), Q value = 0.19

Table S113.  Gene #50: '5p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
5P LOSS MUTATED 15 0 4 15 0 2 4 5 12 11 8 8 0
5P LOSS WILD-TYPE 89 1 32 158 10 1 22 13 71 43 55 18 2

Figure S113.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'5p loss' versus 'ETHNICITY'

P value = 0.0271 (Fisher's exact test), Q value = 0.19

Table S114.  Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
5P LOSS MUTATED 3 51
5P LOSS WILD-TYPE 2 297

Figure S114.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

'5q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S115.  Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
5Q LOSS MUTATED 57 31 33
5Q LOSS WILD-TYPE 288 119 82

Figure S115.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0105 (Wilcoxon-test), Q value = 0.11

Table S116.  Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
5Q LOSS MUTATED 116 3.2 (5.5)
5Q LOSS WILD-TYPE 460 2.0 (4.5)

Figure S116.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'Time to Death'

P value = 0.0309 (logrank test), Q value = 0.2

Table S117.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 593 121 0.0 - 148.0 (20.0)
6P LOSS MUTATED 44 12 1.5 - 45.4 (17.5)
6P LOSS WILD-TYPE 549 109 0.0 - 148.0 (20.1)

Figure S117.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'RACE'

P value = 0.00482 (Fisher's exact test), Q value = 0.066

Table S118.  Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 64 292
6P LOSS MUTATED 0 4 1 23
6P LOSS WILD-TYPE 1 8 63 269

Figure S118.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0356 (Fisher's exact test), Q value = 0.22

Table S119.  Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
6Q LOSS MUTATED 49 7
6Q LOSS WILD-TYPE 397 21

Figure S119.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0333 (Fisher's exact test), Q value = 0.21

Table S120.  Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
6Q LOSS MUTATED 37 7 16 5
6Q LOSS WILD-TYPE 345 53 130 8

Figure S120.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0034 (Fisher's exact test), Q value = 0.055

Table S121.  Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 64 292
6Q LOSS MUTATED 1 4 3 29
6Q LOSS WILD-TYPE 0 8 61 263

Figure S121.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

'7p loss' versus 'ETHNICITY'

P value = 0.0282 (Fisher's exact test), Q value = 0.19

Table S122.  Gene #54: '7p loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
7P LOSS MUTATED 1 1
7P LOSS WILD-TYPE 4 347

Figure S122.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #14: 'ETHNICITY'

'7q loss' versus 'ETHNICITY'

P value = 0.042 (Fisher's exact test), Q value = 0.24

Table S123.  Gene #55: '7q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
7Q LOSS MUTATED 1 2
7Q LOSS WILD-TYPE 4 346

Figure S123.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #14: 'ETHNICITY'

'8p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00284 (Fisher's exact test), Q value = 0.049

Table S124.  Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
8P LOSS MUTATED 141 73
8P LOSS WILD-TYPE 305 89

Figure S124.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0355 (Fisher's exact test), Q value = 0.22

Table S125.  Gene #56: '8p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
8P LOSS MUTATED 29 0 9 51 2 1 11 9 30 24 32 12 1
8P LOSS WILD-TYPE 75 1 27 122 8 2 15 9 53 30 31 14 1

Figure S125.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.011

Table S126.  Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
8P LOSS MUTATED 99 61 55
8P LOSS WILD-TYPE 246 89 60

Figure S126.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00506 (Fisher's exact test), Q value = 0.067

Table S127.  Gene #56: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
8P LOSS MUTATED 148 43
8P LOSS WILD-TYPE 302 45

Figure S127.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00225 (Fisher's exact test), Q value = 0.045

Table S128.  Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
8P LOSS MUTATED 127 12 67 5
8P LOSS WILD-TYPE 255 48 79 8

Figure S128.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.28e-05 (Wilcoxon-test), Q value = 0.004

Table S129.  Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
8P LOSS MUTATED 207 3.2 (6.2)
8P LOSS WILD-TYPE 369 1.7 (3.5)

Figure S129.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'GENDER'

P value = 0.0241 (Fisher's exact test), Q value = 0.18

Table S130.  Gene #57: '8q loss' versus Clinical Feature #8: 'GENDER'

nPatients FEMALE MALE
ALL 287 325
8Q LOSS MUTATED 10 26
8Q LOSS WILD-TYPE 277 299

Figure S130.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #8: 'GENDER'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0254 (Fisher's exact test), Q value = 0.18

Table S131.  Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
9P LOSS MUTATED 51 1 21 1
9P LOSS WILD-TYPE 331 59 125 12

Figure S131.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0359 (Fisher's exact test), Q value = 0.22

Table S132.  Gene #59: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
9Q LOSS MUTATED 52 18
9Q LOSS WILD-TYPE 398 70

Figure S132.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0249 (Fisher's exact test), Q value = 0.18

Table S133.  Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
9Q LOSS MUTATED 51 1 21 1
9Q LOSS WILD-TYPE 331 59 125 12

Figure S133.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'ETHNICITY'

P value = 0.0206 (Fisher's exact test), Q value = 0.16

Table S134.  Gene #59: '9q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
9Q LOSS MUTATED 3 46
9Q LOSS WILD-TYPE 2 302

Figure S134.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #14: 'ETHNICITY'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00496 (Wilcoxon-test), Q value = 0.066

Table S135.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
10P LOSS MUTATED 100 62.9 (13.2)
10P LOSS WILD-TYPE 510 66.9 (12.6)

Figure S135.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'RADIATION_THERAPY'

P value = 0.00835 (Fisher's exact test), Q value = 0.098

Table S136.  Gene #60: '10p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
10P LOSS MUTATED 74 11
10P LOSS WILD-TYPE 372 17

Figure S136.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0221 (Fisher's exact test), Q value = 0.17

Table S137.  Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
10P LOSS MUTATED 60 6 27 6
10P LOSS WILD-TYPE 322 54 119 7

Figure S137.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0197 (Wilcoxon-test), Q value = 0.16

Table S138.  Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
10P LOSS MUTATED 95 2.7 (4.5)
10P LOSS WILD-TYPE 481 2.1 (4.7)

Figure S138.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0203 (Wilcoxon-test), Q value = 0.16

Table S139.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
10Q LOSS MUTATED 110 63.7 (12.8)
10Q LOSS WILD-TYPE 500 66.8 (12.7)

Figure S139.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATION_THERAPY'

P value = 0.00498 (Fisher's exact test), Q value = 0.066

Table S140.  Gene #61: '10q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 446 28
10Q LOSS MUTATED 81 12
10Q LOSS WILD-TYPE 365 16

Figure S140.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0186 (Fisher's exact test), Q value = 0.16

Table S141.  Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
10Q LOSS MUTATED 66 6 31 6
10Q LOSS WILD-TYPE 316 54 115 7

Figure S141.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.011 (Fisher's exact test), Q value = 0.11

Table S142.  Gene #62: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
11P LOSS MUTATED 30 24 20
11P LOSS WILD-TYPE 315 126 95

Figure S142.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000426 (Wilcoxon-test), Q value = 0.016

Table S143.  Gene #62: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
11P LOSS MUTATED 70 3.8 (6.0)
11P LOSS WILD-TYPE 506 2.0 (4.5)

Figure S143.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0104 (Fisher's exact test), Q value = 0.11

Table S144.  Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
12P LOSS MUTATED 45 1 23 0
12P LOSS WILD-TYPE 337 59 123 13

Figure S144.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0233 (Fisher's exact test), Q value = 0.17

Table S145.  Gene #65: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
12Q LOSS MUTATED 29 23 18
12Q LOSS WILD-TYPE 316 127 97

Figure S145.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0114 (Wilcoxon-test), Q value = 0.12

Table S146.  Gene #65: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
12Q LOSS MUTATED 67 3.0 (5.0)
12Q LOSS WILD-TYPE 509 2.1 (4.7)

Figure S146.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0343 (Fisher's exact test), Q value = 0.21

Table S147.  Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
13Q LOSS MUTATED 8 3 6 2
13Q LOSS WILD-TYPE 374 57 140 11

Figure S147.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00705 (Wilcoxon-test), Q value = 0.087

Table S148.  Gene #66: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
13Q LOSS MUTATED 17 8.4 (13.3)
13Q LOSS WILD-TYPE 559 2.0 (4.1)

Figure S148.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'RACE'

P value = 0.0145 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #66: '13q loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 64 292
13Q LOSS MUTATED 1 1 1 7
13Q LOSS WILD-TYPE 0 11 63 285

Figure S149.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #13: 'RACE'

'14q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0196 (Fisher's exact test), Q value = 0.16

Table S150.  Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
14Q LOSS MUTATED 136 66
14Q LOSS WILD-TYPE 310 96

Figure S150.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0402 (Fisher's exact test), Q value = 0.24

Table S151.  Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
14Q LOSS MUTATED 105 63 36
14Q LOSS WILD-TYPE 240 87 79

Figure S151.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S152.  Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
14Q LOSS MUTATED 130 3 64 1
14Q LOSS WILD-TYPE 252 57 82 12

Figure S152.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0168 (Fisher's exact test), Q value = 0.15

Table S153.  Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
15Q LOSS MUTATED 112 66 50
15Q LOSS WILD-TYPE 233 84 65

Figure S153.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00819 (Fisher's exact test), Q value = 0.097

Table S154.  Gene #68: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
15Q LOSS MUTATED 157 44
15Q LOSS WILD-TYPE 293 44

Figure S154.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0122 (Fisher's exact test), Q value = 0.12

Table S155.  Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
15Q LOSS MUTATED 141 12 64 5
15Q LOSS WILD-TYPE 241 48 82 8

Figure S155.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0045 (Wilcoxon-test), Q value = 0.063

Table S156.  Gene #68: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
15Q LOSS MUTATED 213 2.8 (4.9)
15Q LOSS WILD-TYPE 363 1.9 (4.5)

Figure S156.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0168 (Fisher's exact test), Q value = 0.15

Table S157.  Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
17P LOSS MUTATED 232 102
17P LOSS WILD-TYPE 214 60

Figure S157.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00452 (Fisher's exact test), Q value = 0.063

Table S158.  Gene #71: '17p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
17P LOSS MUTATED 46 0 18 86 3 2 14 14 47 36 44 18 2
17P LOSS WILD-TYPE 58 1 18 87 7 1 12 4 36 18 19 8 0

Figure S158.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00194 (Fisher's exact test), Q value = 0.04

Table S159.  Gene #71: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
17P LOSS MUTATED 169 94 74
17P LOSS WILD-TYPE 176 56 41

Figure S159.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0023 (Fisher's exact test), Q value = 0.045

Table S160.  Gene #71: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
17P LOSS MUTATED 238 62
17P LOSS WILD-TYPE 212 26

Figure S160.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S161.  Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
17P LOSS MUTATED 215 14 95 6
17P LOSS WILD-TYPE 167 46 51 7

Figure S161.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000503 (Wilcoxon-test), Q value = 0.018

Table S162.  Gene #71: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
17P LOSS MUTATED 318 2.7 (5.3)
17P LOSS WILD-TYPE 258 1.7 (3.8)

Figure S162.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.11

Table S163.  Gene #72: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
17Q LOSS MUTATED 41 32 23
17Q LOSS WILD-TYPE 304 118 92

Figure S163.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000855 (Wilcoxon-test), Q value = 0.025

Table S164.  Gene #72: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
17Q LOSS MUTATED 89 3.5 (6.7)
17Q LOSS WILD-TYPE 487 2.0 (4.2)

Figure S164.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0415 (Wilcoxon-test), Q value = 0.24

Table S165.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
18P LOSS MUTATED 377 65.7 (12.0)
18P LOSS WILD-TYPE 233 67.3 (13.9)

Figure S165.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.85e-07 (Fisher's exact test), Q value = 0.00028

Table S166.  Gene #73: '18p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
18P LOSS MUTATED 248 126
18P LOSS WILD-TYPE 198 36

Figure S166.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.004

Table S167.  Gene #73: '18p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
18P LOSS MUTATED 57 0 16 99 4 3 11 13 56 36 50 23 1
18P LOSS WILD-TYPE 47 1 20 74 6 0 15 5 27 18 13 3 1

Figure S167.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00383 (Fisher's exact test), Q value = 0.059

Table S168.  Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
18P LOSS MUTATED 193 105 78
18P LOSS WILD-TYPE 152 45 37

Figure S168.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 7.06e-06 (Fisher's exact test), Q value = 0.00096

Table S169.  Gene #73: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
18P LOSS MUTATED 263 73
18P LOSS WILD-TYPE 187 15

Figure S169.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S170.  Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
18P LOSS MUTATED 234 11 119 7
18P LOSS WILD-TYPE 148 49 27 6

Figure S170.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00321 (Wilcoxon-test), Q value = 0.053

Table S171.  Gene #73: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
18P LOSS MUTATED 354 2.4 (4.9)
18P LOSS WILD-TYPE 222 1.9 (4.4)

Figure S171.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0258 (Wilcoxon-test), Q value = 0.18

Table S172.  Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 610 66.3 (12.8)
18Q LOSS MUTATED 407 65.6 (12.1)
18Q LOSS WILD-TYPE 203 67.6 (13.9)

Figure S172.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.73e-09 (Fisher's exact test), Q value = 4.3e-06

Table S173.  Gene #74: '18q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
18Q LOSS MUTATED 267 137
18Q LOSS WILD-TYPE 179 25

Figure S173.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0015

Table S174.  Gene #74: '18q loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
18Q LOSS MUTATED 58 0 20 106 4 3 14 14 60 41 53 24 1
18Q LOSS WILD-TYPE 46 1 16 67 6 0 12 4 23 13 10 2 1

Figure S174.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0042

Table S175.  Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
18Q LOSS MUTATED 204 113 88
18Q LOSS WILD-TYPE 141 37 27

Figure S175.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0015

Table S176.  Gene #74: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
18Q LOSS MUTATED 287 76
18Q LOSS WILD-TYPE 163 12

Figure S176.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S177.  Gene #74: '18q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
18Q LOSS MUTATED 250 14 126 10
18Q LOSS WILD-TYPE 132 46 20 3

Figure S177.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0393 (Fisher's exact test), Q value = 0.23

Table S178.  Gene #74: '18q loss' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 442 5 37 29
18Q LOSS MUTATED 292 3 30 14
18Q LOSS WILD-TYPE 150 2 7 15

Figure S178.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000116 (Wilcoxon-test), Q value = 0.006

Table S179.  Gene #74: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
18Q LOSS MUTATED 384 2.5 (5.0)
18Q LOSS WILD-TYPE 192 1.7 (4.1)

Figure S179.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'PATHOLOGIC_STAGE'

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

Table S180.  Gene #75: '19p loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
19P LOSS MUTATED 8 0 2 10 1 2 5 1 6 9 10 7 1
19P LOSS WILD-TYPE 96 1 34 163 9 1 21 17 77 45 53 19 1

Figure S180.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.011

Table S181.  Gene #75: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
19P LOSS MUTATED 23 16 24
19P LOSS WILD-TYPE 322 134 91

Figure S181.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00597 (Fisher's exact test), Q value = 0.078

Table S182.  Gene #75: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
19P LOSS MUTATED 38 17
19P LOSS WILD-TYPE 412 71

Figure S182.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 3.95e-06 (Wilcoxon-test), Q value = 0.00096

Table S183.  Gene #75: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
19P LOSS MUTATED 59 4.5 (5.9)
19P LOSS WILD-TYPE 517 2.0 (4.5)

Figure S183.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.11

Table S184.  Gene #76: '19q loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
19Q LOSS MUTATED 7 0 2 12 1 2 5 0 5 8 7 5 1
19Q LOSS WILD-TYPE 97 1 34 161 9 1 21 18 78 46 56 21 1

Figure S184.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00153 (Fisher's exact test), Q value = 0.034

Table S185.  Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
19Q LOSS MUTATED 24 10 21
19Q LOSS WILD-TYPE 321 140 94

Figure S185.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000635 (Wilcoxon-test), Q value = 0.02

Table S186.  Gene #76: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
19Q LOSS MUTATED 51 4.5 (6.3)
19Q LOSS WILD-TYPE 525 2.0 (4.5)

Figure S186.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00212 (Fisher's exact test), Q value = 0.043

Table S187.  Gene #79: '21q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 446 162
21Q LOSS MUTATED 124 67
21Q LOSS WILD-TYPE 322 95

Figure S187.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0186 (Fisher's exact test), Q value = 0.16

Table S188.  Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
21Q LOSS MUTATED 94 51 47
21Q LOSS WILD-TYPE 251 99 68

Figure S188.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00025 (Fisher's exact test), Q value = 0.011

Table S189.  Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
21Q LOSS MUTATED 116 8 62 3
21Q LOSS WILD-TYPE 266 52 84 10

Figure S189.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00657 (Wilcoxon-test), Q value = 0.083

Table S190.  Gene #79: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
21Q LOSS MUTATED 184 3.3 (6.7)
21Q LOSS WILD-TYPE 392 1.7 (3.3)

Figure S190.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'ETHNICITY'

P value = 0.0367 (Fisher's exact test), Q value = 0.22

Table S191.  Gene #79: '21q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 348
21Q LOSS MUTATED 4 108
21Q LOSS WILD-TYPE 1 240

Figure S191.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #14: 'ETHNICITY'

'22q loss' versus 'Time to Death'

P value = 0.0403 (logrank test), Q value = 0.24

Table S192.  Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 593 121 0.0 - 148.0 (20.0)
22Q LOSS MUTATED 194 45 0.2 - 140.4 (18.1)
22Q LOSS WILD-TYPE 399 76 0.0 - 148.0 (20.9)

Figure S192.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00294 (Fisher's exact test), Q value = 0.05

Table S193.  Gene #80: '22q loss' versus Clinical Feature #4: '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 104 1 36 173 10 3 26 18 83 54 63 26 2
22Q LOSS MUTATED 24 0 9 47 1 1 9 11 29 22 31 11 0
22Q LOSS WILD-TYPE 80 1 27 126 9 2 17 7 54 32 32 15 2

Figure S193.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0022

Table S194.  Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
22Q LOSS MUTATED 87 67 46
22Q LOSS WILD-TYPE 258 83 69

Figure S194.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00276 (Fisher's exact test), Q value = 0.049

Table S195.  Gene #80: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
22Q LOSS MUTATED 134 41
22Q LOSS WILD-TYPE 316 47

Figure S195.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0311 (Fisher's exact test), Q value = 0.2

Table S196.  Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 60 146 13
22Q LOSS MUTATED 134 10 51 4
22Q LOSS WILD-TYPE 248 50 95 9

Figure S196.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000177 (Wilcoxon-test), Q value = 0.0085

Table S197.  Gene #80: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
22Q LOSS MUTATED 189 2.9 (5.1)
22Q LOSS WILD-TYPE 387 1.9 (4.5)

Figure S197.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0314 (Fisher's exact test), Q value = 0.2

Table S198.  Gene #81: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 345 150 115
XP LOSS MUTATED 43 21 26
XP LOSS WILD-TYPE 302 129 89

Figure S198.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0194 (Wilcoxon-test), Q value = 0.16

Table S199.  Gene #81: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 576 2.2 (4.7)
XP LOSS MUTATED 85 3.2 (5.4)
XP LOSS WILD-TYPE 491 2.1 (4.6)

Figure S199.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.14

Table S200.  Gene #82: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 450 88
XQ LOSS MUTATED 52 19
XQ LOSS WILD-TYPE 398 69

Figure S200.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

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/COADREAD-TP/19781252/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/19775152/COADREAD-TP.merged_data.txt

  • Number of patients = 612

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 14

  • 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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