Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 76 focal events and 12 clinical features across 583 patients, 47 significant findings detected with Q value < 0.25.

  • AMP PEAK 5(6P21.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • AMP PEAK 6(7P21.3) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • AMP PEAK 14(13Q12.13) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 15(13Q12.2) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 16(13Q22.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 18(16P11.2) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • AMP PEAK 24(20Q11.21) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 25(20Q12) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE', and 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 26(20Q13.32) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 10(4P16.1) MUTATION ANALYSIS cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • DEL PEAK 18(8P23.3) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 19(8P23.2) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 20(8P22) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • DEL PEAK 30(14Q11.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 31(14Q31.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 32(14Q31.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 36(16P13.3) MUTATION ANALYSIS cnv correlated to 'Time to Death'.

  • DEL PEAK 38(17P12) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 40(18P11.31) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 41(18Q12.2) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 42(18Q21.2) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 43(18Q22.1) MUTATION ANALYSIS cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 44(19P13.3) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 76 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test
DEL PEAK 20(8P22) MUTATION ANALYSIS 289 (50%) 294 0.347
(1.00) 		0.326
(1.00) 		0.000394
(0.339) 		0.000142
(0.123) 		0.0734
(1.00) 		7.22e-07
(0.000648) 		0.00301
(1.00) 		0.213
(1.00) 		0.000182
(0.158) 		0.0196
(1.00) 		0.0123
(1.00) 		0.000145
(0.126)
DEL PEAK 42(18Q21 2) MUTATION ANALYSIS 409 (70%) 174 0.739
(1.00) 		0.127
(1.00) 		1.22e-09
(1.1e-06) 		5.52e-05
(0.0485) 		0.325
(1.00) 		2.32e-06
(0.00208) 		0.00129
(1.00) 		0.102
(1.00) 		1.05e-16
(9.56e-14) 		0.0638
(1.00) 		0.0495
(1.00) 		0.00247
(1.00)
DEL PEAK 43(18Q22 1) MUTATION ANALYSIS 404 (69%) 179 0.545
(1.00) 		0.306
(1.00) 		2.14e-07
(0.000193) 		0.000123
(0.107) 		0.48
(1.00) 		2.84e-05
(0.0251) 		0.00191
(1.00) 		0.151
(1.00) 		5.8e-16
(5.27e-13) 		0.0632
(1.00) 		0.0933
(1.00) 		0.00431
(1.00)
AMP PEAK 25(20Q12) MUTATION ANALYSIS 447 (77%) 136 0.415
(1.00) 		0.897
(1.00) 		5.02e-06
(0.00448) 		0.000207
(0.18) 		0.383
(1.00) 		0.00126
(1.00) 		0.00129
(1.00) 		0.241
(1.00) 		1.57e-13
(1.43e-10) 		0.693
(1.00) 		0.0517
(1.00) 		0.499
(1.00)
DEL PEAK 18(8P23 3) MUTATION ANALYSIS 276 (47%) 307 0.882
(1.00) 		0.248
(1.00) 		1.09e-05
(0.00966) 		0.0017
(1.00) 		0.0848
(1.00) 		2.98e-05
(0.0263) 		0.0171
(1.00) 		0.157
(1.00) 		1.93e-05
(0.0171) 		0.0155
(1.00) 		0.0219
(1.00) 		0.000548
(0.468)
DEL PEAK 19(8P23 2) MUTATION ANALYSIS 276 (47%) 307 0.732
(1.00) 		0.209
(1.00) 		2.55e-05
(0.0226) 		0.000515
(0.441) 		0.0773
(1.00) 		1.68e-05
(0.0149) 		0.00808
(1.00) 		0.0807
(1.00) 		2.14e-05
(0.019) 		0.0155
(1.00) 		0.00866
(1.00) 		0.000547
(0.468)
DEL PEAK 41(18Q12 2) MUTATION ANALYSIS 392 (67%) 191 0.836
(1.00) 		0.123
(1.00) 		1.82e-09
(1.64e-06) 		0.000596
(0.508) 		0.365
(1.00) 		0.000131
(0.114) 		0.00369
(1.00) 		0.332
(1.00) 		2.48e-18
(2.26e-15) 		0.0343
(1.00) 		0.0488
(1.00) 		0.0168
(1.00)
AMP PEAK 14(13Q12 13) MUTATION ANALYSIS 377 (65%) 206 0.204
(1.00) 		0.246
(1.00) 		0.00254
(1.00) 		0.000334
(0.289) 		0.78
(1.00) 		3.71e-05
(0.0326) 		0.00923
(1.00) 		0.544
(1.00) 		5.03e-10
(4.55e-07) 		1
(1.00) 		0.0498
(1.00) 		0.0474
(1.00)
AMP PEAK 15(13Q12 2) MUTATION ANALYSIS 372 (64%) 211 0.166
(1.00) 		0.185
(1.00) 		0.00197
(1.00) 		0.000879
(0.744) 		0.778
(1.00) 		7.73e-05
(0.0677) 		0.0214
(1.00) 		0.388
(1.00) 		1.16e-09
(1.05e-06) 		1
(1.00) 		0.0901
(1.00) 		0.0489
(1.00)
AMP PEAK 16(13Q22 1) MUTATION ANALYSIS 377 (65%) 206 0.143
(1.00) 		0.358
(1.00) 		0.0255
(1.00) 		0.00714
(1.00) 		0.899
(1.00) 		0.000115
(0.0999) 		0.0226
(1.00) 		0.141
(1.00) 		1.43e-08
(1.29e-05) 		0.504
(1.00) 		0.27
(1.00) 		0.228
(1.00)
AMP PEAK 24(20Q11 21) MUTATION ANALYSIS 445 (76%) 138 0.448
(1.00) 		0.994
(1.00) 		9.63e-06
(0.00857) 		0.000764
(0.647) 		0.29
(1.00) 		0.0017
(1.00) 		0.00538
(1.00) 		0.242
(1.00) 		2.57e-12
(2.33e-09) 		0.693
(1.00) 		0.0508
(1.00) 		0.445
(1.00)
AMP PEAK 26(20Q13 32) MUTATION ANALYSIS 450 (77%) 133 0.521
(1.00) 		0.828
(1.00) 		2.27e-05
(0.0201) 		0.000763
(0.647) 		0.359
(1.00) 		0.00203
(1.00) 		0.00422
(1.00) 		0.429
(1.00) 		2.71e-12
(2.46e-09) 		0.692
(1.00) 		0.0516
(1.00) 		0.332
(1.00)
DEL PEAK 38(17P12) MUTATION ANALYSIS 345 (59%) 238 0.641
(1.00) 		0.151
(1.00) 		0.00125
(1.00) 		0.00188
(1.00) 		0.478
(1.00) 		0.000112
(0.0974) 		0.0242
(1.00) 		0.447
(1.00) 		3.44e-08
(3.1e-05) 		0.322
(1.00) 		0.158
(1.00) 		0.00347
(1.00)
DEL PEAK 40(18P11 31) MUTATION ANALYSIS 347 (60%) 236 0.995
(1.00) 		0.0844
(1.00) 		2.95e-06
(0.00264) 		0.00169
(1.00) 		0.939
(1.00) 		0.0148
(1.00) 		0.000485
(0.417) 		0.8
(1.00) 		5.23e-17
(4.76e-14) 		0.324
(1.00) 		0.0192
(1.00) 		0.573
(1.00)
AMP PEAK 5(6P21 1) MUTATION ANALYSIS 148 (25%) 435 0.954
(1.00) 		0.617
(1.00) 		0.0318
(1.00) 		0.0269
(1.00) 		0.219
(1.00) 		9.3e-05
(0.0813) 		0.144
(1.00) 		0.154
(1.00) 		0.00195
(1.00) 		0.00136
(1.00) 		0.144
(1.00) 		0.00311
(1.00)
AMP PEAK 6(7P21 3) MUTATION ANALYSIS 343 (59%) 240 0.765
(1.00) 		0.0867
(1.00) 		0.0372
(1.00) 		0.000359
(0.31) 		0.937
(1.00) 		8.75e-06
(0.0078) 		0.0284
(1.00) 		0.8
(1.00) 		0.000743
(0.631) 		0.0889
(1.00) 		0.266
(1.00) 		0.0307
(1.00)
AMP PEAK 18(16P11 2) MUTATION ANALYSIS 162 (28%) 421 0.903
(1.00) 		0.339
(1.00) 		0.917
(1.00) 		0.00197
(1.00) 		0.788
(1.00) 		6.89e-05
(0.0604) 		0.161
(1.00) 		0.643
(1.00) 		0.0022
(1.00) 		0.714
(1.00) 		0.246
(1.00) 		0.0204
(1.00)
DEL PEAK 10(4P16 1) MUTATION ANALYSIS 185 (32%) 398 0.12
(1.00) 		0.971
(1.00) 		0.0572
(1.00) 		0.00306
(1.00) 		0.99
(1.00) 		0.000424
(0.365) 		0.00812
(1.00) 		0.0904
(1.00) 		0.023
(1.00) 		2.85e-05
(0.0251) 		0.0679
(1.00) 		0.0019
(1.00)
DEL PEAK 30(14Q11 2) MUTATION ANALYSIS 193 (33%) 390 0.15
(1.00) 		0.518
(1.00) 		0.0131
(1.00) 		0.765
(1.00) 		0.494
(1.00) 		0.0215
(1.00) 		0.262
(1.00) 		1
(1.00) 		6.9e-06
(0.00615) 		0.488
(1.00) 		0.915
(1.00) 		0.681
(1.00)
DEL PEAK 31(14Q31 1) MUTATION ANALYSIS 198 (34%) 385 0.48
(1.00) 		0.28
(1.00) 		0.0183
(1.00) 		0.309
(1.00) 		0.374
(1.00) 		0.023
(1.00) 		0.0253
(1.00) 		0.255
(1.00) 		2.27e-06
(0.00204) 		0.725
(1.00) 		0.686
(1.00) 		0.352
(1.00)
DEL PEAK 32(14Q31 1) MUTATION ANALYSIS 202 (35%) 381 0.279
(1.00) 		0.402
(1.00) 		0.0142
(1.00) 		0.284
(1.00) 		0.287
(1.00) 		0.0332
(1.00) 		0.0425
(1.00) 		0.339
(1.00) 		3.95e-06
(0.00353) 		0.726
(1.00) 		0.704
(1.00) 		0.341
(1.00)
DEL PEAK 36(16P13 3) MUTATION ANALYSIS 59 (10%) 524 7.04e-05
(0.0617) 		0.22
(1.00) 		0.36
(1.00) 		0.0485
(1.00) 		0.0552
(1.00) 		0.187
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.414
(1.00) 		0.609
(1.00) 		0.761
(1.00) 		0.0675
(1.00)
DEL PEAK 44(19P13 3) MUTATION ANALYSIS 93 (16%) 490 0.769
(1.00) 		0.179
(1.00) 		0.0304
(1.00) 		0.00143
(1.00) 		0.386
(1.00) 		5.85e-05
(0.0514) 		0.0143
(1.00) 		0.652
(1.00) 		0.0608
(1.00) 		0.641
(1.00) 		0.163
(1.00) 		0.00283
(1.00)
AMP PEAK 1(1Q31 1) MUTATION ANALYSIS 136 (23%) 447 0.615
(1.00) 		0.312
(1.00) 		0.0274
(1.00) 		0.428
(1.00) 		0.405
(1.00) 		0.0863
(1.00) 		0.203
(1.00) 		0.202
(1.00) 		0.0863
(1.00) 		0.0359
(1.00) 		0.68
(1.00) 		0.0169
(1.00)
AMP PEAK 2(2Q33 1) MUTATION ANALYSIS 125 (21%) 458 0.0656
(1.00) 		0.353
(1.00) 		0.0318
(1.00) 		0.0189
(1.00) 		0.718
(1.00) 		0.00277
(1.00) 		0.344
(1.00) 		0.84
(1.00) 		0.0051
(1.00) 		0.104
(1.00) 		0.495
(1.00) 		0.0319
(1.00)
AMP PEAK 3(5P12) MUTATION ANALYSIS 108 (19%) 475 0.0895
(1.00) 		0.35
(1.00) 		0.151
(1.00) 		0.272
(1.00) 		0.323
(1.00) 		0.0797
(1.00) 		0.352
(1.00) 		0.749
(1.00) 		0.0513
(1.00) 		0.378
(1.00) 		0.0289
(1.00) 		0.081
(1.00)
AMP PEAK 4(5Q22 3) MUTATION ANALYSIS 60 (10%) 523 0.354
(1.00) 		0.957
(1.00) 		0.447
(1.00) 		0.62
(1.00) 		0.915
(1.00) 		0.272
(1.00) 		0.0413
(1.00) 		1
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.0698
(1.00) 		0.546
(1.00)
AMP PEAK 7(8P11 23) MUTATION ANALYSIS 199 (34%) 384 0.279
(1.00) 		0.89
(1.00) 		0.625
(1.00) 		0.21
(1.00) 		0.41
(1.00) 		0.616
(1.00) 		0.355
(1.00) 		0.484
(1.00) 		0.207
(1.00) 		0.499
(1.00) 		0.155
(1.00) 		0.758
(1.00)
AMP PEAK 8(8P11 21) MUTATION ANALYSIS 241 (41%) 342 0.741
(1.00) 		0.743
(1.00) 		0.637
(1.00) 		0.126
(1.00) 		0.507
(1.00) 		0.359
(1.00) 		0.316
(1.00) 		0.207
(1.00) 		0.103
(1.00) 		0.742
(1.00) 		0.0443
(1.00) 		0.535
(1.00)
AMP PEAK 9(8Q12 1) MUTATION ANALYSIS 312 (54%) 271 0.791
(1.00) 		0.289
(1.00) 		0.263
(1.00) 		0.119
(1.00) 		0.166
(1.00) 		0.165
(1.00) 		0.0299
(1.00) 		0.617
(1.00) 		0.00726
(1.00) 		0.0418
(1.00) 		0.1
(1.00) 		0.0465
(1.00)
AMP PEAK 10(8Q24 21) MUTATION ANALYSIS 349 (60%) 234 0.494
(1.00) 		0.331
(1.00) 		0.0868
(1.00) 		0.188
(1.00) 		0.147
(1.00) 		0.235
(1.00) 		0.0726
(1.00) 		0.352
(1.00) 		0.00814
(1.00) 		0.0926
(1.00) 		0.223
(1.00) 		0.102
(1.00)
AMP PEAK 11(10Q22 3) MUTATION ANALYSIS 36 (6%) 547 0.871
(1.00) 		0.385
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.278
(1.00) 		0.0162
(1.00) 		0.904
(1.00) 		0.608
(1.00) 		0.925
(1.00) 		0.439
(1.00) 		0.923
(1.00) 		0.0971
(1.00)
AMP PEAK 12(11P15 5) MUTATION ANALYSIS 130 (22%) 453 0.715
(1.00) 		0.0668
(1.00) 		0.144
(1.00) 		0.98
(1.00) 		0.273
(1.00) 		0.656
(1.00) 		0.338
(1.00) 		0.618
(1.00) 		0.00118
(0.994) 		0.117
(1.00) 		0.891
(1.00) 		0.463
(1.00)
AMP PEAK 13(12P13 32) MUTATION ANALYSIS 144 (25%) 439 0.274
(1.00) 		0.0449
(1.00) 		0.914
(1.00) 		0.165
(1.00) 		0.331
(1.00) 		0.11
(1.00) 		0.124
(1.00) 		0.631
(1.00) 		0.457
(1.00) 		0.696
(1.00) 		0.778
(1.00) 		0.45
(1.00)
AMP PEAK 17(15Q26 1) MUTATION ANALYSIS 43 (7%) 540 0.265
(1.00) 		0.56
(1.00) 		0.287
(1.00) 		0.159
(1.00) 		0.118
(1.00) 		0.00221
(1.00) 		0.615
(1.00) 		0.114
(1.00) 		0.395
(1.00) 		0.137
(1.00) 		0.571
(1.00) 		0.0494
(1.00)
AMP PEAK 19(17Q12) MUTATION ANALYSIS 145 (25%) 438 0.565
(1.00) 		0.358
(1.00) 		0.52
(1.00) 		0.203
(1.00) 		0.503
(1.00) 		0.194
(1.00) 		0.0106
(1.00) 		0.0842
(1.00) 		0.429
(1.00) 		0.463
(1.00) 		0.0615
(1.00) 		0.395
(1.00)
AMP PEAK 20(17Q24 1) MUTATION ANALYSIS 129 (22%) 454 0.0801
(1.00) 		0.237
(1.00) 		0.911
(1.00) 		0.586
(1.00) 		0.797
(1.00) 		0.889
(1.00) 		0.0479
(1.00) 		0.689
(1.00) 		0.0834
(1.00) 		0.692
(1.00) 		0.187
(1.00) 		0.651
(1.00)
AMP PEAK 21(19P13 2) MUTATION ANALYSIS 99 (17%) 484 0.343
(1.00) 		0.596
(1.00) 		0.266
(1.00) 		0.614
(1.00) 		0.508
(1.00) 		0.0391
(1.00) 		0.197
(1.00) 		0.15
(1.00) 		0.0474
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.938
(1.00)
AMP PEAK 22(19Q12) MUTATION ANALYSIS 123 (21%) 460 0.568
(1.00) 		0.889
(1.00) 		0.255
(1.00) 		0.835
(1.00) 		0.676
(1.00) 		0.101
(1.00) 		0.12
(1.00) 		0.186
(1.00) 		0.0255
(1.00) 		0.692
(1.00) 		0.46
(1.00) 		0.415
(1.00)
AMP PEAK 23(20P11 23) MUTATION ANALYSIS 303 (52%) 280 0.97
(1.00) 		0.788
(1.00) 		0.0153
(1.00) 		0.00356
(1.00) 		0.976
(1.00) 		0.0965
(1.00) 		0.0011
(0.927) 		0.046
(1.00) 		0.000493
(0.423) 		0.179
(1.00) 		0.288
(1.00) 		0.475
(1.00)
AMP PEAK 27(XQ28) MUTATION ANALYSIS 124 (21%) 459 0.343
(1.00) 		0.233
(1.00) 		0.426
(1.00) 		0.101
(1.00) 		0.46
(1.00) 		0.0345
(1.00) 		0.261
(1.00) 		0.685
(1.00) 		0.0196
(1.00) 		0.692
(1.00) 		0.281
(1.00) 		0.333
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 223 (38%) 360 0.0605
(1.00) 		0.167
(1.00) 		0.104
(1.00) 		0.0336
(1.00) 		0.259
(1.00) 		0.00194
(1.00) 		0.000706
(0.6) 		0.393
(1.00) 		0.00507
(1.00) 		0.738
(1.00) 		0.108
(1.00) 		0.000655
(0.558)
DEL PEAK 2(1P33) MUTATION ANALYSIS 156 (27%) 427 0.0364
(1.00) 		0.936
(1.00) 		0.343
(1.00) 		0.0302
(1.00) 		0.23
(1.00) 		0.0106
(1.00) 		0.00981
(1.00) 		1
(1.00) 		0.0725
(1.00) 		0.707
(1.00) 		0.311
(1.00) 		0.0163
(1.00)
DEL PEAK 3(1P13 2) MUTATION ANALYSIS 158 (27%) 425 0.193
(1.00) 		0.675
(1.00) 		0.209
(1.00) 		0.00418
(1.00) 		0.136
(1.00) 		0.00208
(1.00) 		0.0015
(1.00) 		0.709
(1.00) 		0.118
(1.00) 		0.262
(1.00) 		0.274
(1.00) 		0.003
(1.00)
DEL PEAK 4(2P12) MUTATION ANALYSIS 20 (3%) 563 0.712
(1.00) 		0.167
(1.00) 		0.00334
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.542
(1.00) 		0.821
(1.00) 		0.0181
(1.00) 		0.271
(1.00) 		0.884
(1.00) 		0.319
(1.00)
DEL PEAK 5(2Q22 1) MUTATION ANALYSIS 34 (6%) 549 0.897
(1.00) 		0.644
(1.00) 		0.843
(1.00) 		0.538
(1.00) 		0.628
(1.00) 		0.715
(1.00) 		0.639
(1.00) 		0.597
(1.00) 		0.982
(1.00) 		1
(1.00) 		1
(1.00) 		0.88
(1.00)
DEL PEAK 6(2Q37 2) MUTATION ANALYSIS 30 (5%) 553 0.742
(1.00) 		0.128
(1.00) 		0.834
(1.00) 		0.183
(1.00) 		0.337
(1.00) 		0.175
(1.00) 		0.125
(1.00) 		0.457
(1.00) 		0.936
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.857
(1.00)
DEL PEAK 7(3P26 3) MUTATION ANALYSIS 85 (15%) 498 0.0116
(1.00) 		0.859
(1.00) 		0.692
(1.00) 		0.0105
(1.00) 		0.0316
(1.00) 		0.0234
(1.00) 		0.00121
(1.00) 		0.638
(1.00) 		0.182
(1.00) 		0.13
(1.00) 		0.0466
(1.00) 		0.032
(1.00)
DEL PEAK 8(3P14 2) MUTATION ANALYSIS 106 (18%) 477 0.367
(1.00) 		0.538
(1.00) 		0.808
(1.00) 		0.148
(1.00) 		0.13
(1.00) 		0.183
(1.00) 		0.0372
(1.00) 		0.52
(1.00) 		0.375
(1.00) 		0.67
(1.00) 		0.205
(1.00) 		0.0271
(1.00)
DEL PEAK 9(3Q26 31) MUTATION ANALYSIS 58 (10%) 525 0.608
(1.00) 		0.971
(1.00) 		0.877
(1.00) 		0.00357
(1.00) 		0.00984
(1.00) 		0.48
(1.00) 		0.477
(1.00) 		0.127
(1.00) 		0.0359
(1.00) 		0.223
(1.00) 		0.258
(1.00) 		0.534
(1.00)
DEL PEAK 11(4Q22 1) MUTATION ANALYSIS 202 (35%) 381 0.49
(1.00) 		0.393
(1.00) 		0.0045
(1.00) 		0.0315
(1.00) 		0.0959
(1.00) 		0.00138
(1.00) 		0.343
(1.00) 		0.139
(1.00) 		0.00118
(0.991) 		0.00119
(1.00) 		0.792
(1.00) 		0.00351
(1.00)
DEL PEAK 12(4Q35 1) MUTATION ANALYSIS 213 (37%) 370 0.543
(1.00) 		0.317
(1.00) 		0.0422
(1.00) 		0.221
(1.00) 		0.502
(1.00) 		0.00406
(1.00) 		0.359
(1.00) 		0.863
(1.00) 		0.0253
(1.00) 		0.00179
(1.00) 		0.724
(1.00) 		0.0302
(1.00)
DEL PEAK 13(5Q11 2) MUTATION ANALYSIS 141 (24%) 442 0.177
(1.00) 		0.134
(1.00) 		0.03
(1.00) 		0.0216
(1.00) 		1
(1.00) 		0.00735
(1.00) 		0.0209
(1.00) 		1
(1.00) 		0.0106
(1.00) 		0.000986
(0.833) 		0.69
(1.00) 		0.0278
(1.00)
DEL PEAK 14(5Q22 2) MUTATION ANALYSIS 173 (30%) 410 0.145
(1.00) 		0.492
(1.00) 		0.129
(1.00) 		0.0585
(1.00) 		0.769
(1.00) 		0.018
(1.00) 		0.0289
(1.00) 		0.586
(1.00) 		0.0525
(1.00) 		0.000359
(0.31) 		0.197
(1.00) 		0.17
(1.00)
DEL PEAK 15(6P25 3) MUTATION ANALYSIS 78 (13%) 505 0.332
(1.00) 		0.0584
(1.00) 		0.891
(1.00) 		0.615
(1.00) 		0.249
(1.00) 		0.455
(1.00) 		0.349
(1.00) 		0.0885
(1.00) 		0.534
(1.00) 		0.344
(1.00) 		0.408
(1.00) 		0.753
(1.00)
DEL PEAK 16(6Q26) MUTATION ANALYSIS 90 (15%) 493 0.0636
(1.00) 		0.962
(1.00) 		0.364
(1.00) 		0.0713
(1.00) 		0.0532
(1.00) 		0.00891
(1.00) 		0.0447
(1.00) 		0.302
(1.00) 		0.0438
(1.00) 		0.635
(1.00) 		0.11
(1.00) 		0.00993
(1.00)
DEL PEAK 17(7Q31 1) MUTATION ANALYSIS 15 (3%) 568 0.726
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.841
(1.00) 		0.523
(1.00) 		0.633
(1.00) 		0.321
(1.00) 		0.306
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.611
(1.00)
DEL PEAK 21(8Q11 1) MUTATION ANALYSIS 45 (8%) 538 0.8
(1.00) 		0.426
(1.00) 		0.217
(1.00) 		0.0334
(1.00) 		0.721
(1.00) 		0.0249
(1.00) 		0.00211
(1.00) 		0.161
(1.00) 		0.439
(1.00) 		0.517
(1.00) 		0.347
(1.00) 		0.273
(1.00)
DEL PEAK 22(9P24 2) MUTATION ANALYSIS 79 (14%) 504 0.0194
(1.00) 		0.114
(1.00) 		0.497
(1.00) 		0.359
(1.00) 		0.537
(1.00) 		0.103
(1.00) 		0.012
(1.00) 		0.0396
(1.00) 		0.426
(1.00) 		0.35
(1.00) 		0.108
(1.00) 		0.232
(1.00)
DEL PEAK 23(10P15 3) MUTATION ANALYSIS 103 (18%) 480 0.4
(1.00) 		0.0297
(1.00) 		0.224
(1.00) 		0.0766
(1.00) 		0.761
(1.00) 		0.00874
(1.00) 		0.194
(1.00) 		1
(1.00) 		0.346
(1.00) 		0.00142
(1.00) 		0.944
(1.00) 		0.05
(1.00)
DEL PEAK 24(10Q21 1) MUTATION ANALYSIS 120 (21%) 463 0.824
(1.00) 		0.0167
(1.00) 		0.489
(1.00) 		0.14
(1.00) 		0.709
(1.00) 		0.0927
(1.00) 		0.54
(1.00) 		0.681
(1.00) 		0.105
(1.00) 		0.00331
(1.00) 		0.358
(1.00) 		0.159
(1.00)
DEL PEAK 25(10Q23 31) MUTATION ANALYSIS 147 (25%) 436 0.476
(1.00) 		0.0115
(1.00) 		0.0414
(1.00) 		0.0359
(1.00) 		0.245
(1.00) 		0.0108
(1.00) 		0.0362
(1.00) 		0.924
(1.00) 		0.0183
(1.00) 		0.0013
(1.00) 		0.589
(1.00) 		0.208
(1.00)
DEL PEAK 26(10Q25 2) MUTATION ANALYSIS 142 (24%) 441 0.976
(1.00) 		0.0802
(1.00) 		0.129
(1.00) 		0.119
(1.00) 		0.171
(1.00) 		0.00735
(1.00) 		0.293
(1.00) 		1
(1.00) 		0.0288
(1.00) 		0.00103
(0.872) 		0.535
(1.00) 		0.158
(1.00)
DEL PEAK 27(11Q22 3) MUTATION ANALYSIS 105 (18%) 478 0.288
(1.00) 		0.454
(1.00) 		0.0857
(1.00) 		0.772
(1.00) 		0.388
(1.00) 		0.0778
(1.00) 		0.641
(1.00) 		0.517
(1.00) 		0.0498
(1.00) 		0.0602
(1.00) 		0.624
(1.00) 		0.0527
(1.00)
DEL PEAK 28(12P13 1) MUTATION ANALYSIS 79 (14%) 504 0.074
(1.00) 		0.412
(1.00) 		0.0279
(1.00) 		0.577
(1.00) 		0.418
(1.00) 		0.0176
(1.00) 		0.0672
(1.00) 		0.467
(1.00) 		0.000559
(0.477) 		0.35
(1.00) 		0.751
(1.00) 		0.88
(1.00)
DEL PEAK 29(12Q21 31) MUTATION ANALYSIS 78 (13%) 505 0.439
(1.00) 		0.538
(1.00) 		0.217
(1.00) 		0.155
(1.00) 		0.623
(1.00) 		0.056
(1.00) 		0.0934
(1.00) 		1
(1.00) 		0.018
(1.00) 		0.344
(1.00) 		0.733
(1.00) 		0.134
(1.00)
DEL PEAK 33(15Q11 2) MUTATION ANALYSIS 235 (40%) 348 0.722
(1.00) 		0.748
(1.00) 		0.184
(1.00) 		0.0923
(1.00) 		0.696
(1.00) 		0.00741
(1.00) 		0.207
(1.00) 		0.446
(1.00) 		0.0442
(1.00) 		0.0345
(1.00) 		0.749
(1.00) 		0.0561
(1.00)
DEL PEAK 34(15Q21 1) MUTATION ANALYSIS 228 (39%) 355 0.491
(1.00) 		0.78
(1.00) 		0.028
(1.00) 		0.18
(1.00) 		0.794
(1.00) 		0.0159
(1.00) 		0.181
(1.00) 		0.27
(1.00) 		0.0101
(1.00) 		0.0321
(1.00) 		0.453
(1.00) 		0.0529
(1.00)
DEL PEAK 35(15Q22 33) MUTATION ANALYSIS 218 (37%) 365 0.621
(1.00) 		0.457
(1.00) 		0.00915
(1.00) 		0.0116
(1.00) 		0.0653
(1.00) 		0.00293
(1.00) 		0.149
(1.00) 		0.668
(1.00) 		0.00417
(1.00) 		0.00214
(1.00) 		0.598
(1.00) 		0.0269
(1.00)
DEL PEAK 37(16Q23 1) MUTATION ANALYSIS 73 (13%) 510 0.0344
(1.00) 		0.23
(1.00) 		0.403
(1.00) 		0.261
(1.00) 		0.18
(1.00) 		0.647
(1.00) 		0.952
(1.00) 		0.133
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.971
(1.00) 		0.279
(1.00)
DEL PEAK 39(17Q24 3) MUTATION ANALYSIS 85 (15%) 498 0.652
(1.00) 		0.359
(1.00) 		0.793
(1.00) 		0.119
(1.00) 		0.253
(1.00) 		0.0043
(1.00) 		0.385
(1.00) 		0.0992
(1.00) 		0.995
(1.00) 		0.626
(1.00) 		0.372
(1.00) 		0.0417
(1.00)
DEL PEAK 45(19Q13 43) MUTATION ANALYSIS 68 (12%) 515 0.414
(1.00) 		0.863
(1.00) 		0.11
(1.00) 		0.00606
(1.00) 		0.438
(1.00) 		0.015
(1.00) 		0.0683
(1.00) 		0.248
(1.00) 		0.369
(1.00) 		0.283
(1.00) 		0.834
(1.00) 		0.0201
(1.00)
DEL PEAK 46(20P12 1) MUTATION ANALYSIS 180 (31%) 403 0.0508
(1.00) 		0.481
(1.00) 		0.0352
(1.00) 		0.238
(1.00) 		0.462
(1.00) 		0.219
(1.00) 		0.756
(1.00) 		0.324
(1.00) 		0.115
(1.00) 		0.0632
(1.00) 		0.321
(1.00) 		0.827
(1.00)
DEL PEAK 47(20P12 1) MUTATION ANALYSIS 180 (31%) 403 0.0508
(1.00) 		0.481
(1.00) 		0.0352
(1.00) 		0.238
(1.00) 		0.462
(1.00) 		0.219
(1.00) 		0.756
(1.00) 		0.324
(1.00) 		0.115
(1.00) 		0.0632
(1.00) 		0.321
(1.00) 		0.827
(1.00)
DEL PEAK 48(21Q11 2) MUTATION ANALYSIS 198 (34%) 385 0.771
(1.00) 		0.732
(1.00) 		0.00571
(1.00) 		0.308
(1.00) 		0.956
(1.00) 		0.052
(1.00) 		0.557
(1.00) 		0.54
(1.00) 		0.000491
(0.422) 		0.176
(1.00) 		0.792
(1.00) 		0.00549
(1.00)
DEL PEAK 49(22Q13 32) MUTATION ANALYSIS 209 (36%) 374 0.0795
(1.00) 		0.697
(1.00) 		0.243
(1.00) 		0.0209
(1.00) 		0.401
(1.00) 		0.000511
(0.438) 		0.022
(1.00) 		0.665
(1.00) 		0.00688
(1.00) 		0.728
(1.00) 		0.534
(1.00) 		0.0129
(1.00)
'AMP PEAK 5(6P21.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 9.3e-05 (Fisher's exact test), Q value = 0.081

Table S1.  Gene #5: 'AMP PEAK 5(6P21.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 5(6P21.1) MUTATED 64 40 43
AMP PEAK 5(6P21.1) WILD-TYPE 265 105 63

Figure S1.  Get High-res Image Gene #5: 'AMP PEAK 5(6P21.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 6(7P21.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 8.75e-06 (Fisher's exact test), Q value = 0.0078

Table S2.  Gene #6: 'AMP PEAK 6(7P21.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 6(7P21.3) MUTATED 165 104 71
AMP PEAK 6(7P21.3) WILD-TYPE 164 41 35

Figure S2.  Get High-res Image Gene #6: 'AMP PEAK 6(7P21.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 3.71e-05 (Fisher's exact test), Q value = 0.033

Table S3.  Gene #14: 'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 14(13Q12.13) MUTATED 187 109 79
AMP PEAK 14(13Q12.13) WILD-TYPE 142 36 27

Figure S3.  Get High-res Image Gene #14: 'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.03e-10 (Fisher's exact test), Q value = 4.6e-07

Table S4.  Gene #14: 'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 14(13Q12.13) MUTATED 239 16 112 5
AMP PEAK 14(13Q12.13) WILD-TYPE 125 39 31 8

Figure S4.  Get High-res Image Gene #14: 'AMP PEAK 14(13Q12.13) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 7.73e-05 (Fisher's exact test), Q value = 0.068

Table S5.  Gene #15: 'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 15(13Q12.2) MUTATED 185 107 78
AMP PEAK 15(13Q12.2) WILD-TYPE 144 38 28

Figure S5.  Get High-res Image Gene #15: 'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.16e-09 (Fisher's exact test), Q value = 1e-06

Table S6.  Gene #15: 'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 15(13Q12.2) MUTATED 235 16 111 5
AMP PEAK 15(13Q12.2) WILD-TYPE 129 39 32 8

Figure S6.  Get High-res Image Gene #15: 'AMP PEAK 15(13Q12.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000115 (Fisher's exact test), Q value = 0.1

Table S7.  Gene #16: 'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 16(13Q22.1) MUTATED 188 109 77
AMP PEAK 16(13Q22.1) WILD-TYPE 141 36 29

Figure S7.  Get High-res Image Gene #16: 'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.43e-08 (Fisher's exact test), Q value = 1.3e-05

Table S8.  Gene #16: 'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 16(13Q22.1) MUTATED 241 18 109 4
AMP PEAK 16(13Q22.1) WILD-TYPE 123 37 34 9

Figure S8.  Get High-res Image Gene #16: 'AMP PEAK 16(13Q22.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'AMP PEAK 18(16P11.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.06

Table S9.  Gene #18: 'AMP PEAK 18(16P11.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
AMP PEAK 18(16P11.2) MUTATED 68 53 40
AMP PEAK 18(16P11.2) WILD-TYPE 261 92 66

Figure S9.  Get High-res Image Gene #18: 'AMP PEAK 18(16P11.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.63e-06 (Fisher's exact test), Q value = 0.0086

Table S10.  Gene #24: 'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
AMP PEAK 24(20Q11.21) MUTATED 301 141
AMP PEAK 24(20Q11.21) WILD-TYPE 119 18

Figure S10.  Get High-res Image Gene #24: 'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.57e-12 (Fisher's exact test), Q value = 2.3e-09

Table S11.  Gene #24: 'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 24(20Q11.21) MUTATED 276 24 132 7
AMP PEAK 24(20Q11.21) WILD-TYPE 88 31 11 6

Figure S11.  Get High-res Image Gene #24: 'AMP PEAK 24(20Q11.21) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'AMP PEAK 25(20Q12) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.02e-06 (Fisher's exact test), Q value = 0.0045

Table S12.  Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
AMP PEAK 25(20Q12) MUTATED 302 142
AMP PEAK 25(20Q12) WILD-TYPE 118 17

Figure S12.  Get High-res Image Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'AMP PEAK 25(20Q12) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000207 (Chi-square test), Q value = 0.18

Table S13.  Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
AMP PEAK 25(20Q12) MUTATED 76 1 24 109 5 3 19 21 59 41 53 24 0
AMP PEAK 25(20Q12) WILD-TYPE 24 0 17 47 5 0 8 1 16 8 6 1 1

Figure S13.  Get High-res Image Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'AMP PEAK 25(20Q12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.57e-13 (Fisher's exact test), Q value = 1.4e-10

Table S14.  Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 25(20Q12) MUTATED 278 23 133 7
AMP PEAK 25(20Q12) WILD-TYPE 86 32 10 6

Figure S14.  Get High-res Image Gene #25: 'AMP PEAK 25(20Q12) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.02

Table S15.  Gene #26: 'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
AMP PEAK 26(20Q13.32) MUTATED 305 141
AMP PEAK 26(20Q13.32) WILD-TYPE 115 18

Figure S15.  Get High-res Image Gene #26: 'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.71e-12 (Fisher's exact test), Q value = 2.5e-09

Table S16.  Gene #26: 'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
AMP PEAK 26(20Q13.32) MUTATED 280 24 132 7
AMP PEAK 26(20Q13.32) WILD-TYPE 84 31 11 6

Figure S16.  Get High-res Image Gene #26: 'AMP PEAK 26(20Q13.32) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 10(4P16.1) MUTATION STATUS' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.85e-05 (Fisher's exact test), Q value = 0.025

Table S17.  Gene #37: 'DEL PEAK 10(4P16.1) MUTATION STATUS' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 574
DEL PEAK 10(4P16.1) MUTATED 9 176
DEL PEAK 10(4P16.1) WILD-TYPE 0 398

Figure S17.  Get High-res Image Gene #37: 'DEL PEAK 10(4P16.1) MUTATION STATUS' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'DEL PEAK 18(8P23.3) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0097

Table S18.  Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 18(8P23.3) MUTATED 175 99
DEL PEAK 18(8P23.3) WILD-TYPE 245 60

Figure S18.  Get High-res Image Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 18(8P23.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.026

Table S19.  Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 18(8P23.3) MUTATED 130 77 67
DEL PEAK 18(8P23.3) WILD-TYPE 199 68 39

Figure S19.  Get High-res Image Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 18(8P23.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.017

Table S20.  Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 18(8P23.3) MUTATED 158 16 90 7
DEL PEAK 18(8P23.3) WILD-TYPE 206 39 53 6

Figure S20.  Get High-res Image Gene #45: 'DEL PEAK 18(8P23.3) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 19(8P23.2) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.023

Table S21.  Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 19(8P23.2) MUTATED 176 98
DEL PEAK 19(8P23.2) WILD-TYPE 244 61

Figure S21.  Get High-res Image Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 19(8P23.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 1.68e-05 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 19(8P23.2) MUTATED 129 78 67
DEL PEAK 19(8P23.2) WILD-TYPE 200 67 39

Figure S22.  Get High-res Image Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 19(8P23.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.019

Table S23.  Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 19(8P23.2) MUTATED 160 15 89 7
DEL PEAK 19(8P23.2) WILD-TYPE 204 40 54 6

Figure S23.  Get High-res Image Gene #46: 'DEL PEAK 19(8P23.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 20(8P22) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000142 (Chi-square test), Q value = 0.12

Table S24.  Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
DEL PEAK 20(8P22) MUTATED 39 0 13 65 3 2 15 13 42 33 42 15 1
DEL PEAK 20(8P22) WILD-TYPE 61 1 28 91 7 1 12 9 33 16 17 10 0

Figure S24.  Get High-res Image Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 20(8P22) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 7.22e-07 (Fisher's exact test), Q value = 0.00065

Table S25.  Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 20(8P22) MUTATED 133 82 72
DEL PEAK 20(8P22) WILD-TYPE 196 63 34

Figure S25.  Get High-res Image Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 20(8P22) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000182 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 20(8P22) MUTATED 172 16 89 7
DEL PEAK 20(8P22) WILD-TYPE 192 39 54 6

Figure S26.  Get High-res Image Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 20(8P22) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000145 (t-test), Q value = 0.13

Table S27.  Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 549 2.2 (4.7)
DEL PEAK 20(8P22) MUTATED 277 3.0 (5.7)
DEL PEAK 20(8P22) WILD-TYPE 272 1.4 (3.4)

Figure S27.  Get High-res Image Gene #47: 'DEL PEAK 20(8P22) MUTATION STATUS' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 30(14Q11.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 6.9e-06 (Fisher's exact test), Q value = 0.0062

Table S28.  Gene #57: 'DEL PEAK 30(14Q11.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 30(14Q11.2) MUTATED 119 5 63 2
DEL PEAK 30(14Q11.2) WILD-TYPE 245 50 80 11

Figure S28.  Get High-res Image Gene #57: 'DEL PEAK 30(14Q11.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 31(14Q31.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.002

Table S29.  Gene #58: 'DEL PEAK 31(14Q31.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 31(14Q31.1) MUTATED 124 5 63 1
DEL PEAK 31(14Q31.1) WILD-TYPE 240 50 80 12

Figure S29.  Get High-res Image Gene #58: 'DEL PEAK 31(14Q31.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 32(14Q31.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.95e-06 (Fisher's exact test), Q value = 0.0035

Table S30.  Gene #59: 'DEL PEAK 32(14Q31.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 32(14Q31.1) MUTATED 125 6 65 1
DEL PEAK 32(14Q31.1) WILD-TYPE 239 49 78 12

Figure S30.  Get High-res Image Gene #59: 'DEL PEAK 32(14Q31.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 36(16P13.3) MUTATION STATUS' versus 'Time to Death'

P value = 7.04e-05 (logrank test), Q value = 0.062

Table S31.  Gene #63: 'DEL PEAK 36(16P13.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 467 76 0.1 - 140.4 (12.3)
DEL PEAK 36(16P13.3) MUTATED 45 15 0.2 - 49.9 (12.6)
DEL PEAK 36(16P13.3) WILD-TYPE 422 61 0.1 - 140.4 (12.2)

Figure S31.  Get High-res Image Gene #63: 'DEL PEAK 36(16P13.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 38(17P12) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000112 (Fisher's exact test), Q value = 0.097

Table S32.  Gene #65: 'DEL PEAK 38(17P12) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 38(17P12) MUTATED 170 97 76
DEL PEAK 38(17P12) WILD-TYPE 159 48 30

Figure S32.  Get High-res Image Gene #65: 'DEL PEAK 38(17P12) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 38(17P12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.44e-08 (Fisher's exact test), Q value = 3.1e-05

Table S33.  Gene #65: 'DEL PEAK 38(17P12) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 38(17P12) MUTATED 215 14 103 6
DEL PEAK 38(17P12) WILD-TYPE 149 41 40 7

Figure S33.  Get High-res Image Gene #65: 'DEL PEAK 38(17P12) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 40(18P11.31) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.95e-06 (Fisher's exact test), Q value = 0.0026

Table S34.  Gene #67: 'DEL PEAK 40(18P11.31) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 40(18P11.31) MUTATED 225 119
DEL PEAK 40(18P11.31) WILD-TYPE 195 40

Figure S34.  Get High-res Image Gene #67: 'DEL PEAK 40(18P11.31) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 40(18P11.31) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.23e-17 (Fisher's exact test), Q value = 4.8e-14

Table S35.  Gene #67: 'DEL PEAK 40(18P11.31) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 40(18P11.31) MUTATED 217 7 113 6
DEL PEAK 40(18P11.31) WILD-TYPE 147 48 30 7

Figure S35.  Get High-res Image Gene #67: 'DEL PEAK 40(18P11.31) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.82e-09 (Fisher's exact test), Q value = 1.6e-06

Table S36.  Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 41(18Q12.2) MUTATED 253 136
DEL PEAK 41(18Q12.2) WILD-TYPE 167 23

Figure S36.  Get High-res Image Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000131 (Fisher's exact test), Q value = 0.11

Table S37.  Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 41(18Q12.2) MUTATED 197 111 81
DEL PEAK 41(18Q12.2) WILD-TYPE 132 34 25

Figure S37.  Get High-res Image Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.48e-18 (Fisher's exact test), Q value = 2.3e-15

Table S38.  Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 41(18Q12.2) MUTATED 241 11 125 10
DEL PEAK 41(18Q12.2) WILD-TYPE 123 44 18 3

Figure S38.  Get High-res Image Gene #68: 'DEL PEAK 41(18Q12.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.22e-09 (Fisher's exact test), Q value = 1.1e-06

Table S39.  Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 42(18Q21.2) MUTATED 266 140
DEL PEAK 42(18Q21.2) WILD-TYPE 154 19

Figure S39.  Get High-res Image Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.52e-05 (Chi-square test), Q value = 0.049

Table S40.  Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
DEL PEAK 42(18Q21.2) MUTATED 60 0 25 98 4 3 17 18 58 40 53 22 1
DEL PEAK 42(18Q21.2) WILD-TYPE 40 1 16 58 6 0 10 4 17 9 6 3 0

Figure S40.  Get High-res Image Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.32e-06 (Fisher's exact test), Q value = 0.0021

Table S41.  Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 42(18Q21.2) MUTATED 203 115 88
DEL PEAK 42(18Q21.2) WILD-TYPE 126 30 18

Figure S41.  Get High-res Image Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.05e-16 (Fisher's exact test), Q value = 9.6e-14

Table S42.  Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 42(18Q21.2) MUTATED 251 14 126 12
DEL PEAK 42(18Q21.2) WILD-TYPE 113 41 17 1

Figure S42.  Get High-res Image Gene #69: 'DEL PEAK 42(18Q21.2) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.14e-07 (Fisher's exact test), Q value = 0.00019

Table S43.  Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 420 159
DEL PEAK 43(18Q22.1) MUTATED 266 135
DEL PEAK 43(18Q22.1) WILD-TYPE 154 24

Figure S43.  Get High-res Image Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000123 (Chi-square test), Q value = 0.11

Table S44.  Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 100 1 41 156 10 3 27 22 75 49 59 25 1
DEL PEAK 43(18Q22.1) MUTATED 60 0 25 98 4 3 15 17 57 40 52 22 1
DEL PEAK 43(18Q22.1) WILD-TYPE 40 1 16 58 6 0 12 5 18 9 7 3 0

Figure S44.  Get High-res Image Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.84e-05 (Fisher's exact test), Q value = 0.025

Table S45.  Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 43(18Q22.1) MUTATED 203 111 87
DEL PEAK 43(18Q22.1) WILD-TYPE 126 34 19

Figure S45.  Get High-res Image Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.8e-16 (Fisher's exact test), Q value = 5.3e-13

Table S46.  Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 364 55 143 13
DEL PEAK 43(18Q22.1) MUTATED 252 13 124 10
DEL PEAK 43(18Q22.1) WILD-TYPE 112 42 19 3

Figure S46.  Get High-res Image Gene #70: 'DEL PEAK 43(18Q22.1) MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'DEL PEAK 44(19P13.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.051

Table S47.  Gene #71: 'DEL PEAK 44(19P13.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 329 145 106
DEL PEAK 44(19P13.3) MUTATED 35 28 30
DEL PEAK 44(19P13.3) WILD-TYPE 294 117 76

Figure S47.  Get High-res Image Gene #71: 'DEL PEAK 44(19P13.3) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 583

  • Number of significantly focal cnvs = 76

  • Number of selected clinical features = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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