Correlation between copy number variation genes (focal events) and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C18S4N70
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18S4N70
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 63 focal events and 11 clinical features across 421 patients, 28 significant findings detected with Q value < 0.25.

  • AMP PEAK 11(13Q12.13) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 12(13Q22.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 13(16P11.2) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • AMP PEAK 14(16Q12.1) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • AMP PEAK 20(20Q11.21) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 21(20Q12) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • AMP PEAK 22(20Q13.12) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 1(1P36.11) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.

  • DEL PEAK 7(4P16.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • DEL PEAK 11(5Q21.3) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • DEL PEAK 16(8P23.3) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • DEL PEAK 17(8P22) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • DEL PEAK 19(8P11.21) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

  • DEL PEAK 25(13Q14.13) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.

  • DEL PEAK 32(17P12) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • DEL PEAK 34(18P11.31) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 35(18Q12.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 36(18Q21.2) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 37(18Q22.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • DEL PEAK 38(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 63 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE 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 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 32(17P12) MUTATION ANALYSIS 231 (55%) 190 0.406
(1.00) 		0.0218
(1.00) 		3.71e-05
(0.0253) 		0.887
(1.00) 		2.14e-05
(0.0146) 		0.00853
(1.00) 		0.282
(1.00) 		3.96e-06
(0.00271) 		0.255
(1.00) 		0.17
(1.00) 		0.000117
(0.0787)
DEL PEAK 36(18Q21 2) MUTATION ANALYSIS 266 (63%) 155 0.652
(1.00) 		0.148
(1.00) 		0.000236
(0.158) 		0.812
(1.00) 		0.000108
(0.073) 		0.00512
(1.00) 		0.0851
(1.00) 		1.95e-09
(1.34e-06) 		0.3
(1.00) 		0.135
(1.00) 		0.0355
(1.00)
AMP PEAK 14(16Q12 1) MUTATION ANALYSIS 103 (24%) 318 0.389
(1.00) 		0.0281
(1.00) 		0.000233
(0.156) 		0.973
(1.00) 		0.000326
(0.217) 		0.28
(1.00) 		0.366
(1.00) 		0.0113
(1.00) 		0.57
(1.00) 		0.737
(1.00) 		0.021
(1.00)
DEL PEAK 17(8P22) MUTATION ANALYSIS 189 (45%) 232 0.33
(1.00) 		0.105
(1.00) 		0.000102
(0.0688) 		0.184
(1.00) 		2.16e-06
(0.00148) 		0.000926
(0.605) 		0.141
(1.00) 		0.0132
(1.00) 		0.59
(1.00) 		0.055
(1.00) 		0.00127
(0.824)
DEL PEAK 37(18Q22 1) MUTATION ANALYSIS 266 (63%) 155 0.471
(1.00) 		0.247
(1.00) 		0.000657
(0.434) 		0.812
(1.00) 		0.00022
(0.147) 		0.00512
(1.00) 		0.0851
(1.00) 		1.97e-10
(1.36e-07) 		0.3
(1.00) 		0.229
(1.00) 		0.0449
(1.00)
AMP PEAK 11(13Q12 13) MUTATION ANALYSIS 256 (61%) 165 0.477
(1.00) 		0.426
(1.00) 		0.0034
(1.00) 		0.972
(1.00) 		0.00246
(1.00) 		0.0044
(1.00) 		0.69
(1.00) 		4.49e-07
(0.000309) 		0.283
(1.00) 		0.0333
(1.00) 		0.0844
(1.00)
AMP PEAK 12(13Q22 1) MUTATION ANALYSIS 260 (62%) 161 0.251
(1.00) 		0.461
(1.00) 		0.00382
(1.00) 		0.975
(1.00) 		0.00112
(0.726) 		0.0064
(1.00) 		0.23
(1.00) 		4.48e-06
(0.00306) 		0.29
(1.00) 		0.0689
(1.00) 		0.125
(1.00)
AMP PEAK 13(16P11 2) MUTATION ANALYSIS 117 (28%) 304 0.759
(1.00) 		0.107
(1.00) 		0.000767
(0.502) 		0.575
(1.00) 		0.000162
(0.109) 		0.449
(1.00) 		0.448
(1.00) 		0.00898
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.00761
(1.00)
AMP PEAK 20(20Q11 21) MUTATION ANALYSIS 302 (72%) 119 0.632
(1.00) 		0.631
(1.00) 		0.00327
(1.00) 		0.28
(1.00) 		0.0237
(1.00) 		0.00954
(1.00) 		0.234
(1.00) 		3.43e-06
(0.00235) 		0.562
(1.00) 		0.129
(1.00) 		0.134
(1.00)
AMP PEAK 21(20Q12) MUTATION ANALYSIS 303 (72%) 118 0.581
(1.00) 		0.671
(1.00) 		0.00131
(0.846) 		0.396
(1.00) 		0.0298
(1.00) 		0.00442
(1.00) 		0.194
(1.00) 		5.53e-07
(0.00038) 		0.563
(1.00) 		0.13
(1.00) 		0.172
(1.00)
AMP PEAK 22(20Q13 12) MUTATION ANALYSIS 306 (73%) 115 0.425
(1.00) 		0.672
(1.00) 		0.000673
(0.444) 		0.51
(1.00) 		0.0194
(1.00) 		0.00236
(1.00) 		0.273
(1.00) 		1.18e-06
(0.000811) 		0.565
(1.00) 		0.126
(1.00) 		0.0586
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 151 (36%) 270 0.0307
(1.00) 		0.238
(1.00) 		0.00743
(1.00) 		0.659
(1.00) 		0.0107
(1.00) 		0.000156
(0.105) 		0.542
(1.00) 		0.00381
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.00756
(1.00)
DEL PEAK 7(4P16 1) MUTATION ANALYSIS 124 (29%) 297 0.0207
(1.00) 		0.629
(1.00) 		0.00109
(0.711) 		0.842
(1.00) 		0.000347
(0.231) 		0.000496
(0.329) 		0.454
(1.00) 		0.0256
(1.00) 		0.0251
(1.00) 		0.0331
(1.00) 		0.0104
(1.00)
DEL PEAK 11(5Q21 3) MUTATION ANALYSIS 118 (28%) 303 0.249
(1.00) 		0.121
(1.00) 		0.00163
(1.00) 		0.968
(1.00) 		6.03e-05
(0.0409) 		0.0197
(1.00) 		0.744
(1.00) 		0.198
(1.00) 		0.0216
(1.00) 		0.249
(1.00) 		0.00699
(1.00)
DEL PEAK 16(8P23 3) MUTATION ANALYSIS 175 (42%) 246 0.845
(1.00) 		0.246
(1.00) 		0.00622
(1.00) 		0.135
(1.00) 		0.000164
(0.11) 		0.0169
(1.00) 		0.0742
(1.00) 		0.0558
(1.00) 		0.573
(1.00) 		0.108
(1.00) 		0.00599
(1.00)
DEL PEAK 19(8P11 21) MUTATION ANALYSIS 44 (10%) 377 0.731
(1.00) 		0.433
(1.00) 		0.00224
(1.00) 		0.132
(1.00) 		0.00022
(0.148) 		0.00992
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.283
(1.00) 		0.111
(1.00) 		0.0172
(1.00)
DEL PEAK 25(13Q14 13) MUTATION ANALYSIS 18 (4%) 403 0.228
(1.00) 		0.296
(1.00) 		0.000699
(0.46) 		0.67
(1.00) 		0.0647
(1.00) 		3.48e-05
(0.0237) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.868
(1.00) 		0.229
(1.00)
DEL PEAK 34(18P11 31) MUTATION ANALYSIS 226 (54%) 195 0.983
(1.00) 		0.0302
(1.00) 		0.0117
(1.00) 		0.94
(1.00) 		0.0602
(1.00) 		0.00309
(1.00) 		0.845
(1.00) 		4.02e-11
(2.79e-08) 		0.252
(1.00) 		0.0286
(1.00) 		0.462
(1.00)
DEL PEAK 35(18Q12 2) MUTATION ANALYSIS 253 (60%) 168 0.92
(1.00) 		0.0826
(1.00) 		0.00211
(1.00) 		0.71
(1.00) 		0.00162
(1.00) 		0.0109
(1.00) 		0.273
(1.00) 		1.41e-10
(9.74e-08) 		0.279
(1.00) 		0.144
(1.00) 		0.128
(1.00)
DEL PEAK 38(19P13 3) MUTATION ANALYSIS 58 (14%) 363 0.66
(1.00) 		0.141
(1.00) 		0.000392
(0.261) 		0.965
(1.00) 		5.88e-05
(0.0399) 		0.02
(1.00) 		0.671
(1.00) 		0.203
(1.00) 		0.36
(1.00) 		0.0791
(1.00) 		0.00175
(1.00)
AMP PEAK 1(2Q33 1) MUTATION ANALYSIS 81 (19%) 340 0.0213
(1.00) 		0.329
(1.00) 		0.208
(1.00) 		0.97
(1.00) 		0.0404
(1.00) 		0.364
(1.00) 		0.387
(1.00) 		0.463
(1.00) 		0.474
(1.00) 		0.101
(1.00) 		0.0969
(1.00)
AMP PEAK 2(5P13 2) MUTATION ANALYSIS 82 (19%) 339 0.959
(1.00) 		0.221
(1.00) 		0.146
(1.00) 		0.448
(1.00) 		0.0591
(1.00) 		0.691
(1.00) 		0.388
(1.00) 		1
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.0594
(1.00)
AMP PEAK 3(5Q22 3) MUTATION ANALYSIS 41 (10%) 380 0.513
(1.00) 		0.668
(1.00) 		0.465
(1.00) 		0.839
(1.00) 		0.309
(1.00) 		0.0122
(1.00) 		0.869
(1.00) 		0.333
(1.00) 		0.265
(1.00) 		0.0962
(1.00) 		0.319
(1.00)
AMP PEAK 4(6P21 1) MUTATION ANALYSIS 91 (22%) 330 0.493
(1.00) 		0.761
(1.00) 		0.0548
(1.00) 		0.472
(1.00) 		0.00347
(1.00) 		0.603
(1.00) 		0.343
(1.00) 		0.0512
(1.00) 		0.00984
(1.00) 		0.573
(1.00) 		0.016
(1.00)
AMP PEAK 5(8P11 23) MUTATION ANALYSIS 147 (35%) 274 0.877
(1.00) 		0.4
(1.00) 		0.365
(1.00) 		0.659
(1.00) 		0.776
(1.00) 		0.472
(1.00) 		0.759
(1.00) 		0.13
(1.00) 		0.28
(1.00) 		0.813
(1.00) 		0.693
(1.00)
AMP PEAK 6(8P11 21) MUTATION ANALYSIS 176 (42%) 245 0.498
(1.00) 		0.604
(1.00) 		0.647
(1.00) 		0.68
(1.00) 		0.569
(1.00) 		0.451
(1.00) 		0.276
(1.00) 		0.145
(1.00) 		0.574
(1.00) 		0.312
(1.00) 		0.963
(1.00)
AMP PEAK 7(8Q12 1) MUTATION ANALYSIS 218 (52%) 203 0.798
(1.00) 		0.196
(1.00) 		0.791
(1.00) 		0.418
(1.00) 		0.577
(1.00) 		0.168
(1.00) 		0.845
(1.00) 		0.0139
(1.00) 		0.249
(1.00) 		0.461
(1.00) 		0.103
(1.00)
AMP PEAK 8(8Q24 21) MUTATION ANALYSIS 243 (58%) 178 0.743
(1.00) 		0.124
(1.00) 		0.347
(1.00) 		0.175
(1.00) 		0.392
(1.00) 		0.11
(1.00) 		0.43
(1.00) 		0.0568
(1.00) 		0.266
(1.00) 		0.401
(1.00) 		0.0881
(1.00)
AMP PEAK 9(11P15 5) MUTATION ANALYSIS 87 (21%) 334 0.723
(1.00) 		0.0455
(1.00) 		0.809
(1.00) 		0.135
(1.00) 		0.18
(1.00) 		0.23
(1.00) 		0.549
(1.00) 		0.00196
(1.00) 		0.11
(1.00) 		0.46
(1.00) 		0.295
(1.00)
AMP PEAK 10(12P13 33) MUTATION ANALYSIS 104 (25%) 317 0.127
(1.00) 		0.0865
(1.00) 		0.214
(1.00) 		0.124
(1.00) 		0.282
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.836
(1.00)
AMP PEAK 15(17Q12) MUTATION ANALYSIS 102 (24%) 319 0.492
(1.00) 		0.445
(1.00) 		0.151
(1.00) 		0.334
(1.00) 		0.151
(1.00) 		0.0109
(1.00) 		0.254
(1.00) 		0.313
(1.00) 		0.566
(1.00) 		0.277
(1.00) 		0.172
(1.00)
AMP PEAK 16(17Q24 1) MUTATION ANALYSIS 93 (22%) 328 0.0947
(1.00) 		0.403
(1.00) 		0.416
(1.00) 		0.421
(1.00) 		0.306
(1.00) 		0.0284
(1.00) 		0.725
(1.00) 		0.0821
(1.00) 		0.528
(1.00) 		0.427
(1.00) 		0.964
(1.00)
AMP PEAK 17(19P13 2) MUTATION ANALYSIS 67 (16%) 354 0.932
(1.00) 		0.754
(1.00) 		0.539
(1.00) 		0.774
(1.00) 		0.0197
(1.00) 		0.0051
(1.00) 		0.0326
(1.00) 		0.168
(1.00) 		0.406
(1.00) 		0.104
(1.00) 		0.305
(1.00)
AMP PEAK 18(19Q13 11) MUTATION ANALYSIS 84 (20%) 337 0.239
(1.00) 		0.625
(1.00) 		0.635
(1.00) 		0.966
(1.00) 		0.122
(1.00) 		0.0166
(1.00) 		0.0511
(1.00) 		0.366
(1.00) 		0.488
(1.00) 		0.598
(1.00) 		0.988
(1.00)
AMP PEAK 19(20P11 23) MUTATION ANALYSIS 205 (49%) 216 0.684
(1.00) 		0.764
(1.00) 		0.000725
(0.476) 		0.966
(1.00) 		0.102
(1.00) 		0.000689
(0.454) 		0.328
(1.00) 		0.0135
(1.00) 		0.115
(1.00) 		0.0305
(1.00) 		0.263
(1.00)
DEL PEAK 2(1P33) MUTATION ANALYSIS 107 (25%) 314 0.00574
(1.00) 		0.631
(1.00) 		0.0294
(1.00) 		0.509
(1.00) 		0.0101
(1.00) 		0.00683
(1.00) 		1
(1.00) 		0.0999
(1.00) 		0.574
(1.00) 		0.263
(1.00) 		0.0171
(1.00)
DEL PEAK 3(2Q37 2) MUTATION ANALYSIS 21 (5%) 400 0.304
(1.00) 		0.417
(1.00) 		0.814
(1.00) 		0.445
(1.00) 		0.82
(1.00) 		0.343
(1.00) 		0.373
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.216
(1.00) 		0.155
(1.00)
DEL PEAK 4(3P26 1) MUTATION ANALYSIS 61 (14%) 360 0.00569
(1.00) 		0.351
(1.00) 		0.00867
(1.00) 		0.0491
(1.00) 		0.0211
(1.00) 		0.000577
(0.382) 		1
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0735
(1.00) 		0.203
(1.00)
DEL PEAK 5(3P14 2) MUTATION ANALYSIS 77 (18%) 344 0.849
(1.00) 		0.56
(1.00) 		0.159
(1.00) 		0.172
(1.00) 		0.0495
(1.00) 		0.0633
(1.00) 		0.45
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.0357
(1.00)
DEL PEAK 6(3Q26 31) MUTATION ANALYSIS 41 (10%) 380 0.162
(1.00) 		0.813
(1.00) 		0.0786
(1.00) 		0.0743
(1.00) 		0.742
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.851
(1.00) 		0.315
(1.00)
DEL PEAK 8(4Q22 1) MUTATION ANALYSIS 130 (31%) 291 0.128
(1.00) 		0.895
(1.00) 		0.00692
(1.00) 		0.256
(1.00) 		0.00117
(0.759) 		0.0975
(1.00) 		0.462
(1.00) 		0.0122
(1.00) 		0.029
(1.00) 		0.897
(1.00) 		0.0206
(1.00)
DEL PEAK 9(4Q35 1) MUTATION ANALYSIS 140 (33%) 281 0.182
(1.00) 		0.305
(1.00) 		0.148
(1.00) 		0.639
(1.00) 		0.0065
(1.00) 		0.165
(1.00) 		0.254
(1.00) 		0.065
(1.00) 		0.0362
(1.00) 		0.324
(1.00) 		0.0737
(1.00)
DEL PEAK 10(5Q11 2) MUTATION ANALYSIS 92 (22%) 329 0.127
(1.00) 		0.0795
(1.00) 		0.0176
(1.00) 		0.933
(1.00) 		0.00278
(1.00) 		0.0504
(1.00) 		0.408
(1.00) 		0.0357
(1.00) 		0.122
(1.00) 		0.719
(1.00) 		0.0186
(1.00)
DEL PEAK 12(5Q23 1) MUTATION ANALYSIS 108 (26%) 313 0.491
(1.00) 		0.424
(1.00) 		0.0749
(1.00) 		0.943
(1.00) 		0.00537
(1.00) 		0.01
(1.00) 		0.264
(1.00) 		0.0989
(1.00) 		0.0165
(1.00) 		0.267
(1.00) 		0.036
(1.00)
DEL PEAK 13(6P25 3) MUTATION ANALYSIS 54 (13%) 367 0.581
(1.00) 		0.0791
(1.00) 		0.649
(1.00) 		0.118
(1.00) 		0.844
(1.00) 		0.18
(1.00) 		0.0805
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.765
(1.00)
DEL PEAK 14(6Q26) MUTATION ANALYSIS 60 (14%) 361 0.0973
(1.00) 		0.857
(1.00) 		0.0531
(1.00) 		0.188
(1.00) 		0.0192
(1.00) 		0.0223
(1.00) 		0.889
(1.00) 		1
(1.00) 		1
(1.00) 		0.078
(1.00) 		0.0163
(1.00)
DEL PEAK 15(7Q31 1) MUTATION ANALYSIS 11 (3%) 410 0.725
(1.00) 		0.612
(1.00) 		0.935
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.36
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.647
(1.00)
DEL PEAK 18(8P11 22) MUTATION ANALYSIS 83 (20%) 338 0.644
(1.00) 		0.21
(1.00) 		0.0131
(1.00) 		0.271
(1.00) 		0.000496
(0.329) 		0.0684
(1.00) 		0.541
(1.00) 		0.365
(1.00) 		0.101
(1.00) 		0.193
(1.00) 		0.03
(1.00)
DEL PEAK 20(9P21 3) MUTATION ANALYSIS 57 (14%) 364 0.0972
(1.00) 		0.0569
(1.00) 		0.469
(1.00) 		0.339
(1.00) 		0.174
(1.00) 		0.0923
(1.00) 		0.203
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.64
(1.00) 		0.315
(1.00)
DEL PEAK 21(10P15 3) MUTATION ANALYSIS 69 (16%) 352 0.999
(1.00) 		0.445
(1.00) 		0.00148
(0.953) 		0.865
(1.00) 		0.00238
(1.00) 		0.00296
(1.00) 		0.895
(1.00) 		0.559
(1.00) 		0.0711
(1.00) 		0.525
(1.00) 		0.0808
(1.00)
DEL PEAK 22(10Q21 1) MUTATION ANALYSIS 84 (20%) 337 0.866
(1.00) 		0.0569
(1.00) 		0.000738
(0.484) 		0.946
(1.00) 		0.0038
(1.00) 		0.0504
(1.00) 		0.541
(1.00) 		0.0727
(1.00) 		0.103
(1.00) 		0.0356
(1.00) 		0.0765
(1.00)
DEL PEAK 23(10Q23 31) MUTATION ANALYSIS 96 (23%) 325 0.83
(1.00) 		0.0215
(1.00) 		0.00111
(0.72) 		0.587
(1.00) 		0.0037
(1.00) 		0.00354
(1.00) 		0.485
(1.00) 		0.166
(1.00) 		0.132
(1.00) 		0.13
(1.00) 		0.106
(1.00)
DEL PEAK 24(10Q25 2) MUTATION ANALYSIS 95 (23%) 326 0.397
(1.00) 		0.18
(1.00) 		0.0135
(1.00) 		0.186
(1.00) 		0.00141
(0.914) 		0.0328
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.129
(1.00) 		0.0413
(1.00) 		0.0754
(1.00)
DEL PEAK 26(14Q32 11) MUTATION ANALYSIS 135 (32%) 286 0.281
(1.00) 		0.695
(1.00) 		0.101
(1.00) 		0.562
(1.00) 		0.0611
(1.00) 		0.022
(1.00) 		0.754
(1.00) 		0.000941
(0.614) 		0.554
(1.00) 		0.276
(1.00) 		0.139
(1.00)
DEL PEAK 27(15Q11 2) MUTATION ANALYSIS 162 (38%) 259 0.822
(1.00) 		0.985
(1.00) 		0.0346
(1.00) 		0.969
(1.00) 		0.00536
(1.00) 		0.0428
(1.00) 		1
(1.00) 		0.0174
(1.00) 		0.0563
(1.00) 		0.475
(1.00) 		0.234
(1.00)
DEL PEAK 28(15Q21 1) MUTATION ANALYSIS 152 (36%) 269 0.198
(1.00) 		0.873
(1.00) 		0.235
(1.00) 		0.977
(1.00) 		0.0433
(1.00) 		0.0638
(1.00) 		0.919
(1.00) 		0.0231
(1.00) 		0.0465
(1.00) 		0.316
(1.00) 		0.448
(1.00)
DEL PEAK 29(15Q22 33) MUTATION ANALYSIS 146 (35%) 275 0.432
(1.00) 		0.604
(1.00) 		0.0497
(1.00) 		0.547
(1.00) 		0.0173
(1.00) 		0.0295
(1.00) 		0.918
(1.00) 		0.00607
(1.00) 		0.0411
(1.00) 		0.87
(1.00) 		0.313
(1.00)
DEL PEAK 30(16P13 3) MUTATION ANALYSIS 46 (11%) 375 0.00145
(0.935) 		0.371
(1.00) 		0.101
(1.00) 		0.028
(1.00) 		0.117
(1.00) 		0.443
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.129
(1.00)
DEL PEAK 31(16Q23 1) MUTATION ANALYSIS 50 (12%) 371 0.0237
(1.00) 		0.248
(1.00) 		0.901
(1.00) 		0.5
(1.00) 		0.579
(1.00) 		0.981
(1.00) 		0.0971
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.201
(1.00)
DEL PEAK 33(17Q24 3) MUTATION ANALYSIS 60 (14%) 361 0.849
(1.00) 		0.596
(1.00) 		0.0533
(1.00) 		0.712
(1.00) 		0.00528
(1.00) 		0.301
(1.00) 		0.328
(1.00) 		1
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.0364
(1.00)
DEL PEAK 39(20P12 1) MUTATION ANALYSIS 79 (19%) 342 0.942
(1.00) 		0.66
(1.00) 		0.469
(1.00) 		0.665
(1.00) 		0.389
(1.00) 		0.982
(1.00) 		0.618
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.73
(1.00) 		0.586
(1.00)
DEL PEAK 40(21Q11 2) MUTATION ANALYSIS 128 (30%) 293 0.922
(1.00) 		0.727
(1.00) 		0.353
(1.00) 		0.352
(1.00) 		0.0479
(1.00) 		0.278
(1.00) 		0.751
(1.00) 		0.00693
(1.00) 		0.221
(1.00) 		0.831
(1.00) 		0.0142
(1.00)
DEL PEAK 41(22Q13 32) MUTATION ANALYSIS 143 (34%) 278 0.326
(1.00) 		0.661
(1.00) 		0.0133
(1.00) 		0.721
(1.00) 		0.00148
(0.954) 		0.0268
(1.00) 		1
(1.00) 		0.00225
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.0116
(1.00)
'AMP PEAK 11(13Q12.13) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.49e-07 (Fisher's exact test), Q value = 0.00031

Table S1.  Gene #11: 'AMP PEAK 11(13Q12.13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
AMP PEAK 11(13Q12.13) MUTATED 239 16
AMP PEAK 11(13Q12.13) WILD-TYPE 125 39

Figure S1.  Get High-res Image Gene #11: 'AMP PEAK 11(13Q12.13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 12(13Q22.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.48e-06 (Fisher's exact test), Q value = 0.0031

Table S2.  Gene #12: 'AMP PEAK 12(13Q22.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
AMP PEAK 12(13Q22.1) MUTATED 241 18
AMP PEAK 12(13Q22.1) WILD-TYPE 123 37

Figure S2.  Get High-res Image Gene #12: 'AMP PEAK 12(13Q22.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 13(16P11.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000162 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #13: 'AMP PEAK 13(16P11.2) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
AMP PEAK 13(16P11.2) MUTATED 50 36 31
AMP PEAK 13(16P11.2) WILD-TYPE 196 64 43

Figure S3.  Get High-res Image Gene #13: 'AMP PEAK 13(16P11.2) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000233 (Chi-square test), Q value = 0.16

Table S4.  Gene #14: 'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus Clinical Feature #3: '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 70 1 33 118 8 1 22 13 52 35 42 16 1
AMP PEAK 14(16Q12.1) MUTATED 12 1 3 21 1 0 5 9 20 13 11 3 0
AMP PEAK 14(16Q12.1) WILD-TYPE 58 0 30 97 7 1 17 4 32 22 31 13 1

Figure S4.  Get High-res Image Gene #14: 'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000326 (Fisher's exact test), Q value = 0.22

Table S5.  Gene #14: 'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
AMP PEAK 14(16Q12.1) MUTATED 43 34 26
AMP PEAK 14(16Q12.1) WILD-TYPE 203 66 48

Figure S5.  Get High-res Image Gene #14: 'AMP PEAK 14(16Q12.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

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

P value = 3.43e-06 (Fisher's exact test), Q value = 0.0023

Table S6.  Gene #20: 'AMP PEAK 20(20Q11.21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
AMP PEAK 20(20Q11.21) MUTATED 276 24
AMP PEAK 20(20Q11.21) WILD-TYPE 88 31

Figure S6.  Get High-res Image Gene #20: 'AMP PEAK 20(20Q11.21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 21(20Q12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 5.53e-07 (Fisher's exact test), Q value = 0.00038

Table S7.  Gene #21: 'AMP PEAK 21(20Q12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
AMP PEAK 21(20Q12) MUTATED 278 23
AMP PEAK 21(20Q12) WILD-TYPE 86 32

Figure S7.  Get High-res Image Gene #21: 'AMP PEAK 21(20Q12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'AMP PEAK 22(20Q13.12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.18e-06 (Fisher's exact test), Q value = 0.00081

Table S8.  Gene #22: 'AMP PEAK 22(20Q13.12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
AMP PEAK 22(20Q13.12) MUTATED 280 24
AMP PEAK 22(20Q13.12) WILD-TYPE 84 31

Figure S8.  Get High-res Image Gene #22: 'AMP PEAK 22(20Q13.12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 1(1P36.11) MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 0.000156 (Chi-square test), Q value = 0.11

Table S9.  Gene #23: 'DEL PEAK 1(1P36.11) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 317 50 7 1 39
DEL PEAK 1(1P36.11) MUTATED 101 33 2 0 14
DEL PEAK 1(1P36.11) WILD-TYPE 216 17 5 1 25

Figure S9.  Get High-res Image Gene #23: 'DEL PEAK 1(1P36.11) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'DEL PEAK 7(4P16.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000347 (Fisher's exact test), Q value = 0.23

Table S10.  Gene #29: 'DEL PEAK 7(4P16.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 7(4P16.1) MUTATED 55 36 33
DEL PEAK 7(4P16.1) WILD-TYPE 191 64 41

Figure S10.  Get High-res Image Gene #29: 'DEL PEAK 7(4P16.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 11(5Q21.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 6.03e-05 (Fisher's exact test), Q value = 0.041

Table S11.  Gene #33: 'DEL PEAK 11(5Q21.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 11(5Q21.3) MUTATED 50 35 33
DEL PEAK 11(5Q21.3) WILD-TYPE 196 65 41

Figure S11.  Get High-res Image Gene #33: 'DEL PEAK 11(5Q21.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 16(8P23.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000164 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #38: 'DEL PEAK 16(8P23.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 16(8P23.3) MUTATED 82 49 43
DEL PEAK 16(8P23.3) WILD-TYPE 164 51 31

Figure S12.  Get High-res Image Gene #38: 'DEL PEAK 16(8P23.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 17(8P22) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000102 (Chi-square test), Q value = 0.069

Table S13.  Gene #39: 'DEL PEAK 17(8P22) MUTATION STATUS' versus Clinical Feature #3: '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 70 1 33 118 8 1 22 13 52 35 42 16 1
DEL PEAK 17(8P22) MUTATED 24 0 9 41 2 0 11 8 27 23 28 12 1
DEL PEAK 17(8P22) WILD-TYPE 46 1 24 77 6 1 11 5 25 12 14 4 0

Figure S13.  Get High-res Image Gene #39: 'DEL PEAK 17(8P22) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 17(8P22) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.16e-06 (Fisher's exact test), Q value = 0.0015

Table S14.  Gene #39: 'DEL PEAK 17(8P22) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 17(8P22) MUTATED 86 53 49
DEL PEAK 17(8P22) WILD-TYPE 160 47 25

Figure S14.  Get High-res Image Gene #39: 'DEL PEAK 17(8P22) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 19(8P11.21) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S15.  Gene #41: 'DEL PEAK 19(8P11.21) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 19(8P11.21) MUTATED 14 14 16
DEL PEAK 19(8P11.21) WILD-TYPE 232 86 58

Figure S15.  Get High-res Image Gene #41: 'DEL PEAK 19(8P11.21) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 25(13Q14.13) MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 3.48e-05 (Chi-square test), Q value = 0.024

Table S16.  Gene #47: 'DEL PEAK 25(13Q14.13) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 317 50 7 1 39
DEL PEAK 25(13Q14.13) MUTATED 12 1 0 1 2
DEL PEAK 25(13Q14.13) WILD-TYPE 305 49 7 0 37

Figure S16.  Get High-res Image Gene #47: 'DEL PEAK 25(13Q14.13) MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'DEL PEAK 32(17P12) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.71e-05 (Chi-square test), Q value = 0.025

Table S17.  Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #3: '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 70 1 33 118 8 1 22 13 52 35 42 16 1
DEL PEAK 32(17P12) MUTATED 34 0 15 49 1 1 13 12 31 26 32 11 1
DEL PEAK 32(17P12) WILD-TYPE 36 1 18 69 7 0 9 1 21 9 10 5 0

Figure S17.  Get High-res Image Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 32(17P12) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.015

Table S18.  Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 32(17P12) MUTATED 112 65 53
DEL PEAK 32(17P12) WILD-TYPE 134 35 21

Figure S18.  Get High-res Image Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 32(17P12) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.96e-06 (Fisher's exact test), Q value = 0.0027

Table S19.  Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
DEL PEAK 32(17P12) MUTATED 215 14
DEL PEAK 32(17P12) WILD-TYPE 149 41

Figure S19.  Get High-res Image Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 32(17P12) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000117 (t-test), Q value = 0.079

Table S20.  Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 397 2.1 (4.5)
DEL PEAK 32(17P12) MUTATED 218 2.8 (5.5)
DEL PEAK 32(17P12) WILD-TYPE 179 1.2 (2.6)

Figure S20.  Get High-res Image Gene #54: 'DEL PEAK 32(17P12) MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 34(18P11.31) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.02e-11 (Fisher's exact test), Q value = 2.8e-08

Table S21.  Gene #56: 'DEL PEAK 34(18P11.31) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
DEL PEAK 34(18P11.31) MUTATED 217 7
DEL PEAK 34(18P11.31) WILD-TYPE 147 48

Figure S21.  Get High-res Image Gene #56: 'DEL PEAK 34(18P11.31) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 35(18Q12.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.41e-10 (Fisher's exact test), Q value = 9.7e-08

Table S22.  Gene #57: 'DEL PEAK 35(18Q12.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
DEL PEAK 35(18Q12.2) MUTATED 241 11
DEL PEAK 35(18Q12.2) WILD-TYPE 123 44

Figure S22.  Get High-res Image Gene #57: 'DEL PEAK 35(18Q12.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000236 (Chi-square test), Q value = 0.16

Table S23.  Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #3: '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 70 1 33 118 8 1 22 13 52 35 42 16 1
DEL PEAK 36(18Q21.2) MUTATED 38 0 18 64 2 1 12 12 35 28 36 13 1
DEL PEAK 36(18Q21.2) WILD-TYPE 32 1 15 54 6 0 10 1 17 7 6 3 0

Figure S23.  Get High-res Image Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000108 (Fisher's exact test), Q value = 0.073

Table S24.  Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 36(18Q21.2) MUTATED 135 72 58
DEL PEAK 36(18Q21.2) WILD-TYPE 111 28 16

Figure S24.  Get High-res Image Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.95e-09 (Fisher's exact test), Q value = 1.3e-06

Table S25.  Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
DEL PEAK 36(18Q21.2) MUTATED 251 14
DEL PEAK 36(18Q21.2) WILD-TYPE 113 41

Figure S25.  Get High-res Image Gene #58: 'DEL PEAK 36(18Q21.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.15

Table S26.  Gene #59: 'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 37(18Q22.1) MUTATED 136 71 58
DEL PEAK 37(18Q22.1) WILD-TYPE 110 29 16

Figure S26.  Get High-res Image Gene #59: 'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.97e-10 (Fisher's exact test), Q value = 1.4e-07

Table S27.  Gene #59: 'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 364 55
DEL PEAK 37(18Q22.1) MUTATED 252 13
DEL PEAK 37(18Q22.1) WILD-TYPE 112 42

Figure S27.  Get High-res Image Gene #59: 'DEL PEAK 37(18Q22.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'DEL PEAK 38(19P13.3) MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.04

Table S28.  Gene #60: 'DEL PEAK 38(19P13.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 246 100 74
DEL PEAK 38(19P13.3) MUTATED 21 15 22
DEL PEAK 38(19P13.3) WILD-TYPE 225 85 52

Figure S28.  Get High-res Image Gene #60: 'DEL PEAK 38(19P13.3) MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 421

  • Number of significantly focal cnvs = 63

  • Number of selected clinical features = 11

  • 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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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