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 89 focal events and 13 clinical features across 441 patients, 25 significant findings detected with Q value < 0.25.

  • amp_1p36.22 cnv correlated to 'GENDER'.

  • amp_1q42.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_6p21.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_6q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_7p22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_17q12 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

  • amp_20q13.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_1p36.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_5q12.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_5q23.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_8p23.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_14q32.32 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_15q15.1 cnv correlated to 'RADIATION_THERAPY'.

  • del_16p13.3 cnv correlated to 'RACE'.

  • del_16q23.1 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_17p12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_17q24.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_18q12.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_18q21.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_19p13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_19q13.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 89 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 25 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 17q12 147 (33%) 294 0.229
(0.839) 		0.329
(0.869) 		0.492
(0.925) 		0.653
(0.986) 		0.506
(0.933) 		0.0405
(0.53) 		0.0456
(0.55) 		0.681
(0.99) 		3e-05
(0.0116) 		0.00011
(0.0212) 		0.506
(0.933) 		0.023
(0.475) 		1
(1.00)
amp 1p36 22 66 (15%) 375 0.625
(0.967) 		0.731
(1.00) 		0.691
(0.99) 		0.157
(0.804) 		0.844
(1.00) 		0.285
(0.844) 		0.00323
(0.207) 		0.0447
(0.547) 		0.926
(1.00) 		1
(1.00) 		0.153
(0.794) 		0.253
(0.839) 		0.524
(0.946)
amp 1q42 3 150 (34%) 291 0.595
(0.965) 		0.481
(0.923) 		0.646
(0.981) 		0.528
(0.948) 		0.413
(0.899) 		0.841
(1.00) 		0.754
(1.00) 		0.0751
(0.688) 		0.00192
(0.159) 		0.73
(1.00) 		0.499
(0.926) 		0.186
(0.809) 		0.665
(0.989)
amp 5p15 33 130 (29%) 311 0.387
(0.89) 		0.0392
(0.53) 		0.926
(1.00) 		0.00395
(0.218) 		0.567
(0.962) 		1
(1.00) 		0.329
(0.869) 		0.672
(0.99) 		0.0204
(0.454) 		0.63
(0.97) 		0.0331
(0.518) 		0.276
(0.844) 		1
(1.00)
amp 6p21 1 124 (28%) 317 0.869
(1.00) 		0.0134
(0.382) 		0.405
(0.892) 		0.0957
(0.705) 		0.421
(0.904) 		0.207
(0.826) 		0.377
(0.887) 		0.776
(1.00) 		6e-05
(0.0139) 		0.537
(0.954) 		0.59
(0.965) 		0.0599
(0.614) 		0.615
(0.965)
amp 6q12 88 (20%) 353 0.51
(0.936) 		0.995
(1.00) 		0.344
(0.869) 		0.53
(0.948) 		0.735
(1.00) 		1
(1.00) 		0.902
(1.00) 		0.329
(0.869) 		0.00044
(0.0566) 		0.313
(0.865) 		0.481
(0.923) 		0.199
(0.819) 		1
(1.00)
amp 7p22 1 229 (52%) 212 0.884
(1.00) 		0.189
(0.81) 		0.795
(1.00) 		0.574
(0.962) 		0.366
(0.883) 		0.449
(0.915) 		0.0476
(0.553) 		0.303
(0.862) 		0.00477
(0.241) 		0.916
(1.00) 		0.204
(0.826) 		0.633
(0.972) 		1
(1.00)
amp 20q13 2 293 (66%) 148 0.516
(0.94) 		0.286
(0.844) 		0.542
(0.954) 		0.318
(0.869) 		0.119
(0.742) 		0.55
(0.955) 		0.0154
(0.382) 		0.272
(0.844) 		3e-05
(0.0116) 		0.452
(0.915) 		0.507
(0.935) 		0.707
(0.996) 		0.66
(0.986)
del 1p36 11 135 (31%) 306 0.377
(0.887) 		0.718
(1.00) 		0.605
(0.965) 		0.122
(0.745) 		0.982
(1.00) 		1
(1.00) 		0.518
(0.942) 		0.024
(0.487) 		0.00267
(0.206) 		0.114
(0.735) 		0.487
(0.925) 		0.47
(0.922) 		1
(1.00)
del 5q12 1 170 (39%) 271 0.921
(1.00) 		0.288
(0.844) 		0.43
(0.905) 		0.582
(0.965) 		0.136
(0.788) 		0.567
(0.962) 		0.76
(1.00) 		0.43
(0.905) 		6e-05
(0.0139) 		0.165
(0.805) 		0.109
(0.719) 		0.841
(1.00) 		1
(1.00)
del 5q23 2 158 (36%) 283 0.741
(1.00) 		0.475
(0.923) 		0.36
(0.883) 		0.364
(0.883) 		0.819
(1.00) 		0.326
(0.869) 		0.606
(0.965) 		0.182
(0.806) 		2e-05
(0.0116) 		0.184
(0.808) 		0.98
(1.00) 		0.607
(0.965) 		1
(1.00)
del 8p23 3 126 (29%) 315 0.94
(1.00) 		0.171
(0.805) 		0.216
(0.835) 		0.42
(0.904) 		0.0388
(0.53) 		0.402
(0.892) 		0.0156
(0.382) 		1
(1.00) 		0.0253
(0.49) 		0.152
(0.794) 		0.00189
(0.159) 		0.263
(0.839) 		0.613
(0.965)
del 10q23 31 116 (26%) 325 0.103
(0.719) 		0.00526
(0.244) 		0.981
(1.00) 		0.101
(0.719) 		0.5
(0.926) 		0.832
(1.00) 		0.822
(1.00) 		0.77
(1.00) 		0.00722
(0.298) 		0.898
(1.00) 		0.0941
(0.705) 		0.251
(0.839) 		0.339
(0.869)
del 12p13 1 77 (17%) 364 0.193
(0.815) 		0.403
(0.892) 		0.336
(0.869) 		0.0175
(0.397) 		0.977
(1.00) 		0.616
(0.965) 		0.897
(1.00) 		0.401
(0.892) 		0.00062
(0.0652) 		0.792
(1.00) 		0.21
(0.829) 		0.725
(1.00) 		0.174
(0.805)
del 14q32 32 133 (30%) 308 0.478
(0.923) 		0.963
(1.00) 		0.169
(0.805) 		0.742
(1.00) 		0.724
(1.00) 		0.00309
(0.207) 		0.59
(0.965) 		0.262
(0.839) 		0.392
(0.89) 		0.31
(0.862) 		0.304
(0.862) 		0.919
(1.00) 		0.328
(0.869)
del 15q15 1 122 (28%) 319 0.826
(1.00) 		0.464
(0.922) 		0.202
(0.826) 		0.0652
(0.634) 		0.688
(0.99) 		0.521
(0.942) 		0.74
(1.00) 		0.00343
(0.207) 		0.0569
(0.593) 		0.472
(0.923) 		0.425
(0.905) 		0.825
(1.00) 		0.62
(0.966)
del 16p13 3 93 (21%) 348 0.768
(1.00) 		0.182
(0.806) 		0.0966
(0.708) 		0.313
(0.865) 		0.429
(0.905) 		0.357
(0.883) 		0.466
(0.922) 		0.529
(0.948) 		0.0472
(0.553) 		0.739
(1.00) 		0.726
(1.00) 		0.00494
(0.241) 		0.587
(0.965)
del 16q23 1 182 (41%) 259 0.745
(1.00) 		0.514
(0.94) 		0.0923
(0.705) 		0.797
(1.00) 		0.552
(0.957) 		0.00358
(0.207) 		0.314
(0.865) 		0.602
(0.965) 		0.134
(0.788) 		0.283
(0.844) 		0.617
(0.965) 		0.925
(1.00) 		1
(1.00)
del 17p12 181 (41%) 260 0.72
(1.00) 		0.724
(1.00) 		0.856
(1.00) 		0.284
(0.844) 		0.683
(0.99) 		0.334
(0.869) 		0.0861
(0.705) 		0.115
(0.737) 		0.00038
(0.055) 		0.149
(0.794) 		0.545
(0.955) 		0.748
(1.00) 		1
(1.00)
del 17q24 3 76 (17%) 365 0.14
(0.792) 		0.148
(0.794) 		0.392
(0.89) 		0.0854
(0.705) 		0.104
(0.719) 		0.802
(1.00) 		0.694
(0.991) 		0.151
(0.794) 		0.208
(0.826) 		0.186
(0.809) 		0.00499
(0.241) 		0.108
(0.719) 		1
(1.00)
del 18q12 2 181 (41%) 260 0.689
(0.99) 		0.34
(0.869) 		0.606
(0.965) 		0.00015
(0.0248) 		0.734
(1.00) 		0.703
(0.995) 		0.364
(0.883) 		0.696
(0.992) 		0.169
(0.805) 		0.469
(0.922) 		0.104
(0.719) 		0.252
(0.839) 		0.398
(0.892)
del 18q21 2 204 (46%) 237 0.929
(1.00) 		0.409
(0.894) 		0.897
(1.00) 		0.00186
(0.159) 		0.71
(0.998) 		0.85
(1.00) 		0.321
(0.869) 		0.699
(0.992) 		0.095
(0.705) 		0.461
(0.922) 		0.0705
(0.663) 		0.188
(0.81) 		0.665
(0.989)
del 19p13 3 162 (37%) 279 0.161
(0.805) 		0.211
(0.829) 		0.969
(1.00) 		0.266
(0.843) 		0.842
(1.00) 		0.845
(1.00) 		0.04
(0.53) 		0.349
(0.869) 		0.00314
(0.207) 		0.272
(0.844) 		0.269
(0.844) 		0.14
(0.792) 		0.667
(0.989)
del 19q13 11 75 (17%) 366 0.751
(1.00) 		0.175
(0.805) 		0.95
(1.00) 		0.835
(1.00) 		0.363
(0.883) 		0.324
(0.869) 		0.692
(0.99) 		0.611
(0.965) 		0.00059
(0.0652) 		0.388
(0.89) 		0.137
(0.788) 		0.495
(0.925) 		0.581
(0.965)
amp 1q21 3 160 (36%) 281 0.942
(1.00) 		0.942
(1.00) 		0.894
(1.00) 		0.385
(0.889) 		0.389
(0.89) 		0.846
(1.00) 		1
(1.00) 		0.0222
(0.467) 		0.118
(0.742) 		0.188
(0.81) 		0.345
(0.869) 		0.399
(0.892) 		0.657
(0.986)
amp 3q26 2 164 (37%) 277 0.703
(0.995) 		0.601
(0.965) 		0.589
(0.965) 		0.167
(0.805) 		0.674
(0.99) 		0.845
(1.00) 		0.918
(1.00) 		0.011
(0.353) 		0.474
(0.923) 		0.938
(1.00) 		0.144
(0.794) 		0.273
(0.844) 		0.052
(0.573)
amp 5p13 1 126 (29%) 315 0.495
(0.925) 		0.0408
(0.53) 		0.979
(1.00) 		0.227
(0.839) 		0.565
(0.962) 		0.53
(0.948) 		0.827
(1.00) 		0.776
(1.00) 		0.224
(0.839) 		0.442
(0.914) 		0.175
(0.805) 		0.637
(0.972) 		1
(1.00)
amp 6q21 82 (19%) 359 0.135
(0.788) 		0.788
(1.00) 		0.224
(0.839) 		0.166
(0.805) 		0.374
(0.883) 		0.23
(0.839) 		0.308
(0.862) 		0.74
(1.00) 		0.048
(0.553) 		0.298
(0.858) 		0.107
(0.719) 		0.122
(0.745) 		1
(1.00)
amp 7p11 2 214 (49%) 227 0.382
(0.889) 		0.0396
(0.53) 		0.554
(0.958) 		0.346
(0.869) 		0.716
(1.00) 		0.191
(0.814) 		0.0918
(0.705) 		0.52
(0.942) 		0.0152
(0.382) 		0.855
(1.00) 		0.176
(0.805) 		0.174
(0.805) 		0.379
(0.888)
amp 7q21 2 204 (46%) 237 0.894
(1.00) 		0.181
(0.806) 		0.939
(1.00) 		0.786
(1.00) 		0.127
(0.769) 		0.345
(0.869) 		0.0288
(0.497) 		0.604
(0.965) 		0.0598
(0.614) 		0.29
(0.846) 		0.0937
(0.705) 		0.0898
(0.705) 		1
(1.00)
amp 7q22 1 202 (46%) 239 0.737
(1.00) 		0.198
(0.819) 		0.759
(1.00) 		0.805
(1.00) 		0.0169
(0.392) 		0.348
(0.869) 		0.0282
(0.497) 		0.697
(0.992) 		0.146
(0.794) 		0.0946
(0.705) 		0.273
(0.844) 		0.0738
(0.683) 		0.657
(0.986)
amp 8p23 1 177 (40%) 264 0.215
(0.835) 		0.0644
(0.634) 		0.494
(0.925) 		0.256
(0.839) 		0.883
(1.00) 		0.446
(0.915) 		0.0115
(0.353) 		0.793
(1.00) 		0.707
(0.996) 		0.344
(0.869) 		0.591
(0.965) 		0.934
(1.00) 		0.391
(0.89)
amp 8q24 21 309 (70%) 132 0.899
(1.00) 		0.0331
(0.518) 		0.642
(0.978) 		0.021
(0.459) 		0.673
(0.99) 		0.837
(1.00) 		0.914
(1.00) 		0.779
(1.00) 		0.251
(0.839) 		0.363
(0.883) 		0.695
(0.992) 		0.0423
(0.532) 		1
(1.00)
amp 9p24 1 65 (15%) 376 0.852
(1.00) 		0.979
(1.00) 		0.541
(0.954) 		0.216
(0.835) 		0.424
(0.905) 		1
(1.00) 		1
(1.00) 		0.373
(0.883) 		0.28
(0.844) 		0.683
(0.99) 		0.59
(0.965) 		0.287
(0.844) 		0.163
(0.805)
amp 9p13 2 91 (21%) 350 0.397
(0.892) 		0.848
(1.00) 		0.0272
(0.497) 		0.286
(0.844) 		0.667
(0.989) 		1
(1.00) 		0.462
(0.922) 		0.159
(0.804) 		0.0157
(0.382) 		0.612
(0.965) 		0.579
(0.965) 		1
(1.00) 		0.0514
(0.573)
amp 9q34 3 122 (28%) 319 0.258
(0.839) 		0.81
(1.00) 		0.466
(0.922) 		0.723
(1.00) 		0.491
(0.925) 		0.833
(1.00) 		0.74
(1.00) 		0.0875
(0.705) 		0.0951
(0.705) 		0.352
(0.874) 		0.435
(0.908) 		0.571
(0.962) 		0.118
(0.742)
amp 10p11 22 119 (27%) 322 0.792
(1.00) 		0.422
(0.905) 		0.179
(0.806) 		0.125
(0.758) 		0.849
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.885
(1.00) 		0.16
(0.805) 		0.708
(0.997) 		0.557
(0.958) 		0.0158
(0.382) 		0.617
(0.965)
amp 10q22 2 88 (20%) 353 0.705
(0.996) 		0.311
(0.862) 		0.0894
(0.705) 		0.59
(0.965) 		0.174
(0.805) 		0.236
(0.839) 		0.902
(1.00) 		0.263
(0.839) 		0.433
(0.906) 		0.372
(0.883) 		0.319
(0.869) 		0.22
(0.839) 		0.587
(0.965)
amp 10q26 13 88 (20%) 353 0.498
(0.926) 		0.687
(0.99) 		0.37
(0.883) 		0.384
(0.889) 		0.474
(0.923) 		0.234
(0.839) 		0.711
(0.998) 		0.517
(0.94) 		0.18
(0.806) 		0.812
(1.00) 		0.717
(1.00) 		0.245
(0.839) 		0.589
(0.965)
amp 11p13 88 (20%) 353 0.243
(0.839) 		0.847
(1.00) 		0.224
(0.839) 		0.0417
(0.532) 		0.307
(0.862) 		0.63
(0.97) 		0.214
(0.835) 		0.331
(0.869) 		0.486
(0.925) 		0.244
(0.839) 		0.0776
(0.696) 		0.324
(0.869) 		0.242
(0.839)
amp 11p11 2 92 (21%) 349 0.595
(0.965) 		0.907
(1.00) 		0.187
(0.809) 		0.606
(0.965) 		0.196
(0.819) 		1
(1.00) 		0.392
(0.89) 		0.148
(0.794) 		0.204
(0.826) 		0.309
(0.862) 		0.153
(0.794) 		0.365
(0.883) 		0.235
(0.839)
amp 11q13 3 115 (26%) 326 0.974
(1.00) 		0.18
(0.806) 		0.699
(0.992) 		0.468
(0.922) 		0.0623
(0.626) 		0.283
(0.844) 		0.652
(0.986) 		0.307
(0.862) 		0.617
(0.965) 		0.733
(1.00) 		0.128
(0.769) 		0.145
(0.794) 		1
(1.00)
amp 12p12 1 128 (29%) 313 0.527
(0.948) 		0.833
(1.00) 		0.681
(0.99) 		0.0255
(0.49) 		0.329
(0.869) 		0.837
(1.00) 		1
(1.00) 		0.673
(0.99) 		0.291
(0.847) 		0.493
(0.925) 		0.466
(0.922) 		0.835
(1.00) 		0.643
(0.978)
amp 12q15 109 (25%) 332 0.151
(0.794) 		0.172
(0.805) 		0.901
(1.00) 		0.783
(1.00) 		0.247
(0.839) 		0.828
(1.00) 		0.565
(0.962) 		0.458
(0.922) 		0.24
(0.839) 		0.556
(0.958) 		0.981
(1.00) 		0.301
(0.862) 		0.603
(0.965)
amp 13q12 3 170 (39%) 271 0.648
(0.982) 		0.574
(0.962) 		0.658
(0.986) 		0.549
(0.955) 		0.768
(1.00) 		1
(1.00) 		0.359
(0.883) 		0.895
(1.00) 		0.221
(0.839) 		0.675
(0.99) 		0.242
(0.839) 		0.243
(0.839) 		1
(1.00)
amp 13q22 1 181 (41%) 260 0.49
(0.925) 		0.9
(1.00) 		0.62
(0.966) 		0.221
(0.839) 		0.44
(0.912) 		1
(1.00) 		0.0339
(0.523) 		0.895
(1.00) 		0.0143
(0.382) 		0.5
(0.926) 		0.411
(0.897) 		0.621
(0.966) 		1
(1.00)
amp 15q26 1 113 (26%) 328 0.815
(1.00) 		0.793
(1.00) 		0.254
(0.839) 		0.499
(0.926) 		0.0881
(0.705) 		0.384
(0.889) 		0.172
(0.805) 		0.054
(0.584) 		0.142
(0.794) 		0.243
(0.839) 		0.31
(0.862) 		0.153
(0.794) 		1
(1.00)
amp 18q11 2 140 (32%) 301 0.248
(0.839) 		0.253
(0.839) 		0.893
(1.00) 		0.47
(0.922) 		0.82
(1.00) 		0.542
(0.954) 		0.915
(1.00) 		0.779
(1.00) 		0.0244
(0.487) 		0.407
(0.894) 		0.447
(0.915) 		0.888
(1.00) 		0.336
(0.869)
amp 19p13 2 47 (11%) 394 0.0654
(0.634) 		0.951
(1.00) 		0.681
(0.99) 		0.712
(0.998) 		0.78
(1.00) 		0.549
(0.955) 		1
(1.00) 		1
(1.00) 		0.819
(1.00) 		0.486
(0.925) 		0.4
(0.892) 		0.194
(0.816) 		1
(1.00)
amp 19q12 130 (29%) 311 0.536
(0.954) 		0.849
(1.00) 		0.757
(1.00) 		0.0837
(0.705) 		0.482
(0.923) 		1
(1.00) 		0.745
(1.00) 		0.159
(0.804) 		0.57
(0.962) 		0.729
(1.00) 		0.154
(0.795) 		0.0772
(0.696) 		1
(1.00)
amp 19q13 32 111 (25%) 330 0.772
(1.00) 		0.943
(1.00) 		0.245
(0.839) 		0.288
(0.844) 		0.107
(0.719) 		1
(1.00) 		0.568
(0.962) 		0.0501
(0.568) 		0.796
(1.00) 		0.438
(0.909) 		0.137
(0.788) 		0.232
(0.839) 		0.343
(0.869)
amp xq27 3 86 (20%) 355 0.337
(0.869) 		0.208
(0.826) 		0.4
(0.892) 		0.476
(0.923) 		0.443
(0.914) 		0.814
(1.00) 		0.901
(1.00) 		0.627
(0.967) 		0.17
(0.805) 		0.678
(0.99) 		0.323
(0.869) 		0.766
(1.00) 		1
(1.00)
del 1p13 2 94 (21%) 347 0.515
(0.94) 		0.935
(1.00) 		0.873
(1.00) 		0.0885
(0.705) 		0.192
(0.815) 		0.819
(1.00) 		0.277
(0.844) 		0.753
(1.00) 		0.0109
(0.353) 		0.105
(0.719) 		0.599
(0.965) 		0.427
(0.905) 		0.587
(0.965)
del 1q44 30 (7%) 411 0.298
(0.858) 		0.0975
(0.71) 		0.916
(1.00) 		0.617
(0.965) 		0.679
(0.99) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.873
(1.00) 		0.811
(1.00) 		0.104
(0.719) 		0.238
(0.839) 		1
(1.00)
del 1q44 26 (6%) 415 0.941
(1.00) 		0.763
(1.00) 		0.399
(0.892) 		0.987
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.294
(0.849) 		1
(1.00) 		0.623
(0.967) 		0.62
(0.966) 		0.385
(0.889) 		0.914
(1.00) 		1
(1.00)
del 2q32 1 64 (15%) 377 0.167
(0.805) 		0.759
(1.00) 		0.842
(1.00) 		0.933
(1.00) 		0.284
(0.844) 		0.599
(0.965) 		0.888
(1.00) 		1
(1.00) 		0.336
(0.869) 		0.799
(1.00) 		0.466
(0.922) 		0.795
(1.00) 		1
(1.00)
del 2q33 3 49 (11%) 392 0.234
(0.839) 		0.673
(0.99) 		0.831
(1.00) 		0.303
(0.862) 		0.414
(0.899) 		1
(1.00) 		0.639
(0.974) 		1
(1.00) 		0.0661
(0.634) 		0.0795
(0.702) 		0.398
(0.892) 		0.348
(0.869) 		1
(1.00)
del 2q37 2 72 (16%) 369 0.449
(0.915) 		0.657
(0.986) 		0.793
(1.00) 		0.924
(1.00) 		0.907
(1.00) 		0.2
(0.821) 		0.107
(0.719) 		1
(1.00) 		0.112
(0.729) 		0.0483
(0.553) 		0.321
(0.869) 		0.966
(1.00) 		1
(1.00)
del 3p26 1 143 (32%) 298 0.541
(0.954) 		0.227
(0.839) 		0.847
(1.00) 		0.967
(1.00) 		0.0287
(0.497) 		0.417
(0.902) 		0.204
(0.826) 		0.891
(1.00) 		0.0302
(0.5) 		0.43
(0.905) 		0.436
(0.908) 		0.433
(0.906) 		1
(1.00)
del 3p14 2 158 (36%) 283 0.131
(0.779) 		0.414
(0.899) 		0.562
(0.961) 		0.845
(1.00) 		0.162
(0.805) 		0.238
(0.839) 		0.836
(1.00) 		0.183
(0.807) 		0.0315
(0.512) 		0.00986
(0.353) 		0.831
(1.00) 		0.149
(0.794) 		1
(1.00)
del 3q26 31 47 (11%) 394 0.689
(0.99) 		0.344
(0.869) 		0.965
(1.00) 		0.233
(0.839) 		0.243
(0.839) 		0.347
(0.869) 		0.873
(1.00) 		0.533
(0.95) 		0.241
(0.839) 		0.427
(0.905) 		0.854
(1.00) 		0.612
(0.965) 		1
(1.00)
del 4p16 3 169 (38%) 272 0.889
(1.00) 		0.453
(0.915) 		0.594
(0.965) 		0.0353
(0.53) 		0.634
(0.972) 		0.083
(0.705) 		0.263
(0.839) 		0.692
(0.99) 		0.216
(0.835) 		0.46
(0.922) 		0.707
(0.996) 		0.572
(0.962) 		1
(1.00)
del 4q22 1 193 (44%) 248 0.328
(0.869) 		0.39
(0.89) 		0.616
(0.965) 		0.149
(0.794) 		0.481
(0.923) 		0.258
(0.839) 		0.549
(0.955) 		0.0681
(0.646) 		0.144
(0.794) 		0.369
(0.883) 		0.0349
(0.53) 		0.265
(0.842) 		1
(1.00)
del 4q34 3 200 (45%) 241 0.893
(1.00) 		0.131
(0.779) 		0.056
(0.589) 		0.529
(0.948) 		0.775
(1.00) 		0.0902
(0.705) 		0.69
(0.99) 		0.0381
(0.53) 		0.0095
(0.353) 		0.118
(0.742) 		0.303
(0.862) 		0.672
(0.99) 		1
(1.00)
del 6p25 3 115 (26%) 326 0.906
(1.00) 		0.15
(0.794) 		0.98
(1.00) 		0.54
(0.954) 		0.923
(1.00) 		0.131
(0.779) 		0.735
(1.00) 		0.56
(0.96) 		0.00628
(0.279) 		0.256
(0.839) 		0.485
(0.925) 		0.903
(1.00) 		1
(1.00)
del 6q14 1 89 (20%) 352 0.876
(1.00) 		0.32
(0.869) 		0.841
(1.00) 		0.185
(0.809) 		0.871
(1.00) 		0.48
(0.923) 		0.173
(0.805) 		0.108
(0.719) 		0.679
(0.99) 		0.49
(0.925) 		0.446
(0.915) 		0.494
(0.925) 		1
(1.00)
del 6q24 3 78 (18%) 363 0.364
(0.883) 		0.372
(0.883) 		0.681
(0.99) 		0.0515
(0.573) 		0.718
(1.00) 		0.0419
(0.532) 		0.0902
(0.705) 		0.609
(0.965) 		0.0755
(0.688) 		0.963
(1.00) 		0.11
(0.726) 		0.0819
(0.705) 		1
(1.00)
del 6q26 102 (23%) 339 0.322
(0.869) 		0.449
(0.915) 		0.276
(0.844) 		0.0468
(0.553) 		0.277
(0.844) 		0.652
(0.986) 		0.346
(0.869) 		0.758
(1.00) 		0.0318
(0.512) 		0.373
(0.883) 		0.0112
(0.353) 		0.67
(0.99) 		1
(1.00)
del 7q31 1 71 (16%) 370 0.452
(0.915) 		0.158
(0.804) 		0.0922
(0.705) 		0.103
(0.719) 		0.0392
(0.53) 		0.199
(0.819) 		0.104
(0.719) 		0.862
(1.00) 		0.307
(0.862) 		0.408
(0.894) 		0.337
(0.869) 		0.0887
(0.705) 		1
(1.00)
del 7q36 3 98 (22%) 343 0.857
(1.00) 		0.98
(1.00) 		0.0915
(0.705) 		0.373
(0.883) 		0.0663
(0.634) 		0.824
(1.00) 		0.635
(0.972) 		0.283
(0.844) 		0.405
(0.892) 		0.229
(0.839) 		0.0117
(0.353) 		0.93
(1.00) 		1
(1.00)
del 9p23 195 (44%) 246 0.98
(1.00) 		0.0827
(0.705) 		0.466
(0.922) 		0.287
(0.844) 		0.344
(0.869) 		0.447
(0.915) 		0.617
(0.965) 		0.603
(0.965) 		0.0634
(0.632) 		0.75
(1.00) 		0.0297
(0.497) 		0.353
(0.874) 		1
(1.00)
del 9p21 3 193 (44%) 248 0.957
(1.00) 		0.0395
(0.53) 		0.557
(0.958) 		0.256
(0.839) 		0.558
(0.958) 		0.452
(0.915) 		0.69
(0.99) 		0.365
(0.883) 		0.0112
(0.353) 		0.258
(0.839) 		0.401
(0.892) 		0.342
(0.869) 		1
(1.00)
del 9q21 11 114 (26%) 327 0.545
(0.955) 		0.778
(1.00) 		0.713
(0.998) 		0.381
(0.889) 		0.86
(1.00) 		0.284
(0.844) 		0.308
(0.862) 		1
(1.00) 		0.206
(0.826) 		0.835
(1.00) 		0.318
(0.869) 		0.218
(0.838) 		1
(1.00)
del 10p12 31 67 (15%) 374 0.205
(0.826) 		0.274
(0.844) 		0.246
(0.839) 		0.886
(1.00) 		0.0272
(0.497) 		1
(1.00) 		0.678
(0.99) 		0.373
(0.883) 		0.259
(0.839) 		0.884
(1.00) 		0.00876
(0.338) 		0.416
(0.901) 		0.549
(0.955)
del 10q22 3 79 (18%) 362 0.119
(0.743) 		0.00812
(0.324) 		0.944
(1.00) 		0.237
(0.839) 		0.367
(0.883) 		0.804
(1.00) 		0.606
(0.965) 		1
(1.00) 		0.036
(0.53) 		0.882
(1.00) 		0.0119
(0.353) 		0.163
(0.805) 		0.198
(0.819)
del 11p15 5 97 (22%) 344 0.851
(1.00) 		0.106
(0.719) 		0.426
(0.905) 		0.0164
(0.388) 		0.598
(0.965) 		0.823
(1.00) 		0.403
(0.892) 		0.0832
(0.705) 		0.0221
(0.467) 		0.223
(0.839) 		0.111
(0.726) 		0.579
(0.965) 		1
(1.00)
del 11q23 2 99 (22%) 342 0.0436
(0.543) 		0.374
(0.883) 		0.684
(0.99) 		0.665
(0.989) 		0.293
(0.849) 		0.247
(0.839) 		0.475
(0.923) 		0.755
(1.00) 		0.48
(0.923) 		0.285
(0.844) 		0.381
(0.889) 		1
(1.00) 		0.293
(0.849)
del 12q12 59 (13%) 382 0.47
(0.922) 		0.616
(0.965) 		0.975
(1.00) 		0.688
(0.99) 		0.926
(1.00) 		0.782
(1.00) 		0.563
(0.961) 		0.14
(0.792) 		0.558
(0.958) 		0.872
(1.00) 		0.52
(0.942) 		0.816
(1.00) 		0.479
(0.923)
del 13q12 11 63 (14%) 378 0.453
(0.915) 		0.268
(0.844) 		0.96
(1.00) 		0.178
(0.806) 		0.636
(0.972) 		0.784
(1.00) 		0.0157
(0.382) 		0.715
(1.00) 		0.756
(1.00) 		0.654
(0.986) 		0.548
(0.955) 		0.962
(1.00) 		0.532
(0.95)
del 14q23 3 136 (31%) 305 0.866
(1.00) 		0.938
(1.00) 		0.241
(0.839) 		0.569
(0.962) 		0.107
(0.719) 		0.04
(0.53) 		0.334
(0.869) 		0.403
(0.892) 		0.0286
(0.497) 		0.115
(0.737) 		0.812
(1.00) 		0.858
(1.00) 		1
(1.00)
del 15q11 2 120 (27%) 321 0.379
(0.888) 		0.215
(0.835) 		0.516
(0.94) 		0.0793
(0.702) 		0.741
(1.00) 		0.831
(1.00) 		0.911
(1.00) 		0.0295
(0.497) 		0.0734
(0.683) 		0.341
(0.869) 		0.835
(1.00) 		0.607
(0.965) 		0.33
(0.869)
del 17p13 3 176 (40%) 265 0.624
(0.967) 		0.881
(1.00) 		0.96
(1.00) 		0.263
(0.839) 		0.96
(1.00) 		0.563
(0.961) 		0.157
(0.804) 		0.432
(0.906) 		0.00691
(0.296) 		0.0915
(0.705) 		0.428
(0.905) 		0.739
(1.00) 		1
(1.00)
del 20p12 1 39 (9%) 402 0.147
(0.794) 		0.828
(1.00) 		0.655
(0.986) 		0.781
(1.00) 		0.93
(1.00) 		0.734
(1.00) 		0.488
(0.925) 		0.0449
(0.547) 		0.484
(0.925) 		0.626
(0.967) 		0.66
(0.986) 		0.78
(1.00) 		1
(1.00)
del 21q11 2 183 (41%) 258 0.753
(1.00) 		0.0136
(0.382) 		0.921
(1.00) 		0.637
(0.972) 		0.238
(0.839) 		0.443
(0.914) 		0.42
(0.904) 		0.239
(0.839) 		0.0528
(0.576) 		0.283
(0.844) 		0.946
(1.00) 		0.66
(0.986) 		1
(1.00)
del 21q22 3 193 (44%) 248 0.766
(1.00) 		0.0605
(0.614) 		0.907
(1.00) 		0.272
(0.844) 		0.263
(0.839) 		0.255
(0.839) 		0.92
(1.00) 		0.193
(0.815) 		0.0554
(0.588) 		0.373
(0.883) 		0.388
(0.89) 		0.609
(0.965) 		1
(1.00)
del 22q13 31 161 (37%) 280 0.572
(0.962) 		0.624
(0.967) 		0.514
(0.94) 		0.509
(0.936) 		0.138
(0.792) 		0.121
(0.745) 		0.258
(0.839) 		0.182
(0.806) 		0.0385
(0.53) 		0.598
(0.965) 		0.0258
(0.49) 		0.541
(0.954) 		1
(1.00)
del xp22 2 85 (19%) 356 0.855
(1.00) 		0.722
(1.00) 		0.167
(0.805) 		0.779
(1.00) 		0.554
(0.958) 		1
(1.00) 		0.208
(0.826) 		0.75
(1.00) 		0.137
(0.788) 		0.605
(0.965) 		0.306
(0.862) 		0.343
(0.869) 		0.261
(0.839)
del xp21 1 74 (17%) 367 0.772
(1.00) 		0.596
(0.965) 		0.459
(0.922) 		0.862
(1.00) 		0.549
(0.955) 		0.801
(1.00) 		0.288
(0.844) 		0.498
(0.926) 		0.268
(0.844) 		0.349
(0.869) 		0.197
(0.819) 		0.405
(0.892) 		0.174
(0.805)
del xq21 33 56 (13%) 385 0.42
(0.904) 		0.98
(1.00) 		0.81
(1.00) 		0.87
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.237
(0.839) 		0.055
(0.588) 		0.807
(1.00) 		0.436
(0.908) 		0.949
(1.00) 		0.906
(1.00) 		0.46
(0.922)
'amp_1p36.22' versus 'GENDER'

P value = 0.00323 (Fisher's exact test), Q value = 0.21

Table S1.  Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 158 283
AMP PEAK 1(1P36.22) MUTATED 13 53
AMP PEAK 1(1P36.22) WILD-TYPE 145 230

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

'amp_1q42.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00192 (Fisher's exact test), Q value = 0.16

Table S2.  Gene #3: 'amp_1q42.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 3(1Q42.3) MUTATED 12 52 29 40 5 7 3
AMP PEAK 3(1Q42.3) WILD-TYPE 60 110 54 39 8 14 5

Figure S2.  Get High-res Image Gene #3: 'amp_1q42.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00395 (Fisher's exact test), Q value = 0.22

Table S3.  Gene #5: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 23 93 196 119
AMP PEAK 5(5P15.33) MUTATED 2 30 70 25
AMP PEAK 5(5P15.33) WILD-TYPE 21 63 126 94

Figure S3.  Get High-res Image Gene #5: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6p21.1' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S4.  Gene #7: 'amp_6p21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 7(6P21.1) MUTATED 5 52 30 30 2 3 2
AMP PEAK 7(6P21.1) WILD-TYPE 67 110 53 49 11 18 6

Figure S4.  Get High-res Image Gene #7: 'amp_6p21.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_6q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00044 (Fisher's exact test), Q value = 0.057

Table S5.  Gene #8: 'amp_6q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 8(6Q12) MUTATED 4 38 27 15 2 1 1
AMP PEAK 8(6Q12) WILD-TYPE 68 124 56 64 11 20 7

Figure S5.  Get High-res Image Gene #8: 'amp_6q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_7p22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00477 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #10: 'amp_7p22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 10(7P22.1) MUTATED 25 81 53 46 9 8 5
AMP PEAK 10(7P22.1) WILD-TYPE 47 81 30 33 4 13 3

Figure S6.  Get High-res Image Gene #10: 'amp_7p22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S7.  Gene #30: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 30(17Q12) MUTATED 9 47 35 38 6 6 4
AMP PEAK 30(17Q12) WILD-TYPE 63 115 48 41 7 15 4

Figure S7.  Get High-res Image Gene #30: 'amp_17q12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'RESIDUAL_TUMOR'

P value = 0.00011 (Fisher's exact test), Q value = 0.021

Table S8.  Gene #30: 'amp_17q12' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 349 18 19 25
AMP PEAK 30(17Q12) MUTATED 121 1 12 3
AMP PEAK 30(17Q12) WILD-TYPE 228 17 7 22

Figure S8.  Get High-res Image Gene #30: 'amp_17q12' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S9.  Gene #35: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
AMP PEAK 35(20Q13.2) MUTATED 32 100 65 65 9 13 6
AMP PEAK 35(20Q13.2) WILD-TYPE 40 62 18 14 4 8 2

Figure S9.  Get High-res Image Gene #35: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00267 (Fisher's exact test), Q value = 0.21

Table S10.  Gene #37: 'del_1p36.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 1(1P36.11) MUTATED 12 41 31 36 5 7 2
DEL PEAK 1(1P36.11) WILD-TYPE 60 121 52 43 8 14 6

Figure S10.  Get High-res Image Gene #37: 'del_1p36.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S11.  Gene #50: 'del_5q12.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 14(5Q12.1) MUTATED 12 60 34 45 4 10 4
DEL PEAK 14(5Q12.1) WILD-TYPE 60 102 49 34 9 11 4

Figure S11.  Get High-res Image Gene #50: 'del_5q12.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_5q23.2' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S12.  Gene #51: 'del_5q23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 15(5Q23.2) MUTATED 9 55 33 46 4 7 3
DEL PEAK 15(5Q23.2) WILD-TYPE 63 107 50 33 9 14 5

Figure S12.  Get High-res Image Gene #51: 'del_5q23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00189 (Wilcoxon-test), Q value = 0.16

Table S13.  Gene #58: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 391 5.6 (8.4)
DEL PEAK 22(8P23.3) MUTATED 111 7.5 (10.3)
DEL PEAK 22(8P23.3) WILD-TYPE 280 4.9 (7.4)

Figure S13.  Get High-res Image Gene #58: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.00526 (Wilcoxon-test), Q value = 0.24

Table S14.  Gene #64: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 432 65.8 (10.8)
DEL PEAK 28(10Q23.31) MUTATED 115 68.1 (9.9)
DEL PEAK 28(10Q23.31) WILD-TYPE 317 64.9 (10.9)

Figure S14.  Get High-res Image Gene #64: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00062 (Fisher's exact test), Q value = 0.065

Table S15.  Gene #67: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 31(12P13.1) MUTATED 4 32 15 20 2 0 4
DEL PEAK 31(12P13.1) WILD-TYPE 68 130 68 59 11 21 4

Figure S15.  Get High-res Image Gene #67: 'del_12p13.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q32.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00309 (Fisher's exact test), Q value = 0.21

Table S16.  Gene #71: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 389 30
DEL PEAK 35(14Q32.32) MUTATED 121 2
DEL PEAK 35(14Q32.32) WILD-TYPE 268 28

Figure S16.  Get High-res Image Gene #71: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q15.1' versus 'RADIATION_THERAPY'

P value = 0.00343 (Fisher's exact test), Q value = 0.21

Table S17.  Gene #73: 'del_15q15.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 314 74
DEL PEAK 37(15Q15.1) MUTATED 75 31
DEL PEAK 37(15Q15.1) WILD-TYPE 239 43

Figure S17.  Get High-res Image Gene #73: 'del_15q15.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_16p13.3' versus 'RACE'

P value = 0.00494 (Fisher's exact test), Q value = 0.24

Table S18.  Gene #74: 'del_16p13.3' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 88 12 1 278
DEL PEAK 38(16P13.3) MUTATED 26 6 0 49
DEL PEAK 38(16P13.3) WILD-TYPE 62 6 1 229

Figure S18.  Get High-res Image Gene #74: 'del_16p13.3' versus Clinical Feature #12: 'RACE'

'del_16q23.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00358 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #75: 'del_16q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 389 30
DEL PEAK 39(16Q23.1) MUTATED 170 5
DEL PEAK 39(16Q23.1) WILD-TYPE 219 25

Figure S19.  Get High-res Image Gene #75: 'del_16q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00038 (Fisher's exact test), Q value = 0.055

Table S20.  Gene #77: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 41(17P12) MUTATED 16 58 43 42 8 9 4
DEL PEAK 41(17P12) WILD-TYPE 56 104 40 37 5 12 4

Figure S20.  Get High-res Image Gene #77: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_17q24.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00499 (Wilcoxon-test), Q value = 0.24

Table S21.  Gene #78: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 391 5.6 (8.4)
DEL PEAK 42(17Q24.3) MUTATED 63 9.7 (13.3)
DEL PEAK 42(17Q24.3) WILD-TYPE 328 4.9 (6.9)

Figure S21.  Get High-res Image Gene #78: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_18q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.025

Table S22.  Gene #79: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 23 93 196 119
DEL PEAK 43(18Q12.2) MUTATED 6 38 101 33
DEL PEAK 43(18Q12.2) WILD-TYPE 17 55 95 86

Figure S22.  Get High-res Image Gene #79: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q21.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00186 (Fisher's exact test), Q value = 0.16

Table S23.  Gene #80: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 23 93 196 119
DEL PEAK 44(18Q21.2) MUTATED 7 43 109 42
DEL PEAK 44(18Q21.2) WILD-TYPE 16 50 87 77

Figure S23.  Get High-res Image Gene #80: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00314 (Fisher's exact test), Q value = 0.21

Table S24.  Gene #81: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 45(19P13.3) MUTATED 16 55 42 34 4 5 5
DEL PEAK 45(19P13.3) WILD-TYPE 56 107 41 45 9 16 3

Figure S24.  Get High-res Image Gene #81: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_19q13.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00059 (Fisher's exact test), Q value = 0.065

Table S25.  Gene #82: 'del_19q13.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
DEL PEAK 46(19Q13.11) MUTATED 5 23 17 26 1 1 2
DEL PEAK 46(19Q13.11) WILD-TYPE 67 139 66 53 12 20 6

Figure S25.  Get High-res Image Gene #82: 'del_19q13.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/19782340/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/19775542/STAD-TP.merged_data.txt

  • Number of patients = 441

  • Number of significantly focal cnvs = 89

  • Number of selected clinical features = 13

  • 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

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.

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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