Correlation between copy number variation genes (focal events) and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18K7862
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18K7862
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 436 patients, 20 significant findings detected with Q value < 0.25.

  • amp_1q42.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_6p21.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_6q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 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 'HISTOLOGICAL_TYPE'.

  • del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_14q32.32 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_16p13.3 cnv correlated to 'RACE'.

  • del_16q23.1 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_17p12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 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, 20 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		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 145 (33%) 291 0.141
(0.739) 		0.269
(0.85) 		0.509
(0.937) 		0.693
(0.978) 		0.546
(0.948) 		0.041
(0.552) 		0.0452
(0.565) 		3e-05
(0.0116) 		1
(1.00) 		9e-05
(0.0174) 		0.438
(0.894) 		0.0104
(0.326) 		0.319
(0.85)
amp 1q42 3 149 (34%) 287 0.425
(0.892) 		0.524
(0.947) 		0.659
(0.971) 		0.464
(0.905) 		0.483
(0.922) 		0.695
(0.978) 		0.753
(1.00) 		0.00326
(0.199) 		0.416
(0.889) 		0.742
(1.00) 		0.431
(0.893) 		0.112
(0.696) 		0.303
(0.85)
amp 6p21 1 121 (28%) 315 0.684
(0.978) 		0.0134
(0.352) 		0.555
(0.951) 		0.19
(0.814) 		0.544
(0.948) 		0.208
(0.823) 		0.437
(0.894) 		1e-05
(0.00578) 		0.354
(0.852) 		0.528
(0.948) 		0.715
(0.99) 		0.054
(0.601) 		1
(1.00)
amp 6q12 86 (20%) 350 0.33
(0.85) 		0.911
(1.00) 		0.398
(0.874) 		0.646
(0.971) 		0.773
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.0005
(0.0578) 		0.338
(0.85) 		0.331
(0.85) 		0.568
(0.951) 		0.191
(0.814) 		1
(1.00)
amp 20q13 2 290 (67%) 146 0.434
(0.893) 		0.252
(0.85) 		0.449
(0.894) 		0.27
(0.85) 		0.0673
(0.639) 		0.549
(0.951) 		0.0115
(0.326) 		6e-05
(0.0139) 		1
(1.00) 		0.435
(0.894) 		0.447
(0.894) 		0.452
(0.896) 		1
(1.00)
del 1p36 11 133 (31%) 303 0.262
(0.85) 		0.774
(1.00) 		0.614
(0.971) 		0.161
(0.765) 		0.947
(1.00) 		1
(1.00) 		0.518
(0.946) 		0.00217
(0.16) 		0.375
(0.863) 		0.108
(0.687) 		0.381
(0.87) 		0.393
(0.87) 		0.578
(0.953)
del 5q12 1 166 (38%) 270 0.537
(0.948) 		0.342
(0.85) 		0.334
(0.85) 		0.659
(0.971) 		0.137
(0.739) 		0.697
(0.978) 		0.838
(1.00) 		6e-05
(0.0139) 		0.678
(0.978) 		0.17
(0.773) 		0.0735
(0.649) 		0.717
(0.99) 		1
(1.00)
del 5q23 2 156 (36%) 280 0.913
(1.00) 		0.507
(0.937) 		0.317
(0.85) 		0.426
(0.892) 		0.861
(1.00) 		0.326
(0.85) 		0.678
(0.978) 		1e-05
(0.00578) 		1
(1.00) 		0.186
(0.806) 		0.924
(1.00) 		0.52
(0.946) 		1
(1.00)
del 8p23 3 123 (28%) 313 0.574
(0.952) 		0.172
(0.773) 		0.149
(0.758) 		0.225
(0.85) 		0.0279
(0.478) 		0.402
(0.88) 		0.0203
(0.454) 		0.0126
(0.34) 		0.676
(0.978) 		0.151
(0.758) 		0.000934
(0.0983) 		0.179
(0.785) 		1
(1.00)
del 10q23 31 114 (26%) 322 0.0633
(0.626) 		0.00662
(0.265) 		0.99
(1.00) 		0.133
(0.739) 		0.5
(0.931) 		0.832
(1.00) 		0.821
(1.00) 		0.00221
(0.16) 		1
(1.00) 		0.903
(1.00) 		0.0612
(0.625) 		0.152
(0.76) 		1
(1.00)
del 12p13 1 74 (17%) 362 0.048
(0.565) 		0.424
(0.892) 		0.547
(0.949) 		0.0587
(0.612) 		0.989
(1.00) 		0.614
(0.971) 		0.791
(1.00) 		0.0002
(0.0289) 		0.064
(0.627) 		0.788
(1.00) 		0.135
(0.739) 		0.657
(0.971) 		0.483
(0.922)
del 14q32 32 131 (30%) 305 0.603
(0.968) 		0.959
(1.00) 		0.176
(0.781) 		0.575
(0.952) 		0.696
(0.978) 		0.0031
(0.199) 		0.664
(0.974) 		0.448
(0.894) 		1
(1.00) 		0.319
(0.85) 		0.305
(0.85) 		0.981
(1.00) 		0.321
(0.85)
del 16p13 3 92 (21%) 344 0.897
(1.00) 		0.143
(0.74) 		0.106
(0.687) 		0.293
(0.85) 		0.39
(0.87) 		0.357
(0.852) 		0.465
(0.905) 		0.0684
(0.64) 		0.611
(0.971) 		0.74
(1.00) 		0.707
(0.982) 		0.00312
(0.199) 		0.585
(0.956)
del 16q23 1 180 (41%) 256 0.987
(1.00) 		0.539
(0.948) 		0.0471
(0.565) 		0.833
(1.00) 		0.484
(0.922) 		0.00359
(0.207) 		0.312
(0.85) 		0.146
(0.75) 		0.086
(0.673) 		0.283
(0.85) 		0.539
(0.948) 		0.986
(1.00) 		1
(1.00)
del 17p12 177 (41%) 259 0.508
(0.937) 		0.807
(1.00) 		0.879
(1.00) 		0.37
(0.863) 		0.528
(0.948) 		0.334
(0.85) 		0.105
(0.687) 		0.00029
(0.0373) 		0.229
(0.85) 		0.154
(0.76) 		0.432
(0.893) 		0.751
(1.00) 		1
(1.00)
del 18q12 2 180 (41%) 256 0.733
(1.00) 		0.3
(0.85) 		0.569
(0.951) 		0.00013
(0.0215) 		0.596
(0.963) 		0.702
(0.978) 		0.312
(0.85) 		0.158
(0.765) 		1
(1.00) 		0.483
(0.922) 		0.0847
(0.666) 		0.304
(0.85) 		1
(1.00)
del 18q21 2 203 (47%) 233 0.975
(1.00) 		0.359
(0.853) 		0.864
(1.00) 		0.00174
(0.144) 		0.655
(0.971) 		0.85
(1.00) 		0.274
(0.85) 		0.11
(0.696) 		0.69
(0.978) 		0.463
(0.905) 		0.0573
(0.608) 		0.267
(0.85) 		1
(1.00)
del 19p13 3 158 (36%) 278 0.0776
(0.664) 		0.257
(0.85) 		0.976
(1.00) 		0.275
(0.85) 		0.91
(1.00) 		0.845
(1.00) 		0.0622
(0.625) 		0.0014
(0.125) 		0.0253
(0.478) 		0.287
(0.85) 		0.194
(0.814) 		0.0701
(0.64) 		1
(1.00)
del 19q13 11 75 (17%) 361 0.539
(0.948) 		0.16
(0.765) 		0.969
(1.00) 		0.871
(1.00) 		0.403
(0.88) 		0.327
(0.85) 		0.6
(0.965) 		0.00128
(0.123) 		1
(1.00) 		0.385
(0.87) 		0.141
(0.739) 		0.393
(0.87) 		0.506
(0.937)
amp 1p36 22 64 (15%) 372 0.986
(1.00) 		0.641
(0.971) 		0.568
(0.951) 		0.161
(0.765) 		0.756
(1.00) 		0.285
(0.85) 		0.00458
(0.252) 		0.882
(1.00) 		0.599
(0.965) 		1
(1.00) 		0.11
(0.696) 		0.266
(0.85) 		1
(1.00)
amp 1q21 3 158 (36%) 278 0.866
(1.00) 		0.838
(1.00) 		0.935
(1.00) 		0.362
(0.854) 		0.486
(0.923) 		0.845
(1.00) 		1
(1.00) 		0.14
(0.739) 		0.0253
(0.478) 		0.2
(0.823) 		0.292
(0.85) 		0.332
(0.85) 		0.301
(0.85)
amp 3q26 2 163 (37%) 273 0.883
(1.00) 		0.653
(0.971) 		0.375
(0.863) 		0.169
(0.773) 		0.553
(0.951) 		0.845
(1.00) 		0.838
(1.00) 		0.463
(0.905) 		1
(1.00) 		0.944
(1.00) 		0.118
(0.698) 		0.18
(0.787) 		0.125
(0.724)
amp 5p15 33 128 (29%) 308 0.535
(0.948) 		0.0283
(0.478) 		0.826
(1.00) 		0.006
(0.265) 		0.637
(0.971) 		1
(1.00) 		0.382
(0.87) 		0.0195
(0.454) 		1
(1.00) 		0.636
(0.971) 		0.0478
(0.565) 		0.201
(0.823) 		1
(1.00)
amp 5p13 1 124 (28%) 312 0.609
(0.971) 		0.0294
(0.479) 		0.916
(1.00) 		0.284
(0.85) 		0.569
(0.951) 		0.532
(0.948) 		0.912
(1.00) 		0.235
(0.85) 		0.679
(0.978) 		0.451
(0.896) 		0.229
(0.85) 		0.573
(0.952) 		1
(1.00)
amp 6q21 81 (19%) 355 0.117
(0.698) 		0.694
(0.978) 		0.3
(0.85) 		0.206
(0.823) 		0.344
(0.85) 		0.233
(0.85) 		0.306
(0.85) 		0.042
(0.553) 		0.31
(0.85) 		0.297
(0.85) 		0.112
(0.696) 		0.0929
(0.676) 		0.535
(0.948)
amp 7p22 1 228 (52%) 208 0.786
(1.00) 		0.194
(0.814) 		0.825
(1.00) 		0.668
(0.978) 		0.271
(0.85) 		0.449
(0.894) 		0.0366
(0.55) 		0.00691
(0.265) 		1
(1.00) 		0.915
(1.00) 		0.21
(0.829) 		0.431
(0.893) 		0.623
(0.971)
amp 7p11 2 213 (49%) 223 0.125
(0.724) 		0.0414
(0.552) 		0.612
(0.971) 		0.491
(0.923) 		0.662
(0.972) 		0.191
(0.814) 		0.0732
(0.649) 		0.0202
(0.454) 		0.686
(0.978) 		0.856
(1.00) 		0.179
(0.787) 		0.0806
(0.664) 		0.627
(0.971)
amp 7q21 2 203 (47%) 233 0.568
(0.951) 		0.189
(0.811) 		0.954
(1.00) 		0.687
(0.978) 		0.091
(0.676) 		0.345
(0.85) 		0.022
(0.454) 		0.0627
(0.625) 		0.69
(0.978) 		0.287
(0.85) 		0.0948
(0.682) 		0.0428
(0.556) 		1
(1.00)
amp 7q22 1 201 (46%) 235 0.83
(1.00) 		0.207
(0.823) 		0.721
(0.991) 		0.809
(1.00) 		0.0108
(0.326) 		0.348
(0.85) 		0.0214
(0.454) 		0.162
(0.765) 		0.691
(0.978) 		0.0927
(0.676) 		0.276
(0.85) 		0.0335
(0.517) 		0.325
(0.85)
amp 8p23 1 175 (40%) 261 0.223
(0.85) 		0.07
(0.64) 		0.564
(0.951) 		0.228
(0.85) 		0.876
(1.00) 		0.446
(0.894) 		0.0113
(0.326) 		0.768
(1.00) 		0.224
(0.85) 		0.339
(0.85) 		0.5
(0.931) 		0.985
(1.00) 		0.305
(0.85)
amp 8q24 21 305 (70%) 131 0.686
(0.978) 		0.0262
(0.478) 		0.566
(0.951) 		0.0274
(0.478) 		0.57
(0.951) 		0.686
(0.978) 		0.914
(1.00) 		0.349
(0.85) 		0.673
(0.978) 		0.37
(0.863) 		0.717
(0.99) 		0.0552
(0.603) 		1
(1.00)
amp 9p24 1 64 (15%) 372 0.759
(1.00) 		0.942
(1.00) 		0.557
(0.951) 		0.138
(0.739) 		0.29
(0.85) 		1
(1.00) 		1
(1.00) 		0.356
(0.852) 		0.0435
(0.56) 		0.696
(0.978) 		0.465
(0.905) 		0.241
(0.85) 		0.106
(0.687)
amp 9p13 2 89 (20%) 347 0.437
(0.894) 		0.891
(1.00) 		0.0491
(0.565) 		0.252
(0.85) 		0.564
(0.951) 		1
(1.00) 		0.388
(0.87) 		0.0225
(0.457) 		0.103
(0.687) 		0.609
(0.971) 		0.565
(0.951) 		1
(1.00) 		0.164
(0.766)
amp 9q34 3 121 (28%) 315 0.183
(0.798) 		0.859
(1.00) 		0.377
(0.864) 		0.648
(0.971) 		0.465
(0.905) 		0.834
(1.00) 		0.739
(1.00) 		0.133
(0.739) 		0.354
(0.852) 		0.35
(0.85) 		0.344
(0.85) 		0.685
(0.978) 		0.0585
(0.612)
amp 10p11 22 118 (27%) 318 0.689
(0.978) 		0.388
(0.87) 		0.083
(0.666) 		0.0995
(0.687) 		0.916
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.214
(0.84) 		0.351
(0.85) 		0.699
(0.978) 		0.635
(0.971) 		0.0107
(0.326) 		1
(1.00)
amp 10q22 2 88 (20%) 348 0.778
(1.00) 		0.336
(0.85) 		0.0914
(0.676) 		0.601
(0.966) 		0.232
(0.85) 		0.165
(0.77) 		1
(1.00) 		0.642
(0.971) 		0.349
(0.85) 		0.357
(0.852) 		0.33
(0.85) 		0.272
(0.85) 		0.587
(0.956)
amp 10q26 13 88 (20%) 348 0.553
(0.951) 		0.719
(0.991) 		0.308
(0.85) 		0.322
(0.85) 		0.426
(0.892) 		0.235
(0.85) 		0.805
(1.00) 		0.257
(0.85) 		0.349
(0.85) 		0.802
(1.00) 		0.7
(0.978) 		0.172
(0.773) 		1
(1.00)
amp 11p13 87 (20%) 349 0.151
(0.758) 		0.883
(1.00) 		0.245
(0.85) 		0.029
(0.479) 		0.208
(0.823) 		0.631
(0.971) 		0.212
(0.836) 		0.503
(0.934) 		0.344
(0.85) 		0.25
(0.85) 		0.0558
(0.604) 		0.269
(0.85) 		0.57
(0.951)
amp 11p11 2 91 (21%) 345 0.392
(0.87) 		0.867
(1.00) 		0.116
(0.698) 		0.518
(0.946) 		0.197
(0.819) 		1
(1.00) 		0.391
(0.87) 		0.215
(0.84) 		0.609
(0.971) 		0.309
(0.85) 		0.117
(0.698) 		0.315
(0.85) 		0.563
(0.951)
amp 11q13 3 115 (26%) 321 0.992
(1.00) 		0.163
(0.765) 		0.867
(1.00) 		0.509
(0.937) 		0.0476
(0.565) 		0.283
(0.85) 		0.573
(0.952) 		0.63
(0.971) 		0.657
(0.971) 		0.74
(1.00) 		0.134
(0.739) 		0.116
(0.698) 		1
(1.00)
amp 12p12 1 127 (29%) 309 0.319
(0.85) 		0.887
(1.00) 		0.649
(0.971) 		0.026
(0.478) 		0.282
(0.85) 		0.837
(1.00) 		1
(1.00) 		0.24
(0.85) 		1
(1.00) 		0.489
(0.923) 		0.467
(0.906) 		0.861
(1.00) 		0.589
(0.958)
amp 12q15 108 (25%) 328 0.0703
(0.64) 		0.147
(0.752) 		0.93
(1.00) 		0.917
(1.00) 		0.351
(0.85) 		0.828
(1.00) 		0.491
(0.923) 		0.139
(0.739) 		0.64
(0.971) 		0.553
(0.951) 		0.979
(1.00) 		0.323
(0.85) 		0.265
(0.85)
amp 13q12 3 168 (39%) 268 0.349
(0.85) 		0.485
(0.922) 		0.526
(0.948) 		0.676
(0.978) 		0.77
(1.00) 		1
(1.00) 		0.357
(0.852) 		0.156
(0.761) 		0.68
(0.978) 		0.694
(0.978) 		0.203
(0.823) 		0.155
(0.76) 		1
(1.00)
amp 13q22 1 179 (41%) 257 0.255
(0.85) 		0.792
(1.00) 		0.491
(0.923) 		0.286
(0.85) 		0.303
(0.85) 		0.851
(1.00) 		0.0333
(0.517) 		0.00734
(0.265) 		0.408
(0.883) 		0.519
(0.946) 		0.359
(0.853) 		0.494
(0.926) 		1
(1.00)
amp 15q26 1 111 (25%) 325 0.856
(1.00) 		0.783
(1.00) 		0.294
(0.85) 		0.558
(0.951) 		0.137
(0.739) 		0.286
(0.85) 		0.171
(0.773) 		0.118
(0.698) 		0.647
(0.971) 		0.24
(0.85) 		0.31
(0.85) 		0.107
(0.687) 		1
(1.00)
amp 18q11 2 137 (31%) 299 0.0923
(0.676) 		0.252
(0.85) 		0.792
(1.00) 		0.518
(0.946) 		0.742
(1.00) 		0.541
(0.948) 		0.83
(1.00) 		0.0285
(0.478) 		0.0809
(0.664) 		0.388
(0.87) 		0.371
(0.863) 		0.867
(1.00) 		0.598
(0.965)
amp 19p13 2 46 (11%) 390 0.0889
(0.676) 		0.924
(1.00) 		0.594
(0.963) 		0.574
(0.952) 		0.68
(0.978) 		0.542
(0.948) 		1
(1.00) 		0.915
(1.00) 		1
(1.00) 		0.458
(0.902) 		0.383
(0.87) 		0.193
(0.814) 		1
(1.00)
amp 19q12 129 (30%) 307 0.705
(0.981) 		0.751
(1.00) 		0.795
(1.00) 		0.0816
(0.664) 		0.529
(0.948) 		1
(1.00) 		0.744
(1.00) 		0.659
(0.971) 		0.0659
(0.635) 		0.746
(1.00) 		0.161
(0.765) 		0.0611
(0.625) 		1
(1.00)
amp 19q13 32 109 (25%) 327 0.948
(1.00) 		0.931
(1.00) 		0.229
(0.85) 		0.253
(0.85) 		0.149
(0.758) 		1
(1.00) 		0.646
(0.971) 		0.829
(1.00) 		0.0365
(0.55) 		0.433
(0.893) 		0.135
(0.739) 		0.173
(0.773) 		0.576
(0.952)
amp xq27 3 83 (19%) 353 0.419
(0.889) 		0.315
(0.85) 		0.316
(0.85) 		0.659
(0.971) 		0.523
(0.946) 		0.814
(1.00) 		1
(1.00) 		0.103
(0.687) 		1
(1.00) 		0.659
(0.971) 		0.28
(0.85) 		0.614
(0.971) 		0.563
(0.951)
del 1p13 2 94 (22%) 342 0.539
(0.948) 		0.89
(1.00) 		0.758
(1.00) 		0.104
(0.687) 		0.173
(0.773) 		0.82
(1.00) 		0.229
(0.85) 		0.0216
(0.454) 		1
(1.00) 		0.107
(0.687) 		0.615
(0.971) 		0.431
(0.893) 		0.587
(0.956)
del 1q44 30 (7%) 406 0.361
(0.854) 		0.0928
(0.676) 		0.832
(1.00) 		0.629
(0.971) 		0.698
(0.978) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.811
(1.00) 		0.107
(0.687) 		0.275
(0.85) 		1
(1.00)
del 1q44 26 (6%) 410 0.903
(1.00) 		0.781
(1.00) 		0.366
(0.858) 		0.988
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.297
(0.85) 		0.634
(0.971) 		1
(1.00) 		0.595
(0.963) 		0.391
(0.87) 		0.91
(1.00) 		1
(1.00)
del 2q32 1 62 (14%) 374 0.0621
(0.625) 		0.712
(0.987) 		0.752
(1.00) 		0.886
(1.00) 		0.225
(0.85) 		0.785
(1.00) 		1
(1.00) 		0.298
(0.85) 		1
(1.00) 		0.775
(1.00) 		0.422
(0.892) 		0.78
(1.00) 		1
(1.00)
del 2q33 3 49 (11%) 387 0.141
(0.739) 		0.701
(0.978) 		0.864
(1.00) 		0.332
(0.85) 		0.457
(0.902) 		1
(1.00) 		0.753
(1.00) 		0.0707
(0.64) 		0.138
(0.739) 		0.0797
(0.664) 		0.406
(0.882) 		0.335
(0.85) 		1
(1.00)
del 2q37 2 72 (17%) 364 0.285
(0.85) 		0.684
(0.978) 		0.808
(1.00) 		0.925
(1.00) 		0.931
(1.00) 		0.201
(0.823) 		0.14
(0.739) 		0.103
(0.687) 		0.259
(0.85) 		0.0472
(0.565) 		0.331
(0.85) 		0.897
(1.00) 		1
(1.00)
del 3p26 1 140 (32%) 296 0.681
(0.978) 		0.28
(0.85) 		0.743
(1.00) 		0.961
(1.00) 		0.0216
(0.454) 		0.317
(0.85) 		0.241
(0.85) 		0.0272
(0.478) 		1
(1.00) 		0.439
(0.894) 		0.403
(0.88) 		0.455
(0.9) 		1
(1.00)
del 3p14 2 156 (36%) 280 0.154
(0.76) 		0.523
(0.946) 		0.527
(0.948) 		0.906
(1.00) 		0.176
(0.781) 		0.235
(0.85) 		0.757
(1.00) 		0.0393
(0.552) 		1
(1.00) 		0.0115
(0.326) 		0.866
(1.00) 		0.204
(0.823) 		0.614
(0.971)
del 3q26 31 47 (11%) 389 0.78
(1.00) 		0.328
(0.85) 		0.962
(1.00) 		0.267
(0.85) 		0.233
(0.85) 		0.348
(0.85) 		0.873
(1.00) 		0.311
(0.85) 		0.498
(0.93) 		0.424
(0.892) 		0.842
(1.00) 		0.541
(0.948) 		1
(1.00)
del 4p16 3 167 (38%) 269 0.832
(1.00) 		0.373
(0.863) 		0.543
(0.948) 		0.0275
(0.478) 		0.487
(0.923) 		0.0821
(0.664) 		0.305
(0.85) 		0.256
(0.85) 		1
(1.00) 		0.444
(0.894) 		0.638
(0.971) 		0.649
(0.971) 		1
(1.00)
del 4q22 1 190 (44%) 246 0.3
(0.85) 		0.374
(0.863) 		0.49
(0.923) 		0.0817
(0.664) 		0.373
(0.863) 		0.258
(0.85) 		0.616
(0.971) 		0.162
(0.765) 		0.411
(0.883) 		0.366
(0.858) 		0.0257
(0.478) 		0.168
(0.773) 		0.638
(0.971)
del 4q34 3 197 (45%) 239 0.64
(0.971) 		0.124
(0.724) 		0.0442
(0.562) 		0.433
(0.893) 		0.7
(0.978) 		0.0903
(0.676) 		0.618
(0.971) 		0.00511
(0.254) 		0.416
(0.889) 		0.118
(0.698) 		0.238
(0.85) 		0.477
(0.92) 		0.634
(0.971)
del 6p25 3 113 (26%) 323 0.876
(1.00) 		0.219
(0.849) 		0.994
(1.00) 		0.444
(0.894) 		0.883
(1.00) 		0.133
(0.739) 		0.651
(0.971) 		0.0116
(0.326) 		1
(1.00) 		0.258
(0.85) 		0.441
(0.894) 		0.918
(1.00) 		1
(1.00)
del 6q14 1 88 (20%) 348 0.839
(1.00) 		0.373
(0.863) 		0.765
(1.00) 		0.161
(0.765) 		0.926
(1.00) 		0.628
(0.971) 		0.172
(0.773) 		0.683
(0.978) 		1
(1.00) 		0.5
(0.931) 		0.416
(0.889) 		0.452
(0.896) 		0.583
(0.956)
del 6q24 3 77 (18%) 359 0.355
(0.852) 		0.442
(0.894) 		0.631
(0.971) 		0.0497
(0.565) 		0.741
(1.00) 		0.0415
(0.552) 		0.089
(0.676) 		0.0835
(0.666) 		0.287
(0.85) 		0.965
(1.00) 		0.0969
(0.687) 		0.065
(0.632) 		1
(1.00)
del 6q26 101 (23%) 335 0.219
(0.849) 		0.389
(0.87) 		0.339
(0.85) 		0.0486
(0.565) 		0.301
(0.85) 		0.651
(0.971) 		0.29
(0.85) 		0.0378
(0.552) 		0.626
(0.971) 		0.377
(0.864) 		0.00973
(0.326) 		0.586
(0.956) 		1
(1.00)
del 7q31 1 70 (16%) 366 0.529
(0.948) 		0.194
(0.814) 		0.154
(0.76) 		0.0881
(0.676) 		0.0807
(0.664) 		0.198
(0.819) 		0.103
(0.687) 		0.3
(0.85) 		1
(1.00) 		0.425
(0.892) 		0.307
(0.85) 		0.0798
(0.664) 		1
(1.00)
del 7q36 3 97 (22%) 339 0.798
(1.00) 		0.922
(1.00) 		0.119
(0.698) 		0.33
(0.85) 		0.0708
(0.64) 		1
(1.00) 		0.634
(0.971) 		0.536
(0.948) 		0.127
(0.727) 		0.228
(0.85) 		0.0125
(0.34) 		0.975
(1.00) 		1
(1.00)
del 9p23 191 (44%) 245 0.937
(1.00) 		0.101
(0.687) 		0.483
(0.922) 		0.24
(0.85) 		0.277
(0.85) 		0.448
(0.894) 		0.689
(0.978) 		0.0553
(0.603) 		1
(1.00) 		0.768
(1.00) 		0.0186
(0.454) 		0.405
(0.882) 		0.638
(0.971)
del 9p21 3 189 (43%) 247 0.927
(1.00) 		0.0495
(0.565) 		0.583
(0.956) 		0.305
(0.85) 		0.431
(0.893) 		0.567
(0.951) 		0.841
(1.00) 		0.00726
(0.265) 		1
(1.00) 		0.263
(0.85) 		0.311
(0.85) 		0.245
(0.85) 		0.65
(0.971)
del 9q21 11 113 (26%) 323 0.489
(0.923) 		0.687
(0.978) 		0.87
(1.00) 		0.348
(0.85) 		0.826
(1.00) 		0.284
(0.85) 		0.306
(0.85) 		0.232
(0.85) 		1
(1.00) 		0.837
(1.00) 		0.33
(0.85) 		0.151
(0.758) 		1
(1.00)
del 10p12 31 66 (15%) 370 0.198
(0.819) 		0.333
(0.85) 		0.26
(0.85) 		0.942
(1.00) 		0.0304
(0.482) 		1
(1.00) 		0.677
(0.978) 		0.207
(0.823) 		1
(1.00) 		0.872
(1.00) 		0.00686
(0.265) 		0.363
(0.857) 		0.475
(0.918)
del 10q22 3 78 (18%) 358 0.107
(0.687) 		0.00706
(0.265) 		0.914
(1.00) 		0.25
(0.85) 		0.336
(0.85) 		0.805
(1.00) 		0.604
(0.969) 		0.0298
(0.479) 		1
(1.00) 		0.882
(1.00) 		0.00725
(0.265) 		0.118
(0.698) 		0.521
(0.946)
del 11p15 5 97 (22%) 339 0.732
(1.00) 		0.0965
(0.687) 		0.406
(0.882) 		0.0102
(0.326) 		0.594
(0.963) 		0.823
(1.00) 		0.34
(0.85) 		0.0216
(0.454) 		1
(1.00) 		0.227
(0.85) 		0.116
(0.698) 		0.523
(0.946) 		0.583
(0.956)
del 11q23 2 97 (22%) 339 0.0403
(0.552) 		0.307
(0.85) 		0.496
(0.929) 		0.655
(0.971) 		0.234
(0.85) 		0.248
(0.85) 		0.475
(0.918) 		0.442
(0.894) 		1
(1.00) 		0.291
(0.85) 		0.312
(0.85) 		1
(1.00) 		1
(1.00)
del 12q12 58 (13%) 378 0.277
(0.85) 		0.72
(0.991) 		0.976
(1.00) 		0.631
(0.971) 		0.874
(1.00) 		0.782
(1.00) 		0.66
(0.971) 		0.447
(0.894) 		1
(1.00) 		0.869
(1.00) 		0.562
(0.951) 		0.747
(1.00) 		0.41
(0.883)
del 13q12 11 61 (14%) 375 0.299
(0.85) 		0.328
(0.85) 		0.919
(1.00) 		0.3
(0.85) 		0.666
(0.975) 		0.784
(1.00) 		0.0215
(0.454) 		0.816
(1.00) 		0.0383
(0.552) 		0.636
(0.971) 		0.393
(0.87) 		1
(1.00) 		1
(1.00)
del 14q23 3 134 (31%) 302 0.784
(1.00) 		0.837
(1.00) 		0.383
(0.87) 		0.626
(0.971) 		0.142
(0.739) 		0.0396
(0.552) 		0.334
(0.85) 		0.027
(0.478) 		0.672
(0.978) 		0.112
(0.696) 		0.729
(1.00) 		0.915
(1.00) 		0.325
(0.85)
del 15q11 2 119 (27%) 317 0.409
(0.883) 		0.246
(0.85) 		0.386
(0.87) 		0.077
(0.664) 		0.652
(0.971) 		0.831
(1.00) 		0.824
(1.00) 		0.0794
(0.664) 		0.0498
(0.565) 		0.347
(0.85) 		0.863
(1.00) 		0.648
(0.971) 		0.577
(0.952)
del 15q15 1 121 (28%) 315 0.884
(1.00) 		0.429
(0.893) 		0.132
(0.739) 		0.0714
(0.64) 		0.569
(0.951) 		0.521
(0.946) 		0.739
(1.00) 		0.0777
(0.664) 		0.0528
(0.593) 		0.47
(0.912) 		0.361
(0.854) 		0.817
(1.00) 		1
(1.00)
del 17p13 3 172 (39%) 264 0.393
(0.87) 		0.791
(1.00) 		0.955
(1.00) 		0.247
(0.85) 		0.901
(1.00) 		0.564
(0.951) 		0.222
(0.85) 		0.00527
(0.254) 		0.0375
(0.552) 		0.0949
(0.682) 		0.329
(0.85) 		0.733
(1.00) 		1
(1.00)
del 17q24 3 76 (17%) 360 0.204
(0.823) 		0.136
(0.739) 		0.41
(0.883) 		0.112
(0.696) 		0.103
(0.687) 		0.802
(1.00) 		0.696
(0.978) 		0.319
(0.85) 		0.596
(0.963) 		0.188
(0.811) 		0.00524
(0.254) 		0.126
(0.726) 		0.542
(0.948)
del 20p12 1 38 (9%) 398 0.0973
(0.687) 		0.982
(1.00) 		0.736
(1.00) 		0.753
(1.00) 		0.91
(1.00) 		0.73
(1.00) 		0.481
(0.922) 		0.338
(0.85) 		0.0887
(0.676) 		0.621
(0.971) 		0.717
(0.99) 		0.767
(1.00) 		1
(1.00)
del 21q11 2 181 (42%) 255 0.966
(1.00) 		0.0206
(0.454) 		0.732
(1.00) 		0.534
(0.948) 		0.205
(0.823) 		0.443
(0.894) 		0.419
(0.889) 		0.0566
(0.607) 		0.238
(0.85) 		0.29
(0.85) 		0.913
(1.00) 		0.541
(0.948) 		0.638
(0.971)
del 21q22 3 191 (44%) 245 0.567
(0.951) 		0.0844
(0.666) 		0.659
(0.971) 		0.178
(0.785) 		0.272
(0.85) 		0.256
(0.85) 		0.92
(1.00) 		0.0668
(0.639) 		0.411
(0.883) 		0.397
(0.874) 		0.366
(0.858) 		0.504
(0.934) 		0.651
(0.971)
del 22q13 31 158 (36%) 278 0.219
(0.849) 		0.756
(1.00) 		0.401
(0.88) 		0.395
(0.873) 		0.105
(0.687) 		0.167
(0.773) 		0.301
(0.85) 		0.0401
(0.552) 		0.196
(0.817) 		0.574
(0.952) 		0.0153
(0.393) 		0.613
(0.971) 		1
(1.00)
del xp22 2 82 (19%) 354 0.89
(1.00) 		0.636
(0.971) 		0.143
(0.74) 		0.892
(1.00) 		0.544
(0.948) 		1
(1.00) 		0.253
(0.85) 		0.133
(0.739) 		1
(1.00) 		0.619
(0.971) 		0.272
(0.85) 		0.419
(0.889) 		0.583
(0.956)
del xp21 1 71 (16%) 365 0.968
(1.00) 		0.681
(0.978) 		0.418
(0.889) 		0.923
(1.00) 		0.545
(0.948) 		0.801
(1.00) 		0.347
(0.85) 		0.263
(0.85) 		1
(1.00) 		0.345
(0.85) 		0.168
(0.773) 		0.465
(0.905) 		0.483
(0.922)
del xq21 33 55 (13%) 381 0.463
(0.905) 		0.947
(1.00) 		0.904
(1.00) 		0.914
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.294
(0.85) 		0.831
(1.00) 		0.557
(0.951) 		0.437
(0.894) 		0.911
(1.00) 		0.903
(1.00) 		1
(1.00)
'amp_1q42.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00326 (Fisher's exact test), Q value = 0.2

Table S1.  Gene #3: 'amp_1q42.3' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 3(1Q42.3) MUTATED 12 53 29 39 7 3 5
AMP PEAK 3(1Q42.3) WILD-TYPE 59 109 52 39 14 5 8

Figure S1.  Get High-res Image Gene #3: 'amp_1q42.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_6p21.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S2.  Gene #7: 'amp_6p21.1' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 7(6P21.1) MUTATED 4 50 30 30 3 2 2
AMP PEAK 7(6P21.1) WILD-TYPE 67 112 51 48 18 6 11

Figure S2.  Get High-res Image Gene #7: 'amp_6p21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_6q12' versus 'HISTOLOGICAL_TYPE'

P value = 5e-04 (Fisher's exact test), Q value = 0.058

Table S3.  Gene #8: 'amp_6q12' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 8(6Q12) MUTATED 4 36 27 15 1 1 2
AMP PEAK 8(6Q12) WILD-TYPE 67 126 54 63 20 7 11

Figure S3.  Get High-res Image Gene #8: 'amp_6q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

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

Table S4.  Gene #30: 'amp_17q12' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 30(17Q12) MUTATED 9 46 35 38 6 4 6
AMP PEAK 30(17Q12) WILD-TYPE 62 116 46 40 15 4 7

Figure S4.  Get High-res Image Gene #30: 'amp_17q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'COMPLETENESS_OF_RESECTION'

P value = 9e-05 (Fisher's exact test), Q value = 0.017

Table S5.  Gene #30: 'amp_17q12' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 347 18 19 25
AMP PEAK 30(17Q12) MUTATED 121 1 12 3
AMP PEAK 30(17Q12) WILD-TYPE 226 17 7 22

Figure S5.  Get High-res Image Gene #30: 'amp_17q12' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

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

Table S6.  Gene #35: 'amp_20q13.2' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 35(20Q13.2) MUTATED 32 101 63 64 13 6 9
AMP PEAK 35(20Q13.2) WILD-TYPE 39 61 18 14 8 2 4

Figure S6.  Get High-res Image Gene #35: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_1p36.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00217 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #37: 'del_1p36.11' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 1(1P36.11) MUTATED 11 42 31 35 7 2 5
DEL PEAK 1(1P36.11) WILD-TYPE 60 120 50 43 14 6 8

Figure S7.  Get High-res Image Gene #37: 'del_1p36.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q12.1' versus 'HISTOLOGICAL_TYPE'

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

Table S8.  Gene #50: 'del_5q12.1' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 14(5Q12.1) MUTATED 11 59 33 44 10 4 4
DEL PEAK 14(5Q12.1) WILD-TYPE 60 103 48 34 11 4 9

Figure S8.  Get High-res Image Gene #50: 'del_5q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q23.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0058

Table S9.  Gene #51: 'del_5q23.2' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 15(5Q23.2) MUTATED 9 56 32 45 7 3 4
DEL PEAK 15(5Q23.2) WILD-TYPE 62 106 49 33 14 5 9

Figure S9.  Get High-res Image Gene #51: 'del_5q23.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_8p23.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000934 (Wilcoxon-test), Q value = 0.098

Table S10.  Gene #58: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 22(8P23.3) MUTATED 109 7.6 (10.3)
DEL PEAK 22(8P23.3) WILD-TYPE 278 4.9 (7.5)

Figure S10.  Get High-res Image Gene #58: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00221 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #64: 'del_10q23.31' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 28(10Q23.31) MUTATED 7 39 31 25 5 3 4
DEL PEAK 28(10Q23.31) WILD-TYPE 64 123 50 53 16 5 9

Figure S11.  Get High-res Image Gene #64: 'del_10q23.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.029

Table S12.  Gene #67: 'del_12p13.1' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 31(12P13.1) MUTATED 3 30 15 20 0 4 2
DEL PEAK 31(12P13.1) WILD-TYPE 68 132 66 58 21 4 11

Figure S12.  Get High-res Image Gene #67: 'del_12p13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_14q32.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.0031 (Fisher's exact test), Q value = 0.2

Table S13.  Gene #71: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 387 30
DEL PEAK 35(14Q32.32) MUTATED 120 2
DEL PEAK 35(14Q32.32) WILD-TYPE 267 28

Figure S13.  Get High-res Image Gene #71: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_16p13.3' versus 'RACE'

P value = 0.00312 (Fisher's exact test), Q value = 0.2

Table S14.  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 11 1 274
DEL PEAK 38(16P13.3) MUTATED 26 6 0 48
DEL PEAK 38(16P13.3) WILD-TYPE 62 5 1 226

Figure S14.  Get High-res Image Gene #74: 'del_16p13.3' versus Clinical Feature #12: 'RACE'

'del_16q23.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00359 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #75: 'del_16q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 387 30
DEL PEAK 39(16Q23.1) MUTATED 169 5
DEL PEAK 39(16Q23.1) WILD-TYPE 218 25

Figure S15.  Get High-res Image Gene #75: 'del_16q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00029 (Fisher's exact test), Q value = 0.037

Table S16.  Gene #77: 'del_17p12' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 41(17P12) MUTATED 15 58 42 41 9 4 8
DEL PEAK 41(17P12) WILD-TYPE 56 104 39 37 12 4 5

Figure S16.  Get High-res Image Gene #77: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_18q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.021

Table S17.  Gene #79: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 22 90 195 119
DEL PEAK 43(18Q12.2) MUTATED 6 37 101 33
DEL PEAK 43(18Q12.2) WILD-TYPE 16 53 94 86

Figure S17.  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 = 0.00174 (Fisher's exact test), Q value = 0.14

Table S18.  Gene #80: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 22 90 195 119
DEL PEAK 44(18Q21.2) MUTATED 7 42 109 42
DEL PEAK 44(18Q21.2) WILD-TYPE 15 48 86 77

Figure S18.  Get High-res Image Gene #80: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0014 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #81: 'del_19p13.3' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 45(19P13.3) MUTATED 15 53 41 34 5 5 4
DEL PEAK 45(19P13.3) WILD-TYPE 56 109 40 44 16 3 9

Figure S19.  Get High-res Image Gene #81: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_19q13.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00128 (Fisher's exact test), Q value = 0.12

Table S20.  Gene #82: 'del_19q13.11' versus Clinical Feature #8: '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 INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 46(19Q13.11) MUTATED 5 24 17 25 1 2 1
DEL PEAK 46(19Q13.11) WILD-TYPE 66 138 64 53 20 6 12

Figure S20.  Get High-res Image Gene #82: 'del_19q13.11' versus Clinical Feature #8: '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/15098840/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/15090008/STAD-TP.merged_data.txt

  • Number of patients = 436

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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