Correlation between copy number variations of arm-level result and selected clinical features
Stomach and Esophageal carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13N22HV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C13N22HV
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 14 clinical features across 609 patients, 29 significant findings detected with Q value < 0.25.

  • 6p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7p gain cnv correlated to 'GENDER'.

  • 11q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 12q gain cnv correlated to 'RACE'.

  • 15q gain cnv correlated to 'COMPLETENESS_OF_RESECTION'.

  • 16q gain cnv correlated to 'Time to Death'.

  • 20q gain cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • xp gain cnv correlated to 'RACE'.

  • xq gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 1p loss cnv correlated to 'COMPLETENESS_OF_RESECTION'.

  • 5p loss cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 8p loss cnv correlated to 'GENDER' and 'NUMBER_OF_LYMPH_NODES'.

  • 10p loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 10q loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 12p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 18q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 19p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • xp loss cnv correlated to 'GENDER' and 'NUMBER_PACK_YEARS_SMOKED'.

  • xq loss cnv correlated to 'GENDER' and 'NUMBER_PACK_YEARS_SMOKED'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 29 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 		NUMBER
PACK
YEARS
SMOKED 		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 Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
20q gain 387 (64%) 222 0.126
(0.576) 		0.183
(0.666) 		0.35
(0.847) 		0.141
(0.589) 		0.0239
(0.339) 		0.494
(0.932) 		0.0013
(0.161) 		0.00047
(0.108) 		1
(1.00) 		0.812
(1.00) 		0.471
(0.918) 		0.293
(0.796) 		0.716
(0.973) 		0.264
(0.753)
xq gain 87 (14%) 522 0.953
(1.00) 		0.454
(0.904) 		0.78
(0.994) 		0.552
(0.957) 		0.347
(0.847) 		1
(1.00) 		1
(1.00) 		0.00585
(0.24) 		0.601
(0.957) 		0.598
(0.957) 		0.403
(0.881) 		0.0712
(0.478) 		0.00285
(0.164) 		1
(1.00)
5p loss 110 (18%) 499 0.127
(0.576) 		0.167
(0.636) 		0.00264
(0.164) 		0.00572
(0.24) 		0.191
(0.674) 		0.658
(0.965) 		0.421
(0.893) 		0.0113
(0.282) 		0.598
(0.957) 		0.834
(1.00) 		0.832
(1.00) 		0.26
(0.748) 		0.267
(0.758) 		0.346
(0.846)
8p loss 146 (24%) 463 0.397
(0.876) 		0.663
(0.965) 		0.106
(0.565) 		0.129
(0.576) 		0.0294
(0.374) 		0.847
(1.00) 		0.00255
(0.164) 		0.00781
(0.282) 		1
(1.00) 		0.19
(0.674) 		0.135
(0.58) 		0.000631
(0.116) 		0.276
(0.773) 		0.651
(0.965)
xp loss 116 (19%) 493 0.368
(0.852) 		0.476
(0.922) 		0.241
(0.737) 		0.379
(0.864) 		0.0539
(0.431) 		0.203
(0.683) 		0.000709
(0.116) 		0.162
(0.634) 		1
(1.00) 		0.00422
(0.211) 		0.45
(0.904) 		0.734
(0.979) 		0.157
(0.618) 		0.62
(0.961)
xq loss 93 (15%) 516 0.902
(1.00) 		0.969
(1.00) 		0.697
(0.972) 		0.33
(0.835) 		0.552
(0.957) 		0.0992
(0.561) 		0.00311
(0.17) 		0.965
(1.00) 		0.229
(0.731) 		0.000988
(0.142) 		0.187
(0.674) 		0.501
(0.934) 		0.972
(1.00) 		1
(1.00)
6p gain 113 (19%) 496 0.279
(0.775) 		0.963
(1.00) 		0.243
(0.737) 		0.367
(0.852) 		0.968
(1.00) 		0.401
(0.88) 		0.91
(1.00) 		0.00268
(0.164) 		0.0809
(0.503) 		0.836
(1.00) 		0.432
(0.9) 		0.794
(1.00) 		0.13
(0.576) 		1
(1.00)
6q gain 96 (16%) 513 0.0771
(0.492) 		0.567
(0.957) 		0.00945
(0.282) 		0.418
(0.893) 		0.796
(1.00) 		0.038
(0.41) 		0.397
(0.876) 		0.00213
(0.164) 		0.053
(0.431) 		0.586
(0.957) 		0.323
(0.828) 		0.923
(1.00) 		0.0609
(0.448) 		1
(1.00)
7p gain 299 (49%) 310 0.836
(1.00) 		0.424
(0.895) 		0.438
(0.9) 		0.0791
(0.502) 		0.997
(1.00) 		0.741
(0.982) 		0.0014
(0.161) 		0.0945
(0.537) 		1
(1.00) 		0.248
(0.737) 		0.479
(0.923) 		0.511
(0.938) 		0.343
(0.846) 		0.0553
(0.437)
11q gain 103 (17%) 506 0.488
(0.929) 		0.0574
(0.437) 		0.56
(0.957) 		0.54
(0.957) 		0.00607
(0.24) 		0.657
(0.965) 		0.479
(0.923) 		0.114
(0.567) 		1
(1.00) 		0.871
(1.00) 		0.375
(0.857) 		0.206
(0.685) 		0.121
(0.568) 		1
(1.00)
12q gain 112 (18%) 497 0.678
(0.967) 		0.013
(0.282) 		0.259
(0.748) 		0.0712
(0.478) 		0.0656
(0.462) 		0.129
(0.576) 		0.17
(0.644) 		0.195
(0.676) 		0.599
(0.957) 		0.016
(0.305) 		0.679
(0.967) 		0.64
(0.963) 		0.00533
(0.235) 		0.141
(0.589)
15q gain 64 (11%) 545 0.0923
(0.532) 		0.794
(1.00) 		0.134
(0.579) 		0.566
(0.957) 		0.293
(0.796) 		0.575
(0.957) 		0.0841
(0.503) 		0.45
(0.904) 		1
(1.00) 		0.0351
(0.407) 		0.00219
(0.164) 		0.191
(0.674) 		0.0111
(0.282) 		1
(1.00)
16q gain 83 (14%) 526 0.00443
(0.212) 		0.753
(0.984) 		0.0234
(0.335) 		0.753
(0.984) 		0.743
(0.984) 		0.0187
(0.317) 		0.0524
(0.431) 		0.248
(0.737) 		0.191
(0.674) 		0.961
(1.00) 		0.144
(0.59) 		0.0328
(0.397) 		0.0556
(0.437) 		1
(1.00)
xp gain 69 (11%) 540 0.356
(0.851) 		0.719
(0.973) 		0.369
(0.852) 		0.35
(0.847) 		0.258
(0.748) 		0.413
(0.889) 		0.489
(0.929) 		0.214
(0.701) 		0.516
(0.938) 		0.283
(0.779) 		0.776
(0.993) 		0.106
(0.565) 		0.00016
(0.108) 		1
(1.00)
1p loss 91 (15%) 518 0.422
(0.893) 		0.34
(0.846) 		0.227
(0.727) 		0.63
(0.961) 		0.661
(0.965) 		0.0153
(0.305) 		1
(1.00) 		0.114
(0.567) 		0.599
(0.957) 		0.345
(0.846) 		0.00347
(0.181) 		0.717
(0.973) 		0.218
(0.711) 		0.601
(0.957)
5q loss 187 (31%) 422 0.302
(0.802) 		0.599
(0.957) 		0.00881
(0.282) 		0.064
(0.46) 		0.0448
(0.42) 		0.591
(0.957) 		0.388
(0.874) 		0.00035
(0.108) 		0.672
(0.967) 		0.847
(1.00) 		0.528
(0.947) 		0.273
(0.77) 		0.745
(0.984) 		1
(1.00)
10p loss 111 (18%) 498 0.105
(0.565) 		0.877
(1.00) 		0.81
(1.00) 		0.0672
(0.47) 		0.189
(0.674) 		0.831
(1.00) 		0.494
(0.932) 		0.195
(0.676) 		1
(1.00) 		0.78
(0.994) 		0.572
(0.957) 		0.00172
(0.164) 		0.282
(0.779) 		1
(1.00)
10q loss 111 (18%) 498 0.44
(0.901) 		0.625
(0.961) 		0.649
(0.964) 		0.443
(0.902) 		0.467
(0.916) 		0.832
(1.00) 		0.494
(0.932) 		0.115
(0.567) 		1
(1.00) 		0.521
(0.943) 		1
(1.00) 		0.00475
(0.218) 		0.0484
(0.431) 		1
(1.00)
12p loss 92 (15%) 517 0.245
(0.737) 		0.0831
(0.503) 		0.91
(1.00) 		0.114
(0.567) 		0.942
(1.00) 		1
(1.00) 		0.389
(0.874) 		0.0027
(0.164) 		1
(1.00) 		0.117
(0.567) 		0.465
(0.913) 		0.396
(0.876) 		0.296
(0.798) 		1
(1.00)
17p loss 229 (38%) 380 0.53
(0.947) 		0.469
(0.916) 		0.899
(1.00) 		0.19
(0.674) 		0.724
(0.973) 		0.492
(0.932) 		0.0999
(0.562) 		0.00278
(0.164) 		0.205
(0.685) 		0.685
(0.967) 		0.195
(0.676) 		0.34
(0.846) 		0.553
(0.957) 		0.691
(0.969)
18q loss 248 (41%) 361 0.974
(1.00) 		0.12
(0.568) 		0.93
(1.00) 		0.00038
(0.108) 		0.937
(1.00) 		0.735
(0.979) 		0.15
(0.602) 		0.542
(0.957) 		0.409
(0.888) 		0.243
(0.737) 		0.986
(1.00) 		0.123
(0.571) 		0.874
(1.00) 		1
(1.00)
19p loss 172 (28%) 437 0.104
(0.565) 		0.924
(1.00) 		0.68
(0.967) 		0.544
(0.957) 		0.634
(0.961) 		0.717
(0.973) 		0.432
(0.9) 		0.0002
(0.108) 		0.677
(0.967) 		0.0657
(0.462) 		0.197
(0.677) 		0.147
(0.594) 		0.0937
(0.535) 		0.685
(0.967)
19q loss 132 (22%) 477 0.747
(0.984) 		0.649
(0.964) 		0.939
(1.00) 		0.438
(0.9) 		0.843
(1.00) 		0.843
(1.00) 		0.668
(0.967) 		0.00169
(0.164) 		1
(1.00) 		0.109
(0.567) 		0.105
(0.565) 		0.69
(0.969) 		0.0564
(0.437) 		1
(1.00)
1p gain 78 (13%) 531 0.131
(0.577) 		0.0448
(0.42) 		0.299
(0.801) 		0.0447
(0.42) 		0.995
(1.00) 		0.208
(0.689) 		0.112
(0.567) 		0.221
(0.717) 		1
(1.00) 		0.902
(1.00) 		0.13
(0.576) 		0.906
(1.00) 		0.649
(0.964) 		1
(1.00)
1q gain 161 (26%) 448 0.12
(0.568) 		0.138
(0.587) 		0.781
(0.994) 		0.0896
(0.525) 		0.943
(1.00) 		0.706
(0.973) 		0.0449
(0.42) 		0.26
(0.748) 		0.657
(0.965) 		0.374
(0.856) 		0.756
(0.984) 		0.513
(0.938) 		0.121
(0.568) 		0.679
(0.967)
2p gain 131 (22%) 478 0.989
(1.00) 		0.315
(0.815) 		0.366
(0.852) 		0.029
(0.374) 		0.613
(0.961) 		1
(1.00) 		0.391
(0.876) 		0.029
(0.374) 		0.35
(0.847) 		0.138
(0.587) 		0.329
(0.835) 		0.909
(1.00) 		0.118
(0.568) 		1
(1.00)
2q gain 106 (17%) 503 0.963
(1.00) 		0.761
(0.988) 		0.493
(0.932) 		0.278
(0.775) 		0.7
(0.972) 		1
(1.00) 		0.416
(0.893) 		0.13
(0.576) 		0.597
(0.957) 		0.939
(1.00) 		0.593
(0.957) 		0.856
(1.00) 		0.607
(0.958) 		1
(1.00)
3p gain 81 (13%) 528 0.397
(0.876) 		0.425
(0.896) 		0.73
(0.976) 		0.951
(1.00) 		0.559
(0.957) 		0.805
(1.00) 		1
(1.00) 		0.514
(0.938) 		1
(1.00) 		0.306
(0.802) 		0.829
(1.00) 		0.452
(0.904) 		0.816
(1.00) 		0.0399
(0.41)
3q gain 163 (27%) 446 0.365
(0.852) 		0.0107
(0.282) 		0.257
(0.748) 		0.872
(1.00) 		0.723
(0.973) 		0.569
(0.957) 		0.369
(0.852) 		0.657
(0.965) 		1
(1.00) 		0.23
(0.731) 		0.73
(0.976) 		0.245
(0.737) 		0.208
(0.689) 		0.364
(0.852)
4p gain 36 (6%) 573 0.387
(0.874) 		0.996
(1.00) 		0.286
(0.785) 		0.619
(0.961) 		0.52
(0.943) 		1
(1.00) 		0.0906
(0.526) 		0.233
(0.733) 		1
(1.00) 		0.575
(0.957) 		0.341
(0.846) 		0.645
(0.964) 		0.682
(0.967) 		0.303
(0.802)
4q gain 31 (5%) 578 0.585
(0.957) 		0.818
(1.00) 		0.658
(0.965) 		0.786
(0.998) 		0.509
(0.938) 		1
(1.00) 		0.107
(0.565) 		0.0907
(0.526) 		1
(1.00) 		0.621
(0.961) 		0.756
(0.984) 		0.53
(0.947) 		0.563
(0.957) 		1
(1.00)
5p gain 167 (27%) 442 0.511
(0.938) 		0.928
(1.00) 		0.669
(0.967) 		0.009
(0.282) 		0.995
(1.00) 		0.354
(0.849) 		0.766
(0.989) 		0.0112
(0.282) 		0.668
(0.967) 		0.717
(0.973) 		0.982
(1.00) 		0.236
(0.736) 		0.984
(1.00) 		1
(1.00)
5q gain 62 (10%) 547 0.434
(0.9) 		0.306
(0.802) 		0.223
(0.719) 		0.0621
(0.451) 		0.249
(0.737) 		1
(1.00) 		0.558
(0.957) 		0.0602
(0.446) 		0.476
(0.922) 		0.749
(0.984) 		0.771
(0.991) 		0.714
(0.973) 		0.592
(0.957) 		1
(1.00)
7q gain 251 (41%) 358 0.621
(0.961) 		0.672
(0.967) 		0.523
(0.944) 		0.0601
(0.446) 		0.786
(0.998) 		0.737
(0.979) 		0.012
(0.282) 		0.157
(0.618) 		1
(1.00) 		0.81
(1.00) 		0.328
(0.835) 		0.412
(0.889) 		0.233
(0.733) 		0.0166
(0.305)
8p gain 243 (40%) 366 0.837
(1.00) 		0.0333
(0.398) 		0.634
(0.961) 		0.974
(1.00) 		0.629
(0.961) 		0.867
(1.00) 		0.03
(0.374) 		0.12
(0.568) 		0.223
(0.719) 		0.257
(0.748) 		0.0378
(0.41) 		0.452
(0.904) 		0.758
(0.985) 		1
(1.00)
8q gain 328 (54%) 281 0.912
(1.00) 		0.0414
(0.414) 		0.132
(0.577) 		0.967
(1.00) 		0.555
(0.957) 		0.405
(0.883) 		0.248
(0.737) 		0.538
(0.956) 		0.225
(0.721) 		0.632
(0.961) 		0.012
(0.282) 		0.604
(0.958) 		0.502
(0.934) 		1
(1.00)
9p gain 73 (12%) 536 0.0531
(0.431) 		0.781
(0.994) 		0.88
(1.00) 		0.853
(1.00) 		0.565
(0.957) 		0.805
(1.00) 		1
(1.00) 		0.0123
(0.282) 		0.155
(0.612) 		0.0392
(0.41) 		0.853
(1.00) 		0.843
(1.00) 		0.351
(0.847) 		0.199
(0.678)
9q gain 104 (17%) 505 0.251
(0.737) 		0.426
(0.896) 		0.97
(1.00) 		0.855
(1.00) 		0.988
(1.00) 		0.83
(1.00) 		0.242
(0.737) 		0.0201
(0.318) 		0.273
(0.77) 		0.0838
(0.503) 		0.723
(0.973) 		0.396
(0.876) 		0.422
(0.893) 		0.346
(0.846)
10p gain 133 (22%) 476 0.921
(1.00) 		0.934
(1.00) 		0.296
(0.798) 		0.115
(0.567) 		0.842
(1.00) 		0.545
(0.957) 		0.749
(0.984) 		0.381
(0.864) 		0.616
(0.961) 		0.437
(0.9) 		0.461
(0.908) 		0.556
(0.957) 		0.106
(0.565) 		0.358
(0.851)
10q gain 97 (16%) 512 0.699
(0.972) 		0.172
(0.648) 		0.0266
(0.365) 		0.0282
(0.374) 		0.53
(0.947) 		0.649
(0.964) 		0.904
(1.00) 		0.652
(0.965) 		0.245
(0.737) 		0.021
(0.321) 		0.575
(0.957) 		0.968
(1.00) 		0.213
(0.701) 		0.605
(0.958)
11p gain 98 (16%) 511 0.512
(0.938) 		0.366
(0.852) 		0.641
(0.963) 		0.0652
(0.462) 		0.0718
(0.479) 		0.649
(0.964) 		0.81
(1.00) 		0.304
(0.802) 		1
(1.00) 		0.439
(0.9) 		0.447
(0.903) 		0.0758
(0.49) 		0.0515
(0.431) 		1
(1.00)
12p gain 142 (23%) 467 0.982
(1.00) 		0.329
(0.835) 		0.0741
(0.489) 		0.00807
(0.282) 		0.456
(0.905) 		0.236
(0.736) 		0.0937
(0.535) 		0.6
(0.957) 		0.345
(0.846) 		0.166
(0.636) 		0.166
(0.636) 		0.639
(0.963) 		0.111
(0.567) 		0.371
(0.853)
13q gain 192 (32%) 417 0.357
(0.851) 		0.818
(1.00) 		0.268
(0.759) 		0.785
(0.998) 		0.123
(0.571) 		0.858
(1.00) 		0.341
(0.846) 		0.214
(0.701) 		0.671
(0.967) 		0.0764
(0.49) 		0.798
(1.00) 		0.342
(0.846) 		0.0823
(0.503) 		0.684
(0.967)
14q gain 71 (12%) 538 0.247
(0.737) 		0.0385
(0.41) 		0.147
(0.594) 		0.484
(0.925) 		0.474
(0.922) 		0.431
(0.9) 		0.0267
(0.365) 		0.477
(0.922) 		1
(1.00) 		0.715
(0.973) 		0.139
(0.587) 		0.0491
(0.431) 		0.599
(0.957) 		0.585
(0.957)
16p gain 95 (16%) 514 0.167
(0.636) 		0.695
(0.972) 		0.0187
(0.317) 		0.664
(0.965) 		0.91
(1.00) 		0.152
(0.606) 		0.0504
(0.431) 		0.813
(1.00) 		0.0516
(0.431) 		0.912
(1.00) 		0.119
(0.568) 		0.0356
(0.408) 		0.0578
(0.437) 		1
(1.00)
17p gain 59 (10%) 550 0.599
(0.957) 		0.852
(1.00) 		0.0612
(0.448) 		0.593
(0.957) 		0.0573
(0.437) 		0.384
(0.868) 		0.0517
(0.431) 		0.0432
(0.42) 		0.459
(0.905) 		0.574
(0.957) 		0.0196
(0.318) 		1
(1.00) 		0.113
(0.567) 		1
(1.00)
17q gain 101 (17%) 508 0.894
(1.00) 		0.917
(1.00) 		0.336
(0.844) 		0.566
(0.957) 		0.937
(1.00) 		0.251
(0.737) 		0.017
(0.305) 		0.297
(0.799) 		1
(1.00) 		0.154
(0.612) 		0.0185
(0.317) 		0.747
(0.984) 		0.00992
(0.282) 		0.6
(0.957)
18p gain 134 (22%) 475 0.017
(0.305) 		0.703
(0.973) 		0.629
(0.961) 		0.634
(0.961) 		0.468
(0.916) 		0.839
(1.00) 		1
(1.00) 		0.106
(0.565) 		0.0233
(0.335) 		0.627
(0.961) 		0.723
(0.973) 		0.599
(0.957) 		0.566
(0.957) 		0.64
(0.963)
18q gain 81 (13%) 528 0.0387
(0.41) 		0.917
(1.00) 		0.0501
(0.431) 		0.0389
(0.41) 		0.647
(0.964) 		1
(1.00) 		0.515
(0.938) 		0.0833
(0.503) 		0.0337
(0.398) 		0.664
(0.965) 		0.532
(0.948) 		0.645
(0.964) 		0.527
(0.947) 		1
(1.00)
19p gain 80 (13%) 529 0.317
(0.815) 		0.147
(0.594) 		0.963
(1.00) 		0.35
(0.847) 		0.441
(0.901) 		0.304
(0.802) 		0.513
(0.938) 		0.112
(0.567) 		0.18
(0.662) 		1
(1.00) 		0.0641
(0.46) 		0.0436
(0.42) 		0.371
(0.853) 		1
(1.00)
19q gain 114 (19%) 495 0.729
(0.976) 		0.413
(0.889) 		0.869
(1.00) 		0.309
(0.807) 		0.116
(0.567) 		0.662
(0.965) 		0.175
(0.653) 		0.692
(0.97) 		0.0129
(0.282) 		0.595
(0.957) 		0.0823
(0.503) 		0.0309
(0.377) 		0.128
(0.576) 		1
(1.00)
20p gain 340 (56%) 269 0.0457
(0.423) 		0.281
(0.779) 		0.412
(0.889) 		0.255
(0.746) 		0.128
(0.576) 		0.621
(0.961) 		0.00984
(0.282) 		0.069
(0.478) 		0.413
(0.889) 		0.802
(1.00) 		0.91
(1.00) 		0.576
(0.957) 		1
(1.00) 		0.476
(0.922)
21q gain 34 (6%) 575 0.885
(1.00) 		0.988
(1.00) 		0.752
(0.984) 		0.753
(0.984) 		0.62
(0.961) 		0.718
(0.973) 		0.847
(1.00) 		0.342
(0.846) 		1
(1.00) 		0.961
(1.00) 		0.721
(0.973) 		0.105
(0.565) 		0.283
(0.779) 		1
(1.00)
22q gain 62 (10%) 547 0.82
(1.00) 		0.0149
(0.305) 		0.312
(0.81) 		0.133
(0.577) 		0.0217
(0.323) 		1
(1.00) 		0.558
(0.957) 		0.482
(0.925) 		1
(1.00) 		0.723
(0.973) 		0.962
(1.00) 		0.931
(1.00) 		0.00847
(0.282) 		0.193
(0.676)
1q loss 45 (7%) 564 0.0277
(0.374) 		0.628
(0.961) 		0.789
(0.998) 		0.315
(0.815) 		0.447
(0.903) 		0.0739
(0.489) 		0.866
(1.00) 		0.565
(0.957) 		1
(1.00) 		0.627
(0.961) 		0.0569
(0.437) 		0.397
(0.876) 		0.947
(1.00) 		1
(1.00)
2p loss 38 (6%) 571 0.854
(1.00) 		0.305
(0.802) 		0.447
(0.903) 		0.0508
(0.431) 		0.7
(0.972) 		0.5
(0.934) 		0.361
(0.852) 		0.117
(0.567) 		0.0485
(0.431) 		0.95
(1.00) 		0.158
(0.618) 		0.395
(0.876) 		0.82
(1.00) 		1
(1.00)
2q loss 51 (8%) 558 0.735
(0.979) 		0.436
(0.9) 		0.86
(1.00) 		0.809
(1.00) 		0.727
(0.976) 		0.563
(0.957) 		0.752
(0.984) 		0.00662
(0.253) 		0.083
(0.503) 		0.503
(0.934) 		0.144
(0.59) 		0.375
(0.857) 		0.214
(0.701) 		1
(1.00)
3p loss 177 (29%) 432 0.781
(0.994) 		0.113
(0.567) 		0.306
(0.802) 		0.422
(0.893) 		0.0188
(0.317) 		0.36
(0.852) 		0.284
(0.779) 		0.0795
(0.502) 		0.678
(0.967) 		0.772
(0.992) 		0.14
(0.589) 		0.767
(0.989) 		0.201
(0.681) 		0.678
(0.967)
3q loss 89 (15%) 520 0.866
(1.00) 		0.698
(0.972) 		0.549
(0.957) 		0.0691
(0.478) 		0.334
(0.841) 		0.175
(0.653) 		0.616
(0.961) 		0.109
(0.567) 		0.6
(0.957) 		0.368
(0.852) 		0.551
(0.957) 		0.766
(0.989) 		0.787
(0.998) 		1
(1.00)
4p loss 263 (43%) 346 0.0761
(0.49) 		0.439
(0.9) 		0.141
(0.589) 		0.117
(0.567) 		0.363
(0.852) 		0.241
(0.737) 		0.13
(0.576) 		0.173
(0.648) 		1
(1.00) 		0.143
(0.59) 		0.931
(1.00) 		0.166
(0.636) 		0.0764
(0.49) 		0.705
(0.973)
4q loss 247 (41%) 362 0.0137
(0.291) 		0.102
(0.565) 		0.261
(0.748) 		0.0751
(0.49) 		0.181
(0.664) 		0.615
(0.961) 		0.528
(0.947) 		0.129
(0.576) 		0.691
(0.969) 		0.68
(0.967) 		0.641
(0.963) 		0.0821
(0.503) 		0.429
(0.899) 		1
(1.00)
6p loss 90 (15%) 519 0.827
(1.00) 		0.576
(0.957) 		0.619
(0.961) 		0.0483
(0.431) 		0.503
(0.934) 		0.145
(0.59) 		0.262
(0.75) 		0.0397
(0.41) 		0.599
(0.957) 		0.24
(0.737) 		0.394
(0.876) 		0.97
(1.00) 		0.844
(1.00) 		1
(1.00)
6q loss 107 (18%) 502 0.817
(1.00) 		0.6
(0.957) 		0.438
(0.9) 		0.0202
(0.318) 		0.69
(0.969) 		0.176
(0.653) 		0.13
(0.576) 		0.104
(0.565) 		0.597
(0.957) 		0.278
(0.775) 		0.705
(0.973) 		0.401
(0.88) 		0.864
(1.00) 		1
(1.00)
7p loss 33 (5%) 576 0.554
(0.957) 		0.998
(1.00) 		0.613
(0.961) 		0.916
(1.00) 		0.299
(0.801) 		1
(1.00) 		0.56
(0.957) 		0.588
(0.957) 		1
(1.00) 		0.03
(0.374) 		0.482
(0.925) 		0.145
(0.59) 		0.0415
(0.414) 		1
(1.00)
7q loss 51 (8%) 558 0.865
(1.00) 		0.289
(0.788) 		0.481
(0.925) 		0.116
(0.567) 		0.457
(0.905) 		0.563
(0.957) 		0.203
(0.683) 		0.708
(0.973) 		1
(1.00) 		0.184
(0.667) 		0.685
(0.967) 		0.329
(0.835) 		0.18
(0.662) 		1
(1.00)
8q loss 56 (9%) 553 0.877
(1.00) 		0.748
(0.984) 		0.251
(0.737) 		0.0213
(0.321) 		0.607
(0.958) 		0.774
(0.992) 		0.169
(0.643) 		0.219
(0.712) 		1
(1.00) 		0.792
(1.00) 		0.109
(0.567) 		0.00951
(0.282) 		0.0382
(0.41) 		1
(1.00)
9p loss 241 (40%) 368 0.485
(0.925) 		0.766
(0.989) 		0.0711
(0.478) 		0.275
(0.773) 		0.0868
(0.516) 		0.736
(0.979) 		0.149
(0.598) 		0.0196
(0.318) 		0.685
(0.967) 		0.5
(0.934) 		0.509
(0.938) 		0.164
(0.635) 		0.189
(0.674) 		0.437
(0.9)
9q loss 169 (28%) 440 0.586
(0.957) 		0.26
(0.748) 		0.223
(0.719) 		0.309
(0.807) 		0.774
(0.992) 		0.58
(0.957) 		0.0384
(0.41) 		0.234
(0.733) 		0.355
(0.851) 		0.232
(0.733) 		0.791
(1) 		0.171
(0.647) 		0.104
(0.565) 		0.111
(0.567)
11p loss 113 (19%) 496 0.368
(0.852) 		0.967
(1.00) 		0.0705
(0.478) 		0.333
(0.841) 		0.579
(0.957) 		0.66
(0.965) 		0.0527
(0.431) 		0.0195
(0.318) 		0.599
(0.957) 		0.883
(1.00) 		0.38
(0.864) 		0.123
(0.571) 		0.631
(0.961) 		0.353
(0.849)
11q loss 114 (19%) 495 0.0508
(0.431) 		0.232
(0.733) 		0.0162
(0.305) 		0.388
(0.874) 		0.237
(0.737) 		0.516
(0.938) 		0.0124
(0.282) 		0.117
(0.567) 		0.6
(0.957) 		0.653
(0.965) 		0.535
(0.952) 		0.0153
(0.305) 		0.765
(0.989) 		0.36
(0.852)
12q loss 79 (13%) 530 0.133
(0.577) 		0.196
(0.677) 		0.295
(0.798) 		0.0397
(0.41) 		0.73
(0.976) 		1
(1.00) 		0.429
(0.899) 		0.0411
(0.414) 		0.567
(0.957) 		0.0212
(0.321) 		0.403
(0.881) 		0.636
(0.962) 		0.023
(0.335) 		0.542
(0.957)
13q loss 97 (16%) 512 0.684
(0.967) 		0.0875
(0.516) 		0.0104
(0.282) 		0.04
(0.41) 		0.0255
(0.357) 		0.247
(0.737) 		0.0298
(0.374) 		0.705
(0.973) 		0.245
(0.737) 		1
(1.00) 		0.145
(0.59) 		0.447
(0.903) 		0.0166
(0.305) 		1
(1.00)
14q loss 155 (25%) 454 0.755
(0.984) 		0.71
(0.973) 		0.0518
(0.431) 		0.199
(0.678) 		0.198
(0.678) 		0.183
(0.666) 		0.839
(1.00) 		0.311
(0.81) 		1
(1.00) 		0.619
(0.961) 		0.417
(0.893) 		0.574
(0.957) 		0.759
(0.986) 		1
(1.00)
15q loss 142 (23%) 467 0.458
(0.905) 		0.199
(0.678) 		0.526
(0.947) 		0.0119
(0.282) 		0.606
(0.958) 		0.696
(0.972) 		0.834
(1.00) 		0.0563
(0.437) 		0.143
(0.59) 		0.696
(0.972) 		0.708
(0.973) 		0.516
(0.938) 		0.496
(0.934) 		1
(1.00)
16p loss 154 (25%) 455 0.835
(1.00) 		0.106
(0.565) 		0.877
(1.00) 		0.204
(0.685) 		0.304
(0.802) 		0.0836
(0.503) 		0.919
(1.00) 		0.0157
(0.305) 		0.646
(0.964) 		0.831
(1.00) 		0.585
(0.957) 		0.469
(0.916) 		0.635
(0.962) 		0.206
(0.685)
16q loss 164 (27%) 445 0.522
(0.944) 		0.358
(0.851) 		0.456
(0.905) 		0.276
(0.773) 		0.964
(1.00) 		0.0582
(0.437) 		0.551
(0.957) 		0.00925
(0.282) 		0.351
(0.847) 		0.718
(0.973) 		0.68
(0.967) 		0.826
(1.00) 		0.888
(1.00) 		0.365
(0.852)
17q loss 97 (16%) 512 0.448
(0.903) 		0.819
(1.00) 		0.578
(0.957) 		0.409
(0.888) 		0.263
(0.752) 		0.176
(0.653) 		0.63
(0.961) 		0.0713
(0.478) 		1
(1.00) 		0.715
(0.973) 		1
(1.00) 		0.163
(0.634) 		0.247
(0.737) 		0.0877
(0.516)
18p loss 181 (30%) 428 0.452
(0.904) 		0.32
(0.821) 		0.865
(1.00) 		0.0428
(0.42) 		0.737
(0.979) 		0.585
(0.957) 		0.0532
(0.431) 		0.854
(1.00) 		0.187
(0.674) 		0.121
(0.568) 		0.677
(0.967) 		0.135
(0.58) 		0.767
(0.989) 		0.421
(0.893)
20p loss 40 (7%) 569 0.756
(0.984) 		0.656
(0.965) 		0.711
(0.973) 		0.613
(0.961) 		0.886
(1.00) 		0.5
(0.934) 		0.722
(0.973) 		0.63
(0.961) 		0.0533
(0.431) 		0.862
(1.00) 		0.569
(0.957) 		0.501
(0.934) 		0.824
(1.00) 		1
(1.00)
20q loss 8 (1%) 601 0.397
(0.876) 		0.57
(0.957) 		0.251
(0.737) 		0.0305
(0.376) 		0.634
(0.961) 		1
(1.00) 		0.446
(0.903) 		1
(1.00) 		0.716
(0.973) 		0.484
(0.925) 		1
(1.00)
21q loss 279 (46%) 330 0.77
(0.991) 		0.193
(0.676) 		0.238
(0.737) 		0.333
(0.841) 		0.574
(0.957) 		0.317
(0.815) 		0.658
(0.965) 		0.199
(0.678) 		0.42
(0.893) 		0.135
(0.58) 		0.682
(0.967) 		0.402
(0.881) 		0.288
(0.787) 		0.453
(0.904)
22q loss 212 (35%) 397 0.043
(0.42) 		0.661
(0.965) 		0.0127
(0.282) 		0.0541
(0.431) 		0.605
(0.958) 		0.606
(0.958) 		0.458
(0.905) 		0.339
(0.846) 		0.19
(0.674) 		0.871
(1.00) 		0.509
(0.938) 		0.0348
(0.407) 		0.498
(0.934) 		1
(1.00)
'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00268 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #11: '6p gain' 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
6P GAIN MUTATED 3 31 22 17 1 1 2
6P GAIN WILD-TYPE 68 131 59 61 20 7 11

Figure S1.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00213 (Fisher's exact test), Q value = 0.16

Table S2.  Gene #12: '6q gain' 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
6Q GAIN MUTATED 2 28 19 12 0 1 2
6Q GAIN WILD-TYPE 69 134 62 66 21 7 11

Figure S2.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'GENDER'

P value = 0.0014 (Fisher's exact test), Q value = 0.16

Table S3.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
7P GAIN MUTATED 71 228
7P GAIN WILD-TYPE 111 199

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00607 (Fisher's exact test), Q value = 0.24

Table S4.  Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 200 182 96 97
11Q GAIN MUTATED 27 28 28 12
11Q GAIN WILD-TYPE 173 154 68 85

Figure S4.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'RACE'

P value = 0.00533 (Fisher's exact test), Q value = 0.24

Table S5.  Gene #24: '12q gain' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
12Q GAIN MUTATED 37 1 0 60
12Q GAIN WILD-TYPE 92 12 1 325

Figure S5.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #13: 'RACE'

'15q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.00219 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #27: '15q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 347 18 19 25
15Q GAIN MUTATED 22 3 6 1
15Q GAIN WILD-TYPE 325 15 13 24

Figure S6.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'16q gain' versus 'Time to Death'

P value = 0.00443 (logrank test), Q value = 0.21

Table S7.  Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 575 221 0.0 - 122.3 (12.8)
16Q GAIN MUTATED 79 35 0.0 - 54.1 (11.5)
16Q GAIN WILD-TYPE 496 186 0.1 - 122.3 (12.9)

Figure S7.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'GENDER'

P value = 0.0013 (Fisher's exact test), Q value = 0.16

Table S8.  Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
20Q GAIN MUTATED 98 289
20Q GAIN WILD-TYPE 84 138

Figure S8.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00047 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #37: '20q gain' 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
20Q GAIN MUTATED 32 95 60 61 12 6 8
20Q GAIN WILD-TYPE 39 67 21 17 9 2 5

Figure S9.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'RACE'

P value = 0.00016 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
XP GAIN MUTATED 17 6 1 35
XP GAIN WILD-TYPE 112 7 0 350

Figure S10.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00585 (Fisher's exact test), Q value = 0.24

Table S11.  Gene #41: 'xq gain' 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
XQ GAIN MUTATED 4 15 12 19 0 1 1
XQ GAIN WILD-TYPE 67 147 69 59 21 7 12

Figure S11.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'RACE'

P value = 0.00285 (Fisher's exact test), Q value = 0.16

Table S12.  Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
XQ GAIN MUTATED 27 4 1 46
XQ GAIN WILD-TYPE 102 9 0 339

Figure S12.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

'1p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.00347 (Fisher's exact test), Q value = 0.18

Table S13.  Gene #42: '1p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 347 18 19 25
1P LOSS MUTATED 41 2 8 1
1P LOSS WILD-TYPE 306 16 11 24

Figure S13.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'5p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00264 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
5P LOSS MUTATED 7 3 3 2 11 19 9 19 11 7 6 1
5P LOSS WILD-TYPE 4 16 45 30 66 65 20 78 61 41 45 3

Figure S14.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00572 (Fisher's exact test), Q value = 0.24

Table S15.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
5P LOSS MUTATED 18 14 47 21
5P LOSS WILD-TYPE 35 112 233 103

Figure S15.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00035 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #51: '5q loss' 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
5Q LOSS MUTATED 6 37 23 33 5 2 3
5Q LOSS WILD-TYPE 65 125 58 45 16 6 10

Figure S16.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'GENDER'

P value = 0.00255 (Fisher's exact test), Q value = 0.16

Table S17.  Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
8P LOSS MUTATED 29 117
8P LOSS WILD-TYPE 153 310

Figure S17.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000631 (Wilcoxon-test), Q value = 0.12

Table S18.  Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
8P LOSS MUTATED 82 8.3 (11.4)
8P LOSS WILD-TYPE 305 5.0 (7.3)

Figure S18.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00172 (Wilcoxon-test), Q value = 0.16

Table S19.  Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
10P LOSS MUTATED 59 7.2 (7.1)
10P LOSS WILD-TYPE 328 5.4 (8.6)

Figure S19.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00475 (Wilcoxon-test), Q value = 0.22

Table S20.  Gene #61: '10q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
10Q LOSS MUTATED 60 7.5 (9.0)
10Q LOSS WILD-TYPE 327 5.3 (8.3)

Figure S20.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0027 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #64: '12p loss' 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
12P LOSS MUTATED 3 23 13 18 0 3 1
12P LOSS WILD-TYPE 68 139 68 60 21 5 12

Figure S21.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00278 (Fisher's exact test), Q value = 0.16

Table S22.  Gene #71: '17p loss' 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
17P LOSS MUTATED 15 52 40 34 10 4 7
17P LOSS WILD-TYPE 56 110 41 44 11 4 6

Figure S22.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00038 (Fisher's exact test), Q value = 0.11

Table S23.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
18Q LOSS MUTATED 18 50 135 33
18Q LOSS WILD-TYPE 35 76 145 91

Figure S23.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #75: '19p loss' 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
19P LOSS MUTATED 9 37 32 27 1 4 3
19P LOSS WILD-TYPE 62 125 49 51 20 4 10

Figure S24.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00169 (Fisher's exact test), Q value = 0.16

Table S25.  Gene #76: '19q loss' 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
19Q LOSS MUTATED 6 27 23 23 2 4 2
19Q LOSS WILD-TYPE 65 135 58 55 19 4 11

Figure S25.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'GENDER'

P value = 0.000709 (Fisher's exact test), Q value = 0.12

Table S26.  Gene #81: 'xp loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
XP LOSS MUTATED 20 96
XP LOSS WILD-TYPE 162 331

Figure S26.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #7: 'GENDER'

'xp loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00422 (Wilcoxon-test), Q value = 0.21

Table S27.  Gene #81: 'xp loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 92 35.2 (21.9)
XP LOSS MUTATED 27 25.6 (16.3)
XP LOSS WILD-TYPE 65 39.1 (22.7)

Figure S27.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'xq loss' versus 'GENDER'

P value = 0.00311 (Fisher's exact test), Q value = 0.17

Table S28.  Gene #82: 'xq loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
XQ LOSS MUTATED 16 77
XQ LOSS WILD-TYPE 166 350

Figure S28.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #7: 'GENDER'

'xq loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000988 (Wilcoxon-test), Q value = 0.14

Table S29.  Gene #82: 'xq loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 92 35.2 (21.9)
XQ LOSS MUTATED 18 20.9 (12.5)
XQ LOSS WILD-TYPE 74 38.6 (22.3)

Figure S29.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/15101919/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/15090071/STES-TP.merged_data.txt

  • Number of patients = 609

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 14

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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