Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1F76C1S
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1F76C1S
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 81 arm-level events and 13 clinical features across 441 patients, 9 significant findings detected with Q value < 0.25.

  • 6p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 15q gain cnv correlated to 'RACE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 8q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 19p loss 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 81 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 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
8p loss 91 (21%) 350 0.829
(1.00) 		0.676
(0.974) 		0.0313
(0.547) 		0.161
(0.732) 		0.0104
(0.324) 		0.644
(0.968) 		0.000856
(0.205) 		0.43
(0.92) 		0.0185
(0.424) 		0.253
(0.809) 		0.00113
(0.205) 		0.314
(0.866) 		0.223
(0.8)
6p gain 81 (18%) 360 0.158
(0.732) 		0.456
(0.922) 		0.531
(0.932) 		0.172
(0.734) 		0.788
(0.988) 		1
(1.00) 		0.799
(0.988) 		0.517
(0.928) 		0.00117
(0.205) 		0.302
(0.852) 		0.908
(1.00) 		0.0382
(0.547) 		0.248
(0.809)
6q gain 66 (15%) 375 0.0168
(0.403) 		0.771
(0.988) 		0.18
(0.737) 		0.175
(0.734) 		0.995
(1.00) 		0.413
(0.919) 		1
(1.00) 		0.862
(1.00) 		0.00164
(0.216) 		0.313
(0.866) 		0.868
(1.00) 		0.0166
(0.403) 		0.163
(0.732)
15q gain 39 (9%) 402 0.0776
(0.621) 		0.624
(0.963) 		0.573
(0.94) 		0.785
(0.988) 		0.0726
(0.621) 		0.175
(0.734) 		0.601
(0.944) 		1
(1.00) 		0.539
(0.932) 		0.00331
(0.274) 		0.205
(0.771) 		0.00194
(0.227) 		1
(1.00)
20q gain 280 (63%) 161 0.47
(0.922) 		0.414
(0.919) 		0.457
(0.922) 		0.159
(0.732) 		0.0893
(0.653) 		0.169
(0.734) 		0.00384
(0.274) 		0.233
(0.8) 		5e-05
(0.0526) 		0.3
(0.85) 		0.401
(0.919) 		0.744
(0.982) 		0.657
(0.969)
5q loss 108 (24%) 333 0.0427
(0.547) 		0.24
(0.801) 		0.00945
(0.302) 		0.607
(0.95) 		0.0784
(0.621) 		0.382
(0.901) 		0.908
(1.00) 		1
(1.00) 		0.00012
(0.0632) 		0.424
(0.919) 		0.256
(0.811) 		0.114
(0.711) 		0.343
(0.881)
8q loss 37 (8%) 404 0.859
(1.00) 		0.883
(1.00) 		0.186
(0.742) 		0.00161
(0.216) 		0.297
(0.847) 		0.734
(0.982) 		0.0728
(0.621) 		0.487
(0.923) 		0.235
(0.8) 		0.141
(0.732) 		0.0612
(0.592) 		0.0463
(0.554) 		1
(1.00)
19p loss 116 (26%) 325 0.078
(0.621) 		0.234
(0.8) 		0.915
(1.00) 		0.936
(1.00) 		0.735
(0.982) 		0.521
(0.929) 		1
(1.00) 		0.774
(0.988) 		0.00045
(0.158) 		0.122
(0.725) 		0.343
(0.881) 		0.112
(0.711) 		1
(1.00)
1p gain 50 (11%) 391 0.225
(0.8) 		0.447
(0.92) 		0.186
(0.742) 		0.203
(0.771) 		0.637
(0.965) 		0.23
(0.8) 		0.273
(0.835) 		0.23
(0.8) 		0.534
(0.932) 		0.382
(0.901) 		0.739
(0.982) 		0.873
(1.00) 		1
(1.00)
1q gain 105 (24%) 336 0.576
(0.94) 		0.816
(0.996) 		0.514
(0.927) 		0.804
(0.988) 		0.0899
(0.653) 		0.502
(0.925) 		0.417
(0.919) 		0.137
(0.732) 		0.168
(0.734) 		0.351
(0.881) 		0.323
(0.873) 		0.221
(0.8) 		0.335
(0.879)
2p gain 78 (18%) 363 0.32
(0.871) 		0.269
(0.835) 		0.679
(0.974) 		0.401
(0.919) 		0.407
(0.919) 		0.626
(0.963) 		0.796
(0.988) 		0.137
(0.732) 		0.0355
(0.547) 		0.299
(0.85) 		0.926
(1.00) 		0.26
(0.821) 		0.591
(0.944)
2q gain 66 (15%) 375 0.88
(1.00) 		0.134
(0.732) 		0.269
(0.835) 		0.619
(0.962) 		0.442
(0.92) 		1
(1.00) 		0.781
(0.988) 		0.113
(0.711) 		0.146
(0.732) 		0.554
(0.938) 		0.93
(1.00) 		0.728
(0.982) 		1
(1.00)
3p gain 52 (12%) 389 0.128
(0.732) 		0.886
(1.00) 		0.926
(1.00) 		0.921
(1.00) 		0.661
(0.971) 		0.56
(0.938) 		0.758
(0.988) 		0.56
(0.938) 		0.609
(0.952) 		1
(1.00) 		0.575
(0.94) 		0.405
(0.919) 		0.0889
(0.653)
3q gain 91 (21%) 350 0.347
(0.881) 		0.573
(0.94) 		0.443
(0.92) 		0.371
(0.889) 		0.556
(0.938) 		0.479
(0.922) 		1
(1.00) 		0.44
(0.92) 		0.632
(0.965) 		0.652
(0.969) 		0.252
(0.809) 		0.201
(0.771) 		0.223
(0.8)
4p gain 21 (5%) 420 0.731
(0.982) 		0.657
(0.969) 		0.0344
(0.547) 		0.287
(0.835) 		0.858
(1.00) 		1
(1.00) 		0.351
(0.881) 		0.759
(0.988) 		0.158
(0.732) 		0.368
(0.889) 		0.467
(0.922) 		1
(1.00) 		1
(1.00)
4q gain 16 (4%) 425 0.75
(0.987) 		0.157
(0.732) 		0.342
(0.881) 		0.819
(0.997) 		0.639
(0.967) 		1
(1.00) 		0.435
(0.92) 		0.736
(0.982) 		0.0547
(0.576) 		0.711
(0.982) 		0.763
(0.988) 		1
(1.00) 		1
(1.00)
5p gain 100 (23%) 341 0.776
(0.988) 		0.428
(0.92) 		0.874
(1.00) 		0.037
(0.547) 		0.778
(0.988) 		0.651
(0.969) 		0.906
(1.00) 		1
(1.00) 		0.00715
(0.279) 		0.981
(1.00) 		0.237
(0.8) 		0.838
(1.00) 		1
(1.00)
5q gain 43 (10%) 398 0.625
(0.963) 		0.351
(0.881) 		0.501
(0.925) 		0.134
(0.732) 		0.761
(0.988) 		1
(1.00) 		0.504
(0.925) 		0.831
(1.00) 		0.0604
(0.592) 		0.813
(0.995) 		0.998
(1.00) 		0.939
(1.00) 		1
(1.00)
7p gain 202 (46%) 239 0.922
(1.00) 		0.213
(0.791) 		0.778
(0.988) 		0.705
(0.982) 		0.464
(0.922) 		0.346
(0.881) 		0.111
(0.711) 		0.899
(1.00) 		0.0616
(0.592) 		0.673
(0.974) 		0.234
(0.8) 		0.307
(0.863) 		0.657
(0.969)
7q gain 171 (39%) 270 0.687
(0.979) 		0.46
(0.922) 		0.739
(0.982) 		0.824
(1) 		0.452
(0.922) 		0.436
(0.92) 		0.154
(0.732) 		0.694
(0.982) 		0.205
(0.771) 		0.328
(0.875) 		0.31
(0.863) 		0.229
(0.8) 		0.364
(0.889)
8p gain 183 (41%) 258 0.549
(0.938) 		0.0126
(0.357) 		0.572
(0.94) 		0.294
(0.844) 		0.539
(0.932) 		1
(1.00) 		0.00869
(0.302) 		0.796
(0.988) 		0.147
(0.732) 		0.0622
(0.592) 		0.494
(0.925) 		0.925
(1.00) 		1
(1.00)
8q gain 240 (54%) 201 0.778
(0.988) 		0.028
(0.547) 		0.374
(0.89) 		0.285
(0.835) 		0.55
(0.938) 		0.452
(0.922) 		0.0739
(0.621) 		1
(1.00) 		0.463
(0.922) 		0.012
(0.35) 		0.764
(0.988) 		0.485
(0.923) 		0.386
(0.904)
9p gain 59 (13%) 382 0.0368
(0.547) 		0.631
(0.965) 		0.988
(1.00) 		0.244
(0.801) 		0.959
(1.00) 		0.783
(0.988) 		0.773
(0.988) 		0.0626
(0.592) 		0.00584
(0.279) 		0.667
(0.973) 		0.888
(1.00) 		0.569
(0.94) 		0.135
(0.732)
9q gain 77 (17%) 364 0.119
(0.721) 		0.229
(0.8) 		0.923
(1.00) 		0.331
(0.876) 		0.958
(1.00) 		0.627
(0.964) 		0.364
(0.889) 		0.0497
(0.557) 		0.0354
(0.547) 		0.417
(0.919) 		0.407
(0.919) 		1
(1.00) 		0.198
(0.771)
10p gain 98 (22%) 343 0.324
(0.873) 		0.932
(1.00) 		0.655
(0.969) 		0.479
(0.922) 		0.724
(0.982) 		1
(1.00) 		0.551
(0.938) 		0.444
(0.92) 		0.308
(0.863) 		0.513
(0.927) 		0.78
(0.988) 		0.00636
(0.279) 		0.594
(0.944)
10q gain 67 (15%) 374 0.739
(0.982) 		0.116
(0.714) 		0.106
(0.703) 		0.551
(0.938) 		0.2
(0.771) 		0.599
(0.944) 		0.583
(0.941) 		0.725
(0.982) 		0.425
(0.919) 		0.744
(0.982) 		0.949
(1.00) 		0.105
(0.701) 		1
(1.00)
11p gain 62 (14%) 379 0.83
(1.00) 		0.386
(0.904) 		0.446
(0.92) 		0.248
(0.809) 		0.0706
(0.621) 		1
(1.00) 		1
(1.00) 		0.0996
(0.685) 		0.35
(0.881) 		0.423
(0.919) 		0.114
(0.711) 		0.0836
(0.63) 		0.497
(0.925)
11q gain 74 (17%) 367 0.596
(0.944) 		0.565
(0.94) 		0.204
(0.771) 		0.633
(0.965) 		0.0353
(0.547) 		0.801
(0.988) 		0.356
(0.881) 		0.041
(0.547) 		0.121
(0.725) 		0.371
(0.889) 		0.198
(0.771) 		0.071
(0.621) 		0.549
(0.938)
12p gain 92 (21%) 349 0.27
(0.835) 		0.397
(0.918) 		0.789
(0.988) 		0.0402
(0.547) 		0.283
(0.835) 		1
(1.00) 		0.714
(0.982) 		1
(1.00) 		0.437
(0.92) 		0.155
(0.732) 		0.534
(0.932) 		0.834
(1.00) 		0.3
(0.85)
12q gain 78 (18%) 363 0.678
(0.974) 		0.0819
(0.625) 		0.755
(0.988) 		0.272
(0.835) 		0.0607
(0.592) 		0.804
(0.988) 		0.516
(0.928) 		0.623
(0.963) 		0.181
(0.737) 		0.653
(0.969) 		0.769
(0.988) 		0.103
(0.701) 		0.242
(0.801)
13q gain 153 (35%) 288 0.278
(0.835) 		0.944
(1.00) 		0.734
(0.982) 		0.504
(0.925) 		0.707
(0.982) 		0.845
(1.00) 		0.175
(0.734) 		0.893
(1.00) 		0.214
(0.791) 		0.796
(0.988) 		0.34
(0.881) 		0.34
(0.881) 		0.661
(0.971)
14q gain 28 (6%) 413 0.184
(0.742) 		0.617
(0.961) 		0.371
(0.889) 		0.875
(1.00) 		0.175
(0.734) 		0.0405
(0.547) 		0.423
(0.919) 		0.453
(0.922) 		0.473
(0.922) 		0.131
(0.732) 		0.0481
(0.557) 		0.409
(0.919) 		0.277
(0.835)
16p gain 58 (13%) 383 0.129
(0.732) 		0.404
(0.919) 		0.0301
(0.547) 		0.526
(0.93) 		0.318
(0.867) 		0.239
(0.801) 		0.884
(1.00) 		0.56
(0.938) 		0.858
(1.00) 		0.115
(0.711) 		0.0603
(0.592) 		0.235
(0.8) 		0.506
(0.925)
16q gain 48 (11%) 393 0.0394
(0.547) 		0.625
(0.963) 		0.17
(0.734) 		0.744
(0.982) 		0.425
(0.919) 		0.054
(0.576) 		0.752
(0.988) 		0.285
(0.835) 		0.241
(0.801) 		0.155
(0.732) 		0.0426
(0.547) 		0.173
(0.734) 		0.431
(0.92)
17p gain 29 (7%) 412 0.346
(0.881) 		0.229
(0.8) 		0.0794
(0.621) 		0.642
(0.967) 		0.595
(0.944) 		0.0935
(0.66) 		0.69
(0.98) 		1
(1.00) 		0.0138
(0.381) 		0.0185
(0.424) 		0.784
(0.988) 		0.0568
(0.58) 		1
(1.00)
17q gain 64 (15%) 377 0.51
(0.926) 		0.798
(0.988) 		0.157
(0.732) 		0.666
(0.973) 		0.469
(0.922) 		0.163
(0.732) 		0.324
(0.873) 		0.59
(0.944) 		0.128
(0.732) 		0.019
(0.425) 		0.945
(1.00) 		0.0437
(0.547) 		0.506
(0.925)
18p gain 85 (19%) 356 0.0496
(0.557) 		0.0838
(0.63) 		0.555
(0.938) 		0.17
(0.734) 		0.356
(0.881) 		1
(1.00) 		0.103
(0.701) 		0.873
(1.00) 		0.0362
(0.547) 		0.733
(0.982) 		0.425
(0.919) 		0.31
(0.863) 		1
(1.00)
18q gain 55 (12%) 386 0.288
(0.835) 		0.526
(0.93) 		0.353
(0.881) 		0.00916
(0.302) 		0.42
(0.919) 		0.767
(0.988) 		0.229
(0.8) 		0.44
(0.92) 		0.021
(0.461) 		0.804
(0.988) 		0.583
(0.941) 		0.536
(0.932) 		0.524
(0.929)
19p gain 53 (12%) 388 0.348
(0.881) 		0.538
(0.932) 		0.726
(0.982) 		0.0806
(0.621) 		0.0649
(0.6) 		0.151
(0.732) 		1
(1.00) 		0.699
(0.982) 		0.287
(0.835) 		0.0808
(0.621) 		0.0258
(0.547) 		0.953
(1.00) 		1
(1.00)
19q gain 79 (18%) 362 0.868
(1.00) 		0.738
(0.982) 		0.88
(1.00) 		0.18
(0.737) 		0.00469
(0.274) 		0.803
(0.988) 		0.606
(0.949) 		0.181
(0.737) 		0.726
(0.982) 		0.0916
(0.659) 		0.0151
(0.388) 		0.147
(0.732) 		0.595
(0.944)
20p gain 242 (55%) 199 0.168
(0.734) 		0.415
(0.919) 		0.822
(0.999) 		0.375
(0.89) 		0.243
(0.801) 		0.253
(0.809) 		0.0363
(0.547) 		0.0553
(0.577) 		0.0432
(0.547) 		0.901
(1.00) 		0.421
(0.919) 		0.625
(0.963) 		0.656
(0.969)
21q gain 22 (5%) 419 0.35
(0.881) 		0.807
(0.991) 		0.566
(0.94) 		0.332
(0.876) 		0.642
(0.967) 		1
(1.00) 		1
(1.00) 		0.548
(0.938) 		0.289
(0.835) 		0.779
(0.988) 		0.105
(0.701) 		0.815
(0.995) 		1
(1.00)
22q gain 32 (7%) 409 0.47
(0.922) 		0.713
(0.982) 		0.289
(0.835) 		0.0526
(0.571) 		0.635
(0.965) 		1
(1.00) 		0.57
(0.94) 		0.634
(0.965) 		0.478
(0.922) 		0.962
(1.00) 		0.938
(1.00) 		0.508
(0.925) 		0.346
(0.881)
xp gain 51 (12%) 390 0.624
(0.963) 		0.738
(0.982) 		0.0305
(0.547) 		0.392
(0.913) 		0.475
(0.922) 		0.767
(0.988) 		0.163
(0.732) 		1
(1.00) 		0.176
(0.734) 		0.785
(0.988) 		0.125
(0.732) 		0.0111
(0.335) 		1
(1.00)
xq gain 55 (12%) 386 0.699
(0.982) 		0.978
(1.00) 		0.146
(0.732) 		0.517
(0.928) 		0.272
(0.835) 		0.4
(0.919) 		0.229
(0.8) 		0.441
(0.92) 		0.00343
(0.274) 		0.398
(0.918) 		0.0869
(0.645) 		0.0406
(0.547) 		0.488
(0.924)
1p loss 58 (13%) 383 0.14
(0.732) 		0.872
(1.00) 		0.447
(0.92) 		0.222
(0.8) 		0.93
(1.00) 		0.0449
(0.547) 		1
(1.00) 		0.572
(0.94) 		0.0417
(0.547) 		0.00338
(0.274) 		0.73
(0.982) 		0.173
(0.734) 		1
(1.00)
1q loss 25 (6%) 416 0.171
(0.734) 		0.997
(1.00) 		0.741
(0.982) 		0.542
(0.935) 		0.643
(0.968) 		0.063
(0.592) 		0.671
(0.974) 		1
(1.00) 		0.792
(0.988) 		0.0452
(0.547) 		0.42
(0.919) 		0.502
(0.925) 		1
(1.00)
2p loss 23 (5%) 418 0.706
(0.982) 		0.549
(0.938) 		0.489
(0.924) 		0.579
(0.941) 		0.667
(0.973) 		0.385
(0.904) 		0.117
(0.718) 		0.411
(0.919) 		0.148
(0.732) 		0.109
(0.711) 		0.522
(0.929) 		0.572
(0.94) 		1
(1.00)
2q loss 30 (7%) 411 0.957
(1.00) 		0.914
(1.00) 		0.782
(0.988) 		0.829
(1.00) 		0.367
(0.889) 		0.709
(0.982) 		1
(1.00) 		0.0808
(0.621) 		0.00665
(0.279) 		0.163
(0.732) 		0.489
(0.924) 		0.132
(0.732) 		1
(1.00)
3p loss 93 (21%) 348 0.31
(0.863) 		0.537
(0.932) 		0.998
(1.00) 		0.868
(1.00) 		0.0162
(0.403) 		0.0995
(0.685) 		1
(1.00) 		1
(1.00) 		0.277
(0.835) 		0.359
(0.887) 		0.94
(1.00) 		0.879
(1.00) 		1
(1.00)
3q loss 56 (13%) 385 0.95
(1.00) 		0.393
(0.913) 		0.651
(0.969) 		0.00705
(0.279) 		0.334
(0.877) 		0.0941
(0.66) 		0.768
(0.988) 		0.573
(0.94) 		0.138
(0.732) 		0.87
(1.00) 		0.791
(0.988) 		0.666
(0.973) 		0.497
(0.925)
4p loss 167 (38%) 274 0.534
(0.932) 		0.397
(0.918) 		0.225
(0.8) 		0.0429
(0.547) 		0.389
(0.908) 		0.118
(0.718) 		0.759
(0.988) 		0.432
(0.92) 		0.18
(0.737) 		0.988
(1.00) 		0.203
(0.771) 		0.73
(0.982) 		1
(1.00)
4q loss 165 (37%) 276 0.153
(0.732) 		0.135
(0.732) 		0.329
(0.876) 		0.13
(0.732) 		0.276
(0.835) 		0.243
(0.801) 		0.758
(0.988) 		0.793
(0.988) 		0.143
(0.732) 		0.873
(1.00) 		0.104
(0.701) 		0.856
(1.00) 		1
(1.00)
5p loss 63 (14%) 378 0.00404
(0.274) 		0.122
(0.725) 		0.149
(0.732) 		0.176
(0.734) 		0.0943
(0.66) 		1
(1.00) 		0.777
(0.988) 		0.477
(0.922) 		0.0739
(0.621) 		0.783
(0.988) 		0.368
(0.889) 		0.0443
(0.547) 		1
(1.00)
6p loss 50 (11%) 391 0.48
(0.922) 		0.998
(1.00) 		0.499
(0.925) 		0.345
(0.881) 		0.649
(0.969) 		0.76
(0.988) 		0.273
(0.835) 		1
(1.00) 		0.074
(0.621) 		0.504
(0.925) 		0.975
(1.00) 		0.79
(0.988) 		1
(1.00)
6q loss 69 (16%) 372 0.325
(0.873) 		0.432
(0.92) 		0.594
(0.944) 		0.161
(0.732) 		0.414
(0.919) 		0.285
(0.835) 		0.22
(0.8) 		1
(1.00) 		0.0775
(0.621) 		0.707
(0.982) 		0.417
(0.919) 		0.508
(0.925) 		1
(1.00)
7p loss 17 (4%) 424 0.695
(0.982) 		0.635
(0.965) 		0.728
(0.982) 		0.159
(0.732) 		0.0391
(0.547) 		1
(1.00) 		0.317
(0.867) 		0.318
(0.867) 		0.458
(0.922) 		0.925
(1.00) 		0.287
(0.835) 		0.158
(0.732) 		1
(1.00)
7q loss 29 (7%) 412 0.678
(0.974) 		0.16
(0.732) 		0.221
(0.8) 		0.0147
(0.388) 		0.0361
(0.547) 		0.709
(0.982) 		0.69
(0.98) 		0.799
(0.988) 		0.212
(0.788) 		0.915
(1.00) 		0.474
(0.922) 		0.289
(0.835) 		1
(1.00)
9p loss 149 (34%) 292 0.181
(0.737) 		0.092
(0.659) 		0.649
(0.969) 		0.834
(1.00) 		0.328
(0.875) 		0.694
(0.982) 		0.601
(0.944) 		0.788
(0.988) 		0.0391
(0.547) 		0.523
(0.929) 		0.185
(0.742) 		0.282
(0.835) 		0.661
(0.971)
9q loss 104 (24%) 337 0.173
(0.734) 		0.414
(0.919) 		0.746
(0.983) 		0.606
(0.949) 		0.758
(0.988) 		1
(1.00) 		0.484
(0.923) 		0.765
(0.988) 		0.36
(0.887) 		0.82
(0.997) 		0.113
(0.711) 		0.182
(0.737) 		1
(1.00)
10p loss 64 (15%) 377 0.191
(0.753) 		0.839
(1.00) 		0.206
(0.771) 		0.331
(0.876) 		0.0695
(0.621) 		0.599
(0.944) 		0.481
(0.922) 		0.111
(0.711) 		0.147
(0.732) 		0.574
(0.94) 		0.00717
(0.279) 		0.24
(0.801) 		0.524
(0.929)
10q loss 68 (15%) 373 0.51
(0.926) 		0.0757
(0.621) 		0.282
(0.835) 		0.67
(0.974) 		0.0482
(0.557) 		0.433
(0.92) 		1
(1.00) 		0.482
(0.922) 		0.0674
(0.617) 		1
(1.00) 		0.0045
(0.274) 		0.325
(0.873) 		0.558
(0.938)
11p loss 64 (15%) 377 0.206
(0.771) 		0.556
(0.938) 		0.236
(0.8) 		0.364
(0.889) 		0.28
(0.835) 		0.176
(0.734) 		0.673
(0.974) 		0.375
(0.89) 		0.00942
(0.302) 		0.371
(0.889) 		0.0486
(0.557) 		0.737
(0.982) 		0.524
(0.929)
11q loss 61 (14%) 380 0.0799
(0.621) 		0.961
(1.00) 		0.203
(0.771) 		0.876
(1.00) 		0.0279
(0.547) 		0.573
(0.94) 		0.196
(0.766) 		0.857
(1.00) 		0.142
(0.732) 		0.536
(0.932) 		0.0146
(0.388) 		0.961
(1.00) 		0.524
(0.929)
12p loss 62 (14%) 379 0.00636
(0.279) 		0.0649
(0.6) 		0.858
(1.00) 		0.272
(0.835) 		0.846
(1.00) 		1
(1.00) 		0.475
(0.922) 		0.857
(1.00) 		0.00641
(0.279) 		0.458
(0.922) 		0.44
(0.92) 		0.496
(0.925) 		0.479
(0.922)
12q loss 52 (12%) 389 0.0284
(0.547) 		0.254
(0.809) 		0.904
(1.00) 		0.133
(0.732) 		0.461
(0.922) 		0.557
(0.938) 		0.538
(0.932) 		0.424
(0.919) 		0.0431
(0.547) 		0.449
(0.92) 		0.524
(0.929) 		0.46
(0.922) 		0.4
(0.919)
13q loss 37 (8%) 404 0.502
(0.925) 		0.346
(0.881) 		0.733
(0.982) 		0.728
(0.982) 		0.738
(0.982) 		0.717
(0.982) 		0.592
(0.944) 		1
(1.00) 		0.58
(0.941) 		0.137
(0.732) 		0.629
(0.964) 		0.775
(0.988) 		0.368
(0.889)
14q loss 111 (25%) 330 0.843
(1.00) 		0.6
(0.944) 		0.262
(0.822) 		0.326
(0.874) 		0.434
(0.92) 		0.0752
(0.621) 		0.732
(0.982) 		1
(1.00) 		0.287
(0.835) 		0.427
(0.92) 		0.556
(0.938) 		1
(1.00) 		0.333
(0.876)
15q loss 90 (20%) 351 0.95
(1.00) 		0.499
(0.925) 		0.565
(0.94) 		0.0544
(0.576) 		0.829
(1.00) 		0.814
(0.995) 		0.712
(0.982) 		0.0561
(0.579) 		0.0337
(0.547) 		0.756
(0.988) 		0.482
(0.922) 		0.449
(0.92) 		0.293
(0.843)
16p loss 100 (23%) 341 0.469
(0.922) 		0.0747
(0.621) 		0.681
(0.974) 		0.683
(0.974) 		0.706
(0.982) 		0.112
(0.711) 		0.636
(0.965) 		0.547
(0.938) 		0.00568
(0.279) 		0.597
(0.944) 		0.583
(0.941) 		0.368
(0.889) 		0.588
(0.944)
16q loss 114 (26%) 327 0.281
(0.835) 		0.786
(0.988) 		0.207
(0.775) 		0.664
(0.973) 		0.903
(1.00) 		0.0325
(0.547) 		0.497
(0.925) 		0.0846
(0.632) 		0.00461
(0.274) 		0.7
(0.982) 		0.737
(0.982) 		0.628
(0.964) 		1
(1.00)
17p loss 164 (37%) 277 0.802
(0.988) 		0.997
(1.00) 		0.673
(0.974) 		0.218
(0.8) 		0.74
(0.982) 		0.441
(0.92) 		0.051
(0.559) 		0.147
(0.732) 		0.00832
(0.302) 		0.191
(0.753) 		0.512
(0.927) 		0.472
(0.922) 		1
(1.00)
17q loss 74 (17%) 367 0.915
(1.00) 		0.836
(1.00) 		0.695
(0.982) 		0.433
(0.92) 		0.27
(0.835) 		0.446
(0.92) 		0.895
(1.00) 		0.863
(1.00) 		0.147
(0.732) 		0.85
(1.00) 		0.253
(0.809) 		0.244
(0.801) 		0.589
(0.944)
18p loss 119 (27%) 322 0.256
(0.811) 		0.854
(1.00) 		0.92
(1.00) 		0.309
(0.863) 		0.59
(0.944) 		0.676
(0.974) 		0.0337
(0.547) 		1
(1.00) 		0.814
(0.995) 		0.704
(0.982) 		0.235
(0.8) 		0.0389
(0.547) 		0.136
(0.732)
18q loss 154 (35%) 287 0.848
(1.00) 		0.19
(0.753) 		0.761
(0.988) 		0.0092
(0.302) 		0.913
(1.00) 		1
(1.00) 		0.533
(0.932) 		0.506
(0.925) 		0.615
(0.96) 		0.939
(1.00) 		0.13
(0.732) 		0.641
(0.967) 		0.341
(0.881)
19q loss 86 (20%) 355 0.73
(0.982) 		0.0697
(0.621) 		0.924
(1.00) 		0.974
(1.00) 		0.716
(0.982) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00353
(0.274) 		0.113
(0.711) 		0.977
(1.00) 		0.416
(0.919) 		1
(1.00)
20p loss 22 (5%) 419 0.356
(0.881) 		0.791
(0.988) 		0.236
(0.8) 		0.356
(0.881) 		0.464
(0.922) 		0.147
(0.732) 		0.174
(0.734) 		0.0346
(0.547) 		0.674
(0.974) 		0.566
(0.94) 		0.494
(0.925) 		0.295
(0.845) 		1
(1.00)
21q loss 181 (41%) 260 0.701
(0.982) 		0.0947
(0.66) 		0.682
(0.974) 		0.578
(0.941) 		0.363
(0.889) 		0.249
(0.809) 		0.314
(0.866) 		0.157
(0.732) 		0.236
(0.8) 		0.654
(0.969) 		0.428
(0.92) 		0.582
(0.941) 		1
(1.00)
22q loss 146 (33%) 295 0.38
(0.899) 		0.982
(1.00) 		0.556
(0.938) 		0.317
(0.867) 		0.256
(0.811) 		0.158
(0.732) 		0.527
(0.93) 		0.14
(0.732) 		0.274
(0.835) 		0.409
(0.919) 		0.0489
(0.557) 		0.582
(0.941) 		0.654
(0.969)
xp loss 61 (14%) 380 0.162
(0.732) 		0.717
(0.982) 		0.218
(0.8) 		0.742
(0.982) 		0.676
(0.974) 		0.407
(0.919) 		0.0609
(0.592) 		0.467
(0.922) 		0.0749
(0.621) 		0.457
(0.922) 		0.731
(0.982) 		0.375
(0.89) 		0.146
(0.732)
xq loss 55 (12%) 386 0.482
(0.922) 		0.682
(0.974) 		0.252
(0.809) 		0.472
(0.922) 		0.991
(1.00) 		0.153
(0.732) 		0.0505
(0.559) 		0.126
(0.732) 		0.82
(0.997) 		0.195
(0.766) 		0.69
(0.98) 		0.486
(0.923) 		0.479
(0.922)
'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00117 (Fisher's exact test), Q value = 0.21

Table S1.  Gene #11: '6p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA, SIGNET RING TYPE STOMACH, ADENOCARCINOMA, DIFFUSE TYPE STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
ALL 13 72 163 21 82 8 79
6P GAIN MUTATED 2 3 34 1 23 1 17
6P GAIN WILD-TYPE 11 69 129 20 59 7 62

Figure S1.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00164 (Fisher's exact test), Q value = 0.22

Table S2.  Gene #12: '6q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA, SIGNET RING TYPE STOMACH, ADENOCARCINOMA, DIFFUSE TYPE STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
ALL 13 72 163 21 82 8 79
6Q GAIN MUTATED 2 2 30 0 19 1 12
6Q GAIN WILD-TYPE 11 70 133 21 63 7 67

Figure S2.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'RACE'

P value = 0.00194 (Fisher's exact test), Q value = 0.23

Table S3.  Gene #27: '15q gain' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 88 12 1 278
15Q GAIN MUTATED 9 4 1 19
15Q GAIN WILD-TYPE 79 8 0 259

Figure S3.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #12: 'RACE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.053

Table S4.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA, SIGNET RING TYPE STOMACH, ADENOCARCINOMA, DIFFUSE TYPE STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
ALL 13 72 163 21 82 8 79
20Q GAIN MUTATED 8 32 96 11 62 6 62
20Q GAIN WILD-TYPE 5 40 67 10 20 2 17

Figure S4.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.063

Table S5.  Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA, SIGNET RING TYPE STOMACH, ADENOCARCINOMA, DIFFUSE TYPE STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
ALL 13 72 163 21 82 8 79
5Q LOSS MUTATED 3 6 35 5 23 2 34
5Q LOSS WILD-TYPE 10 66 128 16 59 6 45

Figure S5.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'GENDER'

P value = 0.000856 (Fisher's exact test), Q value = 0.21

Table S6.  Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 158 283
8P LOSS MUTATED 19 72
8P LOSS WILD-TYPE 139 211

Figure S6.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00113 (Wilcoxon-test), Q value = 0.21

Table S7.  Gene #56: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 391 5.6 (8.4)
8P LOSS MUTATED 83 8.2 (11.4)
8P LOSS WILD-TYPE 308 5.0 (7.3)

Figure S7.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00161 (Fisher's exact test), Q value = 0.22

Table S8.  Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 23 93 196 119
8Q LOSS MUTATED 2 6 26 2
8Q LOSS WILD-TYPE 21 87 170 117

Figure S8.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00045 (Fisher's exact test), Q value = 0.16

Table S9.  Gene #75: '19p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA, SIGNET RING TYPE STOMACH, ADENOCARCINOMA, DIFFUSE TYPE STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
ALL 13 72 163 21 82 8 79
19P LOSS MUTATED 2 10 40 1 31 4 28
19P LOSS WILD-TYPE 11 62 123 20 51 4 51

Figure S9.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

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/STAD-TP/22533931/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/22507291/STAD-TP.merged_data.txt

  • Number of patients = 441

  • Number of significantly arm-level cnvs = 81

  • Number of selected clinical features = 13

  • 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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