Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1JW8D57
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/C1JW8D57
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, 4 significant findings detected with Q value < 0.25.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 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, 4 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
20q gain 279 (63%) 162 0.588
(0.937) 		0.355
(0.888) 		0.365
(0.891) 		0.186
(0.758) 		0.106
(0.653) 		0.171
(0.739) 		0.00533
(0.349) 		0.181
(0.749) 		0.00012
(0.0597) 		0.321
(0.878) 		0.461
(0.937) 		0.692
(0.961) 		0.656
(0.951)
5q loss 106 (24%) 335 0.146
(0.717) 		0.162
(0.739) 		0.0116
(0.392) 		0.686
(0.961) 		0.119
(0.677) 		0.381
(0.897) 		0.908
(1.00) 		1
(1.00) 		0.00017
(0.0597) 		0.555
(0.937) 		0.512
(0.937) 		0.206
(0.764) 		0.594
(0.937)
8q loss 33 (7%) 408 0.37
(0.891) 		0.924
(1.00) 		0.0297
(0.538) 		0.00039
(0.103) 		0.068
(0.596) 		0.491
(0.937) 		0.0885
(0.636) 		0.628
(0.944) 		0.235
(0.787) 		0.0966
(0.636) 		0.00789
(0.378) 		0.0319
(0.538) 		1
(1.00)
19p loss 115 (26%) 326 0.0241
(0.517) 		0.172
(0.739) 		0.966
(1.00) 		0.926
(1.00) 		0.405
(0.906) 		0.521
(0.937) 		0.822
(0.995) 		0.884
(1.00) 		0.00011
(0.0597) 		0.195
(0.762) 		0.14
(0.717) 		0.0326
(0.538) 		1
(1.00)
1p gain 51 (12%) 390 0.444
(0.931) 		0.19
(0.762) 		0.269
(0.825) 		0.198
(0.762) 		0.978
(1.00) 		0.231
(0.787) 		0.354
(0.888) 		0.164
(0.739) 		0.273
(0.829) 		0.274
(0.829) 		0.769
(0.976) 		0.876
(1.00) 		1
(1.00)
1q gain 103 (23%) 338 0.37
(0.891) 		0.666
(0.953) 		0.698
(0.961) 		0.733
(0.966) 		0.197
(0.762) 		0.503
(0.937) 		0.558
(0.937) 		0.287
(0.841) 		0.194
(0.762) 		0.758
(0.972) 		0.494
(0.937) 		0.202
(0.762) 		0.335
(0.888)
2p gain 77 (17%) 364 0.506
(0.937) 		0.296
(0.844) 		0.652
(0.951) 		0.308
(0.862) 		0.371
(0.891) 		0.626
(0.944) 		0.897
(1.00) 		0.0675
(0.596) 		0.0267
(0.533) 		0.318
(0.876) 		0.917
(1.00) 		0.355
(0.888) 		0.593
(0.937)
2q gain 66 (15%) 375 0.97
(1.00) 		0.221
(0.777) 		0.342
(0.888) 		0.589
(0.937) 		0.439
(0.931) 		1
(1.00) 		1
(1.00) 		0.112
(0.659) 		0.105
(0.652) 		0.558
(0.937) 		0.867
(1.00) 		0.778
(0.979) 		1
(1.00)
3p gain 53 (12%) 388 0.14
(0.717) 		0.931
(1.00) 		0.928
(1.00) 		0.944
(1.00) 		0.594
(0.937) 		0.562
(0.937) 		0.544
(0.937) 		0.698
(0.961) 		0.645
(0.949) 		0.813
(0.991) 		0.727
(0.966) 		0.291
(0.841) 		0.0936
(0.636)
3q gain 93 (21%) 348 0.191
(0.762) 		0.753
(0.972) 		0.539
(0.937) 		0.349
(0.888) 		0.605
(0.937) 		0.359
(0.889) 		0.903
(1.00) 		0.435
(0.931) 		0.761
(0.972) 		0.733
(0.966) 		0.234
(0.787) 		0.203
(0.762) 		0.235
(0.787)
4p gain 21 (5%) 420 0.95
(1.00) 		0.986
(1.00) 		0.225
(0.783) 		0.727
(0.966) 		1
(1.00) 		1
(1.00) 		0.351
(0.888) 		0.544
(0.937) 		0.248
(0.793) 		0.365
(0.891) 		0.867
(1.00) 		0.869
(1.00) 		1
(1.00)
4q gain 16 (4%) 425 0.499
(0.937) 		0.353
(0.888) 		0.535
(0.937) 		0.753
(0.972) 		0.597
(0.937) 		1
(1.00) 		0.435
(0.931) 		0.736
(0.966) 		0.146
(0.717) 		0.71
(0.965) 		0.355
(0.888) 		0.643
(0.948) 		1
(1.00)
5p gain 102 (23%) 339 0.776
(0.979) 		0.354
(0.888) 		0.937
(1.00) 		0.0404
(0.538) 		0.613
(0.942) 		0.652
(0.951) 		0.907
(1.00) 		0.76
(0.972) 		0.0104
(0.392) 		0.972
(1.00) 		0.198
(0.762) 		0.883
(1.00) 		1
(1.00)
5q gain 44 (10%) 397 0.822
(0.995) 		0.527
(0.937) 		0.603
(0.937) 		0.12
(0.678) 		0.886
(1.00) 		1
(1.00) 		0.622
(0.944) 		0.529
(0.937) 		0.104
(0.652) 		0.808
(0.991) 		0.695
(0.961) 		0.942
(1.00) 		1
(1.00)
6p gain 78 (18%) 363 0.167
(0.739) 		0.496
(0.937) 		0.528
(0.937) 		0.218
(0.771) 		0.946
(1.00) 		1
(1.00) 		0.796
(0.991) 		0.396
(0.905) 		0.00253
(0.266) 		0.23
(0.787) 		0.89
(1.00) 		0.0457
(0.538) 		0.229
(0.787)
6q gain 64 (15%) 377 0.0498
(0.538) 		0.952
(1.00) 		0.126
(0.693) 		0.276
(0.83) 		0.98
(1.00) 		0.282
(0.836) 		1
(1.00) 		1
(1.00) 		0.00193
(0.254) 		0.266
(0.821) 		0.994
(1.00) 		0.0172
(0.454) 		0.151
(0.735)
7p gain 197 (45%) 244 0.814
(0.991) 		0.217
(0.771) 		0.566
(0.937) 		0.896
(1.00) 		0.542
(0.937) 		0.254
(0.798) 		0.0905
(0.636) 		1
(1.00) 		0.0907
(0.636) 		0.456
(0.937) 		0.345
(0.888) 		0.522
(0.937) 		0.655
(0.951)
7q gain 169 (38%) 272 0.594
(0.937) 		0.376
(0.893) 		0.811
(0.991) 		0.87
(1.00) 		0.444
(0.931) 		0.243
(0.792) 		0.186
(0.758) 		0.894
(1.00) 		0.141
(0.717) 		0.302
(0.852) 		0.405
(0.906) 		0.465
(0.937) 		0.364
(0.891)
8p gain 182 (41%) 259 0.139
(0.717) 		0.00958
(0.392) 		0.486
(0.937) 		0.171
(0.739) 		0.749
(0.972) 		0.701
(0.961) 		0.0342
(0.538) 		0.896
(1.00) 		0.175
(0.739) 		0.0418
(0.538) 		0.592
(0.937) 		0.471
(0.937) 		1
(1.00)
8q gain 237 (54%) 204 0.408
(0.909) 		0.0284
(0.533) 		0.0893
(0.636) 		0.0767
(0.63) 		0.757
(0.972) 		0.343
(0.888) 		0.165
(0.739) 		0.699
(0.961) 		0.704
(0.962) 		0.0178
(0.458) 		0.525
(0.937) 		0.754
(0.972) 		1
(1.00)
9p gain 60 (14%) 381 0.0972
(0.636) 		0.504
(0.937) 		0.893
(1.00) 		0.167
(0.739) 		0.747
(0.972) 		0.783
(0.981) 		1
(1.00) 		0.0648
(0.583) 		0.0099
(0.392) 		0.647
(0.949) 		0.655
(0.951) 		0.617
(0.944) 		0.14
(0.717)
9q gain 78 (18%) 363 0.389
(0.904) 		0.313
(0.873) 		0.851
(1.00) 		0.376
(0.893) 		0.951
(1.00) 		0.626
(0.944) 		0.363
(0.891) 		0.0999
(0.639) 		0.0288
(0.533) 		0.4
(0.905) 		0.459
(0.937) 		1
(1.00) 		0.204
(0.762)
10p gain 98 (22%) 343 0.635
(0.944) 		0.974
(1.00) 		0.508
(0.937) 		0.307
(0.862) 		0.556
(0.937) 		1
(1.00) 		0.551
(0.937) 		0.535
(0.937) 		0.315
(0.873) 		0.516
(0.937) 		0.668
(0.953) 		0.0118
(0.392) 		0.594
(0.937)
10q gain 70 (16%) 371 0.848
(1.00) 		0.0876
(0.636) 		0.0391
(0.538) 		0.493
(0.937) 		0.163
(0.739) 		0.801
(0.991) 		0.341
(0.888) 		0.727
(0.966) 		0.4
(0.905) 		0.63
(0.944) 		0.92
(1.00) 		0.143
(0.717) 		0.594
(0.937)
11p gain 64 (15%) 377 0.846
(1.00) 		0.57
(0.937) 		0.399
(0.905) 		0.19
(0.762) 		0.0754
(0.625) 		1
(1.00) 		0.779
(0.979) 		0.14
(0.717) 		0.278
(0.832) 		0.471
(0.937) 		0.0453
(0.538) 		0.0881
(0.636) 		0.497
(0.937)
11q gain 74 (17%) 367 0.677
(0.954) 		0.565
(0.937) 		0.204
(0.762) 		0.636
(0.944) 		0.0349
(0.538) 		0.801
(0.991) 		0.356
(0.888) 		0.084
(0.636) 		0.126
(0.693) 		0.37
(0.891) 		0.198
(0.762) 		0.0704
(0.599) 		0.549
(0.937)
12p gain 90 (20%) 351 0.36
(0.889) 		0.616
(0.943) 		0.455
(0.937) 		0.0344
(0.538) 		0.379
(0.896) 		1
(1.00) 		0.806
(0.991) 		1
(1.00) 		0.377
(0.893) 		0.163
(0.739) 		0.638
(0.944) 		0.81
(0.991) 		0.293
(0.841)
12q gain 77 (17%) 364 0.929
(1.00) 		0.0519
(0.538) 		0.394
(0.905) 		0.186
(0.758) 		0.0484
(0.538) 		0.803
(0.991) 		0.517
(0.937) 		0.738
(0.967) 		0.217
(0.771) 		0.673
(0.954) 		0.647
(0.949) 		0.0805
(0.631) 		0.235
(0.787)
13q gain 154 (35%) 287 0.425
(0.924) 		0.875
(1.00) 		0.527
(0.937) 		0.514
(0.937) 		0.703
(0.961) 		0.845
(1.00) 		0.146
(0.717) 		1
(1.00) 		0.232
(0.787) 		0.805
(0.991) 		0.352
(0.888) 		0.345
(0.888) 		0.66
(0.952)
14q gain 29 (7%) 412 0.113
(0.659) 		0.445
(0.931) 		0.39
(0.904) 		0.896
(1.00) 		0.235
(0.787) 		0.0464
(0.538) 		0.551
(0.937) 		0.807
(0.991) 		0.545
(0.937) 		0.169
(0.739) 		0.0684
(0.596) 		0.554
(0.937) 		0.289
(0.841)
15q gain 39 (9%) 402 0.111
(0.659) 		0.624
(0.944) 		0.291
(0.841) 		0.784
(0.981) 		0.0709
(0.599) 		0.175
(0.739) 		0.601
(0.937) 		1
(1.00) 		0.55
(0.937) 		0.00342
(0.313) 		0.205
(0.762) 		0.00188
(0.254) 		1
(1.00)
16p gain 59 (13%) 382 0.101
(0.643) 		0.337
(0.888) 		0.0255
(0.533) 		0.576
(0.937) 		0.287
(0.841) 		0.239
(0.792) 		0.773
(0.977) 		0.693
(0.961) 		0.835
(1.00) 		0.124
(0.693) 		0.0559
(0.54) 		0.254
(0.798) 		0.515
(0.937)
16q gain 47 (11%) 394 0.0117
(0.392) 		0.566
(0.937) 		0.115
(0.663) 		0.606
(0.938) 		0.421
(0.923) 		0.0484
(0.538) 		0.631
(0.944) 		0.373
(0.893) 		0.195
(0.762) 		0.14
(0.717) 		0.0371
(0.538) 		0.182
(0.749) 		0.421
(0.923)
17p gain 29 (7%) 412 0.248
(0.793) 		0.0961
(0.636) 		0.091
(0.636) 		0.729
(0.966) 		0.702
(0.961) 		0.0935
(0.636) 		0.69
(0.961) 		0.798
(0.991) 		0.0431
(0.538) 		0.0198
(0.486) 		0.988
(1.00) 		0.0572
(0.54) 		1
(1.00)
17q gain 62 (14%) 379 0.953
(1.00) 		0.952
(1.00) 		0.314
(0.873) 		0.561
(0.937) 		0.762
(0.972) 		0.0999
(0.639) 		0.255
(0.798) 		0.715
(0.965) 		0.281
(0.835) 		0.0185
(0.463) 		0.642
(0.948) 		0.0286
(0.533) 		0.488
(0.937)
18p gain 84 (19%) 357 0.0161
(0.454) 		0.156
(0.737) 		0.61
(0.941) 		0.0809
(0.631) 		0.462
(0.937) 		1
(1.00) 		0.164
(0.739) 		1
(1.00) 		0.096
(0.636) 		0.729
(0.966) 		0.586
(0.937) 		0.385
(0.898) 		1
(1.00)
18q gain 54 (12%) 387 0.0986
(0.639) 		0.593
(0.937) 		0.433
(0.93) 		0.00514
(0.349) 		0.398
(0.905) 		0.764
(0.972) 		0.174
(0.739) 		0.686
(0.961) 		0.051
(0.538) 		0.778
(0.979) 		0.455
(0.937) 		0.573
(0.937) 		0.515
(0.937)
19p gain 54 (12%) 387 0.293
(0.841) 		0.547
(0.937) 		0.621
(0.944) 		0.0826
(0.635) 		0.0532
(0.538) 		0.239
(0.792) 		0.88
(1.00) 		0.693
(0.961) 		0.294
(0.841) 		0.0625
(0.567) 		0.0466
(0.538) 		0.953
(1.00) 		1
(1.00)
19q gain 78 (18%) 363 0.875
(1.00) 		0.747
(0.972) 		0.731
(0.966) 		0.216
(0.771) 		0.00608
(0.351) 		0.625
(0.944) 		0.697
(0.961) 		0.127
(0.693) 		0.67
(0.954) 		0.0804
(0.631) 		0.0206
(0.494) 		0.126
(0.693) 		0.595
(0.937)
20p gain 243 (55%) 198 0.448
(0.933) 		0.357
(0.888) 		0.852
(1.00) 		0.527
(0.937) 		0.29
(0.841) 		0.253
(0.798) 		0.0285
(0.533) 		0.0521
(0.538) 		0.0401
(0.538) 		0.902
(1.00) 		0.651
(0.951) 		0.622
(0.944) 		1
(1.00)
21q gain 21 (5%) 420 0.478
(0.937) 		0.763
(0.972) 		0.319
(0.876) 		0.273
(0.829) 		0.657
(0.951) 		1
(1.00) 		0.819
(0.995) 		0.544
(0.937) 		0.333
(0.888) 		0.722
(0.966) 		0.107
(0.653) 		0.798
(0.991) 		1
(1.00)
22q gain 32 (7%) 409 0.857
(1.00) 		0.713
(0.965) 		0.143
(0.717) 		0.0519
(0.538) 		0.615
(0.943) 		1
(1.00) 		0.57
(0.937) 		1
(1.00) 		0.488
(0.937) 		0.962
(1.00) 		0.938
(1.00) 		0.509
(0.937) 		0.346
(0.888)
xp gain 48 (11%) 393 0.383
(0.898) 		0.377
(0.893) 		0.0921
(0.636) 		0.321
(0.878) 		0.154
(0.737) 		1
(1.00) 		0.079
(0.631) 		1
(1.00) 		0.111
(0.659) 		0.406
(0.906) 		0.023
(0.516) 		0.126
(0.693) 		1
(1.00)
xq gain 56 (13%) 385 0.899
(1.00) 		0.933
(1.00) 		0.094
(0.636) 		0.482
(0.937) 		0.0948
(0.636) 		0.565
(0.937) 		0.1
(0.639) 		0.44
(0.931) 		0.0122
(0.392) 		0.409
(0.909) 		0.0316
(0.538) 		0.391
(0.904) 		0.479
(0.937)
1p loss 59 (13%) 382 0.446
(0.931) 		0.727
(0.966) 		0.695
(0.961) 		0.171
(0.739) 		0.809
(0.991) 		0.0474
(0.538) 		0.884
(1.00) 		0.572
(0.937) 		0.0539
(0.538) 		0.00564
(0.349) 		0.758
(0.972) 		0.203
(0.762) 		1
(1.00)
1q loss 28 (6%) 413 0.246
(0.792) 		0.844
(1.00) 		0.855
(1.00) 		0.556
(0.937) 		0.95
(1.00) 		0.0935
(0.636) 		0.688
(0.961) 		1
(1.00) 		0.505
(0.937) 		0.0448
(0.538) 		0.394
(0.905) 		0.664
(0.953) 		1
(1.00)
2p loss 26 (6%) 415 0.216
(0.771) 		0.42
(0.923) 		0.526
(0.937) 		0.524
(0.937) 		0.592
(0.937) 		1
(1.00) 		0.294
(0.841) 		0.597
(0.937) 		0.115
(0.663) 		0.157
(0.737) 		0.388
(0.903) 		0.608
(0.939) 		1
(1.00)
2q loss 33 (7%) 408 0.374
(0.893) 		0.749
(0.972) 		0.764
(0.972) 		0.957
(1.00) 		0.478
(0.937) 		1
(1.00) 		0.851
(1.00) 		0.33
(0.888) 		0.00634
(0.351) 		0.142
(0.717) 		0.368
(0.891) 		0.0878
(0.636) 		1
(1.00)
3p loss 91 (21%) 350 0.334
(0.888) 		0.537
(0.937) 		0.995
(1.00) 		0.894
(1.00) 		0.0164
(0.454) 		0.095
(0.636) 		0.903
(1.00) 		1
(1.00) 		0.216
(0.771) 		0.142
(0.717) 		0.964
(1.00) 		0.83
(1) 		1
(1.00)
3q loss 54 (12%) 387 0.998
(1.00) 		0.571
(0.937) 		0.592
(0.937) 		0.0108
(0.392) 		0.454
(0.937) 		0.0836
(0.636) 		0.88
(1.00) 		0.44
(0.931) 		0.0559
(0.54) 		0.604
(0.937) 		0.736
(0.966) 		0.543
(0.937) 		0.479
(0.937)
4p loss 167 (38%) 274 0.542
(0.937) 		0.537
(0.937) 		0.258
(0.805) 		0.0568
(0.54) 		0.233
(0.787) 		0.118
(0.675) 		0.759
(0.972) 		0.507
(0.937) 		0.255
(0.798) 		0.932
(1.00) 		0.208
(0.766) 		0.729
(0.966) 		1
(1.00)
4q loss 164 (37%) 277 0.279
(0.832) 		0.209
(0.766) 		0.401
(0.905) 		0.131
(0.708) 		0.239
(0.792) 		0.244
(0.792) 		0.681
(0.958) 		0.792
(0.988) 		0.197
(0.762) 		0.658
(0.951) 		0.131
(0.708) 		0.857
(1.00) 		1
(1.00)
5p loss 60 (14%) 381 0.0219
(0.508) 		0.17
(0.739) 		0.199
(0.762) 		0.194
(0.762) 		0.192
(0.762) 		1
(1.00) 		0.563
(0.937) 		0.459
(0.937) 		0.0462
(0.538) 		0.732
(0.966) 		0.334
(0.888) 		0.0355
(0.538) 		1
(1.00)
6p loss 52 (12%) 389 0.384
(0.898) 		0.909
(1.00) 		0.639
(0.945) 		0.145
(0.717) 		0.796
(0.991) 		0.557
(0.937) 		0.648
(0.949) 		1
(1.00) 		0.049
(0.538) 		0.488
(0.937) 		0.987
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 70 (16%) 371 0.419
(0.923) 		0.487
(0.937) 		0.461
(0.937) 		0.0527
(0.538) 		0.519
(0.937) 		0.286
(0.841) 		0.419
(0.923) 		0.861
(1.00) 		0.105
(0.652) 		0.677
(0.954) 		0.494
(0.937) 		0.612
(0.941) 		1
(1.00)
7p loss 20 (5%) 421 0.513
(0.937) 		0.715
(0.965) 		0.71
(0.965) 		0.224
(0.783) 		0.202
(0.762) 		0.637
(0.944) 		0.157
(0.737) 		0.52
(0.937) 		0.354
(0.888) 		0.478
(0.937) 		0.178
(0.741) 		0.0379
(0.538) 		1
(1.00)
7q loss 30 (7%) 411 0.529
(0.937) 		0.276
(0.83) 		0.5
(0.937) 		0.0137
(0.412) 		0.154
(0.737) 		1
(1.00) 		0.328
(0.887) 		1
(1.00) 		0.502
(0.937) 		0.686
(0.961) 		0.244
(0.792) 		0.178
(0.741) 		1
(1.00)
8p loss 88 (20%) 353 0.669
(0.953) 		0.806
(0.991) 		0.059
(0.542) 		0.0592
(0.542) 		0.0127
(0.392) 		0.635
(0.944) 		0.00419
(0.315) 		0.524
(0.937) 		0.0171
(0.454) 		0.244
(0.792) 		0.00188
(0.254) 		0.308
(0.862) 		0.21
(0.767)
9p loss 150 (34%) 291 0.216
(0.771) 		0.0934
(0.636) 		0.599
(0.937) 		0.666
(0.953) 		0.268
(0.825) 		0.693
(0.961) 		0.675
(0.954) 		0.892
(1.00) 		0.0238
(0.517) 		0.498
(0.937) 		0.2
(0.762) 		0.274
(0.829) 		0.664
(0.953)
9q loss 104 (24%) 337 0.49
(0.937) 		0.597
(0.937) 		0.707
(0.964) 		0.443
(0.931) 		0.893
(1.00) 		1
(1.00) 		0.484
(0.937) 		0.648
(0.949) 		0.421
(0.923) 		0.821
(0.995) 		0.155
(0.737) 		0.211
(0.767) 		1
(1.00)
10p loss 64 (15%) 377 0.056
(0.54) 		0.792
(0.988) 		0.262
(0.813) 		0.328
(0.887) 		0.0377
(0.538) 		0.599
(0.937) 		0.481
(0.937) 		0.207
(0.765) 		0.147
(0.717) 		0.577
(0.937) 		0.00387
(0.313) 		0.356
(0.888) 		0.524
(0.937)
10q loss 67 (15%) 374 0.246
(0.792) 		0.0796
(0.631) 		0.259
(0.805) 		0.672
(0.954) 		0.0275
(0.533) 		0.427
(0.926) 		0.89
(1.00) 		0.593
(0.937) 		0.0858
(0.636) 		0.985
(1.00) 		0.00239
(0.266) 		0.323
(0.88) 		0.549
(0.937)
11p loss 62 (14%) 379 0.382
(0.897) 		0.76
(0.972) 		0.362
(0.891) 		0.248
(0.793) 		0.333
(0.888) 		0.167
(0.739) 		0.394
(0.905) 		0.357
(0.888) 		0.0222
(0.508) 		0.298
(0.847) 		0.124
(0.693) 		0.731
(0.966) 		0.524
(0.937)
11q loss 61 (14%) 380 0.159
(0.739) 		0.961
(1.00) 		0.157
(0.737) 		0.877
(1.00) 		0.0289
(0.533) 		0.573
(0.937) 		0.196
(0.762) 		0.709
(0.965) 		0.144
(0.717) 		0.533
(0.937) 		0.0146
(0.428) 		0.961
(1.00) 		0.524
(0.937)
12p loss 63 (14%) 378 0.0699
(0.599) 		0.0426
(0.538) 		0.863
(1.00) 		0.255
(0.798) 		0.77
(0.976) 		1
(1.00) 		0.482
(0.937) 		1
(1.00) 		0.00736
(0.378) 		0.481
(0.937) 		0.44
(0.931) 		0.497
(0.937) 		0.479
(0.937)
12q loss 52 (12%) 389 0.0495
(0.538) 		0.293
(0.841) 		0.882
(1.00) 		0.145
(0.717) 		0.497
(0.937) 		0.557
(0.937) 		0.758
(0.972) 		0.309
(0.862) 		0.0433
(0.538) 		0.399
(0.905) 		0.627
(0.944) 		0.604
(0.937) 		0.4
(0.905)
13q loss 36 (8%) 405 0.758
(0.972) 		0.519
(0.937) 		0.744
(0.972) 		0.825
(0.997) 		0.854
(1.00) 		0.714
(0.965) 		0.471
(0.937) 		1
(1.00) 		0.636
(0.944) 		0.113
(0.659) 		0.555
(0.937) 		0.823
(0.995) 		0.357
(0.888)
14q loss 111 (25%) 330 0.379
(0.896) 		0.6
(0.937) 		0.182
(0.749) 		0.325
(0.883) 		0.425
(0.924) 		0.0752
(0.625) 		0.732
(0.966) 		0.766
(0.973) 		0.301
(0.852) 		0.431
(0.928) 		0.556
(0.937) 		1
(1.00) 		0.333
(0.888)
15q loss 90 (20%) 351 0.658
(0.951) 		0.499
(0.937) 		0.635
(0.944) 		0.0541
(0.538) 		0.838
(1.00) 		0.814
(0.991) 		0.712
(0.965) 		0.0379
(0.538) 		0.0374
(0.538) 		0.754
(0.972) 		0.482
(0.937) 		0.447
(0.931) 		0.293
(0.841)
16p loss 100 (23%) 341 0.328
(0.887) 		0.0533
(0.538) 		0.633
(0.944) 		0.533
(0.937) 		0.716
(0.965) 		0.112
(0.659) 		0.813
(0.991) 		0.355
(0.888) 		0.0107
(0.392) 		0.616
(0.943) 		0.461
(0.937) 		0.43
(0.928) 		0.589
(0.937)
16q loss 115 (26%) 326 0.175
(0.739) 		0.72
(0.966) 		0.224
(0.783) 		0.589
(0.937) 		0.895
(1.00) 		0.0321
(0.538) 		0.572
(0.937) 		0.0416
(0.538) 		0.0115
(0.392) 		0.701
(0.961) 		0.591
(0.937) 		0.622
(0.944) 		1
(1.00)
17p loss 164 (37%) 277 0.782
(0.981) 		0.814
(0.991) 		0.73
(0.966) 		0.337
(0.888) 		0.826
(0.997) 		0.441
(0.931) 		0.051
(0.538) 		0.109
(0.659) 		0.00383
(0.313) 		0.191
(0.762) 		0.43
(0.928) 		0.474
(0.937) 		1
(1.00)
17q loss 74 (17%) 367 0.477
(0.937) 		0.779
(0.979) 		0.744
(0.972) 		0.424
(0.924) 		0.449
(0.933) 		0.446
(0.931) 		0.692
(0.961) 		1
(1.00) 		0.082
(0.635) 		0.851
(1.00) 		0.111
(0.659) 		0.27
(0.827) 		0.589
(0.937)
18p loss 119 (27%) 322 0.177
(0.741) 		0.635
(0.944) 		0.82
(0.995) 		0.111
(0.659) 		0.73
(0.966) 		0.676
(0.954) 		0.0577
(0.54) 		0.773
(0.977) 		0.889
(1.00) 		0.911
(1.00) 		0.212
(0.767) 		0.0875
(0.636) 		0.14
(0.717)
18q loss 154 (35%) 287 0.574
(0.937) 		0.163
(0.739) 		0.54
(0.937) 		0.00758
(0.378) 		0.954
(1.00) 		1
(1.00) 		0.533
(0.937) 		0.688
(0.961) 		0.738
(0.967) 		0.94
(1.00) 		0.222
(0.78) 		0.483
(0.937) 		0.343
(0.888)
19q loss 87 (20%) 354 0.481
(0.937) 		0.0487
(0.538) 		0.969
(1.00) 		0.967
(1.00) 		0.608
(0.939) 		1
(1.00) 		1
(1.00) 		0.745
(0.972) 		0.00152
(0.254) 		0.105
(0.652) 		0.808
(0.991) 		0.175
(0.739) 		1
(1.00)
20p loss 22 (5%) 419 0.0353
(0.538) 		0.791
(0.988) 		0.21
(0.767) 		0.355
(0.888) 		0.46
(0.937) 		0.147
(0.717) 		0.174
(0.739) 		0.0778
(0.63) 		0.666
(0.953) 		0.568
(0.937) 		0.494
(0.937) 		0.297
(0.844) 		1
(1.00)
21q loss 180 (41%) 261 0.676
(0.954) 		0.0711
(0.599) 		0.891
(1.00) 		0.525
(0.937) 		0.406
(0.906) 		0.25
(0.796) 		0.365
(0.891) 		0.241
(0.792) 		0.241
(0.792) 		0.669
(0.953) 		0.416
(0.921) 		0.586
(0.937) 		1
(1.00)
22q loss 146 (33%) 295 0.594
(0.937) 		0.982
(1.00) 		0.731
(0.966) 		0.319
(0.876) 		0.242
(0.792) 		0.158
(0.737) 		0.527
(0.937) 		0.0777
(0.63) 		0.277
(0.832) 		0.406
(0.906) 		0.0489
(0.538) 		0.585
(0.937) 		0.654
(0.951)
xp loss 59 (13%) 382 0.175
(0.739) 		0.946
(1.00) 		0.234
(0.787) 		0.735
(0.966) 		0.625
(0.944) 		0.403
(0.906) 		0.0412
(0.538) 		0.35
(0.888) 		0.0579
(0.54) 		0.17
(0.739) 		0.661
(0.952) 		0.423
(0.924) 		0.135
(0.717)
xq loss 50 (11%) 391 0.518
(0.937) 		0.551
(0.937) 		0.37
(0.891) 		0.57
(0.937) 		0.859
(1.00) 		0.231
(0.787) 		0.0124
(0.392) 		0.0416
(0.538) 		0.88
(1.00) 		0.0655
(0.584) 		0.567
(0.937) 		0.678
(0.954) 		0.441
(0.931)
'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.06

Table S1.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
20Q GAIN MUTATED 32 95 62 62 8 11 6
20Q GAIN WILD-TYPE 40 67 21 17 5 10 2

Figure S1.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00017 (Fisher's exact test), Q value = 0.06

Table S2.  Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
5Q LOSS MUTATED 6 34 22 33 3 5 3
5Q LOSS WILD-TYPE 66 128 61 46 10 16 5

Figure S2.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.1

Table S3.  Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 23 93 196 119
8Q LOSS MUTATED 1 3 26 2
8Q LOSS WILD-TYPE 22 90 170 117

Figure S3.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.06

Table S4.  Gene #75: '19p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
ALL 72 162 83 79 13 21 8
19P LOSS MUTATED 10 36 33 28 3 1 4
19P LOSS WILD-TYPE 62 126 50 51 10 20 4

Figure S4.  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/19782337/transformed.cor.cli.txt

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

  • Number of patients = 441

  • Number of significantly 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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