Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1DB80XC
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/C1DB80XC
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 436 patients, 5 significant findings detected with Q value < 0.25.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 8p loss cnv correlated to '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, 5 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
20q gain 276 (63%) 160 0.498
(0.938) 		0.319
(0.856) 		0.338
(0.864) 		0.142
(0.687) 		0.0573
(0.553) 		0.17
(0.702) 		0.00516
(0.312) 		0.00033
(0.105) 		0.674
(0.964) 		0.314
(0.855) 		0.404
(0.901) 		0.429
(0.906) 		1
(1.00)
5q loss 105 (24%) 331 0.0583
(0.553) 		0.188
(0.716) 		0.0216
(0.417) 		0.772
(0.993) 		0.125
(0.683) 		0.381
(0.898) 		0.907
(1.00) 		0.0004
(0.105) 		1
(1.00) 		0.573
(0.943) 		0.512
(0.942) 		0.157
(0.702) 		0.577
(0.943)
8p loss 85 (19%) 351 0.335
(0.864) 		0.831
(1.00) 		0.0394
(0.494) 		0.0113
(0.339) 		0.00647
(0.312) 		0.633
(0.962) 		0.00799
(0.312) 		0.00608
(0.312) 		1
(1.00) 		0.247
(0.786) 		0.000816
(0.172) 		0.242
(0.782) 		0.528
(0.943)
8q loss 33 (8%) 403 0.361
(0.873) 		0.945
(1.00) 		0.206
(0.73) 		0.00039
(0.105) 		0.0701
(0.558) 		0.493
(0.937) 		0.0885
(0.608) 		0.222
(0.765) 		1
(1.00) 		0.0984
(0.628) 		0.00817
(0.312) 		0.0259
(0.436) 		1
(1.00)
19p loss 114 (26%) 322 0.0252
(0.435) 		0.195
(0.719) 		0.929
(1.00) 		0.996
(1.00) 		0.421
(0.906) 		0.522
(0.943) 		0.821
(1.00) 		0.00035
(0.105) 		0.654
(0.964) 		0.205
(0.73) 		0.137
(0.687) 		0.0199
(0.416) 		1
(1.00)
1p gain 51 (12%) 385 0.405
(0.901) 		0.201
(0.726) 		0.27
(0.802) 		0.172
(0.702) 		0.978
(1.00) 		0.231
(0.782) 		0.352
(0.873) 		0.272
(0.805) 		1
(1.00) 		0.284
(0.815) 		0.777
(0.995) 		0.829
(1.00) 		1
(1.00)
1q gain 103 (24%) 333 0.456
(0.925) 		0.706
(0.972) 		0.699
(0.971) 		0.685
(0.964) 		0.195
(0.719) 		0.502
(0.938) 		0.482
(0.934) 		0.271
(0.802) 		0.63
(0.961) 		0.758
(0.99) 		0.506
(0.938) 		0.131
(0.686) 		0.576
(0.943)
2p gain 76 (17%) 360 0.535
(0.943) 		0.345
(0.869) 		0.766
(0.99) 		0.458
(0.925) 		0.32
(0.856) 		0.627
(0.961) 		0.896
(1.00) 		0.0295
(0.446) 		0.596
(0.947) 		0.329
(0.859) 		0.909
(1.00) 		0.383
(0.9) 		1
(1.00)
2q gain 65 (15%) 371 0.886
(1.00) 		0.266
(0.802) 		0.684
(0.964) 		0.674
(0.964) 		0.414
(0.904) 		1
(1.00) 		0.89
(1.00) 		0.13
(0.684) 		0.598
(0.947) 		0.591
(0.947) 		0.856
(1.00) 		0.767
(0.99) 		1
(1.00)
3p gain 53 (12%) 383 0.147
(0.687) 		0.9
(1.00) 		0.937
(1.00) 		0.961
(1.00) 		0.644
(0.963) 		0.563
(0.943) 		0.648
(0.964) 		0.611
(0.958) 		1
(1.00) 		0.827
(1.00) 		0.739
(0.978) 		0.291
(0.823) 		0.0617
(0.558)
3q gain 93 (21%) 343 0.189
(0.716) 		0.794
(1.00) 		0.571
(0.943) 		0.361
(0.873) 		0.658
(0.964) 		0.358
(0.873) 		1
(1.00) 		0.723
(0.972) 		1
(1.00) 		0.735
(0.976) 		0.242
(0.782) 		0.153
(0.696) 		0.164
(0.702)
4p gain 21 (5%) 415 0.989
(1.00) 		0.964
(1.00) 		0.243
(0.782) 		0.712
(0.972) 		1
(1.00) 		1
(1.00) 		0.254
(0.79) 		0.247
(0.786) 		1
(1.00) 		0.37
(0.884) 		0.86
(1.00) 		0.865
(1.00) 		1
(1.00)
4q gain 16 (4%) 420 0.606
(0.954) 		0.341
(0.866) 		0.553
(0.943) 		0.734
(0.976) 		0.572
(0.943) 		1
(1.00) 		0.433
(0.912) 		0.146
(0.687) 		1
(1.00) 		0.713
(0.972) 		0.361
(0.873) 		0.521
(0.943) 		1
(1.00)
5p gain 100 (23%) 336 0.981
(1.00) 		0.292
(0.823) 		0.914
(1.00) 		0.0559
(0.553) 		0.675
(0.964) 		0.653
(0.964) 		0.906
(1.00) 		0.0075
(0.312) 		0.624
(0.961) 		0.973
(1.00) 		0.261
(0.798) 		0.948
(1.00) 		1
(1.00)
5q gain 43 (10%) 393 0.96
(1.00) 		0.504
(0.938) 		0.784
(0.997) 		0.129
(0.684) 		0.9
(1.00) 		1
(1.00) 		0.739
(0.978) 		0.0806
(0.582) 		0.466
(0.925) 		0.81
(1.00) 		0.852
(1.00) 		0.94
(1.00) 		1
(1.00)
6p gain 76 (17%) 360 0.099
(0.628) 		0.42
(0.906) 		0.581
(0.943) 		0.364
(0.876) 		0.912
(1.00) 		1
(1.00) 		0.696
(0.968) 		0.00285
(0.254) 		0.0686
(0.558) 		0.238
(0.782) 		0.775
(0.994) 		0.0344
(0.476) 		0.549
(0.943)
6q gain 62 (14%) 374 0.0207
(0.416) 		0.856
(1.00) 		0.144
(0.687) 		0.446
(0.924) 		0.981
(1.00) 		0.284
(0.815) 		0.887
(1.00) 		0.00237
(0.254) 		0.04
(0.495) 		0.269
(0.802) 		0.878
(1.00) 		0.0121
(0.354) 		0.452
(0.925)
7p gain 196 (45%) 240 0.94
(1.00) 		0.229
(0.78) 		0.686
(0.965) 		0.94
(1.00) 		0.492
(0.937) 		0.254
(0.79) 		0.0726
(0.558) 		0.0999
(0.63) 		1
(1.00) 		0.461
(0.925) 		0.351
(0.873) 		0.38
(0.896) 		0.319
(0.856)
7q gain 168 (39%) 268 0.874
(1.00) 		0.402
(0.901) 		0.862
(1.00) 		0.828
(1.00) 		0.397
(0.901) 		0.243
(0.782) 		0.183
(0.71) 		0.16
(0.702) 		1
(1.00) 		0.306
(0.844) 		0.407
(0.901) 		0.352
(0.873) 		0.147
(0.687)
8p gain 180 (41%) 256 0.149
(0.687) 		0.0105
(0.324) 		0.545
(0.943) 		0.133
(0.686) 		0.716
(0.972) 		0.701
(0.971) 		0.0336
(0.472) 		0.17
(0.702) 		0.236
(0.782) 		0.0414
(0.497) 		0.503
(0.938) 		0.587
(0.947) 		1
(1.00)
8q gain 234 (54%) 202 0.507
(0.938) 		0.025
(0.435) 		0.0936
(0.616) 		0.0784
(0.573) 		0.739
(0.978) 		0.342
(0.867) 		0.163
(0.702) 		0.761
(0.99) 		0.223
(0.765) 		0.018
(0.416) 		0.435
(0.913) 		0.819
(1.00) 		0.63
(0.961)
9p gain 59 (14%) 377 0.0716
(0.558) 		0.532
(0.943) 		0.864
(1.00) 		0.0982
(0.628) 		0.589
(0.947) 		0.784
(0.997) 		1
(1.00) 		0.0085
(0.312) 		0.189
(0.716) 		0.64
(0.962) 		0.522
(0.943) 		0.563
(0.943) 		0.0903
(0.613)
9q gain 77 (18%) 359 0.296
(0.827) 		0.339
(0.864) 		0.809
(1.00) 		0.279
(0.815) 		0.898
(1.00) 		0.626
(0.961) 		0.361
(0.873) 		0.0238
(0.435) 		0.287
(0.817) 		0.39
(0.901) 		0.359
(0.873) 		1
(1.00) 		0.136
(0.687)
10p gain 98 (22%) 338 0.553
(0.943) 		0.931
(1.00) 		0.417
(0.906) 		0.357
(0.873) 		0.551
(0.943) 		1
(1.00) 		0.553
(0.943) 		0.424
(0.906) 		0.621
(0.961) 		0.51
(0.942) 		0.651
(0.964) 		0.00935
(0.312) 		0.576
(0.943)
10q gain 70 (16%) 366 0.708
(0.972) 		0.0953
(0.616) 		0.0275
(0.438) 		0.511
(0.942) 		0.142
(0.687) 		0.801
(1.00) 		0.344
(0.868) 		0.547
(0.943) 		0.248
(0.786) 		0.63
(0.961) 		0.905
(1.00) 		0.127
(0.684) 		1
(1.00)
11p gain 64 (15%) 372 0.873
(1.00) 		0.546
(0.943) 		0.673
(0.964) 		0.222
(0.765) 		0.0686
(0.558) 		1
(1.00) 		0.888
(1.00) 		0.257
(0.793) 		1
(1.00) 		0.477
(0.927) 		0.0475
(0.497) 		0.0773
(0.57) 		0.427
(0.906)
11q gain 74 (17%) 362 0.677
(0.964) 		0.541
(0.943) 		0.406
(0.901) 		0.683
(0.964) 		0.027
(0.437) 		0.801
(1.00) 		0.427
(0.906) 		0.117
(0.665) 		1
(1.00) 		0.374
(0.889) 		0.206
(0.73) 		0.0594
(0.558) 		0.475
(0.927)
12p gain 89 (20%) 347 0.465
(0.925) 		0.685
(0.964) 		0.467
(0.925) 		0.0468
(0.497) 		0.308
(0.846) 		1
(1.00) 		0.805
(1.00) 		0.601
(0.947) 		0.354
(0.873) 		0.17
(0.702) 		0.639
(0.962) 		0.746
(0.983) 		0.203
(0.728)
12q gain 76 (17%) 360 0.915
(1.00) 		0.0386
(0.494) 		0.425
(0.906) 		0.199
(0.722) 		0.037
(0.493) 		0.627
(0.961) 		0.6
(0.947) 		0.192
(0.716) 		0.596
(0.947) 		0.676
(0.964) 		0.64
(0.962) 		0.0832
(0.592) 		0.159
(0.702)
13q gain 153 (35%) 283 0.191
(0.716) 		0.978
(1.00) 		0.545
(0.943) 		0.568
(0.943) 		0.656
(0.964) 		0.845
(1.00) 		0.144
(0.687) 		0.167
(0.702) 		0.67
(0.964) 		0.813
(1.00) 		0.367
(0.88) 		0.266
(0.802) 		1
(1.00)
14q gain 29 (7%) 407 0.182
(0.708) 		0.46
(0.925) 		0.391
(0.901) 		0.894
(1.00) 		0.254
(0.79) 		0.0473
(0.497) 		0.554
(0.943) 		0.559
(0.943) 		1
(1.00) 		0.169
(0.702) 		0.0698
(0.558) 		0.493
(0.937) 		0.241
(0.782)
15q gain 39 (9%) 397 0.114
(0.665) 		0.643
(0.963) 		0.27
(0.802) 		0.782
(0.997) 		0.0656
(0.558) 		0.176
(0.704) 		0.491
(0.937) 		0.539
(0.943) 		1
(1.00) 		0.00381
(0.307) 		0.209
(0.737) 		0.00168
(0.254) 		1
(1.00)
16p gain 59 (14%) 377 0.147
(0.687) 		0.316
(0.856) 		0.00717
(0.312) 		0.619
(0.961) 		0.282
(0.815) 		0.24
(0.782) 		0.771
(0.993) 		0.775
(0.994) 		0.035
(0.477) 		0.123
(0.68) 		0.0579
(0.553) 		0.238
(0.782) 		0.444
(0.923)
16q gain 47 (11%) 389 0.0144
(0.379) 		0.544
(0.943) 		0.0301
(0.446) 		0.656
(0.964) 		0.454
(0.925) 		0.0494
(0.5) 		0.63
(0.961) 		0.191
(0.716) 		0.129
(0.684) 		0.14
(0.687) 		0.038
(0.494) 		0.183
(0.71) 		0.357
(0.873)
17p gain 28 (6%) 408 0.429
(0.906) 		0.066
(0.558) 		0.116
(0.665) 		0.677
(0.964) 		0.666
(0.964) 		0.0948
(0.616) 		0.69
(0.968) 		0.0419
(0.497) 		0.33
(0.859) 		0.0203
(0.416) 		1
(1.00) 		0.0433
(0.497) 		1
(1.00)
17q gain 60 (14%) 376 0.963
(1.00) 		0.856
(1.00) 		0.28
(0.815) 		0.726
(0.973) 		0.864
(1.00) 		0.102
(0.632) 		0.313
(0.855) 		0.261
(0.798) 		0.591
(0.947) 		0.0194
(0.416) 		0.76
(0.99) 		0.0176
(0.416) 		1
(1.00)
18p gain 82 (19%) 354 0.00738
(0.312) 		0.162
(0.702) 		0.579
(0.943) 		0.12
(0.667) 		0.316
(0.856) 		1
(1.00) 		0.126
(0.684) 		0.111
(0.665) 		0.0129
(0.359) 		0.728
(0.973) 		0.578
(0.943) 		0.451
(0.925) 		0.57
(0.943)
18q gain 53 (12%) 383 0.0728
(0.558) 		0.506
(0.938) 		0.235
(0.782) 		0.00481
(0.312) 		0.294
(0.826) 		0.765
(0.99) 		0.17
(0.702) 		0.0734
(0.558) 		0.0261
(0.436) 		0.793
(1.00) 		0.463
(0.925) 		0.583
(0.945) 		0.435
(0.913)
19p gain 53 (12%) 383 0.222
(0.765) 		0.466
(0.925) 		0.569
(0.943) 		0.0929
(0.616) 		0.0565
(0.553) 		0.24
(0.782) 		0.879
(1.00) 		0.172
(0.702) 		0.158
(0.702) 		0.0657
(0.558) 		0.0486
(0.497) 		0.951
(1.00) 		1
(1.00)
19q gain 76 (17%) 360 0.74
(0.978) 		0.777
(0.995) 		0.683
(0.964) 		0.198
(0.722) 		0.00909
(0.312) 		0.622
(0.961) 		0.793
(1.00) 		0.624
(0.961) 		0.00974
(0.312) 		0.0701
(0.558) 		0.0194
(0.416) 		0.0889
(0.608) 		1
(1.00)
20p gain 240 (55%) 196 0.322
(0.857) 		0.331
(0.859) 		0.715
(0.972) 		0.458
(0.925) 		0.266
(0.802) 		0.253
(0.79) 		0.0353
(0.477) 		0.0701
(0.558) 		0.415
(0.906) 		0.898
(1.00) 		0.579
(0.943) 		0.665
(0.964) 		1
(1.00)
21q gain 21 (5%) 415 0.298
(0.828) 		0.745
(0.983) 		0.285
(0.815) 		0.238
(0.782) 		0.645
(0.963) 		1
(1.00) 		0.821
(1.00) 		0.34
(0.864) 		1
(1.00) 		0.721
(0.972) 		0.105
(0.643) 		0.79
(1.00) 		1
(1.00)
22q gain 32 (7%) 404 0.956
(1.00) 		0.732
(0.974) 		0.139
(0.687) 		0.0435
(0.497) 		0.647
(0.964) 		1
(1.00) 		0.574
(0.943) 		0.479
(0.929) 		1
(1.00) 		0.962
(1.00) 		0.931
(1.00) 		0.492
(0.937) 		0.291
(0.823)
xp gain 48 (11%) 388 0.296
(0.827) 		0.358
(0.873) 		0.0666
(0.558) 		0.276
(0.813) 		0.142
(0.687) 		1
(1.00) 		0.0813
(0.583) 		0.101
(0.632) 		1
(1.00) 		0.411
(0.901) 		0.0221
(0.417) 		0.106
(0.643) 		1
(1.00)
xq gain 55 (13%) 381 0.945
(1.00) 		0.904
(1.00) 		0.0636
(0.558) 		0.371
(0.886) 		0.075
(0.562) 		0.566
(0.943) 		0.0733
(0.558) 		0.00894
(0.312) 		1
(1.00) 		0.403
(0.901) 		0.0178
(0.416) 		0.349
(0.873) 		0.402
(0.901)
1p loss 59 (14%) 377 0.303
(0.839) 		0.696
(0.968) 		0.685
(0.964) 		0.19
(0.716) 		0.781
(0.997) 		0.0481
(0.497) 		0.885
(1.00) 		0.0608
(0.558) 		1
(1.00) 		0.00605
(0.312) 		0.77
(0.992) 		0.204
(0.73) 		1
(1.00)
1q loss 28 (6%) 408 0.177
(0.704) 		0.863
(1.00) 		0.874
(1.00) 		0.597
(0.947) 		0.95
(1.00) 		0.0948
(0.616) 		0.839
(1.00) 		0.542
(0.943) 		1
(1.00) 		0.0464
(0.497) 		0.4
(0.901) 		0.653
(0.964) 		1
(1.00)
2p loss 26 (6%) 410 0.24
(0.782) 		0.406
(0.901) 		0.591
(0.947) 		0.504
(0.938) 		0.563
(0.943) 		1
(1.00) 		0.297
(0.828) 		0.12
(0.667) 		0.0443
(0.497) 		0.16
(0.702) 		0.395
(0.901) 		0.536
(0.943) 		1
(1.00)
2q loss 33 (8%) 403 0.425
(0.906) 		0.729
(0.973) 		0.802
(1.00) 		0.947
(1.00) 		0.464
(0.925) 		1
(1.00) 		0.851
(1.00) 		0.0062
(0.312) 		0.0688
(0.558) 		0.146
(0.687) 		0.375
(0.889) 		0.0882
(0.608) 		1
(1.00)
3p loss 89 (20%) 347 0.325
(0.859) 		0.714
(0.972) 		0.986
(1.00) 		0.863
(1.00) 		0.00977
(0.312) 		0.0924
(0.616) 		1
(1.00) 		0.196
(0.719) 		1
(1.00) 		0.15
(0.691) 		0.981
(1.00) 		0.893
(1.00) 		1
(1.00)
3q loss 54 (12%) 382 0.979
(1.00) 		0.545
(0.943) 		0.502
(0.938) 		0.0128
(0.359) 		0.408
(0.901) 		0.0848
(0.599) 		0.881
(1.00) 		0.0624
(0.558) 		1
(1.00) 		0.598
(0.947) 		0.722
(0.972) 		0.492
(0.937) 		0.41
(0.901)
4p loss 165 (38%) 271 0.412
(0.901) 		0.448
(0.925) 		0.182
(0.708) 		0.0483
(0.497) 		0.176
(0.704) 		0.118
(0.665) 		0.758
(0.99) 		0.241
(0.782) 		0.677
(0.964) 		0.93
(1.00) 		0.174
(0.702) 		0.674
(0.964) 		1
(1.00)
4q loss 162 (37%) 274 0.178
(0.704) 		0.162
(0.702) 		0.268
(0.802) 		0.138
(0.687) 		0.164
(0.702) 		0.243
(0.782) 		0.68
(0.964) 		0.173
(0.702) 		0.675
(0.964) 		0.644
(0.963) 		0.106
(0.643) 		0.766
(0.99) 		1
(1.00)
5p loss 59 (14%) 377 0.00924
(0.312) 		0.212
(0.741) 		0.256
(0.793) 		0.329
(0.859) 		0.237
(0.782) 		1
(1.00) 		0.561
(0.943) 		0.0467
(0.497) 		1
(1.00) 		0.705
(0.972) 		0.325
(0.859) 		0.0222
(0.417) 		1
(1.00)
6p loss 52 (12%) 384 0.484
(0.934) 		0.88
(1.00) 		0.722
(0.972) 		0.13
(0.684) 		0.756
(0.99) 		0.557
(0.943) 		0.646
(0.963) 		0.0858
(0.602) 		1
(1.00) 		0.477
(0.927) 		0.973
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 69 (16%) 367 0.422
(0.906) 		0.569
(0.943) 		0.472
(0.927) 		0.0574
(0.553) 		0.499
(0.938) 		0.285
(0.815) 		0.495
(0.938) 		0.133
(0.686) 		0.596
(0.947) 		0.702
(0.971) 		0.456
(0.925) 		0.639
(0.962) 		1
(1.00)
7p loss 20 (5%) 416 0.53
(0.943) 		0.694
(0.968) 		0.887
(1.00) 		0.21
(0.738) 		0.387
(0.901) 		0.638
(0.962) 		0.155
(0.702) 		0.589
(0.947) 		1
(1.00) 		0.484
(0.934) 		0.181
(0.708) 		0.0268
(0.437) 		1
(1.00)
7q loss 30 (7%) 406 0.517
(0.943) 		0.261
(0.798) 		0.455
(0.925) 		0.0142
(0.379) 		0.269
(0.802) 		1
(1.00) 		0.326
(0.859) 		0.708
(0.972) 		1
(1.00) 		0.683
(0.964) 		0.25
(0.788) 		0.173
(0.702) 		1
(1.00)
9p loss 146 (33%) 290 0.22
(0.765) 		0.119
(0.667) 		0.652
(0.964) 		0.638
(0.962) 		0.169
(0.702) 		0.695
(0.968) 		0.528
(0.943) 		0.0181
(0.416) 		0.407
(0.901) 		0.525
(0.943) 		0.14
(0.687) 		0.195
(0.719) 		1
(1.00)
9q loss 102 (23%) 334 0.562
(0.943) 		0.617
(0.961) 		0.915
(1.00) 		0.423
(0.906) 		0.881
(1.00) 		1
(1.00) 		0.557
(0.943) 		0.322
(0.857) 		0.143
(0.687) 		0.825
(1.00) 		0.14
(0.687) 		0.113
(0.665) 		1
(1.00)
10p loss 64 (15%) 372 0.127
(0.684) 		0.761
(0.99) 		0.283
(0.815) 		0.284
(0.815) 		0.0389
(0.494) 		0.598
(0.947) 		0.401
(0.901) 		0.151
(0.693) 		1
(1.00) 		0.577
(0.943) 		0.00409
(0.307) 		0.291
(0.823) 		0.452
(0.925)
10q loss 67 (15%) 369 0.443
(0.923) 		0.0728
(0.558) 		0.333
(0.86) 		0.624
(0.961) 		0.0297
(0.446) 		0.429
(0.906) 		0.783
(0.997) 		0.0803
(0.582) 		1
(1.00) 		0.986
(1.00) 		0.00253
(0.254) 		0.266
(0.802) 		0.475
(0.927)
11p loss 62 (14%) 374 0.329
(0.859) 		0.791
(1.00) 		0.47
(0.925) 		0.212
(0.741) 		0.315
(0.856) 		0.168
(0.702) 		0.392
(0.901) 		0.0203
(0.416) 		0.601
(0.947) 		0.301
(0.834) 		0.127
(0.684) 		0.728
(0.973) 		0.452
(0.925)
11q loss 60 (14%) 376 0.0942
(0.616) 		0.86
(1.00) 		0.117
(0.665) 		0.865
(1.00) 		0.0289
(0.446) 		0.574
(0.943) 		0.194
(0.719) 		0.116
(0.665) 		1
(1.00) 		0.539
(0.943) 		0.0153
(0.392) 		0.959
(1.00) 		0.444
(0.923)
12p loss 61 (14%) 375 0.0245
(0.435) 		0.0456
(0.497) 		0.923
(1.00) 		0.353
(0.873) 		0.719
(0.972) 		1
(1.00) 		0.473
(0.927) 		0.00276
(0.254) 		0.597
(0.947) 		0.465
(0.925) 		0.396
(0.901) 		0.379
(0.896) 		0.402
(0.901)
12q loss 52 (12%) 384 0.0317
(0.459) 		0.276
(0.813) 		0.902
(1.00) 		0.156
(0.702) 		0.536
(0.943) 		0.557
(0.943) 		0.759
(0.99) 		0.041
(0.497) 		0.535
(0.943) 		0.403
(0.901) 		0.636
(0.962) 		0.513
(0.942) 		0.339
(0.864)
13q loss 35 (8%) 401 0.159
(0.702) 		0.498
(0.938) 		0.852
(1.00) 		0.757
(0.99) 		0.719
(0.972) 		0.714
(0.972) 		0.464
(0.925) 		0.72
(0.972) 		0.0766
(0.568) 		0.116
(0.665) 		0.418
(0.906) 		0.937
(1.00) 		1
(1.00)
14q loss 110 (25%) 326 0.566
(0.943) 		0.684
(0.964) 		0.208
(0.734) 		0.331
(0.859) 		0.364
(0.876) 		0.0753
(0.562) 		0.731
(0.974) 		0.31
(0.85) 		1
(1.00) 		0.419
(0.906) 		0.574
(0.943) 		1
(1.00) 		0.576
(0.943)
15q loss 89 (20%) 347 0.751
(0.987) 		0.468
(0.925) 		0.41
(0.901) 		0.0577
(0.553) 		0.724
(0.973) 		0.814
(1.00) 		0.711
(0.972) 		0.0461
(0.497) 		0.103
(0.635) 		0.749
(0.986) 		0.4
(0.901) 		0.47
(0.925) 		1
(1.00)
16p loss 99 (23%) 337 0.55
(0.943) 		0.0391
(0.494) 		0.703
(0.971) 		0.506
(0.938) 		0.701
(0.971) 		0.112
(0.665) 		0.813
(1.00) 		0.0209
(0.416) 		0.622
(0.961) 		0.618
(0.961) 		0.445
(0.923) 		0.36
(0.873) 		0.581
(0.943)
16q loss 114 (26%) 322 0.321
(0.857) 		0.674
(0.964) 		0.248
(0.786) 		0.533
(0.943) 		0.908
(1.00) 		0.0319
(0.459) 		0.572
(0.943) 		0.0207
(0.416) 		0.187
(0.716) 		0.68
(0.964) 		0.672
(0.964) 		0.544
(0.943) 		0.576
(0.943)
17p loss 161 (37%) 275 0.553
(0.943) 		0.677
(0.964) 		0.84
(1.00) 		0.336
(0.864) 		0.692
(0.968) 		0.556
(0.943) 		0.0631
(0.558) 		0.0029
(0.254) 		0.2
(0.722) 		0.199
(0.722) 		0.328
(0.859) 		0.477
(0.927) 		1
(1.00)
17q loss 74 (17%) 362 0.798
(1.00) 		0.81
(1.00) 		0.75
(0.986) 		0.468
(0.925) 		0.412
(0.901) 		0.447
(0.924) 		0.791
(1.00) 		0.12
(0.667) 		1
(1.00) 		0.849
(1.00) 		0.115
(0.665) 		0.278
(0.814) 		0.513
(0.942)
18p loss 117 (27%) 319 0.134
(0.687) 		0.692
(0.968) 		0.729
(0.973) 		0.116
(0.665) 		0.636
(0.962) 		0.675
(0.964) 		0.0718
(0.558) 		0.831
(1.00) 		0.35
(0.873) 		0.918
(1.00) 		0.149
(0.687) 		0.0672
(0.558) 		0.32
(0.856)
18q loss 153 (35%) 283 0.536
(0.943) 		0.141
(0.687) 		0.486
(0.935) 		0.00757
(0.312) 		0.939
(1.00) 		1
(1.00) 		0.531
(0.943) 		0.765
(0.99) 		0.67
(0.964) 		0.946
(1.00) 		0.184
(0.71) 		0.577
(0.943) 		0.61
(0.958)
19q loss 87 (20%) 349 0.441
(0.923) 		0.0428
(0.497) 		0.971
(1.00) 		0.933
(1.00) 		0.665
(0.964) 		1
(1.00) 		1
(1.00) 		0.00234
(0.254) 		1
(1.00) 		0.105
(0.643) 		0.823
(1.00) 		0.168
(0.702) 		0.556
(0.943)
20p loss 22 (5%) 414 0.0433
(0.497) 		0.809
(1.00) 		0.385
(0.9) 		0.337
(0.864) 		0.468
(0.925) 		0.149
(0.687) 		0.178
(0.704) 		0.628
(0.961) 		0.0323
(0.459) 		0.572
(0.943) 		0.501
(0.938) 		0.282
(0.815) 		1
(1.00)
21q loss 177 (41%) 259 0.557
(0.943) 		0.0877
(0.608) 		0.625
(0.961) 		0.406
(0.901) 		0.374
(0.889) 		0.252
(0.79) 		0.361
(0.873) 		0.235
(0.782) 		0.229
(0.78) 		0.718
(0.972) 		0.389
(0.901) 		0.494
(0.938) 		0.638
(0.962)
22q loss 142 (33%) 294 0.177
(0.704) 		0.912
(1.00) 		0.611
(0.958) 		0.249
(0.786) 		0.174
(0.702) 		0.158
(0.702) 		0.671
(0.964) 		0.269
(0.802) 		0.0913
(0.616) 		0.384
(0.9) 		0.0295
(0.446) 		0.619
(0.961) 		1
(1.00)
xp loss 56 (13%) 380 0.132
(0.686) 		0.935
(1.00) 		0.189
(0.716) 		0.877
(1.00) 		0.679
(0.964) 		0.402
(0.901) 		0.0736
(0.558) 		0.073
(0.558) 		0.564
(0.943) 		0.172
(0.702) 		0.598
(0.947) 		0.531
(0.943) 		0.427
(0.906)
xq loss 48 (11%) 388 0.689
(0.967) 		0.662
(0.964) 		0.487
(0.936) 		0.707
(0.972) 		0.763
(0.99) 		0.23
(0.782) 		0.0249
(0.435) 		0.913
(1.00) 		0.134
(0.686) 		0.0623
(0.558) 		0.387
(0.901) 		0.723
(0.972) 		1
(1.00)
'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00033 (Fisher's exact test), Q value = 0.11

Table S1.  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 96 60 61 11 6 8
20Q GAIN WILD-TYPE 39 66 21 17 10 2 5

Figure S1.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-04 (Fisher's exact test), Q value = 0.11

Table S2.  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 35 21 32 5 3 3
5Q LOSS WILD-TYPE 65 127 60 46 16 5 10

Figure S2.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000816 (Wilcoxon-test), Q value = 0.17

Table S3.  Gene #56: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
8P LOSS MUTATED 78 8.4 (11.7)
8P LOSS WILD-TYPE 309 5.0 (7.3)

Figure S3.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 22 90 195 119
8Q LOSS MUTATED 1 3 26 2
8Q LOSS WILD-TYPE 21 87 169 117

Figure S4.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S5.  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 10 37 32 27 1 4 3
19P LOSS WILD-TYPE 61 125 49 51 20 4 10

Figure S5.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #8: '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/15098845/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 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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