Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1445KD0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1445KD0
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 79 arm-level events and 12 clinical features across 395 patients, 2 significant findings detected with Q value < 0.25.

  • 16p gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 16q gain cnv correlated to 'PATHOLOGY.M.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE 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
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
16p gain 51 (13%) 344 0.517
(1.00) 		0.277
(1.00) 		0.0102
(1.00) 		0.573
(1.00) 		0.417
(1.00) 		0.00016
(0.152) 		1
(1.00) 		0.936
(1.00) 		0.0306
(1.00) 		0.0387
(1.00) 		0.0337
(1.00) 		0.158
(1.00)
16q gain 41 (10%) 354 0.0833
(1.00) 		0.661
(1.00) 		0.0049
(1.00) 		0.601
(1.00) 		0.596
(1.00) 		2e-05
(0.019) 		0.614
(1.00) 		0.49
(1.00) 		0.121
(1.00) 		0.058
(1.00) 		0.0366
(1.00) 		0.0994
(1.00)
1p gain 46 (12%) 349 0.595
(1.00) 		0.165
(1.00) 		0.44
(1.00) 		0.117
(1.00) 		0.95
(1.00) 		0.451
(1.00) 		0.264
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.91
(1.00) 		1
(1.00)
1q gain 91 (23%) 304 0.632
(1.00) 		0.375
(1.00) 		0.764
(1.00) 		0.389
(1.00) 		0.509
(1.00) 		0.29
(1.00) 		0.54
(1.00) 		0.241
(1.00) 		0.625
(1.00) 		0.654
(1.00) 		0.643
(1.00) 		0.808
(1.00)
2p gain 69 (17%) 326 0.873
(1.00) 		0.517
(1.00) 		0.612
(1.00) 		0.377
(1.00) 		0.622
(1.00) 		0.898
(1.00) 		0.892
(1.00) 		0.1
(1.00) 		0.596
(1.00) 		0.117
(1.00) 		0.773
(1.00) 		0.341
(1.00)
2q gain 59 (15%) 336 0.806
(1.00) 		0.419
(1.00) 		0.622
(1.00) 		0.553
(1.00) 		0.856
(1.00) 		0.497
(1.00) 		0.666
(1.00) 		0.299
(1.00) 		0.598
(1.00) 		0.26
(1.00) 		0.795
(1.00) 		0.357
(1.00)
3p gain 48 (12%) 347 0.0955
(1.00) 		0.567
(1.00) 		0.977
(1.00) 		0.846
(1.00) 		0.643
(1.00) 		0.802
(1.00) 		0.636
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.775
(1.00) 		0.375
(1.00)
3q gain 86 (22%) 309 0.118
(1.00) 		0.405
(1.00) 		0.557
(1.00) 		0.2
(1.00) 		0.609
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.758
(1.00) 		1
(1.00) 		0.78
(1.00) 		0.309
(1.00) 		0.594
(1.00)
4p gain 18 (5%) 377 0.432
(1.00) 		0.878
(1.00) 		0.14
(1.00) 		0.594
(1.00) 		0.986
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.995
(1.00) 		1
(1.00)
4q gain 14 (4%) 381 0.851
(1.00) 		0.49
(1.00) 		0.44
(1.00) 		0.854
(1.00) 		0.411
(1.00) 		0.452
(1.00) 		0.58
(1.00) 		0.0754
(1.00) 		1
(1.00) 		0.735
(1.00) 		0.278
(1.00) 		0.433
(1.00)
5p gain 90 (23%) 305 0.84
(1.00) 		0.209
(1.00) 		0.962
(1.00) 		0.106
(1.00) 		0.757
(1.00) 		0.956
(1.00) 		0.902
(1.00) 		0.00775
(1.00) 		0.623
(1.00) 		0.926
(1.00) 		0.421
(1.00) 		0.929
(1.00)
5q gain 36 (9%) 359 0.58
(1.00) 		0.479
(1.00) 		0.752
(1.00) 		0.25
(1.00) 		0.93
(1.00) 		0.907
(1.00) 		0.858
(1.00) 		0.092
(1.00) 		0.439
(1.00) 		0.569
(1.00) 		0.796
(1.00) 		1
(1.00)
6p gain 69 (17%) 326 0.326
(1.00) 		0.661
(1.00) 		0.532
(1.00) 		0.261
(1.00) 		0.899
(1.00) 		0.512
(1.00) 		0.892
(1.00) 		0.00693
(1.00) 		0.0688
(1.00) 		0.191
(1.00) 		0.813
(1.00) 		0.0608
(1.00)
6q gain 55 (14%) 340 0.0501
(1.00) 		0.961
(1.00) 		0.15
(1.00) 		0.348
(1.00) 		0.953
(1.00) 		0.27
(1.00) 		0.767
(1.00) 		0.00399
(1.00) 		0.0377
(1.00) 		0.207
(1.00) 		0.718
(1.00) 		0.0305
(1.00)
7p gain 174 (44%) 221 0.843
(1.00) 		0.26
(1.00) 		0.551
(1.00) 		0.862
(1.00) 		0.37
(1.00) 		0.0218
(1.00) 		0.0485
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.752
(1.00) 		0.493
(1.00)
7q gain 151 (38%) 244 0.785
(1.00) 		0.545
(1.00) 		0.557
(1.00) 		0.887
(1.00) 		0.176
(1.00) 		0.00135
(1.00) 		0.11
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.486
(1.00) 		0.569
(1.00) 		0.528
(1.00)
8p gain 166 (42%) 229 0.114
(1.00) 		0.0104
(1.00) 		0.746
(1.00) 		0.238
(1.00) 		0.82
(1.00) 		0.613
(1.00) 		0.0757
(1.00) 		0.232
(1.00) 		0.244
(1.00) 		0.0521
(1.00) 		0.61
(1.00) 		0.382
(1.00)
8q gain 214 (54%) 181 0.608
(1.00) 		0.022
(1.00) 		0.103
(1.00) 		0.0637
(1.00) 		0.757
(1.00) 		0.149
(1.00) 		0.3
(1.00) 		0.672
(1.00) 		0.225
(1.00) 		0.0527
(1.00) 		0.48
(1.00) 		0.695
(1.00)
9p gain 54 (14%) 341 0.404
(1.00) 		0.841
(1.00) 		0.838
(1.00) 		0.146
(1.00) 		0.848
(1.00) 		0.578
(1.00) 		0.881
(1.00) 		0.00724
(1.00) 		0.192
(1.00) 		0.591
(1.00) 		0.911
(1.00) 		0.488
(1.00)
9q gain 67 (17%) 328 0.318
(1.00) 		0.749
(1.00) 		0.739
(1.00) 		0.207
(1.00) 		0.985
(1.00) 		0.8
(1.00) 		0.338
(1.00) 		0.0196
(1.00) 		0.27
(1.00) 		0.532
(1.00) 		0.409
(1.00) 		1
(1.00)
10p gain 92 (23%) 303 0.663
(1.00) 		0.772
(1.00) 		0.479
(1.00) 		0.355
(1.00) 		0.563
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.627
(1.00) 		0.285
(1.00) 		0.504
(1.00) 		0.0241
(1.00)
10q gain 66 (17%) 329 0.651
(1.00) 		0.0523
(1.00) 		0.0678
(1.00) 		0.565
(1.00) 		0.162
(1.00) 		0.891
(1.00) 		0.678
(1.00) 		0.665
(1.00) 		0.264
(1.00) 		0.248
(1.00) 		0.92
(1.00) 		0.118
(1.00)
11p gain 56 (14%) 339 0.63
(1.00) 		0.421
(1.00) 		0.784
(1.00) 		0.33
(1.00) 		0.0557
(1.00) 		0.552
(1.00) 		0.883
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.0542
(1.00) 		0.142
(1.00)
11q gain 65 (16%) 330 0.687
(1.00) 		0.393
(1.00) 		0.56
(1.00) 		0.975
(1.00) 		0.00995
(1.00) 		0.944
(1.00) 		0.404
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.24
(1.00) 		0.108
(1.00)
12p gain 79 (20%) 316 0.243
(1.00) 		0.487
(1.00) 		0.604
(1.00) 		0.0701
(1.00) 		0.385
(1.00) 		0.906
(1.00) 		0.797
(1.00) 		0.665
(1.00) 		0.604
(1.00) 		0.176
(1.00) 		0.729
(1.00) 		0.856
(1.00)
12q gain 69 (17%) 326 0.989
(1.00) 		0.057
(1.00) 		0.426
(1.00) 		0.173
(1.00) 		0.0222
(1.00) 		0.851
(1.00) 		0.586
(1.00) 		0.261
(1.00) 		0.596
(1.00) 		0.55
(1.00) 		0.338
(1.00) 		0.0593
(1.00)
13q gain 138 (35%) 257 0.149
(1.00) 		0.767
(1.00) 		0.852
(1.00) 		0.5
(1.00) 		0.85
(1.00) 		0.065
(1.00) 		0.233
(1.00) 		0.235
(1.00) 		0.669
(1.00) 		0.885
(1.00) 		0.469
(1.00) 		0.487
(1.00)
14q gain 22 (6%) 373 0.0439
(1.00) 		0.56
(1.00) 		0.843
(1.00) 		0.693
(1.00) 		0.501
(1.00) 		0.544
(1.00) 		0.503
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.0566
(1.00) 		0.203
(1.00) 		0.744
(1.00)
15q gain 35 (9%) 360 0.259
(1.00) 		0.518
(1.00) 		0.539
(1.00) 		0.758
(1.00) 		0.163
(1.00) 		0.0836
(1.00) 		0.275
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.00555
(1.00) 		0.344
(1.00) 		0.0113
(1.00)
17p gain 24 (6%) 371 0.737
(1.00) 		0.217
(1.00) 		0.185
(1.00) 		0.742
(1.00) 		0.726
(1.00) 		0.0104
(1.00) 		1
(1.00) 		0.0572
(1.00) 		0.315
(1.00) 		0.0137
(1.00) 		0.611
(1.00) 		0.289
(1.00)
17q gain 51 (13%) 344 0.795
(1.00) 		0.927
(1.00) 		0.548
(1.00) 		0.735
(1.00) 		0.733
(1.00) 		0.0175
(1.00) 		0.758
(1.00) 		0.327
(1.00) 		0.566
(1.00) 		0.0183
(1.00) 		0.736
(1.00) 		0.243
(1.00)
18p gain 78 (20%) 317 0.00103
(0.971) 		0.151
(1.00) 		0.768
(1.00) 		0.146
(1.00) 		0.565
(1.00) 		0.603
(1.00) 		0.299
(1.00) 		0.0394
(1.00) 		0.0154
(1.00) 		0.605
(1.00) 		0.737
(1.00) 		0.649
(1.00)
18q gain 51 (13%) 344 0.0368
(1.00) 		0.411
(1.00) 		0.365
(1.00) 		0.00932
(1.00) 		0.289
(1.00) 		0.171
(1.00) 		0.444
(1.00) 		0.027
(1.00) 		0.0306
(1.00) 		0.726
(1.00) 		0.442
(1.00) 		1
(1.00)
19p gain 48 (12%) 347 0.192
(1.00) 		0.459
(1.00) 		0.536
(1.00) 		0.0578
(1.00) 		0.0745
(1.00) 		0.166
(1.00) 		0.636
(1.00) 		0.281
(1.00) 		0.158
(1.00) 		0.0844
(1.00) 		0.0572
(1.00) 		0.936
(1.00)
19q gain 66 (17%) 329 0.349
(1.00) 		0.952
(1.00) 		0.797
(1.00) 		0.207
(1.00) 		0.0258
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.00826
(1.00) 		0.153
(1.00) 		0.0365
(1.00) 		0.101
(1.00)
20p gain 215 (54%) 180 0.822
(1.00) 		0.698
(1.00) 		0.648
(1.00) 		0.242
(1.00) 		0.194
(1.00) 		0.581
(1.00) 		0.0223
(1.00) 		0.0882
(1.00) 		0.418
(1.00) 		0.817
(1.00) 		0.728
(1.00) 		0.345
(1.00)
20q gain 248 (63%) 147 0.635
(1.00) 		0.484
(1.00) 		0.39
(1.00) 		0.119
(1.00) 		0.0556
(1.00) 		0.0775
(1.00) 		0.00737
(1.00) 		0.00127
(1.00) 		0.675
(1.00) 		0.259
(1.00) 		0.53
(1.00) 		0.835
(1.00)
21q gain 21 (5%) 374 0.308
(1.00) 		0.84
(1.00) 		0.344
(1.00) 		0.302
(1.00) 		0.725
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.324
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.11
(1.00) 		0.867
(1.00)
22q gain 31 (8%) 364 0.79
(1.00) 		0.732
(1.00) 		0.171
(1.00) 		0.0638
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.785
(1.00) 		0.792
(1.00) 		0.4
(1.00)
xq gain 51 (13%) 344 0.343
(1.00) 		0.84
(1.00) 		0.0107
(1.00) 		0.449
(1.00) 		0.0817
(1.00) 		1
(1.00) 		0.0298
(1.00) 		0.00133
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.0152
(1.00) 		0.145
(1.00)
1p loss 51 (13%) 344 0.42
(1.00) 		0.873
(1.00) 		0.201
(1.00) 		0.245
(1.00) 		0.764
(1.00) 		0.0142
(1.00) 		0.646
(1.00) 		0.0522
(1.00) 		1
(1.00) 		0.003
(1.00) 		0.828
(1.00) 		0.182
(1.00)
1q loss 25 (6%) 370 0.309
(1.00) 		0.764
(1.00) 		0.779
(1.00) 		0.449
(1.00) 		0.863
(1.00) 		0.0129
(1.00) 		0.532
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.0432
(1.00) 		0.692
(1.00) 		0.421
(1.00)
2p loss 25 (6%) 370 0.283
(1.00) 		0.491
(1.00) 		0.906
(1.00) 		0.565
(1.00) 		0.729
(1.00) 		0.579
(1.00) 		0.298
(1.00) 		0.0193
(1.00) 		0.0494
(1.00) 		0.116
(1.00) 		0.427
(1.00) 		0.875
(1.00)
2q loss 29 (7%) 366 0.494
(1.00) 		0.833
(1.00) 		0.996
(1.00) 		0.989
(1.00) 		0.711
(1.00) 		0.631
(1.00) 		0.843
(1.00) 		0.00197
(1.00) 		0.065
(1.00) 		0.0999
(1.00) 		0.167
(1.00) 		0.0826
(1.00)
3p loss 76 (19%) 319 0.387
(1.00) 		0.669
(1.00) 		0.999
(1.00) 		0.993
(1.00) 		0.0106
(1.00) 		0.183
(1.00) 		1
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.657
(1.00) 		0.759
(1.00)
3q loss 44 (11%) 351 0.905
(1.00) 		0.495
(1.00) 		0.752
(1.00) 		0.0382
(1.00) 		0.293
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.506
(1.00) 		0.618
(1.00)
4p loss 147 (37%) 248 0.487
(1.00) 		0.604
(1.00) 		0.129
(1.00) 		0.097
(1.00) 		0.456
(1.00) 		0.346
(1.00) 		0.831
(1.00) 		0.367
(1.00) 		0.675
(1.00) 		0.966
(1.00) 		0.494
(1.00) 		0.691
(1.00)
4q loss 145 (37%) 250 0.308
(1.00) 		0.3
(1.00) 		0.405
(1.00) 		0.218
(1.00) 		0.229
(1.00) 		0.711
(1.00) 		0.454
(1.00) 		0.551
(1.00) 		0.673
(1.00) 		0.618
(1.00) 		0.259
(1.00) 		0.821
(1.00)
5p loss 50 (13%) 345 0.0534
(1.00) 		0.481
(1.00) 		0.309
(1.00) 		0.506
(1.00) 		0.314
(1.00) 		1
(1.00) 		0.538
(1.00) 		0.0812
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.69
(1.00) 		0.203
(1.00)
5q loss 90 (23%) 305 0.172
(1.00) 		0.299
(1.00) 		0.0673
(1.00) 		0.884
(1.00) 		0.135
(1.00) 		0.405
(1.00) 		0.805
(1.00) 		0.00613
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.831
(1.00) 		0.272
(1.00)
6p loss 49 (12%) 346 0.771
(1.00) 		0.985
(1.00) 		0.792
(1.00) 		0.265
(1.00) 		0.612
(1.00) 		0.16
(1.00) 		0.435
(1.00) 		0.0201
(1.00) 		1
(1.00) 		0.542
(1.00) 		0.973
(1.00) 		0.946
(1.00)
6q loss 62 (16%) 333 0.879
(1.00) 		0.934
(1.00) 		0.792
(1.00) 		0.143
(1.00) 		0.465
(1.00) 		0.0205
(1.00) 		0.321
(1.00) 		0.0803
(1.00) 		0.596
(1.00) 		0.814
(1.00) 		0.536
(1.00) 		0.52
(1.00)
7p loss 18 (5%) 377 0.59
(1.00) 		0.73
(1.00) 		0.812
(1.00) 		0.17
(1.00) 		0.474
(1.00) 		0.35
(1.00) 		0.215
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.173
(1.00) 		0.321
(1.00)
7q loss 29 (7%) 366 0.429
(1.00) 		0.337
(1.00) 		0.843
(1.00) 		0.0171
(1.00) 		0.354
(1.00) 		0.888
(1.00) 		0.241
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.264
(1.00) 		0.301
(1.00)
8p loss 72 (18%) 323 0.113
(1.00) 		0.668
(1.00) 		0.0978
(1.00) 		0.0584
(1.00) 		0.0173
(1.00) 		0.947
(1.00) 		0.0453
(1.00) 		0.0033
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.00107
(1.00) 		0.145
(1.00)
8q loss 26 (7%) 369 0.504
(1.00) 		0.909
(1.00) 		0.404
(1.00) 		0.00537
(1.00) 		0.0761
(1.00) 		0.874
(1.00) 		0.297
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.0564
(1.00) 		0.00308
(1.00) 		0.0408
(1.00)
9p loss 125 (32%) 270 0.51
(1.00) 		0.106
(1.00) 		0.679
(1.00) 		0.385
(1.00) 		0.254
(1.00) 		0.495
(1.00) 		0.374
(1.00) 		0.0677
(1.00) 		0.386
(1.00) 		0.393
(1.00) 		0.519
(1.00) 		0.583
(1.00)
9q loss 88 (22%) 307 0.616
(1.00) 		0.732
(1.00) 		0.926
(1.00) 		0.356
(1.00) 		0.814
(1.00) 		0.434
(1.00) 		0.536
(1.00) 		0.547
(1.00) 		0.127
(1.00) 		0.797
(1.00) 		0.253
(1.00) 		0.748
(1.00)
10p loss 54 (14%) 341 0.123
(1.00) 		0.893
(1.00) 		0.351
(1.00) 		0.156
(1.00) 		0.181
(1.00) 		0.25
(1.00) 		0.455
(1.00) 		0.0498
(1.00) 		0.589
(1.00) 		0.525
(1.00) 		0.0378
(1.00) 		0.504
(1.00)
10q loss 57 (14%) 338 0.591
(1.00) 		0.0471
(1.00) 		0.471
(1.00) 		0.274
(1.00) 		0.212
(1.00) 		0.558
(1.00) 		0.66
(1.00) 		0.0278
(1.00) 		1
(1.00) 		0.949
(1.00) 		0.0569
(1.00) 		0.953
(1.00)
11p loss 55 (14%) 340 0.345
(1.00) 		0.761
(1.00) 		0.8
(1.00) 		0.115
(1.00) 		0.529
(1.00) 		0.474
(1.00) 		0.455
(1.00) 		0.0449
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.178
(1.00) 		0.566
(1.00)
11q loss 51 (13%) 344 0.157
(1.00) 		0.991
(1.00) 		0.254
(1.00) 		0.711
(1.00) 		0.0862
(1.00) 		0.171
(1.00) 		0.354
(1.00) 		0.161
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.0314
(1.00) 		0.791
(1.00)
12p loss 54 (14%) 341 0.263
(1.00) 		0.138
(1.00) 		0.856
(1.00) 		0.45
(1.00) 		0.4
(1.00) 		0.503
(1.00) 		0.228
(1.00) 		0.00201
(1.00) 		0.589
(1.00) 		0.321
(1.00) 		0.835
(1.00) 		0.323
(1.00)
12q loss 43 (11%) 352 0.261
(1.00) 		0.353
(1.00) 		0.814
(1.00) 		0.364
(1.00) 		0.579
(1.00) 		0.0516
(1.00) 		0.409
(1.00) 		0.036
(1.00) 		0.502
(1.00) 		0.835
(1.00) 		0.597
(1.00) 		0.86
(1.00)
13q loss 35 (9%) 360 0.0481
(1.00) 		0.584
(1.00) 		0.808
(1.00) 		0.69
(1.00) 		0.664
(1.00) 		0.111
(1.00) 		0.587
(1.00) 		0.733
(1.00) 		0.0913
(1.00) 		0.141
(1.00) 		0.383
(1.00) 		0.913
(1.00)
14q loss 100 (25%) 295 0.778
(1.00) 		0.568
(1.00) 		0.309
(1.00) 		0.131
(1.00) 		0.148
(1.00) 		0.0668
(1.00) 		1
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.359
(1.00) 		0.696
(1.00) 		1
(1.00)
15q loss 84 (21%) 311 0.36
(1.00) 		0.673
(1.00) 		0.332
(1.00) 		0.0207
(1.00) 		0.663
(1.00) 		0.399
(1.00) 		0.899
(1.00) 		0.0125
(1.00) 		0.113
(1.00) 		0.649
(1.00) 		0.308
(1.00) 		0.468
(1.00)
16p loss 90 (23%) 305 0.285
(1.00) 		0.0589
(1.00) 		0.763
(1.00) 		0.451
(1.00) 		0.47
(1.00) 		0.427
(1.00) 		0.902
(1.00) 		0.0641
(1.00) 		0.623
(1.00) 		0.721
(1.00) 		0.351
(1.00) 		0.482
(1.00)
16q loss 101 (26%) 294 0.336
(1.00) 		0.702
(1.00) 		0.291
(1.00) 		0.335
(1.00) 		0.919
(1.00) 		0.114
(1.00) 		0.477
(1.00) 		0.0549
(1.00) 		0.177
(1.00) 		0.751
(1.00) 		0.814
(1.00) 		0.647
(1.00)
17p loss 143 (36%) 252 0.857
(1.00) 		0.547
(1.00) 		0.891
(1.00) 		0.352
(1.00) 		0.883
(1.00) 		0.712
(1.00) 		0.162
(1.00) 		0.0127
(1.00) 		0.195
(1.00) 		0.344
(1.00) 		0.337
(1.00) 		0.448
(1.00)
17q loss 69 (17%) 326 0.896
(1.00) 		0.757
(1.00) 		0.764
(1.00) 		0.499
(1.00) 		0.219
(1.00) 		0.438
(1.00) 		0.892
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.153
(1.00) 		0.315
(1.00)
18p loss 101 (26%) 294 0.255
(1.00) 		0.62
(1.00) 		0.573
(1.00) 		0.0552
(1.00) 		0.673
(1.00) 		0.884
(1.00) 		0.0759
(1.00) 		0.987
(1.00) 		0.345
(1.00) 		0.948
(1.00) 		0.128
(1.00) 		0.0285
(1.00)
18q loss 133 (34%) 262 0.552
(1.00) 		0.27
(1.00) 		0.573
(1.00) 		0.00195
(1.00) 		0.978
(1.00) 		0.931
(1.00) 		0.913
(1.00) 		0.807
(1.00) 		0.668
(1.00) 		0.902
(1.00) 		0.27
(1.00) 		0.397
(1.00)
19p loss 100 (25%) 295 0.0813
(1.00) 		0.142
(1.00) 		0.958
(1.00) 		0.958
(1.00) 		0.68
(1.00) 		0.881
(1.00) 		0.635
(1.00) 		0.00071
(0.672) 		0.646
(1.00) 		0.102
(1.00) 		0.491
(1.00) 		0.0576
(1.00)
19q loss 77 (19%) 318 0.629
(1.00) 		0.0202
(1.00) 		0.914
(1.00) 		0.718
(1.00) 		0.638
(1.00) 		0.951
(1.00) 		0.794
(1.00) 		0.0122
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.736
(1.00) 		0.321
(1.00)
20p loss 20 (5%) 375 0.00905
(1.00) 		0.777
(1.00) 		0.431
(1.00) 		0.675
(1.00) 		0.523
(1.00) 		0.0168
(1.00) 		0.155
(1.00) 		0.445
(1.00) 		0.0324
(1.00) 		0.466
(1.00) 		0.366
(1.00) 		0.487
(1.00)
21q loss 154 (39%) 241 0.492
(1.00) 		0.136
(1.00) 		0.363
(1.00) 		0.246
(1.00) 		0.628
(1.00) 		0.167
(1.00) 		0.29
(1.00) 		0.424
(1.00) 		0.214
(1.00) 		0.819
(1.00) 		0.57
(1.00) 		0.921
(1.00)
22q loss 125 (32%) 270 0.14
(1.00) 		0.765
(1.00) 		0.386
(1.00) 		0.19
(1.00) 		0.335
(1.00) 		0.536
(1.00) 		0.912
(1.00) 		0.603
(1.00) 		0.0827
(1.00) 		0.336
(1.00) 		0.0322
(1.00) 		0.502
(1.00)
xq loss 42 (11%) 353 0.57
(1.00) 		0.581
(1.00) 		0.85
(1.00) 		0.418
(1.00) 		0.678
(1.00) 		0.651
(1.00) 		0.0447
(1.00) 		0.669
(1.00) 		0.126
(1.00) 		0.0361
(1.00) 		0.289
(1.00) 		0.681
(1.00)
'16p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 353 24 18
16P GAIN MUTATED 37 6 8
16P GAIN WILD-TYPE 316 18 10

Figure S1.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'16q gain' versus 'PATHOLOGY.M.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S2.  Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 353 24 18
16Q GAIN MUTATED 27 6 8
16Q GAIN WILD-TYPE 326 18 10

Figure S2.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = STAD-TP.merged_data.txt

  • Number of patients = 395

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 12

  • 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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