Correlation between copy number variations of arm-level result and selected clinical features
Stomach and Esophageal carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C18C9VRZ
Overview
Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 12 clinical features across 625 patients, 11 significant findings detected with Q value < 0.25.

  • 7p gain cnv correlated to 'GENDER'.

  • 7q gain cnv correlated to 'GENDER'.

  • 12q gain cnv correlated to 'RACE'.

  • 20q gain cnv correlated to 'GENDER'.

  • xp gain cnv correlated to 'RACE'.

  • xq gain cnv correlated to 'RACE'.

  • 5p loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • 5q loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • 8p loss cnv correlated to 'GENDER'.

  • 18q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • xp loss cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 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
KARNOFSKY
PERFORMANCE
SCORE
NUMBER
PACK
YEARS
SMOKED
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 Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
7p gain 308 (49%) 317 0.768
(0.987)
0.551
(0.938)
0.378
(0.84)
0.0408
(0.437)
0.907
(1.00)
1
(1.00)
0.000449
(0.138)
0.918
(1.00)
0.99
(1.00)
0.171
(0.644)
0.0754
(0.515)
0.124
(0.565)
7q gain 257 (41%) 368 0.68
(0.962)
0.975
(1.00)
0.333
(0.811)
0.0625
(0.494)
0.606
(0.96)
1
(1.00)
0.00246
(0.239)
0.834
(1.00)
0.163
(0.626)
0.655
(0.96)
0.123
(0.561)
0.12
(0.558)
12q gain 116 (19%) 509 0.89
(1.00)
0.0289
(0.401)
0.373
(0.838)
0.134
(0.586)
0.112
(0.552)
0.134
(0.586)
0.176
(0.656)
1
(1.00)
0.0616
(0.494)
0.0249
(0.38)
0.00253
(0.239)
0.466
(0.901)
20q gain 395 (63%) 230 0.0863
(0.525)
0.129
(0.578)
0.436
(0.891)
0.166
(0.634)
0.0642
(0.494)
0.499
(0.914)
0.00267
(0.239)
0.134
(0.586)
0.291
(0.793)
0.779
(0.994)
0.855
(1.00)
0.547
(0.938)
xp gain 75 (12%) 550 0.513
(0.923)
0.98
(1.00)
0.3
(0.793)
0.453
(0.9)
0.199
(0.688)
0.295
(0.793)
0.686
(0.963)
0.274
(0.783)
0.699
(0.968)
0.64
(0.96)
0.00019
(0.123)
1
(1.00)
xq gain 93 (15%) 532 0.982
(1.00)
0.252
(0.748)
0.603
(0.959)
0.544
(0.938)
0.318
(0.796)
1
(1.00)
0.806
(1)
0.772
(0.992)
0.829
(1.00)
0.822
(1.00)
0.00056
(0.138)
0.225
(0.718)
5p loss 110 (18%) 515 0.0153
(0.341)
0.197
(0.688)
0.00088
(0.144)
0.0115
(0.341)
0.205
(0.698)
0.657
(0.96)
0.25
(0.748)
0.592
(0.957)
0.671
(0.962)
0.765
(0.987)
0.446
(0.9)
1
(1.00)
5q loss 195 (31%) 430 0.139
(0.586)
0.832
(1.00)
0.00136
(0.191)
0.197
(0.688)
0.031
(0.404)
0.369
(0.838)
0.22
(0.713)
0.825
(1.00)
0.262
(0.767)
0.901
(1.00)
0.209
(0.707)
1
(1.00)
8p loss 156 (25%) 469 0.914
(1.00)
0.743
(0.977)
0.113
(0.552)
0.22
(0.713)
0.0657
(0.494)
1
(1.00)
0.0023
(0.239)
0.721
(0.972)
0.974
(1.00)
0.142
(0.586)
0.286
(0.793)
0.136
(0.586)
18q loss 257 (41%) 368 0.92
(1.00)
0.258
(0.761)
0.906
(1.00)
0.0008
(0.144)
0.97
(1.00)
0.736
(0.972)
0.214
(0.713)
0.601
(0.959)
0.316
(0.795)
0.294
(0.793)
0.805
(1)
0.347
(0.823)
xp loss 123 (20%) 502 0.282
(0.793)
0.494
(0.912)
0.393
(0.853)
0.295
(0.793)
0.0387
(0.437)
0.205
(0.698)
0.000249
(0.123)
0.6
(0.959)
0.864
(1.00)
0.00766
(0.331)
0.38
(0.841)
0.233
(0.734)
1p gain 84 (13%) 541 0.293
(0.793)
0.0299
(0.404)
0.0985
(0.533)
0.0528
(0.486)
0.965
(1.00)
0.21
(0.707)
0.0944
(0.528)
0.0316
(0.404)
0.537
(0.938)
0.959
(1.00)
0.33
(0.807)
0.664
(0.96)
1q gain 170 (27%) 455 0.186
(0.665)
0.0904
(0.528)
0.828
(1.00)
0.203
(0.698)
0.96
(1.00)
0.574
(0.95)
0.0487
(0.461)
0.0642
(0.494)
0.818
(1.00)
0.465
(0.901)
0.0217
(0.373)
0.523
(0.927)
2p gain 137 (22%) 488 0.945
(1.00)
0.47
(0.901)
0.216
(0.713)
0.0564
(0.488)
0.677
(0.962)
0.838
(1.00)
0.525
(0.928)
0.804
(1)
0.437
(0.891)
0.167
(0.635)
0.0438
(0.444)
1
(1.00)
2q gain 113 (18%) 512 0.79
(0.995)
0.876
(1.00)
0.0996
(0.533)
0.11
(0.548)
0.692
(0.966)
1
(1.00)
0.649
(0.96)
0.507
(0.923)
0.703
(0.968)
0.955
(1.00)
0.399
(0.859)
1
(1.00)
3p gain 85 (14%) 540 0.515
(0.923)
0.554
(0.938)
0.4
(0.859)
0.674
(0.962)
0.493
(0.912)
1
(1.00)
0.612
(0.96)
0.237
(0.74)
0.929
(1.00)
0.712
(0.972)
0.478
(0.904)
0.0325
(0.41)
3q gain 170 (27%) 455 0.6
(0.959)
0.00422
(0.279)
0.118
(0.557)
0.922
(1.00)
0.686
(0.963)
0.71
(0.972)
0.325
(0.806)
0.0284
(0.401)
0.884
(1.00)
0.0882
(0.526)
0.0931
(0.528)
0.148
(0.599)
4p gain 37 (6%) 588 0.436
(0.891)
0.988
(1.00)
0.0569
(0.488)
0.62
(0.96)
0.545
(0.938)
1
(1.00)
0.0928
(0.528)
0.655
(0.96)
0.389
(0.853)
0.333
(0.811)
0.274
(0.783)
0.102
(0.533)
4q gain 30 (5%) 595 0.735
(0.972)
0.856
(1.00)
0.402
(0.86)
0.619
(0.96)
0.648
(0.96)
1
(1.00)
0.15
(0.604)
0.813
(1.00)
0.737
(0.972)
0.956
(1.00)
0.221
(0.713)
1
(1.00)
5p gain 179 (29%) 446 0.472
(0.901)
0.743
(0.977)
0.801
(1)
0.00346
(0.277)
0.972
(1.00)
0.46
(0.901)
0.628
(0.96)
0.909
(1.00)
0.975
(1.00)
0.841
(1.00)
0.825
(1.00)
1
(1.00)
5q gain 64 (10%) 561 0.536
(0.938)
0.357
(0.833)
0.271
(0.783)
0.105
(0.534)
0.222
(0.715)
0.785
(0.994)
0.471
(0.901)
0.737
(0.972)
0.263
(0.768)
0.817
(1.00)
0.857
(1.00)
0.61
(0.96)
6p gain 118 (19%) 507 0.0854
(0.525)
0.87
(1.00)
0.141
(0.586)
0.273
(0.783)
0.941
(1.00)
0.401
(0.859)
1
(1.00)
0.437
(0.891)
0.0849
(0.525)
0.463
(0.901)
0.115
(0.554)
1
(1.00)
6q gain 100 (16%) 525 0.021
(0.373)
0.787
(0.994)
0.009
(0.335)
0.291
(0.793)
0.85
(1.00)
0.0369
(0.433)
0.633
(0.96)
1
(1.00)
0.0849
(0.525)
0.266
(0.775)
0.0564
(0.488)
0.681
(0.962)
8p gain 248 (40%) 377 0.807
(1.00)
0.0585
(0.488)
0.469
(0.901)
0.944
(1.00)
0.577
(0.95)
1
(1.00)
0.0158
(0.341)
0.916
(1.00)
0.537
(0.938)
0.14
(0.586)
0.826
(1.00)
0.541
(0.938)
8q gain 337 (54%) 288 0.799
(1)
0.0875
(0.525)
0.286
(0.793)
0.957
(1.00)
0.443
(0.9)
0.407
(0.864)
0.16
(0.622)
0.408
(0.864)
0.964
(1.00)
0.786
(0.994)
0.865
(1.00)
0.554
(0.938)
9p gain 78 (12%) 547 0.00857
(0.335)
0.631
(0.96)
0.909
(1.00)
0.937
(1.00)
0.493
(0.912)
0.457
(0.9)
0.895
(1.00)
0.0188
(0.363)
0.309
(0.793)
0.0196
(0.363)
0.233
(0.734)
0.646
(0.96)
9q gain 109 (17%) 516 0.0577
(0.488)
0.273
(0.783)
0.995
(1.00)
0.927
(1.00)
0.995
(1.00)
0.517
(0.924)
0.106
(0.535)
0.0224
(0.373)
0.0934
(0.528)
0.0423
(0.439)
0.163
(0.626)
0.431
(0.891)
10p gain 136 (22%) 489 0.654
(0.96)
0.921
(1.00)
0.136
(0.586)
0.0824
(0.525)
0.899
(1.00)
0.544
(0.938)
0.832
(1.00)
0.62
(0.96)
0.175
(0.656)
0.274
(0.783)
0.221
(0.713)
0.134
(0.586)
10q gain 98 (16%) 527 0.829
(1.00)
0.104
(0.534)
0.0233
(0.373)
0.0251
(0.38)
0.367
(0.838)
1
(1.00)
1
(1.00)
0.781
(0.994)
0.454
(0.9)
0.0163
(0.341)
0.304
(0.793)
0.225
(0.718)
11p gain 98 (16%) 527 0.497
(0.912)
0.32
(0.798)
0.391
(0.853)
0.0655
(0.494)
0.0757
(0.515)
0.644
(0.96)
0.718
(0.972)
0.396
(0.857)
0.705
(0.968)
0.505
(0.922)
0.0761
(0.515)
1
(1.00)
11q gain 102 (16%) 523 0.412
(0.866)
0.0482
(0.46)
0.21
(0.707)
0.385
(0.849)
0.0045
(0.279)
0.658
(0.96)
0.407
(0.864)
0.329
(0.807)
0.581
(0.95)
0.797
(1)
0.219
(0.713)
1
(1.00)
12p gain 149 (24%) 476 0.563
(0.945)
0.347
(0.823)
0.118
(0.557)
0.0155
(0.341)
0.539
(0.938)
0.326
(0.806)
0.0647
(0.494)
0.185
(0.665)
0.0996
(0.533)
0.181
(0.661)
0.0956
(0.528)
0.483
(0.907)
13q gain 197 (32%) 428 0.599
(0.959)
0.768
(0.987)
0.366
(0.838)
0.872
(1.00)
0.141
(0.586)
0.858
(1.00)
0.346
(0.823)
0.374
(0.838)
0.73
(0.972)
0.046
(0.457)
0.153
(0.607)
0.748
(0.978)
14q gain 76 (12%) 549 0.306
(0.793)
0.0115
(0.341)
0.076
(0.515)
0.301
(0.793)
0.484
(0.907)
0.452
(0.9)
0.0227
(0.373)
0.0918
(0.528)
0.73
(0.972)
0.75
(0.98)
0.52
(0.925)
0.636
(0.96)
15q gain 67 (11%) 558 0.0766
(0.515)
0.729
(0.972)
0.215
(0.713)
0.555
(0.938)
0.299
(0.793)
0.579
(0.95)
0.119
(0.557)
1
(1.00)
0.788
(0.994)
0.0734
(0.515)
0.00791
(0.331)
1
(1.00)
16p gain 100 (16%) 525 0.154
(0.608)
0.801
(1)
0.0704
(0.51)
0.776
(0.992)
0.936
(1.00)
0.159
(0.622)
0.0423
(0.439)
0.196
(0.687)
0.148
(0.599)
0.658
(0.96)
0.0263
(0.392)
1
(1.00)
16q gain 86 (14%) 539 0.0161
(0.341)
0.654
(0.96)
0.047
(0.457)
0.731
(0.972)
0.703
(0.968)
0.0207
(0.373)
0.0743
(0.515)
0.0655
(0.494)
0.783
(0.994)
0.941
(1.00)
0.0309
(0.404)
0.653
(0.96)
17p gain 61 (10%) 564 0.308
(0.793)
0.87
(1.00)
0.00799
(0.331)
0.609
(0.96)
0.0758
(0.515)
0.377
(0.84)
0.0778
(0.515)
0.115
(0.554)
0.957
(1.00)
0.923
(1.00)
0.581
(0.95)
0.611
(0.96)
17q gain 108 (17%) 517 0.746
(0.978)
0.998
(1.00)
0.312
(0.793)
0.496
(0.912)
0.859
(1.00)
0.257
(0.761)
0.0108
(0.341)
0.00596
(0.326)
0.661
(0.96)
0.339
(0.818)
0.0875
(0.525)
1
(1.00)
18p gain 135 (22%) 490 0.0228
(0.373)
0.612
(0.96)
0.638
(0.96)
0.584
(0.953)
0.46
(0.901)
0.685
(0.963)
1
(1.00)
0.455
(0.9)
0.541
(0.938)
0.924
(1.00)
0.773
(0.992)
0.703
(0.968)
18q gain 79 (13%) 546 0.166
(0.634)
0.722
(0.972)
0.0975
(0.533)
0.029
(0.401)
0.618
(0.96)
0.801
(1)
0.511
(0.923)
0.437
(0.891)
0.549
(0.938)
0.507
(0.923)
0.884
(1.00)
1
(1.00)
19p gain 83 (13%) 542 0.182
(0.661)
0.303
(0.793)
0.932
(1.00)
0.0872
(0.525)
0.458
(0.9)
0.306
(0.793)
0.606
(0.96)
0.764
(0.987)
0.722
(0.972)
0.514
(0.923)
0.518
(0.924)
1
(1.00)
19q gain 119 (19%) 506 0.95
(1.00)
0.401
(0.859)
0.876
(1.00)
0.152
(0.607)
0.176
(0.656)
0.666
(0.96)
0.181
(0.661)
1
(1.00)
0.931
(1.00)
0.934
(1.00)
0.242
(0.742)
0.697
(0.968)
20p gain 349 (56%) 276 0.0119
(0.341)
0.363
(0.838)
0.544
(0.938)
0.282
(0.793)
0.204
(0.698)
0.622
(0.96)
0.00808
(0.331)
0.0223
(0.373)
0.0408
(0.437)
0.628
(0.96)
0.957
(1.00)
1
(1.00)
21q gain 39 (6%) 586 0.943
(1.00)
0.717
(0.972)
0.925
(1.00)
0.682
(0.962)
0.465
(0.901)
0.5
(0.915)
0.718
(0.972)
0.669
(0.962)
0.687
(0.963)
0.681
(0.962)
0.218
(0.713)
0.603
(0.959)
22q gain 63 (10%) 562 0.428
(0.889)
0.0192
(0.363)
0.228
(0.724)
0.146
(0.594)
0.0156
(0.341)
1
(1.00)
0.471
(0.901)
0.408
(0.864)
0.239
(0.742)
0.931
(1.00)
0.00725
(0.331)
0.37
(0.838)
1p loss 97 (16%) 528 0.237
(0.74)
0.984
(1.00)
0.32
(0.798)
0.896
(1.00)
0.643
(0.96)
0.0313
(0.404)
0.547
(0.938)
0.393
(0.853)
0.312
(0.793)
0.791
(0.995)
0.247
(0.748)
1
(1.00)
1q loss 47 (8%) 578 0.0385
(0.437)
0.155
(0.609)
0.73
(0.972)
0.446
(0.9)
0.666
(0.96)
0.283
(0.793)
0.869
(1.00)
0.556
(0.938)
0.321
(0.799)
0.262
(0.767)
1
(1.00)
0.603
(0.959)
2p loss 36 (6%) 589 0.457
(0.9)
0.31
(0.793)
0.251
(0.748)
0.0719
(0.515)
0.855
(1.00)
0.156
(0.611)
0.258
(0.761)
0.135
(0.586)
0.95
(1.00)
1
(1.00)
0.884
(1.00)
1
(1.00)
2q loss 49 (8%) 576 0.786
(0.994)
0.439
(0.892)
0.659
(0.96)
0.679
(0.962)
0.815
(1.00)
0.356
(0.833)
1
(1.00)
0.0581
(0.488)
0.294
(0.793)
0.453
(0.9)
0.242
(0.742)
1
(1.00)
3p loss 187 (30%) 438 0.856
(1.00)
0.0543
(0.488)
0.079
(0.515)
0.488
(0.911)
0.0142
(0.341)
0.47
(0.901)
0.444
(0.9)
0.372
(0.838)
0.875
(1.00)
0.586
(0.953)
0.0823
(0.525)
1
(1.00)
3q loss 92 (15%) 533 0.798
(1)
0.811
(1.00)
0.351
(0.828)
0.0963
(0.529)
0.279
(0.793)
0.252
(0.748)
0.806
(1)
0.473
(0.901)
0.364
(0.838)
0.368
(0.838)
0.856
(1.00)
0.673
(0.962)
4p loss 274 (44%) 351 0.139
(0.586)
0.629
(0.96)
0.0843
(0.525)
0.102
(0.533)
0.557
(0.938)
0.183
(0.663)
0.078
(0.515)
0.177
(0.656)
0.99
(1.00)
0.152
(0.607)
0.0401
(0.437)
0.766
(0.987)
4q loss 256 (41%) 369 0.0191
(0.363)
0.0842
(0.525)
0.199
(0.688)
0.0693
(0.507)
0.335
(0.813)
0.866
(1.00)
0.328
(0.807)
0.917
(1.00)
0.914
(1.00)
0.892
(1.00)
0.285
(0.793)
0.758
(0.984)
6p loss 93 (15%) 532 0.812
(1.00)
0.592
(0.957)
0.63
(0.96)
0.128
(0.578)
0.377
(0.84)
0.145
(0.594)
0.112
(0.551)
0.884
(1.00)
0.656
(0.96)
0.178
(0.656)
0.495
(0.912)
0.681
(0.962)
6q loss 112 (18%) 513 0.731
(0.972)
0.664
(0.96)
0.67
(0.962)
0.0289
(0.401)
0.756
(0.984)
0.177
(0.656)
0.0397
(0.437)
0.786
(0.994)
0.884
(1.00)
0.162
(0.626)
0.579
(0.95)
1
(1.00)
7p loss 33 (5%) 592 0.481
(0.907)
0.849
(1.00)
0.389
(0.853)
0.678
(0.962)
0.108
(0.541)
0.714
(0.972)
0.847
(1.00)
0.818
(1.00)
0.269
(0.781)
0.0236
(0.373)
0.236
(0.74)
1
(1.00)
7q loss 50 (8%) 575 0.76
(0.986)
0.0789
(0.515)
0.188
(0.671)
0.101
(0.533)
0.243
(0.742)
0.237
(0.74)
0.63
(0.96)
0.704
(0.968)
0.581
(0.95)
0.122
(0.561)
0.751
(0.98)
1
(1.00)
8q loss 59 (9%) 566 0.539
(0.938)
0.862
(1.00)
0.0461
(0.457)
0.00682
(0.331)
0.732
(0.972)
0.785
(0.994)
0.0528
(0.486)
0.727
(0.972)
0.452
(0.9)
0.413
(0.866)
0.0195
(0.363)
0.567
(0.948)
9p loss 249 (40%) 376 0.524
(0.927)
0.965
(1.00)
0.0334
(0.416)
0.138
(0.586)
0.106
(0.535)
0.736
(0.972)
0.18
(0.661)
0.115
(0.554)
0.545
(0.938)
0.352
(0.828)
0.3
(0.793)
0.114
(0.554)
9q loss 173 (28%) 452 0.305
(0.793)
0.409
(0.864)
0.121
(0.56)
0.227
(0.722)
0.874
(1.00)
0.578
(0.95)
0.0502
(0.471)
0.305
(0.793)
0.311
(0.793)
0.103
(0.534)
0.141
(0.586)
0.19
(0.676)
10p loss 118 (19%) 507 0.0937
(0.528)
0.484
(0.907)
0.828
(1.00)
0.058
(0.488)
0.35
(0.828)
0.835
(1.00)
0.314
(0.793)
0.431
(0.891)
0.0415
(0.439)
0.538
(0.938)
0.0239
(0.373)
0.426
(0.887)
10q loss 118 (19%) 507 0.496
(0.912)
0.938
(1.00)
0.626
(0.96)
0.384
(0.849)
0.495
(0.912)
0.836
(1.00)
0.434
(0.891)
0.36
(0.835)
0.522
(0.927)
0.353
(0.828)
0.00454
(0.279)
0.455
(0.9)
11p loss 117 (19%) 508 0.249
(0.748)
0.747
(0.978)
0.018
(0.363)
0.426
(0.887)
0.454
(0.9)
0.664
(0.96)
0.0927
(0.528)
0.0346
(0.424)
0.105
(0.534)
0.935
(1.00)
0.305
(0.793)
0.118
(0.557)
11q loss 122 (20%) 503 0.0747
(0.515)
0.129
(0.578)
0.014
(0.341)
0.34
(0.818)
0.193
(0.683)
0.666
(0.96)
0.0149
(0.341)
0.0696
(0.507)
0.661
(0.96)
0.476
(0.904)
0.518
(0.924)
0.0395
(0.437)
12p loss 98 (16%) 527 0.104
(0.534)
0.0609
(0.494)
0.858
(1.00)
0.0848
(0.525)
0.766
(0.987)
0.819
(1.00)
0.631
(0.96)
0.0651
(0.494)
0.655
(0.96)
0.0776
(0.515)
0.559
(0.941)
1
(1.00)
12q loss 87 (14%) 538 0.13
(0.578)
0.184
(0.663)
0.288
(0.793)
0.0126
(0.341)
0.569
(0.949)
0.805
(1)
0.613
(0.96)
0.551
(0.938)
0.138
(0.586)
0.0281
(0.401)
0.0373
(0.433)
0.37
(0.838)
13q loss 103 (16%) 522 0.961
(1.00)
0.065
(0.494)
0.00596
(0.326)
0.0354
(0.424)
0.0156
(0.341)
0.25
(0.748)
0.0131
(0.341)
0.0546
(0.488)
0.121
(0.56)
0.848
(1.00)
0.0473
(0.457)
0.387
(0.852)
14q loss 157 (25%) 468 0.776
(0.992)
0.544
(0.938)
0.0686
(0.507)
0.241
(0.742)
0.218
(0.713)
0.244
(0.743)
0.84
(1.00)
0.637
(0.96)
0.477
(0.904)
0.41
(0.864)
0.688
(0.963)
0.472
(0.901)
15q loss 149 (24%) 476 0.546
(0.938)
0.31
(0.793)
0.603
(0.959)
0.0152
(0.341)
0.646
(0.96)
0.701
(0.968)
0.682
(0.962)
0.091
(0.528)
0.689
(0.963)
0.827
(1.00)
0.71
(0.972)
0.297
(0.793)
16p loss 154 (25%) 471 0.935
(1.00)
0.101
(0.533)
0.757
(0.984)
0.215
(0.713)
0.242
(0.742)
0.119
(0.557)
1
(1.00)
0.906
(1.00)
0.976
(1.00)
0.847
(1.00)
0.871
(1.00)
0.714
(0.972)
16q loss 167 (27%) 458 0.554
(0.938)
0.342
(0.821)
0.308
(0.793)
0.41
(0.864)
0.901
(1.00)
0.0581
(0.488)
0.621
(0.96)
0.357
(0.833)
0.828
(1.00)
0.548
(0.938)
0.665
(0.96)
0.14
(0.586)
17p loss 237 (38%) 388 0.917
(1.00)
0.415
(0.868)
0.579
(0.95)
0.28
(0.793)
0.855
(1.00)
0.396
(0.857)
0.0472
(0.457)
0.168
(0.635)
0.0953
(0.528)
0.592
(0.957)
0.51
(0.923)
0.196
(0.687)
17q loss 102 (16%) 523 0.344
(0.823)
0.847
(1.00)
0.569
(0.949)
0.305
(0.793)
0.285
(0.793)
0.372
(0.838)
0.722
(0.972)
0.776
(0.992)
0.105
(0.534)
0.565
(0.947)
0.295
(0.793)
0.0921
(0.528)
18p loss 187 (30%) 438 0.33
(0.807)
0.306
(0.793)
0.956
(1.00)
0.0639
(0.494)
0.847
(1.00)
0.586
(0.953)
0.0849
(0.525)
0.312
(0.793)
0.866
(1.00)
0.146
(0.594)
0.642
(0.96)
0.314
(0.793)
19p loss 182 (29%) 443 0.0553
(0.488)
0.745
(0.978)
0.462
(0.901)
0.575
(0.95)
0.458
(0.9)
0.716
(0.972)
0.21
(0.707)
0.572
(0.95)
0.813
(1.00)
0.0315
(0.404)
0.00976
(0.335)
1
(1.00)
19q loss 142 (23%) 483 0.653
(0.96)
0.904
(1.00)
0.867
(1.00)
0.592
(0.957)
0.653
(0.96)
1
(1.00)
0.347
(0.823)
0.712
(0.972)
0.934
(1.00)
0.0592
(0.49)
0.0152
(0.341)
0.704
(0.968)
20p loss 42 (7%) 583 0.423
(0.884)
0.696
(0.968)
0.627
(0.96)
0.494
(0.912)
0.956
(1.00)
0.726
(0.972)
0.601
(0.959)
0.0374
(0.433)
0.392
(0.853)
0.704
(0.968)
0.51
(0.923)
0.485
(0.907)
20q loss 8 (1%) 617 0.339
(0.818)
0.577
(0.95)
0.245
(0.743)
0.0353
(0.424)
0.649
(0.96)
1
(1.00)
0.447
(0.9)
0.678
(0.962)
0.642
(0.96)
0.512
(0.923)
1
(1.00)
21q loss 287 (46%) 338 0.71
(0.972)
0.142
(0.586)
0.339
(0.818)
0.364
(0.838)
0.665
(0.96)
0.317
(0.795)
0.726
(0.972)
0.214
(0.713)
0.199
(0.688)
0.129
(0.578)
0.375
(0.838)
0.375
(0.838)
22q loss 218 (35%) 407 0.095
(0.528)
0.481
(0.907)
0.00988
(0.335)
0.0437
(0.444)
0.434
(0.891)
0.607
(0.96)
0.358
(0.833)
0.0678
(0.505)
0.475
(0.904)
0.953
(1.00)
0.366
(0.838)
0.752
(0.98)
xq loss 98 (16%) 527 0.6
(0.959)
0.832
(1.00)
0.621
(0.96)
0.291
(0.793)
0.515
(0.923)
0.0999
(0.533)
0.00367
(0.277)
0.314
(0.793)
0.666
(0.96)
0.00965
(0.335)
0.95
(1.00)
0.664
(0.96)
'7p gain' versus 'GENDER'

P value = 0.000449 (Fisher's exact test), Q value = 0.14

Table S1.  Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
7P GAIN MUTATED 71 237
7P GAIN WILD-TYPE 114 203

Figure S1.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'GENDER'

P value = 0.00246 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
7Q GAIN MUTATED 59 198
7Q GAIN WILD-TYPE 126 242

Figure S2.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'RACE'

P value = 0.00253 (Fisher's exact test), Q value = 0.24

Table S3.  Gene #24: '12q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
12Q GAIN MUTATED 39 1 0 62
12Q GAIN WILD-TYPE 95 16 1 330

Figure S3.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #11: 'RACE'

'20q gain' versus 'GENDER'

P value = 0.00267 (Fisher's exact test), Q value = 0.24

Table S4.  Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
20Q GAIN MUTATED 100 295
20Q GAIN WILD-TYPE 85 145

Figure S4.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'RACE'

P value = 0.00019 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
XP GAIN MUTATED 20 7 1 37
XP GAIN WILD-TYPE 114 10 0 355

Figure S5.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

'xq gain' versus 'RACE'

P value = 0.00056 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #41: 'xq gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 134 17 1 392
XQ GAIN MUTATED 29 6 1 48
XQ GAIN WILD-TYPE 105 11 0 344

Figure S6.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00088 (Fisher's exact test), Q value = 0.14

Table S7.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 10 21 47 33 87 87 28 95 72 46 49 4
5P LOSS MUTATED 7 3 2 3 13 18 9 18 11 6 5 1
5P LOSS WILD-TYPE 3 18 45 30 74 69 19 77 61 40 44 3

Figure S7.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00136 (Fisher's exact test), Q value = 0.19

Table S8.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 10 21 47 33 87 87 28 95 72 46 49 4
5Q LOSS MUTATED 7 7 8 9 26 29 11 42 17 11 9 3
5Q LOSS WILD-TYPE 3 14 39 24 61 58 17 53 55 35 40 1

Figure S8.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'GENDER'

P value = 0.0023 (Fisher's exact test), Q value = 0.24

Table S9.  Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
8P LOSS MUTATED 31 125
8P LOSS WILD-TYPE 154 315

Figure S9.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'GENDER'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 55 136 283 124
18Q LOSS MUTATED 18 56 136 34
18Q LOSS WILD-TYPE 37 80 147 90

Figure S10.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'GENDER'

P value = 0.000249 (Fisher's exact test), Q value = 0.12

Table S11.  Gene #81: 'xp loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
XP LOSS MUTATED 20 103
XP LOSS WILD-TYPE 165 337

Figure S11.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #7: 'GENDER'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532763/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/22507048/STES-TP.merged_data.txt

  • Number of patients = 625

  • Number of significantly arm-level cnvs = 82

  • 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)