Correlation between copy number variations of arm-level result and selected clinical features
Stomach and Esophageal carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1D21WXQ
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/C1D21WXQ
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, 7 significant findings detected with Q value < 0.25.

  • 7p gain cnv correlated to 'GENDER'.

  • 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'.

  • 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, 7 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 306 (49%) 319 0.879
(1.00) 		0.532
(0.94) 		0.332
(0.826) 		0.0419
(0.463) 		0.968
(1.00) 		0.741
(0.971) 		0.000631
(0.193) 		0.755
(0.971) 		0.797
(0.988) 		0.285
(0.813) 		0.191
(0.705) 		0.125
(0.612)
20q gain 395 (63%) 230 0.0957
(0.555) 		0.167
(0.677) 		0.325
(0.826) 		0.153
(0.657) 		0.0496
(0.492) 		0.497
(0.936) 		0.00144
(0.233) 		0.106
(0.581) 		0.181
(0.682) 		0.637
(0.971) 		0.852
(1.00) 		0.547
(0.945)
xp gain 71 (11%) 554 0.45
(0.928) 		0.704
(0.971) 		0.394
(0.889) 		0.417
(0.903) 		0.158
(0.666) 		0.416
(0.901) 		0.41
(0.893) 		0.193
(0.706) 		0.711
(0.971) 		0.228
(0.759) 		0.0008
(0.193) 		0.617
(0.971)
xq gain 91 (15%) 534 0.982
(1.00) 		0.387
(0.882) 		0.695
(0.971) 		0.463
(0.928) 		0.331
(0.826) 		1
(1.00) 		1
(1.00) 		0.462
(0.928) 		0.792
(0.985) 		0.624
(0.971) 		0.00166
(0.233) 		0.668
(0.971)
5p loss 112 (18%) 513 0.197
(0.715) 		0.149
(0.647) 		0.00098
(0.193) 		0.00439
(0.288) 		0.168
(0.678) 		0.658
(0.971) 		0.363
(0.862) 		0.685
(0.971) 		0.671
(0.971) 		0.765
(0.971) 		0.498
(0.936) 		1
(1.00)
18q loss 256 (41%) 369 0.878
(1.00) 		0.128
(0.619) 		0.912
(1.00) 		0.0002
(0.125) 		0.99
(1.00) 		0.735
(0.971) 		0.182
(0.682) 		0.673
(0.971) 		0.218
(0.745) 		0.298
(0.813) 		0.83
(1.00) 		0.347
(0.85)
xp loss 122 (20%) 503 0.297
(0.813) 		0.513
(0.936) 		0.248
(0.777) 		0.286
(0.813) 		0.0428
(0.463) 		0.204
(0.722) 		0.000253
(0.125) 		0.509
(0.936) 		0.671
(0.971) 		0.00531
(0.29) 		0.381
(0.88) 		0.233
(0.771)
1p gain 82 (13%) 543 0.126
(0.615) 		0.0257
(0.434) 		0.329
(0.826) 		0.052
(0.496) 		0.991
(1.00) 		0.208
(0.727) 		0.12
(0.603) 		0.0273
(0.434) 		0.63
(0.971) 		0.855
(1.00) 		0.29
(0.813) 		0.66
(0.971)
1q gain 167 (27%) 458 0.0603
(0.51) 		0.079
(0.521) 		0.826
(1.00) 		0.124
(0.609) 		0.964
(1.00) 		0.71
(0.971) 		0.0474
(0.481) 		0.1
(0.557) 		0.818
(1) 		0.465
(0.928) 		0.0608
(0.51) 		0.736
(0.971)
2p gain 137 (22%) 488 0.867
(1.00) 		0.315
(0.813) 		0.14
(0.636) 		0.0255
(0.434) 		0.525
(0.94) 		0.838
(1.00) 		0.397
(0.889) 		0.707
(0.971) 		0.631
(0.971) 		0.167
(0.677) 		0.0427
(0.463) 		1
(1.00)
2q gain 111 (18%) 514 0.885
(1.00) 		0.737
(0.971) 		0.0991
(0.557) 		0.235
(0.774) 		0.592
(0.97) 		1
(1.00) 		0.423
(0.907) 		0.283
(0.813) 		0.703
(0.971) 		0.954
(1.00) 		0.463
(0.928) 		1
(1.00)
3p gain 83 (13%) 542 0.492
(0.936) 		0.365
(0.862) 		0.626
(0.971) 		0.901
(1.00) 		0.464
(0.928) 		0.805
(0.996) 		1
(1.00) 		0.226
(0.757) 		0.948
(1.00) 		0.404
(0.893) 		0.46
(0.928) 		0.0325
(0.463)
3q gain 170 (27%) 455 0.334
(0.83) 		0.00516
(0.29) 		0.272
(0.807) 		0.923
(1.00) 		0.695
(0.971) 		0.456
(0.928) 		0.431
(0.919) 		0.0268
(0.434) 		0.671
(0.971) 		0.155
(0.662) 		0.101
(0.558) 		0.148
(0.647)
4p gain 39 (6%) 586 0.742
(0.971) 		0.954
(1.00) 		0.0708
(0.521) 		0.686
(0.971) 		0.435
(0.923) 		1
(1.00) 		0.0468
(0.48) 		0.659
(0.971) 		0.692
(0.971) 		0.494
(0.936) 		0.364
(0.862) 		0.11
(0.594)
4q gain 33 (5%) 592 0.939
(1.00) 		0.7
(0.971) 		0.521
(0.939) 		0.76
(0.971) 		0.512
(0.936) 		1
(1.00) 		0.0767
(0.521) 		1
(1.00) 		0.415
(0.901) 		0.573
(0.965) 		0.117
(0.603) 		0.39
(0.886)
5p gain 177 (28%) 448 0.921
(1.00) 		0.71
(0.971) 		0.789
(0.984) 		0.00568
(0.294) 		0.983
(1.00) 		0.457
(0.928) 		0.56
(0.957) 		0.908
(1.00) 		0.975
(1.00) 		0.841
(1.00) 		0.802
(0.994) 		1
(1.00)
5q gain 63 (10%) 562 0.767
(0.971) 		0.282
(0.813) 		0.253
(0.777) 		0.0541
(0.496) 		0.25
(0.777) 		1
(1.00) 		0.471
(0.928) 		0.737
(0.971) 		0.263
(0.787) 		0.817
(1) 		0.82
(1) 		0.61
(0.971)
6p gain 117 (19%) 508 0.238
(0.776) 		0.925
(1.00) 		0.205
(0.722) 		0.326
(0.826) 		0.94
(1.00) 		0.396
(0.889) 		0.911
(1.00) 		0.506
(0.936) 		0.0849
(0.521) 		0.727
(0.971) 		0.141
(0.636) 		1
(1.00)
6q gain 100 (16%) 525 0.0721
(0.521) 		0.598
(0.97) 		0.00784
(0.331) 		0.383
(0.88) 		0.734
(0.971) 		0.0369
(0.463) 		0.473
(0.928) 		1
(1.00) 		0.0849
(0.521) 		0.502
(0.936) 		0.0672
(0.512) 		0.681
(0.971)
7q gain 257 (41%) 368 0.623
(0.971) 		0.728
(0.971) 		0.465
(0.928) 		0.0559
(0.505) 		0.79
(0.984) 		0.736
(0.971) 		0.0076
(0.331) 		0.672
(0.971) 		0.272
(0.807) 		0.963
(1.00) 		0.234
(0.773) 		0.121
(0.606)
8p gain 248 (40%) 377 0.883
(1.00) 		0.0189
(0.434) 		0.616
(0.971) 		0.996
(1.00) 		0.598
(0.97) 		1
(1.00) 		0.0398
(0.463) 		0.915
(1.00) 		0.537
(0.94) 		0.14
(0.636) 		0.749
(0.971) 		0.542
(0.94)
8q gain 338 (54%) 287 0.68
(0.971) 		0.0334
(0.463) 		0.162
(0.669) 		0.947
(1.00) 		0.529
(0.94) 		0.406
(0.893) 		0.253
(0.777) 		0.602
(0.971) 		0.768
(0.971) 		0.786
(0.983) 		0.828
(1.00) 		0.56
(0.957)
9p gain 77 (12%) 548 0.107
(0.585) 		0.672
(0.971) 		0.809
(0.998) 		0.933
(1.00) 		0.438
(0.927) 		0.805
(0.996) 		0.894
(1.00) 		0.0273
(0.434) 		0.527
(0.94) 		0.0271
(0.434) 		0.262
(0.787) 		0.636
(0.971)
9q gain 109 (17%) 516 0.409
(0.893) 		0.314
(0.813) 		0.982
(1.00) 		0.929
(1.00) 		0.981
(1.00) 		0.83
(1.00) 		0.166
(0.677) 		0.0585
(0.505) 		0.16
(0.666) 		0.0577
(0.505) 		0.25
(0.777) 		0.422
(0.907)
10p gain 135 (22%) 490 0.81
(0.998) 		1
(1.00) 		0.202
(0.722) 		0.0859
(0.521) 		0.916
(1.00) 		0.543
(0.94) 		0.75
(0.971) 		0.708
(0.971) 		0.175
(0.682) 		0.274
(0.809) 		0.204
(0.722) 		0.133
(0.631)
10q gain 98 (16%) 527 0.717
(0.971) 		0.181
(0.682) 		0.0399
(0.463) 		0.0203
(0.434) 		0.532
(0.94) 		0.647
(0.971) 		0.904
(1.00) 		0.888
(1.00) 		0.454
(0.928) 		0.0163
(0.434) 		0.303
(0.813) 		0.225
(0.757)
11p gain 99 (16%) 526 0.537
(0.94) 		0.395
(0.889) 		0.377
(0.878) 		0.0643
(0.51) 		0.0822
(0.521) 		0.647
(0.971) 		0.811
(0.998) 		0.481
(0.928) 		0.705
(0.971) 		0.505
(0.936) 		0.0863
(0.521) 		1
(1.00)
11q gain 104 (17%) 521 0.56
(0.957) 		0.0664
(0.512) 		0.201
(0.722) 		0.49
(0.936) 		0.00701
(0.331) 		0.657
(0.971) 		0.481
(0.928) 		0.486
(0.935) 		0.893
(1.00) 		0.895
(1.00) 		0.114
(0.601) 		0.673
(0.971)
12p gain 148 (24%) 477 0.783
(0.981) 		0.276
(0.809) 		0.0616
(0.51) 		0.0143
(0.434) 		0.56
(0.957) 		0.244
(0.777) 		0.0797
(0.521) 		0.222
(0.755) 		0.0996
(0.557) 		0.181
(0.682) 		0.0809
(0.521) 		0.481
(0.928)
12q gain 115 (18%) 510 0.856
(1.00) 		0.0186
(0.434) 		0.226
(0.757) 		0.108
(0.589) 		0.0971
(0.555) 		0.131
(0.628) 		0.213
(0.736) 		1
(1.00) 		0.0616
(0.51) 		0.0249
(0.434) 		0.0023
(0.251) 		0.46
(0.928)
13q gain 197 (32%) 428 0.856
(1.00) 		0.768
(0.971) 		0.226
(0.757) 		0.871
(1.00) 		0.14
(0.636) 		0.858
(1.00) 		0.346
(0.849) 		0.313
(0.813) 		0.73
(0.971) 		0.046
(0.479) 		0.154
(0.657) 		0.748
(0.971)
14q gain 75 (12%) 550 0.185
(0.694) 		0.0148
(0.434) 		0.0793
(0.521) 		0.305
(0.813) 		0.44
(0.928) 		0.446
(0.928) 		0.0305
(0.455) 		0.218
(0.745) 		0.768
(0.971) 		0.75
(0.971) 		0.476
(0.928) 		0.632
(0.971)
15q gain 67 (11%) 558 0.0912
(0.54) 		0.729
(0.971) 		0.124
(0.609) 		0.553
(0.952) 		0.29
(0.813) 		0.579
(0.969) 		0.119
(0.603) 		0.62
(0.971) 		0.788
(0.984) 		0.0734
(0.521) 		0.00788
(0.331) 		1
(1.00)
16p gain 99 (16%) 526 0.148
(0.647) 		0.887
(1.00) 		0.0529
(0.496) 		0.779
(0.98) 		0.932
(1.00) 		0.159
(0.666) 		0.0544
(0.496) 		0.189
(0.7) 		0.396
(0.889) 		1
(1.00) 		0.0194
(0.434) 		0.402
(0.893)
16q gain 86 (14%) 539 0.00902
(0.355) 		0.654
(0.971) 		0.0537
(0.496) 		0.731
(0.971) 		0.694
(0.971) 		0.0207
(0.434) 		0.0743
(0.521) 		0.0893
(0.532) 		0.783
(0.981) 		0.941
(1.00) 		0.0305
(0.455) 		0.653
(0.971)
17p gain 62 (10%) 563 0.467
(0.928) 		0.994
(1.00) 		0.0224
(0.434) 		0.652
(0.971) 		0.0537
(0.496) 		0.384
(0.88) 		0.0778
(0.521) 		0.119
(0.603) 		0.976
(1.00) 		0.829
(1.00) 		0.263
(0.787) 		0.61
(0.971)
17q gain 106 (17%) 519 0.816
(1) 		0.865
(1.00) 		0.359
(0.858) 		0.422
(0.907) 		0.917
(1.00) 		0.252
(0.777) 		0.0145
(0.434) 		0.0368
(0.463) 		0.601
(0.971) 		0.293
(0.813) 		0.0791
(0.521) 		1
(1.00)
18p gain 137 (22%) 488 0.0294
(0.454) 		0.67
(0.971) 		0.595
(0.97) 		0.57
(0.965) 		0.584
(0.969) 		0.839
(1.00) 		1
(1.00) 		0.254
(0.777) 		0.573
(0.965) 		0.711
(0.971) 		0.72
(0.971) 		0.706
(0.971)
18q gain 82 (13%) 543 0.0627
(0.51) 		0.919
(1.00) 		0.0807
(0.521) 		0.0358
(0.463) 		0.752
(0.971) 		1
(1.00) 		0.517
(0.936) 		0.529
(0.94) 		0.366
(0.862) 		0.757
(0.971) 		0.408
(0.893) 		1
(1.00)
19p gain 83 (13%) 542 0.282
(0.813) 		0.159
(0.666) 		0.95
(1.00) 		0.262
(0.787) 		0.452
(0.928) 		0.306
(0.813) 		0.606
(0.971) 		0.76
(0.971) 		0.722
(0.971) 		0.894
(1.00) 		0.496
(0.936) 		1
(1.00)
19q gain 117 (19%) 508 0.846
(1.00) 		0.351
(0.855) 		0.902
(1.00) 		0.331
(0.826) 		0.0971
(0.555) 		0.662
(0.971) 		0.146
(0.642) 		0.894
(1.00) 		0.629
(0.971) 		0.704
(0.971) 		0.245
(0.777) 		0.698
(0.971)
20p gain 349 (56%) 276 0.0544
(0.496) 		0.31
(0.813) 		0.48
(0.928) 		0.301
(0.813) 		0.149
(0.647) 		0.622
(0.971) 		0.00808
(0.331) 		0.0273
(0.434) 		0.0408
(0.463) 		0.614
(0.971) 		0.991
(1.00) 		0.763
(0.971)
21q gain 36 (6%) 589 0.707
(0.971) 		0.905
(1.00) 		0.731
(0.971) 		0.743
(0.971) 		0.571
(0.965) 		0.5
(0.936) 		1
(1.00) 		0.821
(1) 		0.616
(0.971) 		0.887
(1.00) 		0.246
(0.777) 		0.591
(0.97)
22q gain 64 (10%) 561 0.648
(0.971) 		0.0114
(0.401) 		0.175
(0.682) 		0.0983
(0.557) 		0.0102
(0.379) 		1
(1.00) 		0.471
(0.928) 		1
(1.00) 		0.211
(0.733) 		0.834
(1.00) 		0.00351
(0.288) 		0.627
(0.971)
1p loss 95 (15%) 530 0.626
(0.971) 		0.582
(0.969) 		0.26
(0.787) 		0.684
(0.971) 		0.713
(0.971) 		0.0184
(0.434) 		0.903
(1.00) 		0.243
(0.777) 		0.238
(0.776) 		0.424
(0.907) 		0.258
(0.787) 		1
(1.00)
1q loss 47 (8%) 578 0.0625
(0.51) 		0.419
(0.904) 		0.622
(0.971) 		0.603
(0.971) 		0.542
(0.94) 		0.0851
(0.521) 		1
(1.00) 		0.843
(1.00) 		0.321
(0.821) 		0.51
(0.936) 		0.78
(0.98) 		0.603
(0.971)
2p loss 38 (6%) 587 0.92
(1.00) 		0.287
(0.813) 		0.253
(0.777) 		0.0634
(0.51) 		0.727
(0.971) 		0.5
(0.936) 		0.359
(0.858) 		0.143
(0.636) 		0.95
(1.00) 		1
(1.00) 		0.941
(1.00) 		1
(1.00)
2q loss 51 (8%) 574 0.666
(0.971) 		0.41
(0.893) 		0.677
(0.971) 		0.777
(0.98) 		0.764
(0.971) 		0.764
(0.971) 		0.873
(1.00) 		0.134
(0.632) 		0.294
(0.813) 		0.453
(0.928) 		0.271
(0.807) 		1
(1.00)
3p loss 187 (30%) 438 0.898
(1.00) 		0.0853
(0.521) 		0.0861
(0.521) 		0.478
(0.928) 		0.014
(0.434) 		0.47
(0.928) 		0.339
(0.838) 		0.652
(0.971) 		0.631
(0.971) 		0.586
(0.969) 		0.0815
(0.521) 		1
(1.00)
3q loss 90 (14%) 535 0.989
(1.00) 		0.749
(0.971) 		0.409
(0.893) 		0.0743
(0.521) 		0.381
(0.88) 		0.172
(0.682) 		0.536
(0.94) 		0.382
(0.88) 		0.364
(0.862) 		0.368
(0.862) 		0.921
(1.00) 		0.668
(0.971)
4p loss 271 (43%) 354 0.165
(0.677) 		0.276
(0.809) 		0.16
(0.666) 		0.138
(0.636) 		0.533
(0.94) 		0.241
(0.777) 		0.112
(0.596) 		0.207
(0.726) 		0.947
(1.00) 		0.131
(0.627) 		0.0463
(0.479) 		0.767
(0.971)
4q loss 251 (40%) 374 0.0323
(0.463) 		0.109
(0.591) 		0.35
(0.854) 		0.066
(0.512) 		0.285
(0.813) 		0.735
(0.971) 		0.475
(0.928) 		0.75
(0.971) 		0.385
(0.881) 		0.509
(0.936) 		0.296
(0.813) 		1
(1.00)
5q loss 195 (31%) 430 0.368
(0.862) 		0.757
(0.971) 		0.00392
(0.288) 		0.0703
(0.521) 		0.0295
(0.454) 		0.59
(0.97) 		0.299
(0.813) 		0.823
(1.00) 		0.281
(0.813) 		0.901
(1.00) 		0.492
(0.936) 		1
(1.00)
6p loss 93 (15%) 532 0.59
(0.97) 		0.817
(1) 		0.496
(0.936) 		0.0634
(0.51) 		0.479
(0.928) 		0.145
(0.642) 		0.218
(0.745) 		1
(1.00) 		0.656
(0.971) 		0.178
(0.682) 		0.701
(0.971) 		0.681
(0.971)
6q loss 110 (18%) 515 0.655
(0.971) 		0.613
(0.971) 		0.519
(0.939) 		0.0205
(0.434) 		0.738
(0.971) 		0.176
(0.682) 		0.0855
(0.521) 		0.784
(0.981) 		0.884
(1.00) 		0.288
(0.813) 		0.81
(0.998) 		1
(1.00)
7p loss 33 (5%) 592 0.574
(0.965) 		0.972
(1.00) 		0.407
(0.893) 		0.861
(1.00) 		0.316
(0.813) 		1
(1.00) 		0.561
(0.957) 		0.354
(0.857) 		0.644
(0.971) 		0.0236
(0.434) 		0.0968
(0.555) 		1
(1.00)
7q loss 51 (8%) 574 0.855
(1.00) 		0.273
(0.808) 		0.354
(0.857) 		0.0959
(0.555) 		0.508
(0.936) 		0.764
(0.971) 		0.205
(0.722) 		1
(1.00) 		0.62
(0.971) 		0.151
(0.652) 		0.24
(0.777) 		1
(1.00)
8p loss 153 (24%) 472 0.726
(0.971) 		0.683
(0.971) 		0.172
(0.682) 		0.329
(0.826) 		0.0766
(0.521) 		0.849
(1.00) 		0.0042
(0.288) 		1
(1.00) 		0.974
(1.00) 		0.142
(0.636) 		0.319
(0.817) 		0.135
(0.634)
8q loss 57 (9%) 568 0.893
(1.00) 		0.672
(0.971) 		0.0813
(0.521) 		0.026
(0.434) 		0.598
(0.97) 		0.774
(0.977) 		0.171
(0.682) 		0.594
(0.97) 		0.452
(0.928) 		0.858
(1.00) 		0.0243
(0.434) 		0.579
(0.969)
9p loss 250 (40%) 375 0.564
(0.959) 		0.873
(1.00) 		0.0369
(0.463) 		0.204
(0.722) 		0.0868
(0.521) 		0.735
(0.971) 		0.18
(0.682) 		0.136
(0.636) 		0.311
(0.813) 		0.507
(0.936) 		0.357
(0.858) 		0.118
(0.603)
9q loss 175 (28%) 450 0.516
(0.936) 		0.3
(0.813) 		0.119
(0.603) 		0.279
(0.813) 		0.701
(0.971) 		0.583
(0.969) 		0.0403
(0.463) 		0.299
(0.813) 		0.505
(0.936) 		0.178
(0.682) 		0.187
(0.698) 		0.309
(0.813)
10p loss 117 (19%) 508 0.05
(0.492) 		0.539
(0.94) 		0.759
(0.971) 		0.0678
(0.512) 		0.302
(0.813) 		0.833
(1.00) 		0.314
(0.813) 		0.69
(0.971) 		0.0415
(0.463) 		0.538
(0.94) 		0.0237
(0.434) 		0.426
(0.91)
10q loss 117 (19%) 508 0.309
(0.813) 		0.966
(1.00) 		0.607
(0.971) 		0.398
(0.889) 		0.513
(0.936) 		0.835
(1.00) 		0.434
(0.923) 		0.595
(0.97) 		0.522
(0.94) 		0.353
(0.857) 		0.00364
(0.288) 		0.45
(0.928)
11p loss 118 (19%) 507 0.46
(0.928) 		0.862
(1.00) 		0.0537
(0.496) 		0.316
(0.813) 		0.516
(0.936) 		0.664
(0.971) 		0.0565
(0.505) 		0.0229
(0.434) 		0.191
(0.705) 		0.955
(1.00) 		0.341
(0.838) 		0.118
(0.603)
11q loss 120 (19%) 505 0.14
(0.636) 		0.179
(0.682) 		0.0176
(0.434) 		0.298
(0.813) 		0.283
(0.813) 		0.662
(0.971) 		0.0196
(0.434) 		0.0336
(0.463) 		0.468
(0.928) 		0.528
(0.94) 		0.643
(0.971) 		0.128
(0.619)
12p loss 95 (15%) 530 0.38
(0.88) 		0.0672
(0.512) 		0.92
(1.00) 		0.123
(0.609) 		0.878
(1.00) 		1
(1.00) 		0.542
(0.94) 		0.143
(0.636) 		0.743
(0.971) 		0.0967
(0.555) 		0.499
(0.936) 		1
(1.00)
12q loss 82 (13%) 543 0.16
(0.666) 		0.261
(0.787) 		0.258
(0.787) 		0.0173
(0.434) 		0.774
(0.977) 		1
(1.00) 		0.517
(0.936) 		1
(1.00) 		0.083
(0.521) 		0.0352
(0.463) 		0.013
(0.434) 		0.339
(0.838)
13q loss 102 (16%) 523 0.92
(1.00) 		0.0423
(0.463) 		0.00496
(0.29) 		0.0385
(0.463) 		0.0196
(0.434) 		0.25
(0.777) 		0.0174
(0.434) 		0.0495
(0.492) 		0.121
(0.606) 		0.864
(1.00) 		0.0346
(0.463) 		0.387
(0.882)
14q loss 158 (25%) 467 0.763
(0.971) 		0.598
(0.97) 		0.0453
(0.479) 		0.202
(0.722) 		0.223
(0.755) 		0.244
(0.777) 		0.763
(0.971) 		0.904
(1.00) 		0.452
(0.928) 		0.41
(0.893) 		0.663
(0.971) 		0.473
(0.928)
15q loss 149 (24%) 476 0.356
(0.858) 		0.31
(0.813) 		0.715
(0.971) 		0.0156
(0.434) 		0.667
(0.971) 		0.701
(0.971) 		0.682
(0.971) 		0.0681
(0.512) 		0.689
(0.971) 		0.827
(1.00) 		0.71
(0.971) 		0.297
(0.813)
16p loss 156 (25%) 469 0.966
(1.00) 		0.0785
(0.521) 		0.815
(1) 		0.193
(0.706) 		0.286
(0.813) 		0.119
(0.603) 		0.84
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.585
(0.969) 		0.926
(1.00) 		0.718
(0.971)
16q loss 168 (27%) 457 0.476
(0.928) 		0.315
(0.813) 		0.381
(0.88) 		0.374
(0.873) 		0.907
(1.00) 		0.058
(0.505) 		0.693
(0.971) 		0.243
(0.777) 		0.828
(1.00) 		0.548
(0.946) 		0.671
(0.971) 		0.142
(0.636)
17p loss 236 (38%) 389 0.688
(0.971) 		0.471
(0.928) 		0.674
(0.971) 		0.239
(0.777) 		0.846
(1.00) 		0.397
(0.889) 		0.0576
(0.505) 		0.236
(0.774) 		0.0754
(0.521) 		0.66
(0.971) 		0.556
(0.956) 		0.194
(0.707)
17q loss 99 (16%) 526 0.404
(0.893) 		0.751
(0.971) 		0.572
(0.965) 		0.327
(0.826) 		0.291
(0.813) 		0.177
(0.682) 		0.719
(0.971) 		1
(1.00) 		0.0718
(0.521) 		0.656
(0.971) 		0.303
(0.813) 		0.0841
(0.521)
18p loss 187 (30%) 438 0.495
(0.936) 		0.208
(0.727) 		0.853
(1.00) 		0.0395
(0.463) 		0.853
(1.00) 		0.586
(0.969) 		0.0849
(0.521) 		0.112
(0.596) 		0.917
(1.00) 		0.115
(0.603) 		0.754
(0.971) 		0.311
(0.813)
19p loss 177 (28%) 448 0.0679
(0.512) 		0.821
(1) 		0.564
(0.959) 		0.521
(0.939) 		0.482
(0.928) 		0.717
(0.971) 		0.331
(0.826) 		0.642
(0.971) 		0.585
(0.969) 		0.0399
(0.463) 		0.0334
(0.463) 		1
(1.00)
19q loss 136 (22%) 489 0.699
(0.971) 		0.874
(1.00) 		0.934
(1.00) 		0.467
(0.928) 		0.844
(1.00) 		0.844
(1.00) 		0.525
(0.94) 		0.899
(1.00) 		0.978
(1.00) 		0.0641
(0.51) 		0.0104
(0.379) 		0.466
(0.928)
20p loss 41 (7%) 584 0.923
(1.00) 		0.514
(0.936) 		0.615
(0.971) 		0.471
(0.928) 		0.948
(1.00) 		0.723
(0.971) 		0.727
(0.971) 		0.143
(0.636) 		0.392
(0.889) 		0.704
(0.971) 		0.529
(0.94) 		0.47
(0.928)
20q loss 8 (1%) 617 0.34
(0.838) 		0.577
(0.968) 		0.23
(0.765) 		0.0357
(0.463) 		0.651
(0.971) 		1
(1.00) 		0.447
(0.928) 		0.676
(0.971) 		0.642
(0.971) 		0.509
(0.936) 		1
(1.00)
21q loss 289 (46%) 336 0.705
(0.971) 		0.177
(0.682) 		0.504
(0.936) 		0.327
(0.826) 		0.64
(0.971) 		0.249
(0.777) 		0.861
(1.00) 		0.21
(0.729) 		0.181
(0.682) 		0.176
(0.682) 		0.301
(0.813) 		0.537
(0.94)
22q loss 218 (35%) 407 0.166
(0.677) 		0.481
(0.928) 		0.0233
(0.434) 		0.0435
(0.465) 		0.447
(0.928) 		0.607
(0.971) 		0.358
(0.858) 		0.0382
(0.463) 		0.475
(0.928) 		0.953
(1.00) 		0.368
(0.862) 		0.752
(0.971)
xq loss 96 (15%) 529 0.874
(1.00) 		0.764
(0.971) 		0.53
(0.94) 		0.319
(0.817) 		0.599
(0.97) 		0.0994
(0.557) 		0.00227
(0.251) 		0.306
(0.813) 		0.796
(0.988) 		0.0038
(0.288) 		0.925
(1.00) 		0.657
(0.971)
'7p gain' versus 'GENDER'

P value = 0.000631 (Fisher's exact test), Q value = 0.19

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

nPatients FEMALE MALE
ALL 185 440
7P GAIN MUTATED 71 235
7P GAIN WILD-TYPE 114 205

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

'20q gain' versus 'GENDER'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S2.  Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
20Q GAIN MUTATED 99 296
20Q GAIN WILD-TYPE 86 144

Figure S2.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'RACE'

P value = 8e-04 (Fisher's exact test), Q value = 0.19

Table S3.  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 19 6 1 35
XP GAIN WILD-TYPE 115 11 0 357

Figure S3.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #11: 'RACE'

'xq gain' versus 'RACE'

P value = 0.00166 (Fisher's exact test), Q value = 0.23

Table S4.  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 5 1 47
XQ GAIN WILD-TYPE 105 12 0 345

Figure S4.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #11: 'RACE'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00098 (Fisher's exact test), Q value = 0.19

Table S5.  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 11 20 47 33 87 88 29 97 73 46 51 4
5P LOSS MUTATED 7 3 2 2 14 20 9 19 11 6 6 1
5P LOSS WILD-TYPE 4 17 45 31 73 68 20 78 62 40 45 3

Figure S5.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.12

Table S6.  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 55 137 33
18Q LOSS WILD-TYPE 37 81 146 91

Figure S6.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'GENDER'

P value = 0.000253 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #81: 'xp loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 185 440
XP LOSS MUTATED 20 102
XP LOSS WILD-TYPE 165 338

Figure S7.  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/19785966/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/19775559/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)
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