Correlation between copy number variations of arm-level result and selected clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1F47N74
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/C1F47N74
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 15 clinical features across 493 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

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 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		COMPLETENESS
OF
RESECTION 		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 Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 89 (18%) 404 0.416
(0.929) 		0.706
(0.987) 		0.0461
(0.704) 		0.59
(0.975) 		0.544
(0.971) 		0.0318
(0.652) 		0.689
(0.987) 		0.448
(0.932) 		0.0409
(0.704) 		1
(1.00) 		0.677
(0.987) 		0.996
(1.00) 		0.678
(0.987) 		0.941
(1.00) 		1
(1.00)
1q gain 200 (41%) 293 0.152
(0.804) 		0.357
(0.907) 		0.0246
(0.572) 		0.138
(0.8) 		0.57
(0.975) 		0.0453
(0.704) 		0.175
(0.821) 		0.331
(0.907) 		0.00271
(0.303) 		0.257
(0.883) 		0.903
(1.00) 		0.474
(0.938) 		0.897
(1.00) 		0.753
(0.995) 		0.72
(0.987)
2p gain 218 (44%) 275 0.00591
(0.455) 		0.601
(0.975) 		0.384
(0.92) 		0.241
(0.883) 		0.241
(0.883) 		1
(1.00) 		0.00183
(0.268) 		0.344
(0.907) 		0.0284
(0.614) 		0.26
(0.883) 		0.306
(0.89) 		0.155
(0.81) 		0.271
(0.883) 		0.291
(0.883) 		0.0834
(0.79)
2q gain 138 (28%) 355 0.0697
(0.732) 		0.794
(1.00) 		0.449
(0.932) 		0.333
(0.907) 		0.535
(0.961) 		1
(1.00) 		0.0296
(0.627) 		0.617
(0.975) 		0.064
(0.718) 		0.206
(0.871) 		0.586
(0.975) 		0.497
(0.947) 		0.338
(0.907) 		0.686
(0.987) 		0.444
(0.932)
3p gain 105 (21%) 388 0.936
(1.00) 		0.838
(1.00) 		0.151
(0.804) 		0.802
(1.00) 		0.291
(0.883) 		1
(1.00) 		0.134
(0.798) 		0.984
(1.00) 		0.349
(0.907) 		0.489
(0.943) 		0.599
(0.975) 		0.5
(0.95) 		0.333
(0.907) 		0.394
(0.92) 		1
(1.00)
3q gain 311 (63%) 182 0.969
(1.00) 		0.835
(1.00) 		0.121
(0.79) 		0.331
(0.907) 		0.884
(1.00) 		0.0512
(0.704) 		0.67
(0.987) 		0.815
(1.00) 		0.00355
(0.323) 		0.389
(0.92) 		0.504
(0.952) 		0.455
(0.933) 		0.969
(1.00) 		0.449
(0.932) 		1
(1.00)
4p gain 32 (6%) 461 0.286
(0.883) 		0.599
(0.975) 		0.668
(0.987) 		0.688
(0.987) 		0.941
(1.00) 		1
(1.00) 		0.0939
(0.79) 		0.455
(0.933) 		0.178
(0.828) 		0.587
(0.975) 		0.936
(1.00) 		0.732
(0.987) 		0.691
(0.987) 		0.457
(0.933) 		1
(1.00)
4q gain 23 (5%) 470 0.562
(0.975) 		0.026
(0.592) 		0.12
(0.79) 		0.93
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.221
(0.883) 		0.596
(0.975) 		0.0919
(0.79) 		0.467
(0.934) 		0.249
(0.883) 		0.916
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 305 (62%) 188 0.404
(0.92) 		0.0243
(0.572) 		0.715
(0.987) 		0.57
(0.975) 		0.11
(0.79) 		0.715
(0.987) 		0.597
(0.975) 		0.939
(1.00) 		0.424
(0.931) 		0.572
(0.975) 		0.0803
(0.79) 		0.164
(0.812) 		0.0438
(0.704) 		0.188
(0.847) 		0.267
(0.883)
5q gain 92 (19%) 401 0.508
(0.953) 		0.372
(0.92) 		0.985
(1.00) 		0.712
(0.987) 		0.971
(1.00) 		1
(1.00) 		0.511
(0.953) 		0.845
(1.00) 		0.329
(0.907) 		1
(1.00) 		0.365
(0.917) 		0.11
(0.79) 		0.307
(0.89) 		0.493
(0.946) 		0.359
(0.907)
6p gain 108 (22%) 385 0.715
(0.987) 		0.567
(0.975) 		0.895
(1.00) 		0.618
(0.975) 		0.644
(0.987) 		1
(1.00) 		0.71
(0.987) 		0.0504
(0.704) 		0.285
(0.883) 		1
(1.00) 		0.93
(1.00) 		0.196
(0.854) 		0.372
(0.92) 		0.124
(0.79) 		1
(1.00)
6q gain 92 (19%) 401 0.85
(1.00) 		0.846
(1.00) 		0.445
(0.932) 		0.91
(1.00) 		0.221
(0.883) 		0.359
(0.907) 		0.694
(0.987) 		0.118
(0.79) 		0.328
(0.907) 		1
(1.00) 		0.905
(1.00) 		0.81
(1.00) 		0.766
(1.00) 		0.443
(0.932) 		0.205
(0.871)
7p gain 238 (48%) 255 0.009
(0.461) 		0.0612
(0.718) 		0.0131
(0.555) 		0.00073
(0.268) 		0.327
(0.907) 		0.718
(0.987) 		0.217
(0.882) 		0.288
(0.883) 		0.354
(0.907) 		0.579
(0.975) 		0.134
(0.798) 		0.104
(0.79) 		0.793
(1.00) 		0.0214
(0.555) 		0.292
(0.883)
7q gain 218 (44%) 275 0.272
(0.883) 		0.301
(0.89) 		0.145
(0.802) 		0.0518
(0.704) 		0.164
(0.812) 		0.251
(0.883) 		0.215
(0.88) 		0.0182
(0.555) 		0.577
(0.975) 		0.782
(1.00) 		0.203
(0.871) 		0.112
(0.79) 		0.763
(1.00) 		0.14
(0.8) 		0.473
(0.938)
8p gain 128 (26%) 365 0.886
(1.00) 		0.00697
(0.456) 		0.0616
(0.718) 		0.0854
(0.79) 		0.464
(0.934) 		0.0862
(0.79) 		1
(1.00) 		0.167
(0.812) 		0.384
(0.92) 		0.749
(0.995) 		0.989
(1.00) 		0.555
(0.975) 		0.0476
(0.704) 		0.265
(0.883) 		0.426
(0.931)
8q gain 255 (52%) 238 0.275
(0.883) 		0.325
(0.907) 		0.0361
(0.696) 		0.113
(0.79) 		0.457
(0.933) 		0.126
(0.79) 		0.918
(1.00) 		0.111
(0.79) 		0.654
(0.987) 		0.579
(0.975) 		0.202
(0.871) 		0.601
(0.975) 		0.232
(0.883) 		0.136
(0.8) 		0.724
(0.987)
9p gain 61 (12%) 432 0.801
(1.00) 		0.206
(0.871) 		0.29
(0.883) 		0.421
(0.931) 		0.0167
(0.555) 		1
(1.00) 		1
(1.00) 		0.562
(0.975) 		0.363
(0.914) 		1
(1.00) 		0.357
(0.907) 		0.882
(1.00) 		0.855
(1.00) 		0.306
(0.89) 		0.227
(0.883)
9q gain 91 (18%) 402 0.475
(0.938) 		0.741
(0.992) 		0.318
(0.897) 		0.525
(0.954) 		0.0507
(0.704) 		1
(1.00) 		0.691
(0.987) 		0.695
(0.987) 		0.607
(0.975) 		0.14
(0.8) 		0.708
(0.987) 		0.922
(1.00) 		0.607
(0.975) 		0.553
(0.975) 		0.638
(0.987)
10p gain 78 (16%) 415 0.716
(0.987) 		0.89
(1.00) 		0.216
(0.881) 		0.724
(0.987) 		0.544
(0.971) 		0.306
(0.89) 		0.0485
(0.704) 		0.131
(0.795) 		0.92
(1.00) 		1
(1.00) 		0.05
(0.704) 		0.0158
(0.555) 		0.343
(0.907) 		0.0984
(0.79) 		1
(1.00)
10q gain 44 (9%) 449 0.895
(1.00) 		0.356
(0.907) 		0.653
(0.987) 		0.805
(1.00) 		0.684
(0.987) 		0.486
(0.941) 		0.28
(0.883) 		0.663
(0.987) 		1
(1.00) 		0.326
(0.907) 		0.263
(0.883) 		0.00885
(0.461) 		0.769
(1.00) 		0.137
(0.8) 		0.589
(0.975)
11p gain 73 (15%) 420 0.778
(1.00) 		0.309
(0.893) 		0.669
(0.987) 		0.771
(1.00) 		0.256
(0.883) 		0.601
(0.975) 		0.193
(0.851) 		0.00838
(0.461) 		1
(1.00) 		1
(1.00) 		0.96
(1.00) 		0.734
(0.988) 		0.401
(0.92) 		0.304
(0.89) 		1
(1.00)
11q gain 90 (18%) 403 0.631
(0.984) 		0.552
(0.975) 		0.433
(0.932) 		0.239
(0.883) 		0.214
(0.88) 		0.129
(0.793) 		1
(1.00) 		0.242
(0.883) 		0.417
(0.929) 		0.479
(0.941) 		0.644
(0.987) 		0.946
(1.00) 		0.69
(0.987) 		0.45
(0.932) 		1
(1.00)
12p gain 225 (46%) 268 0.781
(1.00) 		0.681
(0.987) 		0.325
(0.907) 		0.0744
(0.763) 		0.295
(0.884) 		0.461
(0.934) 		0.00196
(0.268) 		0.0136
(0.555) 		0.965
(1.00) 		0.583
(0.975) 		0.174
(0.821) 		0.962
(1.00) 		0.933
(1.00) 		0.924
(1.00) 		1
(1.00)
12q gain 150 (30%) 343 0.858
(1.00) 		0.572
(0.975) 		0.449
(0.932) 		0.143
(0.802) 		0.0508
(0.704) 		1
(1.00) 		0.00502
(0.412) 		0.0841
(0.79) 		0.9
(1.00) 		1
(1.00) 		0.95
(1.00) 		0.512
(0.953) 		0.964
(1.00) 		0.725
(0.987) 		0.702
(0.987)
13q gain 35 (7%) 458 0.595
(0.975) 		0.52
(0.953) 		0.815
(1.00) 		0.761
(1.00) 		0.524
(0.954) 		0.381
(0.92) 		0.842
(1.00) 		0.899
(1.00) 		0.396
(0.92) 		1
(1.00) 		0.193
(0.851) 		0.151
(0.804) 		0.703
(0.987) 		0.0237
(0.572) 		1
(1.00)
14q gain 128 (26%) 365 0.0333
(0.671) 		0.0921
(0.79) 		0.114
(0.79) 		0.0399
(0.704) 		0.248
(0.883) 		1
(1.00) 		1
(1.00) 		0.317
(0.897) 		1
(1.00) 		1
(1.00) 		0.391
(0.92) 		0.414
(0.929) 		0.607
(0.975) 		0.659
(0.987) 		0.0226
(0.568)
15q gain 103 (21%) 390 0.436
(0.932) 		0.51
(0.953) 		0.139
(0.8) 		0.279
(0.883) 		0.0526
(0.704) 		0.19
(0.849) 		0.205
(0.871) 		0.944
(1.00) 		0.424
(0.931) 		1
(1.00) 		0.334
(0.907) 		0.257
(0.883) 		0.749
(0.995) 		0.89
(1.00) 		0.689
(0.987)
16p gain 82 (17%) 411 0.987
(1.00) 		0.73
(0.987) 		0.497
(0.947) 		0.679
(0.987) 		0.408
(0.927) 		0.611
(0.975) 		0.169
(0.812) 		0.723
(0.987) 		0.0601
(0.718) 		1
(1.00) 		0.169
(0.812) 		0.905
(1.00) 		0.934
(1.00) 		0.502
(0.952) 		1
(1.00)
16q gain 83 (17%) 410 0.969
(1.00) 		0.412
(0.929) 		0.409
(0.929) 		0.871
(1.00) 		0.661
(0.987) 		1
(1.00) 		0.0089
(0.461) 		0.746
(0.994) 		0.0895
(0.79) 		1
(1.00) 		0.485
(0.941) 		0.426
(0.931) 		0.772
(1.00) 		0.134
(0.798) 		1
(1.00)
17p gain 66 (13%) 427 0.282
(0.883) 		0.0956
(0.79) 		0.827
(1.00) 		0.518
(0.953) 		0.967
(1.00) 		1
(1.00) 		0.289
(0.883) 		0.531
(0.959) 		0.593
(0.975) 		0.233
(0.883) 		0.09
(0.79) 		0.0202
(0.555) 		0.487
(0.941) 		1
(1.00) 		0.337
(0.907)
17q gain 154 (31%) 339 0.571
(0.975) 		0.131
(0.797) 		0.106
(0.79) 		0.00687
(0.456) 		0.144
(0.802) 		0.683
(0.987) 		0.0012
(0.268) 		0.55
(0.975) 		0.492
(0.946) 		1
(1.00) 		0.252
(0.883) 		0.0931
(0.79) 		0.508
(0.953) 		0.162
(0.812) 		0.254
(0.883)
18p gain 149 (30%) 344 0.602
(0.975) 		0.211
(0.873) 		0.652
(0.987) 		0.566
(0.975) 		0.185
(0.844) 		0.68
(0.987) 		0.37
(0.92) 		0.102
(0.79) 		0.93
(1.00) 		0.0708
(0.732) 		0.643
(0.987) 		0.415
(0.929) 		0.168
(0.812) 		0.0134
(0.555) 		1
(1.00)
18q gain 104 (21%) 389 0.826
(1.00) 		0.875
(1.00) 		0.481
(0.941) 		0.116
(0.79) 		0.515
(0.953) 		0.356
(0.907) 		0.529
(0.958) 		0.00705
(0.456) 		0.795
(1.00) 		0.0362
(0.696) 		0.0669
(0.723) 		0.578
(0.975) 		0.371
(0.92) 		0.0161
(0.555) 		0.678
(0.987)
19p gain 110 (22%) 383 0.224
(0.883) 		0.583
(0.975) 		0.467
(0.934) 		0.581
(0.975) 		0.435
(0.932) 		0.358
(0.907) 		0.805
(1.00) 		0.0562
(0.704) 		0.204
(0.871) 		0.0469
(0.704) 		0.532
(0.959) 		0.109
(0.79) 		1
(1.00) 		0.945
(1.00) 		0.682
(0.987)
19q gain 157 (32%) 336 0.487
(0.941) 		0.247
(0.883) 		0.517
(0.953) 		0.291
(0.883) 		0.249
(0.883) 		1
(1.00) 		1
(1.00) 		0.316
(0.897) 		0.0421
(0.704) 		0.764
(1.00) 		0.0562
(0.704) 		0.00306
(0.313) 		0.699
(0.987) 		0.464
(0.934) 		0.702
(0.987)
20p gain 256 (52%) 237 0.89
(1.00) 		0.228
(0.883) 		0.417
(0.929) 		0.148
(0.804) 		0.591
(0.975) 		0.125
(0.79) 		0.00983
(0.483) 		0.914
(1.00) 		0.398
(0.92) 		0.265
(0.883) 		0.401
(0.92) 		0.993
(1.00) 		0.867
(1.00) 		0.732
(0.987) 		0.0687
(0.728)
20q gain 245 (50%) 248 0.603
(0.975) 		0.336
(0.907) 		0.432
(0.932) 		0.362
(0.913) 		0.184
(0.844) 		0.122
(0.79) 		0.000974
(0.268) 		0.717
(0.987) 		0.123
(0.79) 		0.415
(0.929) 		0.688
(0.987) 		0.608
(0.975) 		0.74
(0.991) 		0.631
(0.984) 		0.283
(0.883)
21q gain 56 (11%) 437 0.0609
(0.718) 		0.402
(0.92) 		0.164
(0.812) 		0.0377
(0.704) 		0.0265
(0.592) 		1
(1.00) 		0.331
(0.907) 		0.261
(0.883) 		0.0511
(0.704) 		0.175
(0.821) 		0.828
(1.00) 		0.456
(0.933) 		0.0495
(0.704) 		0.306
(0.89) 		1
(1.00)
22q gain 216 (44%) 277 0.159
(0.812) 		0.0203
(0.555) 		0.0519
(0.704) 		0.156
(0.812) 		0.251
(0.883) 		0.252
(0.883) 		0.12
(0.79) 		0.844
(1.00) 		0.303
(0.89) 		0.783
(1.00) 		0.148
(0.804) 		0.0414
(0.704) 		0.157
(0.812) 		0.129
(0.793) 		1
(1.00)
xp gain 65 (13%) 428 0.862
(1.00) 		0.354
(0.907) 		0.718
(0.987) 		0.28
(0.883) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		0.109
(0.79) 		0.0818
(0.79) 		1
(1.00) 		0.124
(0.79) 		0.712
(0.987) 		0.536
(0.961) 		0.567
(0.975) 		0.604
(0.975)
xq gain 82 (17%) 411 0.604
(0.975) 		0.373
(0.92) 		0.097
(0.79) 		0.0206
(0.555) 		0.698
(0.987) 		0.347
(0.907) 		0.272
(0.883) 		0.575
(0.975) 		0.923
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.467
(0.934) 		0.739
(0.991) 		0.34
(0.907) 		0.359
(0.907)
1p loss 147 (30%) 346 0.892
(1.00) 		0.0624
(0.718) 		0.617
(0.975) 		0.916
(1.00) 		0.0102
(0.484) 		0.679
(0.987) 		0.0554
(0.704) 		0.522
(0.953) 		0.931
(1.00) 		0.222
(0.883) 		0.555
(0.975) 		0.655
(0.987) 		0.823
(1.00) 		0.75
(0.995) 		0.0485
(0.704)
1q loss 59 (12%) 434 0.0983
(0.79) 		0.754
(0.995) 		0.0277
(0.609) 		0.862
(1.00) 		0.153
(0.804) 		1
(1.00) 		0.207
(0.871) 		0.794
(1.00) 		0.45
(0.932) 		0.195
(0.854) 		0.574
(0.975) 		0.521
(0.953) 		0.0521
(0.704) 		0.229
(0.883) 		0.267
(0.883)
2p loss 20 (4%) 473 0.865
(1.00) 		0.598
(0.975) 		0.586
(0.975) 		0.504
(0.952) 		0.114
(0.79) 		1
(1.00) 		0.0641
(0.718) 		0.832
(1.00) 		0.622
(0.978) 		0.42
(0.931) 		0.376
(0.92) 		0.695
(0.987) 		0.813
(1.00) 		0.754
(0.995) 		0.287
(0.883)
2q loss 40 (8%) 453 0.498
(0.947) 		0.512
(0.953) 		0.787
(1.00) 		0.545
(0.972) 		0.0502
(0.704) 		0.446
(0.932) 		0.346
(0.907) 		0.806
(1.00) 		0.673
(0.987) 		1
(1.00) 		0.0549
(0.704) 		0.842
(1.00) 		0.922
(1.00) 		0.872
(1.00) 		1
(1.00)
3p loss 307 (62%) 186 0.994
(1.00) 		0.402
(0.92) 		0.792
(1.00) 		0.988
(1.00) 		0.584
(0.975) 		0.261
(0.883) 		0.457
(0.933) 		0.287
(0.883) 		0.726
(0.987) 		0.775
(1.00) 		0.51
(0.953) 		0.876
(1.00) 		0.231
(0.883) 		0.167
(0.812) 		0.479
(0.941)
3q loss 69 (14%) 424 0.471
(0.935) 		0.164
(0.812) 		0.441
(0.932) 		0.0661
(0.723) 		0.466
(0.934) 		0.601
(0.975) 		0.301
(0.89) 		0.886
(1.00) 		0.521
(0.953) 		1
(1.00) 		0.123
(0.79) 		0.145
(0.802) 		0.819
(1.00) 		0.306
(0.89) 		1
(1.00)
4p loss 310 (63%) 183 0.151
(0.804) 		0.0982
(0.79) 		0.283
(0.883) 		0.28
(0.883) 		0.873
(1.00) 		0.433
(0.932) 		0.456
(0.933) 		1
(1.00) 		0.056
(0.704) 		0.145
(0.802) 		0.832
(1.00) 		0.586
(0.975) 		0.598
(0.975) 		0.0897
(0.79) 		1
(1.00)
4q loss 292 (59%) 201 0.191
(0.849) 		0.448
(0.932) 		0.252
(0.883) 		0.147
(0.804) 		0.486
(0.941) 		0.453
(0.933) 		0.917
(1.00) 		0.788
(1.00) 		0.237
(0.883) 		0.0842
(0.79) 		0.167
(0.812) 		0.776
(1.00) 		0.629
(0.983) 		0.591
(0.975) 		0.729
(0.987)
5p loss 75 (15%) 418 0.31
(0.894) 		0.28
(0.883) 		0.612
(0.975) 		0.17
(0.813) 		0.352
(0.907) 		0.601
(0.975) 		0.252
(0.883) 		0.728
(0.987) 		0.558
(0.975) 		0.12
(0.79) 		0.0977
(0.79) 		0.0433
(0.704) 		0.176
(0.823) 		1
(1.00) 		0.0998
(0.79)
5q loss 285 (58%) 208 0.836
(1.00) 		0.711
(0.987) 		0.794
(1.00) 		0.485
(0.941) 		0.378
(0.92) 		0.247
(0.883) 		0.677
(0.987) 		0.919
(1.00) 		0.376
(0.92) 		0.254
(0.883) 		0.578
(0.975) 		0.0197
(0.555) 		0.809
(1.00) 		0.239
(0.883) 		0.477
(0.941)
6p loss 112 (23%) 381 0.879
(1.00) 		0.852
(1.00) 		0.455
(0.933) 		0.42
(0.931) 		0.211
(0.873) 		0.667
(0.987) 		0.39
(0.92) 		0.519
(0.953) 		0.946
(1.00) 		0.742
(0.992) 		0.942
(1.00) 		0.695
(0.987) 		0.377
(0.92) 		0.798
(1.00) 		1
(1.00)
6q loss 113 (23%) 380 0.69
(0.987) 		0.593
(0.975) 		0.273
(0.883) 		0.462
(0.934) 		0.357
(0.907) 		0.667
(0.987) 		0.808
(1.00) 		0.718
(0.987) 		0.391
(0.92) 		1
(1.00) 		0.918
(1.00) 		0.536
(0.961) 		0.465
(0.934) 		1
(1.00) 		0.395
(0.92)
7p loss 57 (12%) 436 0.829
(1.00) 		0.848
(1.00) 		0.417
(0.929) 		0.578
(0.975) 		0.422
(0.931) 		0.575
(0.975) 		0.263
(0.883) 		0.856
(1.00) 		1
(1.00) 		0.654
(0.987) 		0.107
(0.79) 		0.866
(1.00) 		0.103
(0.79) 		0.824
(1.00) 		1
(1.00)
7q loss 50 (10%) 443 0.778
(1.00) 		0.876
(1.00) 		0.836
(1.00) 		0.775
(1.00) 		0.982
(1.00) 		1
(1.00) 		0.395
(0.92) 		0.865
(1.00) 		1
(1.00) 		1
(1.00) 		0.167
(0.812) 		0.229
(0.883) 		0.385
(0.92) 		0.186
(0.844) 		0.589
(0.975)
8p loss 239 (48%) 254 0.468
(0.934) 		0.000918
(0.268) 		0.318
(0.897) 		0.392
(0.92) 		0.484
(0.941) 		0.45
(0.932) 		0.473
(0.938) 		0.267
(0.883) 		0.271
(0.883) 		0.783
(1.00) 		0.352
(0.907) 		0.181
(0.836) 		0.959
(1.00) 		0.963
(1.00) 		0.727
(0.987)
8q loss 47 (10%) 446 0.754
(0.995) 		0.185
(0.844) 		0.138
(0.8) 		0.468
(0.934) 		0.369
(0.92) 		0.505
(0.953) 		0.38
(0.92) 		0.423
(0.931) 		0.845
(1.00) 		1
(1.00) 		0.0997
(0.79) 		0.00144
(0.268) 		0.604
(0.975) 		0.189
(0.847) 		0.514
(0.953)
9p loss 304 (62%) 189 0.984
(1.00) 		0.632
(0.984) 		0.13
(0.793) 		0.529
(0.958) 		0.38
(0.92) 		0.711
(0.987) 		0.751
(0.995) 		0.5
(0.95) 		0.031
(0.647) 		1
(1.00) 		0.245
(0.883) 		0.45
(0.932) 		0.814
(1.00) 		0.812
(1.00) 		0.479
(0.941)
9q loss 241 (49%) 252 0.646
(0.987) 		0.00232
(0.285) 		0.392
(0.92) 		0.153
(0.804) 		0.787
(1.00) 		0.266
(0.883) 		0.918
(1.00) 		0.265
(0.883) 		0.0704
(0.732) 		0.262
(0.883) 		0.735
(0.988) 		0.0217
(0.555) 		0.351
(0.907) 		0.562
(0.975) 		0.067
(0.723)
10p loss 210 (43%) 283 0.284
(0.883) 		0.705
(0.987) 		0.512
(0.953) 		0.857
(1.00) 		0.759
(1.00) 		0.145
(0.802) 		0.3
(0.89) 		0.692
(0.987) 		0.96
(1.00) 		0.571
(0.975) 		0.46
(0.934) 		0.289
(0.883) 		0.34
(0.907) 		0.415
(0.929) 		0.732
(0.987)
10q loss 224 (45%) 269 0.128
(0.793) 		0.166
(0.812) 		0.383
(0.92) 		0.224
(0.883) 		0.836
(1.00) 		0.135
(0.798) 		0.121
(0.79) 		0.432
(0.932) 		0.854
(1.00) 		0.399
(0.92) 		0.816
(1.00) 		0.33
(0.907) 		0.23
(0.883) 		0.278
(0.883) 		1
(1.00)
11p loss 170 (34%) 323 0.885
(1.00) 		0.171
(0.814) 		0.336
(0.907) 		0.293
(0.884) 		0.437
(0.932) 		0.241
(0.883) 		0.449
(0.932) 		0.0876
(0.79) 		0.572
(0.975) 		0.773
(1.00) 		0.102
(0.79) 		0.485
(0.941) 		0.634
(0.986) 		0.179
(0.831) 		0.717
(0.987)
11q loss 140 (28%) 353 0.652
(0.987) 		0.163
(0.812) 		0.402
(0.92) 		0.317
(0.897) 		0.0646
(0.718) 		1
(1.00) 		0.111
(0.79) 		0.818
(1.00) 		0.795
(1.00) 		0.766
(1.00) 		0.882
(1.00) 		0.313
(0.897) 		0.173
(0.821) 		0.469
(0.934) 		1
(1.00)
12p loss 38 (8%) 455 0.593
(0.975) 		0.468
(0.934) 		0.197
(0.854) 		0.195
(0.854) 		0.271
(0.883) 		1
(1.00) 		0.7
(0.987) 		0.815
(1.00) 		0.0866
(0.79) 		0.612
(0.975) 		0.0197
(0.555) 		0.369
(0.92) 		1
(1.00) 		0.189
(0.847) 		1
(1.00)
12q loss 47 (10%) 446 0.684
(0.987) 		0.68
(0.987) 		0.144
(0.802) 		0.212
(0.873) 		0.352
(0.907) 		1
(1.00) 		0.729
(0.987) 		0.322
(0.903) 		0.101
(0.79) 		1
(1.00) 		0.145
(0.802) 		0.592
(0.975) 		0.761
(1.00) 		0.126
(0.79) 		0.605
(0.975)
13q loss 308 (62%) 185 0.125
(0.79) 		0.609
(0.975) 		0.265
(0.883) 		0.373
(0.92) 		0.512
(0.953) 		0.431
(0.932) 		1
(1.00) 		0.796
(1.00) 		0.00161
(0.268) 		1
(1.00) 		0.561
(0.975) 		0.388
(0.92) 		0.903
(1.00) 		0.0547
(0.704) 		0.0232
(0.57)
14q loss 161 (33%) 332 0.152
(0.804) 		0.96
(1.00) 		0.095
(0.79) 		0.0197
(0.555) 		0.0682
(0.728) 		0.101
(0.79) 		0.585
(0.975) 		0.208
(0.872) 		0.221
(0.883) 		1
(1.00) 		0.397
(0.92) 		0.438
(0.932) 		0.753
(0.995) 		0.877
(1.00) 		0.271
(0.883)
15q loss 140 (28%) 353 0.811
(1.00) 		0.27
(0.883) 		0.118
(0.79) 		0.535
(0.961) 		0.0901
(0.79) 		0.402
(0.92) 		0.496
(0.947) 		0.377
(0.92) 		0.347
(0.907) 		0.208
(0.872) 		0.443
(0.932) 		0.583
(0.975) 		0.719
(0.987) 		0.122
(0.79) 		1
(1.00)
16p loss 160 (32%) 333 0.416
(0.929) 		0.787
(1.00) 		0.265
(0.883) 		0.288
(0.883) 		0.492
(0.946) 		1
(1.00) 		0.442
(0.932) 		0.694
(0.987) 		0.104
(0.79) 		1
(1.00) 		0.237
(0.883) 		0.693
(0.987) 		0.158
(0.812) 		0.0566
(0.704) 		1
(1.00)
16q loss 179 (36%) 314 0.242
(0.883) 		0.677
(0.987) 		0.781
(1.00) 		0.669
(0.987) 		0.73
(0.987) 		1
(1.00) 		0.108
(0.79) 		0.616
(0.975) 		0.202
(0.871) 		0.242
(0.883) 		0.0478
(0.704) 		0.981
(1.00) 		0.519
(0.953) 		0.251
(0.883) 		0.718
(0.987)
17p loss 288 (58%) 205 0.254
(0.883) 		0.108
(0.79) 		0.868
(1.00) 		0.403
(0.92) 		0.0492
(0.704) 		0.704
(0.987) 		0.917
(1.00) 		0.129
(0.793) 		0.66
(0.987) 		0.255
(0.883) 		0.0174
(0.555) 		0.437
(0.932) 		0.642
(0.987) 		0.702
(0.987) 		0.735
(0.988)
17q loss 94 (19%) 399 0.259
(0.883) 		0.0579
(0.713) 		0.82
(1.00) 		0.256
(0.883) 		0.0935
(0.79) 		0.626
(0.98) 		0.0881
(0.79) 		0.27
(0.883) 		0.284
(0.883) 		0.081
(0.79) 		0.063
(0.718) 		0.779
(1.00) 		0.627
(0.98) 		0.0648
(0.718) 		0.669
(0.987)
18p loss 139 (28%) 354 0.683
(0.987) 		0.72
(0.987) 		0.0534
(0.704) 		0.348
(0.907) 		0.975
(1.00) 		0.0211
(0.555) 		0.304
(0.89) 		0.651
(0.987) 		0.962
(1.00) 		0.123
(0.79) 		0.675
(0.987) 		0.611
(0.975) 		0.818
(1.00) 		0.525
(0.954) 		0.69
(0.987)
18q loss 187 (38%) 306 0.302
(0.89) 		0.425
(0.931) 		0.0187
(0.555) 		0.0788
(0.79) 		0.497
(0.947) 		0.106
(0.79) 		0.397
(0.92) 		0.11
(0.79) 		0.927
(1.00) 		0.387
(0.92) 		0.578
(0.975) 		0.163
(0.812) 		0.125
(0.79) 		0.433
(0.932) 		0.716
(0.987)
19p loss 161 (33%) 332 0.25
(0.883) 		0.382
(0.92) 		0.743
(0.992) 		0.972
(1.00) 		0.0172
(0.555) 		0.226
(0.883) 		0.272
(0.883) 		0.0588
(0.716) 		0.389
(0.92) 		0.369
(0.92) 		0.658
(0.987) 		0.343
(0.907) 		0.539
(0.965) 		0.841
(1.00) 		1
(1.00)
19q loss 107 (22%) 386 0.658
(0.987) 		0.147
(0.804) 		0.426
(0.931) 		0.997
(1.00) 		0.706
(0.987) 		0.651
(0.987) 		0.0339
(0.673) 		0.101
(0.79) 		0.315
(0.897) 		0.168
(0.812) 		0.114
(0.79) 		0.0159
(0.555) 		0.673
(0.987) 		0.845
(1.00) 		1
(1.00)
20p loss 42 (9%) 451 0.336
(0.907) 		0.693
(0.987) 		0.894
(1.00) 		0.352
(0.907) 		0.585
(0.975) 		1
(1.00) 		0.359
(0.907) 		0.321
(0.903) 		1
(1.00) 		1
(1.00) 		0.332
(0.907) 		0.431
(0.932) 		0.711
(0.987) 		0.89
(1.00) 		1
(1.00)
20q loss 46 (9%) 447 0.743
(0.992) 		0.84
(1.00) 		0.655
(0.987) 		0.191
(0.849) 		0.547
(0.974) 		1
(1.00) 		0.724
(0.987) 		0.469
(0.934) 		0.618
(0.975) 		0.622
(0.978) 		0.349
(0.907) 		0.434
(0.932) 		0.614
(0.975) 		1
(1.00) 		0.527
(0.956)
21q loss 259 (53%) 234 0.731
(0.987) 		0.0888
(0.79) 		0.395
(0.92) 		0.711
(0.987) 		0.517
(0.953) 		0.134
(0.798) 		0.000297
(0.268) 		0.636
(0.987) 		0.58
(0.975) 		1
(1.00) 		0.933
(1.00) 		0.159
(0.812) 		0.944
(1.00) 		0.399
(0.92) 		0.284
(0.883)
22q loss 97 (20%) 396 0.516
(0.953) 		0.00367
(0.323) 		0.252
(0.883) 		0.618
(0.975) 		0.0209
(0.555) 		0.624
(0.98) 		0.897
(1.00) 		0.514
(0.953) 		0.308
(0.891) 		0.726
(0.987) 		0.903
(1.00) 		0.011
(0.501) 		0.485
(0.941) 		0.237
(0.883) 		0.642
(0.987)
xp loss 141 (29%) 352 0.602
(0.975) 		0.315
(0.897) 		0.624
(0.98) 		0.181
(0.836) 		0.375
(0.92) 		0.679
(0.987) 		0.733
(0.987) 		0.295
(0.884) 		0.668
(0.987) 		1
(1.00) 		0.616
(0.975) 		0.998
(1.00) 		0.315
(0.897) 		0.59
(0.975) 		0.45
(0.932)
xq loss 109 (22%) 384 0.236
(0.883) 		0.814
(1.00) 		0.335
(0.907) 		0.00771
(0.461) 		0.707
(0.987) 		0.354
(0.907) 		0.264
(0.883) 		0.693
(0.987) 		0.294
(0.884) 		1
(1.00) 		0.293
(0.884) 		0.6
(0.975) 		0.643
(0.987) 		0.283
(0.883) 		0.211
(0.873)
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/LUSC-TP/15093662/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/15084586/LUSC-TP.merged_data.txt

  • Number of patients = 493

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 15

  • 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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