Correlation between copy number variations of arm-level result and selected clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1R20ZQK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R20ZQK
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 80 arm-level events and 13 clinical features across 391 patients, one significant finding detected with Q value < 0.25.

  • 20Q LOSS MUTATION ANALYSIS cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test
20Q LOSS MUTATION ANALYSIS 35 (9%) 356 0.985
(1.00) 		0.615
(1.00) 		0.0646
(1.00) 		0.133
(1.00) 		0.414
(1.00) 		0.557
(1.00) 		0.84
(1.00) 		2e-06
(0.00208) 		0.78
(1.00) 		0.612
(1.00) 		0.168
(1.00) 		0.303
(1.00) 		0.467
(1.00)
1P GAIN MUTATION ANALYSIS 75 (19%) 316 0.811
(1.00) 		0.886
(1.00) 		0.0364
(1.00) 		0.136
(1.00) 		0.958
(1.00) 		0.0883
(1.00) 		0.883
(1.00) 		0.273
(1.00) 		0.0394
(1.00) 		0.256
(1.00) 		0.281
(1.00) 		0.282
(1.00) 		0.361
(1.00)
1Q GAIN MUTATION ANALYSIS 162 (41%) 229 0.65
(1.00) 		0.561
(1.00) 		0.121
(1.00) 		0.103
(1.00) 		0.943
(1.00) 		0.494
(1.00) 		0.556
(1.00) 		0.481
(1.00) 		0.00371
(1.00) 		0.768
(1.00) 		0.141
(1.00) 		0.465
(1.00) 		0.747
(1.00)
2P GAIN MUTATION ANALYSIS 166 (42%) 225 0.238
(1.00) 		0.791
(1.00) 		0.54
(1.00) 		0.328
(1.00) 		0.336
(1.00) 		0.874
(1.00) 		0.0453
(1.00) 		0.708
(1.00) 		0.0483
(1.00) 		0.135
(1.00) 		0.03
(1.00) 		0.108
(1.00) 		0.21
(1.00)
2Q GAIN MUTATION ANALYSIS 107 (27%) 284 0.773
(1.00) 		0.753
(1.00) 		0.282
(1.00) 		0.387
(1.00) 		0.456
(1.00) 		0.947
(1.00) 		0.514
(1.00) 		0.575
(1.00) 		0.028
(1.00) 		0.0975
(1.00) 		0.142
(1.00) 		0.618
(1.00) 		0.275
(1.00)
3P GAIN MUTATION ANALYSIS 83 (21%) 308 0.341
(1.00) 		0.925
(1.00) 		0.182
(1.00) 		0.554
(1.00) 		0.367
(1.00) 		0.823
(1.00) 		0.2
(1.00) 		0.522
(1.00) 		0.506
(1.00) 		0.723
(1.00) 		0.198
(1.00) 		0.889
(1.00) 		0.811
(1.00)
3Q GAIN MUTATION ANALYSIS 243 (62%) 148 0.987
(1.00) 		0.917
(1.00) 		0.601
(1.00) 		0.817
(1.00) 		0.79
(1.00) 		0.169
(1.00) 		0.339
(1.00) 		0.826
(1.00) 		0.0135
(1.00) 		0.547
(1.00) 		0.667
(1.00) 		0.962
(1.00) 		0.96
(1.00)
4P GAIN MUTATION ANALYSIS 23 (6%) 368 0.116
(1.00) 		0.904
(1.00) 		0.377
(1.00) 		0.187
(1.00) 		1
(1.00) 		1
(1.00) 		0.219
(1.00) 		0.729
(1.00) 		0.673
(1.00) 		0.522
(1.00) 		0.821
(1.00) 		0.418
(1.00) 		0.312
(1.00)
4Q GAIN MUTATION ANALYSIS 15 (4%) 376 0.832
(1.00) 		0.0813
(1.00) 		0.314
(1.00) 		0.727
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.683
(1.00) 		0.513
(1.00) 		0.379
(1.00) 		0.517
(1.00) 		0.734
(1.00) 		0.686
(1.00)
5P GAIN MUTATION ANALYSIS 239 (61%) 152 0.425
(1.00) 		0.105
(1.00) 		0.746
(1.00) 		0.238
(1.00) 		0.239
(1.00) 		0.765
(1.00) 		0.905
(1.00) 		0.824
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.282
(1.00) 		0.379
(1.00) 		0.00381
(1.00)
5Q GAIN MUTATION ANALYSIS 71 (18%) 320 0.39
(1.00) 		0.293
(1.00) 		0.0733
(1.00) 		0.553
(1.00) 		0.489
(1.00) 		0.872
(1.00) 		0.88
(1.00) 		0.923
(1.00) 		0.9
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.0985
(1.00) 		0.451
(1.00)
6P GAIN MUTATION ANALYSIS 85 (22%) 306 0.979
(1.00) 		0.661
(1.00) 		0.75
(1.00) 		0.217
(1.00) 		0.531
(1.00) 		0.777
(1.00) 		0.573
(1.00) 		0.0189
(1.00) 		0.355
(1.00) 		0.728
(1.00) 		0.921
(1.00) 		0.3
(1.00) 		0.322
(1.00)
6Q GAIN MUTATION ANALYSIS 74 (19%) 317 0.91
(1.00) 		0.994
(1.00) 		0.463
(1.00) 		0.459
(1.00) 		0.614
(1.00) 		0.936
(1.00) 		0.551
(1.00) 		0.0254
(1.00) 		0.281
(1.00) 		0.706
(1.00) 		0.643
(1.00) 		0.694
(1.00) 		0.775
(1.00)
7P GAIN MUTATION ANALYSIS 184 (47%) 207 0.061
(1.00) 		0.165
(1.00) 		0.0732
(1.00) 		0.0126
(1.00) 		0.163
(1.00) 		0.389
(1.00) 		0.244
(1.00) 		0.58
(1.00) 		0.547
(1.00) 		0.39
(1.00) 		0.0264
(1.00) 		0.251
(1.00) 		0.479
(1.00)
7Q GAIN MUTATION ANALYSIS 173 (44%) 218 0.434
(1.00) 		0.576
(1.00) 		0.17
(1.00) 		0.116
(1.00) 		0.336
(1.00) 		0.0993
(1.00) 		0.24
(1.00) 		0.0354
(1.00) 		0.614
(1.00) 		0.561
(1.00) 		0.0739
(1.00) 		0.466
(1.00) 		0.349
(1.00)
8P GAIN MUTATION ANALYSIS 108 (28%) 283 0.617
(1.00) 		0.0466
(1.00) 		0.00533
(1.00) 		0.0101
(1.00) 		0.639
(1.00) 		0.0098
(1.00) 		0.24
(1.00) 		0.252
(1.00) 		0.437
(1.00) 		0.0229
(1.00) 		0.948
(1.00) 		0.916
(1.00) 		0.0751
(1.00)
8Q GAIN MUTATION ANALYSIS 199 (51%) 192 0.682
(1.00) 		0.507
(1.00) 		0.0233
(1.00) 		0.0813
(1.00) 		0.0795
(1.00) 		0.0438
(1.00) 		0.352
(1.00) 		0.401
(1.00) 		0.474
(1.00) 		0.141
(1.00) 		0.538
(1.00) 		0.583
(1.00) 		0.0424
(1.00)
9P GAIN MUTATION ANALYSIS 43 (11%) 348 0.634
(1.00) 		0.313
(1.00) 		0.0579
(1.00) 		0.577
(1.00) 		0.124
(1.00) 		0.209
(1.00) 		0.709
(1.00) 		0.12
(1.00) 		0.305
(1.00) 		0.377
(1.00) 		0.475
(1.00) 		0.768
(1.00) 		1
(1.00)
9Q GAIN MUTATION ANALYSIS 71 (18%) 320 0.973
(1.00) 		0.771
(1.00) 		0.361
(1.00) 		0.678
(1.00) 		0.574
(1.00) 		0.0152
(1.00) 		0.364
(1.00) 		0.167
(1.00) 		0.588
(1.00) 		0.135
(1.00) 		0.436
(1.00) 		0.965
(1.00) 		0.302
(1.00)
10P GAIN MUTATION ANALYSIS 57 (15%) 334 0.522
(1.00) 		0.497
(1.00) 		0.173
(1.00) 		0.659
(1.00) 		0.49
(1.00) 		0.528
(1.00) 		0.187
(1.00) 		0.272
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.0277
(1.00) 		0.432
(1.00)
10Q GAIN MUTATION ANALYSIS 33 (8%) 358 0.379
(1.00) 		0.542
(1.00) 		0.402
(1.00) 		0.307
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.936
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.0737
(1.00) 		0.682
(1.00)
11P GAIN MUTATION ANALYSIS 54 (14%) 337 0.937
(1.00) 		0.0111
(1.00) 		0.916
(1.00) 		0.0947
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.125
(1.00) 		0.751
(1.00) 		0.675
(1.00) 		0.215
(1.00) 		0.318
(1.00) 		0.64
(1.00)
11Q GAIN MUTATION ANALYSIS 66 (17%) 325 0.53
(1.00) 		0.134
(1.00) 		0.895
(1.00) 		0.128
(1.00) 		0.364
(1.00) 		0.239
(1.00) 		0.877
(1.00) 		0.412
(1.00) 		0.8
(1.00) 		0.699
(1.00) 		0.0791
(1.00) 		0.844
(1.00) 		0.497
(1.00)
12P GAIN MUTATION ANALYSIS 178 (46%) 213 0.945
(1.00) 		0.902
(1.00) 		0.334
(1.00) 		0.237
(1.00) 		0.556
(1.00) 		0.502
(1.00) 		0.00153
(1.00) 		0.105
(1.00) 		0.783
(1.00) 		0.393
(1.00) 		0.948
(1.00) 		0.821
(1.00) 		1
(1.00)
12Q GAIN MUTATION ANALYSIS 120 (31%) 271 0.92
(1.00) 		0.553
(1.00) 		0.371
(1.00) 		0.301
(1.00) 		0.193
(1.00) 		0.865
(1.00) 		0.0113
(1.00) 		0.924
(1.00) 		0.941
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.778
(1.00) 		0.974
(1.00)
13Q GAIN MUTATION ANALYSIS 29 (7%) 362 0.721
(1.00) 		0.173
(1.00) 		0.996
(1.00) 		0.494
(1.00) 		0.538
(1.00) 		0.303
(1.00) 		0.824
(1.00) 		0.197
(1.00) 		0.406
(1.00) 		0.609
(1.00) 		0.0682
(1.00) 		0.163
(1.00) 		0.477
(1.00)
14Q GAIN MUTATION ANALYSIS 93 (24%) 298 0.0403
(1.00) 		0.0216
(1.00) 		0.484
(1.00) 		0.171
(1.00) 		0.489
(1.00) 		0.269
(1.00) 		0.681
(1.00) 		0.71
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.321
(1.00) 		0.758
(1.00)
15Q GAIN MUTATION ANALYSIS 87 (22%) 304 0.798
(1.00) 		0.847
(1.00) 		0.559
(1.00) 		0.559
(1.00) 		0.158
(1.00) 		0.229
(1.00) 		0.327
(1.00) 		0.652
(1.00) 		0.365
(1.00) 		0.478
(1.00) 		0.0164
(1.00) 		0.352
(1.00) 		0.884
(1.00)
16P GAIN MUTATION ANALYSIS 65 (17%) 326 0.287
(1.00) 		0.402
(1.00) 		0.472
(1.00) 		0.81
(1.00) 		0.401
(1.00) 		0.435
(1.00) 		0.0593
(1.00) 		0.0681
(1.00) 		0.208
(1.00) 		1
(1.00) 		0.0833
(1.00) 		0.449
(1.00) 		0.953
(1.00)
16Q GAIN MUTATION ANALYSIS 65 (17%) 326 0.604
(1.00) 		0.152
(1.00) 		0.227
(1.00) 		0.677
(1.00) 		0.671
(1.00) 		0.239
(1.00) 		0.00276
(1.00) 		0.287
(1.00) 		0.229
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.0324
(1.00) 		0.78
(1.00)
17P GAIN MUTATION ANALYSIS 54 (14%) 337 0.555
(1.00) 		0.0231
(1.00) 		0.28
(1.00) 		0.947
(1.00) 		0.926
(1.00) 		0.506
(1.00) 		0.736
(1.00) 		0.889
(1.00) 		0.643
(1.00) 		0.385
(1.00) 		0.0127
(1.00) 		0.0423
(1.00) 		0.872
(1.00)
17Q GAIN MUTATION ANALYSIS 119 (30%) 272 0.167
(1.00) 		0.213
(1.00) 		0.377
(1.00) 		0.191
(1.00) 		0.332
(1.00) 		0.349
(1.00) 		0.00748
(1.00) 		0.816
(1.00) 		0.941
(1.00) 		0.761
(1.00) 		0.634
(1.00) 		0.0793
(1.00) 		0.73
(1.00)
18P GAIN MUTATION ANALYSIS 120 (31%) 271 0.61
(1.00) 		0.367
(1.00) 		0.426
(1.00) 		0.424
(1.00) 		0.312
(1.00) 		0.665
(1.00) 		0.315
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.2
(1.00) 		0.563
(1.00) 		0.832
(1.00) 		0.223
(1.00)
18Q GAIN MUTATION ANALYSIS 92 (24%) 299 0.827
(1.00) 		0.575
(1.00) 		0.262
(1.00) 		0.0278
(1.00) 		0.576
(1.00) 		0.406
(1.00) 		0.492
(1.00) 		0.044
(1.00) 		0.543
(1.00) 		0.163
(1.00) 		0.0691
(1.00) 		0.474
(1.00) 		0.306
(1.00)
19P GAIN MUTATION ANALYSIS 83 (21%) 308 0.21
(1.00) 		0.652
(1.00) 		0.563
(1.00) 		0.773
(1.00) 		0.806
(1.00) 		0.684
(1.00) 		0.776
(1.00) 		0.0454
(1.00) 		0.0723
(1.00) 		0.291
(1.00) 		0.929
(1.00) 		0.119
(1.00) 		0.82
(1.00)
19Q GAIN MUTATION ANALYSIS 122 (31%) 269 0.941
(1.00) 		0.21
(1.00) 		0.696
(1.00) 		0.0852
(1.00) 		0.263
(1.00) 		0.824
(1.00) 		0.532
(1.00) 		0.133
(1.00) 		0.0711
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.00636
(1.00) 		0.724
(1.00)
20P GAIN MUTATION ANALYSIS 198 (51%) 193 0.352
(1.00) 		0.0936
(1.00) 		0.245
(1.00) 		0.807
(1.00) 		0.619
(1.00) 		0.298
(1.00) 		0.13
(1.00) 		0.779
(1.00) 		0.824
(1.00) 		0.381
(1.00) 		0.35
(1.00) 		0.782
(1.00) 		0.725
(1.00)
20Q GAIN MUTATION ANALYSIS 192 (49%) 199 0.438
(1.00) 		0.222
(1.00) 		0.559
(1.00) 		0.473
(1.00) 		0.169
(1.00) 		0.43
(1.00) 		0.0625
(1.00) 		0.133
(1.00) 		0.474
(1.00) 		0.569
(1.00) 		0.703
(1.00) 		0.395
(1.00) 		0.798
(1.00)
21Q GAIN MUTATION ANALYSIS 40 (10%) 351 0.122
(1.00) 		0.947
(1.00) 		0.00416
(1.00) 		0.0613
(1.00) 		0.0132
(1.00) 		0.671
(1.00) 		0.335
(1.00) 		0.686
(1.00) 		0.0993
(1.00) 		0.114
(1.00) 		0.474
(1.00) 		0.323
(1.00) 		0.0311
(1.00)
22Q GAIN MUTATION ANALYSIS 174 (45%) 217 0.778
(1.00) 		0.0425
(1.00) 		0.0826
(1.00) 		0.112
(1.00) 		0.387
(1.00) 		0.807
(1.00) 		0.726
(1.00) 		0.971
(1.00) 		0.59
(1.00) 		0.56
(1.00) 		0.232
(1.00) 		0.121
(1.00) 		0.209
(1.00)
XQ GAIN MUTATION ANALYSIS 62 (16%) 329 0.384
(1.00) 		0.71
(1.00) 		0.377
(1.00) 		0.119
(1.00) 		0.85
(1.00) 		0.285
(1.00) 		0.523
(1.00) 		0.987
(1.00) 		0.531
(1.00) 		0.7
(1.00) 		0.927
(1.00) 		0.277
(1.00) 		0.715
(1.00)
1P LOSS MUTATION ANALYSIS 109 (28%) 282 0.351
(1.00) 		0.697
(1.00) 		0.744
(1.00) 		0.484
(1.00) 		0.369
(1.00) 		0.24
(1.00) 		0.0682
(1.00) 		0.973
(1.00) 		0.931
(1.00) 		0.745
(1.00) 		0.36
(1.00) 		0.748
(1.00) 		0.61
(1.00)
1Q LOSS MUTATION ANALYSIS 39 (10%) 352 0.731
(1.00) 		0.473
(1.00) 		0.382
(1.00) 		0.475
(1.00) 		0.096
(1.00) 		0.764
(1.00) 		0.564
(1.00) 		0.656
(1.00) 		0.798
(1.00) 		0.107
(1.00) 		0.265
(1.00) 		0.875
(1.00) 		0.0429
(1.00)
2P LOSS MUTATION ANALYSIS 15 (4%) 376 0.534
(1.00) 		0.115
(1.00) 		0.178
(1.00) 		0.293
(1.00) 		0.0615
(1.00) 		0.372
(1.00) 		0.221
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.379
(1.00) 		0.239
(1.00) 		0.697
(1.00) 		1
(1.00)
2Q LOSS MUTATION ANALYSIS 30 (8%) 361 0.68
(1.00) 		0.14
(1.00) 		0.849
(1.00) 		0.319
(1.00) 		0.0317
(1.00) 		0.495
(1.00) 		0.515
(1.00) 		0.963
(1.00) 		1
(1.00) 		1
(1.00) 		0.0462
(1.00) 		0.768
(1.00) 		0.671
(1.00)
3P LOSS MUTATION ANALYSIS 242 (62%) 149 0.547
(1.00) 		0.0316
(1.00) 		0.651
(1.00) 		0.941
(1.00) 		0.587
(1.00) 		0.697
(1.00) 		0.149
(1.00) 		0.454
(1.00) 		0.825
(1.00) 		0.547
(1.00) 		0.173
(1.00) 		0.356
(1.00) 		1
(1.00)
3Q LOSS MUTATION ANALYSIS 63 (16%) 328 0.617
(1.00) 		0.929
(1.00) 		0.808
(1.00) 		0.0612
(1.00) 		0.889
(1.00) 		0.0883
(1.00) 		0.43
(1.00) 		0.478
(1.00) 		0.355
(1.00) 		1
(1.00) 		0.273
(1.00) 		0.548
(1.00) 		0.733
(1.00)
4P LOSS MUTATION ANALYSIS 237 (61%) 154 0.146
(1.00) 		0.703
(1.00) 		0.0987
(1.00) 		0.438
(1.00) 		0.774
(1.00) 		0.313
(1.00) 		0.474
(1.00) 		0.651
(1.00) 		0.248
(1.00) 		0.379
(1.00) 		0.713
(1.00) 		0.939
(1.00) 		0.48
(1.00)
4Q LOSS MUTATION ANALYSIS 217 (55%) 174 0.133
(1.00) 		0.901
(1.00) 		0.298
(1.00) 		0.55
(1.00) 		0.471
(1.00) 		0.291
(1.00) 		0.413
(1.00) 		0.248
(1.00) 		0.815
(1.00) 		0.24
(1.00) 		0.374
(1.00) 		0.472
(1.00) 		0.609
(1.00)
5P LOSS MUTATION ANALYSIS 65 (17%) 326 0.193
(1.00) 		0.34
(1.00) 		0.587
(1.00) 		0.107
(1.00) 		0.261
(1.00) 		0.934
(1.00) 		0.756
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.0826
(1.00) 		0.19
(1.00) 		0.211
(1.00)
5Q LOSS MUTATION ANALYSIS 229 (59%) 162 0.269
(1.00) 		0.837
(1.00) 		0.0113
(1.00) 		0.611
(1.00) 		0.188
(1.00) 		0.291
(1.00) 		0.556
(1.00) 		0.706
(1.00) 		0.773
(1.00) 		0.373
(1.00) 		0.964
(1.00) 		0.0841
(1.00) 		0.477
(1.00)
6P LOSS MUTATION ANALYSIS 79 (20%) 312 0.463
(1.00) 		0.446
(1.00) 		0.342
(1.00) 		0.284
(1.00) 		0.0812
(1.00) 		1
(1.00) 		0.469
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.473
(1.00) 		0.897
(1.00) 		0.649
(1.00) 		0.226
(1.00)
6Q LOSS MUTATION ANALYSIS 84 (21%) 307 0.869
(1.00) 		0.522
(1.00) 		0.152
(1.00) 		0.32
(1.00) 		0.474
(1.00) 		0.731
(1.00) 		0.778
(1.00) 		0.818
(1.00) 		0.554
(1.00) 		0.475
(1.00) 		0.823
(1.00) 		0.253
(1.00) 		0.652
(1.00)
7P LOSS MUTATION ANALYSIS 49 (13%) 342 0.479
(1.00) 		0.321
(1.00) 		0.072
(1.00) 		0.299
(1.00) 		0.286
(1.00) 		0.531
(1.00) 		0.293
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.0478
(1.00) 		0.922
(1.00) 		0.123
(1.00)
7Q LOSS MUTATION ANALYSIS 44 (11%) 347 0.612
(1.00) 		0.527
(1.00) 		0.755
(1.00) 		0.524
(1.00) 		0.945
(1.00) 		0.701
(1.00) 		0.854
(1.00) 		0.567
(1.00) 		1
(1.00) 		1
(1.00) 		0.0497
(1.00) 		0.333
(1.00) 		0.622
(1.00)
8P LOSS MUTATION ANALYSIS 186 (48%) 205 0.515
(1.00) 		0.019
(1.00) 		0.124
(1.00) 		0.231
(1.00) 		0.963
(1.00) 		0.0595
(1.00) 		0.0806
(1.00) 		0.255
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.375
(1.00) 		0.431
(1.00) 		0.649
(1.00)
8Q LOSS MUTATION ANALYSIS 36 (9%) 355 0.691
(1.00) 		0.698
(1.00) 		0.386
(1.00) 		0.309
(1.00) 		0.491
(1.00) 		0.648
(1.00) 		0.156
(1.00) 		0.344
(1.00) 		0.146
(1.00) 		0.613
(1.00) 		0.552
(1.00) 		0.178
(1.00) 		0.391
(1.00)
9P LOSS MUTATION ANALYSIS 245 (63%) 146 0.645
(1.00) 		0.288
(1.00) 		0.241
(1.00) 		0.669
(1.00) 		0.507
(1.00) 		0.761
(1.00) 		0.719
(1.00) 		0.846
(1.00) 		0.112
(1.00) 		1
(1.00) 		0.147
(1.00) 		0.21
(1.00) 		0.771
(1.00)
9Q LOSS MUTATION ANALYSIS 184 (47%) 207 0.87
(1.00) 		0.00509
(1.00) 		0.443
(1.00) 		0.328
(1.00) 		0.483
(1.00) 		0.088
(1.00) 		0.726
(1.00) 		0.535
(1.00) 		0.154
(1.00) 		0.39
(1.00) 		0.886
(1.00) 		0.0517
(1.00) 		0.96
(1.00)
10P LOSS MUTATION ANALYSIS 161 (41%) 230 0.764
(1.00) 		0.873
(1.00) 		0.307
(1.00) 		0.946
(1.00) 		0.155
(1.00) 		0.385
(1.00) 		0.236
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.768
(1.00) 		0.365
(1.00) 		0.172
(1.00) 		0.444
(1.00)
10Q LOSS MUTATION ANALYSIS 164 (42%) 227 0.766
(1.00) 		0.117
(1.00) 		0.226
(1.00) 		0.906
(1.00) 		0.269
(1.00) 		0.337
(1.00) 		0.347
(1.00) 		0.633
(1.00) 		0.913
(1.00) 		0.768
(1.00) 		0.965
(1.00) 		0.11
(1.00) 		0.351
(1.00)
11P LOSS MUTATION ANALYSIS 133 (34%) 258 0.574
(1.00) 		0.042
(1.00) 		0.234
(1.00) 		0.897
(1.00) 		0.155
(1.00) 		0.0667
(1.00) 		0.806
(1.00) 		0.247
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.0445
(1.00) 		0.394
(1.00) 		0.777
(1.00)
11Q LOSS MUTATION ANALYSIS 110 (28%) 281 0.704
(1.00) 		0.0309
(1.00) 		0.882
(1.00) 		0.793
(1.00) 		0.0413
(1.00) 		0.686
(1.00) 		0.156
(1.00) 		0.694
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.085
(1.00) 		0.181
(1.00) 		0.13
(1.00)
12P LOSS MUTATION ANALYSIS 31 (8%) 360 0.139
(1.00) 		0.812
(1.00) 		0.317
(1.00) 		0.206
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.547
(1.00) 		0.0524
(1.00) 		0.61
(1.00) 		0.691
(1.00) 		0.296
(1.00) 		0.759
(1.00)
12Q LOSS MUTATION ANALYSIS 35 (9%) 356 0.871
(1.00) 		0.615
(1.00) 		0.68
(1.00) 		0.459
(1.00) 		0.753
(1.00) 		0.638
(1.00) 		0.683
(1.00) 		0.588
(1.00) 		0.0326
(1.00) 		0.612
(1.00) 		0.728
(1.00) 		0.519
(1.00) 		1
(1.00)
13Q LOSS MUTATION ANALYSIS 234 (60%) 157 0.295
(1.00) 		0.422
(1.00) 		0.651
(1.00) 		0.697
(1.00) 		0.65
(1.00) 		0.675
(1.00) 		0.476
(1.00) 		0.626
(1.00) 		0.0169
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.677
(1.00) 		0.754
(1.00)
14Q LOSS MUTATION ANALYSIS 127 (32%) 264 0.107
(1.00) 		0.613
(1.00) 		0.484
(1.00) 		0.12
(1.00) 		0.174
(1.00) 		0.297
(1.00) 		0.619
(1.00) 		0.899
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.2
(1.00) 		0.568
(1.00)
15Q LOSS MUTATION ANALYSIS 100 (26%) 291 0.896
(1.00) 		0.148
(1.00) 		0.0623
(1.00) 		0.152
(1.00) 		0.0501
(1.00) 		0.547
(1.00) 		0.289
(1.00) 		0.969
(1.00) 		0.187
(1.00) 		0.0844
(1.00) 		0.585
(1.00) 		0.55
(1.00) 		0.686
(1.00)
16P LOSS MUTATION ANALYSIS 121 (31%) 270 0.0813
(1.00) 		0.975
(1.00) 		0.131
(1.00) 		0.22
(1.00) 		0.629
(1.00) 		0.217
(1.00) 		0.257
(1.00) 		0.23
(1.00) 		0.0694
(1.00) 		0.762
(1.00) 		0.266
(1.00) 		0.805
(1.00) 		0.473
(1.00)
16Q LOSS MUTATION ANALYSIS 137 (35%) 254 0.199
(1.00) 		0.319
(1.00) 		0.438
(1.00) 		0.598
(1.00) 		0.687
(1.00) 		0.0818
(1.00) 		0.113
(1.00) 		0.221
(1.00) 		0.211
(1.00) 		0.76
(1.00) 		0.639
(1.00) 		0.768
(1.00) 		0.483
(1.00)
17P LOSS MUTATION ANALYSIS 217 (55%) 174 0.655
(1.00) 		0.0152
(1.00) 		0.706
(1.00) 		0.573
(1.00) 		0.0485
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.0667
(1.00) 		0.917
(1.00) 		0.0737
(1.00) 		0.00315
(1.00) 		0.133
(1.00) 		0.652
(1.00)
17Q LOSS MUTATION ANALYSIS 72 (18%) 319 0.542
(1.00) 		0.21
(1.00) 		0.459
(1.00) 		0.262
(1.00) 		0.33
(1.00) 		0.871
(1.00) 		0.0968
(1.00) 		0.348
(1.00) 		0.291
(1.00) 		0.0506
(1.00) 		0.402
(1.00) 		0.607
(1.00) 		0.924
(1.00)
18P LOSS MUTATION ANALYSIS 106 (27%) 285 0.739
(1.00) 		0.402
(1.00) 		0.107
(1.00) 		0.428
(1.00) 		0.913
(1.00) 		0.0865
(1.00) 		0.6
(1.00) 		0.754
(1.00) 		0.711
(1.00) 		0.193
(1.00) 		0.606
(1.00) 		0.987
(1.00) 		0.847
(1.00)
18Q LOSS MUTATION ANALYSIS 141 (36%) 250 0.36
(1.00) 		0.737
(1.00) 		0.0911
(1.00) 		0.119
(1.00) 		0.824
(1.00) 		0.265
(1.00) 		0.332
(1.00) 		0.682
(1.00) 		0.265
(1.00) 		0.549
(1.00) 		0.205
(1.00) 		0.353
(1.00) 		0.293
(1.00)
19P LOSS MUTATION ANALYSIS 122 (31%) 269 0.132
(1.00) 		0.254
(1.00) 		0.582
(1.00) 		0.517
(1.00) 		0.0226
(1.00) 		0.202
(1.00) 		0.615
(1.00) 		0.0126
(1.00) 		0.533
(1.00) 		0.204
(1.00) 		0.245
(1.00) 		0.319
(1.00) 		0.438
(1.00)
19Q LOSS MUTATION ANALYSIS 81 (21%) 310 0.611
(1.00) 		0.173
(1.00) 		0.609
(1.00) 		0.736
(1.00) 		0.656
(1.00) 		0.822
(1.00) 		0.251
(1.00) 		0.0353
(1.00) 		0.147
(1.00) 		0.281
(1.00) 		0.0968
(1.00) 		0.0128
(1.00) 		0.281
(1.00)
20P LOSS MUTATION ANALYSIS 35 (9%) 356 0.505
(1.00) 		0.964
(1.00) 		0.502
(1.00) 		0.133
(1.00) 		0.438
(1.00) 		0.751
(1.00) 		0.311
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.76
(1.00) 		0.373
(1.00)
21Q LOSS MUTATION ANALYSIS 207 (53%) 184 0.512
(1.00) 		0.719
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.11
(1.00) 		0.000269
(0.279) 		0.532
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.441
(1.00) 		0.572
(1.00)
22Q LOSS MUTATION ANALYSIS 71 (18%) 320 0.999
(1.00) 		0.0453
(1.00) 		0.142
(1.00) 		0.717
(1.00) 		0.0126
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.124
(1.00) 		0.463
(1.00) 		0.676
(1.00) 		0.0389
(1.00) 		0.568
(1.00)
XQ LOSS MUTATION ANALYSIS 94 (24%) 297 0.492
(1.00) 		0.505
(1.00) 		0.894
(1.00) 		0.0947
(1.00) 		0.496
(1.00) 		0.597
(1.00) 		0.343
(1.00) 		0.268
(1.00) 		0.426
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.313
(1.00) 		0.729
(1.00)
'20Q LOSS MUTATION STATUS' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2e-06 (t-test), Q value = 0.0021

Table S1.  Gene #77: '20Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 54 28.5 (39.7)
20Q LOSS MUTATED 4 0.0 (0.0)
20Q LOSS WILD-TYPE 50 30.8 (40.4)

Figure S1.  Get High-res Image Gene #77: '20Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'KARNOFSKY.PERFORMANCE.SCORE'

Methods & Data
Input

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

  • Clinical data file = LUSC-TP.clin.merged.picked.txt

  • Number of patients = 391

  • Number of significantly arm-level cnvs = 80

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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