Correlation between copy number variation genes (focal) and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1F769JP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Lung Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1F769JP
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level results and 14 clinical features across 389 patients, 7 significant findings detected with Q value < 0.25.

  • Amp Peak 17(10p15.1) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

  • Amp Peak 18(11q13.3) cnv correlated to 'AGE'.

  • Del Peak 6(3p21.31) cnv correlated to 'YEAROFTOBACCOSMOKINGONSET'.

  • Del Peak 13(5q22.1) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

  • Del Peak 24(10p15.3) cnv correlated to 'GENDER'.

  • Del Peak 44(19p13.2) cnv correlated to 'GENDER'.

  • Del Peak 45(19p12) cnv correlated to 'TUMOR.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level results and 14 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 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test Fisher's exact test t-test Fisher's exact test
Amp Peak 17(10p15 1) 0 (0%) 280 0.098
(1.00) 		0.497
(1.00) 		0.00662
(1.00) 		0.436
(1.00) 		0.321
(1.00) 		0.678
(1.00) 		0.0271
(1.00) 		0.687
(1.00) 		0.544
(1.00) 		0.609
(1.00) 		0.00204
(1.00) 		2.87e-05
(0.0329) 		0.889
(1.00) 		0.368
(1.00)
Amp Peak 18(11q13 3) 0 (0%) 252 0.953
(1.00) 		4.09e-05
(0.0468) 		0.201
(1.00) 		0.579
(1.00) 		0.443
(1.00) 		0.823
(1.00) 		0.576
(1.00) 		0.642
(1.00) 		0.144
(1.00) 		0.811
(1.00) 		0.802
(1.00) 		0.00989
(1.00) 		0.33
(1.00) 		0.306
(1.00)
Del Peak 6(3p21 31) 0 (0%) 202 0.664
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.068
(1.00) 		0.689
(1.00) 		0.00795
(1.00) 		0.0569
(1.00) 		0.516
(1.00) 		0.311
(1.00) 		0.258
(1.00) 		0.74
(1.00) 		0.0105
(1.00) 		0.000219
(0.249) 		0.916
(1.00)
Del Peak 13(5q22 1) 0 (0%) 230 0.261
(1.00) 		0.00111
(1.00) 		0.535
(1.00) 		0.528
(1.00) 		0.26
(1.00) 		0.466
(1.00) 		0.0507
(1.00) 		0.966
(1.00) 		0.0671
(1.00) 		0.165
(1.00) 		0.0224
(1.00) 		2.96e-05
(0.0339) 		0.149
(1.00) 		0.338
(1.00)
Del Peak 24(10p15 3) 0 (0%) 299 0.145
(1.00) 		0.465
(1.00) 		0.000101
(0.116) 		0.816
(1.00) 		0.522
(1.00) 		0.195
(1.00) 		0.805
(1.00) 		0.198
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.00381
(1.00) 		0.629
(1.00) 		0.966
(1.00)
Del Peak 44(19p13 2) 0 (0%) 181 0.332
(1.00) 		0.0328
(1.00) 		0.000154
(0.176) 		0.876
(1.00) 		0.483
(1.00) 		0.335
(1.00) 		0.16
(1.00) 		0.241
(1.00) 		0.0719
(1.00) 		0.82
(1.00) 		0.738
(1.00) 		0.0278
(1.00) 		0.295
(1.00) 		0.538
(1.00)
Del Peak 45(19p12) 0 (0%) 222 0.00503
(1.00) 		0.00406
(1.00) 		0.0104
(1.00) 		0.91
(1.00) 		0.506
(1.00) 		0.118
(1.00) 		0.00419
(1.00) 		0.124
(1.00) 		7.92e-05
(0.0905) 		1
(1.00) 		0.357
(1.00) 		0.172
(1.00) 		0.124
(1.00) 		0.924
(1.00)
Amp Peak 1(1p34 3) 0 (0%) 283 0.768
(1.00) 		0.0221
(1.00) 		0.819
(1.00) 		0.401
(1.00) 		0.698
(1.00) 		0.815
(1.00) 		0.384
(1.00) 		0.516
(1.00) 		0.789
(1.00) 		0.609
(1.00) 		0.901
(1.00) 		0.354
(1.00) 		0.918
(1.00) 		0.241
(1.00)
Amp Peak 2(1p22 3) 0 (0%) 285 0.906
(1.00) 		0.00157
(1.00) 		0.909
(1.00) 		0.648
(1.00) 		0.22
(1.00) 		0.892
(1.00) 		0.189
(1.00) 		0.539
(1.00) 		0.455
(1.00) 		0.437
(1.00) 		0.598
(1.00) 		0.752
(1.00) 		0.654
(1.00) 		0.557
(1.00)
Amp Peak 3(1q21 3) 0 (0%) 108 0.368
(1.00) 		0.121
(1.00) 		0.0228
(1.00) 		0.302
(1.00) 		0.00313
(1.00) 		0.819
(1.00) 		0.641
(1.00) 		0.623
(1.00) 		0.93
(1.00) 		0.304
(1.00) 		0.495
(1.00) 		0.17
(1.00) 		0.283
(1.00) 		0.474
(1.00)
Amp Peak 4(3q26 2) 0 (0%) 258 0.847
(1.00) 		0.349
(1.00) 		0.668
(1.00) 		0.781
(1.00) 		0.775
(1.00) 		0.782
(1.00) 		0.215
(1.00) 		0.444
(1.00) 		0.232
(1.00) 		0.474
(1.00) 		0.15
(1.00) 		0.029
(1.00) 		0.0969
(1.00) 		0.428
(1.00)
Amp Peak 5(4q12) 0 (0%) 313 0.244
(1.00) 		0.0162
(1.00) 		0.609
(1.00) 		0.994
(1.00) 		0.458
(1.00) 		0.0223
(1.00) 		0.756
(1.00) 		0.311
(1.00) 		0.648
(1.00) 		0.776
(1.00) 		0.712
(1.00) 		0.991
(1.00) 		0.262
(1.00) 		0.574
(1.00)
Amp Peak 6(5p15 33) 0 (0%) 136 0.136
(1.00) 		0.00291
(1.00) 		0.166
(1.00) 		0.0273
(1.00) 		0.0219
(1.00) 		0.0444
(1.00) 		0.505
(1.00) 		0.403
(1.00) 		0.538
(1.00) 		0.471
(1.00) 		0.0146
(1.00) 		0.208
(1.00) 		0.325
(1.00) 		0.27
(1.00)
Amp Peak 7(5p13 1) 0 (0%) 159 0.0458
(1.00) 		0.00248
(1.00) 		0.148
(1.00) 		0.929
(1.00) 		0.0739
(1.00) 		0.0184
(1.00) 		0.261
(1.00) 		0.22
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.0112
(1.00) 		0.188
(1.00) 		0.395
(1.00) 		0.0882
(1.00)
Amp Peak 8(5q35 1) 0 (0%) 299 0.102
(1.00) 		0.177
(1.00) 		0.0158
(1.00) 		0.994
(1.00) 		0.759
(1.00) 		0.5
(1.00) 		0.456
(1.00) 		0.653
(1.00) 		0.608
(1.00) 		0.425
(1.00) 		0.396
(1.00) 		0.109
(1.00) 		0.0975
(1.00) 		0.694
(1.00)
Amp Peak 9(6p21 1) 0 (0%) 244 0.657
(1.00) 		0.291
(1.00) 		0.833
(1.00) 		0.877
(1.00) 		0.58
(1.00) 		0.427
(1.00) 		0.252
(1.00) 		0.107
(1.00) 		0.606
(1.00) 		0.637
(1.00) 		0.909
(1.00) 		0.0136
(1.00) 		0.508
(1.00) 		0.184
(1.00)
Amp Peak 10(7p21 1) 0 (0%) 172 0.882
(1.00) 		0.569
(1.00) 		0.413
(1.00) 		0.966
(1.00) 		0.234
(1.00) 		0.307
(1.00) 		0.0573
(1.00) 		0.779
(1.00) 		0.334
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.0604
(1.00) 		0.961
(1.00) 		0.249
(1.00)
Amp Peak 11(7p11 2) 0 (0%) 180 0.237
(1.00) 		0.241
(1.00) 		0.36
(1.00) 		0.755
(1.00) 		0.274
(1.00) 		0.101
(1.00) 		0.00673
(1.00) 		0.739
(1.00) 		0.141
(1.00) 		0.819
(1.00) 		0.214
(1.00) 		0.155
(1.00) 		0.349
(1.00) 		0.819
(1.00)
Amp Peak 12(7q31 2) 0 (0%) 226 0.761
(1.00) 		0.0214
(1.00) 		0.837
(1.00) 		0.35
(1.00) 		0.266
(1.00) 		0.477
(1.00) 		0.249
(1.00) 		0.639
(1.00) 		0.555
(1.00) 		0.25
(1.00) 		0.348
(1.00) 		0.222
(1.00) 		0.919
(1.00) 		0.379
(1.00)
Amp Peak 13(8p11 23) 0 (0%) 283 0.982
(1.00) 		0.0076
(1.00) 		0.109
(1.00) 		0.119
(1.00) 		0.26
(1.00) 		0.732
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.973
(1.00) 		1
(1.00) 		0.877
(1.00) 		0.0304
(1.00) 		0.286
(1.00) 		0.94
(1.00)
Amp Peak 14(8p11 21) 0 (0%) 256 0.29
(1.00) 		0.0596
(1.00) 		0.0013
(1.00) 		0.972
(1.00) 		0.0246
(1.00) 		0.852
(1.00) 		0.184
(1.00) 		0.282
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.0397
(1.00) 		0.777
(1.00) 		1
(1.00)
Amp Peak 15(8q11 1) 0 (0%) 208 0.641
(1.00) 		0.0115
(1.00) 		0.222
(1.00) 		0.997
(1.00) 		0.057
(1.00) 		0.393
(1.00) 		0.473
(1.00) 		0.72
(1.00) 		0.539
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.0224
(1.00) 		0.101
(1.00) 		0.739
(1.00)
Amp Peak 16(8q24 21) 0 (0%) 141 0.307
(1.00) 		0.0889
(1.00) 		0.916
(1.00) 		0.844
(1.00) 		0.0175
(1.00) 		0.31
(1.00) 		0.833
(1.00) 		0.92
(1.00) 		0.895
(1.00) 		0.639
(1.00) 		0.691
(1.00) 		0.121
(1.00) 		0.907
(1.00) 		0.53
(1.00)
Amp Peak 19(12p12 1) 0 (0%) 256 0.0272
(1.00) 		0.372
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.393
(1.00) 		0.352
(1.00) 		0.226
(1.00) 		0.354
(1.00) 		0.545
(1.00) 		0.631
(1.00) 		0.854
(1.00) 		0.242
(1.00) 		0.199
(1.00) 		0.0295
(1.00)
Amp Peak 20(12q14 1) 0 (0%) 267 0.151
(1.00) 		0.0466
(1.00) 		0.381
(1.00) 		0.625
(1.00) 		0.347
(1.00) 		0.337
(1.00) 		0.361
(1.00) 		0.523
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.0656
(1.00) 		0.000439
(0.5) 		0.265
(1.00)
Amp Peak 21(12q15) 0 (0%) 263 0.348
(1.00) 		0.327
(1.00) 		0.514
(1.00) 		0.305
(1.00) 		0.414
(1.00) 		0.315
(1.00) 		0.282
(1.00) 		0.567
(1.00) 		0.402
(1.00) 		0.809
(1.00) 		0.207
(1.00) 		0.0398
(1.00) 		0.00488
(1.00) 		0.283
(1.00)
Amp Peak 22(13q33 3) 0 (0%) 324 0.838
(1.00) 		0.654
(1.00) 		0.221
(1.00) 		0.87
(1.00) 		0.602
(1.00) 		0.595
(1.00) 		0.585
(1.00) 		0.808
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.642
(1.00) 		0.898
(1.00) 		0.555
(1.00)
Amp Peak 23(14q13 3) 0 (0%) 221 0.38
(1.00) 		0.47
(1.00) 		0.758
(1.00) 		0.495
(1.00) 		0.317
(1.00) 		0.383
(1.00) 		0.87
(1.00) 		0.215
(1.00) 		0.901
(1.00) 		0.496
(1.00) 		0.604
(1.00) 		0.464
(1.00) 		0.157
(1.00) 		0.872
(1.00)
Amp Peak 24(17q12) 0 (0%) 217 0.827
(1.00) 		0.629
(1.00) 		0.682
(1.00) 		0.0892
(1.00) 		0.416
(1.00) 		0.525
(1.00) 		0.59
(1.00) 		0.146
(1.00) 		0.507
(1.00) 		0.0655
(1.00) 		0.00759
(1.00) 		0.327
(1.00) 		0.748
(1.00) 		0.00656
(1.00)
Amp Peak 25(17q23 1) 0 (0%) 200 0.498
(1.00) 		0.145
(1.00) 		0.541
(1.00) 		0.532
(1.00) 		0.14
(1.00) 		0.335
(1.00) 		0.41
(1.00) 		0.22
(1.00) 		0.583
(1.00) 		0.648
(1.00) 		0.0416
(1.00) 		0.523
(1.00) 		0.189
(1.00) 		0.0255
(1.00)
Amp Peak 26(18q11 2) 0 (0%) 307 0.84
(1.00) 		0.357
(1.00) 		0.134
(1.00) 		0.855
(1.00) 		0.101
(1.00) 		0.976
(1.00) 		0.672
(1.00) 		0.175
(1.00) 		0.49
(1.00) 		0.271
(1.00) 		0.458
(1.00) 		0.344
(1.00) 		0.811
(1.00) 		0.351
(1.00)
Amp Peak 27(19q12) 0 (0%) 278 0.922
(1.00) 		0.451
(1.00) 		0.0243
(1.00) 		0.252
(1.00) 		0.474
(1.00) 		0.604
(1.00) 		0.602
(1.00) 		0.733
(1.00) 		0.519
(1.00) 		0.21
(1.00) 		0.0673
(1.00) 		0.76
(1.00) 		0.172
(1.00) 		0.781
(1.00)
Amp Peak 28(20p11 21) 0 (0%) 244 0.52
(1.00) 		0.879
(1.00) 		0.916
(1.00) 		0.196
(1.00) 		0.284
(1.00) 		0.109
(1.00) 		0.0146
(1.00) 		0.32
(1.00) 		0.00812
(1.00) 		0.637
(1.00) 		0.634
(1.00) 		0.134
(1.00) 		0.248
(1.00) 		0.532
(1.00)
Amp Peak 29(20q13 33) 0 (0%) 202 0.394
(1.00) 		0.237
(1.00) 		0.919
(1.00) 		0.304
(1.00) 		0.0632
(1.00) 		0.104
(1.00) 		0.126
(1.00) 		0.17
(1.00) 		0.0378
(1.00) 		0.499
(1.00) 		0.473
(1.00) 		0.211
(1.00) 		0.497
(1.00) 		0.833
(1.00)
Amp Peak 30(22q11 22) 0 (0%) 323 0.31
(1.00) 		0.967
(1.00) 		0.418
(1.00) 		0.279
(1.00) 		0.389
(1.00) 		0.349
(1.00) 		0.0797
(1.00) 		0.322
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.851
(1.00) 		0.506
(1.00) 		0.951
(1.00)
Amp Peak 31(Xq28) 0 (0%) 261 0.285
(1.00) 		0.213
(1.00) 		0.129
(1.00) 		0.334
(1.00) 		0.431
(1.00) 		0.514
(1.00) 		0.337
(1.00) 		0.421
(1.00) 		0.288
(1.00) 		0.811
(1.00) 		0.488
(1.00) 		0.00511
(1.00) 		0.752
(1.00) 		0.952
(1.00)
Del Peak 1(1p36 13) 0 (0%) 300 0.0373
(1.00) 		0.366
(1.00) 		0.0526
(1.00) 		0.427
(1.00) 		0.58
(1.00) 		0.0635
(1.00) 		0.0953
(1.00) 		0.497
(1.00) 		0.11
(1.00) 		0.42
(1.00) 		0.632
(1.00) 		0.786
(1.00) 		0.965
(1.00) 		0.191
(1.00)
Del Peak 2(1p13 3) 0 (0%) 272 0.749
(1.00) 		0.332
(1.00) 		0.824
(1.00) 		0.646
(1.00) 		0.925
(1.00) 		0.537
(1.00) 		0.654
(1.00) 		0.63
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.989
(1.00) 		0.861
(1.00) 		0.274
(1.00)
Del Peak 3(1p13 1) 0 (0%) 276 0.414
(1.00) 		0.179
(1.00) 		0.823
(1.00) 		0.783
(1.00) 		0.894
(1.00) 		0.619
(1.00) 		0.543
(1.00) 		0.564
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.767
(1.00) 		0.778
(1.00) 		0.532
(1.00)
Del Peak 4(2q22 1) 0 (0%) 346 0.732
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.242
(1.00) 		0.411
(1.00) 		0.36
(1.00) 		0.193
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.0639
(1.00) 		0.0838
(1.00) 		0.48
(1.00) 		0.751
(1.00)
Del Peak 5(2q37 3) 0 (0%) 331 0.263
(1.00) 		0.906
(1.00) 		0.0648
(1.00) 		0.548
(1.00) 		0.128
(1.00) 		0.926
(1.00) 		0.108
(1.00) 		0.364
(1.00) 		0.687
(1.00) 		0.0545
(1.00) 		0.85
(1.00) 		0.359
(1.00) 		0.374
(1.00) 		0.86
(1.00)
Del Peak 7(3q11 1) 0 (0%) 276 0.426
(1.00) 		0.27
(1.00) 		0.737
(1.00) 		0.0885
(1.00) 		0.897
(1.00) 		0.991
(1.00) 		0.775
(1.00) 		0.66
(1.00) 		0.507
(1.00) 		0.804
(1.00) 		0.316
(1.00) 		0.652
(1.00) 		0.0663
(1.00) 		0.756
(1.00)
Del Peak 8(3q29) 0 (0%) 280 0.799
(1.00) 		0.358
(1.00) 		0.652
(1.00) 		0.404
(1.00) 		0.695
(1.00) 		0.497
(1.00) 		0.222
(1.00) 		0.746
(1.00) 		0.108
(1.00) 		0.609
(1.00) 		0.277
(1.00) 		0.624
(1.00) 		0.348
(1.00) 		0.352
(1.00)
Del Peak 9(4p16 3) 0 (0%) 295 0.139
(1.00) 		0.0453
(1.00) 		0.813
(1.00) 		0.598
(1.00) 		0.486
(1.00) 		0.617
(1.00) 		0.566
(1.00) 		0.948
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.0115
(1.00) 		0.0769
(1.00) 		0.797
(1.00)
Del Peak 10(4q22 1) 0 (0%) 269 0.508
(1.00) 		0.506
(1.00) 		0.661
(1.00) 		0.174
(1.00) 		0.231
(1.00) 		0.483
(1.00) 		0.0156
(1.00) 		0.556
(1.00) 		0.105
(1.00) 		0.456
(1.00) 		0.528
(1.00) 		0.133
(1.00) 		0.232
(1.00) 		0.405
(1.00)
Del Peak 11(4q35 1) 0 (0%) 246 0.915
(1.00) 		0.213
(1.00) 		0.115
(1.00) 		0.212
(1.00) 		0.222
(1.00) 		0.17
(1.00) 		0.349
(1.00) 		0.393
(1.00) 		0.705
(1.00) 		0.237
(1.00) 		0.523
(1.00) 		0.00201
(1.00) 		0.155
(1.00) 		0.887
(1.00)
Del Peak 12(5q11 2) 0 (0%) 251 0.238
(1.00) 		0.0187
(1.00) 		0.75
(1.00) 		0.528
(1.00) 		0.169
(1.00) 		0.51
(1.00) 		0.0225
(1.00) 		0.402
(1.00) 		0.143
(1.00) 		0.35
(1.00) 		0.0398
(1.00) 		0.0553
(1.00) 		0.378
(1.00) 		0.547
(1.00)
Del Peak 14(6q12) 0 (0%) 254 0.128
(1.00) 		0.507
(1.00) 		0.749
(1.00) 		0.174
(1.00) 		0.341
(1.00) 		0.692
(1.00) 		0.0899
(1.00) 		0.395
(1.00) 		0.0114
(1.00) 		0.341
(1.00) 		0.0135
(1.00) 		0.0294
(1.00) 		0.0676
(1.00) 		0.332
(1.00)
Del Peak 15(6q22 31) 0 (0%) 195 0.637
(1.00) 		0.155
(1.00) 		0.542
(1.00) 		0.174
(1.00) 		0.921
(1.00) 		0.773
(1.00) 		0.637
(1.00) 		0.556
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0398
(1.00) 		0.189
(1.00) 		0.235
(1.00) 		0.706
(1.00)
Del Peak 16(6q26) 0 (0%) 193 0.618
(1.00) 		0.137
(1.00) 		0.542
(1.00) 		0.252
(1.00) 		0.864
(1.00) 		0.943
(1.00) 		0.416
(1.00) 		0.143
(1.00) 		0.0618
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.249
(1.00) 		0.171
(1.00) 		0.692
(1.00)
Del Peak 17(8p23 2) 0 (0%) 202 0.712
(1.00) 		0.262
(1.00) 		0.187
(1.00) 		0.0429
(1.00) 		0.0156
(1.00) 		0.293
(1.00) 		0.606
(1.00) 		0.63
(1.00) 		0.984
(1.00) 		0.359
(1.00) 		0.644
(1.00) 		0.162
(1.00) 		0.224
(1.00) 		0.904
(1.00)
Del Peak 18(8p12) 0 (0%) 221 0.7
(1.00) 		0.631
(1.00) 		0.182
(1.00) 		0.211
(1.00) 		0.0232
(1.00) 		0.321
(1.00) 		0.545
(1.00) 		0.414
(1.00) 		0.904
(1.00) 		0.821
(1.00) 		0.397
(1.00) 		0.558
(1.00) 		0.697
(1.00) 		0.319
(1.00)
Del Peak 19(8p11 21) 0 (0%) 304 0.531
(1.00) 		0.927
(1.00) 		0.00946
(1.00) 		0.125
(1.00) 		0.0971
(1.00) 		0.521
(1.00) 		0.446
(1.00) 		0.804
(1.00) 		0.477
(1.00) 		0.404
(1.00) 		0.617
(1.00) 		0.842
(1.00) 		0.38
(1.00) 		0.0966
(1.00)
Del Peak 20(8q11 21) 0 (0%) 343 0.539
(1.00) 		0.111
(1.00) 		0.212
(1.00) 		0.00461
(1.00) 		0.0934
(1.00) 		0.318
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.314
(1.00) 		1
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.229
(1.00)
Del Peak 21(9p23) 0 (0%) 181 0.0984
(1.00) 		0.23
(1.00) 		0.476
(1.00) 		0.559
(1.00) 		0.631
(1.00) 		0.899
(1.00) 		0.00969
(1.00) 		0.831
(1.00) 		0.215
(1.00) 		0.36
(1.00) 		0.961
(1.00) 		0.261
(1.00) 		0.414
(1.00) 		0.969
(1.00)
Del Peak 22(9p21 3) 0 (0%) 175 0.489
(1.00) 		0.111
(1.00) 		0.0665
(1.00) 		0.755
(1.00) 		0.472
(1.00) 		0.934
(1.00) 		0.00258
(1.00) 		0.949
(1.00) 		0.0321
(1.00) 		1
(1.00) 		0.541
(1.00) 		0.297
(1.00) 		0.308
(1.00) 		0.968
(1.00)
Del Peak 23(9q21 11) 0 (0%) 199 0.281
(1.00) 		0.949
(1.00) 		0.919
(1.00) 		0.841
(1.00) 		0.0332
(1.00) 		0.354
(1.00) 		0.262
(1.00) 		0.259
(1.00) 		0.315
(1.00) 		0.108
(1.00) 		0.0714
(1.00) 		0.45
(1.00) 		0.528
(1.00) 		0.352
(1.00)
Del Peak 25(10q26 3) 0 (0%) 285 0.52
(1.00) 		0.568
(1.00) 		0.0857
(1.00) 		0.261
(1.00) 		0.757
(1.00) 		0.101
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.117
(1.00) 		0.0215
(1.00) 		0.114
(1.00) 		0.187
(1.00) 		0.393
(1.00)
Del Peak 26(11p15 5) 0 (0%) 286 0.619
(1.00) 		0.0739
(1.00) 		0.0835
(1.00) 		0.369
(1.00) 		0.216
(1.00) 		0.944
(1.00) 		0.743
(1.00) 		0.103
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.147
(1.00) 		0.00652
(1.00) 		0.141
(1.00) 		0.969
(1.00)
Del Peak 27(11q23 2) 0 (0%) 301 0.85
(1.00) 		0.648
(1.00) 		0.275
(1.00) 		0.507
(1.00) 		0.676
(1.00) 		0.792
(1.00) 		0.371
(1.00) 		0.473
(1.00) 		0.839
(1.00) 		0.584
(1.00) 		0.463
(1.00) 		0.503
(1.00) 		0.199
(1.00) 		0.491
(1.00)
Del Peak 28(11q25) 0 (0%) 306 0.232
(1.00) 		0.627
(1.00) 		0.138
(1.00) 		0.507
(1.00) 		0.797
(1.00) 		0.931
(1.00) 		0.251
(1.00) 		0.349
(1.00) 		0.759
(1.00) 		0.587
(1.00) 		0.333
(1.00) 		0.287
(1.00) 		0.195
(1.00) 		0.562
(1.00)
Del Peak 29(12p13 2) 0 (0%) 278 0.273
(1.00) 		0.905
(1.00) 		0.00104
(1.00) 		0.893
(1.00) 		0.847
(1.00) 		0.767
(1.00) 		0.709
(1.00) 		0.308
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.0318
(1.00) 		0.419
(1.00) 		0.0964
(1.00) 		0.342
(1.00)
Del Peak 30(12q12) 0 (0%) 314 0.253
(1.00) 		0.0913
(1.00) 		0.122
(1.00) 		0.794
(1.00) 		0.655
(1.00) 		0.553
(1.00) 		0.577
(1.00) 		0.0369
(1.00) 		0.48
(1.00) 		0.777
(1.00) 		0.0868
(1.00) 		0.668
(1.00) 		0.372
(1.00) 		0.291
(1.00)
Del Peak 31(12q24 33) 0 (0%) 296 0.513
(1.00) 		0.98
(1.00) 		0.0433
(1.00) 		0.374
(1.00) 		0.207
(1.00) 		0.167
(1.00) 		0.822
(1.00) 		0.268
(1.00) 		0.705
(1.00) 		0.181
(1.00) 		0.408
(1.00) 		0.0378
(1.00) 		0.329
(1.00) 		0.769
(1.00)
Del Peak 32(13q12 11) 0 (0%) 174 0.444
(1.00) 		0.0902
(1.00) 		0.0106
(1.00) 		0.0264
(1.00) 		0.0618
(1.00) 		0.546
(1.00) 		0.941
(1.00) 		0.15
(1.00) 		0.849
(1.00) 		0.365
(1.00) 		0.00158
(1.00) 		0.0752
(1.00) 		0.186
(1.00) 		0.909
(1.00)
Del Peak 33(13q12 13) 0 (0%) 172 0.541
(1.00) 		0.194
(1.00) 		0.0518
(1.00) 		0.0422
(1.00) 		0.0253
(1.00) 		0.861
(1.00) 		0.901
(1.00) 		0.15
(1.00) 		0.875
(1.00) 		0.169
(1.00) 		0.0143
(1.00) 		0.219
(1.00) 		0.162
(1.00) 		0.933
(1.00)
Del Peak 34(13q14 2) 0 (0%) 181 0.882
(1.00) 		0.103
(1.00) 		0.61
(1.00) 		0.7
(1.00) 		0.206
(1.00) 		0.779
(1.00) 		0.751
(1.00) 		0.355
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.209
(1.00) 		0.166
(1.00) 		0.854
(1.00)
Del Peak 35(13q34) 0 (0%) 214 0.986
(1.00) 		0.0819
(1.00) 		0.759
(1.00) 		0.627
(1.00) 		0.384
(1.00) 		0.759
(1.00) 		0.988
(1.00) 		0.14
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.157
(1.00) 		0.223
(1.00) 		0.269
(1.00)
Del Peak 36(14q32 33) 0 (0%) 270 0.402
(1.00) 		0.715
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.423
(1.00) 		0.313
(1.00) 		0.179
(1.00) 		0.315
(1.00) 		0.226
(1.00) 		0.627
(1.00) 		0.261
(1.00) 		0.258
(1.00) 		0.074
(1.00) 		0.0723
(1.00)
Del Peak 37(15q11 2) 0 (0%) 188 0.322
(1.00) 		0.0156
(1.00) 		0.186
(1.00) 		0.261
(1.00) 		0.043
(1.00) 		0.407
(1.00) 		0.903
(1.00) 		0.971
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.901
(1.00) 		0.388
(1.00) 		0.162
(1.00) 		0.552
(1.00)
Del Peak 38(16q23 1) 0 (0%) 257 0.968
(1.00) 		0.578
(1.00) 		0.915
(1.00) 		0.553
(1.00) 		0.815
(1.00) 		0.676
(1.00) 		0.343
(1.00) 		0.85
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.131
(1.00) 		0.793
(1.00) 		0.823
(1.00)
Del Peak 39(16q24 3) 0 (0%) 245 0.697
(1.00) 		0.404
(1.00) 		0.916
(1.00) 		0.637
(1.00) 		0.807
(1.00) 		0.958
(1.00) 		0.188
(1.00) 		0.89
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.0576
(1.00) 		0.779
(1.00) 		0.94
(1.00)
Del Peak 40(17p13 3) 0 (0%) 178 0.634
(1.00) 		0.0603
(1.00) 		0.0837
(1.00) 		0.831
(1.00) 		0.0438
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.862
(1.00) 		0.491
(1.00) 		0.713
(1.00) 		0.432
(1.00) 		0.0139
(1.00) 		0.35
(1.00)
Del Peak 41(18q21 32) 0 (0%) 192 0.221
(1.00) 		0.269
(1.00) 		0.155
(1.00) 		0.348
(1.00) 		0.43
(1.00) 		0.473
(1.00) 		0.357
(1.00) 		0.211
(1.00) 		0.258
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.253
(1.00) 		0.195
(1.00) 		0.0307
(1.00)
Del Peak 42(18q23) 0 (0%) 198 0.303
(1.00) 		0.0981
(1.00) 		0.154
(1.00) 		0.367
(1.00) 		0.284
(1.00) 		0.174
(1.00) 		0.196
(1.00) 		0.52
(1.00) 		0.0313
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.202
(1.00) 		0.0651
(1.00) 		0.0314
(1.00)
Del Peak 43(19p13 3) 0 (0%) 174 0.069
(1.00) 		0.155
(1.00) 		0.000736
(0.838) 		0.763
(1.00) 		0.303
(1.00) 		0.188
(1.00) 		0.123
(1.00) 		0.498
(1.00) 		0.0161
(1.00) 		0.818
(1.00) 		0.616
(1.00) 		0.15
(1.00) 		0.198
(1.00) 		0.28
(1.00)
Del Peak 46(19q13 33) 0 (0%) 246 0.0265
(1.00) 		0.339
(1.00) 		0.462
(1.00) 		0.409
(1.00) 		0.373
(1.00) 		0.678
(1.00) 		0.678
(1.00) 		0.187
(1.00) 		0.21
(1.00) 		0.813
(1.00) 		0.773
(1.00) 		0.299
(1.00) 		0.752
(1.00) 		0.236
(1.00)
Del Peak 47(20p13) 0 (0%) 291 0.718
(1.00) 		0.937
(1.00) 		0.0786
(1.00) 		0.6
(1.00) 		0.28
(1.00) 		0.639
(1.00) 		0.0494
(1.00) 		0.798
(1.00) 		0.128
(1.00) 		0.602
(1.00) 		0.223
(1.00) 		0.204
(1.00) 		0.0428
(1.00) 		0.939
(1.00)
Del Peak 48(21q11 2) 0 (0%) 257 0.695
(1.00) 		0.362
(1.00) 		0.454
(1.00) 		0.707
(1.00) 		0.45
(1.00) 		0.823
(1.00) 		0.96
(1.00) 		0.696
(1.00) 		0.685
(1.00) 		0.333
(1.00) 		0.298
(1.00) 		0.0247
(1.00) 		0.0803
(1.00) 		0.82
(1.00)
Del Peak 49(21q21 3) 0 (0%) 261 0.545
(1.00) 		0.722
(1.00) 		0.083
(1.00) 		0.578
(1.00) 		0.307
(1.00) 		0.659
(1.00) 		0.929
(1.00) 		0.91
(1.00) 		0.613
(1.00) 		0.234
(1.00) 		0.171
(1.00) 		0.00793
(1.00) 		0.315
(1.00) 		0.44
(1.00)
Del Peak 50(22q13 32) 0 (0%) 202 0.363
(1.00) 		0.000871
(0.99) 		0.0667
(1.00) 		0.58
(1.00) 		0.223
(1.00) 		0.976
(1.00) 		0.399
(1.00) 		0.852
(1.00) 		0.698
(1.00) 		0.822
(1.00) 		0.809
(1.00) 		0.0165
(1.00) 		0.00358
(1.00) 		0.546
(1.00)
Del Peak 51(Xp22 2) 0 (0%) 276 0.532
(1.00) 		0.193
(1.00) 		0.0436
(1.00) 		0.833
(1.00) 		0.605
(1.00) 		0.819
(1.00) 		0.417
(1.00) 		0.66
(1.00) 		0.506
(1.00) 		0.804
(1.00) 		0.74
(1.00) 		0.605
(1.00) 		0.0598
(1.00) 		0.784
(1.00)
'Amp Peak 17(10p15.1)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.033

Table S1.  Gene #17: 'Amp Peak 17(10p15.1)' versus Clinical Feature #12: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT SMOKER LIFELONG NON-SMOKER
ALL 100 77 62 36
AMP PEAK 17(10P15.1) CNV 39 14 24 2
AMP PEAK 17(10P15.1) WILD-TYPE 61 63 38 34

Figure S1.  Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Clinical Feature #12: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Amp Peak 18(11q13.3)' versus 'AGE'

P value = 4.09e-05 (t-test), Q value = 0.047

Table S2.  Gene #18: 'Amp Peak 18(11q13.3)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 358 65.2 (9.8)
AMP PEAK 18(11Q13.3) CNV 128 62.4 (9.8)
AMP PEAK 18(11Q13.3) WILD-TYPE 230 66.8 (9.5)

Figure S2.  Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Clinical Feature #2: 'AGE'

'Del Peak 6(3p21.31)' versus 'YEAROFTOBACCOSMOKINGONSET'

P value = 0.000219 (t-test), Q value = 0.25

Table S3.  Gene #37: 'Del Peak 6(3p21.31)' versus Clinical Feature #13: 'YEAROFTOBACCOSMOKINGONSET'

nPatients Mean (Std.Dev)
ALL 206 1965.4 (12.6)
DEL PEAK 6(3P21.31) CNV 98 1968.7 (12.7)
DEL PEAK 6(3P21.31) WILD-TYPE 108 1962.3 (11.6)

Figure S3.  Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Clinical Feature #13: 'YEAROFTOBACCOSMOKINGONSET'

'Del Peak 13(5q22.1)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.96e-05 (Fisher's exact test), Q value = 0.034

Table S4.  Gene #44: 'Del Peak 13(5q22.1)' versus Clinical Feature #12: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT SMOKER LIFELONG NON-SMOKER
ALL 100 77 62 36
DEL PEAK 13(5Q22.1) CNV 47 21 40 10
DEL PEAK 13(5Q22.1) WILD-TYPE 53 56 22 26

Figure S4.  Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Clinical Feature #12: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 24(10p15.3)' versus 'GENDER'

P value = 0.000101 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #55: 'Del Peak 24(10p15.3)' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 211 178
DEL PEAK 24(10P15.3) CNV 65 25
DEL PEAK 24(10P15.3) WILD-TYPE 146 153

Figure S5.  Get High-res Image Gene #55: 'Del Peak 24(10p15.3)' versus Clinical Feature #3: 'GENDER'

'Del Peak 44(19p13.2)' versus 'GENDER'

P value = 0.000154 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #75: 'Del Peak 44(19p13.2)' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 211 178
DEL PEAK 44(19P13.2) CNV 94 114
DEL PEAK 44(19P13.2) WILD-TYPE 117 64

Figure S6.  Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Clinical Feature #3: 'GENDER'

'Del Peak 45(19p12)' versus 'TUMOR.STAGE'

P value = 7.92e-05 (Fisher's exact test), Q value = 0.09

Table S7.  Gene #76: 'Del Peak 45(19p12)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 149 61 57 16
DEL PEAK 45(19P12) CNV 47 31 36 10
DEL PEAK 45(19P12) WILD-TYPE 102 30 21 6

Figure S7.  Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Clinical Feature #9: 'TUMOR.STAGE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 389

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 14

  • Exclude genes 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

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

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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