Correlation between copy number variation genes (focal events) and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1S46Q84
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1S46Q84
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 79 focal events and 13 clinical features across 450 patients, 2 significant findings detected with Q value < 0.25.

  • AMP PEAK 18(11Q13.3) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • DEL PEAK 42(19P13.2) MUTATION ANALYSIS cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings 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 Chi-square test Fisher's exact test t-test Chi-square test Fisher's exact test t-test t-test Fisher's exact test
AMP PEAK 18(11Q13 3) MUTATION ANALYSIS 154 (34%) 296 0.918
(1.00) 		0.000162
(0.166) 		0.74
(1.00) 		0.396
(1.00) 		0.726
(1.00) 		0.515
(1.00) 		0.37
(1.00) 		0.196
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.479
(1.00) 		0.133
(1.00) 		0.764
(1.00)
DEL PEAK 42(19P13 2) MUTATION ANALYSIS 243 (54%) 207 0.111
(1.00) 		0.0489
(1.00) 		0.0268
(1.00) 		0.305
(1.00) 		0.0393
(1.00) 		0.0192
(1.00) 		0.000214
(0.219) 		0.32
(1.00) 		0.454
(1.00) 		0.82
(1.00) 		0.842
(1.00) 		0.276
(1.00) 		0.447
(1.00)
AMP PEAK 1(1P34 3) MUTATION ANALYSIS 121 (27%) 329 0.794
(1.00) 		0.0188
(1.00) 		0.759
(1.00) 		0.736
(1.00) 		0.308
(1.00) 		0.798
(1.00) 		0.594
(1.00) 		0.351
(1.00) 		0.88
(1.00) 		0.61
(1.00) 		0.742
(1.00) 		0.382
(1.00) 		0.29
(1.00)
AMP PEAK 2(1P22 3) MUTATION ANALYSIS 121 (27%) 329 0.746
(1.00) 		0.00197
(1.00) 		0.493
(1.00) 		0.766
(1.00) 		0.216
(1.00) 		0.838
(1.00) 		0.915
(1.00) 		0.526
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.877
(1.00) 		0.787
(1.00) 		0.375
(1.00)
AMP PEAK 3(1Q21 3) MUTATION ANALYSIS 322 (72%) 128 0.99
(1.00) 		0.108
(1.00) 		0.248
(1.00) 		0.426
(1.00) 		0.952
(1.00) 		0.517
(1.00) 		0.0597
(1.00) 		0.486
(1.00) 		0.00689
(1.00) 		0.212
(1.00) 		0.282
(1.00) 		0.161
(1.00) 		0.492
(1.00)
AMP PEAK 4(3Q26 2) MUTATION ANALYSIS 147 (33%) 303 0.413
(1.00) 		0.347
(1.00) 		0.75
(1.00) 		0.942
(1.00) 		0.332
(1.00) 		0.524
(1.00) 		0.841
(1.00) 		0.557
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.0382
(1.00) 		0.0625
(1.00) 		0.344
(1.00)
AMP PEAK 5(4Q12) MUTATION ANALYSIS 88 (20%) 362 0.372
(1.00) 		0.0235
(1.00) 		0.113
(1.00) 		0.505
(1.00) 		0.17
(1.00) 		0.921
(1.00) 		0.634
(1.00) 		0.824
(1.00) 		0.265
(1.00) 		0.391
(1.00) 		0.731
(1.00) 		0.188
(1.00) 		0.673
(1.00)
AMP PEAK 6(5P15 33) MUTATION ANALYSIS 293 (65%) 157 0.42
(1.00) 		0.0162
(1.00) 		0.762
(1.00) 		0.567
(1.00) 		0.476
(1.00) 		0.854
(1.00) 		0.234
(1.00) 		0.00736
(1.00) 		0.0246
(1.00) 		0.473
(1.00) 		0.00371
(1.00) 		0.222
(1.00) 		0.794
(1.00)
AMP PEAK 7(5P13 1) MUTATION ANALYSIS 270 (60%) 180 0.076
(1.00) 		0.0197
(1.00) 		0.18
(1.00) 		0.121
(1.00) 		0.619
(1.00) 		0.648
(1.00) 		0.289
(1.00) 		0.829
(1.00) 		0.059
(1.00) 		1
(1.00) 		0.0027
(1.00) 		0.392
(1.00) 		0.257
(1.00)
AMP PEAK 8(5Q35 1) MUTATION ANALYSIS 103 (23%) 347 0.505
(1.00) 		0.151
(1.00) 		0.415
(1.00) 		0.277
(1.00) 		0.816
(1.00) 		0.76
(1.00) 		0.0924
(1.00) 		0.907
(1.00) 		0.653
(1.00) 		1
(1.00) 		0.518
(1.00) 		0.0956
(1.00) 		0.815
(1.00)
AMP PEAK 9(6P21 1) MUTATION ANALYSIS 167 (37%) 283 0.259
(1.00) 		0.291
(1.00) 		0.494
(1.00) 		0.664
(1.00) 		0.312
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.945
(1.00) 		0.424
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.363
(1.00)
AMP PEAK 10(7P21 1) MUTATION ANALYSIS 247 (55%) 203 0.336
(1.00) 		0.142
(1.00) 		0.74
(1.00) 		0.405
(1.00) 		0.00676
(1.00) 		0.289
(1.00) 		0.569
(1.00) 		0.729
(1.00) 		0.227
(1.00) 		0.37
(1.00) 		0.403
(1.00) 		0.379
(1.00) 		0.592
(1.00)
AMP PEAK 11(7P11 2) MUTATION ANALYSIS 242 (54%) 208 0.0532
(1.00) 		0.0253
(1.00) 		0.374
(1.00) 		0.234
(1.00) 		0.00149
(1.00) 		0.33
(1.00) 		0.636
(1.00) 		0.926
(1.00) 		0.273
(1.00) 		0.82
(1.00) 		0.302
(1.00) 		0.0983
(1.00) 		0.746
(1.00)
AMP PEAK 12(7Q31 2) MUTATION ANALYSIS 194 (43%) 256 0.689
(1.00) 		0.00446
(1.00) 		0.246
(1.00) 		0.223
(1.00) 		0.0497
(1.00) 		0.642
(1.00) 		0.567
(1.00) 		0.899
(1.00) 		0.352
(1.00) 		0.356
(1.00) 		0.202
(1.00) 		0.987
(1.00) 		0.42
(1.00)
AMP PEAK 13(8P11 23) MUTATION ANALYSIS 120 (27%) 330 0.618
(1.00) 		0.0137
(1.00) 		0.982
(1.00) 		0.66
(1.00) 		0.913
(1.00) 		0.977
(1.00) 		0.043
(1.00) 		0.762
(1.00) 		0.607
(1.00) 		0.796
(1.00) 		0.85
(1.00) 		0.452
(1.00) 		0.584
(1.00)
AMP PEAK 14(8P11 21) MUTATION ANALYSIS 157 (35%) 293 0.157
(1.00) 		0.0357
(1.00) 		0.878
(1.00) 		0.294
(1.00) 		0.532
(1.00) 		0.465
(1.00) 		0.00147
(1.00) 		0.979
(1.00) 		0.0449
(1.00) 		0.636
(1.00) 		0.659
(1.00) 		0.647
(1.00) 		0.98
(1.00)
AMP PEAK 15(8Q11 1) MUTATION ANALYSIS 207 (46%) 243 0.321
(1.00) 		0.00288
(1.00) 		0.472
(1.00) 		0.284
(1.00) 		0.403
(1.00) 		0.773
(1.00) 		0.129
(1.00) 		0.762
(1.00) 		0.0654
(1.00) 		0.82
(1.00) 		0.955
(1.00) 		0.103
(1.00) 		0.807
(1.00)
AMP PEAK 16(8Q24 21) MUTATION ANALYSIS 287 (64%) 163 0.0605
(1.00) 		0.0442
(1.00) 		0.735
(1.00) 		0.0545
(1.00) 		0.717
(1.00) 		0.68
(1.00) 		0.432
(1.00) 		0.884
(1.00) 		0.0134
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.49
(1.00) 		0.493
(1.00)
AMP PEAK 17(10P15 1) MUTATION ANALYSIS 126 (28%) 324 0.342
(1.00) 		0.148
(1.00) 		0.798
(1.00) 		0.231
(1.00) 		0.0387
(1.00) 		0.933
(1.00) 		0.00108
(1.00) 		0.179
(1.00) 		0.253
(1.00) 		0.214
(1.00) 		0.00907
(1.00) 		0.838
(1.00) 		0.299
(1.00)
AMP PEAK 19(12P12 1) MUTATION ANALYSIS 155 (34%) 295 0.00942
(1.00) 		0.277
(1.00) 		0.668
(1.00) 		0.525
(1.00) 		0.903
(1.00) 		0.804
(1.00) 		0.551
(1.00) 		0.881
(1.00) 		0.227
(1.00) 		0.633
(1.00) 		0.613
(1.00) 		0.142
(1.00) 		0.0612
(1.00)
AMP PEAK 20(12Q14 1) MUTATION ANALYSIS 144 (32%) 306 0.0724
(1.00) 		0.0622
(1.00) 		0.831
(1.00) 		0.323
(1.00) 		0.819
(1.00) 		0.288
(1.00) 		0.156
(1.00) 		0.5
(1.00) 		0.34
(1.00) 		0.808
(1.00) 		0.762
(1.00) 		0.000282
(0.289) 		0.234
(1.00)
AMP PEAK 21(12Q15) MUTATION ANALYSIS 147 (33%) 303 0.219
(1.00) 		0.423
(1.00) 		0.869
(1.00) 		0.612
(1.00) 		0.766
(1.00) 		0.478
(1.00) 		0.16
(1.00) 		0.201
(1.00) 		0.448
(1.00) 		0.473
(1.00) 		0.532
(1.00) 		0.00361
(1.00) 		0.377
(1.00)
AMP PEAK 22(13Q33 3) MUTATION ANALYSIS 70 (16%) 380 0.371
(1.00) 		0.941
(1.00) 		0.297
(1.00) 		0.258
(1.00) 		0.43
(1.00) 		0.0773
(1.00) 		0.192
(1.00) 		0.587
(1.00) 		0.884
(1.00) 		0.532
(1.00) 		0.302
(1.00) 		0.956
(1.00) 		0.455
(1.00)
AMP PEAK 23(14Q13 3) MUTATION ANALYSIS 202 (45%) 248 0.62
(1.00) 		0.353
(1.00) 		0.383
(1.00) 		0.732
(1.00) 		0.93
(1.00) 		0.0039
(1.00) 		0.849
(1.00) 		0.681
(1.00) 		0.154
(1.00) 		0.25
(1.00) 		0.279
(1.00) 		0.156
(1.00) 		0.892
(1.00)
AMP PEAK 24(16P11 2) MUTATION ANALYSIS 143 (32%) 307 0.333
(1.00) 		0.158
(1.00) 		0.965
(1.00) 		0.547
(1.00) 		0.467
(1.00) 		0.679
(1.00) 		0.418
(1.00) 		0.614
(1.00) 		0.724
(1.00) 		1
(1.00) 		0.117
(1.00) 		0.803
(1.00) 		0.907
(1.00)
AMP PEAK 25(17Q12) MUTATION ANALYSIS 203 (45%) 247 0.795
(1.00) 		0.166
(1.00) 		0.679
(1.00) 		0.58
(1.00) 		0.511
(1.00) 		0.809
(1.00) 		0.255
(1.00) 		0.182
(1.00) 		0.271
(1.00) 		0.25
(1.00) 		0.0166
(1.00) 		0.815
(1.00) 		0.0207
(1.00)
AMP PEAK 26(17Q23 1) MUTATION ANALYSIS 222 (49%) 228 0.814
(1.00) 		0.0414
(1.00) 		0.437
(1.00) 		0.202
(1.00) 		0.414
(1.00) 		0.803
(1.00) 		0.777
(1.00) 		0.267
(1.00) 		0.0366
(1.00) 		1
(1.00) 		0.0987
(1.00) 		0.137
(1.00) 		0.0988
(1.00)
AMP PEAK 27(18Q11 2) MUTATION ANALYSIS 90 (20%) 360 0.534
(1.00) 		0.436
(1.00) 		0.476
(1.00) 		0.977
(1.00) 		0.969
(1.00) 		0.407
(1.00) 		0.156
(1.00) 		0.659
(1.00) 		0.174
(1.00) 		0.391
(1.00) 		0.454
(1.00) 		0.873
(1.00) 		0.349
(1.00)
AMP PEAK 28(19Q12) MUTATION ANALYSIS 126 (28%) 324 0.687
(1.00) 		0.442
(1.00) 		0.912
(1.00) 		0.593
(1.00) 		0.596
(1.00) 		0.962
(1.00) 		0.0736
(1.00) 		0.137
(1.00) 		0.28
(1.00) 		0.611
(1.00) 		0.0714
(1.00) 		0.197
(1.00) 		0.974
(1.00)
AMP PEAK 29(20P11 21) MUTATION ANALYSIS 172 (38%) 278 0.414
(1.00) 		0.7
(1.00) 		0.101
(1.00) 		0.111
(1.00) 		0.063
(1.00) 		0.467
(1.00) 		0.383
(1.00) 		0.238
(1.00) 		0.0881
(1.00) 		0.49
(1.00) 		0.266
(1.00) 		0.218
(1.00) 		0.684
(1.00)
AMP PEAK 30(20Q13 33) MUTATION ANALYSIS 218 (48%) 232 0.465
(1.00) 		0.212
(1.00) 		0.242
(1.00) 		0.138
(1.00) 		0.295
(1.00) 		0.332
(1.00) 		0.571
(1.00) 		0.178
(1.00) 		0.0278
(1.00) 		0.822
(1.00) 		0.226
(1.00) 		0.777
(1.00) 		0.867
(1.00)
AMP PEAK 31(22Q11 22) MUTATION ANALYSIS 78 (17%) 372 0.345
(1.00) 		0.948
(1.00) 		0.291
(1.00) 		0.574
(1.00) 		0.867
(1.00) 		0.242
(1.00) 		0.215
(1.00) 		0.641
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.537
(1.00) 		0.808
(1.00)
AMP PEAK 32(XQ28) MUTATION ANALYSIS 144 (32%) 306 0.642
(1.00) 		0.236
(1.00) 		0.981
(1.00) 		0.49
(1.00) 		0.106
(1.00) 		0.48
(1.00) 		0.224
(1.00) 		0.344
(1.00) 		0.456
(1.00) 		0.224
(1.00) 		0.592
(1.00) 		0.862
(1.00) 		0.869
(1.00)
DEL PEAK 1(1P36 13) MUTATION ANALYSIS 102 (23%) 348 0.101
(1.00) 		0.251
(1.00) 		0.0824
(1.00) 		0.362
(1.00) 		0.0232
(1.00) 		0.377
(1.00) 		0.0902
(1.00) 		0.285
(1.00) 		0.334
(1.00) 		0.787
(1.00) 		0.963
(1.00) 		0.924
(1.00) 		0.412
(1.00)
DEL PEAK 2(1P13 2) MUTATION ANALYSIS 135 (30%) 315 0.953
(1.00) 		0.273
(1.00) 		0.287
(1.00) 		0.457
(1.00) 		0.467
(1.00) 		0.344
(1.00) 		0.918
(1.00) 		0.682
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.867
(1.00) 		0.726
(1.00)
DEL PEAK 3(2Q22 1) MUTATION ANALYSIS 46 (10%) 404 0.593
(1.00) 		0.876
(1.00) 		0.569
(1.00) 		0.472
(1.00) 		0.492
(1.00) 		0.509
(1.00) 		0.876
(1.00) 		0.942
(1.00) 		0.534
(1.00) 		1
(1.00) 		0.0482
(1.00) 		0.662
(1.00) 		0.766
(1.00)
DEL PEAK 4(2Q37 3) MUTATION ANALYSIS 60 (13%) 390 0.128
(1.00) 		0.928
(1.00) 		0.0641
(1.00) 		0.873
(1.00) 		0.142
(1.00) 		0.432
(1.00) 		0.0368
(1.00) 		0.45
(1.00) 		0.234
(1.00) 		0.091
(1.00) 		0.962
(1.00) 		0.644
(1.00) 		0.77
(1.00)
DEL PEAK 5(3P21 31) MUTATION ANALYSIS 215 (48%) 235 0.193
(1.00) 		0.272
(1.00) 		0.258
(1.00) 		0.00237
(1.00) 		0.0109
(1.00) 		0.343
(1.00) 		0.509
(1.00) 		0.127
(1.00) 		0.65
(1.00) 		0.823
(1.00) 		0.961
(1.00) 		0.00169
(1.00) 		0.51
(1.00)
DEL PEAK 6(3Q11 1) MUTATION ANALYSIS 130 (29%) 320 0.0345
(1.00) 		0.284
(1.00) 		0.749
(1.00) 		0.584
(1.00) 		0.322
(1.00) 		0.941
(1.00) 		0.678
(1.00) 		0.121
(1.00) 		0.84
(1.00) 		0.805
(1.00) 		0.281
(1.00) 		0.159
(1.00) 		0.811
(1.00)
DEL PEAK 7(3Q29) MUTATION ANALYSIS 125 (28%) 325 0.447
(1.00) 		0.393
(1.00) 		0.821
(1.00) 		0.566
(1.00) 		0.975
(1.00) 		0.767
(1.00) 		0.673
(1.00) 		0.859
(1.00) 		0.66
(1.00) 		0.306
(1.00) 		0.349
(1.00) 		0.534
(1.00) 		0.147
(1.00)
DEL PEAK 8(4P16 3) MUTATION ANALYSIS 109 (24%) 341 0.0867
(1.00) 		0.0649
(1.00) 		0.616
(1.00) 		0.779
(1.00) 		0.798
(1.00) 		0.96
(1.00) 		0.912
(1.00) 		0.148
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.0357
(1.00) 		0.101
(1.00) 		0.724
(1.00)
DEL PEAK 9(4Q22 1) MUTATION ANALYSIS 134 (30%) 316 0.423
(1.00) 		0.577
(1.00) 		0.495
(1.00) 		0.648
(1.00) 		0.044
(1.00) 		0.876
(1.00) 		0.68
(1.00) 		0.0675
(1.00) 		0.158
(1.00) 		0.322
(1.00) 		0.288
(1.00) 		0.17
(1.00) 		0.347
(1.00)
DEL PEAK 10(4Q35 1) MUTATION ANALYSIS 163 (36%) 287 0.245
(1.00) 		0.0797
(1.00) 		0.476
(1.00) 		0.314
(1.00) 		0.12
(1.00) 		0.276
(1.00) 		0.0621
(1.00) 		0.296
(1.00) 		0.165
(1.00) 		0.234
(1.00) 		0.528
(1.00) 		0.0577
(1.00) 		0.931
(1.00)
DEL PEAK 11(5Q11 2) MUTATION ANALYSIS 165 (37%) 285 0.22
(1.00) 		0.00887
(1.00) 		0.885
(1.00) 		0.91
(1.00) 		0.148
(1.00) 		0.464
(1.00) 		0.624
(1.00) 		0.452
(1.00) 		0.0587
(1.00) 		0.346
(1.00) 		0.0184
(1.00) 		0.36
(1.00) 		0.458
(1.00)
DEL PEAK 12(5Q31 1) MUTATION ANALYSIS 190 (42%) 260 0.181
(1.00) 		0.00184
(1.00) 		0.65
(1.00) 		0.975
(1.00) 		0.679
(1.00) 		0.802
(1.00) 		0.445
(1.00) 		0.622
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.0114
(1.00) 		0.174
(1.00) 		0.723
(1.00)
DEL PEAK 13(6Q12) MUTATION ANALYSIS 164 (36%) 286 0.383
(1.00) 		0.209
(1.00) 		0.057
(1.00) 		0.478
(1.00) 		0.0687
(1.00) 		0.675
(1.00) 		0.695
(1.00) 		0.156
(1.00) 		0.301
(1.00) 		0.236
(1.00) 		0.0373
(1.00) 		0.0603
(1.00) 		0.464
(1.00)
DEL PEAK 14(6Q22 31) MUTATION ANALYSIS 227 (50%) 223 0.782
(1.00) 		0.187
(1.00) 		0.782
(1.00) 		0.64
(1.00) 		0.774
(1.00) 		0.681
(1.00) 		0.187
(1.00) 		0.0858
(1.00) 		0.697
(1.00) 		1
(1.00) 		0.0292
(1.00) 		0.0919
(1.00) 		0.787
(1.00)
DEL PEAK 15(6Q26) MUTATION ANALYSIS 229 (51%) 221 0.726
(1.00) 		0.226
(1.00) 		0.886
(1.00) 		0.813
(1.00) 		0.728
(1.00) 		0.306
(1.00) 		0.345
(1.00) 		0.142
(1.00) 		0.526
(1.00) 		0.82
(1.00) 		0.365
(1.00) 		0.154
(1.00) 		0.881
(1.00)
DEL PEAK 16(8P23 2) MUTATION ANALYSIS 221 (49%) 229 0.823
(1.00) 		0.341
(1.00) 		0.52
(1.00) 		0.526
(1.00) 		0.95
(1.00) 		0.414
(1.00) 		0.059
(1.00) 		0.162
(1.00) 		0.0463
(1.00) 		1
(1.00) 		0.221
(1.00) 		0.487
(1.00) 		0.679
(1.00)
DEL PEAK 17(8P12) MUTATION ANALYSIS 197 (44%) 253 0.493
(1.00) 		0.972
(1.00) 		0.793
(1.00) 		0.551
(1.00) 		0.463
(1.00) 		0.206
(1.00) 		0.0873
(1.00) 		0.388
(1.00) 		0.0608
(1.00) 		0.252
(1.00) 		0.938
(1.00) 		0.962
(1.00) 		0.667
(1.00)
DEL PEAK 18(8P11 21) MUTATION ANALYSIS 101 (22%) 349 0.418
(1.00) 		0.922
(1.00) 		0.612
(1.00) 		0.311
(1.00) 		0.889
(1.00) 		0.785
(1.00) 		0.00455
(1.00) 		0.0545
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.368
(1.00) 		0.41
(1.00)
DEL PEAK 19(8Q11 21) MUTATION ANALYSIS 55 (12%) 395 0.796
(1.00) 		0.209
(1.00) 		0.707
(1.00) 		0.573
(1.00) 		0.0883
(1.00) 		0.906
(1.00) 		0.149
(1.00) 		0.0192
(1.00) 		0.121
(1.00) 		0.153
(1.00) 		0.834
(1.00) 		0.342
(1.00) 		0.381
(1.00)
DEL PEAK 20(9P23) MUTATION ANALYSIS 244 (54%) 206 0.26
(1.00) 		0.276
(1.00) 		0.673
(1.00) 		0.931
(1.00) 		0.02
(1.00) 		0.47
(1.00) 		0.343
(1.00) 		0.394
(1.00) 		0.501
(1.00) 		0.652
(1.00) 		0.979
(1.00) 		0.32
(1.00) 		0.935
(1.00)
DEL PEAK 21(9P21 3) MUTATION ANALYSIS 249 (55%) 201 0.534
(1.00) 		0.127
(1.00) 		0.403
(1.00) 		0.944
(1.00) 		0.0105
(1.00) 		0.235
(1.00) 		0.0707
(1.00) 		0.562
(1.00) 		0.247
(1.00) 		0.652
(1.00) 		0.579
(1.00) 		0.324
(1.00) 		0.906
(1.00)
DEL PEAK 22(9Q21 11) MUTATION ANALYSIS 222 (49%) 228 0.311
(1.00) 		0.979
(1.00) 		0.955
(1.00) 		0.34
(1.00) 		0.728
(1.00) 		0.815
(1.00) 		0.705
(1.00) 		0.7
(1.00) 		0.141
(1.00) 		0.253
(1.00) 		0.0985
(1.00) 		0.449
(1.00) 		0.501
(1.00)
DEL PEAK 23(10P15 3) MUTATION ANALYSIS 107 (24%) 343 0.173
(1.00) 		0.673
(1.00) 		0.55
(1.00) 		0.37
(1.00) 		0.429
(1.00) 		0.821
(1.00) 		0.000246
(0.252) 		0.305
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.766
(1.00) 		0.835
(1.00) 		0.492
(1.00)
DEL PEAK 24(10Q26 3) MUTATION ANALYSIS 127 (28%) 323 0.999
(1.00) 		0.809
(1.00) 		0.659
(1.00) 		0.168
(1.00) 		0.507
(1.00) 		0.822
(1.00) 		0.116
(1.00) 		0.337
(1.00) 		0.4
(1.00) 		0.213
(1.00) 		0.0266
(1.00) 		0.272
(1.00) 		0.544
(1.00)
DEL PEAK 25(11P15 5) MUTATION ANALYSIS 122 (27%) 328 0.485
(1.00) 		0.0127
(1.00) 		0.671
(1.00) 		0.689
(1.00) 		0.891
(1.00) 		0.168
(1.00) 		0.0258
(1.00) 		0.551
(1.00) 		0.299
(1.00) 		0.61
(1.00) 		0.186
(1.00) 		0.0538
(1.00) 		0.64
(1.00)
DEL PEAK 26(11Q25) MUTATION ANALYSIS 99 (22%) 351 0.402
(1.00) 		0.636
(1.00) 		0.611
(1.00) 		0.73
(1.00) 		0.259
(1.00) 		0.655
(1.00) 		0.04
(1.00) 		0.929
(1.00) 		0.934
(1.00) 		0.586
(1.00) 		0.289
(1.00) 		0.442
(1.00) 		0.84
(1.00)
DEL PEAK 27(12P13 2) MUTATION ANALYSIS 120 (27%) 330 0.874
(1.00) 		0.992
(1.00) 		0.147
(1.00) 		0.942
(1.00) 		0.466
(1.00) 		0.721
(1.00) 		0.00532
(1.00) 		0.208
(1.00) 		0.781
(1.00) 		0.305
(1.00) 		0.0832
(1.00) 		0.17
(1.00) 		0.364
(1.00)
DEL PEAK 28(12Q12) MUTATION ANALYSIS 85 (19%) 365 0.323
(1.00) 		0.158
(1.00) 		0.246
(1.00) 		0.269
(1.00) 		0.319
(1.00) 		0.159
(1.00) 		0.148
(1.00) 		0.732
(1.00) 		0.914
(1.00) 		0.144
(1.00) 		0.151
(1.00) 		0.624
(1.00) 		0.555
(1.00)
DEL PEAK 29(12Q24 33) MUTATION ANALYSIS 107 (24%) 343 0.541
(1.00) 		0.896
(1.00) 		0.179
(1.00) 		0.0425
(1.00) 		0.735
(1.00) 		0.103
(1.00) 		0.0453
(1.00) 		0.339
(1.00) 		0.464
(1.00) 		0.0563
(1.00) 		0.503
(1.00) 		0.385
(1.00) 		0.73
(1.00)
DEL PEAK 30(13Q12 11) MUTATION ANALYSIS 251 (56%) 199 0.673
(1.00) 		0.161
(1.00) 		0.546
(1.00) 		0.359
(1.00) 		0.959
(1.00) 		0.72
(1.00) 		0.0101
(1.00) 		0.0113
(1.00) 		0.0896
(1.00) 		0.17
(1.00) 		0.000455
(0.465) 		0.255
(1.00) 		0.803
(1.00)
DEL PEAK 31(13Q12 13) MUTATION ANALYSIS 251 (56%) 199 0.876
(1.00) 		0.321
(1.00) 		0.625
(1.00) 		0.41
(1.00) 		0.856
(1.00) 		0.656
(1.00) 		0.0455
(1.00) 		0.0163
(1.00) 		0.0515
(1.00) 		0.0664
(1.00) 		0.00741
(1.00) 		0.222
(1.00) 		0.814
(1.00)
DEL PEAK 32(13Q14 2) MUTATION ANALYSIS 242 (54%) 208 0.94
(1.00) 		0.279
(1.00) 		0.981
(1.00) 		0.597
(1.00) 		0.93
(1.00) 		0.57
(1.00) 		0.57
(1.00) 		0.46
(1.00) 		0.247
(1.00) 		0.82
(1.00) 		0.0839
(1.00) 		0.381
(1.00) 		0.828
(1.00)
DEL PEAK 33(13Q34) MUTATION ANALYSIS 204 (45%) 246 0.745
(1.00) 		0.146
(1.00) 		0.793
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.635
(1.00) 		0.574
(1.00) 		0.487
(1.00) 		0.654
(1.00) 		0.147
(1.00) 		0.422
(1.00) 		0.309
(1.00)
DEL PEAK 34(14Q32 33) MUTATION ANALYSIS 136 (30%) 314 0.837
(1.00) 		0.483
(1.00) 		0.168
(1.00) 		0.408
(1.00) 		0.0837
(1.00) 		0.881
(1.00) 		0.681
(1.00) 		0.319
(1.00) 		0.524
(1.00) 		0.328
(1.00) 		0.156
(1.00) 		0.0552
(1.00) 		0.108
(1.00)
DEL PEAK 35(15Q11 2) MUTATION ANALYSIS 229 (51%) 221 0.676
(1.00) 		0.00518
(1.00) 		0.0971
(1.00) 		0.435
(1.00) 		0.885
(1.00) 		0.785
(1.00) 		0.637
(1.00) 		0.0487
(1.00) 		0.0566
(1.00) 		0.365
(1.00) 		0.524
(1.00) 		0.195
(1.00) 		0.662
(1.00)
DEL PEAK 36(16Q23 1) MUTATION ANALYSIS 150 (33%) 300 0.855
(1.00) 		0.428
(1.00) 		0.615
(1.00) 		0.825
(1.00) 		0.437
(1.00) 		0.734
(1.00) 		0.764
(1.00) 		0.391
(1.00) 		0.547
(1.00) 		0.628
(1.00) 		0.97
(1.00) 		0.923
(1.00) 		0.905
(1.00)
DEL PEAK 37(17P13 3) MUTATION ANALYSIS 245 (54%) 205 0.833
(1.00) 		0.0375
(1.00) 		0.507
(1.00) 		0.157
(1.00) 		0.874
(1.00) 		0.436
(1.00) 		0.184
(1.00) 		0.996
(1.00) 		0.113
(1.00) 		0.251
(1.00) 		0.431
(1.00) 		0.00442
(1.00) 		0.468
(1.00)
DEL PEAK 38(17P11 2) MUTATION ANALYSIS 200 (44%) 250 0.911
(1.00) 		0.0448
(1.00) 		0.298
(1.00) 		0.0667
(1.00) 		0.445
(1.00) 		0.381
(1.00) 		0.183
(1.00) 		0.113
(1.00) 		0.238
(1.00) 		0.0359
(1.00) 		0.374
(1.00) 		0.0414
(1.00) 		0.774
(1.00)
DEL PEAK 39(18Q21 32) MUTATION ANALYSIS 226 (50%) 224 0.0212
(1.00) 		0.21
(1.00) 		0.0266
(1.00) 		0.269
(1.00) 		0.056
(1.00) 		0.134
(1.00) 		0.344
(1.00) 		0.847
(1.00) 		0.502
(1.00) 		0.178
(1.00) 		0.886
(1.00) 		0.0964
(1.00) 		0.0354
(1.00)
DEL PEAK 40(18Q23) MUTATION ANALYSIS 223 (50%) 227 0.0559
(1.00) 		0.0842
(1.00) 		0.0147
(1.00) 		0.186
(1.00) 		0.0436
(1.00) 		0.358
(1.00) 		0.187
(1.00) 		0.814
(1.00) 		0.2
(1.00) 		0.253
(1.00) 		0.823
(1.00) 		0.0526
(1.00) 		0.0352
(1.00)
DEL PEAK 41(19P13 3) MUTATION ANALYSIS 249 (55%) 201 0.0417
(1.00) 		0.296
(1.00) 		0.0275
(1.00) 		0.124
(1.00) 		0.106
(1.00) 		0.0715
(1.00) 		0.0102
(1.00) 		0.249
(1.00) 		0.371
(1.00) 		0.819
(1.00) 		0.513
(1.00) 		0.201
(1.00) 		0.763
(1.00)
DEL PEAK 43(19Q13 33) MUTATION ANALYSIS 173 (38%) 277 0.0807
(1.00) 		0.537
(1.00) 		0.579
(1.00) 		0.448
(1.00) 		0.565
(1.00) 		0.147
(1.00) 		0.333
(1.00) 		0.401
(1.00) 		0.383
(1.00) 		0.489
(1.00) 		0.94
(1.00) 		0.677
(1.00) 		0.578
(1.00)
DEL PEAK 44(20Q13 12) MUTATION ANALYSIS 79 (18%) 371 0.323
(1.00) 		0.903
(1.00) 		0.151
(1.00) 		0.463
(1.00) 		0.273
(1.00) 		0.028
(1.00) 		0.267
(1.00) 		0.00615
(1.00) 		0.142
(1.00) 		0.55
(1.00) 		0.0882
(1.00) 		0.252
(1.00) 		0.593
(1.00)
DEL PEAK 45(21Q11 2) MUTATION ANALYSIS 150 (33%) 300 0.632
(1.00) 		0.404
(1.00) 		0.235
(1.00) 		0.471
(1.00) 		0.955
(1.00) 		0.943
(1.00) 		0.133
(1.00) 		0.455
(1.00) 		0.32
(1.00) 		0.331
(1.00) 		0.174
(1.00) 		0.112
(1.00) 		0.526
(1.00)
DEL PEAK 46(22Q13 32) MUTATION ANALYSIS 215 (48%) 235 0.294
(1.00) 		0.00029
(0.297) 		0.541
(1.00) 		0.998
(1.00) 		0.912
(1.00) 		0.318
(1.00) 		0.0107
(1.00) 		0.0775
(1.00) 		0.221
(1.00) 		0.503
(1.00) 		0.961
(1.00) 		0.00387
(1.00) 		0.707
(1.00)
DEL PEAK 47(XP22 2) MUTATION ANALYSIS 130 (29%) 320 0.571
(1.00) 		0.211
(1.00) 		0.291
(1.00) 		0.746
(1.00) 		0.222
(1.00) 		0.792
(1.00) 		0.0473
(1.00) 		0.782
(1.00) 		0.629
(1.00) 		0.457
(1.00) 		0.521
(1.00) 		0.0889
(1.00) 		0.807
(1.00)
'AMP PEAK 18(11Q13.3) MUTATION STATUS' versus 'AGE'

P value = 0.000162 (t-test), Q value = 0.17

Table S1.  Gene #18: 'AMP PEAK 18(11Q13.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 419 65.5 (9.7)
AMP PEAK 18(11Q13.3) MUTATED 145 63.0 (9.8)
AMP PEAK 18(11Q13.3) WILD-TYPE 274 66.8 (9.4)

Figure S1.  Get High-res Image Gene #18: 'AMP PEAK 18(11Q13.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 42(19P13.2) MUTATION STATUS' versus 'GENDER'

P value = 0.000214 (Fisher's exact test), Q value = 0.22

Table S2.  Gene #74: 'DEL PEAK 42(19P13.2) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 242 208
DEL PEAK 42(19P13.2) MUTATED 111 132
DEL PEAK 42(19P13.2) WILD-TYPE 131 76

Figure S2.  Get High-res Image Gene #74: 'DEL PEAK 42(19P13.2) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

Methods & Data
Input

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

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

  • Number of patients = 450

  • Number of significantly focal cnvs = 79

  • Number of selected clinical features = 13

  • 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

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle