Correlation between copy number variation genes (focal events) 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/C19C6WHD
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C19C6WHD
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 83 focal events and 15 clinical features across 493 patients, 4 significant findings detected with Q value < 0.25.

  • amp_7p11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_20q11.21 cnv correlated to 'GENDER'.

  • amp_xq28 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_2q22.1 cnv correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 83 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 significant findings 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
amp 7p11 2 252 (51%) 241 0.00106
(0.264) 		0.523
(0.917) 		0.00246
(0.269) 		0.00033
(0.187) 		0.181
(0.816) 		0.45
(0.893) 		0.257
(0.86) 		0.587
(0.937) 		0.176
(0.804) 		0.784
(0.975) 		0.31
(0.892) 		0.435
(0.892) 		0.671
(0.963) 		0.013
(0.415) 		0.284
(0.882)
amp 20q11 21 301 (61%) 192 0.396
(0.892) 		0.319
(0.892) 		0.644
(0.957) 		0.111
(0.741) 		0.0369
(0.572) 		0.264
(0.86) 		0.000133
(0.165) 		0.361
(0.892) 		0.0487
(0.598) 		0.774
(0.975) 		0.953
(1.00) 		0.38
(0.892) 		0.783
(0.975) 		0.96
(1.00) 		0.152
(0.783)
amp xq28 121 (25%) 372 0.332
(0.892) 		0.961
(1.00) 		0.0623
(0.616) 		0.0006
(0.187) 		0.285
(0.882) 		0.679
(0.963) 		0.0945
(0.715) 		0.0391
(0.572) 		0.954
(1.00) 		1
(1.00) 		0.506
(0.91) 		0.148
(0.783) 		0.747
(0.965) 		0.62
(0.947) 		0.206
(0.827)
del 2q22 1 129 (26%) 364 0.623
(0.948) 		0.000574
(0.187) 		0.119
(0.757) 		0.74
(0.965) 		0.0318
(0.544) 		0.685
(0.963) 		0.161
(0.796) 		0.764
(0.973) 		0.571
(0.931) 		0.529
(0.917) 		0.886
(1.00) 		0.00666
(0.389) 		0.343
(0.892) 		0.456
(0.893) 		0.686
(0.963)
amp 1q21 2 254 (52%) 239 0.0615
(0.616) 		0.103
(0.715) 		0.193
(0.824) 		0.0287
(0.544) 		0.213
(0.834) 		0.129
(0.776) 		0.149
(0.783) 		0.513
(0.915) 		0.00924
(0.41) 		0.578
(0.933) 		0.866
(1.00) 		0.371
(0.892) 		0.656
(0.962) 		0.624
(0.948) 		0.725
(0.965)
amp 2p16 1 269 (55%) 224 0.0745
(0.675) 		0.996
(1.00) 		0.136
(0.783) 		0.127
(0.776) 		0.0524
(0.604) 		1
(1.00) 		0.0071
(0.389) 		0.398
(0.892) 		0.0245
(0.514) 		0.78
(0.975) 		0.185
(0.823) 		0.148
(0.783) 		0.467
(0.893) 		0.208
(0.827) 		0.0305
(0.544)
amp 2q31 2 170 (34%) 323 0.191
(0.823) 		0.334
(0.892) 		0.15
(0.783) 		0.645
(0.957) 		0.542
(0.927) 		1
(1.00) 		0.0394
(0.572) 		0.686
(0.963) 		0.401
(0.892) 		0.557
(0.927) 		0.00975
(0.41) 		0.0564
(0.605) 		0.428
(0.892) 		0.594
(0.937) 		1
(1.00)
amp 3q26 33 444 (90%) 49 0.0248
(0.514) 		0.614
(0.941) 		0.167
(0.797) 		0.786
(0.975) 		0.964
(1.00) 		1
(1.00) 		0.0378
(0.572) 		0.412
(0.892) 		0.0395
(0.572) 		0.629
(0.949) 		0.565
(0.929) 		0.635
(0.951) 		0.796
(0.982) 		0.078
(0.676) 		0.577
(0.933)
amp 4q12 117 (24%) 376 0.394
(0.892) 		0.0606
(0.616) 		0.454
(0.893) 		0.358
(0.892) 		0.886
(1.00) 		0.359
(0.892) 		1
(1.00) 		0.628
(0.949) 		0.234
(0.855) 		1
(1.00) 		0.419
(0.892) 		0.0323
(0.544) 		1
(1.00) 		0.487
(0.901) 		0.207
(0.827)
amp 5p15 33 382 (77%) 111 0.428
(0.892) 		0.602
(0.937) 		0.0979
(0.715) 		0.35
(0.892) 		0.0115
(0.413) 		0.653
(0.959) 		0.392
(0.892) 		0.884
(1.00) 		0.629
(0.949) 		0.502
(0.909) 		0.384
(0.892) 		0.766
(0.973) 		0.857
(1.00) 		0.172
(0.797) 		0.686
(0.963)
amp 5p12 349 (71%) 144 0.988
(1.00) 		0.326
(0.892) 		0.183
(0.823) 		0.179
(0.812) 		0.171
(0.797) 		1
(1.00) 		0.0172
(0.458) 		0.406
(0.892) 		0.0998
(0.715) 		1
(1.00) 		0.132
(0.776) 		0.282
(0.881) 		0.32
(0.892) 		0.212
(0.831) 		1
(1.00)
amp 6p12 1 163 (33%) 330 0.687
(0.963) 		0.152
(0.783) 		0.405
(0.892) 		0.04
(0.572) 		0.821
(0.99) 		0.43
(0.892) 		0.444
(0.892) 		0.638
(0.954) 		0.441
(0.892) 		0.767
(0.973) 		0.961
(1.00) 		0.313
(0.892) 		0.74
(0.965) 		0.337
(0.892) 		0.723
(0.965)
amp 6q12 150 (30%) 343 0.683
(0.963) 		0.0966
(0.715) 		0.59
(0.937) 		0.647
(0.959) 		0.835
(0.992) 		0.445
(0.892) 		0.0939
(0.715) 		0.648
(0.959) 		0.601
(0.937) 		0.547
(0.927) 		0.401
(0.892) 		0.0759
(0.676) 		0.84
(0.992) 		0.202
(0.827) 		1
(1.00)
amp 7q21 2 260 (53%) 233 0.0421
(0.584) 		0.45
(0.893) 		0.348
(0.892) 		0.0123
(0.413) 		0.188
(0.823) 		0.459
(0.893) 		0.0301
(0.544) 		0.0422
(0.584) 		0.227
(0.848) 		0.401
(0.892) 		0.501
(0.909) 		0.409
(0.892) 		0.55
(0.927) 		0.301
(0.892) 		0.723
(0.965)
amp 8p11 23 235 (48%) 258 0.0771
(0.676) 		0.688
(0.963) 		0.862
(1.00) 		0.416
(0.892) 		0.996
(1.00) 		0.714
(0.965) 		0.00545
(0.387) 		0.0807
(0.693) 		0.324
(0.892) 		0.781
(0.975) 		0.651
(0.959) 		0.513
(0.915) 		0.0151
(0.448) 		0.418
(0.892) 		0.299
(0.892)
amp 8q24 21 349 (71%) 144 0.278
(0.881) 		0.918
(1.00) 		0.0314
(0.544) 		0.0144
(0.438) 		0.112
(0.741) 		0.198
(0.827) 		0.141
(0.783) 		0.0872
(0.715) 		0.356
(0.892) 		0.764
(0.973) 		0.494
(0.906) 		0.84
(0.992) 		0.188
(0.823) 		0.37
(0.892) 		0.443
(0.892)
amp 9p13 3 132 (27%) 361 0.385
(0.892) 		0.234
(0.855) 		0.154
(0.785) 		0.631
(0.949) 		0.24
(0.86) 		0.402
(0.892) 		0.907
(1.00) 		0.375
(0.892) 		0.0457
(0.598) 		1
(1.00) 		0.614
(0.941) 		0.549
(0.927) 		0.102
(0.715) 		0.55
(0.927) 		1
(1.00)
amp 11q13 3 182 (37%) 311 0.729
(0.965) 		0.728
(0.965) 		0.456
(0.893) 		0.408
(0.892) 		0.626
(0.949) 		0.434
(0.892) 		0.165
(0.797) 		0.588
(0.937) 		0.569
(0.929) 		0.146
(0.783) 		0.84
(0.992) 		0.482
(0.898) 		0.8
(0.984) 		0.427
(0.892) 		1
(1.00)
amp 12p13 33 251 (51%) 242 0.447
(0.893) 		0.909
(1.00) 		0.205
(0.827) 		0.102
(0.715) 		0.287
(0.885) 		0.449
(0.893) 		0.0307
(0.544) 		0.253
(0.86) 		0.716
(0.965) 		0.41
(0.892) 		0.946
(1.00) 		0.819
(0.99) 		0.847
(0.996) 		0.157
(0.786) 		1
(1.00)
amp 12q15 173 (35%) 320 0.744
(0.965) 		0.602
(0.937) 		0.723
(0.965) 		0.831
(0.991) 		0.518
(0.917) 		1
(1.00) 		0.107
(0.733) 		0.239
(0.86) 		0.855
(1.00) 		0.557
(0.927) 		0.674
(0.963) 		0.774
(0.975) 		0.983
(1.00) 		0.577
(0.933) 		0.467
(0.893)
amp 13q34 86 (17%) 407 0.485
(0.899) 		0.228
(0.848) 		0.528
(0.917) 		0.109
(0.74) 		0.243
(0.86) 		1
(1.00) 		0.497
(0.909) 		0.814
(0.99) 		0.0552
(0.605) 		1
(1.00) 		0.249
(0.86) 		0.541
(0.927) 		0.438
(0.892) 		0.675
(0.963) 		1
(1.00)
amp 14q13 3 157 (32%) 336 0.123
(0.767) 		0.00678
(0.389) 		0.168
(0.797) 		0.31
(0.892) 		0.135
(0.779) 		1
(1.00) 		0.912
(1.00) 		0.58
(0.933) 		0.907
(1.00) 		0.764
(0.973) 		0.36
(0.892) 		0.593
(0.937) 		0.434
(0.892) 		0.958
(1.00) 		0.00975
(0.41)
amp 14q32 33 155 (31%) 338 0.1
(0.715) 		0.357
(0.892) 		0.483
(0.898) 		0.0201
(0.471) 		0.819
(0.99) 		0.685
(0.963) 		0.222
(0.842) 		0.83
(0.991) 		0.829
(0.991) 		0.763
(0.973) 		0.465
(0.893) 		0.642
(0.956) 		0.715
(0.965) 		0.754
(0.971) 		0.0507
(0.598)
amp 15q26 3 175 (35%) 318 0.281
(0.881) 		0.238
(0.86) 		0.806
(0.987) 		0.258
(0.86) 		0.0986
(0.715) 		0.715
(0.965) 		0.392
(0.892) 		0.613
(0.941) 		0.3
(0.892) 		1
(1.00) 		0.828
(0.991) 		0.868
(1.00) 		0.353
(0.892) 		0.417
(0.892) 		0.719
(0.965)
amp 17q25 1 231 (47%) 262 0.383
(0.892) 		0.132
(0.776) 		0.0312
(0.544) 		0.00234
(0.269) 		0.0026
(0.269) 		0.264
(0.86) 		0.00281
(0.269) 		0.71
(0.965) 		0.371
(0.892) 		0.4
(0.892) 		0.779
(0.975) 		0.00383
(0.318) 		0.479
(0.895) 		0.549
(0.927) 		0.735
(0.965)
amp 18p11 32 178 (36%) 315 0.736
(0.965) 		0.0918
(0.715) 		0.808
(0.988) 		0.249
(0.86) 		0.372
(0.892) 		1
(1.00) 		0.335
(0.892) 		0.217
(0.834) 		0.881
(1.00) 		0.241
(0.86) 		0.743
(0.965) 		0.14
(0.783) 		0.318
(0.892) 		0.0961
(0.715) 		0.717
(0.965)
amp 18q11 2 150 (30%) 343 0.887
(1.00) 		0.364
(0.892) 		0.833
(0.992) 		0.103
(0.715) 		0.00991
(0.41) 		0.445
(0.892) 		1
(1.00) 		0.04
(0.572) 		0.901
(1.00) 		0.229
(0.848) 		0.845
(0.994) 		0.85
(0.998) 		0.666
(0.963) 		0.351
(0.892) 		1
(1.00)
amp 19q12 219 (44%) 274 0.278
(0.881) 		0.522
(0.917) 		0.047
(0.598) 		0.52
(0.917) 		0.0173
(0.458) 		0.707
(0.965) 		0.3
(0.892) 		0.836
(0.992) 		0.408
(0.892) 		0.262
(0.86) 		0.165
(0.797) 		0.0485
(0.598) 		0.804
(0.987) 		0.618
(0.944) 		1
(1.00)
amp 19q13 2 231 (47%) 262 0.321
(0.892) 		0.488
(0.902) 		0.492
(0.904) 		0.228
(0.848) 		0.163
(0.797) 		1
(1.00) 		0.018
(0.458) 		0.214
(0.834) 		0.116
(0.753) 		0.4
(0.892) 		0.0303
(0.544) 		0.00848
(0.41) 		0.958
(1.00) 		0.856
(1.00) 		0.734
(0.965)
amp 20p12 2 274 (56%) 219 0.169
(0.797) 		0.145
(0.783) 		0.231
(0.852) 		0.0289
(0.544) 		0.815
(0.99) 		0.145
(0.783) 		0.00269
(0.269) 		0.262
(0.86) 		0.709
(0.965) 		1
(1.00) 		0.484
(0.899) 		0.558
(0.927) 		0.782
(0.975) 		0.762
(0.973) 		0.0748
(0.675)
amp 22q11 21 251 (51%) 242 0.101
(0.715) 		0.204
(0.827) 		0.0205
(0.472) 		0.0949
(0.715) 		0.122
(0.767) 		0.456
(0.893) 		0.123
(0.767) 		0.51
(0.914) 		0.189
(0.823) 		0.41
(0.892) 		0.143
(0.783) 		0.04
(0.572) 		0.0517
(0.602) 		0.0896
(0.715) 		1
(1.00)
del 1p36 11 223 (45%) 270 0.144
(0.783) 		0.013
(0.415) 		0.303
(0.892) 		0.524
(0.917) 		0.269
(0.868) 		1
(1.00) 		0.0383
(0.572) 		0.203
(0.827) 		0.32
(0.892) 		0.581
(0.933) 		0.952
(1.00) 		0.0492
(0.598) 		0.91
(1.00) 		0.96
(1.00) 		0.474
(0.894)
del 1p13 1 216 (44%) 277 0.931
(1.00) 		0.00226
(0.269) 		0.434
(0.892) 		0.928
(1.00) 		0.0466
(0.598) 		0.466
(0.893) 		0.255
(0.86) 		0.351
(0.892) 		0.963
(1.00) 		0.405
(0.892) 		0.347
(0.892) 		0.0184
(0.458) 		0.767
(0.973) 		0.387
(0.892) 		0.0825
(0.703)
del 2p25 3 49 (10%) 444 0.83
(0.991) 		0.117
(0.753) 		0.245
(0.86) 		0.111
(0.741) 		0.218
(0.834) 		0.541
(0.927) 		0.301
(0.892) 		0.133
(0.776) 		0.253
(0.86) 		1
(1.00) 		0.468
(0.893) 		0.766
(0.973) 		0.931
(1.00) 		0.0576
(0.611) 		0.54
(0.927)
del 2q37 1 154 (31%) 339 0.544
(0.927) 		0.00591
(0.387) 		0.845
(0.994) 		0.823
(0.991) 		0.152
(0.783) 		0.68
(0.963) 		0.374
(0.892) 		0.622
(0.948) 		0.875
(1.00) 		0.362
(0.892) 		0.786
(0.975) 		0.0176
(0.458) 		0.465
(0.893) 		0.915
(1.00) 		0.706
(0.965)
del 3p25 3 390 (79%) 103 0.638
(0.954) 		0.381
(0.892) 		0.716
(0.965) 		0.748
(0.965) 		0.397
(0.892) 		1
(1.00) 		0.705
(0.965) 		0.361
(0.892) 		0.0706
(0.652) 		0.319
(0.892) 		0.38
(0.892) 		0.521
(0.917) 		0.573
(0.931) 		0.475
(0.894) 		1
(1.00)
del 3p13 426 (86%) 67 0.666
(0.963) 		0.496
(0.908) 		0.343
(0.892) 		0.65
(0.959) 		0.917
(1.00) 		0.6
(0.937) 		0.652
(0.959) 		0.13
(0.776) 		0.088
(0.715) 		1
(1.00) 		0.624
(0.948) 		0.602
(0.937) 		0.193
(0.824) 		0.0443
(0.598) 		0.607
(0.941)
del 3p12 3 419 (85%) 74 0.513
(0.915) 		0.444
(0.892) 		0.568
(0.929) 		0.438
(0.892) 		0.778
(0.975) 		0.601
(0.937) 		0.567
(0.929) 		0.0459
(0.598) 		0.15
(0.783) 		1
(1.00) 		0.688
(0.963) 		0.845
(0.994) 		0.285
(0.882) 		0.112
(0.741) 		0.363
(0.892)
del 3p12 3 413 (84%) 80 0.719
(0.965) 		0.381
(0.892) 		0.55
(0.927) 		0.307
(0.892) 		0.559
(0.927) 		0.607
(0.941) 		0.678
(0.963) 		0.0848
(0.708) 		0.206
(0.827) 		1
(1.00) 		0.844
(0.994) 		0.819
(0.99) 		0.394
(0.892) 		0.114
(0.741) 		0.361
(0.892)
del 3q11 1 78 (16%) 415 0.0306
(0.544) 		0.717
(0.965) 		0.603
(0.937) 		0.503
(0.909) 		0.702
(0.965) 		0.279
(0.881) 		0.888
(1.00) 		0.342
(0.892) 		0.231
(0.852) 		0.703
(0.965) 		0.174
(0.804) 		0.473
(0.894) 		0.661
(0.963) 		0.926
(1.00) 		0.0332
(0.544)
del 4p15 2 312 (63%) 181 0.295
(0.892) 		0.145
(0.783) 		0.631
(0.949) 		0.155
(0.786) 		0.746
(0.965) 		0.713
(0.965) 		0.393
(0.892) 		0.885
(1.00) 		0.196
(0.827) 		0.146
(0.783) 		0.804
(0.987) 		0.384
(0.892) 		0.546
(0.927) 		0.0845
(0.708) 		1
(1.00)
del 4q22 1 280 (57%) 213 0.248
(0.86) 		0.34
(0.892) 		0.0189
(0.463) 		0.0561
(0.605) 		0.525
(0.917) 		0.249
(0.86) 		0.35
(0.892) 		0.97
(1.00) 		0.338
(0.892) 		0.0477
(0.598) 		0.0611
(0.616) 		0.824
(0.991) 		0.594
(0.937) 		0.195
(0.827) 		0.735
(0.965)
del 4q32 3 321 (65%) 172 0.372
(0.892) 		0.168
(0.797) 		0.0109
(0.41) 		0.0194
(0.464) 		0.434
(0.892) 		0.249
(0.86) 		0.388
(0.892) 		0.595
(0.937) 		0.0221
(0.5) 		0.236
(0.857) 		0.107
(0.733) 		0.658
(0.963) 		0.594
(0.937) 		0.354
(0.892) 		1
(1.00)
del 4q35 2 323 (66%) 170 0.874
(1.00) 		0.5
(0.909) 		0.0273
(0.544) 		0.13
(0.776) 		0.16
(0.795) 		0.243
(0.86) 		0.746
(0.965) 		0.61
(0.941) 		0.0622
(0.616) 		0.235
(0.857) 		0.0604
(0.616) 		0.964
(1.00) 		0.727
(0.965) 		0.242
(0.86) 		1
(1.00)
del 5q12 1 362 (73%) 131 0.878
(1.00) 		0.798
(0.982) 		0.554
(0.927) 		0.283
(0.882) 		0.383
(0.892) 		0.197
(0.827) 		0.0622
(0.616) 		0.88
(1.00) 		0.295
(0.892) 		0.2
(0.827) 		0.467
(0.893) 		0.125
(0.77) 		0.381
(0.892) 		0.0695
(0.652) 		1
(1.00)
del 5q31 1 379 (77%) 114 0.83
(0.991) 		0.267
(0.864) 		0.169
(0.797) 		0.716
(0.965) 		0.692
(0.965) 		0.36
(0.892) 		0.394
(0.892) 		0.579
(0.933) 		0.334
(0.892) 		0.316
(0.892) 		0.895
(1.00) 		0.0638
(0.625) 		0.426
(0.892) 		0.0927
(0.715) 		1
(1.00)
del 6p25 3 132 (27%) 361 0.714
(0.965) 		0.281
(0.881) 		0.211
(0.83) 		0.771
(0.974) 		0.417
(0.892) 		0.399
(0.892) 		0.201
(0.827) 		0.574
(0.931) 		0.92
(1.00) 		0.529
(0.917) 		0.806
(0.987) 		0.769
(0.974) 		0.189
(0.823) 		0.532
(0.921) 		0.219
(0.836)
del 6q22 31 121 (25%) 372 0.294
(0.892) 		0.303
(0.892) 		0.142
(0.783) 		0.126
(0.773) 		0.916
(1.00) 		1
(1.00) 		1
(1.00) 		0.564
(0.929) 		0.416
(0.892) 		0.531
(0.92) 		0.666
(0.963) 		0.0554
(0.605) 		0.305
(0.892) 		0.95
(1.00) 		1
(1.00)
del 6q26 132 (27%) 361 0.528
(0.917) 		0.635
(0.951) 		0.952
(1.00) 		0.82
(0.99) 		0.739
(0.965) 		0.679
(0.963) 		0.727
(0.965) 		0.9
(1.00) 		0.68
(0.963) 		0.754
(0.971) 		0.426
(0.892) 		0.189
(0.823) 		0.469
(0.893) 		0.903
(1.00) 		1
(1.00)
del 7q11 22 46 (9%) 447 0.772
(0.975) 		0.435
(0.892) 		0.414
(0.892) 		0.95
(1.00) 		0.928
(1.00) 		1
(1.00) 		0.724
(0.965) 		0.256
(0.86) 		1
(1.00) 		0.346
(0.892) 		0.922
(1.00) 		0.969
(1.00) 		0.34
(0.892) 		1
(1.00) 		1
(1.00)
del 7q36 3 101 (20%) 392 0.879
(1.00) 		0.113
(0.741) 		0.54
(0.927) 		0.517
(0.917) 		0.6
(0.937) 		0.354
(0.892) 		1
(1.00) 		0.567
(0.929) 		0.351
(0.892) 		0.735
(0.965) 		0.37
(0.892) 		0.0173
(0.458) 		0.599
(0.937) 		0.612
(0.941) 		0.665
(0.963)
del 8p23 2 336 (68%) 157 0.597
(0.937) 		0.00496
(0.386) 		0.254
(0.86) 		0.61
(0.941) 		0.218
(0.834) 		0.202
(0.827) 		0.322
(0.892) 		0.22
(0.837) 		0.402
(0.892) 		0.764
(0.973) 		0.423
(0.892) 		0.668
(0.963) 		0.573
(0.931) 		0.641
(0.956) 		1
(1.00)
del 9p23 325 (66%) 168 0.916
(1.00) 		0.556
(0.927) 		0.457
(0.893) 		0.554
(0.927) 		0.422
(0.892) 		0.43
(0.892) 		0.233
(0.854) 		0.347
(0.892) 		0.0252
(0.514) 		0.771
(0.974) 		0.388
(0.892) 		0.559
(0.927) 		0.926
(1.00) 		0.257
(0.86) 		0.452
(0.893)
del 9p21 3 381 (77%) 112 0.461
(0.893) 		0.717
(0.965) 		0.1
(0.715) 		0.882
(1.00) 		0.0175
(0.458) 		1
(1.00) 		0.0859
(0.713) 		0.396
(0.892) 		0.00901
(0.41) 		0.504
(0.909) 		0.527
(0.917) 		0.957
(1.00) 		0.418
(0.892) 		0.724
(0.965) 		0.408
(0.892)
del 9p21 1 320 (65%) 173 0.741
(0.965) 		0.334
(0.892) 		0.0495
(0.598) 		0.259
(0.86) 		0.371
(0.892) 		0.258
(0.86) 		0.915
(1.00) 		0.349
(0.892) 		0.0103
(0.41) 		0.393
(0.892) 		0.188
(0.823) 		0.609
(0.941) 		0.593
(0.937) 		0.271
(0.872) 		0.446
(0.893)
del 9q21 11 248 (50%) 245 0.44
(0.892) 		0.00718
(0.389) 		0.904
(1.00) 		0.305
(0.892) 		0.865
(1.00) 		0.721
(0.965) 		0.15
(0.783) 		0.124
(0.768) 		0.058
(0.611) 		0.172
(0.797) 		0.879
(1.00) 		0.162
(0.797) 		0.122
(0.767) 		0.629
(0.949) 		0.0669
(0.636)
del 10p15 2 216 (44%) 277 0.2
(0.827) 		0.684
(0.963) 		0.665
(0.963) 		0.649
(0.959) 		0.986
(1.00) 		0.141
(0.783) 		0.756
(0.972) 		0.864
(1.00) 		0.962
(1.00) 		1
(1.00) 		0.444
(0.892) 		0.178
(0.811) 		0.886
(1.00) 		0.47
(0.894) 		1
(1.00)
del 10q23 31 264 (54%) 229 0.133
(0.776) 		0.899
(1.00) 		0.736
(0.965) 		0.298
(0.892) 		0.744
(0.965) 		0.0548
(0.605) 		0.0642
(0.625) 		0.513
(0.915) 		0.576
(0.933) 		0.779
(0.975) 		0.52
(0.917) 		0.694
(0.965) 		0.795
(0.982) 		0.473
(0.894) 		1
(1.00)
del 11p15 5 242 (49%) 251 0.458
(0.893) 		0.258
(0.86) 		0.442
(0.892) 		0.072
(0.659) 		0.684
(0.963) 		0.724
(0.965) 		0.217
(0.834) 		0.0118
(0.413) 		0.983
(1.00) 		0.41
(0.892) 		0.432
(0.892) 		0.99
(1.00) 		0.848
(0.996) 		0.179
(0.812) 		0.292
(0.892)
del 11q22 1 159 (32%) 334 0.786
(0.975) 		0.819
(0.99) 		0.255
(0.86) 		0.348
(0.892) 		0.0509
(0.598) 		1
(1.00) 		0.322
(0.892) 		0.797
(0.982) 		0.856
(1.00) 		1
(1.00) 		0.614
(0.941) 		0.757
(0.972) 		0.648
(0.959) 		0.837
(0.992) 		0.723
(0.965)
del 11q25 182 (37%) 311 0.776
(0.975) 		0.476
(0.894) 		0.52
(0.917) 		0.319
(0.892) 		0.0507
(0.598) 		1
(1.00) 		0.109
(0.74) 		0.641
(0.956) 		0.567
(0.929) 		1
(1.00) 		0.361
(0.892) 		0.581
(0.933) 		0.68
(0.963) 		0.811
(0.988) 		0.715
(0.965)
del 12q24 31 83 (17%) 410 0.0839
(0.708) 		0.345
(0.892) 		0.0584
(0.611) 		0.114
(0.741) 		0.383
(0.892) 		1
(1.00) 		0.169
(0.797) 		0.353
(0.892) 		0.792
(0.98) 		1
(1.00) 		0.14
(0.783) 		0.432
(0.892) 		0.428
(0.892) 		0.0405
(0.572) 		0.363
(0.892)
del 13q12 11 329 (67%) 164 0.634
(0.951) 		0.396
(0.892) 		0.0251
(0.514) 		0.167
(0.797) 		0.723
(0.965) 		0.688
(0.963) 		0.743
(0.965) 		0.686
(0.963) 		0.092
(0.715) 		0.559
(0.927) 		0.733
(0.965) 		0.0547
(0.605) 		0.739
(0.965) 		0.462
(0.893) 		0.266
(0.864)
del 13q14 2 340 (69%) 153 0.562
(0.929) 		0.644
(0.957) 		0.3
(0.892) 		0.797
(0.982) 		0.824
(0.991) 		0.435
(0.892) 		0.505
(0.909) 		0.545
(0.927) 		0.0182
(0.458) 		0.362
(0.892) 		0.528
(0.917) 		0.673
(0.963) 		0.786
(0.975) 		0.304
(0.892) 		0.0545
(0.605)
del 14q11 2 172 (35%) 321 0.0336
(0.544) 		0.454
(0.893) 		0.334
(0.892) 		0.191
(0.823) 		0.854
(1.00) 		0.101
(0.715) 		0.829
(0.991) 		0.986
(1.00) 		0.192
(0.823) 		0.775
(0.975) 		0.553
(0.927) 		0.81
(0.988) 		0.882
(1.00) 		0.596
(0.937) 		0.717
(0.965)
del 15q11 2 165 (33%) 328 0.299
(0.892) 		0.121
(0.767) 		0.0251
(0.514) 		0.392
(0.892) 		0.0119
(0.413) 		0.689
(0.963) 		0.103
(0.715) 		0.246
(0.86) 		0.499
(0.909) 		0.375
(0.892) 		0.416
(0.892) 		0.565
(0.929) 		0.717
(0.965) 		0.209
(0.827) 		1
(1.00)
del 15q21 1 168 (34%) 325 0.58
(0.933) 		0.101
(0.715) 		0.0356
(0.569) 		0.557
(0.927) 		0.0107
(0.41) 		0.689
(0.963) 		0.329
(0.892) 		0.319
(0.892) 		0.207
(0.827) 		0.381
(0.892) 		0.525
(0.917) 		0.402
(0.892) 		0.81
(0.988) 		0.0944
(0.715) 		0.72
(0.965)
del 16p13 3 184 (37%) 309 0.355
(0.892) 		0.0704
(0.652) 		0.204
(0.827) 		0.149
(0.783) 		0.417
(0.892) 		1
(1.00) 		0.596
(0.937) 		0.905
(1.00) 		0.39
(0.892) 		1
(1.00) 		0.301
(0.892) 		0.368
(0.892) 		0.0663
(0.635) 		0.316
(0.892) 		1
(1.00)
del 16q23 1 204 (41%) 289 0.154
(0.785) 		0.995
(1.00) 		0.596
(0.937) 		0.227
(0.848) 		0.834
(0.992) 		0.704
(0.965) 		0.21
(0.828) 		0.514
(0.915) 		0.143
(0.783) 		0.159
(0.795) 		0.033
(0.544) 		0.362
(0.892) 		0.817
(0.99) 		0.427
(0.892) 		0.475
(0.894)
del 17p11 2 268 (54%) 225 0.701
(0.965) 		0.176
(0.804) 		0.903
(1.00) 		0.492
(0.904) 		0.509
(0.914) 		0.461
(0.893) 		0.303
(0.892) 		0.808
(0.988) 		0.46
(0.893) 		0.156
(0.786) 		0.00567
(0.387) 		0.204
(0.827) 		0.476
(0.894) 		0.923
(1.00) 		1
(1.00)
del 17q11 2 131 (27%) 362 0.428
(0.892) 		0.0505
(0.598) 		0.198
(0.827) 		0.218
(0.834) 		0.00353
(0.314) 		0.381
(0.892) 		0.485
(0.899) 		0.952
(1.00) 		0.386
(0.892) 		0.529
(0.917) 		0.456
(0.893) 		0.315
(0.892) 		0.375
(0.892) 		0.167
(0.797) 		0.689
(0.963)
del 17q25 3 101 (20%) 392 0.189
(0.823) 		0.133
(0.776) 		0.465
(0.893) 		0.148
(0.783) 		0.144
(0.783) 		0.353
(0.892) 		0.372
(0.892) 		0.38
(0.892) 		0.881
(1.00) 		0.735
(0.965) 		0.885
(1.00) 		0.0656
(0.633) 		0.585
(0.937) 		0.329
(0.892) 		0.381
(0.892)
del 18q23 231 (47%) 262 0.403
(0.892) 		0.0499
(0.598) 		0.258
(0.86) 		0.19
(0.823) 		0.55
(0.927) 		0.261
(0.86) 		0.00281
(0.269) 		0.264
(0.86) 		0.933
(1.00) 		1
(1.00) 		0.831
(0.991) 		0.117
(0.753) 		0.422
(0.892) 		0.924
(1.00) 		0.479
(0.895)
del 19p13 3 229 (46%) 264 0.631
(0.949) 		0.758
(0.972) 		0.729
(0.965) 		0.872
(1.00) 		0.0983
(0.715) 		1
(1.00) 		0.256
(0.86) 		0.28
(0.881) 		0.82
(0.99) 		1
(1.00) 		0.344
(0.892) 		0.502
(0.909) 		0.908
(1.00) 		0.0766
(0.676) 		0.726
(0.965)
del 19q13 32 144 (29%) 349 0.87
(1.00) 		0.207
(0.827) 		0.961
(1.00) 		0.829
(0.991) 		0.701
(0.965) 		1
(1.00) 		0.0707
(0.652) 		0.957
(1.00) 		0.214
(0.834) 		0.537
(0.927) 		0.686
(0.963) 		0.0501
(0.598) 		0.175
(0.804) 		0.684
(0.963) 		1
(1.00)
del 21q11 2 241 (49%) 252 0.374
(0.892) 		0.572
(0.931) 		0.13
(0.776) 		0.947
(1.00) 		0.424
(0.892) 		0.449
(0.893) 		0.0237
(0.514) 		0.744
(0.965) 		0.564
(0.929) 		0.262
(0.86) 		0.781
(0.975) 		0.569
(0.929) 		0.791
(0.98) 		0.702
(0.965) 		0.156
(0.786)
del 21q22 3 274 (56%) 219 0.689
(0.963) 		0.311
(0.892) 		0.424
(0.892) 		0.477
(0.895) 		0.874
(1.00) 		0.247
(0.86) 		0.00269
(0.269) 		0.264
(0.86) 		0.757
(0.972) 		1
(1.00) 		0.963
(1.00) 		0.363
(0.892) 		1
(1.00) 		0.267
(0.864) 		0.295
(0.892)
del 22q11 21 93 (19%) 400 0.26
(0.86) 		0.00878
(0.41) 		0.471
(0.894) 		0.929
(1.00) 		0.432
(0.892) 		0.361
(0.892) 		0.895
(1.00) 		0.545
(0.927) 		0.432
(0.892) 		0.28
(0.881) 		0.896
(1.00) 		0.0909
(0.715) 		0.343
(0.892) 		0.465
(0.893) 		1
(1.00)
del 22q13 32 125 (25%) 368 0.975
(1.00) 		0.0139
(0.431) 		0.452
(0.893) 		0.586
(0.937) 		0.258
(0.86) 		1
(1.00) 		0.407
(0.892) 		0.837
(0.992) 		0.17
(0.797) 		0.747
(0.965) 		0.369
(0.892) 		0.0905
(0.715) 		0.807
(0.987) 		0.693
(0.965) 		0.686
(0.963)
del xp22 2 151 (31%) 342 0.404
(0.892) 		0.721
(0.965) 		0.0553
(0.605) 		0.272
(0.873) 		0.0984
(0.715) 		0.445
(0.892) 		0.146
(0.783) 		0.229
(0.848) 		0.474
(0.894) 		0.549
(0.927) 		0.6
(0.937) 		0.49
(0.904) 		0.747
(0.965) 		0.43
(0.892) 		0.445
(0.892)
del xp21 1 148 (30%) 345 0.615
(0.942) 		0.0781
(0.676) 		0.761
(0.973) 		0.48
(0.896) 		0.277
(0.881) 		0.68
(0.963) 		0.503
(0.909) 		0.274
(0.878) 		0.559
(0.927) 		1
(1.00) 		0.863
(1.00) 		0.909
(1.00) 		0.617
(0.944) 		0.652
(0.959) 		0.448
(0.893)
del xp11 3 144 (29%) 349 0.92
(1.00) 		0.747
(0.965) 		0.611
(0.941) 		0.184
(0.823) 		0.432
(0.892) 		0.679
(0.963) 		0.91
(1.00) 		0.128
(0.776) 		0.833
(0.992) 		1
(1.00) 		0.966
(1.00) 		0.226
(0.848) 		0.558
(0.927) 		0.785
(0.975) 		0.686
(0.963)
del xq22 3 111 (23%) 382 0.491
(0.904) 		0.522
(0.917) 		0.684
(0.963) 		0.286
(0.884) 		0.501
(0.909) 		1
(1.00) 		0.217
(0.834) 		0.693
(0.965) 		0.164
(0.797) 		1
(1.00) 		0.0334
(0.544) 		0.342
(0.892) 		0.0772
(0.676) 		0.0945
(0.715) 		0.361
(0.892)
'amp_7p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #10: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 111 290 69 23
AMP PEAK 10(7P11.2) MUTATED 39 169 35 9
AMP PEAK 10(7P11.2) WILD-TYPE 72 121 34 14

Figure S1.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_20q11.21' versus 'GENDER'

P value = 0.000133 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #28: 'amp_20q11.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 127 366
AMP PEAK 28(20Q11.21) MUTATED 59 242
AMP PEAK 28(20Q11.21) WILD-TYPE 68 124

Figure S2.  Get High-res Image Gene #28: 'amp_20q11.21' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 6e-04 (Fisher's exact test), Q value = 0.19

Table S3.  Gene #30: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 111 290 69 23
AMP PEAK 30(XQ28) MUTATED 13 76 23 9
AMP PEAK 30(XQ28) WILD-TYPE 98 214 46 14

Figure S3.  Get High-res Image Gene #30: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000574 (Wilcoxon-test), Q value = 0.19

Table S4.  Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 67.3 (8.6)
DEL PEAK 4(2Q22.1) MUTATED 127 65.4 (8.1)
DEL PEAK 4(2Q22.1) WILD-TYPE 357 68.0 (8.6)

Figure S4.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/15093660/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 focal cnvs = 83

  • Number of selected clinical features = 15

  • 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

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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