Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C13T9G1X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C13T9G1X
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 57 arm-level events and 17 clinical features across 486 patients, 8 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'AGE',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 5p gain cnv correlated to 'AGE'.

  • 5q gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 20p gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 20q gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 11q loss cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 8 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATIONEXPOSURE EXTRATHYROIDAL
EXTENSION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		MULTIFOCALITY TUMOR
SIZE 		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 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 Wilcoxon-test Fisher's exact test Fisher's exact test
1q gain 24 (5%) 462 0.193
(1.00) 		9.33e-05
(0.0886) 		0.00012
(0.114) 		0.00013
(0.123) 		0.00115
(1.00) 		0.704
(1.00) 		0.478
(1.00) 		0.022
(1.00) 		0.513
(1.00) 		0.601
(1.00) 		0.00031
(0.292) 		0.0341
(1.00) 		0.0325
(1.00) 		0.0368
(1.00) 		0.0185
(1.00) 		0.00232
(1.00) 		0.259
(1.00)
5p gain 20 (4%) 466 0.108
(1.00) 		0.000239
(0.225) 		0.00337
(1.00) 		0.423
(1.00) 		0.202
(1.00) 		0.0041
(1.00) 		0.796
(1.00) 		0.135
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.0402
(1.00) 		0.5
(1.00) 		0.0263
(1.00) 		0.651
(1.00) 		0.0508
(1.00) 		0.47
(1.00) 		1
(1.00)
5q gain 16 (3%) 470 0.0208
(1.00) 		0.0113
(1.00) 		0.0053
(1.00) 		0.687
(1.00) 		0.00571
(1.00) 		0.00019
(0.179) 		0.773
(1.00) 		0.0422
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.0285
(1.00) 		0.409
(1.00) 		0.000546
(0.512) 		0.802
(1.00) 		0.134
(1.00) 		0.766
(1.00) 		0.607
(1.00)
20p gain 12 (2%) 474 0.33
(1.00) 		0.0798
(1.00) 		0.0105
(1.00) 		0.555
(1.00) 		0.0678
(1.00) 		0.00011
(0.104) 		0.528
(1.00) 		0.00425
(1.00) 		1
(1.00) 		1
(1.00) 		0.0229
(1.00) 		0.855
(1.00) 		0.005
(1.00) 		0.779
(1.00) 		0.087
(1.00) 		1
(1.00) 		1
(1.00)
20q gain 12 (2%) 474 0.33
(1.00) 		0.0798
(1.00) 		0.0105
(1.00) 		0.552
(1.00) 		0.0678
(1.00) 		0.00015
(0.142) 		0.528
(1.00) 		0.00434
(1.00) 		1
(1.00) 		1
(1.00) 		0.0218
(1.00) 		0.854
(1.00) 		0.005
(1.00) 		0.779
(1.00) 		0.087
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 9 (2%) 477 0.00326
(1.00) 		0.000181
(0.171) 		0.00347
(1.00) 		0.198
(1.00) 		0.503
(1.00) 		0.12
(1.00) 		0.00179
(1.00) 		1
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.797
(1.00) 		0.511
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.00211
(1.00) 		0.36
(1.00) 		1
(1.00)
1p gain 3 (1%) 483 0.921
(1.00) 		0.457
(1.00) 		0.0403
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.0783
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.969
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
3p gain 3 (1%) 483 0.0117
(1.00) 		0.0148
(1.00) 		0.0336
(1.00) 		0.118
(1.00) 		1
(1.00) 		0.0117
(1.00) 		0.569
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.0224
(1.00) 		1
(1.00) 		0.533
(1.00) 		1
(1.00)
4p gain 5 (1%) 481 0.025
(1.00) 		0.0283
(1.00) 		0.186
(1.00) 		0.631
(1.00) 		0.0611
(1.00) 		0.0293
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.137
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.0271
(1.00) 		0.185
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00)
4q gain 5 (1%) 481 0.025
(1.00) 		0.0283
(1.00) 		0.183
(1.00) 		0.631
(1.00) 		0.0611
(1.00) 		0.0286
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.137
(1.00) 		1
(1.00) 		1
(1.00) 		0.388
(1.00) 		0.0271
(1.00) 		0.185
(1.00) 		0.231
(1.00) 		1
(1.00) 		1
(1.00)
7p gain 17 (3%) 469 0.365
(1.00) 		0.0638
(1.00) 		0.00588
(1.00) 		0.793
(1.00) 		0.003
(1.00) 		0.00612
(1.00) 		1
(1.00) 		0.0179
(1.00) 		1
(1.00) 		1
(1.00) 		0.0099
(1.00) 		0.413
(1.00) 		0.000315
(0.296) 		1
(1.00) 		0.543
(1.00) 		0.766
(1.00) 		0.607
(1.00)
7q gain 19 (4%) 467 0.379
(1.00) 		0.0526
(1.00) 		0.00895
(1.00) 		0.947
(1.00) 		0.003
(1.00) 		0.00854
(1.00) 		0.792
(1.00) 		0.0114
(1.00) 		1
(1.00) 		1
(1.00) 		0.0219
(1.00) 		0.256
(1.00) 		0.000315
(0.296) 		1
(1.00) 		0.549
(1.00) 		0.641
(1.00) 		0.607
(1.00)
8p gain 6 (1%) 480 0.631
(1.00) 		0.652
(1.00) 		0.71
(1.00) 		0.906
(1.00) 		0.623
(1.00) 		0.19
(1.00) 		1
(1.00) 		0.785
(1.00) 		1
(1.00) 		1
(1.00) 		0.351
(1.00) 		0.457
(1.00) 		0.202
(1.00) 		0.225
(1.00) 		0.319
(1.00) 		0.633
(1.00) 		1
(1.00)
8q gain 7 (1%) 479 0.104
(1.00) 		0.345
(1.00) 		0.0561
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.0933
(1.00) 		0.681
(1.00) 		0.821
(1.00) 		1
(1.00) 		1
(1.00) 		0.00861
(1.00) 		0.386
(1.00) 		0.202
(1.00) 		0.131
(1.00) 		0.21
(1.00) 		0.699
(1.00) 		1
(1.00)
9p gain 3 (1%) 483 0.705
(1.00) 		0.0768
(1.00) 		0.0463
(1.00) 		0.806
(1.00) 		0.248
(1.00) 		0.608
(1.00) 		1
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.0577
(1.00) 		1
(1.00)
9q gain 4 (1%) 482 0.699
(1.00) 		0.0312
(1.00) 		0.0413
(1.00) 		0.63
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.338
(1.00) 		0.0237
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 6 (1%) 480 0.562
(1.00) 		0.759
(1.00) 		0.711
(1.00) 		0.696
(1.00) 		0.123
(1.00) 		0.19
(1.00) 		0.193
(1.00) 		0.255
(1.00) 		1
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.46
(1.00) 		0.0485
(1.00) 		0.225
(1.00) 		0.605
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 5 (1%) 481 0.565
(1.00) 		0.745
(1.00) 		0.796
(1.00) 		0.799
(1.00) 		0.248
(1.00) 		0.248
(1.00) 		0.612
(1.00) 		0.565
(1.00) 		1
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.386
(1.00) 		0.088
(1.00) 		0.0652
(1.00) 		0.982
(1.00) 		1
(1.00) 		1
(1.00)
12p gain 14 (3%) 472 0.516
(1.00) 		0.199
(1.00) 		0.0948
(1.00) 		0.916
(1.00) 		0.00176
(1.00) 		0.00066
(0.617) 		1
(1.00) 		0.0166
(1.00) 		1
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.455
(1.00) 		0.000949
(0.884) 		0.791
(1.00) 		0.925
(1.00) 		0.731
(1.00) 		1
(1.00)
12q gain 15 (3%) 471 0.516
(1.00) 		0.173
(1.00) 		0.127
(1.00) 		0.922
(1.00) 		0.00176
(1.00) 		0.00036
(0.338) 		0.769
(1.00) 		0.00661
(1.00) 		1
(1.00) 		1
(1.00) 		0.203
(1.00) 		0.544
(1.00) 		0.000949
(0.884) 		1
(1.00) 		0.925
(1.00) 		0.749
(1.00) 		1
(1.00)
13q gain 5 (1%) 481 0.732
(1.00) 		0.149
(1.00) 		0.0575
(1.00) 		0.705
(1.00) 		0.123
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.184
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0485
(1.00) 		0.665
(1.00) 		0.673
(1.00) 		1
(1.00)
14q gain 11 (2%) 475 0.539
(1.00) 		0.0343
(1.00) 		0.00668
(1.00) 		0.378
(1.00) 		0.0678
(1.00) 		0.0344
(1.00) 		0.302
(1.00) 		0.0625
(1.00) 		1
(1.00) 		1
(1.00) 		0.824
(1.00) 		0.492
(1.00) 		0.0671
(1.00) 		0.122
(1.00) 		0.253
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 15 (3%) 471 0.23
(1.00) 		0.193
(1.00) 		0.0384
(1.00) 		0.878
(1.00) 		0.0201
(1.00) 		0.016
(1.00) 		0.769
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00) 		0.0349
(1.00) 		0.128
(1.00) 		0.00165
(1.00) 		0.794
(1.00) 		0.651
(1.00) 		0.769
(1.00) 		1
(1.00)
16q gain 13 (3%) 473 0.222
(1.00) 		0.128
(1.00) 		0.0206
(1.00) 		0.713
(1.00) 		0.0372
(1.00) 		0.00997
(1.00) 		1
(1.00) 		0.0515
(1.00) 		1
(1.00) 		1
(1.00) 		0.0167
(1.00) 		0.235
(1.00) 		0.00287
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.731
(1.00) 		1
(1.00)
17p gain 16 (3%) 470 0.422
(1.00) 		0.078
(1.00) 		0.00386
(1.00) 		0.849
(1.00) 		0.036
(1.00) 		0.0086
(1.00) 		1
(1.00) 		0.0413
(1.00) 		1
(1.00) 		1
(1.00) 		0.767
(1.00) 		0.325
(1.00) 		0.0144
(1.00) 		1
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.607
(1.00)
17q gain 17 (3%) 469 0.422
(1.00) 		0.145
(1.00) 		0.00562
(1.00) 		0.863
(1.00) 		0.0206
(1.00) 		0.00558
(1.00) 		1
(1.00) 		0.0639
(1.00) 		1
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.327
(1.00) 		0.00847
(1.00) 		0.806
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.607
(1.00)
18p gain 6 (1%) 480 0.62
(1.00) 		0.717
(1.00) 		0.713
(1.00) 		0.699
(1.00) 		0.0611
(1.00) 		0.473
(1.00) 		0.658
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.0485
(1.00) 		0.692
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00)
18q gain 6 (1%) 480 0.62
(1.00) 		0.717
(1.00) 		0.711
(1.00) 		0.697
(1.00) 		0.0611
(1.00) 		0.474
(1.00) 		0.658
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.39
(1.00) 		0.0485
(1.00) 		0.692
(1.00) 		0.789
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 8 (2%) 478 0.735
(1.00) 		0.0519
(1.00) 		0.623
(1.00) 		0.581
(1.00) 		0.0302
(1.00) 		0.00245
(1.00) 		0.217
(1.00) 		0.00852
(1.00) 		1
(1.00) 		1
(1.00) 		0.592
(1.00) 		0.456
(1.00) 		0.00874
(1.00) 		0.151
(1.00) 		0.147
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 10 (2%) 476 0.0315
(1.00) 		0.0154
(1.00) 		0.602
(1.00) 		0.318
(1.00) 		0.0149
(1.00) 		0.00088
(0.821) 		0.139
(1.00) 		0.00538
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.684
(1.00) 		0.005
(1.00) 		0.524
(1.00) 		0.0771
(1.00) 		1
(1.00) 		1
(1.00)
21q gain 5 (1%) 481 0.62
(1.00) 		0.317
(1.00) 		0.578
(1.00) 		0.557
(1.00) 		0.248
(1.00) 		0.689
(1.00) 		0.612
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.311
(1.00) 		0.088
(1.00) 		0.0652
(1.00) 		0.129
(1.00) 		1
(1.00) 		1
(1.00)
xq gain 9 (2%) 477 0.0849
(1.00) 		0.0536
(1.00) 		0.015
(1.00) 		0.485
(1.00) 		0.285
(1.00) 		0.0242
(1.00) 		0.456
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.309
(1.00) 		0.0231
(1.00) 		0.0826
(1.00) 		0.108
(1.00) 		0.313
(1.00) 		0.45
(1.00) 		1
(1.00) 		1
(1.00)
1p loss 4 (1%) 482 0.604
(1.00) 		0.539
(1.00) 		0.154
(1.00) 		0.63
(1.00) 		0.248
(1.00) 		0.372
(1.00) 		0.578
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.11
(1.00) 		0.452
(1.00) 		1
(1.00)
1q loss 3 (1%) 483 0.608
(1.00) 		0.816
(1.00) 		0.332
(1.00) 		0.692
(1.00) 		0.499
(1.00) 		0.137
(1.00) 		0.569
(1.00) 		0.23
(1.00) 		1
(1.00) 		1
(1.00) 		0.608
(1.00) 		1
(1.00) 		1
(1.00) 		0.11
(1.00) 		1
(1.00)
2p loss 10 (2%) 476 0.722
(1.00) 		0.28
(1.00) 		0.0283
(1.00) 		0.695
(1.00) 		0.00732
(1.00) 		0.0141
(1.00) 		0.729
(1.00) 		0.00575
(1.00) 		1
(1.00) 		1
(1.00) 		0.145
(1.00) 		0.555
(1.00) 		0.00287
(1.00) 		1
(1.00) 		0.986
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 10 (2%) 476 0.579
(1.00) 		0.256
(1.00) 		0.0277
(1.00) 		0.825
(1.00) 		0.0149
(1.00) 		0.013
(1.00) 		0.729
(1.00) 		0.00538
(1.00) 		1
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.556
(1.00) 		0.005
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 3 (1%) 483 0.664
(1.00) 		0.568
(1.00) 		0.332
(1.00) 		0.693
(1.00) 		0.499
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.643
(1.00) 		1
(1.00) 		1
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.0748
(1.00) 		1
(1.00) 		1
(1.00)
3q loss 4 (1%) 482 0.601
(1.00) 		0.593
(1.00) 		0.153
(1.00) 		0.631
(1.00) 		0.248
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.462
(1.00) 		1
(1.00) 		1
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.088
(1.00) 		1
(1.00) 		0.0896
(1.00) 		1
(1.00) 		1
(1.00)
6p loss 4 (1%) 482 0.636
(1.00) 		0.32
(1.00) 		0.735
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.107
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.0547
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 7 (1%) 479 0.00749
(1.00) 		0.0784
(1.00) 		0.199
(1.00) 		0.79
(1.00) 		0.372
(1.00) 		0.00967
(1.00) 		0.389
(1.00) 		0.822
(1.00) 		0.186
(1.00) 		0.218
(1.00) 		0.384
(1.00) 		0.755
(1.00) 		0.202
(1.00) 		0.46
(1.00) 		0.00834
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 4 (1%) 482 0.873
(1.00) 		0.903
(1.00) 		0.175
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.369
(1.00) 		0.0591
(1.00) 		0.462
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.0485
(1.00) 		1
(1.00) 		0.728
(1.00) 		1
(1.00)
8q loss 4 (1%) 482 0.873
(1.00) 		0.903
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.372
(1.00) 		0.0591
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.0485
(1.00) 		1
(1.00) 		0.728
(1.00) 		1
(1.00)
9p loss 19 (4%) 467 0.481
(1.00) 		0.0918
(1.00) 		0.0282
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.0548
(1.00) 		0.297
(1.00) 		0.766
(1.00) 		1
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.563
(1.00) 		0.29
(1.00) 		0.486
(1.00) 		0.107
(1.00) 		0.733
(1.00) 		0.378
(1.00)
9q loss 23 (5%) 463 0.0433
(1.00) 		0.00485
(1.00) 		0.00063
(0.59) 		0.228
(1.00) 		0.493
(1.00) 		0.0259
(1.00) 		0.343
(1.00) 		0.723
(1.00) 		0.498
(1.00) 		0.601
(1.00) 		0.0793
(1.00) 		0.681
(1.00) 		0.507
(1.00) 		0.528
(1.00) 		0.0513
(1.00) 		0.78
(1.00) 		1
(1.00)
10p loss 7 (1%) 479 0.59
(1.00) 		0.327
(1.00) 		0.123
(1.00) 		0.243
(1.00) 		0.0302
(1.00) 		0.096
(1.00) 		0.389
(1.00) 		0.392
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		0.0271
(1.00) 		0.708
(1.00) 		0.0104
(1.00) 		0.632
(1.00) 		1
(1.00)
10q loss 6 (1%) 480 0.651
(1.00) 		0.305
(1.00) 		0.257
(1.00) 		0.31
(1.00) 		0.0611
(1.00) 		0.188
(1.00) 		0.193
(1.00) 		0.783
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0485
(1.00) 		0.421
(1.00) 		0.00765
(1.00) 		0.63
(1.00) 		1
(1.00)
11p loss 7 (1%) 479 0.00114
(1.00) 		0.000622
(0.583) 		0.00586
(1.00) 		0.216
(1.00) 		0.449
(1.00) 		0.0959
(1.00) 		0.0161
(1.00) 		0.822
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.524
(1.00) 		0.242
(1.00) 		0.708
(1.00) 		0.00714
(1.00) 		0.418
(1.00) 		1
(1.00)
13q loss 14 (3%) 472 0.372
(1.00) 		0.0292
(1.00) 		0.462
(1.00) 		0.562
(1.00) 		0.0108
(1.00) 		0.363
(1.00) 		0.538
(1.00) 		0.465
(1.00) 		0.34
(1.00) 		0.000713
(0.666) 		0.624
(1.00) 		0.67
(1.00) 		0.00689
(1.00) 		0.791
(1.00) 		0.0858
(1.00) 		1
(1.00) 		0.607
(1.00)
15q loss 8 (2%) 478 0.563
(1.00) 		0.76
(1.00) 		0.241
(1.00) 		0.685
(1.00) 		0.122
(1.00) 		0.0612
(1.00) 		0.688
(1.00) 		0.0535
(1.00) 		1
(1.00) 		1
(1.00) 		0.592
(1.00) 		0.784
(1.00) 		0.156
(1.00) 		0.731
(1.00) 		0.0706
(1.00) 		0.632
(1.00) 		0.412
(1.00)
17p loss 7 (1%) 479 0.579
(1.00) 		0.838
(1.00) 		0.259
(1.00) 		0.14
(1.00) 		0.449
(1.00) 		0.337
(1.00) 		0.681
(1.00) 		0.133
(1.00) 		0.0149
(1.00) 		0.25
(1.00) 		0.183
(1.00) 		0.752
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.04
(1.00) 		0.546
(1.00) 		1
(1.00)
17q loss 4 (1%) 482 0.807
(1.00) 		0.467
(1.00) 		0.473
(1.00) 		0.628
(1.00) 		0.123
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.111
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.088
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00)
18p loss 4 (1%) 482 0.76
(1.00) 		0.681
(1.00) 		0.176
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.628
(1.00) 		0.657
(1.00) 		0.191
(1.00)
18q loss 4 (1%) 482 0.76
(1.00) 		0.681
(1.00) 		0.176
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.628
(1.00) 		0.657
(1.00) 		0.191
(1.00)
19p loss 5 (1%) 481 0.123
(1.00) 		0.489
(1.00) 		0.251
(1.00) 		1
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.612
(1.00) 		1
(1.00) 		1
(1.00) 		0.014
(1.00) 		1
(1.00) 		0.632
(1.00) 		0.38
(1.00) 		0.00887
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 8 (2%) 478 0.85
(1.00) 		0.113
(1.00) 		0.0121
(1.00) 		0.174
(1.00) 		0.724
(1.00) 		0.774
(1.00) 		0.443
(1.00) 		0.856
(1.00) 		1
(1.00) 		1
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.151
(1.00) 		0.489
(1.00) 		0.302
(1.00) 		1
(1.00)
22q loss 85 (17%) 401 0.506
(1.00) 		0.771
(1.00) 		0.554
(1.00) 		0.474
(1.00) 		0.261
(1.00) 		0.58
(1.00) 		0.502
(1.00) 		0.271
(1.00) 		0.481
(1.00) 		0.332
(1.00) 		0.3
(1.00) 		0.483
(1.00) 		0.482
(1.00) 		0.276
(1.00) 		0.82
(1.00) 		0.666
(1.00) 		1
(1.00)
xq loss 3 (1%) 483 0.754
(1.00) 		0.418
(1.00) 		0.00625
(1.00) 		0.225
(1.00) 		0.248
(1.00) 		0.135
(1.00) 		0.173
(1.00) 		0.645
(1.00) 		1
(1.00) 		1
(1.00) 		0.608
(1.00) 		1
(1.00) 		0.088
(1.00) 		1
(1.00) 		1
(1.00)
'1q gain' versus 'AGE'

P value = 9.33e-05 (Wilcoxon-test), Q value = 0.089

Table S1.  Gene #2: '1q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 486 47.2 (15.6)
1Q GAIN MUTATED 24 60.2 (15.7)
1Q GAIN WILD-TYPE 462 46.5 (15.3)

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'AGE'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 275 50 107 2 44 6
1Q GAIN MUTATED 6 0 10 1 7 0
1Q GAIN WILD-TYPE 269 50 97 1 37 6

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 139 163 161 21
1Q GAIN MUTATED 2 3 15 4
1Q GAIN WILD-TYPE 137 160 146 17

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p gain' versus 'AGE'

P value = 0.000239 (Wilcoxon-test), Q value = 0.23

Table S4.  Gene #6: '5p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 486 47.2 (15.6)
5P GAIN MUTATED 20 60.8 (15.5)
5P GAIN WILD-TYPE 466 46.6 (15.4)

Figure S4.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #2: 'AGE'

'5q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.18

Table S5.  Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 267 9 209
5Q GAIN MUTATED 1 0 15
5Q GAIN WILD-TYPE 266 9 194

Figure S5.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 267 9 209
20P GAIN MUTATED 0 0 12
20P GAIN WILD-TYPE 267 9 197

Figure S6.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.14

Table S7.  Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 267 9 209
20Q GAIN MUTATED 0 0 12
20Q GAIN WILD-TYPE 267 9 197

Figure S7.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'11q loss' versus 'AGE'

P value = 0.000181 (Wilcoxon-test), Q value = 0.17

Table S8.  Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 486 47.2 (15.6)
11Q LOSS MUTATED 9 67.0 (8.9)
11Q LOSS WILD-TYPE 477 46.8 (15.5)

Figure S8.  Get High-res Image Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

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

  • Clinical data file = THCA-TP.merged_data.txt

  • Number of patients = 486

  • Number of significantly arm-level cnvs = 57

  • Number of selected clinical features = 17

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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