Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1H99437
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/C1H99437
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 79 arm-level events and 11 clinical features across 516 patients, 21 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 5p gain cnv correlated to 'AGE'.

  • 20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 20q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 3q loss cnv correlated to 'GENDER'.

  • 4p loss cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 4q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 5p loss cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 13q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 14q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 15q loss cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 18p loss cnv correlated to 'PATHOLOGY.T.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED 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 Wilcoxon-test Fisher's exact test Fisher's exact test
20p gain 110 (21%) 406 0.256
(1.00) 		0.264
(1.00) 		3e-05
(0.0227) 		1e-05
(0.00766) 		0.546
(1.00) 		0.00686
(1.00) 		0.00048
(0.355) 		0.973
(1.00) 		0.378
(1.00) 		0.442
(1.00)
20q gain 113 (22%) 403 0.12
(1.00) 		0.0911
(1.00) 		3e-05
(0.0227) 		2e-05
(0.0152) 		0.236
(1.00) 		0.00964
(1.00) 		0.00265
(1.00) 		0.973
(1.00) 		0.363
(1.00) 		0.318
(1.00)
4q loss 65 (13%) 451 0.905
(1.00) 		0.836
(1.00) 		1e-05
(0.00766) 		2e-05
(0.0152) 		0.463
(1.00) 		0.00185
(1.00) 		0.269
(1.00) 		0.477
(1.00) 		0.0531
(1.00) 		0.76
(1.00)
9p loss 147 (28%) 369 0.414
(1.00) 		0.0656
(1.00) 		2e-05
(0.0152) 		5e-05
(0.0377) 		0.103
(1.00) 		0.00215
(1.00) 		0.00054
(0.399) 		0.546
(1.00) 		0.797
(1.00) 		0.215
(1.00) 		0.654
(1.00)
9q loss 148 (29%) 368 0.86
(1.00) 		0.0465
(1.00) 		1e-05
(0.00766) 		2e-05
(0.0152) 		0.172
(1.00) 		0.00585
(1.00) 		0.000388
(0.288) 		0.317
(1.00) 		0.779
(1.00) 		0.187
(1.00) 		0.824
(1.00)
13q loss 70 (14%) 446 0.00637
(1.00) 		0.942
(1.00) 		0.00013
(0.0978) 		1e-05
(0.00766) 		0.492
(1.00) 		0.0559
(1.00) 		0.286
(1.00) 		0.949
(1.00) 		0.274
(1.00) 		0.228
(1.00)
14q loss 213 (41%) 303 0.0851
(1.00) 		0.254
(1.00) 		4e-05
(0.0302) 		6e-05
(0.0452) 		0.00233
(1.00) 		0.00186
(1.00) 		0.0199
(1.00) 		0.184
(1.00) 		0.251
(1.00) 		0.0471
(1.00) 		0.838
(1.00)
3q gain 60 (12%) 456 0.837
(1.00) 		0.918
(1.00) 		0.00103
(0.756) 		0.0001
(0.0753) 		0.00848
(1.00) 		0.00572
(1.00) 		0.671
(1.00) 		0.477
(1.00) 		0.535
(1.00) 		1
(1.00)
5p gain 191 (37%) 325 0.238
(1.00) 		0.000235
(0.176) 		0.108
(1.00) 		0.196
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.0175
(1.00) 		0.505
(1.00) 		0.119
(1.00) 		0.835
(1.00)
3q loss 97 (19%) 419 0.105
(1.00) 		0.0141
(1.00) 		0.481
(1.00) 		0.239
(1.00) 		0.747
(1.00) 		0.971
(1.00) 		0.000154
(0.115) 		0.38
(1.00) 		0.664
(1.00) 		0.783
(1.00)
4p loss 72 (14%) 444 0.559
(1.00) 		0.75
(1.00) 		0.00036
(0.268) 		0.00022
(0.165) 		0.731
(1.00) 		0.0357
(1.00) 		0.895
(1.00) 		0.609
(1.00) 		0.152
(1.00) 		0.564
(1.00)
5p loss 7 (1%) 509 0.251
(1.00) 		0.00167
(1.00) 		0.00022
(0.165) 		1
(1.00) 		0.138
(1.00) 		0.259
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 35 (7%) 481 0.975
(1.00) 		0.992
(1.00) 		0.00067
(0.493) 		0.00023
(0.172) 		1
(1.00) 		0.0228
(1.00) 		0.045
(1.00) 		0.943
(1.00) 		0.0776
(1.00) 		0.383
(1.00)
18p loss 92 (18%) 424 0.0341
(1.00) 		0.123
(1.00) 		0.00038
(0.283) 		0.00032
(0.239) 		1
(1.00) 		0.0747
(1.00) 		0.152
(1.00) 		0.826
(1.00) 		0.383
(1.00) 		0.0987
(1.00)
1p gain 24 (5%) 492 0.179
(1.00) 		0.168
(1.00) 		0.174
(1.00) 		0.286
(1.00) 		0.212
(1.00) 		0.464
(1.00) 		0.832
(1.00) 		0.482
(1.00) 		0.495
(1.00) 		1
(1.00)
1q gain 51 (10%) 465 0.577
(1.00) 		0.0301
(1.00) 		0.0627
(1.00) 		0.0998
(1.00) 		0.425
(1.00) 		0.815
(1.00) 		0.54
(1.00) 		0.763
(1.00) 		0.912
(1.00) 		0.733
(1.00)
2p gain 75 (15%) 441 0.402
(1.00) 		0.154
(1.00) 		0.124
(1.00) 		0.517
(1.00) 		0.743
(1.00) 		0.445
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.281
(1.00) 		0.76
(1.00)
2q gain 77 (15%) 439 0.81
(1.00) 		0.246
(1.00) 		0.301
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.441
(1.00) 		0.703
(1.00) 		0.248
(1.00) 		0.371
(1.00)
3p gain 19 (4%) 497 0.666
(1.00) 		0.518
(1.00) 		0.153
(1.00) 		0.211
(1.00) 		0.0464
(1.00) 		0.15
(1.00) 		0.333
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 13 (3%) 503 0.00921
(1.00) 		0.773
(1.00) 		0.419
(1.00) 		0.18
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.394
(1.00) 		1
(1.00) 		1
(1.00)
4q gain 13 (3%) 503 0.0116
(1.00) 		0.773
(1.00) 		0.551
(1.00) 		0.717
(1.00) 		0.456
(1.00) 		0.821
(1.00) 		0.778
(1.00) 		1
(1.00) 		1
(1.00)
5q gain 204 (40%) 312 0.154
(1.00) 		0.000636
(0.469) 		0.346
(1.00) 		0.358
(1.00) 		1
(1.00) 		1
(1.00) 		0.0193
(1.00) 		0.505
(1.00) 		0.046
(1.00) 		0.837
(1.00)
6p gain 11 (2%) 505 0.423
(1.00) 		0.796
(1.00) 		0.344
(1.00) 		0.236
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.342
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 9 (2%) 507 0.299
(1.00) 		0.361
(1.00) 		0.236
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.627
(1.00) 		1
(1.00)
7p gain 170 (33%) 346 0.904
(1.00) 		0.283
(1.00) 		0.0779
(1.00) 		0.133
(1.00) 		0.45
(1.00) 		0.0513
(1.00) 		0.00337
(1.00) 		0.394
(1.00) 		0.345
(1.00) 		0.104
(1.00) 		0.51
(1.00)
7q gain 171 (33%) 345 0.437
(1.00) 		0.321
(1.00) 		0.0195
(1.00) 		0.0651
(1.00) 		0.444
(1.00) 		0.00776
(1.00) 		0.00854
(1.00) 		0.174
(1.00) 		0.345
(1.00) 		0.0955
(1.00) 		0.269
(1.00)
8p gain 30 (6%) 486 0.576
(1.00) 		0.162
(1.00) 		0.0018
(1.00) 		0.00183
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.56
(1.00) 		0.491
(1.00) 		0.481
(1.00) 		0.381
(1.00)
8q gain 61 (12%) 455 0.4
(1.00) 		0.0424
(1.00) 		0.00695
(1.00) 		0.0106
(1.00) 		0.449
(1.00) 		0.201
(1.00) 		0.118
(1.00) 		0.897
(1.00) 		0.923
(1.00) 		0.497
(1.00)
9p gain 13 (3%) 503 0.349
(1.00) 		0.679
(1.00) 		0.947
(1.00) 		0.0539
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.0172
(1.00) 		0.446
(1.00) 		0.563
(1.00)
9q gain 12 (2%) 504 0.728
(1.00) 		0.34
(1.00) 		0.237
(1.00) 		0.00252
(1.00) 		1
(1.00) 		1
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.563
(1.00)
10p gain 17 (3%) 499 0.174
(1.00) 		0.0962
(1.00) 		0.355
(1.00) 		0.12
(1.00) 		0.107
(1.00) 		0.863
(1.00) 		0.619
(1.00) 		0.244
(1.00) 		0.533
(1.00) 		1
(1.00)
10q gain 12 (2%) 504 0.0509
(1.00) 		0.0152
(1.00) 		0.847
(1.00) 		0.883
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.366
(1.00) 		0.626
(1.00) 		0.679
(1.00) 		1
(1.00)
11p gain 31 (6%) 485 0.211
(1.00) 		0.996
(1.00) 		0.0341
(1.00) 		0.0164
(1.00) 		1
(1.00) 		0.205
(1.00) 		0.704
(1.00) 		0.943
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 29 (6%) 487 0.689
(1.00) 		0.938
(1.00) 		0.195
(1.00) 		0.1
(1.00) 		1
(1.00) 		0.592
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12p gain 119 (23%) 397 0.297
(1.00) 		0.142
(1.00) 		0.00057
(0.421) 		0.00201
(1.00) 		0.0885
(1.00) 		0.0237
(1.00) 		0.447
(1.00) 		0.0246
(1.00) 		0.127
(1.00) 		0.224
(1.00)
12q gain 120 (23%) 396 0.324
(1.00) 		0.269
(1.00) 		0.00043
(0.319) 		0.00135
(0.987) 		0.0885
(1.00) 		0.0278
(1.00) 		0.386
(1.00) 		0.0246
(1.00) 		0.112
(1.00) 		0.225
(1.00)
13q gain 22 (4%) 494 0.119
(1.00) 		0.253
(1.00) 		0.15
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.257
(1.00) 		0.129
(1.00) 		0.0972
(1.00)
14q gain 16 (3%) 500 0.585
(1.00) 		0.472
(1.00) 		0.244
(1.00) 		0.00652
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.796
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 26 (5%) 490 0.682
(1.00) 		0.459
(1.00) 		0.594
(1.00) 		0.425
(1.00) 		0.212
(1.00) 		0.619
(1.00) 		0.677
(1.00) 		0.0304
(1.00) 		0.814
(1.00) 		1
(1.00)
16p gain 105 (20%) 411 0.953
(1.00) 		0.216
(1.00) 		0.178
(1.00) 		0.0944
(1.00) 		0.134
(1.00) 		0.526
(1.00) 		0.733
(1.00) 		0.835
(1.00) 		0.253
(1.00) 		1
(1.00)
16q gain 97 (19%) 419 0.651
(1.00) 		0.299
(1.00) 		0.187
(1.00) 		0.064
(1.00) 		0.211
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.988
(1.00) 		0.428
(1.00) 		0.786
(1.00)
17p gain 25 (5%) 491 0.966
(1.00) 		0.399
(1.00) 		0.0852
(1.00) 		0.836
(1.00) 		0.212
(1.00) 		0.0387
(1.00) 		0.831
(1.00) 		0.159
(1.00) 		0.0405
(1.00) 		0.611
(1.00)
17q gain 32 (6%) 484 0.789
(1.00) 		0.238
(1.00) 		0.509
(1.00) 		0.69
(1.00) 		0.325
(1.00) 		0.312
(1.00) 		0.851
(1.00) 		0.461
(1.00) 		0.058
(1.00) 		0.629
(1.00)
18p gain 25 (5%) 491 0.235
(1.00) 		0.811
(1.00) 		0.686
(1.00) 		0.873
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.133
(1.00) 		0.809
(1.00) 		0.347
(1.00)
18q gain 25 (5%) 491 0.249
(1.00) 		0.624
(1.00) 		0.513
(1.00) 		0.771
(1.00) 		0.602
(1.00) 		0.483
(1.00) 		0.133
(1.00) 		0.811
(1.00) 		0.347
(1.00)
19p gain 51 (10%) 465 0.624
(1.00) 		0.681
(1.00) 		0.00687
(1.00) 		0.0173
(1.00) 		0.404
(1.00) 		0.00852
(1.00) 		0.219
(1.00) 		0.369
(1.00) 		0.135
(1.00) 		0.733
(1.00)
19q gain 57 (11%) 459 0.713
(1.00) 		0.396
(1.00) 		0.00162
(1.00) 		0.00668
(1.00) 		0.436
(1.00) 		0.00312
(1.00) 		0.242
(1.00) 		0.369
(1.00) 		0.107
(1.00) 		1
(1.00)
21q gain 49 (9%) 467 0.595
(1.00) 		0.0959
(1.00) 		0.217
(1.00) 		0.104
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.438
(1.00) 		0.765
(1.00) 		0.179
(1.00) 		0.719
(1.00)
22q gain 40 (8%) 476 0.456
(1.00) 		0.566
(1.00) 		0.749
(1.00) 		0.0986
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.304
(1.00) 		0.304
(1.00) 		0.332
(1.00) 		1
(1.00)
xq gain 30 (6%) 486 0.265
(1.00) 		0.797
(1.00) 		0.106
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.0337
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.629
(1.00)
1p loss 55 (11%) 461 0.0728
(1.00) 		0.0944
(1.00) 		0.593
(1.00) 		0.0177
(1.00) 		0.702
(1.00) 		0.221
(1.00) 		0.182
(1.00) 		0.765
(1.00) 		0.502
(1.00) 		0.203
(1.00)
1q loss 36 (7%) 480 0.666
(1.00) 		0.661
(1.00) 		0.813
(1.00) 		0.0778
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.59
(1.00) 		0.943
(1.00) 		0.552
(1.00) 		0.462
(1.00)
2p loss 14 (3%) 502 0.00654
(1.00) 		0.834
(1.00) 		0.455
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.779
(1.00) 		0.0397
(1.00) 		1
(1.00)
2q loss 14 (3%) 502 0.102
(1.00) 		0.81
(1.00) 		0.562
(1.00) 		0.229
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.779
(1.00) 		0.0982
(1.00) 		1
(1.00)
3p loss 371 (72%) 145 0.894
(1.00) 		0.683
(1.00) 		0.0243
(1.00) 		0.032
(1.00) 		0.792
(1.00) 		0.254
(1.00) 		0.0108
(1.00) 		0.43
(1.00) 		0.251
(1.00) 		0.108
(1.00) 		0.654
(1.00)
5q loss 6 (1%) 510 0.15
(1.00) 		0.0059
(1.00) 		0.00039
(0.289) 		1
(1.00) 		0.396
(1.00) 		0.672
(1.00) 		1
(1.00) 		1
(1.00)
6p loss 100 (19%) 416 0.207
(1.00) 		0.276
(1.00) 		0.0765
(1.00) 		0.0283
(1.00) 		0.00564
(1.00) 		0.371
(1.00) 		0.0011
(0.807) 		0.033
(1.00) 		0.779
(1.00) 		0.166
(1.00) 		1
(1.00)
6q loss 128 (25%) 388 0.563
(1.00) 		0.679
(1.00) 		0.423
(1.00) 		0.245
(1.00) 		0.00134
(0.981) 		0.844
(1.00) 		0.0564
(1.00) 		0.444
(1.00) 		0.0591
(1.00) 		0.381
(1.00) 		0.485
(1.00)
7q loss 3 (1%) 513 0.597
(1.00) 		0.122
(1.00) 		0.0103
(1.00) 		0.0723
(1.00) 		1
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.138
(1.00)
8p loss 135 (26%) 381 0.387
(1.00) 		0.806
(1.00) 		0.308
(1.00) 		0.175
(1.00) 		0.775
(1.00) 		0.152
(1.00) 		0.0285
(1.00) 		0.377
(1.00) 		0.731
(1.00) 		0.18
(1.00) 		0.0566
(1.00)
8q loss 63 (12%) 453 0.971
(1.00) 		0.648
(1.00) 		0.536
(1.00) 		0.234
(1.00) 		0.436
(1.00) 		0.745
(1.00) 		0.0168
(1.00) 		0.41
(1.00) 		0.213
(1.00) 		0.0519
(1.00)
10p loss 65 (13%) 451 0.821
(1.00) 		0.481
(1.00) 		0.0511
(1.00) 		0.00642
(1.00) 		0.141
(1.00) 		0.196
(1.00) 		0.269
(1.00) 		0.0408
(1.00) 		0.462
(1.00) 		0.203
(1.00)
10q loss 87 (17%) 429 0.851
(1.00) 		0.676
(1.00) 		0.0807
(1.00) 		0.00167
(1.00) 		0.322
(1.00) 		0.0961
(1.00) 		0.0862
(1.00) 		0.231
(1.00) 		0.196
(1.00) 		0.276
(1.00)
11p loss 18 (3%) 498 0.46
(1.00) 		0.0541
(1.00) 		0.386
(1.00) 		0.435
(1.00) 		0.157
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.611
(1.00)
11q loss 23 (4%) 493 0.119
(1.00) 		0.00592
(1.00) 		0.66
(1.00) 		0.566
(1.00) 		0.24
(1.00) 		0.507
(1.00) 		0.378
(1.00) 		0.244
(1.00) 		0.797
(1.00) 		1
(1.00)
12p loss 3 (1%) 513 0.675
(1.00) 		0.812
(1.00) 		0.481
(1.00) 		0.741
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 4 (1%) 512 0.675
(1.00) 		0.315
(1.00) 		0.167
(1.00) 		0.417
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
16p loss 9 (2%) 507 0.624
(1.00) 		0.984
(1.00) 		0.244
(1.00) 		0.00813
(1.00) 		0.366
(1.00) 		1
(1.00) 		1
(1.00) 		0.625
(1.00) 		1
(1.00)
16q loss 14 (3%) 502 0.522
(1.00) 		0.559
(1.00) 		0.165
(1.00) 		0.00252
(1.00) 		0.456
(1.00) 		0.559
(1.00) 		0.779
(1.00) 		0.479
(1.00) 		1
(1.00)
17p loss 45 (9%) 471 0.0287
(1.00) 		0.286
(1.00) 		0.238
(1.00) 		0.202
(1.00) 		0.374
(1.00) 		0.0814
(1.00) 		0.195
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.712
(1.00)
17q loss 28 (5%) 488 0.661
(1.00) 		0.793
(1.00) 		0.328
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.258
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00)
18q loss 94 (18%) 422 0.00266
(1.00) 		0.149
(1.00) 		0.00904
(1.00) 		0.00444
(1.00) 		1
(1.00) 		0.084
(1.00) 		0.122
(1.00) 		0.851
(1.00) 		0.391
(1.00) 		0.281
(1.00)
19p loss 11 (2%) 505 0.0926
(1.00) 		0.0263
(1.00) 		0.00069
(0.507) 		1
(1.00) 		0.602
(1.00) 		0.754
(1.00) 		0.213
(1.00) 		1
(1.00)
19q loss 4 (1%) 512 0.846
(1.00) 		0.235
(1.00) 		0.00312
(1.00) 		1
(1.00) 		0.244
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 8 (2%) 508 0.569
(1.00) 		0.701
(1.00) 		0.758
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.144
(1.00) 		0.257
(1.00)
20q loss 3 (1%) 513 0.114
(1.00) 		0.234
(1.00) 		0.111
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		0.0714
(1.00)
21q loss 54 (10%) 462 0.67
(1.00) 		0.709
(1.00) 		0.183
(1.00) 		0.00214
(1.00) 		0.0916
(1.00) 		0.91
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00)
22q loss 39 (8%) 477 0.0132
(1.00) 		0.246
(1.00) 		0.0244
(1.00) 		0.18
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.863
(1.00) 		0.357
(1.00) 		0.877
(1.00) 		0.0112
(1.00)
xq loss 46 (9%) 470 0.111
(1.00) 		0.505
(1.00) 		0.752
(1.00) 		0.19
(1.00) 		0.325
(1.00) 		0.896
(1.00) 		0.0782
(1.00) 		0.715
(1.00) 		0.149
(1.00)
'3q gain' versus 'PATHOLOGY.T.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.075

Table S1.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
3Q GAIN MUTATED 17 6 33 4
3Q GAIN WILD-TYPE 241 63 145 7

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p gain' versus 'AGE'

P value = 0.000235 (Wilcoxon-test), Q value = 0.18

Table S2.  Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 515 60.5 (12.1)
5P GAIN MUTATED 191 63.1 (11.8)
5P GAIN WILD-TYPE 324 59.0 (12.0)

Figure S2.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S3.  Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
20P GAIN MUTATED 33 12 39 26
20P GAIN WILD-TYPE 220 45 87 54

Figure S3.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S4.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
20P GAIN MUTATED 34 13 57 6
20P GAIN WILD-TYPE 224 56 121 5

Figure S4.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S5.  Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
20Q GAIN MUTATED 34 12 41 26
20Q GAIN WILD-TYPE 219 45 85 54

Figure S5.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S6.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
20Q GAIN MUTATED 36 13 59 5
20Q GAIN WILD-TYPE 222 56 119 6

Figure S6.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3q loss' versus 'GENDER'

P value = 0.000154 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #46: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 186 330
3Q LOSS MUTATED 19 78
3Q LOSS WILD-TYPE 167 252

Figure S7.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S8.  Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
4P LOSS MUTATED 22 8 38 4
4P LOSS WILD-TYPE 236 61 140 7

Figure S8.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S9.  Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
4Q LOSS MUTATED 15 6 24 20
4Q LOSS WILD-TYPE 238 51 102 60

Figure S9.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
4Q LOSS MUTATED 16 8 36 5
4Q LOSS WILD-TYPE 242 61 142 6

Figure S10.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
5P LOSS MUTATED 0 3 2 2
5P LOSS WILD-TYPE 258 66 176 9

Figure S11.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S12.  Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
9P LOSS MUTATED 51 11 50 35
9P LOSS WILD-TYPE 202 46 76 45

Figure S12.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.038

Table S13.  Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
9P LOSS MUTATED 54 15 73 5
9P LOSS WILD-TYPE 204 54 105 6

Figure S13.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S14.  Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
9Q LOSS MUTATED 48 14 52 34
9Q LOSS WILD-TYPE 205 43 74 46

Figure S14.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S15.  Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
9Q LOSS MUTATED 50 18 76 4
9Q LOSS WILD-TYPE 208 51 102 7

Figure S15.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.098

Table S16.  Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
13Q LOSS MUTATED 24 2 25 19
13Q LOSS WILD-TYPE 229 55 101 61

Figure S16.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0077

Table S17.  Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
13Q LOSS MUTATED 26 3 34 7
13Q LOSS WILD-TYPE 232 66 144 4

Figure S17.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'14q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.03

Table S18.  Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 253 57 126 80
14Q LOSS MUTATED 78 26 64 45
14Q LOSS WILD-TYPE 175 31 62 35

Figure S18.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'14q loss' versus 'PATHOLOGY.T.STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.045

Table S19.  Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
14Q LOSS MUTATED 83 34 93 3
14Q LOSS WILD-TYPE 175 35 85 8

Figure S19.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'15q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
15Q LOSS MUTATED 9 2 21 3
15Q LOSS WILD-TYPE 249 67 157 8

Figure S20.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.24

Table S21.  Gene #71: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 258 69 178 11
18P LOSS MUTATED 32 9 46 5
18P LOSS WILD-TYPE 226 60 132 6

Figure S21.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

Methods & Data
Input

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

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

  • Number of patients = 516

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 11

  • 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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