Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C16H4G5N
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/C16H4G5N
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 505 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'.

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

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

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

  • 5q 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'.

  • 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 (22%) 395 0.192
(1.00) 		0.259
(1.00) 		0.0001
(0.0751) 		1e-05
(0.00762) 		0.546
(1.00) 		0.0248
(1.00) 		0.000712
(0.521) 		0.878
(1.00) 		0.747
(1.00) 		0.435
(1.00)
20q gain 113 (22%) 392 0.0904
(1.00) 		0.0889
(1.00) 		8e-05
(0.0602) 		4e-05
(0.0302) 		0.237
(1.00) 		0.0339
(1.00) 		0.00504
(1.00) 		0.878
(1.00) 		0.798
(1.00) 		0.436
(1.00)
4p loss 71 (14%) 434 0.265
(1.00) 		0.9
(1.00) 		0.00026
(0.193) 		0.00023
(0.171) 		0.726
(1.00) 		0.0366
(1.00) 		0.894
(1.00) 		0.327
(1.00) 		0.142
(1.00) 		0.38
(1.00)
4q loss 65 (13%) 440 0.517
(1.00) 		0.828
(1.00) 		2e-05
(0.0151) 		1e-05
(0.00762) 		0.464
(1.00) 		0.00716
(1.00) 		0.331
(1.00) 		0.542
(1.00) 		0.178
(1.00) 		0.541
(1.00)
9p loss 144 (29%) 361 0.133
(1.00) 		0.058
(1.00) 		1e-05
(0.00762) 		4e-05
(0.0302) 		0.0997
(1.00) 		0.00071
(0.52) 		0.00063
(0.464) 		0.824
(1.00) 		0.145
(1.00) 		0.817
(1.00)
9q loss 145 (29%) 360 0.388
(1.00) 		0.0409
(1.00) 		1e-05
(0.00762) 		1e-05
(0.00762) 		0.171
(1.00) 		0.00163
(1.00) 		0.000443
(0.328) 		0.539
(1.00) 		0.148
(1.00) 		0.643
(1.00)
13q loss 69 (14%) 436 0.00206
(1.00) 		0.783
(1.00) 		0.00011
(0.0825) 		1e-05
(0.00762) 		0.321
(1.00) 		0.0632
(1.00) 		0.279
(1.00) 		0.752
(1.00) 		0.279
(1.00) 		0.224
(1.00)
14q loss 211 (42%) 294 0.0366
(1.00) 		0.184
(1.00) 		2e-05
(0.0151) 		0.00015
(0.112) 		0.0024
(1.00) 		0.00306
(1.00) 		0.0376
(1.00) 		0.126
(1.00) 		0.465
(1.00) 		0.145
(1.00) 		0.529
(1.00)
3q gain 60 (12%) 445 0.539
(1.00) 		0.919
(1.00) 		0.00126
(0.917) 		0.00013
(0.0974) 		0.00868
(1.00) 		0.0136
(1.00) 		0.776
(1.00) 		0.542
(1.00) 		0.754
(1.00) 		1
(1.00)
5p gain 187 (37%) 318 0.144
(1.00) 		0.000207
(0.154) 		0.138
(1.00) 		0.233
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.0264
(1.00) 		0.629
(1.00) 		0.0561
(1.00) 		1
(1.00)
5p loss 7 (1%) 498 0.143
(1.00) 		0.253
(1.00) 		0.0019
(1.00) 		0.00014
(0.105) 		1
(1.00) 		0.191
(1.00) 		0.249
(1.00) 		1
(1.00) 		1
(1.00)
5q loss 6 (1%) 499 0.143
(1.00) 		0.151
(1.00) 		0.00567
(1.00) 		0.00033
(0.245) 		1
(1.00) 		0.323
(1.00) 		0.43
(1.00) 		1
(1.00) 		1
(1.00)
18p loss 91 (18%) 414 0.0624
(1.00) 		0.112
(1.00) 		0.00034
(0.252) 		0.00032
(0.238) 		1
(1.00) 		0.0711
(1.00) 		0.148
(1.00) 		0.771
(1.00) 		0.585
(1.00) 		0.0946
(1.00)
1p gain 23 (5%) 482 0.205
(1.00) 		0.212
(1.00) 		0.294
(1.00) 		0.361
(1.00) 		0.213
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.45
(1.00) 		0.45
(1.00) 		1
(1.00)
1q gain 50 (10%) 455 0.678
(1.00) 		0.0375
(1.00) 		0.126
(1.00) 		0.164
(1.00) 		0.426
(1.00) 		0.75
(1.00) 		0.644
(1.00) 		0.7
(1.00) 		0.898
(1.00) 		0.719
(1.00)
2p gain 75 (15%) 430 0.263
(1.00) 		0.152
(1.00) 		0.159
(1.00) 		0.597
(1.00) 		0.744
(1.00) 		0.345
(1.00) 		0.896
(1.00) 		0.252
(1.00) 		0.788
(1.00) 		0.541
(1.00)
2q gain 77 (15%) 428 0.583
(1.00) 		0.245
(1.00) 		0.359
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.364
(1.00) 		0.588
(1.00) 		0.739
(1.00) 		0.353
(1.00)
3p gain 19 (4%) 486 0.169
(1.00) 		0.518
(1.00) 		0.169
(1.00) 		0.222
(1.00) 		0.0468
(1.00) 		0.156
(1.00) 		0.328
(1.00) 		0.976
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 13 (3%) 492 0.0161
(1.00) 		0.776
(1.00) 		0.467
(1.00) 		0.2
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.677
(1.00) 		1
(1.00)
4q gain 13 (3%) 492 0.0196
(1.00) 		0.776
(1.00) 		0.573
(1.00) 		0.719
(1.00) 		0.458
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.679
(1.00) 		1
(1.00)
5q gain 200 (40%) 305 0.0858
(1.00) 		0.000568
(0.419) 		0.392
(1.00) 		0.401
(1.00) 		1
(1.00) 		1
(1.00) 		0.029
(1.00) 		0.629
(1.00) 		0.0257
(1.00) 		0.833
(1.00)
6p gain 11 (2%) 494 0.477
(1.00) 		0.795
(1.00) 		0.373
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.343
(1.00) 		0.613
(1.00) 		1
(1.00)
6q gain 9 (2%) 496 0.344
(1.00) 		0.362
(1.00) 		0.255
(1.00) 		0.295
(1.00) 		1
(1.00) 		1
(1.00) 		0.17
(1.00) 		0.54
(1.00) 		1
(1.00)
7p gain 167 (33%) 338 0.965
(1.00) 		0.393
(1.00) 		0.0804
(1.00) 		0.136
(1.00) 		0.448
(1.00) 		0.05
(1.00) 		0.00401
(1.00) 		0.546
(1.00) 		0.102
(1.00) 		0.365
(1.00)
7q gain 168 (33%) 337 0.361
(1.00) 		0.439
(1.00) 		0.0168
(1.00) 		0.0627
(1.00) 		0.442
(1.00) 		0.00617
(1.00) 		0.0101
(1.00) 		0.258
(1.00) 		0.0988
(1.00) 		0.169
(1.00)
8p gain 29 (6%) 476 0.0445
(1.00) 		0.199
(1.00) 		0.00547
(1.00) 		0.00329
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.693
(1.00) 		0.441
(1.00) 		0.524
(1.00) 		0.622
(1.00)
8q gain 60 (12%) 445 0.067
(1.00) 		0.051
(1.00) 		0.0169
(1.00) 		0.0207
(1.00) 		0.451
(1.00) 		0.191
(1.00) 		0.152
(1.00) 		0.828
(1.00) 		0.915
(1.00) 		0.491
(1.00)
9p gain 13 (3%) 492 0.325
(1.00) 		0.676
(1.00) 		0.948
(1.00) 		0.0516
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.0155
(1.00) 		0.365
(1.00) 		0.543
(1.00)
9q gain 12 (2%) 493 0.803
(1.00) 		0.339
(1.00) 		0.236
(1.00) 		0.00288
(1.00) 		1
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.648
(1.00) 		0.543
(1.00)
10p gain 17 (3%) 488 0.218
(1.00) 		0.0957
(1.00) 		0.36
(1.00) 		0.108
(1.00) 		0.107
(1.00) 		0.81
(1.00) 		0.797
(1.00) 		0.222
(1.00) 		0.711
(1.00) 		1
(1.00)
10q gain 12 (2%) 493 0.0708
(1.00) 		0.0153
(1.00) 		0.827
(1.00) 		0.884
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.36
(1.00) 		0.587
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 31 (6%) 474 0.285
(1.00) 		0.992
(1.00) 		0.0449
(1.00) 		0.0196
(1.00) 		1
(1.00) 		0.143
(1.00) 		0.847
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 29 (6%) 476 0.796
(1.00) 		0.941
(1.00) 		0.23
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.29
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12p gain 119 (24%) 386 0.0924
(1.00) 		0.139
(1.00) 		0.00098
(0.716) 		0.00318
(1.00) 		0.0892
(1.00) 		0.0405
(1.00) 		0.583
(1.00) 		0.0163
(1.00) 		0.514
(1.00) 		0.223
(1.00)
12q gain 120 (24%) 385 0.105
(1.00) 		0.265
(1.00) 		0.00063
(0.464) 		0.00233
(1.00) 		0.0892
(1.00) 		0.044
(1.00) 		0.512
(1.00) 		0.0163
(1.00) 		0.515
(1.00) 		0.221
(1.00)
13q gain 22 (4%) 483 0.146
(1.00) 		0.254
(1.00) 		0.172
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.258
(1.00) 		0.182
(1.00) 		0.0855
(1.00)
14q gain 16 (3%) 489 0.662
(1.00) 		0.476
(1.00) 		0.265
(1.00) 		0.00779
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.798
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 26 (5%) 479 0.609
(1.00) 		0.451
(1.00) 		0.636
(1.00) 		0.455
(1.00) 		0.213
(1.00) 		0.742
(1.00) 		0.68
(1.00) 		0.0275
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 104 (21%) 401 0.852
(1.00) 		0.219
(1.00) 		0.201
(1.00) 		0.108
(1.00) 		0.133
(1.00) 		0.726
(1.00) 		0.731
(1.00) 		0.708
(1.00) 		0.486
(1.00) 		1
(1.00)
16q gain 96 (19%) 409 0.863
(1.00) 		0.304
(1.00) 		0.217
(1.00) 		0.071
(1.00) 		0.211
(1.00) 		1
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.632
(1.00) 		1
(1.00)
17p gain 25 (5%) 480 0.464
(1.00) 		0.398
(1.00) 		0.0827
(1.00) 		0.823
(1.00) 		0.213
(1.00) 		0.0471
(1.00) 		0.832
(1.00) 		0.139
(1.00) 		0.0229
(1.00) 		0.611
(1.00)
17q gain 31 (6%) 474 0.599
(1.00) 		0.366
(1.00) 		0.529
(1.00) 		0.729
(1.00) 		0.298
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.0624
(1.00) 		0.617
(1.00)
18p gain 25 (5%) 480 0.214
(1.00) 		0.806
(1.00) 		0.695
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.0862
(1.00) 		1
(1.00) 		0.323
(1.00)
18q gain 25 (5%) 480 0.227
(1.00) 		0.62
(1.00) 		0.541
(1.00) 		0.775
(1.00) 		0.604
(1.00) 		0.62
(1.00) 		0.0862
(1.00) 		1
(1.00) 		0.323
(1.00)
19p gain 51 (10%) 454 0.359
(1.00) 		0.677
(1.00) 		0.00895
(1.00) 		0.0214
(1.00) 		0.404
(1.00) 		0.0212
(1.00) 		0.279
(1.00) 		0.312
(1.00) 		0.379
(1.00) 		0.723
(1.00)
19q gain 57 (11%) 448 0.437
(1.00) 		0.393
(1.00) 		0.00237
(1.00) 		0.00847
(1.00) 		0.438
(1.00) 		0.00768
(1.00) 		0.243
(1.00) 		0.312
(1.00) 		0.245
(1.00) 		0.749
(1.00)
21q gain 49 (10%) 456 0.333
(1.00) 		0.0951
(1.00) 		0.253
(1.00) 		0.124
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.532
(1.00) 		0.84
(1.00) 		0.418
(1.00) 		0.479
(1.00)
22q gain 40 (8%) 465 0.391
(1.00) 		0.563
(1.00) 		0.817
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.307
(1.00) 		0.291
(1.00) 		0.653
(1.00) 		1
(1.00)
xq gain 29 (6%) 476 0.327
(1.00) 		0.84
(1.00) 		0.0792
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.0367
(1.00) 		0.842
(1.00) 		0.976
(1.00) 		0.443
(1.00) 		0.617
(1.00)
1p loss 55 (11%) 450 0.0329
(1.00) 		0.0926
(1.00) 		0.543
(1.00) 		0.0155
(1.00) 		0.702
(1.00) 		0.501
(1.00) 		0.232
(1.00) 		0.84
(1.00) 		0.228
(1.00) 		0.184
(1.00)
1q loss 36 (7%) 469 0.308
(1.00) 		0.656
(1.00) 		0.795
(1.00) 		0.0785
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.443
(1.00)
2p loss 14 (3%) 491 0.0125
(1.00) 		0.836
(1.00) 		0.434
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.773
(1.00) 		0.779
(1.00) 		0.0362
(1.00) 		1
(1.00)
2q loss 14 (3%) 491 0.142
(1.00) 		0.812
(1.00) 		0.561
(1.00) 		0.223
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.779
(1.00) 		0.0666
(1.00) 		1
(1.00)
3p loss 364 (72%) 141 0.735
(1.00) 		0.859
(1.00) 		0.0251
(1.00) 		0.038
(1.00) 		0.791
(1.00) 		0.242
(1.00) 		0.0223
(1.00) 		0.248
(1.00) 		0.121
(1.00) 		0.486
(1.00)
3q loss 96 (19%) 409 0.0634
(1.00) 		0.0169
(1.00) 		0.647
(1.00) 		0.282
(1.00) 		0.747
(1.00) 		0.886
(1.00) 		0.000347
(0.257) 		0.421
(1.00) 		0.879
(1.00) 		0.571
(1.00)
6p loss 98 (19%) 407 0.126
(1.00) 		0.271
(1.00) 		0.0598
(1.00) 		0.0357
(1.00) 		0.00494
(1.00) 		0.196
(1.00) 		0.0014
(1.00) 		0.0689
(1.00) 		0.107
(1.00) 		0.791
(1.00)
6q loss 125 (25%) 380 0.738
(1.00) 		0.754
(1.00) 		0.339
(1.00) 		0.237
(1.00) 		0.00118
(0.858) 		0.9
(1.00) 		0.0527
(1.00) 		0.626
(1.00) 		0.0347
(1.00) 		0.219
(1.00) 		0.627
(1.00)
7q loss 3 (1%) 502 0.597
(1.00) 		0.127
(1.00) 		0.011
(1.00) 		0.0726
(1.00) 		1
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.131
(1.00)
8p loss 134 (27%) 371 0.542
(1.00) 		0.683
(1.00) 		0.354
(1.00) 		0.292
(1.00) 		0.776
(1.00) 		0.33
(1.00) 		0.0577
(1.00) 		0.449
(1.00) 		0.291
(1.00) 		0.41
(1.00) 		0.0267
(1.00)
8q loss 62 (12%) 443 0.847
(1.00) 		0.805
(1.00) 		0.534
(1.00) 		0.356
(1.00) 		0.438
(1.00) 		0.742
(1.00) 		0.0325
(1.00) 		0.449
(1.00) 		0.213
(1.00) 		0.0363
(1.00)
10p loss 65 (13%) 440 0.537
(1.00) 		0.477
(1.00) 		0.0701
(1.00) 		0.00825
(1.00) 		0.14
(1.00) 		0.564
(1.00) 		0.331
(1.00) 		0.0521
(1.00) 		0.693
(1.00) 		0.184
(1.00)
10q loss 87 (17%) 418 0.637
(1.00) 		0.668
(1.00) 		0.109
(1.00) 		0.00253
(1.00) 		0.322
(1.00) 		0.436
(1.00) 		0.11
(1.00) 		0.282
(1.00) 		0.457
(1.00) 		0.253
(1.00)
11p loss 18 (4%) 487 0.0705
(1.00) 		0.0546
(1.00) 		0.452
(1.00) 		0.442
(1.00) 		0.158
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.587
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 23 (5%) 482 0.0164
(1.00) 		0.00599
(1.00) 		0.678
(1.00) 		0.602
(1.00) 		0.241
(1.00) 		0.6
(1.00) 		0.383
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00)
12p loss 3 (1%) 502 0.66
(1.00) 		0.813
(1.00) 		0.489
(1.00) 		0.742
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 4 (1%) 501 0.66
(1.00) 		0.315
(1.00) 		0.174
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 35 (7%) 470 0.407
(1.00) 		0.991
(1.00) 		0.00099
(0.723) 		0.00047
(0.347) 		1
(1.00) 		0.0386
(1.00) 		0.0654
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.381
(1.00)
16p loss 9 (2%) 496 0.605
(1.00) 		0.983
(1.00) 		0.249
(1.00) 		0.00885
(1.00) 		0.367
(1.00) 		1
(1.00) 		1
(1.00) 		0.541
(1.00) 		1
(1.00)
16q loss 13 (3%) 492 0.518
(1.00) 		0.688
(1.00) 		0.298
(1.00) 		0.00381
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.677
(1.00) 		1
(1.00)
17p loss 44 (9%) 461 0.0427
(1.00) 		0.407
(1.00) 		0.206
(1.00) 		0.17
(1.00) 		0.376
(1.00) 		0.0927
(1.00) 		0.186
(1.00) 		0.101
(1.00) 		1
(1.00) 		0.708
(1.00)
17q loss 28 (6%) 477 0.777
(1.00) 		0.789
(1.00) 		0.343
(1.00) 		0.325
(1.00) 		1
(1.00) 		0.324
(1.00) 		0.31
(1.00) 		0.809
(1.00) 		1
(1.00)
18q loss 93 (18%) 412 0.00697
(1.00) 		0.136
(1.00) 		0.00921
(1.00) 		0.0048
(1.00) 		1
(1.00) 		0.0954
(1.00) 		0.118
(1.00) 		0.916
(1.00) 		0.59
(1.00) 		0.276
(1.00)
19p loss 11 (2%) 494 0.0935
(1.00) 		0.028
(1.00) 		0.00069
(0.506) 		1
(1.00) 		0.504
(1.00) 		0.754
(1.00) 		0.19
(1.00) 		1
(1.00)
19q loss 4 (1%) 501 0.847
(1.00) 		0.241
(1.00) 		0.00307
(1.00) 		1
(1.00) 		0.179
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 8 (2%) 497 0.547
(1.00) 		0.704
(1.00) 		0.728
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.132
(1.00) 		0.246
(1.00)
20q loss 3 (1%) 502 0.116
(1.00) 		0.24
(1.00) 		0.111
(1.00) 		0.433
(1.00) 		1
(1.00) 		1
(1.00) 		0.0678
(1.00)
21q loss 53 (10%) 452 0.782
(1.00) 		0.546
(1.00) 		0.176
(1.00) 		0.00365
(1.00) 		0.0927
(1.00) 		0.878
(1.00) 		0.651
(1.00) 		0.962
(1.00) 		0.638
(1.00) 		1
(1.00)
22q loss 38 (8%) 467 0.00183
(1.00) 		0.249
(1.00) 		0.0173
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.149
(1.00) 		0.725
(1.00) 		0.398
(1.00) 		0.86
(1.00) 		0.0315
(1.00)
xq loss 45 (9%) 460 0.0344
(1.00) 		0.358
(1.00) 		0.714
(1.00) 		0.199
(1.00) 		0.326
(1.00) 		0.858
(1.00) 		0.141
(1.00) 		0.675
(1.00) 		0.245
(1.00)
'3q gain' versus 'PATHOLOGY.T.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.097

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
3Q GAIN MUTATED 17 6 33 4
3Q GAIN WILD-TYPE 233 61 144 7

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

'5p gain' versus 'AGE'

P value = 0.000207 (Wilcoxon-test), Q value = 0.15

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

nPatients Mean (Std.Dev)
ALL 504 60.5 (12.1)
5P GAIN MUTATED 187 63.2 (11.8)
5P GAIN WILD-TYPE 317 59.0 (12.1)

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

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

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

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
20P GAIN MUTATED 33 12 39 26
20P GAIN WILD-TYPE 211 44 87 53

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 = 0.0076

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
20P GAIN MUTATED 34 13 57 6
20P GAIN WILD-TYPE 216 54 120 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 = 8e-05 (Fisher's exact test), Q value = 0.06

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
20Q GAIN MUTATED 34 12 41 26
20Q GAIN WILD-TYPE 210 44 85 53

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

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

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

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
20Q GAIN MUTATED 36 13 59 5
20Q GAIN WILD-TYPE 214 54 118 6

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

'4p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #47: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
4P LOSS MUTATED 20 6 26 19
4P LOSS WILD-TYPE 224 50 100 60

Figure S7.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

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

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
4P LOSS MUTATED 21 8 38 4
4P LOSS WILD-TYPE 229 59 139 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 = 2e-05 (Fisher's exact test), Q value = 0.015

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
4Q LOSS MUTATED 15 6 24 20
4Q LOSS WILD-TYPE 229 50 102 59

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

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

P value = 1e-05 (Fisher's exact test), Q value = 0.0076

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
4Q LOSS MUTATED 16 8 36 5
4Q LOSS WILD-TYPE 234 59 141 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 = 0.00014 (Fisher's exact test), Q value = 0.1

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

nPatients T1 T2 T3 T4
ALL 250 67 177 11
5P LOSS MUTATED 0 3 2 2
5P LOSS WILD-TYPE 250 64 175 9

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

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

P value = 0.00033 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 250 67 177 11
5Q LOSS MUTATED 0 2 2 2
5Q LOSS WILD-TYPE 250 65 175 9

Figure S12.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0076

Table S13.  Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
9P LOSS MUTATED 48 11 50 35
9P LOSS WILD-TYPE 196 45 76 44

Figure S13.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

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

Table S14.  Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 250 67 177 11
9P LOSS MUTATED 52 15 72 5
9P LOSS WILD-TYPE 198 52 105 6

Figure S14.  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 = 0.0076

Table S15.  Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
9Q LOSS MUTATED 45 14 52 34
9Q LOSS WILD-TYPE 199 42 74 45

Figure S15.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1e-05 (Fisher's exact test), Q value = 0.0076

Table S16.  Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 250 67 177 11
9Q LOSS MUTATED 48 18 75 4
9Q LOSS WILD-TYPE 202 49 102 7

Figure S16.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.082

Table S17.  Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
13Q LOSS MUTATED 23 2 25 19
13Q LOSS WILD-TYPE 221 54 101 60

Figure S17.  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 = 0.0076

Table S18.  Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 250 67 177 11
13Q LOSS MUTATED 25 3 34 7
13Q LOSS WILD-TYPE 225 64 143 4

Figure S18.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'14q loss' versus 'NEOPLASM.DISEASESTAGE'

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

Table S19.  Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 244 56 126 79
14Q LOSS MUTATED 76 26 64 45
14Q LOSS WILD-TYPE 168 30 62 34

Figure S19.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 0.00015 (Fisher's exact test), Q value = 0.11

Table S20.  Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 250 67 177 11
14Q LOSS MUTATED 82 34 92 3
14Q LOSS WILD-TYPE 168 33 85 8

Figure S20.  Get High-res Image Gene #65: '14q 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 250 67 177 11
18P LOSS MUTATED 31 9 46 5
18P LOSS WILD-TYPE 219 58 131 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 = 505

  • 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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