Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1R78CPV
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/C1R78CPV
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 80 arm-level events and 6 clinical features across 562 patients, 15 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'AGE'.

  • 2p gain cnv correlated to 'AGE'.

  • 3q gain cnv correlated to 'AGE'.

  • 6p gain cnv correlated to 'AGE'.

  • 6q gain cnv correlated to 'AGE'.

  • 7p gain cnv correlated to 'AGE'.

  • 10p gain cnv correlated to 'AGE'.

  • 12p gain cnv correlated to 'AGE'.

  • 12q gain cnv correlated to 'AGE'.

  • 20p gain cnv correlated to 'AGE'.

  • 20q gain cnv correlated to 'AGE'.

  • 21q gain cnv correlated to 'AGE'.

  • 9q loss cnv correlated to 'AGE'.

  • 15q loss cnv correlated to 'AGE'.

  • 16q 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 80 arm-level events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		KARNOFSKY
PERFORMANCE
SCORE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test Fisher's exact test
1q gain 216 (38%) 346 0.731
(1.00) 		0.000434
(0.199) 		0.266
(1.00) 		0.0241
(1.00) 		1
(1.00) 		1
(1.00)
2p gain 176 (31%) 386 0.1
(1.00) 		5.55e-06
(0.00258) 		1
(1.00) 		0.695
(1.00) 		1
(1.00) 		0.837
(1.00)
3q gain 265 (47%) 297 0.554
(1.00) 		2.13e-08
(1e-05) 		0.175
(1.00) 		0.564
(1.00) 		0.251
(1.00) 		0.759
(1.00)
6p gain 163 (29%) 399 0.3
(1.00) 		2.24e-05
(0.0103) 		0.747
(1.00) 		0.0837
(1.00) 		0.56
(1.00) 		1
(1.00)
6q gain 96 (17%) 466 0.434
(1.00) 		0.000175
(0.0808) 		1
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.741
(1.00)
7p gain 178 (32%) 384 0.857
(1.00) 		0.00041
(0.188) 		0.378
(1.00) 		0.0632
(1.00) 		0.555
(1.00) 		1
(1.00)
10p gain 181 (32%) 381 0.363
(1.00) 		3.85e-08
(1.8e-05) 		0.102
(1.00) 		0.323
(1.00) 		0.244
(1.00) 		0.664
(1.00)
12p gain 249 (44%) 313 0.295
(1.00) 		2.81e-10
(1.33e-07) 		0.347
(1.00) 		0.0292
(1.00) 		1
(1.00) 		0.574
(1.00)
12q gain 173 (31%) 389 0.155
(1.00) 		2.93e-08
(1.37e-05) 		0.0849
(1.00) 		0.00638
(1.00) 		1
(1.00) 		0.664
(1.00)
20p gain 280 (50%) 282 0.0181
(1.00) 		1.05e-06
(0.000488) 		0.749
(1.00) 		0.0983
(1.00) 		0.623
(1.00) 		0.869
(1.00)
20q gain 317 (56%) 245 0.053
(1.00) 		1.21e-05
(0.00559) 		0.758
(1.00) 		0.215
(1.00) 		1
(1.00) 		1
(1.00)
21q gain 109 (19%) 453 1
(1.00) 		0.000518
(0.237) 		0.0719
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.576
(1.00)
9q loss 280 (50%) 282 0.364
(1.00) 		4.57e-07
(0.000213) 		0.494
(1.00) 		0.985
(1.00) 		0.623
(1.00) 		0.867
(1.00)
15q loss 272 (48%) 290 0.365
(1.00) 		0.000217
(0.0997) 		0.483
(1.00) 		0.985
(1.00) 		0.613
(1.00) 		0.751
(1.00)
16q loss 400 (71%) 162 0.13
(1.00) 		8.74e-06
(0.00406) 		0.749
(1.00) 		0.152
(1.00) 		0.561
(1.00) 		0.662
(1.00)
1p gain 166 (30%) 396 0.317
(1.00) 		0.0462
(1.00) 		0.337
(1.00) 		0.0649
(1.00) 		0.21
(1.00) 		0.299
(1.00)
2q gain 148 (26%) 414 0.115
(1.00) 		0.000894
(0.407) 		1
(1.00) 		0.991
(1.00) 		0.171
(1.00) 		1
(1.00)
3p gain 154 (27%) 408 0.568
(1.00) 		0.000717
(0.327) 		0.723
(1.00) 		0.636
(1.00) 		0.565
(1.00) 		0.217
(1.00)
4p gain 57 (10%) 505 0.053
(1.00) 		0.0243
(1.00) 		0.349
(1.00) 		0.417
(1.00) 		0.275
(1.00) 		0.411
(1.00)
4q gain 32 (6%) 530 0.241
(1.00) 		0.0435
(1.00) 		1
(1.00) 		0.497
(1.00) 		0.162
(1.00)
5p gain 193 (34%) 369 0.364
(1.00) 		0.00211
(0.956) 		0.115
(1.00) 		0.429
(1.00) 		1
(1.00) 		0.0524
(1.00)
5q gain 59 (10%) 503 0.91
(1.00) 		0.171
(1.00) 		0.354
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.121
(1.00)
7q gain 193 (34%) 369 0.521
(1.00) 		0.00223
(1.00) 		0.797
(1.00) 		0.0736
(1.00) 		0.555
(1.00) 		0.574
(1.00)
8p gain 116 (21%) 446 0.888
(1.00) 		0.974
(1.00) 		0.608
(1.00) 		0.733
(1.00) 		0.501
(1.00) 		0.664
(1.00)
8q gain 236 (42%) 326 0.423
(1.00) 		0.112
(1.00) 		0.327
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.0733
(1.00)
9p gain 88 (16%) 474 0.464
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.401
(1.00) 		1
(1.00)
9q gain 43 (8%) 519 0.64
(1.00) 		0.154
(1.00) 		1
(1.00) 		0.00339
(1.00) 		0.213
(1.00) 		1
(1.00)
10q gain 105 (19%) 457 0.683
(1.00) 		0.00238
(1.00) 		0.163
(1.00) 		0.809
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 75 (13%) 487 0.116
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.35
(1.00)
11q gain 111 (20%) 451 0.945
(1.00) 		0.803
(1.00) 		1
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.576
(1.00)
13q gain 60 (11%) 502 0.63
(1.00) 		0.00586
(1.00) 		1
(1.00) 		0.541
(1.00) 		0.288
(1.00) 		0.675
(1.00)
14q gain 57 (10%) 505 0.0599
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.0284
(1.00) 		0.722
(1.00)
15q gain 38 (7%) 524 0.169
(1.00) 		0.765
(1.00) 		1
(1.00) 		0.0326
(1.00) 		1
(1.00)
16p gain 58 (10%) 504 0.904
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.0757
(1.00) 		1
(1.00) 		0.277
(1.00)
16q gain 30 (5%) 532 0.819
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.22
(1.00) 		1
(1.00) 		0.377
(1.00)
17p gain 22 (4%) 540 0.17
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.921
(1.00) 		1
(1.00)
17q gain 49 (9%) 513 0.819
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.417
(1.00) 		1
(1.00) 		0.00697
(1.00)
18p gain 117 (21%) 445 0.17
(1.00) 		0.0404
(1.00) 		1
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.812
(1.00)
18q gain 71 (13%) 491 0.327
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.722
(1.00)
19p gain 165 (29%) 397 0.456
(1.00) 		0.0641
(1.00) 		0.752
(1.00) 		0.595
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 159 (28%) 403 0.689
(1.00) 		0.00627
(1.00) 		0.155
(1.00) 		0.903
(1.00) 		0.194
(1.00) 		0.859
(1.00)
22q gain 25 (4%) 537 0.0507
(1.00) 		0.643
(1.00) 		0.17
(1.00) 		0.00338
(1.00) 		1
(1.00) 		1
(1.00)
xq gain 104 (19%) 458 0.661
(1.00) 		0.124
(1.00) 		0.0692
(1.00) 		0.935
(1.00) 		1
(1.00) 		1
(1.00)
1p loss 60 (11%) 502 0.915
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.331
(1.00) 		0.288
(1.00) 		1
(1.00)
1q loss 39 (7%) 523 0.883
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.194
(1.00)
2p loss 53 (9%) 509 0.93
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.181
(1.00) 		1
(1.00)
2q loss 59 (10%) 503 0.986
(1.00) 		0.0166
(1.00) 		0.359
(1.00) 		0.181
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 93 (17%) 469 0.933
(1.00) 		0.0113
(1.00) 		0.523
(1.00) 		0.437
(1.00) 		0.419
(1.00) 		0.0386
(1.00)
3q loss 41 (7%) 521 0.299
(1.00) 		0.155
(1.00) 		0.266
(1.00) 		0.753
(1.00) 		0.204
(1.00)
4p loss 308 (55%) 254 0.462
(1.00) 		0.963
(1.00) 		0.167
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.659
(1.00)
4q loss 352 (63%) 210 0.366
(1.00) 		0.577
(1.00) 		0.778
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.645
(1.00)
5p loss 127 (23%) 435 0.805
(1.00) 		0.0532
(1.00) 		0.646
(1.00) 		0.0319
(1.00) 		1
(1.00) 		0.741
(1.00)
5q loss 216 (38%) 346 0.437
(1.00) 		0.023
(1.00) 		1
(1.00) 		0.144
(1.00) 		1
(1.00) 		0.778
(1.00)
6p loss 162 (29%) 400 0.231
(1.00) 		0.11
(1.00) 		0.744
(1.00) 		0.853
(1.00) 		1
(1.00) 		0.493
(1.00)
6q loss 235 (42%) 327 0.587
(1.00) 		0.131
(1.00) 		0.149
(1.00) 		0.68
(1.00) 		1
(1.00) 		1
(1.00)
7p loss 117 (21%) 445 0.76
(1.00) 		0.767
(1.00) 		0.608
(1.00) 		0.0452
(1.00) 		1
(1.00) 		0.356
(1.00)
7q loss 81 (14%) 481 0.289
(1.00) 		0.198
(1.00) 		0.471
(1.00) 		0.0326
(1.00) 		0.374
(1.00) 		0.476
(1.00)
8p loss 267 (48%) 295 0.138
(1.00) 		0.0321
(1.00) 		0.175
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.339
(1.00)
8q loss 87 (15%) 475 0.0758
(1.00) 		0.00876
(1.00) 		1
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.741
(1.00)
9p loss 255 (45%) 307 0.753
(1.00) 		0.0171
(1.00) 		0.455
(1.00) 		0.31
(1.00) 		0.593
(1.00) 		0.382
(1.00)
10p loss 93 (17%) 469 0.449
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.419
(1.00) 		0.62
(1.00)
10q loss 122 (22%) 440 0.81
(1.00) 		0.0689
(1.00) 		0.619
(1.00) 		0.948
(1.00) 		0.01
(1.00) 		1
(1.00)
11p loss 191 (34%) 371 0.916
(1.00) 		0.0039
(1.00) 		1
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.658
(1.00)
11q loss 144 (26%) 418 0.603
(1.00) 		0.0377
(1.00) 		0.274
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.601
(1.00)
12p loss 77 (14%) 485 0.809
(1.00) 		0.0843
(1.00) 		1
(1.00) 		0.243
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 102 (18%) 460 0.346
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 298 (53%) 264 0.508
(1.00) 		0.432
(1.00) 		0.751
(1.00) 		0.83
(1.00) 		0.603
(1.00) 		0.645
(1.00)
14q loss 206 (37%) 356 0.52
(1.00) 		0.00124
(0.564) 		0.784
(1.00) 		0.684
(1.00) 		0.302
(1.00) 		0.632
(1.00)
16p loss 322 (57%) 240 0.361
(1.00) 		0.106
(1.00) 		0.759
(1.00) 		0.866
(1.00) 		0.265
(1.00) 		0.871
(1.00)
17p loss 466 (83%) 96 0.808
(1.00) 		0.48
(1.00) 		0.527
(1.00) 		0.862
(1.00) 		0.431
(1.00) 		0.0968
(1.00)
17q loss 372 (66%) 190 0.54
(1.00) 		0.779
(1.00) 		0.798
(1.00) 		0.0108
(1.00) 		0.554
(1.00) 		0.0627
(1.00)
18p loss 230 (41%) 332 0.0745
(1.00) 		0.973
(1.00) 		0.765
(1.00) 		0.981
(1.00) 		0.068
(1.00) 		0.871
(1.00)
18q loss 286 (51%) 276 0.113
(1.00) 		0.3
(1.00) 		0.492
(1.00) 		0.952
(1.00) 		0.249
(1.00) 		1
(1.00)
19p loss 180 (32%) 382 0.169
(1.00) 		0.0128
(1.00) 		0.195
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.308
(1.00)
19q loss 170 (30%) 392 0.771
(1.00) 		0.336
(1.00) 		0.172
(1.00) 		0.232
(1.00) 		0.557
(1.00) 		0.164
(1.00)
20p loss 48 (9%) 514 0.0923
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.00337
(1.00) 		0.235
(1.00)
20q loss 31 (6%) 531 0.142
(1.00) 		0.908
(1.00) 		1
(1.00) 		0.00338
(1.00) 		1
(1.00)
21q loss 190 (34%) 372 0.792
(1.00) 		0.344
(1.00) 		0.406
(1.00) 		0.365
(1.00) 		1
(1.00) 		1
(1.00)
22q loss 419 (75%) 143 0.121
(1.00) 		0.0556
(1.00) 		0.271
(1.00) 		0.88
(1.00) 		0.574
(1.00) 		0.0627
(1.00)
xq loss 270 (48%) 292 0.769
(1.00) 		0.00522
(1.00) 		0.75
(1.00) 		0.799
(1.00) 		0.11
(1.00) 		0.867
(1.00)
'1q gain' versus 'AGE'

P value = 0.000434 (t-test), Q value = 0.2

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
1Q GAIN MUTATED 206 62.0 (10.7)
1Q GAIN WILD-TYPE 335 58.5 (12.0)

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

'2p gain' versus 'AGE'

P value = 5.55e-06 (t-test), Q value = 0.0026

Table S2.  Gene #3: '2p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
2P GAIN MUTATED 167 63.1 (11.2)
2P GAIN WILD-TYPE 374 58.3 (11.5)

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #2: 'AGE'

'3q gain' versus 'AGE'

P value = 2.13e-08 (t-test), Q value = 1e-05

Table S3.  Gene #6: '3q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
3Q GAIN MUTATED 258 62.7 (11.2)
3Q GAIN WILD-TYPE 283 57.2 (11.4)

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'AGE'

'6p gain' versus 'AGE'

P value = 2.24e-05 (t-test), Q value = 0.01

Table S4.  Gene #11: '6p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
6P GAIN MUTATED 159 63.0 (11.0)
6P GAIN WILD-TYPE 382 58.5 (11.6)

Figure S4.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #2: 'AGE'

'6q gain' versus 'AGE'

P value = 0.000175 (t-test), Q value = 0.081

Table S5.  Gene #12: '6q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
6Q GAIN MUTATED 92 63.7 (10.6)
6Q GAIN WILD-TYPE 449 59.0 (11.7)

Figure S5.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #2: 'AGE'

'7p gain' versus 'AGE'

P value = 0.00041 (t-test), Q value = 0.19

Table S6.  Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
7P GAIN MUTATED 170 62.3 (10.9)
7P GAIN WILD-TYPE 371 58.6 (11.8)

Figure S6.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

'10p gain' versus 'AGE'

P value = 3.85e-08 (t-test), Q value = 1.8e-05

Table S7.  Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
10P GAIN MUTATED 175 63.7 (10.9)
10P GAIN WILD-TYPE 366 57.9 (11.5)

Figure S7.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

'12p gain' versus 'AGE'

P value = 2.81e-10 (t-test), Q value = 1.3e-07

Table S8.  Gene #23: '12p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
12P GAIN MUTATED 236 63.3 (11.1)
12P GAIN WILD-TYPE 305 57.1 (11.3)

Figure S8.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'AGE'

'12q gain' versus 'AGE'

P value = 2.93e-08 (t-test), Q value = 1.4e-05

Table S9.  Gene #24: '12q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
12Q GAIN MUTATED 163 63.8 (10.4)
12Q GAIN WILD-TYPE 378 58.1 (11.7)

Figure S9.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'AGE'

P value = 1.05e-06 (t-test), Q value = 0.00049

Table S10.  Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
20P GAIN MUTATED 271 62.2 (11.7)
20P GAIN WILD-TYPE 270 57.4 (11.1)

Figure S10.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'AGE'

P value = 1.21e-05 (t-test), Q value = 0.0056

Table S11.  Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
20Q GAIN MUTATED 306 61.7 (11.8)
20Q GAIN WILD-TYPE 235 57.3 (10.9)

Figure S11.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'21q gain' versus 'AGE'

P value = 0.000518 (t-test), Q value = 0.24

Table S12.  Gene #38: '21q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
21Q GAIN MUTATED 106 63.1 (10.5)
21Q GAIN WILD-TYPE 435 59.0 (11.7)

Figure S12.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'AGE'

'9q loss' versus 'AGE'

P value = 4.57e-07 (t-test), Q value = 0.00021

Table S13.  Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
9Q LOSS MUTATED 266 62.3 (11.3)
9Q LOSS WILD-TYPE 275 57.3 (11.4)

Figure S13.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

'15q loss' versus 'AGE'

P value = 0.000217 (t-test), Q value = 0.1

Table S14.  Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
15Q LOSS MUTATED 264 61.7 (11.3)
15Q LOSS WILD-TYPE 277 58.0 (11.6)

Figure S14.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'AGE'

P value = 8.74e-06 (t-test), Q value = 0.0041

Table S15.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
16Q LOSS MUTATED 385 61.2 (11.4)
16Q LOSS WILD-TYPE 156 56.3 (11.5)

Figure S15.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

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

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

  • Number of patients = 562

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 6

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

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

Q value calculation

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

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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