Correlation between copy number variation genes (focal events) and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1DR2TX5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2TX5
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 73 focal events and 7 clinical features across 573 patients, 28 significant findings detected with Q value < 0.25.

  • amp_1p34.3 cnv correlated to 'Time to Death'.

  • amp_1q21.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_1q42.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_3q26.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_5p15.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_6p22.3 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_8p11.21 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_10p15.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_12p13.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_12p12.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_12q15 cnv correlated to 'YEARS_TO_BIRTH' and 'TUMOR_TISSUE_SITE'.

  • amp_19q12 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_19q13.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_20p13 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_20q11.21 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_20q13.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_3p26.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_6q27 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_11p15.5 cnv correlated to 'TUMOR_TISSUE_SITE'.

  • del_12q23.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_13q14.2 cnv correlated to 'Time to Death'.

  • del_15q11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_15q15.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_17q11.2 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 73 focal events and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		RESIDUAL
TUMOR 		ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 6p22 3 300 (52%) 273 0.0105
(0.208) 		0.00267
(0.091) 		1
(1.00) 		1
(1.00) 		0.289
(0.941) 		0.872
(1.00) 		0.342
(0.974)
amp 12q15 221 (39%) 352 0.257
(0.912) 		4.56e-07
(5.83e-05) 		0.00742
(0.175) 		0.373
(0.989) 		0.343
(0.974) 		0.402
(0.994) 		0.739
(1.00)
amp 19q13 2 242 (42%) 331 0.00655
(0.167) 		3.06e-06
(0.000313) 		0.0746
(0.508) 		1
(1.00) 		0.845
(1.00) 		0.739
(1.00) 		0.747
(1.00)
amp 1p34 3 291 (51%) 282 0.00821
(0.182) 		0.0164
(0.27) 		1
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.398
(0.994) 		1
(1.00)
amp 1q21 3 364 (64%) 209 0.291
(0.941) 		8.07e-06
(0.000589) 		0.382
(0.989) 		0.36
(0.989) 		0.364
(0.989) 		0.0885
(0.552) 		1
(1.00)
amp 1q42 2 317 (55%) 256 0.196
(0.798) 		0.000784
(0.0308) 		0.174
(0.761) 		0.182
(0.775) 		0.749
(1.00) 		0.883
(1.00) 		0.53
(1.00)
amp 3q26 2 479 (84%) 94 0.693
(1.00) 		0.00206
(0.0751) 		1
(1.00) 		0.189
(0.784) 		0.0256
(0.336) 		0.828
(1.00) 		0.648
(1.00)
amp 5p15 33 305 (53%) 268 0.0985
(0.579) 		0.011
(0.209) 		0.509
(1.00) 		0.187
(0.784) 		0.735
(1.00) 		0.165
(0.761) 		0.752
(1.00)
amp 8p11 21 210 (37%) 363 0.0626
(0.498) 		0.000568
(0.0242) 		0.115
(0.615) 		1
(1.00) 		0.941
(1.00) 		0.784
(1.00) 		1
(1.00)
amp 10p15 3 250 (44%) 323 0.0797
(0.534) 		0.000468
(0.0218) 		0.318
(0.966) 		0.659
(1.00) 		0.979
(1.00) 		0.651
(1.00) 		0.197
(0.798)
amp 12p13 33 328 (57%) 245 0.431
(1.00) 		1.86e-07
(3.18e-05) 		0.401
(0.994) 		0.0729
(0.508) 		0.79
(1.00) 		0.277
(0.926) 		1
(1.00)
amp 12p12 1 311 (54%) 262 0.0859
(0.546) 		1.45e-08
(5.3e-06) 		0.128
(0.659) 		1
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00)
amp 19q12 319 (56%) 254 0.0419
(0.42) 		2.94e-05
(0.00188) 		0.0437
(0.429) 		0.659
(1.00) 		0.715
(1.00) 		0.229
(0.854) 		1
(1.00)
amp 20p13 315 (55%) 258 0.227
(0.853) 		0.00526
(0.157) 		0.327
(0.966) 		0.659
(1.00) 		0.169
(0.761) 		0.752
(1.00) 		0.524
(1.00)
amp 20q11 21 344 (60%) 229 0.0865
(0.546) 		2.07e-08
(5.3e-06) 		1
(1.00) 		1
(1.00) 		0.361
(0.989) 		0.699
(1.00) 		0.748
(1.00)
amp 20q13 33 399 (70%) 174 0.565
(1.00) 		6.57e-06
(0.000559) 		0.595
(1.00) 		0.641
(1.00) 		0.475
(1.00) 		0.0633
(0.498) 		0.731
(1.00)
del 3p26 2 208 (36%) 365 0.474
(1.00) 		0.00382
(0.122) 		0.277
(0.926) 		1
(1.00) 		0.405
(0.994) 		0.537
(1.00) 		1
(1.00)
del 6q27 375 (65%) 198 0.0222
(0.32) 		0.000102
(0.00578) 		0.368
(0.989) 		0.662
(1.00) 		0.968
(1.00) 		0.783
(1.00) 		1
(1.00)
del 11p15 5 340 (59%) 233 0.0474
(0.432) 		0.363
(0.989) 		0.0106
(0.208) 		0.653
(1.00) 		0.539
(1.00) 		0.752
(1.00) 		1
(1.00)
del 12q23 1 193 (34%) 380 0.29
(0.941) 		0.00753
(0.175) 		0.801
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.957
(1.00) 		1
(1.00)
del 13q14 2 359 (63%) 214 0.00892
(0.19) 		0.403
(0.994) 		0.382
(0.989) 		0.371
(0.989) 		0.843
(1.00) 		0.253
(0.905) 		0.746
(1.00)
del 15q11 2 296 (52%) 277 0.603
(1.00) 		0.00582
(0.157) 		0.624
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.465
(1.00) 		0.752
(1.00)
del 15q15 1 359 (63%) 214 0.69
(1.00) 		0.00571
(0.157) 		0.793
(1.00) 		1
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.327
(0.966)
del 16q23 1 447 (78%) 126 0.227
(0.853) 		0.000464
(0.0218) 		0.712
(1.00) 		0.59
(1.00) 		0.0657
(0.501) 		0.051
(0.45) 		0.249
(0.894)
del 17q11 2 467 (82%) 106 0.528
(1.00) 		0.0125
(0.228) 		0.0225
(0.32) 		1
(1.00) 		0.994
(1.00) 		1
(1.00) 		0.697
(1.00)
amp 2p23 2 247 (43%) 326 0.52
(1.00) 		0.0926
(0.564) 		1
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.785
(1.00) 		1
(1.00)
amp 2q31 2 259 (45%) 314 0.232
(0.854) 		0.0245
(0.329) 		0.325
(0.966) 		0.662
(1.00) 		0.903
(1.00) 		0.847
(1.00) 		0.338
(0.974)
amp 4p16 3 162 (28%) 411 0.583
(1.00) 		0.698
(1.00) 		0.583
(1.00) 		0.626
(1.00) 		0.209
(0.823) 		0.745
(1.00) 		0.468
(1.00)
amp 4q13 3 113 (20%) 460 0.151
(0.744) 		0.198
(0.798) 		0.261
(0.912) 		0.265
(0.915) 		0.555
(1.00) 		0.105
(0.588) 		1
(1.00)
amp 7q36 3 316 (55%) 257 0.149
(0.744) 		0.715
(1.00) 		1
(1.00) 		1
(1.00) 		0.0805
(0.534) 		0.849
(1.00) 		0.342
(0.974)
amp 8q24 21 455 (79%) 118 0.712
(1.00) 		0.0981
(0.579) 		1
(1.00) 		0.273
(0.926) 		0.801
(1.00) 		0.923
(1.00) 		0.428
(1.00)
amp 10q22 3 182 (32%) 391 0.475
(1.00) 		0.111
(0.611) 		0.0537
(0.458) 		0.659
(1.00) 		0.852
(1.00) 		0.461
(1.00) 		1
(1.00)
amp 11q14 1 252 (44%) 321 0.652
(1.00) 		0.507
(1.00) 		0.634
(1.00) 		0.391
(0.994) 		0.76
(1.00) 		0.719
(1.00) 		0.526
(1.00)
amp 14q11 2 146 (25%) 427 0.174
(0.761) 		0.0461
(0.429) 		0.0815
(0.534) 		1
(1.00) 		0.469
(1.00) 		0.741
(1.00) 		0.139
(0.703)
amp 14q32 33 156 (27%) 417 0.267
(0.915) 		0.0187
(0.29) 		0.392
(0.994) 		0.122
(0.635) 		0.991
(1.00) 		0.956
(1.00) 		0.72
(1.00)
amp 15q26 3 160 (28%) 413 0.024
(0.329) 		0.204
(0.813) 		1
(1.00) 		1
(1.00) 		0.833
(1.00) 		0.869
(1.00) 		0.733
(1.00)
amp 17q25 3 212 (37%) 361 0.215
(0.826) 		0.768
(1.00) 		0.622
(1.00) 		0.656
(1.00) 		0.925
(1.00) 		0.0535
(0.458) 		1
(1.00)
amp 18q11 2 139 (24%) 434 0.474
(1.00) 		0.11
(0.608) 		0.0724
(0.508) 		1
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.26
(0.912)
amp 19p13 12 314 (55%) 259 0.784
(1.00) 		0.0414
(0.42) 		0.797
(1.00) 		1
(1.00) 		0.318
(0.966) 		0.265
(0.915) 		1
(1.00)
amp 22q12 2 91 (16%) 482 0.868
(1.00) 		0.0413
(0.42) 		0.0927
(0.564) 		1
(1.00) 		0.302
(0.964) 		0.622
(1.00) 		0.173
(0.761)
amp xp11 23 159 (28%) 414 0.232
(0.854) 		0.104
(0.588) 		0.0347
(0.42) 		1
(1.00) 		0.554
(1.00) 		0.191
(0.786) 		1
(1.00)
amp xq28 217 (38%) 356 0.631
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.373
(0.989) 		0.245
(0.887) 		0.53
(1.00) 		0.327
(0.966)
del 1p36 11 266 (46%) 307 0.0388
(0.42) 		0.289
(0.941) 		0.626
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.757
(1.00) 		0.525
(1.00)
del 1q41 95 (17%) 478 0.309
(0.966) 		0.442
(1.00) 		1
(1.00) 		0.189
(0.784) 		0.979
(1.00) 		0.591
(1.00) 		0.377
(0.989)
del 2p25 3 120 (21%) 453 0.915
(1.00) 		0.467
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.0388
(0.42) 		0.45
(1.00)
del 2q22 1 133 (23%) 440 0.647
(1.00) 		0.334
(0.971) 		0.492
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.666
(1.00) 		0.0614
(0.498)
del 2q37 3 172 (30%) 401 0.498
(1.00) 		0.0175
(0.28) 		0.783
(1.00) 		0.167
(0.761) 		0.166
(0.761) 		0.514
(1.00) 		0.491
(1.00)
del 3q13 31 84 (15%) 489 0.449
(1.00) 		0.811
(1.00) 		1
(1.00) 		1
(1.00) 		0.225
(0.853) 		0.433
(1.00) 		1
(1.00)
del 4q22 1 390 (68%) 183 0.0604
(0.498) 		0.879
(1.00) 		0.797
(1.00) 		0.659
(1.00) 		0.736
(1.00) 		0.852
(1.00) 		0.174
(0.761)
del 4q34 3 416 (73%) 157 0.481
(1.00) 		0.46
(1.00) 		0.572
(1.00) 		0.329
(0.966) 		0.152
(0.744) 		0.407
(0.995) 		0.0674
(0.501)
del 5q12 1 350 (61%) 223 0.79
(1.00) 		0.678
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.243
(0.885) 		0.377
(0.989) 		1
(1.00)
del 5q13 2 414 (72%) 159 0.0677
(0.501) 		0.998
(1.00) 		0.402
(0.994) 		0.62
(1.00) 		0.177
(0.761) 		0.214
(0.826) 		0.733
(1.00)
del 7p22 2 251 (44%) 322 0.0643
(0.498) 		0.0199
(0.299) 		0.402
(0.994) 		0.659
(1.00) 		0.626
(1.00) 		0.577
(1.00) 		0.754
(1.00)
del 8p23 3 384 (67%) 189 0.215
(0.826) 		0.0691
(0.505) 		1
(1.00) 		0.668
(1.00) 		0.555
(1.00) 		0.522
(1.00) 		0.175
(0.761)
del 8p21 2 401 (70%) 172 0.613
(1.00) 		0.0738
(0.508) 		1
(1.00) 		0.641
(1.00) 		0.894
(1.00) 		0.561
(1.00) 		0.293
(0.941)
del 9p24 3 259 (45%) 314 0.751
(1.00) 		0.0153
(0.26) 		0.321
(0.966) 		1
(1.00) 		0.554
(1.00) 		0.814
(1.00) 		1
(1.00)
del 9q34 13 341 (60%) 232 0.314
(0.966) 		0.0614
(0.498) 		0.501
(1.00) 		1
(1.00) 		0.962
(1.00) 		0.68
(1.00) 		1
(1.00)
del 10p15 3 117 (20%) 456 0.46
(1.00) 		0.881
(1.00) 		0.681
(1.00) 		0.589
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.697
(1.00)
del 10q23 31 222 (39%) 351 0.0509
(0.45) 		0.799
(1.00) 		1
(1.00) 		0.383
(0.989) 		0.644
(1.00) 		0.868
(1.00) 		1
(1.00)
del 10q25 1 238 (42%) 335 0.122
(0.635) 		0.467
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.529
(1.00) 		0.949
(1.00) 		0.532
(1.00)
del 11q25 200 (35%) 373 0.502
(1.00) 		0.041
(0.42) 		0.16
(0.761) 		1
(1.00) 		0.322
(0.966) 		0.709
(1.00) 		0.0382
(0.42)
del 12q24 33 214 (37%) 359 0.935
(1.00) 		0.0741
(0.508) 		0.382
(0.989) 		0.655
(1.00) 		0.636
(1.00) 		0.046
(0.429) 		0.0368
(0.42)
del 14q23 3 303 (53%) 270 0.898
(1.00) 		0.498
(1.00) 		0.177
(0.761) 		0.668
(1.00) 		0.0965
(0.579) 		0.374
(0.989) 		0.115
(0.615)
del 16p13 3 309 (54%) 264 0.835
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.667
(1.00) 		0.501
(1.00) 		0.905
(1.00) 		0.521
(1.00)
del 16q22 1 457 (80%) 116 0.798
(1.00) 		0.0145
(0.255) 		0.274
(0.926) 		0.589
(1.00) 		0.133
(0.679) 		0.0454
(0.429) 		0.428
(1.00)
del 17p12 486 (85%) 87 0.477
(1.00) 		0.772
(1.00) 		0.171
(0.761) 		1
(1.00) 		0.831
(1.00) 		0.494
(1.00) 		0.656
(1.00)
del 18q23 377 (66%) 196 0.569
(1.00) 		0.615
(1.00) 		0.154
(0.744) 		1
(1.00) 		0.653
(1.00) 		0.105
(0.588) 		1
(1.00)
del 19p13 3 506 (88%) 67 0.418
(1.00) 		0.0263
(0.336) 		1
(1.00) 		1
(1.00) 		0.102
(0.588) 		1
(1.00) 		1
(1.00)
del 19q13 33 296 (52%) 277 0.154
(0.744) 		0.548
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.0847
(0.546) 		0.326
(0.966) 		0.114
(0.615)
del 19q13 43 282 (49%) 291 0.51
(1.00) 		0.0336
(0.419) 		1
(1.00) 		0.373
(0.989) 		0.0408
(0.42) 		0.373
(0.989) 		0.209
(0.823)
del 21q22 3 224 (39%) 349 0.326
(0.966) 		0.426
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.329
(0.966) 		0.357
(0.989) 		0.331
(0.966)
del 22q13 32 499 (87%) 74 0.577
(1.00) 		0.914
(1.00) 		0.282
(0.937) 		1
(1.00) 		0.432
(1.00) 		0.819
(1.00) 		1
(1.00)
del xp21 1 354 (62%) 219 0.439
(1.00) 		0.396
(0.994) 		1
(1.00) 		0.655
(1.00) 		0.948
(1.00) 		0.759
(1.00) 		0.746
(1.00)
'amp_1p34.3' versus 'Time to Death'

P value = 0.00821 (logrank test), Q value = 0.18

Table S1.  Gene #1: 'amp_1p34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 559 331 0.3 - 180.2 (32.9)
AMP PEAK 1(1P34.3) MUTATED 286 156 0.4 - 180.2 (34.5)
AMP PEAK 1(1P34.3) WILD-TYPE 273 175 0.3 - 134.0 (31.0)

Figure S1.  Get High-res Image Gene #1: 'amp_1p34.3' versus Clinical Feature #1: 'Time to Death'

'amp_1q21.3' versus 'YEARS_TO_BIRTH'

P value = 8.07e-06 (Wilcoxon-test), Q value = 0.00059

Table S2.  Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED 351 61.5 (10.9)
AMP PEAK 2(1Q21.3) WILD-TYPE 201 56.9 (12.1)

Figure S2.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q42.2' versus 'YEARS_TO_BIRTH'

P value = 0.000784 (Wilcoxon-test), Q value = 0.031

Table S3.  Gene #3: 'amp_1q42.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 3(1Q42.2) MUTATED 304 61.3 (11.2)
AMP PEAK 3(1Q42.2) WILD-TYPE 248 58.1 (11.8)

Figure S3.  Get High-res Image Gene #3: 'amp_1q42.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.2' versus 'YEARS_TO_BIRTH'

P value = 0.00206 (Wilcoxon-test), Q value = 0.075

Table S4.  Gene #6: 'amp_3q26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 6(3Q26.2) MUTATED 462 60.5 (11.3)
AMP PEAK 6(3Q26.2) WILD-TYPE 90 56.2 (12.3)

Figure S4.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.011 (Wilcoxon-test), Q value = 0.21

Table S5.  Gene #9: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 9(5P15.33) MUTATED 296 61.0 (11.5)
AMP PEAK 9(5P15.33) WILD-TYPE 256 58.5 (11.5)

Figure S5.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_6p22.3' versus 'Time to Death'

P value = 0.0105 (logrank test), Q value = 0.21

Table S6.  Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 559 331 0.3 - 180.2 (32.9)
AMP PEAK 10(6P22.3) MUTATED 291 158 0.5 - 153.4 (31.3)
AMP PEAK 10(6P22.3) WILD-TYPE 268 173 0.3 - 180.2 (34.0)

Figure S6.  Get High-res Image Gene #10: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

'amp_6p22.3' versus 'YEARS_TO_BIRTH'

P value = 0.00267 (Wilcoxon-test), Q value = 0.091

Table S7.  Gene #10: 'amp_6p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 10(6P22.3) MUTATED 290 61.2 (11.8)
AMP PEAK 10(6P22.3) WILD-TYPE 262 58.3 (11.2)

Figure S7.  Get High-res Image Gene #10: 'amp_6p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p11.21' versus 'YEARS_TO_BIRTH'

P value = 0.000568 (Wilcoxon-test), Q value = 0.024

Table S8.  Gene #12: 'amp_8p11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 12(8P11.21) MUTATED 200 62.1 (10.9)
AMP PEAK 12(8P11.21) WILD-TYPE 352 58.5 (11.8)

Figure S8.  Get High-res Image Gene #12: 'amp_8p11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 0.000468 (Wilcoxon-test), Q value = 0.022

Table S9.  Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED 244 61.7 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE 308 58.4 (11.7)

Figure S9.  Get High-res Image Gene #14: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p13.33' versus 'YEARS_TO_BIRTH'

P value = 1.86e-07 (Wilcoxon-test), Q value = 3.2e-05

Table S10.  Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED 316 62.1 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE 236 56.8 (11.9)

Figure S10.  Get High-res Image Gene #17: 'amp_12p13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p12.1' versus 'YEARS_TO_BIRTH'

P value = 1.45e-08 (Wilcoxon-test), Q value = 5.3e-06

Table S11.  Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED 297 62.4 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE 255 56.8 (11.2)

Figure S11.  Get High-res Image Gene #18: 'amp_12p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 4.56e-07 (Wilcoxon-test), Q value = 5.8e-05

Table S12.  Gene #19: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 19(12Q15) MUTATED 207 63.0 (11.2)
AMP PEAK 19(12Q15) WILD-TYPE 345 57.9 (11.4)

Figure S12.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'TUMOR_TISSUE_SITE'

P value = 0.00742 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #19: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients OMENTUM OVARY PERITONEUM OVARY
ALL 3 558 2
AMP PEAK 19(12Q15) MUTATED 3 209 2
AMP PEAK 19(12Q15) WILD-TYPE 0 349 0

Figure S13.  Get High-res Image Gene #19: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 2.94e-05 (Wilcoxon-test), Q value = 0.0019

Table S14.  Gene #26: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 26(19Q12) MUTATED 308 61.7 (11.1)
AMP PEAK 26(19Q12) WILD-TYPE 244 57.5 (11.7)

Figure S14.  Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q13.2' versus 'Time to Death'

P value = 0.00655 (logrank test), Q value = 0.17

Table S15.  Gene #27: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 559 331 0.3 - 180.2 (32.9)
AMP PEAK 27(19Q13.2) MUTATED 237 149 0.3 - 180.2 (29.0)
AMP PEAK 27(19Q13.2) WILD-TYPE 322 182 0.4 - 134.0 (35.0)

Figure S15.  Get High-res Image Gene #27: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

'amp_19q13.2' versus 'YEARS_TO_BIRTH'

P value = 3.06e-06 (Wilcoxon-test), Q value = 0.00031

Table S16.  Gene #27: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 27(19Q13.2) MUTATED 235 62.5 (11.2)
AMP PEAK 27(19Q13.2) WILD-TYPE 317 57.8 (11.5)

Figure S16.  Get High-res Image Gene #27: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20p13' versus 'YEARS_TO_BIRTH'

P value = 0.00526 (Wilcoxon-test), Q value = 0.16

Table S17.  Gene #28: 'amp_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 28(20P13) MUTATED 305 61.1 (11.7)
AMP PEAK 28(20P13) WILD-TYPE 247 58.2 (11.2)

Figure S17.  Get High-res Image Gene #28: 'amp_20p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q11.21' versus 'YEARS_TO_BIRTH'

P value = 2.07e-08 (Wilcoxon-test), Q value = 5.3e-06

Table S18.  Gene #29: 'amp_20q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 29(20Q11.21) MUTATED 331 62.1 (11.5)
AMP PEAK 29(20Q11.21) WILD-TYPE 221 56.4 (10.9)

Figure S18.  Get High-res Image Gene #29: 'amp_20q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.33' versus 'YEARS_TO_BIRTH'

P value = 6.57e-06 (Wilcoxon-test), Q value = 0.00056

Table S19.  Gene #30: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
AMP PEAK 30(20Q13.33) MUTATED 386 61.3 (11.5)
AMP PEAK 30(20Q13.33) WILD-TYPE 166 56.5 (11.1)

Figure S19.  Get High-res Image Gene #30: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3p26.2' versus 'YEARS_TO_BIRTH'

P value = 0.00382 (Wilcoxon-test), Q value = 0.12

Table S20.  Gene #39: 'del_3p26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 6(3P26.2) MUTATED 200 61.8 (11.6)
DEL PEAK 6(3P26.2) WILD-TYPE 352 58.7 (11.4)

Figure S20.  Get High-res Image Gene #39: 'del_3p26.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 0.000102 (Wilcoxon-test), Q value = 0.0058

Table S21.  Gene #45: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 12(6Q27) MUTATED 360 58.5 (11.4)
DEL PEAK 12(6Q27) WILD-TYPE 192 62.4 (11.5)

Figure S21.  Get High-res Image Gene #45: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'TUMOR_TISSUE_SITE'

P value = 0.0106 (Fisher's exact test), Q value = 0.21

Table S22.  Gene #54: 'del_11p15.5' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients OMENTUM OVARY PERITONEUM OVARY
ALL 3 558 2
DEL PEAK 21(11P15.5) MUTATED 0 336 0
DEL PEAK 21(11P15.5) WILD-TYPE 3 222 2

Figure S22.  Get High-res Image Gene #54: 'del_11p15.5' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_12q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00753 (Wilcoxon-test), Q value = 0.17

Table S23.  Gene #56: 'del_12q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 23(12Q23.1) MUTATED 188 58.0 (10.6)
DEL PEAK 23(12Q23.1) WILD-TYPE 364 60.8 (11.9)

Figure S23.  Get High-res Image Gene #56: 'del_12q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'Time to Death'

P value = 0.00892 (logrank test), Q value = 0.19

Table S24.  Gene #58: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 559 331 0.3 - 180.2 (32.9)
DEL PEAK 25(13Q14.2) MUTATED 348 199 0.3 - 153.4 (34.8)
DEL PEAK 25(13Q14.2) WILD-TYPE 211 132 0.3 - 180.2 (29.2)

Figure S24.  Get High-res Image Gene #58: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_15q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00582 (Wilcoxon-test), Q value = 0.16

Table S25.  Gene #60: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 27(15Q11.2) MUTATED 285 61.1 (11.4)
DEL PEAK 27(15Q11.2) WILD-TYPE 267 58.4 (11.6)

Figure S25.  Get High-res Image Gene #60: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q15.1' versus 'YEARS_TO_BIRTH'

P value = 0.00571 (Wilcoxon-test), Q value = 0.16

Table S26.  Gene #61: 'del_15q15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 28(15Q15.1) MUTATED 346 60.9 (11.1)
DEL PEAK 28(15Q15.1) WILD-TYPE 206 58.1 (12.1)

Figure S26.  Get High-res Image Gene #61: 'del_15q15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000464 (Wilcoxon-test), Q value = 0.022

Table S27.  Gene #64: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 31(16Q23.1) MUTATED 433 60.8 (11.5)
DEL PEAK 31(16Q23.1) WILD-TYPE 119 56.4 (11.3)

Figure S27.  Get High-res Image Gene #64: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0125 (Wilcoxon-test), Q value = 0.23

Table S28.  Gene #66: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
DEL PEAK 33(17Q11.2) MUTATED 450 59.3 (11.5)
DEL PEAK 33(17Q11.2) WILD-TYPE 102 62.2 (11.7)

Figure S28.  Get High-res Image Gene #66: 'del_17q11.2' 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/OV-TP/22534546/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/22507289/OV-TP.merged_data.txt

  • Number of patients = 573

  • Number of significantly focal cnvs = 73

  • Number of selected clinical features = 7

  • 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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