Correlation between copy number variation genes (focal events) and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1K64GD3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1K64GD3
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 70 focal events and 6 clinical features across 562 patients, 12 significant findings detected with Q value < 0.25.

  • AMP PEAK 2(1Q21.3) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 3(1Q42.2) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 12(8P11.21) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 14(10P15.3) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 17(12P13.33) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 18(12P12.1) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 19(12Q15) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 26(19Q12) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 27(19Q13.2) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 29(20Q11.21) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • AMP PEAK 30(20Q13.33) MUTATION ANALYSIS cnv correlated to 'AGE'.

  • DEL PEAK 28(16Q23.1) MUTATION ANALYSIS cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 focal events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 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
AMP PEAK 2(1Q21 3) MUTATION ANALYSIS 353 (63%) 209 0.289
(1.00) 		3.74e-06
(0.00155) 		0.128
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.349
(1.00)
AMP PEAK 3(1Q42 2) MUTATION ANALYSIS 306 (54%) 256 0.275
(1.00) 		0.000591
(0.241) 		0.252
(1.00) 		0.736
(1.00) 		0.594
(1.00) 		0.875
(1.00)
AMP PEAK 12(8P11 21) MUTATION ANALYSIS 202 (36%) 360 0.281
(1.00) 		0.000504
(0.206) 		0.121
(1.00) 		0.662
(1.00) 		0.294
(1.00) 		0.161
(1.00)
AMP PEAK 14(10P15 3) MUTATION ANALYSIS 239 (43%) 323 0.111
(1.00) 		0.000403
(0.165) 		0.154
(1.00) 		0.923
(1.00) 		0.578
(1.00) 		0.76
(1.00)
AMP PEAK 17(12P13 33) MUTATION ANALYSIS 315 (56%) 247 0.753
(1.00) 		3.97e-07
(0.000165) 		0.756
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.339
(1.00)
AMP PEAK 18(12P12 1) MUTATION ANALYSIS 300 (53%) 262 0.101
(1.00) 		1.08e-08
(4.52e-06) 		0.251
(1.00) 		0.335
(1.00) 		0.601
(1.00) 		1
(1.00)
AMP PEAK 19(12Q15) MUTATION ANALYSIS 209 (37%) 353 0.108
(1.00) 		1.82e-07
(7.59e-05) 		0.0176
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.659
(1.00)
AMP PEAK 26(19Q12) MUTATION ANALYSIS 310 (55%) 252 0.665
(1.00) 		1.08e-05
(0.00443) 		0.162
(1.00) 		0.51
(1.00) 		1
(1.00) 		1
(1.00)
AMP PEAK 27(19Q13 2) MUTATION ANALYSIS 235 (42%) 327 0.0169
(1.00) 		3.09e-06
(0.00128) 		0.15
(1.00) 		0.989
(1.00) 		0.574
(1.00) 		0.211
(1.00)
AMP PEAK 29(20Q11 21) MUTATION ANALYSIS 328 (58%) 234 0.0969
(1.00) 		6.66e-08
(2.78e-05) 		1
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.584
(1.00)
AMP PEAK 30(20Q13 33) MUTATION ANALYSIS 389 (69%) 173 0.327
(1.00) 		9.79e-06
(0.00404) 		1
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.0802
(1.00)
DEL PEAK 28(16Q23 1) MUTATION ANALYSIS 437 (78%) 125 0.135
(1.00) 		8.12e-05
(0.0334) 		0.636
(1.00) 		0.0778
(1.00) 		1
(1.00) 		0.195
(1.00)
AMP PEAK 1(1P34 3) MUTATION ANALYSIS 280 (50%) 282 0.0305
(1.00) 		0.00905
(1.00) 		1
(1.00) 		0.985
(1.00) 		0.123
(1.00) 		0.478
(1.00)
AMP PEAK 4(2P23 2) MUTATION ANALYSIS 235 (42%) 327 0.935
(1.00) 		0.0822
(1.00) 		0.762
(1.00) 		0.988
(1.00) 		1
(1.00) 		0.664
(1.00)
AMP PEAK 5(2Q31 2) MUTATION ANALYSIS 248 (44%) 314 0.197
(1.00) 		0.0142
(1.00) 		0.756
(1.00) 		0.693
(1.00) 		0.0853
(1.00) 		0.873
(1.00)
AMP PEAK 6(3Q26 2) MUTATION ANALYSIS 466 (83%) 96 0.95
(1.00) 		0.000788
(0.32) 		0.527
(1.00) 		0.00131
(0.53) 		1
(1.00) 		0.778
(1.00)
AMP PEAK 7(4P16 3) MUTATION ANALYSIS 155 (28%) 407 0.372
(1.00) 		0.67
(1.00) 		0.723
(1.00) 		0.0728
(1.00) 		1
(1.00) 		0.529
(1.00)
AMP PEAK 8(4Q13 3) MUTATION ANALYSIS 106 (19%) 456 0.235
(1.00) 		0.204
(1.00) 		0.571
(1.00) 		0.42
(1.00) 		1
(1.00) 		0.411
(1.00)
AMP PEAK 9(5P15 33) MUTATION ANALYSIS 296 (53%) 266 0.0791
(1.00) 		0.00255
(1.00) 		0.751
(1.00) 		0.798
(1.00) 		0.605
(1.00) 		0.0469
(1.00)
AMP PEAK 10(6P22 3) MUTATION ANALYSIS 285 (51%) 277 0.147
(1.00) 		0.00508
(1.00) 		1
(1.00) 		0.545
(1.00) 		0.619
(1.00) 		0.514
(1.00)
AMP PEAK 11(7Q36 3) MUTATION ANALYSIS 300 (53%) 262 0.253
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.1
(1.00) 		0.601
(1.00) 		0.161
(1.00)
AMP PEAK 13(8Q24 21) MUTATION ANALYSIS 441 (78%) 121 0.573
(1.00) 		0.0972
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.518
(1.00) 		0.391
(1.00)
AMP PEAK 15(10Q22 3) MUTATION ANALYSIS 174 (31%) 388 0.545
(1.00) 		0.216
(1.00) 		0.0934
(1.00) 		0.989
(1.00) 		1
(1.00) 		0.415
(1.00)
AMP PEAK 16(11Q14 1) MUTATION ANALYSIS 248 (44%) 314 0.287
(1.00) 		0.326
(1.00) 		0.256
(1.00) 		0.474
(1.00) 		1
(1.00) 		1
(1.00)
AMP PEAK 20(14Q11 2) MUTATION ANALYSIS 142 (25%) 420 0.818
(1.00) 		0.0633
(1.00) 		0.124
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.812
(1.00)
AMP PEAK 21(14Q32 33) MUTATION ANALYSIS 150 (27%) 412 0.284
(1.00) 		0.0168
(1.00) 		0.711
(1.00) 		0.113
(1.00) 		0.175
(1.00) 		1
(1.00)
AMP PEAK 22(15Q26 3) MUTATION ANALYSIS 154 (27%) 408 0.0566
(1.00) 		0.291
(1.00) 		0.728
(1.00) 		0.42
(1.00) 		0.565
(1.00) 		1
(1.00)
AMP PEAK 23(17Q25 3) MUTATION ANALYSIS 204 (36%) 358 0.0402
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.0901
(1.00)
AMP PEAK 24(18Q11 2) MUTATION ANALYSIS 136 (24%) 426 0.956
(1.00) 		0.0427
(1.00) 		0.114
(1.00) 		0.18
(1.00) 		0.565
(1.00) 		0.837
(1.00)
AMP PEAK 25(19P13 12) MUTATION ANALYSIS 304 (54%) 258 0.181
(1.00) 		0.0684
(1.00) 		0.461
(1.00) 		0.597
(1.00) 		0.596
(1.00) 		0.413
(1.00)
AMP PEAK 28(20P13) MUTATION ANALYSIS 309 (55%) 253 0.311
(1.00) 		0.00193
(0.781) 		0.754
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.381
(1.00)
AMP PEAK 31(22Q12 2) MUTATION ANALYSIS 88 (16%) 474 0.506
(1.00) 		0.0234
(1.00) 		1
(1.00) 		0.419
(1.00) 		1
(1.00) 		1
(1.00)
AMP PEAK 32(XP11 23) MUTATION ANALYSIS 163 (29%) 399 0.174
(1.00) 		0.0215
(1.00) 		0.0781
(1.00) 		0.275
(1.00) 		0.56
(1.00) 		0.192
(1.00)
AMP PEAK 33(XQ28) MUTATION ANALYSIS 221 (39%) 341 0.337
(1.00) 		0.956
(1.00) 		0.77
(1.00) 		0.654
(1.00) 		0.0603
(1.00) 		0.871
(1.00)
DEL PEAK 1(1P36 11) MUTATION ANALYSIS 261 (46%) 301 0.205
(1.00) 		0.194
(1.00) 		0.751
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.871
(1.00)
DEL PEAK 2(1Q32 3) MUTATION ANALYSIS 92 (16%) 470 0.886
(1.00) 		0.512
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.416
(1.00)
DEL PEAK 3(2P25 3) MUTATION ANALYSIS 118 (21%) 444 0.827
(1.00) 		0.452
(1.00) 		0.615
(1.00) 		0.875
(1.00) 		0.508
(1.00) 		0.0216
(1.00)
DEL PEAK 4(2Q22 1) MUTATION ANALYSIS 131 (23%) 431 0.302
(1.00) 		0.378
(1.00) 		0.656
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.467
(1.00)
DEL PEAK 5(2Q37 3) MUTATION ANALYSIS 171 (30%) 391 0.467
(1.00) 		0.0991
(1.00) 		0.359
(1.00) 		0.432
(1.00) 		0.221
(1.00) 		0.253
(1.00)
DEL PEAK 6(3P26 2) MUTATION ANALYSIS 207 (37%) 355 0.771
(1.00) 		0.00233
(0.938) 		0.126
(1.00) 		0.246
(1.00) 		0.0495
(1.00) 		0.287
(1.00)
DEL PEAK 7(4Q22 1) MUTATION ANALYSIS 379 (67%) 183 0.581
(1.00) 		0.938
(1.00) 		1
(1.00) 		0.925
(1.00) 		1
(1.00) 		0.363
(1.00)
DEL PEAK 8(4Q34 3) MUTATION ANALYSIS 407 (72%) 155 0.887
(1.00) 		0.353
(1.00) 		0.728
(1.00) 		0.171
(1.00) 		0.565
(1.00) 		0.386
(1.00)
DEL PEAK 9(5Q11 2) MUTATION ANALYSIS 335 (60%) 227 0.662
(1.00) 		0.641
(1.00) 		0.767
(1.00) 		0.325
(1.00) 		0.568
(1.00) 		0.209
(1.00)
DEL PEAK 10(5Q13 2) MUTATION ANALYSIS 400 (71%) 162 0.206
(1.00) 		0.934
(1.00) 		0.747
(1.00) 		0.216
(1.00) 		0.201
(1.00) 		0.238
(1.00)
DEL PEAK 11(6Q27) MUTATION ANALYSIS 375 (67%) 187 0.301
(1.00) 		0.00067
(0.273) 		1
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.872
(1.00)
DEL PEAK 12(7P22 1) MUTATION ANALYSIS 244 (43%) 318 0.0635
(1.00) 		0.0274
(1.00) 		0.758
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.133
(1.00)
DEL PEAK 13(8P23 3) MUTATION ANALYSIS 377 (67%) 185 0.273
(1.00) 		0.0597
(1.00) 		1
(1.00) 		0.95
(1.00) 		1
(1.00) 		0.859
(1.00)
DEL PEAK 14(8P21 2) MUTATION ANALYSIS 392 (70%) 170 0.594
(1.00) 		0.0667
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00) 		0.658
(1.00)
DEL PEAK 15(9P24 3) MUTATION ANALYSIS 253 (45%) 309 0.86
(1.00) 		0.0238
(1.00) 		0.45
(1.00) 		0.928
(1.00) 		0.591
(1.00) 		0.584
(1.00)
DEL PEAK 16(9Q34 13) MUTATION ANALYSIS 336 (60%) 226 0.664
(1.00) 		0.0421
(1.00) 		0.767
(1.00) 		0.623
(1.00) 		0.277
(1.00) 		0.18
(1.00)
DEL PEAK 17(10P15 3) MUTATION ANALYSIS 118 (21%) 444 0.293
(1.00) 		0.839
(1.00) 		0.608
(1.00) 		0.72
(1.00) 		0.508
(1.00) 		1
(1.00)
DEL PEAK 18(10Q23 31) MUTATION ANALYSIS 219 (39%) 343 0.258
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.563
(1.00) 		0.601
(1.00)
DEL PEAK 19(10Q26 3) MUTATION ANALYSIS 189 (34%) 373 0.0587
(1.00) 		0.817
(1.00) 		0.8
(1.00) 		0.77
(1.00) 		1
(1.00) 		1
(1.00)
DEL PEAK 20(11P15 5) MUTATION ANALYSIS 332 (59%) 230 0.0523
(1.00) 		0.55
(1.00) 		0.0267
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.664
(1.00)
DEL PEAK 21(11Q25) MUTATION ANALYSIS 193 (34%) 369 0.605
(1.00) 		0.0771
(1.00) 		0.225
(1.00) 		0.631
(1.00) 		0.272
(1.00) 		0.253
(1.00)
DEL PEAK 22(12Q24 33) MUTATION ANALYSIS 211 (38%) 351 0.757
(1.00) 		0.106
(1.00) 		0.13
(1.00) 		0.652
(1.00) 		0.295
(1.00) 		0.0793
(1.00)
DEL PEAK 23(13Q14 2) MUTATION ANALYSIS 349 (62%) 213 0.0572
(1.00) 		0.549
(1.00) 		0.777
(1.00) 		0.592
(1.00) 		0.56
(1.00) 		0.272
(1.00)
DEL PEAK 24(14Q23 3) MUTATION ANALYSIS 295 (52%) 267 0.408
(1.00) 		0.604
(1.00) 		0.475
(1.00) 		0.0123
(1.00) 		0.107
(1.00) 		0.478
(1.00)
DEL PEAK 25(15Q15 1) MUTATION ANALYSIS 353 (63%) 209 0.714
(1.00) 		0.00534
(1.00) 		0.411
(1.00) 		0.253
(1.00) 		0.298
(1.00) 		0.87
(1.00)
DEL PEAK 26(16P13 3) MUTATION ANALYSIS 299 (53%) 263 0.839
(1.00) 		0.867
(1.00) 		0.751
(1.00) 		0.578
(1.00) 		0.602
(1.00) 		0.759
(1.00)
DEL PEAK 27(16Q22 1) MUTATION ANALYSIS 447 (80%) 115 0.56
(1.00) 		0.00438
(1.00) 		0.193
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.329
(1.00)
DEL PEAK 29(17P12) MUTATION ANALYSIS 475 (85%) 87 0.716
(1.00) 		0.99
(1.00) 		0.493
(1.00) 		0.73
(1.00) 		1
(1.00) 		0.47
(1.00)
DEL PEAK 30(17Q11 2) MUTATION ANALYSIS 460 (82%) 102 0.65
(1.00) 		0.0323
(1.00) 		0.0666
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.873
(1.00)
DEL PEAK 31(18Q23) MUTATION ANALYSIS 368 (65%) 194 0.754
(1.00) 		0.464
(1.00) 		0.225
(1.00) 		0.544
(1.00) 		1
(1.00) 		1
(1.00)
DEL PEAK 32(19P13 3) MUTATION ANALYSIS 495 (88%) 67 0.291
(1.00) 		0.0168
(1.00) 		1
(1.00) 		0.00833
(1.00) 		1
(1.00) 		0.423
(1.00)
DEL PEAK 33(19Q13 33) MUTATION ANALYSIS 291 (52%) 271 0.572
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.25
(1.00) 		0.354
(1.00)
DEL PEAK 34(19Q13 43) MUTATION ANALYSIS 276 (49%) 286 0.367
(1.00) 		0.03
(1.00) 		1
(1.00) 		0.283
(1.00) 		1
(1.00) 		0.339
(1.00)
DEL PEAK 35(21Q22 3) MUTATION ANALYSIS 217 (39%) 345 0.495
(1.00) 		0.341
(1.00) 		0.774
(1.00) 		0.665
(1.00) 		1
(1.00) 		0.664
(1.00)
DEL PEAK 36(22Q13 32) MUTATION ANALYSIS 487 (87%) 75 0.887
(1.00) 		0.909
(1.00) 		0.443
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.675
(1.00)
DEL PEAK 37(XP21 1) MUTATION ANALYSIS 360 (64%) 202 0.913
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.987
(1.00) 		0.556
(1.00) 		0.759
(1.00)
'AMP PEAK 2(1Q21.3) MUTATION STATUS' versus 'AGE'

P value = 3.74e-06 (t-test), Q value = 0.0015

Table S1.  Gene #2: 'AMP PEAK 2(1Q21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED 341 61.6 (11.0)
AMP PEAK 2(1Q21.3) WILD-TYPE 200 56.7 (12.0)

Figure S1.  Get High-res Image Gene #2: 'AMP PEAK 2(1Q21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 3(1Q42.2) MUTATION STATUS' versus 'AGE'

P value = 0.000591 (t-test), Q value = 0.24

Table S2.  Gene #3: 'AMP PEAK 3(1Q42.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 3(1Q42.2) MUTATED 293 61.4 (11.3)
AMP PEAK 3(1Q42.2) WILD-TYPE 248 57.9 (11.7)

Figure S2.  Get High-res Image Gene #3: 'AMP PEAK 3(1Q42.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 12(8P11.21) MUTATION STATUS' versus 'AGE'

P value = 0.000504 (t-test), Q value = 0.21

Table S3.  Gene #12: 'AMP PEAK 12(8P11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 12(8P11.21) MUTATED 192 62.1 (10.8)
AMP PEAK 12(8P11.21) WILD-TYPE 349 58.5 (11.8)

Figure S3.  Get High-res Image Gene #12: 'AMP PEAK 12(8P11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 14(10P15.3) MUTATION STATUS' versus 'AGE'

P value = 0.000403 (t-test), Q value = 0.17

Table S4.  Gene #14: 'AMP PEAK 14(10P15.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED 233 61.8 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE 308 58.3 (11.7)

Figure S4.  Get High-res Image Gene #14: 'AMP PEAK 14(10P15.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 17(12P13.33) MUTATION STATUS' versus 'AGE'

P value = 3.97e-07 (t-test), Q value = 0.00016

Table S5.  Gene #17: 'AMP PEAK 17(12P13.33) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED 303 62.0 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE 238 56.9 (12.0)

Figure S5.  Get High-res Image Gene #17: 'AMP PEAK 17(12P13.33) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 18(12P12.1) MUTATION STATUS' versus 'AGE'

P value = 1.08e-08 (t-test), Q value = 4.5e-06

Table S6.  Gene #18: 'AMP PEAK 18(12P12.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED 286 62.5 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE 255 56.8 (11.4)

Figure S6.  Get High-res Image Gene #18: 'AMP PEAK 18(12P12.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 19(12Q15) MUTATION STATUS' versus 'AGE'

P value = 1.82e-07 (t-test), Q value = 7.6e-05

Table S7.  Gene #19: 'AMP PEAK 19(12Q15) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 19(12Q15) MUTATED 195 63.2 (11.3)
AMP PEAK 19(12Q15) WILD-TYPE 346 57.8 (11.4)

Figure S7.  Get High-res Image Gene #19: 'AMP PEAK 19(12Q15) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 26(19Q12) MUTATION STATUS' versus 'AGE'

P value = 1.08e-05 (t-test), Q value = 0.0044

Table S8.  Gene #26: 'AMP PEAK 26(19Q12) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 26(19Q12) MUTATED 300 61.8 (11.1)
AMP PEAK 26(19Q12) WILD-TYPE 241 57.3 (11.8)

Figure S8.  Get High-res Image Gene #26: 'AMP PEAK 26(19Q12) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 27(19Q13.2) MUTATION STATUS' versus 'AGE'

P value = 3.09e-06 (t-test), Q value = 0.0013

Table S9.  Gene #27: 'AMP PEAK 27(19Q13.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 27(19Q13.2) MUTATED 228 62.5 (11.2)
AMP PEAK 27(19Q13.2) WILD-TYPE 313 57.8 (11.5)

Figure S9.  Get High-res Image Gene #27: 'AMP PEAK 27(19Q13.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 29(20Q11.21) MUTATION STATUS' versus 'AGE'

P value = 6.66e-08 (t-test), Q value = 2.8e-05

Table S10.  Gene #29: 'AMP PEAK 29(20Q11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 29(20Q11.21) MUTATED 315 62.0 (11.5)
AMP PEAK 29(20Q11.21) WILD-TYPE 226 56.7 (11.0)

Figure S10.  Get High-res Image Gene #29: 'AMP PEAK 29(20Q11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 30(20Q13.33) MUTATION STATUS' versus 'AGE'

P value = 9.79e-06 (t-test), Q value = 0.004

Table S11.  Gene #30: 'AMP PEAK 30(20Q13.33) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
AMP PEAK 30(20Q13.33) MUTATED 376 61.2 (11.5)
AMP PEAK 30(20Q13.33) WILD-TYPE 165 56.5 (11.1)

Figure S11.  Get High-res Image Gene #30: 'AMP PEAK 30(20Q13.33) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 28(16Q23.1) MUTATION STATUS' versus 'AGE'

P value = 8.12e-05 (t-test), Q value = 0.033

Table S12.  Gene #61: 'DEL PEAK 28(16Q23.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
DEL PEAK 28(16Q23.1) MUTATED 423 60.8 (11.5)
DEL PEAK 28(16Q23.1) WILD-TYPE 118 56.1 (11.2)

Figure S12.  Get High-res Image Gene #61: 'DEL PEAK 28(16Q23.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

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

  • Clinical data file = OV-TP.clin.merged.picked.txt

  • Number of patients = 562

  • Number of significantly focal cnvs = 70

  • Number of selected clinical features = 6

  • 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

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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