Correlation between copy number variations of arm-level result and selected clinical features
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 8 clinical features across 472 patients, 93 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 1q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 3q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 4p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 7q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 9q gain cnv correlated to 'GENDER'.

  • 10p gain cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.

  • 11p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'Time to Death'.

  • 16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p gain cnv correlated to 'Time to Death'.

  • 17q gain cnv correlated to 'Time to Death'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 19q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 20p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 20q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • xp gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • xq gain cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • 1p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 1q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 3q loss cnv correlated to 'Time to Death'.

  • 4p loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 4q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 6p loss cnv correlated to 'Time to Death'.

  • 6q loss cnv correlated to 'Time to Death',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 8p loss cnv correlated to 'Time to Death'.

  • 8q loss cnv correlated to 'Time to Death'.

  • 9p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 9q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 10p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 10q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 11p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 11q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 12q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 13q loss cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 14q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 16p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 17p loss cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 17q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 18p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 18q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • 21q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'HISTOLOGICAL_TYPE'.

  • 22q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • xq loss cnv correlated to 'Time to Death'.

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 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 93 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
10p loss 74 (16%) 398 0
(0) 		3.96e-17
(8.46e-15) 		0.703
(1.00) 		0.00324
(0.0493) 		0.00019
(0.00486) 		0.524
(0.934) 		0.0132
(0.136) 		0.751
(1.00)
10q loss 87 (18%) 385 0
(0) 		1.05e-14
(1.69e-12) 		0.475
(0.895) 		0.0166
(0.161) 		5e-05
(0.00139) 		0.654
(1.00) 		0.0344
(0.241) 		0.546
(0.948)
10p gain 53 (11%) 419 0.742
(1.00) 		0.0236
(0.199) 		0.243
(0.688) 		0.0695
(0.367) 		0.00072
(0.0132) 		0.0255
(0.204) 		1
(1.00) 		0.034
(0.241)
1p loss 171 (36%) 301 0.00267
(0.0438) 		0.000263
(0.00625) 		0.847
(1.00) 		0.751
(1.00) 		1e-05
(0.000427) 		0.0153
(0.153) 		0.314
(0.736) 		1
(1.00)
20p gain 38 (8%) 434 1.14e-07
(9.12e-06) 		3.59e-07
(2.56e-05) 		0.733
(1.00) 		0.0317
(0.241) 		0.252
(0.688) 		1
(1.00) 		0.366
(0.797) 		1
(1.00)
6q loss 55 (12%) 417 3.39e-05
(0.00114) 		0.0878
(0.422) 		0.567
(0.962) 		0.0032
(0.0493) 		0.00051
(0.0105) 		0.146
(0.559) 		0.111
(0.475) 		1
(1.00)
9p loss 104 (22%) 368 0.000495
(0.0105) 		0.0322
(0.241) 		0.823
(1.00) 		0.0813
(0.406) 		0.176
(0.593) 		0.0356
(0.245) 		0.939
(1.00) 		1
(1.00)
19q loss 193 (41%) 279 0.0191
(0.18) 		0.0258
(0.204) 		0.925
(1.00) 		0.618
(0.987) 		1e-05
(0.000427) 		0.126
(0.506) 		0.904
(1.00) 		0.467
(0.894)
22q loss 50 (11%) 422 1.93e-05
(0.000688) 		1.87e-05
(0.000688) 		0.548
(0.948) 		0.0284
(0.221) 		0.253
(0.688) 		0.853
(1.00) 		0.168
(0.585) 		1
(1.00)
1p gain 11 (2%) 461 0.0116
(0.126) 		0.0456
(0.286) 		0.223
(0.664) 		0.975
(1.00) 		0.00822
(0.0939) 		0.455
(0.875) 		1
(1.00) 		1
(1.00)
3p gain 11 (2%) 461 0.00348
(0.0518) 		0.0888
(0.424) 		0.545
(0.948) 		0.753
(1.00) 		0.0258
(0.204) 		0.455
(0.875) 		1
(1.00) 		1
(1.00)
3q gain 8 (2%) 464 0.000903
(0.0161) 		0.0347
(0.241) 		0.305
(0.734) 		0.293
(0.728) 		0.0805
(0.406) 		0.191
(0.622) 		1
(1.00) 		1
(1.00)
7p gain 110 (23%) 362 9.45e-06
(0.000427) 		3.39e-08
(3.1e-06) 		0.19
(0.622) 		0.106
(0.464) 		0.214
(0.648) 		0.681
(1.00) 		0.041
(0.269) 		0.778
(1.00)
7q gain 141 (30%) 331 5e-05
(0.00139) 		1e-08
(1.28e-06) 		0.417
(0.84) 		0.308
(0.734) 		0.0597
(0.338) 		0.377
(0.806) 		0.0659
(0.358) 		0.8
(1.00)
11p gain 30 (6%) 442 0.517
(0.928) 		0.0244
(0.201) 		0.182
(0.608) 		0.936
(1.00) 		0.0121
(0.129) 		1
(1.00) 		1
(1.00) 		0.339
(0.766)
19p gain 91 (19%) 381 0.641
(1) 		0.0155
(0.153) 		0.412
(0.834) 		0.0986
(0.454) 		1e-05
(0.000427) 		0.661
(1.00) 		0.692
(1.00) 		0.764
(1.00)
19q gain 22 (5%) 450 1.49e-05
(0.000597) 		4.07e-05
(0.00124) 		0.83
(1.00) 		0.234
(0.681) 		0.257
(0.688) 		0.782
(1.00) 		0.155
(0.574) 		0.595
(0.978)
20q gain 38 (8%) 434 2.28e-08
(2.43e-06) 		4.76e-07
(3.05e-05) 		0.306
(0.734) 		0.0562
(0.324) 		0.442
(0.862) 		0.831
(1.00) 		0.698
(1.00) 		1
(1.00)
xq gain 34 (7%) 438 0.515
(0.928) 		0.196
(0.625) 		0.00394
(0.0549) 		0.147
(0.561) 		0.0218
(0.191) 		0.506
(0.928) 		0.308
(0.734) 		0.118
(0.497)
4p loss 63 (13%) 409 0.67
(1.00) 		0.00371
(0.054) 		0.101
(0.461) 		0.615
(0.987) 		0.00054
(0.0108) 		0.231
(0.681) 		0.273
(0.709) 		0.489
(0.91)
5p loss 33 (7%) 439 0.925
(1.00) 		0.3
(0.731) 		1
(1.00) 		0.0749
(0.387) 		0.0138
(0.14) 		0.0201
(0.181) 		0.803
(1.00) 		0.629
(0.992)
11q loss 20 (4%) 452 0.00213
(0.0359) 		0.173
(0.585) 		1
(1.00) 		0.0401
(0.267) 		0.0169
(0.161) 		0.391
(0.81) 		1
(1.00) 		0.577
(0.969)
14q loss 70 (15%) 402 3.62e-05
(0.00116) 		0.00031
(0.00685) 		0.897
(1.00) 		0.14
(0.544) 		0.172
(0.585) 		0.513
(0.928) 		0.249
(0.688) 		0.489
(0.91)
17p loss 12 (3%) 460 0.00732
(0.0867) 		0.0513
(0.301) 		0.38
(0.806) 		0.00311
(0.0493) 		0.71
(1.00) 		0.476
(0.895) 		1
(1.00) 		0.0828
(0.411)
21q loss 29 (6%) 443 0.89
(1.00) 		0.653
(1.00) 		0.7
(1.00) 		0.000655
(0.0123) 		0.0218
(0.191) 		0.628
(0.992) 		0.779
(1.00) 		1
(1.00)
1q gain 20 (4%) 452 0.428
(0.852) 		0.000188
(0.00486) 		0.647
(1.00) 		0.246
(0.688) 		0.16
(0.585) 		0.563
(0.96) 		0.407
(0.826) 		1
(1.00)
4p gain 11 (2%) 461 0.238
(0.684) 		0.847
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.0245
(0.201) 		0.7
(1.00) 		0.449
(0.873) 		1
(1.00)
9q gain 22 (5%) 450 0.165
(0.585) 		0.0419
(0.269) 		0.00706
(0.0867) 		0.281
(0.726) 		0.0692
(0.367) 		0.592
(0.978) 		0.336
(0.765) 		0.595
(0.978)
12q gain 14 (3%) 458 0.0236
(0.199) 		0.314
(0.736) 		0.286
(0.727) 		0.122
(0.497) 		1
(1.00) 		1
(1.00) 		0.301
(0.731) 		1
(1.00)
16q gain 18 (4%) 454 0.421
(0.844) 		0.801
(1.00) 		0.338
(0.766) 		0.849
(1.00) 		0.0229
(0.198) 		0.365
(0.797) 		0.603
(0.978) 		1
(1.00)
17p gain 18 (4%) 454 0.0324
(0.241) 		0.07
(0.367) 		0.226
(0.671) 		0.634
(0.998) 		0.0862
(0.421) 		0.763
(1.00) 		0.363
(0.797) 		0.518
(0.928)
17q gain 20 (4%) 452 0.00649
(0.0815) 		0.189
(0.622) 		0.253
(0.688) 		0.986
(1.00) 		0.161
(0.585) 		1
(1.00) 		0.384
(0.809) 		0.518
(0.928)
21q gain 23 (5%) 449 0.181
(0.606) 		0.011
(0.124) 		0.4
(0.821) 		0.237
(0.684) 		0.963
(1.00) 		0.788
(1.00) 		0.478
(0.895) 		0.614
(0.987)
22q gain 17 (4%) 455 0.533
(0.943) 		0.0426
(0.27) 		1
(1.00) 		0.206
(0.635) 		0.00478
(0.0624) 		1
(1.00) 		1
(1.00) 		0.45
(0.873)
xp gain 18 (4%) 454 0.987
(1.00) 		0.674
(1.00) 		0.149
(0.566) 		0.033
(0.241) 		0.127
(0.509) 		0.365
(0.797) 		0.258
(0.688) 		1
(1.00)
1q loss 24 (5%) 448 0.883
(1.00) 		0.049
(0.295) 		0.836
(1.00) 		0.838
(1.00) 		0.0124
(0.13) 		0.438
(0.86) 		0.169
(0.585) 		1
(1.00)
3p loss 26 (6%) 446 0.0369
(0.251) 		0.79
(1.00) 		0.223
(0.664) 		0.000594
(0.0115) 		0.935
(1.00) 		0.799
(1.00) 		0.516
(0.928) 		0.0763
(0.391)
3q loss 25 (5%) 447 0.00785
(0.0913) 		0.564
(0.96) 		0.301
(0.731) 		0.203
(0.634) 		1
(1.00) 		0.603
(0.978) 		0.395
(0.815) 		0.259
(0.688)
4q loss 82 (17%) 390 0.495
(0.913) 		0.211
(0.645) 		0.271
(0.708) 		0.89
(1.00) 		0.00415
(0.0565) 		0.36
(0.797) 		0.545
(0.948) 		0.335
(0.765)
5q loss 33 (7%) 439 0.11
(0.474) 		0.267
(0.701) 		0.367
(0.797) 		0.357
(0.797) 		0.0201
(0.181) 		0.0645
(0.353) 		0.804
(1.00) 		1
(1.00)
6p loss 26 (6%) 446 8.82e-06
(0.000427) 		0.0912
(0.433) 		0.84
(1.00) 		0.156
(0.574) 		0.199
(0.625) 		1
(1.00) 		0.0927
(0.436) 		1
(1.00)
8p loss 15 (3%) 457 0.0287
(0.222) 		0.234
(0.681) 		1
(1.00) 		0.185
(0.612) 		0.173
(0.585) 		0.506
(0.928) 		0.197
(0.625) 		0.473
(0.895)
8q loss 9 (2%) 463 0.0199
(0.181) 		0.151
(0.567) 		0.513
(0.928) 		0.345
(0.777) 		0.435
(0.857) 		0.69
(1.00) 		0.192
(0.624) 		0.318
(0.736)
9q loss 44 (9%) 428 0.0511
(0.301) 		0.0526
(0.306) 		1
(1.00) 		0.00135
(0.0234) 		0.959
(1.00) 		1
(1.00) 		0.306
(0.734) 		0.688
(1.00)
11p loss 57 (12%) 415 0.206
(0.635) 		0.26
(0.688) 		0.257
(0.688) 		0.156
(0.574) 		0.00387
(0.0549) 		0.29
(0.728) 		0.71
(1.00) 		1
(1.00)
12q loss 46 (10%) 426 0.722
(1.00) 		0.0708
(0.368) 		1
(1.00) 		0.259
(0.688) 		0.00562
(0.0719) 		0.696
(1.00) 		0.54
(0.948) 		0.238
(0.684)
13q loss 105 (22%) 367 0.642
(1) 		0.853
(1.00) 		0.0941
(0.44) 		0.172
(0.585) 		0.544
(0.948) 		0.0115
(0.126) 		0.389
(0.81) 		0.774
(1.00)
16p loss 11 (2%) 461 0.115
(0.487) 		0.000239
(0.00588) 		0.362
(0.797) 		0.156
(0.574) 		0.545
(0.948) 		1
(1.00) 		1
(1.00) 		0.374
(0.803)
16q loss 19 (4%) 453 0.123
(0.497) 		0.000301
(0.00685) 		1
(1.00) 		0.387
(0.809) 		0.365
(0.797) 		0.39
(0.81) 		0.645
(1.00) 		0.558
(0.956)
17q loss 8 (2%) 464 0.38
(0.806) 		0.165
(0.585) 		0.733
(1.00) 		0.0344
(0.241) 		0.826
(1.00) 		1
(1.00) 		1
(1.00) 		0.0388
(0.261)
18p loss 63 (13%) 409 0.862
(1.00) 		0.00447
(0.0596) 		0.172
(0.585) 		0.511
(0.928) 		0.284
(0.727) 		0.735
(1.00) 		0.0631
(0.348) 		0.715
(1.00)
18q loss 58 (12%) 414 0.477
(0.895) 		0.0346
(0.241) 		0.573
(0.967) 		0.884
(1.00) 		0.106
(0.464) 		1
(1.00) 		0.0475
(0.295) 		0.469
(0.895)
xq loss 65 (14%) 407 0.00725
(0.0867) 		0.249
(0.688) 		0.591
(0.978) 		0.196
(0.625) 		0.729
(1.00) 		0.868
(1.00) 		0.403
(0.822) 		0.73
(1.00)
2p gain 13 (3%) 459 0.301
(0.731) 		0.133
(0.52) 		0.573
(0.967) 		0.291
(0.728) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		0.4
(0.821)
2q gain 12 (3%) 460 0.598
(0.978) 		0.279
(0.724) 		0.38
(0.806) 		0.291
(0.728) 		0.709
(1.00) 		1
(1.00) 		1
(1.00) 		0.374
(0.803)
4q gain 5 (1%) 467 0.241
(0.688) 		0.318
(0.736) 		1
(1.00) 		0.223
(0.664) 		0.588
(0.978) 		1
(1.00) 		1
(1.00)
5p gain 9 (2%) 463 0.256
(0.688) 		0.112
(0.477) 		1
(1.00) 		0.902
(1.00) 		0.133
(0.52) 		1
(1.00) 		0.168
(0.585) 		1
(1.00)
5q gain 6 (1%) 466 0.696
(1.00) 		0.264
(0.695) 		1
(1.00) 		0.984
(1.00) 		0.587
(0.978) 		0.602
(0.978) 		0.104
(0.464) 		1
(1.00)
6p gain 7 (1%) 465 0.698
(1.00) 		0.122
(0.497) 		0.248
(0.688) 		0.984
(1.00) 		0.206
(0.635) 		0.627
(0.992) 		1
(1.00) 		1
(1.00)
8p gain 43 (9%) 429 0.913
(1.00) 		0.894
(1.00) 		0.422
(0.844) 		0.618
(0.987) 		0.325
(0.746) 		0.689
(1.00) 		1
(1.00) 		0.682
(1.00)
8q gain 51 (11%) 421 0.823
(1.00) 		0.285
(0.727) 		0.372
(0.803) 		0.943
(1.00) 		0.078
(0.396) 		1
(1.00) 		0.76
(1.00) 		0.433
(0.856)
9p gain 15 (3%) 457 0.123
(0.497) 		0.0487
(0.295) 		0.109
(0.474) 		0.315
(0.736) 		0.3
(0.731) 		1
(1.00) 		1
(1.00) 		1
(1.00)
10q gain 9 (2%) 463 0.948
(1.00) 		0.492
(0.912) 		0.738
(1.00) 		0.218
(0.658) 		0.0413
(0.269) 		0.387
(0.809) 		0.0868
(0.421) 		0.288
(0.728)
11q gain 56 (12%) 416 0.234
(0.681) 		0.0608
(0.34) 		0.199
(0.625) 		0.574
(0.967) 		0.359
(0.797) 		1
(1.00) 		0.688
(1.00) 		1
(1.00)
12p gain 30 (6%) 442 0.677
(1.00) 		0.402
(0.822) 		0.26
(0.688) 		0.973
(1.00) 		0.311
(0.736) 		1
(1.00) 		0.597
(0.978) 		1
(1.00)
13q gain 6 (1%) 466 0.431
(0.853) 		0.935
(1.00) 		1
(1.00) 		0.042
(0.269) 		0.888
(1.00) 		0.602
(0.978) 		1
(1.00) 		1
(1.00)
14q gain 3 (1%) 469 0.385
(0.809) 		0.212
(0.645) 		1
(1.00) 		1
(1.00) 		0.0986
(0.454) 		1
(1.00) 		1
(1.00)
15q gain 9 (2%) 463 0.048
(0.295) 		0.0494
(0.295) 		0.738
(1.00) 		0.325
(0.746) 		0.243
(0.688) 		0.69
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 16 (3%) 456 0.693
(1.00) 		0.119
(0.497) 		0.317
(0.736) 		0.524
(0.934) 		0.122
(0.497) 		0.528
(0.939) 		0.559
(0.956) 		1
(1.00)
18p gain 15 (3%) 457 0.0685
(0.367) 		0.925
(1.00) 		0.799
(1.00) 		0.493
(0.912) 		0.295
(0.73) 		0.746
(1.00) 		0.557
(0.956) 		1
(1.00)
18q gain 10 (2%) 462 0.0597
(0.338) 		0.923
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.477
(0.895) 		0.695
(1.00) 		0.417
(0.84) 		1
(1.00)
2p loss 19 (4%) 453 0.199
(0.625) 		0.722
(1.00) 		0.64
(1) 		0.321
(0.742) 		0.363
(0.797) 		1
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 16 (3%) 456 0.907
(1.00) 		0.285
(0.727) 		0.799
(1.00) 		0.145
(0.558) 		0.105
(0.464) 		1
(1.00) 		1
(1.00) 		1
(1.00)
7p loss 3 (1%) 469 0.601
(0.978) 		0.637
(0.999) 		0.583
(0.977) 		0.629
(0.992) 		1
(1.00) 		1
(1.00) 		1
(1.00)
7q loss 3 (1%) 469 0.782
(1.00) 		0.936
(1.00) 		1
(1.00) 		0.931
(1.00) 		0.629
(0.992) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12p loss 24 (5%) 448 0.771
(1.00) 		0.0611
(0.34) 		0.534
(0.943) 		0.293
(0.728) 		0.0849
(0.418) 		0.795
(1.00) 		1
(1.00) 		0.614
(0.987)
15q loss 46 (10%) 426 0.44
(0.861) 		0.428
(0.852) 		0.757
(1.00) 		0.618
(0.987) 		0.547
(0.948) 		0.845
(1.00) 		0.453
(0.875) 		1
(1.00)
19p loss 22 (5%) 450 0.697
(1.00) 		0.84
(1.00) 		1
(1.00) 		0.103
(0.464) 		1
(1.00) 		0.164
(0.585) 		0.132
(0.52) 		0.166
(0.585)
20p loss 5 (1%) 467 0.766
(1.00) 		0.993
(1.00) 		0.657
(1.00) 		0.551
(0.951) 		0.252
(0.688) 		0.105
(0.464) 		1
(1.00)
xp loss 89 (19%) 383 0.199
(0.625) 		0.836
(1.00) 		0.478
(0.895) 		0.171
(0.585) 		0.775
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.13
(0.516)
'1p gain' versus 'Time to Death'

P value = 0.0116 (logrank test), Q value = 0.13

Table S1.  Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
1P GAIN MUTATED 11 4 0.2 - 42.7 (15.0)
1P GAIN WILD-TYPE 459 90 0.0 - 211.2 (18.7)

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00822 (Fisher's exact test), Q value = 0.094

Table S2.  Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
1P GAIN MUTATED 9 0 2
1P GAIN WILD-TYPE 167 118 176

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000188 (Wilcoxon-test), Q value = 0.0049

Table S3.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
1Q GAIN MUTATED 20 54.1 (11.6)
1Q GAIN WILD-TYPE 451 42.6 (13.3)

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'Time to Death'

P value = 0.00348 (logrank test), Q value = 0.052

Table S4.  Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
3P GAIN MUTATED 11 4 0.2 - 47.8 (8.8)
3P GAIN WILD-TYPE 459 90 0.0 - 211.2 (18.8)

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0258 (Fisher's exact test), Q value = 0.2

Table S5.  Gene #5: '3p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
3P GAIN MUTATED 8 0 3
3P GAIN WILD-TYPE 168 118 175

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 0.000903 (logrank test), Q value = 0.016

Table S6.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
3Q GAIN MUTATED 8 4 0.2 - 47.8 (13.1)
3Q GAIN WILD-TYPE 462 90 0.0 - 211.2 (18.7)

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0347 (Wilcoxon-test), Q value = 0.24

Table S7.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
3Q GAIN MUTATED 8 52.8 (11.4)
3Q GAIN WILD-TYPE 463 42.9 (13.4)

Figure S7.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0245 (Fisher's exact test), Q value = 0.2

Table S8.  Gene #7: '4p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
4P GAIN MUTATED 8 0 3
4P GAIN WILD-TYPE 168 118 175

Figure S8.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'Time to Death'

P value = 9.45e-06 (logrank test), Q value = 0.00043

Table S9.  Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
7P GAIN MUTATED 110 37 0.1 - 211.2 (16.7)
7P GAIN WILD-TYPE 360 57 0.0 - 182.3 (19.2)

Figure S9.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 3.39e-08 (Wilcoxon-test), Q value = 3.1e-06

Table S10.  Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
7P GAIN MUTATED 110 49.3 (13.1)
7P GAIN WILD-TYPE 361 41.1 (13.0)

Figure S10.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'Time to Death'

P value = 5e-05 (logrank test), Q value = 0.0014

Table S11.  Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
7Q GAIN MUTATED 141 43 0.1 - 211.2 (17.4)
7Q GAIN WILD-TYPE 329 51 0.0 - 182.3 (19.6)

Figure S11.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 1e-08 (Wilcoxon-test), Q value = 1.3e-06

Table S12.  Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
7Q GAIN MUTATED 141 48.5 (13.2)
7Q GAIN WILD-TYPE 330 40.7 (12.9)

Figure S12.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'GENDER'

P value = 0.00706 (Fisher's exact test), Q value = 0.087

Table S13.  Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 206 266
9Q GAIN MUTATED 16 6
9Q GAIN WILD-TYPE 190 260

Figure S13.  Get High-res Image Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0236 (Wilcoxon-test), Q value = 0.2

Table S14.  Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
10P GAIN MUTATED 53 38.4 (10.9)
10P GAIN WILD-TYPE 418 43.6 (13.6)

Figure S14.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00072 (Fisher's exact test), Q value = 0.013

Table S15.  Gene #18: '10p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
10P GAIN MUTATED 28 17 8
10P GAIN WILD-TYPE 148 101 170

Figure S15.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0255 (Fisher's exact test), Q value = 0.2

Table S16.  Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
10P GAIN MUTATED 17 36
10P GAIN WILD-TYPE 75 344

Figure S16.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10p gain' versus 'ETHNICITY'

P value = 0.034 (Fisher's exact test), Q value = 0.24

Table S17.  Gene #18: '10p gain' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 18 419
10P GAIN MUTATED 5 42
10P GAIN WILD-TYPE 13 377

Figure S17.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #8: 'ETHNICITY'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0244 (Wilcoxon-test), Q value = 0.2

Table S18.  Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
11P GAIN MUTATED 30 48.9 (14.7)
11P GAIN WILD-TYPE 441 42.7 (13.3)

Figure S18.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0121 (Fisher's exact test), Q value = 0.13

Table S19.  Gene #20: '11p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
11P GAIN MUTATED 4 10 16
11P GAIN WILD-TYPE 172 108 162

Figure S19.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'Time to Death'

P value = 0.0236 (logrank test), Q value = 0.2

Table S20.  Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
12Q GAIN MUTATED 14 6 1.2 - 77.9 (17.2)
12Q GAIN WILD-TYPE 456 88 0.0 - 211.2 (18.7)

Figure S20.  Get High-res Image Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0229 (Fisher's exact test), Q value = 0.2

Table S21.  Gene #28: '16q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
16Q GAIN MUTATED 12 1 5
16Q GAIN WILD-TYPE 164 117 173

Figure S21.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0324 (logrank test), Q value = 0.24

Table S22.  Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
17P GAIN MUTATED 18 6 7.2 - 62.2 (18.3)
17P GAIN WILD-TYPE 452 88 0.0 - 211.2 (18.7)

Figure S22.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'Time to Death'

P value = 0.00649 (logrank test), Q value = 0.081

Table S23.  Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
17Q GAIN MUTATED 20 7 5.8 - 62.2 (17.4)
17Q GAIN WILD-TYPE 450 87 0.0 - 211.2 (18.7)

Figure S23.  Get High-res Image Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0155 (Wilcoxon-test), Q value = 0.15

Table S24.  Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
19P GAIN MUTATED 90 46.3 (14.2)
19P GAIN WILD-TYPE 381 42.3 (13.2)

Figure S24.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S25.  Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
19P GAIN MUTATED 18 17 56
19P GAIN WILD-TYPE 158 101 122

Figure S25.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'Time to Death'

P value = 1.49e-05 (logrank test), Q value = 6e-04

Table S26.  Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
19Q GAIN MUTATED 22 8 0.2 - 49.5 (15.7)
19Q GAIN WILD-TYPE 448 86 0.0 - 211.2 (18.8)

Figure S26.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 4.07e-05 (Wilcoxon-test), Q value = 0.0012

Table S27.  Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
19Q GAIN MUTATED 22 55.1 (12.1)
19Q GAIN WILD-TYPE 449 42.5 (13.2)

Figure S27.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'Time to Death'

P value = 1.14e-07 (logrank test), Q value = 9.1e-06

Table S28.  Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
20P GAIN MUTATED 38 14 0.5 - 49.5 (14.0)
20P GAIN WILD-TYPE 432 80 0.0 - 211.2 (18.8)

Figure S28.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 3.59e-07 (Wilcoxon-test), Q value = 2.6e-05

Table S29.  Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
20P GAIN MUTATED 38 54.4 (12.8)
20P GAIN WILD-TYPE 433 42.1 (13.0)

Figure S29.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0317 (Wilcoxon-test), Q value = 0.24

Table S30.  Gene #35: '20p gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
20P GAIN MUTATED 22 83.6 (12.2)
20P GAIN WILD-TYPE 247 88.1 (11.9)

Figure S30.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'Time to Death'

P value = 2.28e-08 (logrank test), Q value = 2.4e-06

Table S31.  Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
20Q GAIN MUTATED 38 14 0.5 - 49.5 (14.0)
20Q GAIN WILD-TYPE 432 80 0.0 - 211.2 (19.0)

Figure S31.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 4.76e-07 (Wilcoxon-test), Q value = 3e-05

Table S32.  Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
20Q GAIN MUTATED 38 54.3 (13.0)
20Q GAIN WILD-TYPE 433 42.1 (13.0)

Figure S32.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.011 (Wilcoxon-test), Q value = 0.12

Table S33.  Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
21Q GAIN MUTATED 23 51.8 (17.3)
21Q GAIN WILD-TYPE 448 42.6 (13.1)

Figure S33.  Get High-res Image Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00478 (Fisher's exact test), Q value = 0.062

Table S34.  Gene #38: '22q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
22Q GAIN MUTATED 2 2 13
22Q GAIN WILD-TYPE 174 116 165

Figure S34.  Get High-res Image Gene #38: '22q gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.033 (Wilcoxon-test), Q value = 0.24

Table S35.  Gene #39: 'xp gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
XP GAIN MUTATED 10 95.0 (5.3)
XP GAIN WILD-TYPE 259 87.5 (12.1)

Figure S35.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'GENDER'

P value = 0.00394 (Fisher's exact test), Q value = 0.055

Table S36.  Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 206 266
XQ GAIN MUTATED 23 11
XQ GAIN WILD-TYPE 183 255

Figure S36.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0218 (Fisher's exact test), Q value = 0.19

Table S37.  Gene #40: 'xq gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
XQ GAIN MUTATED 15 13 6
XQ GAIN WILD-TYPE 161 105 172

Figure S37.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'Time to Death'

P value = 0.00267 (logrank test), Q value = 0.044

Table S38.  Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
1P LOSS MUTATED 170 23 0.1 - 182.3 (20.2)
1P LOSS WILD-TYPE 300 71 0.0 - 211.2 (18.5)

Figure S38.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000263 (Wilcoxon-test), Q value = 0.0062

Table S39.  Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
1P LOSS MUTATED 170 45.8 (12.7)
1P LOSS WILD-TYPE 301 41.5 (13.6)

Figure S39.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S40.  Gene #41: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
1P LOSS MUTATED 9 34 128
1P LOSS WILD-TYPE 167 84 50

Figure S40.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0153 (Fisher's exact test), Q value = 0.15

Table S41.  Gene #41: '1p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
1P LOSS MUTATED 23 148
1P LOSS WILD-TYPE 69 232

Figure S41.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0124 (Fisher's exact test), Q value = 0.13

Table S42.  Gene #42: '1q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
1Q LOSS MUTATED 4 4 16
1Q LOSS WILD-TYPE 172 114 162

Figure S42.  Get High-res Image Gene #42: '1q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000594 (Wilcoxon-test), Q value = 0.012

Table S43.  Gene #45: '3p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
3P LOSS MUTATED 19 78.9 (13.3)
3P LOSS WILD-TYPE 250 88.4 (11.6)

Figure S43.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'Time to Death'

P value = 0.00785 (logrank test), Q value = 0.091

Table S44.  Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
3Q LOSS MUTATED 25 12 0.0 - 117.4 (21.4)
3Q LOSS WILD-TYPE 445 82 0.1 - 211.2 (18.4)

Figure S44.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00371 (Wilcoxon-test), Q value = 0.054

Table S45.  Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
4P LOSS MUTATED 63 47.4 (12.5)
4P LOSS WILD-TYPE 408 42.4 (13.5)

Figure S45.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.011

Table S46.  Gene #47: '4p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
4P LOSS MUTATED 12 14 37
4P LOSS WILD-TYPE 164 104 141

Figure S46.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00415 (Fisher's exact test), Q value = 0.057

Table S47.  Gene #48: '4q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
4Q LOSS MUTATED 20 18 44
4Q LOSS WILD-TYPE 156 100 134

Figure S47.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0138 (Fisher's exact test), Q value = 0.14

Table S48.  Gene #49: '5p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
5P LOSS MUTATED 17 11 5
5P LOSS WILD-TYPE 159 107 173

Figure S48.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0201 (Fisher's exact test), Q value = 0.18

Table S49.  Gene #49: '5p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
5P LOSS MUTATED 12 21
5P LOSS WILD-TYPE 80 359

Figure S49.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0201 (Fisher's exact test), Q value = 0.18

Table S50.  Gene #50: '5q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
5Q LOSS MUTATED 20 6 7
5Q LOSS WILD-TYPE 156 112 171

Figure S50.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'Time to Death'

P value = 8.82e-06 (logrank test), Q value = 0.00043

Table S51.  Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
6P LOSS MUTATED 26 11 0.2 - 50.9 (18.6)
6P LOSS WILD-TYPE 444 83 0.0 - 211.2 (18.7)

Figure S51.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'Time to Death'

P value = 3.39e-05 (logrank test), Q value = 0.0011

Table S52.  Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
6Q LOSS MUTATED 54 16 0.1 - 57.9 (17.7)
6Q LOSS WILD-TYPE 416 78 0.0 - 211.2 (18.8)

Figure S52.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0032 (Wilcoxon-test), Q value = 0.049

Table S53.  Gene #52: '6q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
6Q LOSS MUTATED 34 82.4 (12.8)
6Q LOSS WILD-TYPE 235 88.5 (11.7)

Figure S53.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00051 (Fisher's exact test), Q value = 0.011

Table S54.  Gene #52: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
6Q LOSS MUTATED 34 10 11
6Q LOSS WILD-TYPE 142 108 167

Figure S54.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'Time to Death'

P value = 0.0287 (logrank test), Q value = 0.22

Table S55.  Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
8P LOSS MUTATED 14 5 0.2 - 50.9 (19.5)
8P LOSS WILD-TYPE 456 89 0.0 - 211.2 (18.6)

Figure S55.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'Time to Death'

P value = 0.0199 (logrank test), Q value = 0.18

Table S56.  Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
8Q LOSS MUTATED 9 3 0.2 - 41.1 (15.7)
8Q LOSS WILD-TYPE 461 91 0.0 - 211.2 (18.7)

Figure S56.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'Time to Death'

P value = 0.000495 (logrank test), Q value = 0.011

Table S57.  Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
9P LOSS MUTATED 103 32 0.1 - 169.8 (18.4)
9P LOSS WILD-TYPE 367 62 0.0 - 211.2 (18.7)

Figure S57.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0322 (Wilcoxon-test), Q value = 0.24

Table S58.  Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
9P LOSS MUTATED 103 45.4 (13.1)
9P LOSS WILD-TYPE 368 42.4 (13.5)

Figure S58.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0356 (Fisher's exact test), Q value = 0.24

Table S59.  Gene #57: '9p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
9P LOSS MUTATED 28 76
9P LOSS WILD-TYPE 64 304

Figure S59.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00135 (Wilcoxon-test), Q value = 0.023

Table S60.  Gene #58: '9q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
9Q LOSS MUTATED 27 81.5 (12.0)
9Q LOSS WILD-TYPE 242 88.4 (11.8)

Figure S60.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S61.  Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
10P LOSS MUTATED 74 37 0.1 - 134.3 (15.0)
10P LOSS WILD-TYPE 396 57 0.0 - 211.2 (20.0)

Figure S61.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 3.96e-17 (Wilcoxon-test), Q value = 8.5e-15

Table S62.  Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
10P LOSS MUTATED 74 55.5 (11.3)
10P LOSS WILD-TYPE 397 40.7 (12.5)

Figure S62.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00324 (Wilcoxon-test), Q value = 0.049

Table S63.  Gene #59: '10p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
10P LOSS MUTATED 44 83.0 (13.7)
10P LOSS WILD-TYPE 225 88.7 (11.4)

Figure S63.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0049

Table S64.  Gene #59: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
10P LOSS MUTATED 44 14 16
10P LOSS WILD-TYPE 132 104 162

Figure S64.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.0132 (Fisher's exact test), Q value = 0.14

Table S65.  Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 15 437
10P LOSS MUTATED 1 1 6 65
10P LOSS WILD-TYPE 0 7 9 372

Figure S65.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'

'10q loss' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S66.  Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
10Q LOSS MUTATED 87 43 0.1 - 172.8 (15.7)
10Q LOSS WILD-TYPE 383 51 0.0 - 211.2 (19.6)

Figure S66.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 1.05e-14 (Wilcoxon-test), Q value = 1.7e-12

Table S67.  Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
10Q LOSS MUTATED 87 53.3 (12.7)
10Q LOSS WILD-TYPE 384 40.7 (12.5)

Figure S67.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0166 (Wilcoxon-test), Q value = 0.16

Table S68.  Gene #60: '10q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
10Q LOSS MUTATED 51 84.3 (13.2)
10Q LOSS WILD-TYPE 218 88.5 (11.6)

Figure S68.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0014

Table S69.  Gene #60: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
10Q LOSS MUTATED 51 17 19
10Q LOSS WILD-TYPE 125 101 159

Figure S69.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.0344 (Fisher's exact test), Q value = 0.24

Table S70.  Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 15 437
10Q LOSS MUTATED 1 1 6 78
10Q LOSS WILD-TYPE 0 7 9 359

Figure S70.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00387 (Fisher's exact test), Q value = 0.055

Table S71.  Gene #61: '11p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
11P LOSS MUTATED 32 13 12
11P LOSS WILD-TYPE 144 105 166

Figure S71.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 0.00213 (logrank test), Q value = 0.036

Table S72.  Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
11Q LOSS MUTATED 20 7 0.2 - 49.5 (18.7)
11Q LOSS WILD-TYPE 450 87 0.0 - 211.2 (18.6)

Figure S72.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0169 (Fisher's exact test), Q value = 0.16

Table S73.  Gene #62: '11q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
11Q LOSS MUTATED 12 6 2
11Q LOSS WILD-TYPE 164 112 176

Figure S73.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00562 (Fisher's exact test), Q value = 0.072

Table S74.  Gene #64: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
12Q LOSS MUTATED 25 13 8
12Q LOSS WILD-TYPE 151 105 170

Figure S74.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0115 (Fisher's exact test), Q value = 0.13

Table S75.  Gene #65: '13q loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
13Q LOSS MUTATED 30 75
13Q LOSS WILD-TYPE 62 305

Figure S75.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'14q loss' versus 'Time to Death'

P value = 3.62e-05 (logrank test), Q value = 0.0012

Table S76.  Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
14Q LOSS MUTATED 69 24 0.1 - 130.8 (18.8)
14Q LOSS WILD-TYPE 401 70 0.0 - 211.2 (18.6)

Figure S76.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00031 (Wilcoxon-test), Q value = 0.0068

Table S77.  Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
14Q LOSS MUTATED 70 48.5 (13.2)
14Q LOSS WILD-TYPE 401 42.1 (13.3)

Figure S77.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000239 (Wilcoxon-test), Q value = 0.0059

Table S78.  Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
16P LOSS MUTATED 11 58.5 (10.3)
16P LOSS WILD-TYPE 460 42.7 (13.3)

Figure S78.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000301 (Wilcoxon-test), Q value = 0.0068

Table S79.  Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
16Q LOSS MUTATED 19 55.3 (14.3)
16Q LOSS WILD-TYPE 452 42.5 (13.2)

Figure S79.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'Time to Death'

P value = 0.00732 (logrank test), Q value = 0.087

Table S80.  Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
17P LOSS MUTATED 12 3 0.1 - 23.7 (14.6)
17P LOSS WILD-TYPE 458 91 0.0 - 211.2 (18.8)

Figure S80.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00311 (Wilcoxon-test), Q value = 0.049

Table S81.  Gene #70: '17p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
17P LOSS MUTATED 6 73.3 (10.3)
17P LOSS WILD-TYPE 263 88.1 (11.8)

Figure S81.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0344 (Wilcoxon-test), Q value = 0.24

Table S82.  Gene #71: '17q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
17Q LOSS MUTATED 4 75.0 (12.9)
17Q LOSS WILD-TYPE 265 87.9 (11.9)

Figure S82.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00447 (Wilcoxon-test), Q value = 0.06

Table S83.  Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
18P LOSS MUTATED 63 47.9 (14.4)
18P LOSS WILD-TYPE 408 42.3 (13.1)

Figure S83.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0346 (Wilcoxon-test), Q value = 0.24

Table S84.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
18Q LOSS MUTATED 58 46.9 (14.4)
18Q LOSS WILD-TYPE 413 42.5 (13.2)

Figure S84.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'Time to Death'

P value = 0.0191 (logrank test), Q value = 0.18

Table S85.  Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
19Q LOSS MUTATED 192 31 0.1 - 182.3 (20.2)
19Q LOSS WILD-TYPE 278 63 0.0 - 211.2 (18.2)

Figure S85.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0258 (Wilcoxon-test), Q value = 0.2

Table S86.  Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
19Q LOSS MUTATED 192 44.5 (12.6)
19Q LOSS WILD-TYPE 279 42.1 (13.9)

Figure S86.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00043

Table S87.  Gene #75: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
19Q LOSS MUTATED 21 38 134
19Q LOSS WILD-TYPE 155 80 44

Figure S87.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000655 (Wilcoxon-test), Q value = 0.012

Table S88.  Gene #77: '21q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
21Q LOSS MUTATED 21 78.6 (14.6)
21Q LOSS WILD-TYPE 248 88.5 (11.4)

Figure S88.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0218 (Fisher's exact test), Q value = 0.19

Table S89.  Gene #77: '21q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
21Q LOSS MUTATED 18 5 6
21Q LOSS WILD-TYPE 158 113 172

Figure S89.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 1.93e-05 (logrank test), Q value = 0.00069

Table S90.  Gene #78: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
22Q LOSS MUTATED 50 20 0.1 - 156.2 (18.1)
22Q LOSS WILD-TYPE 420 74 0.0 - 211.2 (18.7)

Figure S90.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 1.87e-05 (Wilcoxon-test), Q value = 0.00069

Table S91.  Gene #78: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
22Q LOSS MUTATED 50 51.3 (14.0)
22Q LOSS WILD-TYPE 421 42.1 (13.0)

Figure S91.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0284 (Wilcoxon-test), Q value = 0.22

Table S92.  Gene #78: '22q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
22Q LOSS MUTATED 28 82.1 (15.2)
22Q LOSS WILD-TYPE 241 88.4 (11.4)

Figure S92.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'Time to Death'

P value = 0.00725 (logrank test), Q value = 0.087

Table S93.  Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
XQ LOSS MUTATED 64 19 0.1 - 134.3 (16.6)
XQ LOSS WILD-TYPE 406 75 0.0 - 211.2 (19.0)

Figure S93.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/15087637/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/15082624/LGG-TP.merged_data.txt

  • Number of patients = 472

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 8

  • 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.

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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