Correlation between copy number variations of arm-level result and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5TSH
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 81 arm-level events and 8 clinical features across 512 patients, 157 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', 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'.

  • 4q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 5q gain cnv correlated to 'Time to Death' and 'RACE'.

  • 7p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

  • 7q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 8q gain cnv correlated to 'RADIATION_THERAPY'.

  • 9p gain cnv correlated to 'GENDER' and 'RADIATION_THERAPY'.

  • 9q gain cnv correlated to 'GENDER',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • 10q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 12p gain cnv correlated to 'RADIATION_THERAPY'.

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

  • 13q gain cnv correlated to 'RADIATION_THERAPY'.

  • 15q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 16p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

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

  • 18p gain cnv correlated to 'Time to Death'.

  • 18q gain cnv correlated to 'Time to Death'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', 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',  'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • xp gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • xq gain cnv correlated to 'YEARS_TO_BIRTH',  'GENDER',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

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

  • 1q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 2p loss cnv correlated to 'RADIATION_THERAPY'.

  • 2q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

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

  • 4q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 5q loss cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • 6p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RADIATION_THERAPY'.

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

  • 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',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 9q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

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

  • 11p loss cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and '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 'RADIATION_THERAPY'.

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

  • 16p loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

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

  • 18p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 18q loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 19p loss cnv correlated to 'RACE' and 'ETHNICITY'.

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

  • 20p loss cnv correlated to 'RADIATION_THERAPY'.

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

  • 22q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', 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 81 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 157 significant findings detected.

Clinical
Features
Time
to
Death
YEARS
TO
BIRTH
GENDER RADIATION
THERAPY
KARNOFSKY
PERFORMANCE
SCORE
HISTOLOGICAL
TYPE
RACE 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 Fisher's exact test
7q gain 150 (29%) 362 2.81e-07
(1.21e-05)
1.96e-10
(1.82e-08)
0.435
(0.775)
0.00116
(0.0153)
0.00576
(0.0541)
0.0514
(0.228)
0.00939
(0.0761)
0.557
(0.849)
6q loss 62 (12%) 450 7.35e-05
(0.0017)
0.0291
(0.161)
0.414
(0.755)
0.0253
(0.15)
0.00121
(0.0157)
0.00115
(0.0153)
0.0504
(0.225)
0.563
(0.849)
10p loss 83 (16%) 429 0
(0)
5.96e-20
(1.29e-17)
0.81
(0.973)
9.18e-05
(0.00205)
0.000203
(0.00387)
0.00011
(0.0022)
0.00867
(0.0723)
0.804
(0.973)
10q loss 97 (19%) 415 0
(0)
2.9e-17
(4.69e-15)
0.734
(0.942)
2.96e-06
(0.000107)
0.000212
(0.0039)
3e-05
(0.000778)
0.0278
(0.159)
0.485
(0.813)
7p gain 120 (23%) 392 9.05e-08
(4.89e-06)
1.63e-10
(1.76e-08)
0.174
(0.457)
0.000773
(0.0111)
0.000962
(0.0133)
0.239
(0.553)
0.0159
(0.106)
0.834
(0.986)
9p loss 117 (23%) 395 1.11e-06
(4.48e-05)
0.00204
(0.0245)
1
(1.00)
0.000609
(0.00918)
0.00199
(0.0243)
0.0589
(0.247)
0.605
(0.875)
0.669
(0.896)
1p gain 13 (3%) 499 0.016
(0.106)
0.0126
(0.0946)
0.263
(0.578)
0.0344
(0.175)
0.799
(0.973)
0.00907
(0.0744)
0.556
(0.849)
1
(1.00)
20p gain 45 (9%) 467 2.94e-12
(3.8e-10)
7.25e-09
(5.22e-07)
0.757
(0.957)
0.0282
(0.159)
0.00967
(0.0764)
0.186
(0.473)
0.47
(0.804)
0.343
(0.668)
20q gain 44 (9%) 468 2.04e-09
(1.65e-07)
2.04e-08
(1.2e-06)
0.341
(0.668)
0.0282
(0.159)
0.0145
(0.102)
0.234
(0.549)
0.64
(0.885)
0.507
(0.819)
xq gain 41 (8%) 471 0.159
(0.433)
0.0539
(0.236)
0.0136
(0.1)
0.229
(0.549)
0.519
(0.831)
0.00437
(0.0442)
0.611
(0.875)
0.0254
(0.15)
1p loss 184 (36%) 328 0.000112
(0.0022)
0.000914
(0.0129)
0.853
(1.00)
1.83e-07
(8.9e-06)
0.293
(0.615)
1e-05
(0.000282)
0.315
(0.636)
0.704
(0.924)
9q loss 50 (10%) 462 0.0035
(0.0372)
0.00595
(0.0551)
1
(1.00)
0.011
(0.084)
0.000364
(0.0059)
0.877
(1.00)
0.136
(0.403)
1
(1.00)
17p loss 14 (3%) 498 0.0587
(0.247)
0.0397
(0.196)
0.174
(0.457)
1
(1.00)
0.0168
(0.109)
0.551
(0.849)
1
(1.00)
0.0599
(0.247)
19q loss 209 (41%) 303 0.0024
(0.0273)
0.0437
(0.207)
0.928
(1.00)
4.3e-06
(0.000147)
0.353
(0.681)
1e-05
(0.000282)
0.918
(1.00)
0.0929
(0.328)
22q loss 57 (11%) 455 1.94e-08
(1.2e-06)
2.06e-06
(7.84e-05)
0.482
(0.813)
0.0483
(0.22)
0.00505
(0.0496)
0.121
(0.375)
0.173
(0.457)
0.56
(0.849)
9q gain 24 (5%) 488 0.373
(0.713)
0.0775
(0.299)
0.00268
(0.03)
0.00177
(0.0225)
0.557
(0.849)
0.0586
(0.247)
0.212
(0.521)
0.661
(0.892)
10p gain 57 (11%) 455 0.536
(0.848)
0.0215
(0.131)
0.258
(0.576)
0.0159
(0.106)
0.217
(0.53)
0.00026
(0.00443)
1
(1.00)
0.136
(0.403)
15q gain 11 (2%) 501 0.0166
(0.109)
0.0259
(0.15)
1
(1.00)
0.543
(0.848)
0.0135
(0.1)
0.406
(0.748)
0.496
(0.815)
1
(1.00)
17p gain 20 (4%) 492 0.0143
(0.102)
0.0176
(0.112)
0.106
(0.355)
0.49
(0.813)
0.678
(0.901)
0.059
(0.247)
0.223
(0.54)
1
(1.00)
19p gain 99 (19%) 413 0.629
(0.885)
0.00964
(0.0764)
0.262
(0.578)
0.043
(0.206)
0.464
(0.802)
1e-05
(0.000282)
0.5
(0.816)
0.108
(0.36)
4p loss 72 (14%) 440 0.74
(0.945)
0.0188
(0.118)
0.0413
(0.201)
1
(1.00)
0.956
(1.00)
0.00049
(0.00774)
0.562
(0.849)
0.798
(0.973)
6p loss 30 (6%) 482 0.000108
(0.0022)
0.0548
(0.237)
0.573
(0.853)
0.0583
(0.247)
0.0745
(0.289)
0.233
(0.549)
0.0616
(0.252)
1
(1.00)
11p loss 63 (12%) 449 0.0307
(0.166)
0.265
(0.58)
0.343
(0.668)
0.00629
(0.0574)
0.168
(0.45)
0.00063
(0.00928)
0.562
(0.849)
0.784
(0.972)
14q loss 81 (16%) 431 2.47e-05
(0.000666)
3.84e-05
(0.000958)
1
(1.00)
0.194
(0.481)
0.035
(0.177)
0.2
(0.495)
0.218
(0.53)
0.452
(0.795)
3p gain 11 (2%) 501 0.039
(0.194)
0.0849
(0.311)
0.551
(0.849)
1
(1.00)
0.805
(0.973)
0.0288
(0.161)
1
(1.00)
1
(1.00)
3q gain 8 (2%) 504 0.0022
(0.0259)
0.0332
(0.172)
0.476
(0.81)
0.414
(0.755)
0.302
(0.621)
0.0914
(0.325)
1
(1.00)
1
(1.00)
5p gain 11 (2%) 501 0.0305
(0.166)
0.0321
(0.17)
1
(1.00)
0.543
(0.848)
0.791
(0.973)
0.243
(0.555)
0.079
(0.301)
1
(1.00)
5q gain 9 (2%) 503 0.042
(0.203)
0.0627
(0.256)
0.521
(0.831)
1
(1.00)
0.97
(1.00)
0.584
(0.857)
0.0548
(0.237)
1
(1.00)
9p gain 17 (3%) 495 0.58
(0.857)
0.104
(0.35)
0.0442
(0.207)
0.0353
(0.177)
0.574
(0.853)
0.236
(0.549)
0.653
(0.891)
1
(1.00)
11p gain 30 (6%) 482 0.179
(0.459)
0.0295
(0.162)
0.348
(0.672)
0.181
(0.464)
0.639
(0.885)
0.0081
(0.07)
1
(1.00)
0.431
(0.77)
19q gain 25 (5%) 487 1.92e-07
(8.9e-06)
7.02e-06
(0.000228)
0.416
(0.755)
0.069
(0.274)
0.0675
(0.271)
0.155
(0.429)
0.0983
(0.337)
0.67
(0.896)
22q gain 23 (4%) 489 0.645
(0.888)
0.0457
(0.213)
0.831
(0.985)
0.121
(0.375)
0.19
(0.478)
0.00383
(0.04)
0.731
(0.94)
0.159
(0.433)
3p loss 30 (6%) 482 0.0496
(0.223)
0.883
(1.00)
0.45
(0.795)
0.243
(0.555)
0.00192
(0.024)
0.915
(1.00)
0.312
(0.633)
0.431
(0.77)
5p loss 35 (7%) 477 0.871
(1.00)
0.254
(0.571)
0.862
(1.00)
0.00747
(0.0658)
0.357
(0.686)
0.00983
(0.0767)
0.57
(0.853)
0.153
(0.427)
5q loss 32 (6%) 480 0.28
(0.595)
0.29
(0.611)
0.583
(0.857)
0.00504
(0.0496)
0.67
(0.896)
0.04
(0.196)
0.662
(0.892)
0.712
(0.924)
11q loss 21 (4%) 491 9.86e-05
(0.00213)
0.149
(0.418)
1
(1.00)
0.081
(0.304)
0.0821
(0.304)
0.0141
(0.102)
1
(1.00)
1
(1.00)
16p loss 14 (3%) 498 0.052
(0.229)
0.000244
(0.00427)
1
(1.00)
0.266
(0.581)
0.149
(0.418)
0.741
(0.945)
0.582
(0.857)
0.239
(0.553)
16q loss 22 (4%) 490 0.0745
(0.289)
0.000217
(0.0039)
0.664
(0.892)
0.0212
(0.131)
0.0737
(0.289)
0.513
(0.825)
0.491
(0.813)
0.652
(0.891)
18q loss 62 (12%) 450 0.573
(0.853)
0.0236
(0.141)
0.499
(0.816)
0.885
(1.00)
0.858
(1.00)
0.0326
(0.172)
0.104
(0.35)
0.784
(0.972)
19p loss 26 (5%) 486 0.909
(1.00)
0.677
(0.901)
0.843
(0.993)
0.3
(0.621)
0.0817
(0.304)
0.934
(1.00)
0.0219
(0.133)
0.0594
(0.247)
21q loss 38 (7%) 474 0.694
(0.917)
0.495
(0.815)
0.737
(0.944)
0.148
(0.418)
0.00752
(0.0658)
0.00412
(0.0424)
0.586
(0.857)
1
(1.00)
1q gain 23 (4%) 489 0.457
(0.8)
5.1e-05
(0.00122)
0.522
(0.831)
0.655
(0.891)
0.112
(0.364)
0.0831
(0.306)
0.276
(0.59)
0.385
(0.722)
4q gain 7 (1%) 505 0.11
(0.364)
0.0109
(0.084)
0.47
(0.804)
0.259
(0.576)
0.157
(0.432)
1
(1.00)
1
(1.00)
8q gain 55 (11%) 457 0.719
(0.932)
0.23
(0.549)
0.774
(0.969)
0.0159
(0.106)
0.335
(0.661)
0.176
(0.457)
0.63
(0.885)
0.369
(0.707)
10q gain 11 (2%) 501 0.856
(1.00)
0.24
(0.553)
1
(1.00)
0.543
(0.848)
0.336
(0.661)
0.0087
(0.0723)
0.0933
(0.328)
0.14
(0.409)
12p gain 32 (6%) 480 0.301
(0.621)
0.462
(0.8)
0.273
(0.589)
0.0336
(0.173)
0.832
(0.985)
0.471
(0.804)
0.345
(0.669)
0.711
(0.924)
12q gain 15 (3%) 497 0.00551
(0.0525)
0.324
(0.648)
0.193
(0.481)
0.581
(0.857)
0.12
(0.375)
0.8
(0.973)
0.154
(0.427)
0.613
(0.875)
13q gain 6 (1%) 506 0.41
(0.753)
0.94
(1.00)
1
(1.00)
0.0332
(0.172)
0.0678
(0.271)
1
(1.00)
1
(1.00)
1
(1.00)
16p gain 16 (3%) 496 0.616
(0.877)
0.0319
(0.17)
0.445
(0.787)
0.426
(0.767)
0.708
(0.924)
0.146
(0.418)
0.609
(0.875)
0.613
(0.875)
16q gain 19 (4%) 493 0.417
(0.755)
0.606
(0.875)
0.49
(0.813)
0.461
(0.8)
0.638
(0.885)
0.0153
(0.106)
0.677
(0.901)
0.623
(0.88)
17q gain 23 (4%) 489 0.00836
(0.0713)
0.118
(0.374)
0.0858
(0.312)
0.663
(0.892)
0.961
(1.00)
0.27
(0.586)
0.26
(0.577)
0.636
(0.885)
18p gain 18 (4%) 494 0.0174
(0.112)
0.906
(1.00)
0.639
(0.885)
0.806
(0.973)
0.383
(0.722)
0.564
(0.849)
0.306
(0.626)
0.619
(0.879)
18q gain 13 (3%) 499 0.000572
(0.00883)
0.781
(0.972)
1
(1.00)
0.145
(0.418)
0.507
(0.819)
0.46
(0.8)
0.192
(0.481)
1
(1.00)
21q gain 23 (4%) 489 0.276
(0.59)
0.00537
(0.0519)
0.285
(0.603)
0.177
(0.457)
0.0995
(0.339)
0.829
(0.985)
0.391
(0.724)
0.389
(0.722)
xp gain 22 (4%) 490 0.54
(0.848)
0.897
(1.00)
0.19
(0.478)
0.177
(0.457)
0.502
(0.817)
0.0197
(0.123)
0.278
(0.593)
1
(1.00)
1q loss 26 (5%) 486 0.42
(0.759)
0.113
(0.364)
1
(1.00)
0.83
(0.985)
0.609
(0.875)
0.00319
(0.0345)
0.229
(0.549)
1
(1.00)
2p loss 21 (4%) 491 0.307
(0.627)
0.528
(0.837)
0.656
(0.891)
0.0138
(0.101)
0.0677
(0.271)
0.232
(0.549)
1
(1.00)
0.385
(0.722)
2q loss 18 (4%) 494 0.909
(1.00)
0.48
(0.813)
0.81
(0.973)
0.121
(0.375)
0.223
(0.54)
0.0488
(0.221)
1
(1.00)
0.623
(0.88)
3q loss 28 (5%) 484 0.0258
(0.15)
0.443
(0.787)
0.697
(0.917)
0.3
(0.621)
0.0955
(0.332)
0.97
(1.00)
0.276
(0.59)
0.7
(0.92)
4q loss 94 (18%) 418 0.471
(0.804)
0.38
(0.722)
0.207
(0.509)
0.809
(0.973)
0.745
(0.948)
0.0158
(0.106)
0.823
(0.983)
0.816
(0.977)
8p loss 17 (3%) 495 0.0474
(0.218)
0.174
(0.457)
0.81
(0.973)
0.0912
(0.325)
0.327
(0.65)
0.386
(0.722)
0.113
(0.364)
0.317
(0.638)
8q loss 11 (2%) 501 0.0439
(0.207)
0.111
(0.364)
0.551
(0.849)
0.163
(0.442)
0.507
(0.819)
0.798
(0.973)
0.0936
(0.328)
0.164
(0.442)
12q loss 52 (10%) 460 0.748
(0.951)
0.177
(0.457)
0.77
(0.967)
0.125
(0.382)
0.795
(0.973)
0.00291
(0.032)
0.791
(0.973)
0.233
(0.549)
13q loss 115 (22%) 397 0.248
(0.564)
0.721
(0.933)
0.136
(0.403)
0.000328
(0.00545)
0.137
(0.403)
0.509
(0.82)
0.294
(0.615)
0.388
(0.722)
18p loss 67 (13%) 445 0.613
(0.875)
0.00237
(0.0273)
0.147
(0.418)
1
(1.00)
0.458
(0.8)
0.184
(0.468)
0.097
(0.335)
0.784
(0.972)
20p loss 7 (1%) 505 0.904
(1.00)
0.858
(1.00)
0.251
(0.566)
0.0472
(0.218)
0.43
(0.77)
0.495
(0.815)
0.147
(0.418)
0.386
(0.722)
xq loss 70 (14%) 442 0.00654
(0.0589)
0.149
(0.418)
0.607
(0.875)
0.0959
(0.332)
0.157
(0.432)
0.707
(0.924)
0.651
(0.891)
1
(1.00)
2p gain 14 (3%) 498 0.149
(0.418)
0.0783
(0.3)
0.787
(0.972)
0.387
(0.722)
0.485
(0.813)
0.548
(0.849)
1
(1.00)
0.599
(0.872)
2q gain 13 (3%) 499 0.321
(0.645)
0.172
(0.457)
0.577
(0.856)
0.142
(0.414)
0.485
(0.813)
0.559
(0.849)
1
(1.00)
0.569
(0.853)
4p gain 12 (2%) 500 0.903
(1.00)
0.122
(0.376)
1
(1.00)
0.386
(0.722)
0.695
(0.917)
0.0813
(0.304)
0.168
(0.45)
1
(1.00)
6p gain 7 (1%) 505 0.539
(0.848)
0.123
(0.377)
0.251
(0.566)
0.0867
(0.314)
0.824
(0.983)
0.235
(0.549)
1
(1.00)
1
(1.00)
8p gain 45 (9%) 467 0.62
(0.879)
0.867
(1.00)
0.638
(0.885)
0.073
(0.288)
0.127
(0.386)
0.299
(0.621)
0.552
(0.849)
0.753
(0.955)
11q gain 58 (11%) 454 0.129
(0.388)
0.122
(0.376)
0.263
(0.578)
0.886
(1.00)
0.807
(0.973)
0.235
(0.549)
0.901
(1.00)
0.767
(0.966)
14q gain 4 (1%) 508 0.333
(0.66)
0.252
(0.567)
1
(1.00)
0.64
(0.885)
0.978
(1.00)
0.839
(0.991)
1
(1.00)
0.243
(0.555)
7p loss 3 (1%) 509 0.73
(0.94)
0.643
(0.887)
0.588
(0.858)
0.526
(0.835)
0.787
(0.972)
1
(1.00)
1
(1.00)
7q loss 4 (1%) 508 0.884
(1.00)
0.889
(1.00)
0.633
(0.885)
0.289
(0.61)
0.49
(0.813)
0.456
(0.8)
1
(1.00)
1
(1.00)
12p loss 28 (5%) 484 0.855
(1.00)
0.111
(0.364)
0.563
(0.849)
0.417
(0.755)
0.486
(0.813)
0.136
(0.403)
1
(1.00)
1
(1.00)
15q loss 51 (10%) 461 0.313
(0.633)
0.342
(0.668)
0.658
(0.892)
0.269
(0.584)
0.774
(0.969)
0.647
(0.888)
0.784
(0.972)
0.759
(0.957)
17q loss 9 (2%) 503 0.572
(0.853)
0.081
(0.304)
0.521
(0.831)
1
(1.00)
0.119
(0.375)
0.759
(0.957)
1
(1.00)
0.116
(0.372)
20q loss 3 (1%) 509 0.926
(1.00)
0.966
(1.00)
0.0877
(0.316)
1
(1.00)
0.325
(0.648)
0.47
(0.804)
1
(1.00)
0.188
(0.476)
xp loss 98 (19%) 414 0.392
(0.724)
0.725
(0.936)
0.498
(0.816)
0.115
(0.369)
0.306
(0.626)
0.711
(0.924)
0.688
(0.911)
0.103
(0.349)
'1p gain' versus 'Time to Death'

P value = 0.016 (logrank test), Q value = 0.11

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

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
1P GAIN MUTATED 13 6 0.2 - 51.9 (19.9)
1P GAIN WILD-TYPE 495 119 0.0 - 211.2 (22.4)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0126 (Wilcoxon-test), Q value = 0.095

Table S2.  Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
1P GAIN MUTATED 13 52.4 (12.7)
1P GAIN WILD-TYPE 498 42.7 (13.3)

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0344 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #1: '1p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
1P GAIN MUTATED 1 11
1P GAIN WILD-TYPE 183 284

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00907 (Fisher's exact test), Q value = 0.074

Table S4.  Gene #1: '1p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
1P GAIN MUTATED 10 0 3
1P GAIN WILD-TYPE 184 129 186

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 5.1e-05 (Wilcoxon-test), Q value = 0.0012

Table S5.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
1Q GAIN MUTATED 23 54.0 (11.1)
1Q GAIN WILD-TYPE 488 42.5 (13.2)

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'Time to Death'

P value = 0.039 (logrank test), Q value = 0.19

Table S6.  Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
3P GAIN MUTATED 11 4 0.2 - 49.9 (17.3)
3P GAIN WILD-TYPE 497 121 0.0 - 211.2 (22.6)

Figure S6.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0288 (Fisher's exact test), Q value = 0.16

Table S7.  Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
3P GAIN MUTATED 8 0 3
3P GAIN WILD-TYPE 186 129 186

Figure S7.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 0.0022 (logrank test), Q value = 0.026

Table S8.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
3Q GAIN MUTATED 8 4 0.2 - 47.8 (13.1)
3Q GAIN WILD-TYPE 500 121 0.0 - 211.2 (22.5)

Figure S8.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0332 (Wilcoxon-test), Q value = 0.17

Table S9.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
3Q GAIN MUTATED 8 52.8 (11.4)
3Q GAIN WILD-TYPE 503 42.8 (13.3)

Figure S9.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0109 (Wilcoxon-test), Q value = 0.084

Table S10.  Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
4Q GAIN MUTATED 7 57.0 (15.2)
4Q GAIN WILD-TYPE 504 42.8 (13.2)

Figure S10.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'Time to Death'

P value = 0.0305 (logrank test), Q value = 0.17

Table S11.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
5P GAIN MUTATED 11 6 2.5 - 62.2 (24.4)
5P GAIN WILD-TYPE 497 119 0.0 - 211.2 (22.3)

Figure S11.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0321 (Wilcoxon-test), Q value = 0.17

Table S12.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
5P GAIN MUTATED 11 51.5 (12.3)
5P GAIN WILD-TYPE 500 42.8 (13.3)

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'Time to Death'

P value = 0.042 (logrank test), Q value = 0.2

Table S13.  Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
5Q GAIN MUTATED 9 5 2.5 - 62.2 (24.4)
5Q GAIN WILD-TYPE 499 120 0.0 - 211.2 (22.3)

Figure S13.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'RACE'

P value = 0.0548 (Fisher's exact test), Q value = 0.24

Table S14.  Gene #10: '5q gain' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
5Q GAIN MUTATED 0 1 1 6
5Q GAIN WILD-TYPE 1 7 20 466

Figure S14.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'RACE'

'7p gain' versus 'Time to Death'

P value = 9.05e-08 (logrank test), Q value = 4.9e-06

Table S15.  Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
7P GAIN MUTATED 120 48 0.1 - 211.2 (18.9)
7P GAIN WILD-TYPE 388 77 0.0 - 182.3 (24.8)

Figure S15.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 1.63e-10 (Wilcoxon-test), Q value = 1.8e-08

Table S16.  Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
7P GAIN MUTATED 120 49.8 (12.8)
7P GAIN WILD-TYPE 391 40.9 (12.8)

Figure S16.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'RADIATION_THERAPY'

P value = 0.000773 (Fisher's exact test), Q value = 0.011

Table S17.  Gene #12: '7p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
7P GAIN MUTATED 27 82
7P GAIN WILD-TYPE 157 213

Figure S17.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000962 (Wilcoxon-test), Q value = 0.013

Table S18.  Gene #12: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
7P GAIN MUTATED 74 81.9 (15.3)
7P GAIN WILD-TYPE 232 88.2 (11.2)

Figure S18.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7p gain' versus 'RACE'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #12: '7p gain' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
7P GAIN MUTATED 1 2 10 107
7P GAIN WILD-TYPE 0 6 11 365

Figure S19.  Get High-res Image Gene #12: '7p gain' versus Clinical Feature #7: 'RACE'

'7q gain' versus 'Time to Death'

P value = 2.81e-07 (logrank test), Q value = 1.2e-05

Table S20.  Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
7Q GAIN MUTATED 150 57 0.1 - 211.2 (19.2)
7Q GAIN WILD-TYPE 358 68 0.0 - 182.3 (24.4)

Figure S20.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 1.96e-10 (Wilcoxon-test), Q value = 1.8e-08

Table S21.  Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
7Q GAIN MUTATED 150 48.8 (13.1)
7Q GAIN WILD-TYPE 361 40.6 (12.7)

Figure S21.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'RADIATION_THERAPY'

P value = 0.00116 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #13: '7q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
7Q GAIN MUTATED 36 99
7Q GAIN WILD-TYPE 148 196

Figure S22.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00576 (Wilcoxon-test), Q value = 0.054

Table S23.  Gene #13: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
7Q GAIN MUTATED 89 83.1 (14.6)
7Q GAIN WILD-TYPE 217 88.1 (11.4)

Figure S23.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0514 (Fisher's exact test), Q value = 0.23

Table S24.  Gene #13: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
7Q GAIN MUTATED 67 39 44
7Q GAIN WILD-TYPE 127 90 145

Figure S24.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'RACE'

P value = 0.00939 (Fisher's exact test), Q value = 0.076

Table S25.  Gene #13: '7q gain' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
7Q GAIN MUTATED 1 3 12 134
7Q GAIN WILD-TYPE 0 5 9 338

Figure S25.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #7: 'RACE'

'8q gain' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #15: '8q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
8Q GAIN MUTATED 12 40
8Q GAIN WILD-TYPE 172 255

Figure S26.  Get High-res Image Gene #15: '8q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9p gain' versus 'GENDER'

P value = 0.0442 (Fisher's exact test), Q value = 0.21

Table S27.  Gene #16: '9p gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
9P GAIN MUTATED 12 5
9P GAIN WILD-TYPE 216 279

Figure S27.  Get High-res Image Gene #16: '9p gain' versus Clinical Feature #3: 'GENDER'

'9p gain' versus 'RADIATION_THERAPY'

P value = 0.0353 (Fisher's exact test), Q value = 0.18

Table S28.  Gene #16: '9p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
9P GAIN MUTATED 2 14
9P GAIN WILD-TYPE 182 281

Figure S28.  Get High-res Image Gene #16: '9p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q gain' versus 'GENDER'

P value = 0.00268 (Fisher's exact test), Q value = 0.03

Table S29.  Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
9Q GAIN MUTATED 18 6
9Q GAIN WILD-TYPE 210 278

Figure S29.  Get High-res Image Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

'9q gain' versus 'RADIATION_THERAPY'

P value = 0.00177 (Fisher's exact test), Q value = 0.023

Table S30.  Gene #17: '9q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
9Q GAIN MUTATED 2 21
9Q GAIN WILD-TYPE 182 274

Figure S30.  Get High-res Image Gene #17: '9q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0586 (Fisher's exact test), Q value = 0.25

Table S31.  Gene #17: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
9Q GAIN MUTATED 14 6 4
9Q GAIN WILD-TYPE 180 123 185

Figure S31.  Get High-res Image Gene #17: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0215 (Wilcoxon-test), Q value = 0.13

Table S32.  Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
10P GAIN MUTATED 57 38.5 (10.9)
10P GAIN WILD-TYPE 454 43.6 (13.5)

Figure S32.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #18: '10p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
10P GAIN MUTATED 12 41
10P GAIN WILD-TYPE 172 254

Figure S33.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0044

Table S34.  Gene #18: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
10P GAIN MUTATED 32 17 8
10P GAIN WILD-TYPE 162 112 181

Figure S34.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0087 (Fisher's exact test), Q value = 0.072

Table S35.  Gene #19: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
10Q GAIN MUTATED 9 0 2
10Q GAIN WILD-TYPE 185 129 187

Figure S35.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0295 (Wilcoxon-test), Q value = 0.16

Table S36.  Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
11P GAIN MUTATED 30 48.8 (14.9)
11P GAIN WILD-TYPE 481 42.6 (13.2)

Figure S36.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0081 (Fisher's exact test), Q value = 0.07

Table S37.  Gene #20: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
11P GAIN MUTATED 4 9 17
11P GAIN WILD-TYPE 190 120 172

Figure S37.  Get High-res Image Gene #20: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.0336 (Fisher's exact test), Q value = 0.17

Table S38.  Gene #22: '12p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
12P GAIN MUTATED 6 24
12P GAIN WILD-TYPE 178 271

Figure S38.  Get High-res Image Gene #22: '12p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'12q gain' versus 'Time to Death'

P value = 0.00551 (logrank test), Q value = 0.053

Table S39.  Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
12Q GAIN MUTATED 15 9 1.2 - 84.3 (30.2)
12Q GAIN WILD-TYPE 493 116 0.0 - 211.2 (22.1)

Figure S39.  Get High-res Image Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0332 (Fisher's exact test), Q value = 0.17

Table S40.  Gene #24: '13q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
13Q GAIN MUTATED 5 1
13Q GAIN WILD-TYPE 179 294

Figure S40.  Get High-res Image Gene #24: '13q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'15q gain' versus 'Time to Death'

P value = 0.0166 (logrank test), Q value = 0.11

Table S41.  Gene #26: '15q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
15Q GAIN MUTATED 11 7 2.4 - 117.4 (32.5)
15Q GAIN WILD-TYPE 497 118 0.0 - 211.2 (22.3)

Figure S41.  Get High-res Image Gene #26: '15q gain' versus Clinical Feature #1: 'Time to Death'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0259 (Wilcoxon-test), Q value = 0.15

Table S42.  Gene #26: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
15Q GAIN MUTATED 11 51.8 (13.3)
15Q GAIN WILD-TYPE 500 42.8 (13.3)

Figure S42.  Get High-res Image Gene #26: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0135 (Wilcoxon-test), Q value = 0.1

Table S43.  Gene #26: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
15Q GAIN MUTATED 10 72.0 (19.9)
15Q GAIN WILD-TYPE 296 87.2 (12.0)

Figure S43.  Get High-res Image Gene #26: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0319 (Wilcoxon-test), Q value = 0.17

Table S44.  Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
16P GAIN MUTATED 16 49.8 (11.8)
16P GAIN WILD-TYPE 495 42.8 (13.3)

Figure S44.  Get High-res Image Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0153 (Fisher's exact test), Q value = 0.11

Table S45.  Gene #28: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
16Q GAIN MUTATED 13 1 5
16Q GAIN WILD-TYPE 181 128 184

Figure S45.  Get High-res Image Gene #28: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0143 (logrank test), Q value = 0.1

Table S46.  Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
17P GAIN MUTATED 20 8 8.1 - 62.2 (21.6)
17P GAIN WILD-TYPE 488 117 0.0 - 211.2 (22.5)

Figure S46.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0176 (Wilcoxon-test), Q value = 0.11

Table S47.  Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
17P GAIN MUTATED 20 49.9 (13.4)
17P GAIN WILD-TYPE 491 42.7 (13.3)

Figure S47.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.059 (Fisher's exact test), Q value = 0.25

Table S48.  Gene #29: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
17P GAIN MUTATED 11 1 8
17P GAIN WILD-TYPE 183 128 181

Figure S48.  Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 0.00836 (logrank test), Q value = 0.071

Table S49.  Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
17Q GAIN MUTATED 23 9 5.8 - 62.2 (21.0)
17Q GAIN WILD-TYPE 485 116 0.0 - 211.2 (22.4)

Figure S49.  Get High-res Image Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'Time to Death'

P value = 0.0174 (logrank test), Q value = 0.11

Table S50.  Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
18P GAIN MUTATED 18 9 0.2 - 117.5 (25.0)
18P GAIN WILD-TYPE 490 116 0.0 - 211.2 (22.4)

Figure S50.  Get High-res Image Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'Time to Death'

P value = 0.000572 (logrank test), Q value = 0.0088

Table S51.  Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
18Q GAIN MUTATED 13 8 0.2 - 51.9 (29.1)
18Q GAIN WILD-TYPE 495 117 0.0 - 211.2 (22.3)

Figure S51.  Get High-res Image Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00964 (Wilcoxon-test), Q value = 0.076

Table S52.  Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
19P GAIN MUTATED 98 46.3 (14.2)
19P GAIN WILD-TYPE 413 42.2 (13.0)

Figure S52.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'RADIATION_THERAPY'

P value = 0.043 (Fisher's exact test), Q value = 0.21

Table S53.  Gene #33: '19p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
19P GAIN MUTATED 44 48
19P GAIN WILD-TYPE 140 247

Figure S53.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S54.  Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
19P GAIN MUTATED 20 19 60
19P GAIN WILD-TYPE 174 110 129

Figure S54.  Get High-res Image Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'Time to Death'

P value = 1.92e-07 (logrank test), Q value = 8.9e-06

Table S55.  Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
19Q GAIN MUTATED 25 11 0.2 - 54.8 (16.8)
19Q GAIN WILD-TYPE 483 114 0.0 - 211.2 (23.5)

Figure S55.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 7.02e-06 (Wilcoxon-test), Q value = 0.00023

Table S56.  Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
19Q GAIN MUTATED 25 55.2 (11.7)
19Q GAIN WILD-TYPE 486 42.4 (13.1)

Figure S56.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'Time to Death'

P value = 2.94e-12 (logrank test), Q value = 3.8e-10

Table S57.  Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
20P GAIN MUTATED 45 23 0.5 - 54.8 (17.7)
20P GAIN WILD-TYPE 463 102 0.0 - 211.2 (23.5)

Figure S57.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 7.25e-09 (Wilcoxon-test), Q value = 5.2e-07

Table S58.  Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
20P GAIN MUTATED 45 54.4 (11.8)
20P GAIN WILD-TYPE 466 41.9 (13.0)

Figure S58.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'RADIATION_THERAPY'

P value = 0.0282 (Fisher's exact test), Q value = 0.16

Table S59.  Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
20P GAIN MUTATED 9 32
20P GAIN WILD-TYPE 175 263

Figure S59.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00967 (Wilcoxon-test), Q value = 0.076

Table S60.  Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
20P GAIN MUTATED 28 81.4 (13.5)
20P GAIN WILD-TYPE 278 87.2 (12.4)

Figure S60.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'Time to Death'

P value = 2.04e-09 (logrank test), Q value = 1.6e-07

Table S61.  Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
20Q GAIN MUTATED 44 22 0.5 - 117.5 (17.6)
20Q GAIN WILD-TYPE 464 103 0.0 - 211.2 (23.5)

Figure S61.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 2.04e-08 (Wilcoxon-test), Q value = 1.2e-06

Table S62.  Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
20Q GAIN MUTATED 44 54.3 (12.2)
20Q GAIN WILD-TYPE 467 41.9 (13.0)

Figure S62.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'RADIATION_THERAPY'

P value = 0.0282 (Fisher's exact test), Q value = 0.16

Table S63.  Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
20Q GAIN MUTATED 9 32
20Q GAIN WILD-TYPE 175 263

Figure S63.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0145 (Wilcoxon-test), Q value = 0.1

Table S64.  Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
20Q GAIN MUTATED 27 81.5 (13.8)
20Q GAIN WILD-TYPE 279 87.2 (12.4)

Figure S64.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00537 (Wilcoxon-test), Q value = 0.052

Table S65.  Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
21Q GAIN MUTATED 23 52.5 (17.3)
21Q GAIN WILD-TYPE 488 42.5 (13.0)

Figure S65.  Get High-res Image Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0457 (Wilcoxon-test), Q value = 0.21

Table S66.  Gene #38: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
22Q GAIN MUTATED 23 48.0 (11.3)
22Q GAIN WILD-TYPE 488 42.8 (13.4)

Figure S66.  Get High-res Image Gene #38: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00383 (Fisher's exact test), Q value = 0.04

Table S67.  Gene #38: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
22Q GAIN MUTATED 3 4 16
22Q GAIN WILD-TYPE 191 125 173

Figure S67.  Get High-res Image Gene #38: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0197 (Fisher's exact test), Q value = 0.12

Table S68.  Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
XP GAIN MUTATED 14 5 3
XP GAIN WILD-TYPE 180 124 186

Figure S68.  Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.0539 (Wilcoxon-test), Q value = 0.24

Table S69.  Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
XQ GAIN MUTATED 41 39.5 (12.1)
XQ GAIN WILD-TYPE 470 43.3 (13.4)

Figure S69.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'GENDER'

P value = 0.0136 (Fisher's exact test), Q value = 0.1

Table S70.  Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
XQ GAIN MUTATED 26 15
XQ GAIN WILD-TYPE 202 269

Figure S70.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00437 (Fisher's exact test), Q value = 0.044

Table S71.  Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
XQ GAIN MUTATED 20 15 6
XQ GAIN WILD-TYPE 174 114 183

Figure S71.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0254 (Fisher's exact test), Q value = 0.15

Table S72.  Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 446
XQ GAIN MUTATED 6 30
XQ GAIN WILD-TYPE 26 416

Figure S72.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

'1p loss' versus 'Time to Death'

P value = 0.000112 (logrank test), Q value = 0.0022

Table S73.  Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
1P LOSS MUTATED 181 27 0.1 - 182.3 (23.2)
1P LOSS WILD-TYPE 327 98 0.0 - 211.2 (21.3)

Figure S73.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000914 (Wilcoxon-test), Q value = 0.013

Table S74.  Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
1P LOSS MUTATED 183 45.4 (12.8)
1P LOSS WILD-TYPE 328 41.6 (13.5)

Figure S74.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'RADIATION_THERAPY'

P value = 1.83e-07 (Fisher's exact test), Q value = 8.9e-06

Table S75.  Gene #41: '1p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
1P LOSS MUTATED 93 79
1P LOSS WILD-TYPE 91 216

Figure S75.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S76.  Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
1P LOSS MUTATED 10 38 136
1P LOSS WILD-TYPE 184 91 53

Figure S76.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00319 (Fisher's exact test), Q value = 0.034

Table S77.  Gene #42: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
1Q LOSS MUTATED 4 4 18
1Q LOSS WILD-TYPE 190 125 171

Figure S77.  Get High-res Image Gene #42: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'RADIATION_THERAPY'

P value = 0.0138 (Fisher's exact test), Q value = 0.1

Table S78.  Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
2P LOSS MUTATED 2 17
2P LOSS WILD-TYPE 182 278

Figure S78.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0488 (Fisher's exact test), Q value = 0.22

Table S79.  Gene #44: '2q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
2Q LOSS MUTATED 12 3 3
2Q LOSS WILD-TYPE 182 126 186

Figure S79.  Get High-res Image Gene #44: '2q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.0496 (logrank test), Q value = 0.22

Table S80.  Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
3P LOSS MUTATED 29 11 0.1 - 84.3 (24.3)
3P LOSS WILD-TYPE 479 114 0.0 - 211.2 (22.3)

Figure S80.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00192 (Wilcoxon-test), Q value = 0.024

Table S81.  Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
3P LOSS MUTATED 21 78.6 (13.9)
3P LOSS WILD-TYPE 285 87.3 (12.3)

Figure S81.  Get High-res Image Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'Time to Death'

P value = 0.0258 (logrank test), Q value = 0.15

Table S82.  Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
3Q LOSS MUTATED 28 13 0.0 - 117.4 (24.2)
3Q LOSS WILD-TYPE 480 112 0.1 - 211.2 (22.3)

Figure S82.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0188 (Wilcoxon-test), Q value = 0.12

Table S83.  Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
4P LOSS MUTATED 72 46.3 (12.8)
4P LOSS WILD-TYPE 439 42.5 (13.4)

Figure S83.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'GENDER'

P value = 0.0413 (Fisher's exact test), Q value = 0.2

Table S84.  Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
4P LOSS MUTATED 24 48
4P LOSS WILD-TYPE 204 236

Figure S84.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0077

Table S85.  Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
4P LOSS MUTATED 14 19 39
4P LOSS WILD-TYPE 180 110 150

Figure S85.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0158 (Fisher's exact test), Q value = 0.11

Table S86.  Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
4Q LOSS MUTATED 25 23 46
4Q LOSS WILD-TYPE 169 106 143

Figure S86.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00747 (Fisher's exact test), Q value = 0.066

Table S87.  Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
5P LOSS MUTATED 5 27
5P LOSS WILD-TYPE 179 268

Figure S87.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00983 (Fisher's exact test), Q value = 0.077

Table S88.  Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
5P LOSS MUTATED 19 11 5
5P LOSS WILD-TYPE 175 118 184

Figure S88.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00504 (Fisher's exact test), Q value = 0.05

Table S89.  Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
5Q LOSS MUTATED 4 25
5Q LOSS WILD-TYPE 180 270

Figure S89.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.04 (Fisher's exact test), Q value = 0.2

Table S90.  Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
5Q LOSS MUTATED 19 6 7
5Q LOSS WILD-TYPE 175 123 182

Figure S90.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'Time to Death'

P value = 0.000108 (logrank test), Q value = 0.0022

Table S91.  Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
6P LOSS MUTATED 30 13 0.2 - 65.4 (19.3)
6P LOSS WILD-TYPE 478 112 0.0 - 211.2 (22.5)

Figure S91.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0548 (Wilcoxon-test), Q value = 0.24

Table S92.  Gene #51: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
6P LOSS MUTATED 30 47.7 (14.7)
6P LOSS WILD-TYPE 481 42.7 (13.2)

Figure S92.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'RADIATION_THERAPY'

P value = 0.0583 (Fisher's exact test), Q value = 0.25

Table S93.  Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
6P LOSS MUTATED 5 20
6P LOSS WILD-TYPE 179 275

Figure S93.  Get High-res Image Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'Time to Death'

P value = 7.35e-05 (logrank test), Q value = 0.0017

Table S94.  Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
6Q LOSS MUTATED 61 20 0.1 - 65.4 (18.0)
6Q LOSS WILD-TYPE 447 105 0.0 - 211.2 (23.6)

Figure S94.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0291 (Wilcoxon-test), Q value = 0.16

Table S95.  Gene #52: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
6Q LOSS MUTATED 62 46.4 (13.7)
6Q LOSS WILD-TYPE 449 42.5 (13.2)

Figure S95.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0253 (Fisher's exact test), Q value = 0.15

Table S96.  Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
6Q LOSS MUTATED 13 41
6Q LOSS WILD-TYPE 171 254

Figure S96.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00121 (Wilcoxon-test), Q value = 0.016

Table S97.  Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
6Q LOSS MUTATED 40 81.0 (13.2)
6Q LOSS WILD-TYPE 266 87.5 (12.3)

Figure S97.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00115 (Fisher's exact test), Q value = 0.015

Table S98.  Gene #52: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
6Q LOSS MUTATED 37 10 15
6Q LOSS WILD-TYPE 157 119 174

Figure S98.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0504 (Fisher's exact test), Q value = 0.23

Table S99.  Gene #52: '6q loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
6Q LOSS MUTATED 1 1 5 55
6Q LOSS WILD-TYPE 0 7 16 417

Figure S99.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #7: 'RACE'

'8p loss' versus 'Time to Death'

P value = 0.0474 (logrank test), Q value = 0.22

Table S100.  Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
8P LOSS MUTATED 16 6 0.2 - 51.9 (19.9)
8P LOSS WILD-TYPE 492 119 0.0 - 211.2 (22.5)

Figure S100.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'Time to Death'

P value = 0.0439 (logrank test), Q value = 0.21

Table S101.  Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
8Q LOSS MUTATED 11 4 0.2 - 51.9 (19.1)
8Q LOSS WILD-TYPE 497 121 0.0 - 211.2 (22.6)

Figure S101.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'Time to Death'

P value = 1.11e-06 (logrank test), Q value = 4.5e-05

Table S102.  Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
9P LOSS MUTATED 116 46 0.1 - 169.8 (21.2)
9P LOSS WILD-TYPE 392 79 0.0 - 211.2 (22.5)

Figure S102.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00204 (Wilcoxon-test), Q value = 0.024

Table S103.  Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
9P LOSS MUTATED 116 46.2 (13.2)
9P LOSS WILD-TYPE 395 42.0 (13.3)

Figure S103.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000609 (Fisher's exact test), Q value = 0.0092

Table S104.  Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
9P LOSS MUTATED 25 79
9P LOSS WILD-TYPE 159 216

Figure S104.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00199 (Wilcoxon-test), Q value = 0.024

Table S105.  Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
9P LOSS MUTATED 75 83.1 (13.0)
9P LOSS WILD-TYPE 231 87.8 (12.3)

Figure S105.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0589 (Fisher's exact test), Q value = 0.25

Table S106.  Gene #57: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
9P LOSS MUTATED 55 23 39
9P LOSS WILD-TYPE 139 106 150

Figure S106.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'Time to Death'

P value = 0.0035 (logrank test), Q value = 0.037

Table S107.  Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
9Q LOSS MUTATED 50 21 0.1 - 169.8 (21.6)
9Q LOSS WILD-TYPE 458 104 0.0 - 211.2 (22.5)

Figure S107.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00595 (Wilcoxon-test), Q value = 0.055

Table S108.  Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
9Q LOSS MUTATED 50 48.1 (14.7)
9Q LOSS WILD-TYPE 461 42.4 (13.1)

Figure S108.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'RADIATION_THERAPY'

P value = 0.011 (Fisher's exact test), Q value = 0.084

Table S109.  Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
9Q LOSS MUTATED 8 33
9Q LOSS WILD-TYPE 176 262

Figure S109.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000364 (Wilcoxon-test), Q value = 0.0059

Table S110.  Gene #58: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
9Q LOSS MUTATED 32 80.0 (12.2)
9Q LOSS WILD-TYPE 274 87.4 (12.4)

Figure S110.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'Time to Death'

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

Table S111.  Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
10P LOSS MUTATED 83 49 0.1 - 134.3 (16.2)
10P LOSS WILD-TYPE 425 76 0.0 - 211.2 (25.6)

Figure S111.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 5.96e-20 (Wilcoxon-test), Q value = 1.3e-17

Table S112.  Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
10P LOSS MUTATED 83 55.6 (11.0)
10P LOSS WILD-TYPE 428 40.5 (12.4)

Figure S112.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'RADIATION_THERAPY'

P value = 9.18e-05 (Fisher's exact test), Q value = 0.0021

Table S113.  Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
10P LOSS MUTATED 14 61
10P LOSS WILD-TYPE 170 234

Figure S113.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000203 (Wilcoxon-test), Q value = 0.0039

Table S114.  Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
10P LOSS MUTATED 52 80.4 (14.9)
10P LOSS WILD-TYPE 254 88.0 (11.7)

Figure S114.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0022

Table S115.  Gene #59: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
10P LOSS MUTATED 49 16 18
10P LOSS WILD-TYPE 145 113 171

Figure S115.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00867 (Fisher's exact test), Q value = 0.072

Table S116.  Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
10P LOSS MUTATED 1 1 8 72
10P LOSS WILD-TYPE 0 7 13 400

Figure S116.  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 S117.  Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
10Q LOSS MUTATED 97 55 0.1 - 172.8 (17.6)
10Q LOSS WILD-TYPE 411 70 0.0 - 211.2 (25.5)

Figure S117.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 2.9e-17 (Wilcoxon-test), Q value = 4.7e-15

Table S118.  Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
10Q LOSS MUTATED 97 53.4 (12.3)
10Q LOSS WILD-TYPE 414 40.5 (12.4)

Figure S118.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATION_THERAPY'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.00011

Table S119.  Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
10Q LOSS MUTATED 15 73
10Q LOSS WILD-TYPE 169 222

Figure S119.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000212 (Wilcoxon-test), Q value = 0.0039

Table S120.  Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
10Q LOSS MUTATED 60 80.8 (14.9)
10Q LOSS WILD-TYPE 246 88.1 (11.6)

Figure S120.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00078

Table S121.  Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
10Q LOSS MUTATED 57 19 21
10Q LOSS WILD-TYPE 137 110 168

Figure S121.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.0278 (Fisher's exact test), Q value = 0.16

Table S122.  Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
10Q LOSS MUTATED 1 1 8 86
10Q LOSS WILD-TYPE 0 7 13 386

Figure S122.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

'11p loss' versus 'Time to Death'

P value = 0.0307 (logrank test), Q value = 0.17

Table S123.  Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
11P LOSS MUTATED 63 24 0.2 - 156.2 (20.5)
11P LOSS WILD-TYPE 445 101 0.0 - 211.2 (22.5)

Figure S123.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.00629 (Fisher's exact test), Q value = 0.057

Table S124.  Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
11P LOSS MUTATED 13 46
11P LOSS WILD-TYPE 171 249

Figure S124.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0093

Table S125.  Gene #61: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
11P LOSS MUTATED 37 14 12
11P LOSS WILD-TYPE 157 115 177

Figure S125.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 9.86e-05 (logrank test), Q value = 0.0021

Table S126.  Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
11Q LOSS MUTATED 21 9 0.2 - 54.8 (18.7)
11Q LOSS WILD-TYPE 487 116 0.0 - 211.2 (23.2)

Figure S126.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0141 (Fisher's exact test), Q value = 0.1

Table S127.  Gene #62: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
11Q LOSS MUTATED 13 6 2
11Q LOSS WILD-TYPE 181 123 187

Figure S127.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00291 (Fisher's exact test), Q value = 0.032

Table S128.  Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
12Q LOSS MUTATED 29 14 9
12Q LOSS WILD-TYPE 165 115 180

Figure S128.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.000328 (Fisher's exact test), Q value = 0.0054

Table S129.  Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
13Q LOSS MUTATED 26 83
13Q LOSS WILD-TYPE 158 212

Figure S129.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'14q loss' versus 'Time to Death'

P value = 2.47e-05 (logrank test), Q value = 0.00067

Table S130.  Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
14Q LOSS MUTATED 80 33 0.1 - 130.8 (21.3)
14Q LOSS WILD-TYPE 428 92 0.0 - 211.2 (22.9)

Figure S130.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 3.84e-05 (Wilcoxon-test), Q value = 0.00096

Table S131.  Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
14Q LOSS MUTATED 81 48.7 (13.2)
14Q LOSS WILD-TYPE 430 41.9 (13.1)

Figure S131.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.035 (Wilcoxon-test), Q value = 0.18

Table S132.  Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
14Q LOSS MUTATED 51 83.5 (13.1)
14Q LOSS WILD-TYPE 255 87.3 (12.4)

Figure S132.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p loss' versus 'Time to Death'

P value = 0.052 (logrank test), Q value = 0.23

Table S133.  Gene #68: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
16P LOSS MUTATED 14 7 2.4 - 78.3 (28.6)
16P LOSS WILD-TYPE 494 118 0.0 - 211.2 (22.2)

Figure S133.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000244 (Wilcoxon-test), Q value = 0.0043

Table S134.  Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
16P LOSS MUTATED 14 56.1 (10.7)
16P LOSS WILD-TYPE 497 42.6 (13.2)

Figure S134.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000217 (Wilcoxon-test), Q value = 0.0039

Table S135.  Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
16Q LOSS MUTATED 22 54.3 (13.8)
16Q LOSS WILD-TYPE 489 42.5 (13.1)

Figure S135.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.0212 (Fisher's exact test), Q value = 0.13

Table S136.  Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
16Q LOSS MUTATED 3 18
16Q LOSS WILD-TYPE 181 277

Figure S136.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'17p loss' versus 'Time to Death'

P value = 0.0587 (logrank test), Q value = 0.25

Table S137.  Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
17P LOSS MUTATED 14 3 0.1 - 33.3 (15.0)
17P LOSS WILD-TYPE 494 122 0.0 - 211.2 (23.2)

Figure S137.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0397 (Wilcoxon-test), Q value = 0.2

Table S138.  Gene #70: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
17P LOSS MUTATED 14 49.9 (12.3)
17P LOSS WILD-TYPE 497 42.8 (13.3)

Figure S138.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0168 (Wilcoxon-test), Q value = 0.11

Table S139.  Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
17P LOSS MUTATED 7 77.1 (9.5)
17P LOSS WILD-TYPE 299 86.9 (12.6)

Figure S139.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'ETHNICITY'

P value = 0.0599 (Fisher's exact test), Q value = 0.25

Table S140.  Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 446
17P LOSS MUTATED 3 11
17P LOSS WILD-TYPE 29 435

Figure S140.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00237 (Wilcoxon-test), Q value = 0.027

Table S141.  Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
18P LOSS MUTATED 67 48.1 (14.6)
18P LOSS WILD-TYPE 444 42.2 (13.0)

Figure S141.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0236 (Wilcoxon-test), Q value = 0.14

Table S142.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
18Q LOSS MUTATED 62 47.1 (14.7)
18Q LOSS WILD-TYPE 449 42.4 (13.1)

Figure S142.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0326 (Fisher's exact test), Q value = 0.17

Table S143.  Gene #73: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
18Q LOSS MUTATED 20 10 32
18Q LOSS WILD-TYPE 174 119 157

Figure S143.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.0219 (Fisher's exact test), Q value = 0.13

Table S144.  Gene #74: '19p loss' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
19P LOSS MUTATED 0 1 4 20
19P LOSS WILD-TYPE 1 7 17 452

Figure S144.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #7: 'RACE'

'19p loss' versus 'ETHNICITY'

P value = 0.0594 (Fisher's exact test), Q value = 0.25

Table S145.  Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 446
19P LOSS MUTATED 4 19
19P LOSS WILD-TYPE 28 427

Figure S145.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

'19q loss' versus 'Time to Death'

P value = 0.0024 (logrank test), Q value = 0.027

Table S146.  Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
19Q LOSS MUTATED 206 38 0.1 - 182.3 (24.7)
19Q LOSS WILD-TYPE 302 87 0.0 - 211.2 (20.8)

Figure S146.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0437 (Wilcoxon-test), Q value = 0.21

Table S147.  Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
19Q LOSS MUTATED 208 44.2 (12.5)
19Q LOSS WILD-TYPE 303 42.2 (13.8)

Figure S147.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'RADIATION_THERAPY'

P value = 4.3e-06 (Fisher's exact test), Q value = 0.00015

Table S148.  Gene #75: '19q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
19Q LOSS MUTATED 100 97
19Q LOSS WILD-TYPE 84 198

Figure S148.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S149.  Gene #75: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
19Q LOSS MUTATED 23 44 142
19Q LOSS WILD-TYPE 171 85 47

Figure S149.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0472 (Fisher's exact test), Q value = 0.22

Table S150.  Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
20P LOSS MUTATED 0 7
20P LOSS WILD-TYPE 184 288

Figure S150.  Get High-res Image Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00752 (Wilcoxon-test), Q value = 0.066

Table S151.  Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
21Q LOSS MUTATED 28 80.7 (13.9)
21Q LOSS WILD-TYPE 278 87.3 (12.3)

Figure S151.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00412 (Fisher's exact test), Q value = 0.042

Table S152.  Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
21Q LOSS MUTATED 24 7 7
21Q LOSS WILD-TYPE 170 122 182

Figure S152.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 1.94e-08 (logrank test), Q value = 1.2e-06

Table S153.  Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
22Q LOSS MUTATED 57 28 0.1 - 156.2 (19.5)
22Q LOSS WILD-TYPE 451 97 0.0 - 211.2 (23.2)

Figure S153.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 2.06e-06 (Wilcoxon-test), Q value = 7.8e-05

Table S154.  Gene #79: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
22Q LOSS MUTATED 57 51.5 (13.8)
22Q LOSS WILD-TYPE 454 41.9 (12.9)

Figure S154.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.0483 (Fisher's exact test), Q value = 0.22

Table S155.  Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 295
22Q LOSS MUTATED 13 38
22Q LOSS WILD-TYPE 171 257

Figure S155.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00505 (Wilcoxon-test), Q value = 0.05

Table S156.  Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.6)
22Q LOSS MUTATED 35 80.6 (15.1)
22Q LOSS WILD-TYPE 271 87.5 (12.0)

Figure S156.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'Time to Death'

P value = 0.00654 (logrank test), Q value = 0.059

Table S157.  Gene #81: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 508 125 0.0 - 211.2 (22.4)
XQ LOSS MUTATED 69 23 0.1 - 134.3 (18.6)
XQ LOSS WILD-TYPE 439 102 0.0 - 211.2 (23.6)

Figure S157.  Get High-res Image Gene #81: '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/22533657/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/22506744/LGG-TP.merged_data.txt

  • Number of patients = 512

  • Number of significantly arm-level cnvs = 81

  • 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.

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)