Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 52 focal events and 8 clinical features across 512 patients, 145 significant findings detected with Q value < 0.25.

  • amp_1q22 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_1q32.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • amp_2p24.3 cnv correlated to 'Time to Death'.

  • amp_3q26.33 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • amp_4q12 cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_7p11.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_7q31.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_7q32.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_8q24.13 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_9q34.3 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • amp_10p15.3 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_12p13.32 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

  • amp_12q14.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_13q34 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • amp_15q26.3 cnv correlated to 'Time to Death'.

  • amp_17q25.1 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_19p13.3 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_19p13.2 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_xp11.22 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • amp_xp11.22 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • del_1p36.32 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_1p32.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_2q37.3 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_3p21.31 cnv correlated to 'RADIATION_THERAPY' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_3q13.31 cnv correlated to 'Time to Death' and 'RADIATION_THERAPY'.

  • del_3q29 cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_5p15.33 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • del_5q34 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • del_6p25.3 cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_6q22.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_6q24.3 cnv correlated to 'Time to Death',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_9p23 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_9p21.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_10q26.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_11p15.1 cnv correlated to 'Time to Death',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_12p13.1 cnv correlated to 'Time to Death'.

  • del_12q12 cnv correlated to 'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_13q14.2 cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_13q14.2 cnv correlated to 'Time to Death',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_13q34 cnv correlated to 'Time to Death' and 'RADIATION_THERAPY'.

  • del_14q24.3 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_18q23 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_19q13.41 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_19q13.42 cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_22q13.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_xq21.1 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 52 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 145 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
amp 7q31 2 174 (34%) 338 4.64e-05
(0.000536) 		4.58e-08
(2.72e-06) 		0.0495
(0.16) 		0.0027
(0.0154) 		0.0282
(0.101) 		0.0515
(0.165) 		0.00979
(0.0448) 		0.447
(0.694)
amp 7q32 3 182 (36%) 330 2.23e-05
(0.000265) 		7.84e-09
(5.43e-07) 		0.0325
(0.115) 		0.00116
(0.00723) 		0.04
(0.133) 		0.0576
(0.18) 		0.0177
(0.07) 		0.346
(0.582)
amp 7p11 2 128 (25%) 384 3.12e-11
(3.25e-09) 		6.09e-12
(8.44e-10) 		0.307
(0.536) 		0.000705
(0.00473) 		0.000435
(0.00348) 		0.0632
(0.193) 		0.0318
(0.113) 		1
(1.00)
del 10q26 3 151 (29%) 361 1.71e-14
(7.11e-12) 		6.91e-08
(3.59e-06) 		0.0641
(0.193) 		4.78e-06
(0.000117) 		0.0168
(0.069) 		2e-05
(0.000245) 		0.238
(0.454) 		0.845
(0.935)
del 6q22 31 77 (15%) 435 4.4e-06
(0.000114) 		0.0803
(0.234) 		0.385
(0.629) 		0.00682
(0.0334) 		0.00106
(0.00668) 		7e-05
(0.000747) 		0.124
(0.31) 		1
(1.00)
del 9p23 149 (29%) 363 1.97e-06
(5.45e-05) 		0.000504
(0.00381) 		0.494
(0.724) 		0.000111
(0.0011) 		0.000101
(0.00102) 		0.00841
(0.0398) 		0.678
(0.842) 		1
(1.00)
del 9p21 3 175 (34%) 337 6.21e-13
(1.29e-10) 		9.28e-08
(3.86e-06) 		0.191
(0.401) 		1.42e-06
(4.54e-05) 		1.26e-05
(0.000181) 		0.00186
(0.0112) 		0.49
(0.721) 		0.565
(0.773)
del 22q13 31 77 (15%) 435 1e-05
(0.000149) 		0.000444
(0.00348) 		0.62
(0.801) 		0.00782
(0.0374) 		0.0542
(0.171) 		0.00088
(0.00572) 		0.155
(0.353) 		0.603
(0.794)
amp 1q32 1 43 (8%) 469 0.000553
(0.00408) 		8.98e-08
(3.86e-06) 		1
(1.00) 		0.0641
(0.193) 		0.0141
(0.0619) 		0.153
(0.352) 		0.149
(0.352) 		0.0964
(0.265)
amp 3q26 33 21 (4%) 491 1.55e-06
(4.6e-05) 		0.043
(0.141) 		0.825
(0.928) 		0.461
(0.697) 		0.0406
(0.134) 		0.00106
(0.00668) 		0.129
(0.319) 		0.629
(0.801)
amp 12q14 1 37 (7%) 475 2.8e-10
(2.33e-08) 		0.00148
(0.00906) 		0.865
(0.945) 		0.0192
(0.0752) 		0.152
(0.352) 		0.0228
(0.0869) 		0.27
(0.497) 		0.498
(0.726)
del 1p36 32 206 (40%) 306 0.0262
(0.0946) 		8.3e-07
(3.14e-05) 		0.587
(0.787) 		1.48e-05
(0.000205) 		0.444
(0.694) 		1e-05
(0.000149) 		0.282
(0.508) 		1
(1.00)
del 1p32 3 196 (38%) 316 0.00317
(0.0173) 		5.46e-06
(0.000126) 		0.784
(0.903) 		1.07e-06
(3.7e-05) 		0.211
(0.422) 		1e-05
(0.000149) 		0.396
(0.642) 		0.852
(0.94)
del 6q24 3 81 (16%) 431 1.7e-05
(0.000228) 		0.386
(0.629) 		0.18
(0.394) 		0.0251
(0.0925) 		0.000703
(0.00473) 		0.00012
(0.00113) 		0.144
(0.347) 		1
(1.00)
del 11p15 1 72 (14%) 440 0.00718
(0.0347) 		0.236
(0.454) 		0.0959
(0.265) 		0.00682
(0.0334) 		0.0542
(0.171) 		0.00022
(0.00183) 		0.717
(0.865) 		1
(1.00)
del 13q14 2 144 (28%) 368 0.0334
(0.116) 		0.933
(0.996) 		0.237
(0.454) 		0.000182
(0.00161) 		0.00625
(0.0317) 		0.0819
(0.236) 		0.116
(0.296) 		0.426
(0.677)
del 19q13 41 267 (52%) 245 0.00299
(0.0166) 		0.0589
(0.183) 		0.478
(0.71) 		0.000337
(0.00275) 		0.624
(0.801) 		1e-05
(0.000149) 		0.423
(0.674) 		0.717
(0.865)
amp 4q12 30 (6%) 482 0.000578
(0.00408) 		0.197
(0.404) 		0.706
(0.864) 		0.0171
(0.0691) 		0.151
(0.352) 		0.00074
(0.00489) 		1
(1.00) 		0.711
(0.864)
amp 8q24 13 100 (20%) 412 0.224
(0.439) 		0.0203
(0.0782) 		0.316
(0.547) 		0.00663
(0.0332) 		0.894
(0.963) 		0.00401
(0.0214) 		0.623
(0.801) 		0.245
(0.463)
amp 10p15 3 71 (14%) 441 0.499
(0.726) 		0.000195
(0.00169) 		0.159
(0.358) 		0.0596
(0.184) 		0.258
(0.482) 		1e-05
(0.000149) 		0.838
(0.932) 		0.174
(0.386)
amp 19p13 3 129 (25%) 383 0.442
(0.694) 		0.0347
(0.119) 		0.539
(0.75) 		0.00489
(0.0254) 		0.511
(0.734) 		1e-05
(0.000149) 		0.722
(0.865) 		0.294
(0.523)
amp 19p13 2 122 (24%) 390 0.987
(1.00) 		0.00919
(0.0425) 		0.144
(0.347) 		0.011
(0.0491) 		0.974
(1.00) 		1e-05
(0.000149) 		0.62
(0.801) 		0.201
(0.411)
del 2q37 3 77 (15%) 435 0.642
(0.809) 		0.0779
(0.229) 		0.456
(0.696) 		0.0169
(0.069) 		0.37
(0.617) 		0.01
(0.0453) 		0.733
(0.874) 		0.322
(0.553)
del 11p15 5 104 (20%) 408 0.103
(0.275) 		0.014
(0.0619) 		0.0979
(0.266) 		0.00346
(0.0187) 		0.153
(0.352) 		1e-05
(0.000149) 		0.454
(0.696) 		0.822
(0.928)
del 12q12 72 (14%) 440 0.903
(0.966) 		0.522
(0.734) 		0.898
(0.963) 		0.0151
(0.064) 		0.629
(0.801) 		7e-05
(0.000747) 		0.462
(0.697) 		0.0679
(0.202)
del 13q14 2 142 (28%) 370 0.0373
(0.126) 		0.941
(1.00) 		0.234
(0.454) 		0.000161
(0.00148) 		0.00578
(0.0297) 		0.104
(0.275) 		0.109
(0.284) 		0.542
(0.752)
del 19q13 42 278 (54%) 234 0.000117
(0.00113) 		0.257
(0.482) 		0.722
(0.865) 		0.000467
(0.0036) 		0.608
(0.795) 		1e-05
(0.000149) 		0.385
(0.629) 		1
(1.00)
amp 9q34 3 46 (9%) 466 0.823
(0.928) 		0.71
(0.864) 		0.0899
(0.254) 		0.00485
(0.0254) 		0.521
(0.734) 		0.0239
(0.0895) 		0.0993
(0.268) 		0.193
(0.401)
amp 12p13 32 72 (14%) 440 0.265
(0.493) 		0.0366
(0.125) 		0.127
(0.316) 		0.0169
(0.069) 		0.576
(0.778) 		0.123
(0.31) 		0.838
(0.932) 		0.6
(0.794)
amp 17q25 1 43 (8%) 469 0.026
(0.0946) 		0.0334
(0.116) 		0.525
(0.735) 		0.742
(0.879) 		0.189
(0.401) 		0.303
(0.531) 		0.153
(0.352) 		0.318
(0.549)
amp xp11 22 48 (9%) 464 0.18
(0.394) 		0.887
(0.961) 		0.761
(0.887) 		0.000632
(0.00438) 		0.639
(0.809) 		0.00239
(0.0138) 		0.276
(0.503) 		0.193
(0.401)
amp xp11 22 63 (12%) 449 0.397
(0.642) 		0.719
(0.865) 		0.343
(0.581) 		0.000578
(0.00408) 		0.465
(0.699) 		1e-05
(0.000149) 		0.678
(0.842) 		0.569
(0.773)
del 3p21 31 49 (10%) 463 0.188
(0.401) 		0.84
(0.932) 		0.764
(0.887) 		0.00275
(0.0154) 		0.0242
(0.0898) 		0.557
(0.765) 		0.787
(0.903) 		0.218
(0.433)
del 3q13 31 39 (8%) 473 0.0168
(0.069) 		0.839
(0.932) 		0.738
(0.878) 		0.0782
(0.229) 		0.191
(0.401) 		0.549
(0.756) 		0.6
(0.794) 		1
(1.00)
del 3q29 47 (9%) 465 0.0392
(0.132) 		0.972
(1.00) 		0.878
(0.954) 		0.107
(0.282) 		0.066
(0.198) 		0.0888
(0.253) 		0.488
(0.72) 		0.516
(0.734)
del 5p15 33 50 (10%) 462 0.571
(0.774) 		0.373
(0.617) 		0.766
(0.887) 		0.000101
(0.00102) 		0.133
(0.327) 		0.00218
(0.013) 		0.789
(0.903) 		0.759
(0.887)
del 5q34 64 (12%) 448 0.11
(0.284) 		0.696
(0.855) 		0.505
(0.732) 		0.000578
(0.00408) 		0.518
(0.734) 		2e-05
(0.000245) 		0.258
(0.482) 		0.407
(0.653)
del 6p25 3 50 (10%) 462 0.000202
(0.00172) 		0.373
(0.617) 		1
(1.00) 		0.186
(0.401) 		0.0176
(0.07) 		0.325
(0.557) 		0.173
(0.386) 		0.228
(0.445)
del 13q34 110 (21%) 402 0.0149
(0.0638) 		0.482
(0.714) 		0.449
(0.694) 		0.00905
(0.0423) 		0.206
(0.415) 		0.897
(0.963) 		0.277
(0.503) 		0.826
(0.928)
del 14q24 3 121 (24%) 391 1.76e-05
(0.000228) 		0.0144
(0.0623) 		0.0948
(0.265) 		0.152
(0.352) 		0.214
(0.425) 		0.412
(0.66) 		0.184
(0.4) 		1
(1.00)
amp 1q22 42 (8%) 470 0.189
(0.401) 		0.000163
(0.00148) 		1
(1.00) 		0.241
(0.458) 		0.456
(0.696) 		0.221
(0.436) 		0.209
(0.42) 		0.0963
(0.265)
amp 2p24 3 24 (5%) 488 0.0237
(0.0895) 		0.803
(0.915) 		1
(1.00) 		0.655
(0.821) 		0.626
(0.801) 		0.206
(0.415) 		0.749
(0.882) 		0.159
(0.358)
amp 13q34 22 (4%) 490 0.568
(0.773) 		0.765
(0.887) 		0.828
(0.928) 		1
(1.00) 		0.0455
(0.148) 		0.621
(0.801) 		0.733
(0.874) 		0.644
(0.809)
amp 15q26 3 19 (4%) 493 6.15e-05
(0.000691) 		0.953
(1.00) 		0.818
(0.928) 		0.339
(0.578) 		0.194
(0.401) 		0.11
(0.284) 		0.697
(0.855) 		0.343
(0.581)
del 12p13 1 38 (7%) 474 0.00222
(0.013) 		0.349
(0.585) 		1
(1.00) 		0.859
(0.943) 		0.584
(0.786) 		0.113
(0.29) 		1
(1.00) 		0.155
(0.353)
del 18q23 78 (15%) 434 0.877
(0.954) 		0.0196
(0.0763) 		0.267
(0.493) 		0.604
(0.794) 		0.861
(0.943) 		0.238
(0.454) 		0.196
(0.403) 		0.445
(0.694)
del xq21 1 78 (15%) 434 0.083
(0.238) 		0.1
(0.269) 		0.459
(0.696) 		0.149
(0.352) 		0.778
(0.899) 		0.591
(0.791) 		0.468
(0.7) 		1
(1.00)
amp 11q24 1 87 (17%) 425 0.521
(0.734) 		0.527
(0.735) 		0.478
(0.71) 		1
(1.00) 		0.744
(0.879) 		0.509
(0.734) 		0.618
(0.801) 		1
(1.00)
del 1q43 30 (6%) 482 0.862
(0.943) 		0.137
(0.334) 		0.188
(0.401) 		0.117
(0.296) 		0.593
(0.791) 		0.374
(0.617) 		0.311
(0.541) 		1
(1.00)
del 4q34 3 138 (27%) 374 0.522
(0.734) 		0.144
(0.347) 		0.548
(0.756) 		0.456
(0.696) 		0.694
(0.855) 		0.791
(0.903) 		0.666
(0.832) 		0.681
(0.843)
del 7p22 3 23 (4%) 489 0.0968
(0.265) 		0.75
(0.882) 		0.522
(0.734) 		0.177
(0.392) 		0.605
(0.794) 		0.891
(0.963) 		0.293
(0.523) 		0.644
(0.809)
del 8q24 3 29 (6%) 483 0.276
(0.503) 		0.438
(0.693) 		0.447
(0.694) 		0.3
(0.529) 		0.298
(0.528) 		0.282
(0.508) 		0.29
(0.52) 		0.405
(0.653)
'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.000163 (Wilcoxon-test), Q value = 0.0015

Table S1.  Gene #1: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 1(1Q22) MUTATED 42 50.4 (12.8)
AMP PEAK 1(1Q22) WILD-TYPE 469 42.3 (13.2)

Figure S1.  Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q32.1' versus 'Time to Death'

P value = 0.000553 (logrank test), Q value = 0.0041

Table S2.  Gene #2: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 2(1Q32.1) MUTATED 43 21 0.2 - 211.2 (19.1)
AMP PEAK 2(1Q32.1) WILD-TYPE 466 100 0.0 - 182.3 (21.3)

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 8.98e-08 (Wilcoxon-test), Q value = 3.9e-06

Table S3.  Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 2(1Q32.1) MUTATED 43 53.7 (11.9)
AMP PEAK 2(1Q32.1) WILD-TYPE 468 42.0 (13.0)

Figure S3.  Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q32.1' versus 'RADIATION_THERAPY'

P value = 0.0641 (Fisher's exact test), Q value = 0.19

Table S4.  Gene #2: 'amp_1q32.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 2(1Q32.1) MUTATED 10 31
AMP PEAK 2(1Q32.1) WILD-TYPE 174 262

Figure S4.  Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_1q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0141 (Wilcoxon-test), Q value = 0.062

Table S5.  Gene #2: 'amp_1q32.1' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 2(1Q32.1) MUTATED 27 81.5 (12.6)
AMP PEAK 2(1Q32.1) WILD-TYPE 279 87.1 (12.5)

Figure S5.  Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_2p24.3' versus 'Time to Death'

P value = 0.0237 (logrank test), Q value = 0.089

Table S6.  Gene #3: 'amp_2p24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 3(2P24.3) MUTATED 24 10 0.1 - 94.5 (20.4)
AMP PEAK 3(2P24.3) WILD-TYPE 485 111 0.0 - 211.2 (21.0)

Figure S6.  Get High-res Image Gene #3: 'amp_2p24.3' versus Clinical Feature #1: 'Time to Death'

'amp_3q26.33' versus 'Time to Death'

P value = 1.55e-06 (logrank test), Q value = 4.6e-05

Table S7.  Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 4(3Q26.33) MUTATED 20 10 0.2 - 47.8 (17.6)
AMP PEAK 4(3Q26.33) WILD-TYPE 489 111 0.0 - 211.2 (21.3)

Figure S7.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

'amp_3q26.33' versus 'YEARS_TO_BIRTH'

P value = 0.043 (Wilcoxon-test), Q value = 0.14

Table S8.  Gene #4: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 4(3Q26.33) MUTATED 21 48.3 (12.0)
AMP PEAK 4(3Q26.33) WILD-TYPE 490 42.8 (13.4)

Figure S8.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0406 (Wilcoxon-test), Q value = 0.13

Table S9.  Gene #4: 'amp_3q26.33' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 4(3Q26.33) MUTATED 14 81.4 (11.0)
AMP PEAK 4(3Q26.33) WILD-TYPE 292 86.9 (12.6)

Figure S9.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00106 (Fisher's exact test), Q value = 0.0067

Table S10.  Gene #4: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 4(3Q26.33) MUTATED 16 1 4
AMP PEAK 4(3Q26.33) WILD-TYPE 178 128 185

Figure S10.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_4q12' versus 'Time to Death'

P value = 0.000578 (logrank test), Q value = 0.0041

Table S11.  Gene #5: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 5(4Q12) MUTATED 30 12 2.8 - 60.3 (20.1)
AMP PEAK 5(4Q12) WILD-TYPE 479 109 0.0 - 211.2 (21.0)

Figure S11.  Get High-res Image Gene #5: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

'amp_4q12' versus 'RADIATION_THERAPY'

P value = 0.0171 (Fisher's exact test), Q value = 0.069

Table S12.  Gene #5: 'amp_4q12' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 5(4Q12) MUTATED 5 24
AMP PEAK 5(4Q12) WILD-TYPE 179 269

Figure S12.  Get High-res Image Gene #5: 'amp_4q12' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00074 (Fisher's exact test), Q value = 0.0049

Table S13.  Gene #5: 'amp_4q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 5(4Q12) MUTATED 21 2 7
AMP PEAK 5(4Q12) WILD-TYPE 173 127 182

Figure S13.  Get High-res Image Gene #5: 'amp_4q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

P value = 3.12e-11 (logrank test), Q value = 3.2e-09

Table S14.  Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 6(7P11.2) MUTATED 128 54 0.1 - 211.2 (18.0)
AMP PEAK 6(7P11.2) WILD-TYPE 381 67 0.0 - 182.3 (23.2)

Figure S14.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'YEARS_TO_BIRTH'

P value = 6.09e-12 (Wilcoxon-test), Q value = 8.4e-10

Table S15.  Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 6(7P11.2) MUTATED 128 50.1 (13.1)
AMP PEAK 6(7P11.2) WILD-TYPE 383 40.6 (12.6)

Figure S15.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7p11.2' versus 'RADIATION_THERAPY'

P value = 0.000705 (Fisher's exact test), Q value = 0.0047

Table S16.  Gene #6: 'amp_7p11.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 6(7P11.2) MUTATED 30 88
AMP PEAK 6(7P11.2) WILD-TYPE 154 205

Figure S16.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_7p11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000435 (Wilcoxon-test), Q value = 0.0035

Table S17.  Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 6(7P11.2) MUTATED 77 81.8 (15.1)
AMP PEAK 6(7P11.2) WILD-TYPE 229 88.3 (11.2)

Figure S17.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0632 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #6: 'amp_7p11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 6(7P11.2) MUTATED 58 33 37
AMP PEAK 6(7P11.2) WILD-TYPE 136 96 152

Figure S18.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'RACE'

P value = 0.0318 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #6: 'amp_7p11.2' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
AMP PEAK 6(7P11.2) MUTATED 1 2 10 115
AMP PEAK 6(7P11.2) WILD-TYPE 0 6 11 357

Figure S19.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #7: 'RACE'

'amp_7q31.2' versus 'Time to Death'

P value = 4.64e-05 (logrank test), Q value = 0.00054

Table S20.  Gene #7: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 7(7Q31.2) MUTATED 174 60 0.1 - 211.2 (18.5)
AMP PEAK 7(7Q31.2) WILD-TYPE 335 61 0.0 - 182.3 (23.5)

Figure S20.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 4.58e-08 (Wilcoxon-test), Q value = 2.7e-06

Table S21.  Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 7(7Q31.2) MUTATED 174 47.5 (13.3)
AMP PEAK 7(7Q31.2) WILD-TYPE 337 40.6 (12.8)

Figure S21.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'GENDER'

P value = 0.0495 (Fisher's exact test), Q value = 0.16

Table S22.  Gene #7: 'amp_7q31.2' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
AMP PEAK 7(7Q31.2) MUTATED 88 86
AMP PEAK 7(7Q31.2) WILD-TYPE 140 198

Figure S22.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #3: 'GENDER'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 0.0027 (Fisher's exact test), Q value = 0.015

Table S23.  Gene #7: 'amp_7q31.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 7(7Q31.2) MUTATED 46 113
AMP PEAK 7(7Q31.2) WILD-TYPE 138 180

Figure S23.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0282 (Wilcoxon-test), Q value = 0.1

Table S24.  Gene #7: 'amp_7q31.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 7(7Q31.2) MUTATED 102 83.8 (14.8)
AMP PEAK 7(7Q31.2) WILD-TYPE 204 88.0 (11.1)

Figure S24.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0515 (Fisher's exact test), Q value = 0.16

Table S25.  Gene #7: 'amp_7q31.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 7(7Q31.2) MUTATED 75 47 52
AMP PEAK 7(7Q31.2) WILD-TYPE 119 82 137

Figure S25.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'RACE'

P value = 0.00979 (Fisher's exact test), Q value = 0.045

Table S26.  Gene #7: 'amp_7q31.2' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
AMP PEAK 7(7Q31.2) MUTATED 1 4 13 156
AMP PEAK 7(7Q31.2) WILD-TYPE 0 4 8 316

Figure S26.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #7: 'RACE'

'amp_7q32.3' versus 'Time to Death'

P value = 2.23e-05 (logrank test), Q value = 0.00027

Table S27.  Gene #8: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 8(7Q32.3) MUTATED 182 63 0.1 - 211.2 (18.5)
AMP PEAK 8(7Q32.3) WILD-TYPE 327 58 0.0 - 182.3 (23.6)

Figure S27.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

'amp_7q32.3' versus 'YEARS_TO_BIRTH'

P value = 7.84e-09 (Wilcoxon-test), Q value = 5.4e-07

Table S28.  Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 8(7Q32.3) MUTATED 182 47.6 (13.1)
AMP PEAK 8(7Q32.3) WILD-TYPE 329 40.5 (12.8)

Figure S28.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q32.3' versus 'GENDER'

P value = 0.0325 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #8: 'amp_7q32.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
AMP PEAK 8(7Q32.3) MUTATED 93 89
AMP PEAK 8(7Q32.3) WILD-TYPE 135 195

Figure S29.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #3: 'GENDER'

'amp_7q32.3' versus 'RADIATION_THERAPY'

P value = 0.00116 (Fisher's exact test), Q value = 0.0072

Table S30.  Gene #8: 'amp_7q32.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 8(7Q32.3) MUTATED 48 119
AMP PEAK 8(7Q32.3) WILD-TYPE 136 174

Figure S30.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_7q32.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.04 (Wilcoxon-test), Q value = 0.13

Table S31.  Gene #8: 'amp_7q32.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 8(7Q32.3) MUTATED 107 84.1 (14.6)
AMP PEAK 8(7Q32.3) WILD-TYPE 199 88.0 (11.1)

Figure S31.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q32.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0576 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #8: 'amp_7q32.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 8(7Q32.3) MUTATED 78 49 55
AMP PEAK 8(7Q32.3) WILD-TYPE 116 80 134

Figure S32.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7q32.3' versus 'RACE'

P value = 0.0177 (Fisher's exact test), Q value = 0.07

Table S33.  Gene #8: 'amp_7q32.3' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
AMP PEAK 8(7Q32.3) MUTATED 1 4 13 164
AMP PEAK 8(7Q32.3) WILD-TYPE 0 4 8 308

Figure S33.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #7: 'RACE'

'amp_8q24.13' versus 'YEARS_TO_BIRTH'

P value = 0.0203 (Wilcoxon-test), Q value = 0.078

Table S34.  Gene #9: 'amp_8q24.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 9(8Q24.13) MUTATED 100 40.4 (13.0)
AMP PEAK 9(8Q24.13) WILD-TYPE 411 43.6 (13.4)

Figure S34.  Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.13' versus 'RADIATION_THERAPY'

P value = 0.00663 (Fisher's exact test), Q value = 0.033

Table S35.  Gene #9: 'amp_8q24.13' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 9(8Q24.13) MUTATED 25 70
AMP PEAK 9(8Q24.13) WILD-TYPE 159 223

Figure S35.  Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_8q24.13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00401 (Fisher's exact test), Q value = 0.021

Table S36.  Gene #9: 'amp_8q24.13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 9(8Q24.13) MUTATED 48 29 23
AMP PEAK 9(8Q24.13) WILD-TYPE 146 100 166

Figure S36.  Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_9q34.3' versus 'RADIATION_THERAPY'

P value = 0.00485 (Fisher's exact test), Q value = 0.025

Table S37.  Gene #10: 'amp_9q34.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 10(9Q34.3) MUTATED 8 35
AMP PEAK 10(9Q34.3) WILD-TYPE 176 258

Figure S37.  Get High-res Image Gene #10: 'amp_9q34.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0239 (Fisher's exact test), Q value = 0.089

Table S38.  Gene #10: 'amp_9q34.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 10(9Q34.3) MUTATED 24 13 9
AMP PEAK 10(9Q34.3) WILD-TYPE 170 116 180

Figure S38.  Get High-res Image Gene #10: 'amp_9q34.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 0.000195 (Wilcoxon-test), Q value = 0.0017

Table S39.  Gene #11: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 11(10P15.3) MUTATED 71 37.0 (10.3)
AMP PEAK 11(10P15.3) WILD-TYPE 440 44.0 (13.5)

Figure S39.  Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p15.3' versus 'RADIATION_THERAPY'

P value = 0.0596 (Fisher's exact test), Q value = 0.18

Table S40.  Gene #11: 'amp_10p15.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 11(10P15.3) MUTATED 19 49
AMP PEAK 11(10P15.3) WILD-TYPE 165 244

Figure S40.  Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_10p15.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S41.  Gene #11: 'amp_10p15.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 11(10P15.3) MUTATED 38 24 9
AMP PEAK 11(10P15.3) WILD-TYPE 156 105 180

Figure S41.  Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_12p13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0366 (Wilcoxon-test), Q value = 0.12

Table S42.  Gene #13: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 13(12P13.32) MUTATED 72 40.4 (12.9)
AMP PEAK 13(12P13.32) WILD-TYPE 439 43.4 (13.4)

Figure S42.  Get High-res Image Gene #13: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p13.32' versus 'RADIATION_THERAPY'

P value = 0.0169 (Fisher's exact test), Q value = 0.069

Table S43.  Gene #13: 'amp_12p13.32' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 13(12P13.32) MUTATED 18 52
AMP PEAK 13(12P13.32) WILD-TYPE 166 241

Figure S43.  Get High-res Image Gene #13: 'amp_12p13.32' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'Time to Death'

P value = 2.8e-10 (logrank test), Q value = 2.3e-08

Table S44.  Gene #14: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 14(12Q14.1) MUTATED 37 21 0.2 - 84.3 (17.5)
AMP PEAK 14(12Q14.1) WILD-TYPE 472 100 0.0 - 211.2 (21.4)

Figure S44.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_12q14.1' versus 'YEARS_TO_BIRTH'

P value = 0.00148 (Wilcoxon-test), Q value = 0.0091

Table S45.  Gene #14: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 14(12Q14.1) MUTATED 37 50.2 (14.3)
AMP PEAK 14(12Q14.1) WILD-TYPE 474 42.4 (13.1)

Figure S45.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'RADIATION_THERAPY'

P value = 0.0192 (Fisher's exact test), Q value = 0.075

Table S46.  Gene #14: 'amp_12q14.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 14(12Q14.1) MUTATED 7 28
AMP PEAK 14(12Q14.1) WILD-TYPE 177 265

Figure S46.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0228 (Fisher's exact test), Q value = 0.087

Table S47.  Gene #14: 'amp_12q14.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 14(12Q14.1) MUTATED 22 5 10
AMP PEAK 14(12Q14.1) WILD-TYPE 172 124 179

Figure S47.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_13q34' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0455 (Wilcoxon-test), Q value = 0.15

Table S48.  Gene #15: 'amp_13q34' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
AMP PEAK 15(13Q34) MUTATED 14 77.1 (18.6)
AMP PEAK 15(13Q34) WILD-TYPE 292 87.1 (12.1)

Figure S48.  Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_15q26.3' versus 'Time to Death'

P value = 6.15e-05 (logrank test), Q value = 0.00069

Table S49.  Gene #16: 'amp_15q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 16(15Q26.3) MUTATED 19 11 2.4 - 51.9 (24.9)
AMP PEAK 16(15Q26.3) WILD-TYPE 490 110 0.0 - 211.2 (20.8)

Figure S49.  Get High-res Image Gene #16: 'amp_15q26.3' versus Clinical Feature #1: 'Time to Death'

'amp_17q25.1' versus 'Time to Death'

P value = 0.026 (logrank test), Q value = 0.095

Table S50.  Gene #17: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
AMP PEAK 17(17Q25.1) MUTATED 43 14 0.2 - 85.5 (21.0)
AMP PEAK 17(17Q25.1) WILD-TYPE 466 107 0.0 - 211.2 (20.8)

Figure S50.  Get High-res Image Gene #17: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

'amp_17q25.1' versus 'YEARS_TO_BIRTH'

P value = 0.0334 (Wilcoxon-test), Q value = 0.12

Table S51.  Gene #17: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 17(17Q25.1) MUTATED 43 46.7 (12.4)
AMP PEAK 17(17Q25.1) WILD-TYPE 468 42.7 (13.4)

Figure S51.  Get High-res Image Gene #17: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 0.0347 (Wilcoxon-test), Q value = 0.12

Table S52.  Gene #18: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 18(19P13.3) MUTATED 128 45.1 (13.8)
AMP PEAK 18(19P13.3) WILD-TYPE 383 42.3 (13.1)

Figure S52.  Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.3' versus 'RADIATION_THERAPY'

P value = 0.00489 (Fisher's exact test), Q value = 0.025

Table S53.  Gene #18: 'amp_19p13.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 18(19P13.3) MUTATED 60 61
AMP PEAK 18(19P13.3) WILD-TYPE 124 232

Figure S53.  Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S54.  Gene #18: 'amp_19p13.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 18(19P13.3) MUTATED 26 29 74
AMP PEAK 18(19P13.3) WILD-TYPE 168 100 115

Figure S54.  Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_19p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.00919 (Wilcoxon-test), Q value = 0.042

Table S55.  Gene #19: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
AMP PEAK 19(19P13.2) MUTATED 121 45.9 (13.7)
AMP PEAK 19(19P13.2) WILD-TYPE 390 42.1 (13.1)

Figure S55.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.2' versus 'RADIATION_THERAPY'

P value = 0.011 (Fisher's exact test), Q value = 0.049

Table S56.  Gene #19: 'amp_19p13.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 19(19P13.2) MUTATED 56 58
AMP PEAK 19(19P13.2) WILD-TYPE 128 235

Figure S56.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S57.  Gene #19: 'amp_19p13.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 19(19P13.2) MUTATED 24 25 73
AMP PEAK 19(19P13.2) WILD-TYPE 170 104 116

Figure S57.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xp11.22' versus 'RADIATION_THERAPY'

P value = 0.000632 (Fisher's exact test), Q value = 0.0044

Table S58.  Gene #20: 'amp_xp11.22' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 20(XP11.22) MUTATED 7 38
AMP PEAK 20(XP11.22) WILD-TYPE 177 255

Figure S58.  Get High-res Image Gene #20: 'amp_xp11.22' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_xp11.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00239 (Fisher's exact test), Q value = 0.014

Table S59.  Gene #20: 'amp_xp11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 20(XP11.22) MUTATED 28 12 8
AMP PEAK 20(XP11.22) WILD-TYPE 166 117 181

Figure S59.  Get High-res Image Gene #20: 'amp_xp11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xp11.22' versus 'RADIATION_THERAPY'

P value = 0.000578 (Fisher's exact test), Q value = 0.0041

Table S60.  Gene #21: 'amp_xp11.22' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
AMP PEAK 21(XP11.22) MUTATED 11 48
AMP PEAK 21(XP11.22) WILD-TYPE 173 245

Figure S60.  Get High-res Image Gene #21: 'amp_xp11.22' versus Clinical Feature #4: 'RADIATION_THERAPY'

'amp_xp11.22' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S61.  Gene #21: 'amp_xp11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
AMP PEAK 21(XP11.22) MUTATED 39 15 9
AMP PEAK 21(XP11.22) WILD-TYPE 155 114 180

Figure S61.  Get High-res Image Gene #21: 'amp_xp11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_1p36.32' versus 'Time to Death'

P value = 0.0262 (logrank test), Q value = 0.095

Table S62.  Gene #22: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 1(1P36.32) MUTATED 204 37 0.1 - 182.3 (20.6)
DEL PEAK 1(1P36.32) WILD-TYPE 305 84 0.0 - 211.2 (21.0)

Figure S62.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'YEARS_TO_BIRTH'

P value = 8.3e-07 (Wilcoxon-test), Q value = 3.1e-05

Table S63.  Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 1(1P36.32) MUTATED 205 46.3 (12.8)
DEL PEAK 1(1P36.32) WILD-TYPE 306 40.7 (13.3)

Figure S63.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.32' versus 'RADIATION_THERAPY'

P value = 1.48e-05 (Fisher's exact test), Q value = 0.00021

Table S64.  Gene #22: 'del_1p36.32' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 1(1P36.32) MUTATED 97 95
DEL PEAK 1(1P36.32) WILD-TYPE 87 198

Figure S64.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_1p36.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S65.  Gene #22: 'del_1p36.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 1(1P36.32) MUTATED 22 46 138
DEL PEAK 1(1P36.32) WILD-TYPE 172 83 51

Figure S65.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_1p32.3' versus 'Time to Death'

P value = 0.00317 (logrank test), Q value = 0.017

Table S66.  Gene #23: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 2(1P32.3) MUTATED 194 32 0.1 - 182.3 (21.4)
DEL PEAK 2(1P32.3) WILD-TYPE 315 89 0.0 - 211.2 (20.8)

Figure S66.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

'del_1p32.3' versus 'YEARS_TO_BIRTH'

P value = 5.46e-06 (Wilcoxon-test), Q value = 0.00013

Table S67.  Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 2(1P32.3) MUTATED 195 46.3 (13.1)
DEL PEAK 2(1P32.3) WILD-TYPE 316 40.9 (13.1)

Figure S67.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p32.3' versus 'RADIATION_THERAPY'

P value = 1.07e-06 (Fisher's exact test), Q value = 3.7e-05

Table S68.  Gene #23: 'del_1p32.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 2(1P32.3) MUTATED 95 85
DEL PEAK 2(1P32.3) WILD-TYPE 89 208

Figure S68.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_1p32.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S69.  Gene #23: 'del_1p32.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 2(1P32.3) MUTATED 16 42 138
DEL PEAK 2(1P32.3) WILD-TYPE 178 87 51

Figure S69.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.0779 (Wilcoxon-test), Q value = 0.23

Table S70.  Gene #25: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 4(2Q37.3) MUTATED 77 40.8 (13.3)
DEL PEAK 4(2Q37.3) WILD-TYPE 434 43.4 (13.3)

Figure S70.  Get High-res Image Gene #25: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'RADIATION_THERAPY'

P value = 0.0169 (Fisher's exact test), Q value = 0.069

Table S71.  Gene #25: 'del_2q37.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 4(2Q37.3) MUTATED 18 53
DEL PEAK 4(2Q37.3) WILD-TYPE 166 240

Figure S71.  Get High-res Image Gene #25: 'del_2q37.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.01 (Fisher's exact test), Q value = 0.045

Table S72.  Gene #25: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 4(2Q37.3) MUTATED 37 23 17
DEL PEAK 4(2Q37.3) WILD-TYPE 157 106 172

Figure S72.  Get High-res Image Gene #25: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.00275 (Fisher's exact test), Q value = 0.015

Table S73.  Gene #26: 'del_3p21.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 5(3P21.31) MUTATED 9 39
DEL PEAK 5(3P21.31) WILD-TYPE 175 254

Figure S73.  Get High-res Image Gene #26: 'del_3p21.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_3p21.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0242 (Wilcoxon-test), Q value = 0.09

Table S74.  Gene #26: 'del_3p21.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 5(3P21.31) MUTATED 32 81.2 (15.4)
DEL PEAK 5(3P21.31) WILD-TYPE 274 87.3 (12.1)

Figure S74.  Get High-res Image Gene #26: 'del_3p21.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3q13.31' versus 'Time to Death'

P value = 0.0168 (logrank test), Q value = 0.069

Table S75.  Gene #27: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 6(3Q13.31) MUTATED 39 16 0.2 - 117.4 (23.2)
DEL PEAK 6(3Q13.31) WILD-TYPE 470 105 0.0 - 211.2 (20.7)

Figure S75.  Get High-res Image Gene #27: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

'del_3q13.31' versus 'RADIATION_THERAPY'

P value = 0.0782 (Fisher's exact test), Q value = 0.23

Table S76.  Gene #27: 'del_3q13.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 6(3Q13.31) MUTATED 9 28
DEL PEAK 6(3Q13.31) WILD-TYPE 175 265

Figure S76.  Get High-res Image Gene #27: 'del_3q13.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_3q29' versus 'Time to Death'

P value = 0.0392 (logrank test), Q value = 0.13

Table S77.  Gene #28: 'del_3q29' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 7(3Q29) MUTATED 47 18 0.0 - 122.5 (24.2)
DEL PEAK 7(3Q29) WILD-TYPE 462 103 0.1 - 211.2 (20.6)

Figure S77.  Get High-res Image Gene #28: 'del_3q29' versus Clinical Feature #1: 'Time to Death'

'del_3q29' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.066 (Wilcoxon-test), Q value = 0.2

Table S78.  Gene #28: 'del_3q29' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 7(3Q29) MUTATED 33 82.7 (14.2)
DEL PEAK 7(3Q29) WILD-TYPE 273 87.1 (12.3)

Figure S78.  Get High-res Image Gene #28: 'del_3q29' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.000101 (Fisher's exact test), Q value = 0.001

Table S79.  Gene #30: 'del_5p15.33' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 9(5P15.33) MUTATED 6 40
DEL PEAK 9(5P15.33) WILD-TYPE 178 253

Figure S79.  Get High-res Image Gene #30: 'del_5p15.33' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00218 (Fisher's exact test), Q value = 0.013

Table S80.  Gene #30: 'del_5p15.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 9(5P15.33) MUTATED 23 19 8
DEL PEAK 9(5P15.33) WILD-TYPE 171 110 181

Figure S80.  Get High-res Image Gene #30: 'del_5p15.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_5q34' versus 'RADIATION_THERAPY'

P value = 0.000578 (Fisher's exact test), Q value = 0.0041

Table S81.  Gene #31: 'del_5q34' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 10(5Q34) MUTATED 11 48
DEL PEAK 10(5Q34) WILD-TYPE 173 245

Figure S81.  Get High-res Image Gene #31: 'del_5q34' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_5q34' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00024

Table S82.  Gene #31: 'del_5q34' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 10(5Q34) MUTATED 41 13 10
DEL PEAK 10(5Q34) WILD-TYPE 153 116 179

Figure S82.  Get High-res Image Gene #31: 'del_5q34' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 0.000202 (logrank test), Q value = 0.0017

Table S83.  Gene #32: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 11(6P25.3) MUTATED 49 21 0.2 - 145.1 (19.2)
DEL PEAK 11(6P25.3) WILD-TYPE 460 100 0.0 - 211.2 (21.0)

Figure S83.  Get High-res Image Gene #32: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6p25.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0176 (Wilcoxon-test), Q value = 0.07

Table S84.  Gene #32: 'del_6p25.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 11(6P25.3) MUTATED 35 82.6 (12.4)
DEL PEAK 11(6P25.3) WILD-TYPE 271 87.2 (12.5)

Figure S84.  Get High-res Image Gene #32: 'del_6p25.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'Time to Death'

P value = 4.4e-06 (logrank test), Q value = 0.00011

Table S85.  Gene #33: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 12(6Q22.31) MUTATED 76 28 0.1 - 117.4 (18.0)
DEL PEAK 12(6Q22.31) WILD-TYPE 433 93 0.0 - 211.2 (21.5)

Figure S85.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'YEARS_TO_BIRTH'

P value = 0.0803 (Wilcoxon-test), Q value = 0.23

Table S86.  Gene #33: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 12(6Q22.31) MUTATED 77 45.5 (13.8)
DEL PEAK 12(6Q22.31) WILD-TYPE 434 42.5 (13.2)

Figure S86.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q22.31' versus 'RADIATION_THERAPY'

P value = 0.00682 (Fisher's exact test), Q value = 0.033

Table S87.  Gene #33: 'del_6q22.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 12(6Q22.31) MUTATED 16 52
DEL PEAK 12(6Q22.31) WILD-TYPE 168 241

Figure S87.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00106 (Wilcoxon-test), Q value = 0.0067

Table S88.  Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 12(6Q22.31) MUTATED 51 81.4 (13.7)
DEL PEAK 12(6Q22.31) WILD-TYPE 255 87.7 (12.1)

Figure S88.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.00075

Table S89.  Gene #33: 'del_6q22.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 12(6Q22.31) MUTATED 47 11 19
DEL PEAK 12(6Q22.31) WILD-TYPE 147 118 170

Figure S89.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6q24.3' versus 'Time to Death'

P value = 1.7e-05 (logrank test), Q value = 0.00023

Table S90.  Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 13(6Q24.3) MUTATED 80 29 0.0 - 130.8 (18.0)
DEL PEAK 13(6Q24.3) WILD-TYPE 429 92 0.1 - 211.2 (21.5)

Figure S90.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

'del_6q24.3' versus 'RADIATION_THERAPY'

P value = 0.0251 (Fisher's exact test), Q value = 0.092

Table S91.  Gene #34: 'del_6q24.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 13(6Q24.3) MUTATED 19 53
DEL PEAK 13(6Q24.3) WILD-TYPE 165 240

Figure S91.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_6q24.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000703 (Wilcoxon-test), Q value = 0.0047

Table S92.  Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 13(6Q24.3) MUTATED 52 81.3 (13.6)
DEL PEAK 13(6Q24.3) WILD-TYPE 254 87.7 (12.1)

Figure S92.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0011

Table S93.  Gene #34: 'del_6q24.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 13(6Q24.3) MUTATED 48 12 21
DEL PEAK 13(6Q24.3) WILD-TYPE 146 117 168

Figure S93.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'Time to Death'

P value = 1.97e-06 (logrank test), Q value = 5.5e-05

Table S94.  Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 16(9P23) MUTATED 148 52 0.1 - 169.8 (20.4)
DEL PEAK 16(9P23) WILD-TYPE 361 69 0.0 - 211.2 (21.3)

Figure S94.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.000504 (Wilcoxon-test), Q value = 0.0038

Table S95.  Gene #37: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 16(9P23) MUTATED 148 46.2 (13.5)
DEL PEAK 16(9P23) WILD-TYPE 363 41.7 (13.1)

Figure S95.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'RADIATION_THERAPY'

P value = 0.000111 (Fisher's exact test), Q value = 0.0011

Table S96.  Gene #37: 'del_9p23' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 16(9P23) MUTATED 34 102
DEL PEAK 16(9P23) WILD-TYPE 150 191

Figure S96.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_9p23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000101 (Wilcoxon-test), Q value = 0.001

Table S97.  Gene #37: 'del_9p23' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 16(9P23) MUTATED 96 82.6 (13.6)
DEL PEAK 16(9P23) WILD-TYPE 210 88.5 (11.6)

Figure S97.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00841 (Fisher's exact test), Q value = 0.04

Table S98.  Gene #37: 'del_9p23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 16(9P23) MUTATED 72 33 44
DEL PEAK 16(9P23) WILD-TYPE 122 96 145

Figure S98.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'Time to Death'

P value = 6.21e-13 (logrank test), Q value = 1.3e-10

Table S99.  Gene #38: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 17(9P21.3) MUTATED 174 67 0.1 - 169.8 (19.3)
DEL PEAK 17(9P21.3) WILD-TYPE 335 54 0.0 - 211.2 (22.5)

Figure S99.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 9.28e-08 (Wilcoxon-test), Q value = 3.9e-06

Table S100.  Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 17(9P21.3) MUTATED 174 47.6 (14.0)
DEL PEAK 17(9P21.3) WILD-TYPE 337 40.6 (12.4)

Figure S100.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'RADIATION_THERAPY'

P value = 1.42e-06 (Fisher's exact test), Q value = 4.5e-05

Table S101.  Gene #38: 'del_9p21.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 17(9P21.3) MUTATED 37 121
DEL PEAK 17(9P21.3) WILD-TYPE 147 172

Figure S101.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.26e-05 (Wilcoxon-test), Q value = 0.00018

Table S102.  Gene #38: 'del_9p21.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 17(9P21.3) MUTATED 105 82.1 (14.3)
DEL PEAK 17(9P21.3) WILD-TYPE 201 89.0 (10.9)

Figure S102.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00186 (Fisher's exact test), Q value = 0.011

Table S103.  Gene #38: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 17(9P21.3) MUTATED 85 36 54
DEL PEAK 17(9P21.3) WILD-TYPE 109 93 135

Figure S103.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'Time to Death'

P value = 1.71e-14 (logrank test), Q value = 7.1e-12

Table S104.  Gene #39: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 18(10Q26.3) MUTATED 150 67 0.1 - 172.8 (17.9)
DEL PEAK 18(10Q26.3) WILD-TYPE 359 54 0.0 - 211.2 (23.8)

Figure S104.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 6.91e-08 (Wilcoxon-test), Q value = 3.6e-06

Table S105.  Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 18(10Q26.3) MUTATED 151 48.1 (13.9)
DEL PEAK 18(10Q26.3) WILD-TYPE 360 40.8 (12.5)

Figure S105.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'GENDER'

P value = 0.0641 (Fisher's exact test), Q value = 0.19

Table S106.  Gene #39: 'del_10q26.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 228 284
DEL PEAK 18(10Q26.3) MUTATED 77 74
DEL PEAK 18(10Q26.3) WILD-TYPE 151 210

Figure S106.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #3: 'GENDER'

'del_10q26.3' versus 'RADIATION_THERAPY'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.00012

Table S107.  Gene #39: 'del_10q26.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 18(10Q26.3) MUTATED 32 108
DEL PEAK 18(10Q26.3) WILD-TYPE 152 185

Figure S107.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_10q26.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0168 (Wilcoxon-test), Q value = 0.069

Table S108.  Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 18(10Q26.3) MUTATED 90 83.3 (15.0)
DEL PEAK 18(10Q26.3) WILD-TYPE 216 88.0 (11.2)

Figure S108.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00024

Table S109.  Gene #39: 'del_10q26.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 18(10Q26.3) MUTATED 81 33 37
DEL PEAK 18(10Q26.3) WILD-TYPE 113 96 152

Figure S109.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.014 (Wilcoxon-test), Q value = 0.062

Table S110.  Gene #40: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 19(11P15.5) MUTATED 104 40.1 (11.4)
DEL PEAK 19(11P15.5) WILD-TYPE 407 43.7 (13.7)

Figure S110.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.00346 (Fisher's exact test), Q value = 0.019

Table S111.  Gene #40: 'del_11p15.5' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 19(11P15.5) MUTATED 25 73
DEL PEAK 19(11P15.5) WILD-TYPE 159 220

Figure S111.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S112.  Gene #40: 'del_11p15.5' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 19(11P15.5) MUTATED 57 30 17
DEL PEAK 19(11P15.5) WILD-TYPE 137 99 172

Figure S112.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11p15.1' versus 'Time to Death'

P value = 0.00718 (logrank test), Q value = 0.035

Table S113.  Gene #41: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 20(11P15.1) MUTATED 71 27 0.2 - 156.2 (20.5)
DEL PEAK 20(11P15.1) WILD-TYPE 438 94 0.0 - 211.2 (20.9)

Figure S113.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

'del_11p15.1' versus 'RADIATION_THERAPY'

P value = 0.00682 (Fisher's exact test), Q value = 0.033

Table S114.  Gene #41: 'del_11p15.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 20(11P15.1) MUTATED 16 52
DEL PEAK 20(11P15.1) WILD-TYPE 168 241

Figure S114.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_11p15.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0542 (Wilcoxon-test), Q value = 0.17

Table S115.  Gene #41: 'del_11p15.1' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 20(11P15.1) MUTATED 53 84.5 (11.5)
DEL PEAK 20(11P15.1) WILD-TYPE 253 87.1 (12.8)

Figure S115.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S116.  Gene #41: 'del_11p15.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 20(11P15.1) MUTATED 43 15 14
DEL PEAK 20(11P15.1) WILD-TYPE 151 114 175

Figure S116.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'Time to Death'

P value = 0.00222 (logrank test), Q value = 0.013

Table S117.  Gene #42: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 21(12P13.1) MUTATED 37 14 0.1 - 95.1 (20.7)
DEL PEAK 21(12P13.1) WILD-TYPE 472 107 0.0 - 211.2 (20.9)

Figure S117.  Get High-res Image Gene #42: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

'del_12q12' versus 'RADIATION_THERAPY'

P value = 0.0151 (Fisher's exact test), Q value = 0.064

Table S118.  Gene #43: 'del_12q12' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 22(12Q12) MUTATED 17 51
DEL PEAK 22(12Q12) WILD-TYPE 167 242

Figure S118.  Get High-res Image Gene #43: 'del_12q12' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_12q12' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.00075

Table S119.  Gene #43: 'del_12q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 22(12Q12) MUTATED 43 16 13
DEL PEAK 22(12Q12) WILD-TYPE 151 113 176

Figure S119.  Get High-res Image Gene #43: 'del_12q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_12q12' versus 'ETHNICITY'

P value = 0.0679 (Fisher's exact test), Q value = 0.2

Table S120.  Gene #43: 'del_12q12' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 446
DEL PEAK 22(12Q12) MUTATED 1 66
DEL PEAK 22(12Q12) WILD-TYPE 31 380

Figure S120.  Get High-res Image Gene #43: 'del_12q12' versus Clinical Feature #8: 'ETHNICITY'

'del_13q14.2' versus 'Time to Death'

P value = 0.0373 (logrank test), Q value = 0.13

Table S121.  Gene #44: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 23(13Q14.2) MUTATED 141 46 0.1 - 211.2 (20.0)
DEL PEAK 23(13Q14.2) WILD-TYPE 368 75 0.0 - 182.3 (22.2)

Figure S121.  Get High-res Image Gene #44: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.000161 (Fisher's exact test), Q value = 0.0015

Table S122.  Gene #44: 'del_13q14.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 23(13Q14.2) MUTATED 34 101
DEL PEAK 23(13Q14.2) WILD-TYPE 150 192

Figure S122.  Get High-res Image Gene #44: 'del_13q14.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00578 (Wilcoxon-test), Q value = 0.03

Table S123.  Gene #44: 'del_13q14.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 23(13Q14.2) MUTATED 90 83.6 (13.5)
DEL PEAK 23(13Q14.2) WILD-TYPE 216 87.9 (12.0)

Figure S123.  Get High-res Image Gene #44: 'del_13q14.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q14.2' versus 'Time to Death'

P value = 0.0334 (logrank test), Q value = 0.12

Table S124.  Gene #45: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 24(13Q14.2) MUTATED 143 47 0.1 - 211.2 (20.0)
DEL PEAK 24(13Q14.2) WILD-TYPE 366 74 0.0 - 182.3 (21.7)

Figure S124.  Get High-res Image Gene #45: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.000182 (Fisher's exact test), Q value = 0.0016

Table S125.  Gene #45: 'del_13q14.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 24(13Q14.2) MUTATED 35 102
DEL PEAK 24(13Q14.2) WILD-TYPE 149 191

Figure S125.  Get High-res Image Gene #45: 'del_13q14.2' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00625 (Wilcoxon-test), Q value = 0.032

Table S126.  Gene #45: 'del_13q14.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 24(13Q14.2) MUTATED 91 83.6 (13.5)
DEL PEAK 24(13Q14.2) WILD-TYPE 215 87.9 (12.0)

Figure S126.  Get High-res Image Gene #45: 'del_13q14.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0819 (Fisher's exact test), Q value = 0.24

Table S127.  Gene #45: 'del_13q14.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 24(13Q14.2) MUTATED 64 37 43
DEL PEAK 24(13Q14.2) WILD-TYPE 130 92 146

Figure S127.  Get High-res Image Gene #45: 'del_13q14.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_13q34' versus 'Time to Death'

P value = 0.0149 (logrank test), Q value = 0.064

Table S128.  Gene #46: 'del_13q34' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 25(13Q34) MUTATED 110 38 0.1 - 211.2 (18.9)
DEL PEAK 25(13Q34) WILD-TYPE 399 83 0.0 - 182.3 (22.6)

Figure S128.  Get High-res Image Gene #46: 'del_13q34' versus Clinical Feature #1: 'Time to Death'

'del_13q34' versus 'RADIATION_THERAPY'

P value = 0.00905 (Fisher's exact test), Q value = 0.042

Table S129.  Gene #46: 'del_13q34' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 25(13Q34) MUTATED 29 77
DEL PEAK 25(13Q34) WILD-TYPE 155 216

Figure S129.  Get High-res Image Gene #46: 'del_13q34' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_14q24.3' versus 'Time to Death'

P value = 1.76e-05 (logrank test), Q value = 0.00023

Table S130.  Gene #47: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 26(14Q24.3) MUTATED 120 45 0.1 - 130.8 (21.4)
DEL PEAK 26(14Q24.3) WILD-TYPE 389 76 0.0 - 211.2 (20.7)

Figure S130.  Get High-res Image Gene #47: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

'del_14q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.0144 (Wilcoxon-test), Q value = 0.062

Table S131.  Gene #47: 'del_14q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 26(14Q24.3) MUTATED 121 45.6 (13.0)
DEL PEAK 26(14Q24.3) WILD-TYPE 390 42.2 (13.4)

Figure S131.  Get High-res Image Gene #47: 'del_14q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'YEARS_TO_BIRTH'

P value = 0.0196 (Wilcoxon-test), Q value = 0.076

Table S132.  Gene #48: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 27(18Q23) MUTATED 78 46.7 (14.6)
DEL PEAK 27(18Q23) WILD-TYPE 433 42.3 (13.0)

Figure S132.  Get High-res Image Gene #48: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'Time to Death'

P value = 0.00299 (logrank test), Q value = 0.017

Table S133.  Gene #49: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 28(19Q13.41) MUTATED 264 49 0.0 - 182.3 (21.5)
DEL PEAK 28(19Q13.41) WILD-TYPE 245 72 0.1 - 211.2 (20.5)

Figure S133.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

'del_19q13.41' versus 'YEARS_TO_BIRTH'

P value = 0.0589 (Wilcoxon-test), Q value = 0.18

Table S134.  Gene #49: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 28(19Q13.41) MUTATED 266 43.9 (12.6)
DEL PEAK 28(19Q13.41) WILD-TYPE 245 42.0 (14.1)

Figure S134.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'RADIATION_THERAPY'

P value = 0.000337 (Fisher's exact test), Q value = 0.0028

Table S135.  Gene #49: 'del_19q13.41' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 28(19Q13.41) MUTATED 115 133
DEL PEAK 28(19Q13.41) WILD-TYPE 69 160

Figure S135.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_19q13.41' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S136.  Gene #49: 'del_19q13.41' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 28(19Q13.41) MUTATED 54 60 153
DEL PEAK 28(19Q13.41) WILD-TYPE 140 69 36

Figure S136.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19q13.42' versus 'Time to Death'

P value = 0.000117 (logrank test), Q value = 0.0011

Table S137.  Gene #50: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 29(19Q13.42) MUTATED 275 51 0.0 - 182.3 (22.3)
DEL PEAK 29(19Q13.42) WILD-TYPE 234 70 0.1 - 211.2 (20.0)

Figure S137.  Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'RADIATION_THERAPY'

P value = 0.000467 (Fisher's exact test), Q value = 0.0036

Table S138.  Gene #50: 'del_19q13.42' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 29(19Q13.42) MUTATED 119 141
DEL PEAK 29(19Q13.42) WILD-TYPE 65 152

Figure S138.  Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_19q13.42' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00015

Table S139.  Gene #50: 'del_19q13.42' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 29(19Q13.42) MUTATED 60 64 154
DEL PEAK 29(19Q13.42) WILD-TYPE 134 65 35

Figure S139.  Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q13.31' versus 'Time to Death'

P value = 1e-05 (logrank test), Q value = 0.00015

Table S140.  Gene #51: 'del_22q13.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 30(22Q13.31) MUTATED 77 34 0.1 - 156.2 (20.5)
DEL PEAK 30(22Q13.31) WILD-TYPE 432 87 0.0 - 211.2 (20.9)

Figure S140.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #1: 'Time to Death'

'del_22q13.31' versus 'YEARS_TO_BIRTH'

P value = 0.000444 (Wilcoxon-test), Q value = 0.0035

Table S141.  Gene #51: 'del_22q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 43.0 (13.3)
DEL PEAK 30(22Q13.31) MUTATED 77 48.4 (14.5)
DEL PEAK 30(22Q13.31) WILD-TYPE 434 42.0 (12.9)

Figure S141.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.31' versus 'RADIATION_THERAPY'

P value = 0.00782 (Fisher's exact test), Q value = 0.037

Table S142.  Gene #51: 'del_22q13.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 184 293
DEL PEAK 30(22Q13.31) MUTATED 17 53
DEL PEAK 30(22Q13.31) WILD-TYPE 167 240

Figure S142.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #4: 'RADIATION_THERAPY'

'del_22q13.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0542 (Wilcoxon-test), Q value = 0.17

Table S143.  Gene #51: 'del_22q13.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.6 (12.6)
DEL PEAK 30(22Q13.31) MUTATED 49 83.3 (14.3)
DEL PEAK 30(22Q13.31) WILD-TYPE 257 87.3 (12.1)

Figure S143.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_22q13.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00088 (Fisher's exact test), Q value = 0.0057

Table S144.  Gene #51: 'del_22q13.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 129 189
DEL PEAK 30(22Q13.31) MUTATED 44 15 18
DEL PEAK 30(22Q13.31) WILD-TYPE 150 114 171

Figure S144.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq21.1' versus 'Time to Death'

P value = 0.083 (logrank test), Q value = 0.24

Table S145.  Gene #52: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 121 0.0 - 211.2 (20.8)
DEL PEAK 31(XQ21.1) MUTATED 77 25 0.1 - 156.2 (19.0)
DEL PEAK 31(XQ21.1) WILD-TYPE 432 96 0.0 - 211.2 (21.4)

Figure S145.  Get High-res Image Gene #52: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/19781933/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/19775312/LGG-TP.merged_data.txt

  • Number of patients = 512

  • Number of significantly focal cnvs = 52

  • Number of selected clinical features = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

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

Q value calculation

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

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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