Correlation between copy number variation genes (focal events) and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1R49PS8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R49PS8
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 472 patients, 93 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' and 'YEARS_TO_BIRTH'.

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

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

  • amp_7p11.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

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

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

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

  • amp_9q34.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • amp_12p13.32 cnv correlated to 'YEARS_TO_BIRTH'.

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

  • 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' and 'HISTOLOGICAL_TYPE'.

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

  • amp_xp11.22 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_xp11.22 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_1p36.32 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

  • del_2q37.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

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

  • del_3q29 cnv correlated to 'Time to Death'.

  • del_5p15.33 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • del_5q34 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

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

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

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

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

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

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

  • del_11p15.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'HISTOLOGICAL_TYPE'.

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

  • del_12q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_13q14.2 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_13q14.2 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 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', and 'HISTOLOGICAL_TYPE'.

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

  • del_22q13.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', 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, 93 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
del 9p23 134 (28%) 338 0.000222
(0.0028) 		0.00424
(0.036) 		0.609
(0.86) 		0.0162
(0.109) 		0.0286
(0.155) 		0.0281
(0.155) 		0.95
(1.00) 		0.6
(0.857)
del 9p21 3 161 (34%) 311 6.44e-10
(1.24e-07) 		3.11e-06
(9.96e-05) 		0.282
(0.647) 		0.00441
(0.0365) 		0.00592
(0.0443) 		0.0203
(0.13) 		1
(1.00) 		0.621
(0.86)
amp 7q31 2 164 (35%) 308 0.00109
(0.0116) 		6.09e-07
(2.53e-05) 		0.0511
(0.236) 		0.331
(0.672) 		0.059
(0.259) 		0.331
(0.672) 		0.0555
(0.249) 		1
(1.00)
amp 7q32 3 170 (36%) 302 0.0017
(0.0168) 		1.17e-07
(8.09e-06) 		0.0262
(0.153) 		0.445
(0.749) 		0.0538
(0.246) 		0.276
(0.641) 		0.0771
(0.297) 		0.807
(0.945)
del 1p32 3 181 (38%) 291 0.0214
(0.132) 		1.47e-06
(5.09e-05) 		0.569
(0.842) 		0.55
(0.832) 		1e-05
(0.000208) 		0.00396
(0.0343) 		0.374
(0.704) 		0.806
(0.945)
amp 12q14 1 34 (7%) 438 3.62e-08
(3.31e-06) 		0.00504
(0.0403) 		0.721
(0.91) 		0.274
(0.641) 		0.0337
(0.169) 		0.367
(0.704) 		0.323
(0.668) 		1
(1.00)
del 1p36 32 191 (40%) 281 0.154
(0.442) 		3.25e-07
(1.69e-05) 		0.396
(0.713) 		0.673
(0.874) 		1e-05
(0.000208) 		0.033
(0.167) 		0.302
(0.665) 		0.628
(0.86)
del 5p15 33 46 (10%) 426 0.951
(1.00) 		0.399
(0.715) 		0.536
(0.826) 		0.0326
(0.167) 		0.00291
(0.0269) 		0.0291
(0.155) 		0.545
(0.828) 		0.7
(0.892)
del 6q22 31 69 (15%) 403 1.28e-05
(0.000254) 		0.203
(0.524) 		0.694
(0.891) 		0.0442
(0.211) 		3e-05
(0.000499) 		0.412
(0.726) 		0.185
(0.491) 		0.733
(0.916)
del 6q24 3 72 (15%) 400 0.00021
(0.00273) 		0.646
(0.868) 		0.369
(0.704) 		0.0442
(0.211) 		8e-05
(0.00119) 		0.335
(0.674) 		0.21
(0.539) 		0.331
(0.672)
del 10q26 3 135 (29%) 337 3.75e-12
(1.56e-09) 		2.23e-07
(1.33e-05) 		0.0653
(0.269) 		0.165
(0.454) 		3e-05
(0.000499) 		0.7
(0.892) 		0.175
(0.472) 		1
(1.00)
del 19q13 41 247 (52%) 225 0.0192
(0.126) 		0.0247
(0.147) 		0.578
(0.843) 		0.641
(0.865) 		1e-05
(0.000208) 		0.487
(0.779) 		0.395
(0.713) 		1
(1.00)
del 22q13 31 68 (14%) 404 0.000626
(0.00723) 		0.00252
(0.0239) 		0.511
(0.793) 		0.126
(0.402) 		0.00121
(0.0123) 		0.619
(0.86) 		0.134
(0.416) 		1
(1.00)
amp 1q32 1 39 (8%) 433 0.00121
(0.0123) 		9.21e-07
(3.48e-05) 		0.866
(0.982) 		0.0587
(0.259) 		0.302
(0.665) 		0.297
(0.661) 		0.162
(0.449) 		0.385
(0.712)
amp 3q26 33 19 (4%) 453 1.85e-05
(0.000349) 		0.0801
(0.298) 		0.482
(0.779) 		0.161
(0.449) 		0.00447
(0.0365) 		0.231
(0.564) 		0.0609
(0.26) 		1
(1.00)
amp 4q12 27 (6%) 445 0.014
(0.0955) 		0.232
(0.564) 		0.843
(0.961) 		0.317
(0.668) 		0.00385
(0.0341) 		0.626
(0.86) 		0.772
(0.941) 		1
(1.00)
amp 7p11 2 117 (25%) 355 3.98e-08
(3.31e-06) 		8.98e-10
(1.24e-07) 		0.333
(0.673) 		0.0646
(0.269) 		0.0661
(0.269) 		0.42
(0.731) 		0.0667
(0.269) 		0.786
(0.942)
amp 8q24 13 93 (20%) 379 0.462
(0.771) 		0.0466
(0.218) 		0.296
(0.661) 		0.419
(0.731) 		0.00204
(0.0197) 		1
(1.00) 		0.615
(0.86) 		0.373
(0.704)
amp 10p15 3 66 (14%) 406 0.44
(0.749) 		0.000326
(0.00399) 		0.229
(0.564) 		0.0691
(0.271) 		7e-05
(0.00108) 		0.0945
(0.336) 		0.815
(0.947) 		0.0804
(0.298)
amp 17q25 1 39 (8%) 433 0.00926
(0.0653) 		0.0302
(0.157) 		0.614
(0.86) 		0.361
(0.704) 		0.211
(0.539) 		0.673
(0.874) 		0.202
(0.524) 		0.647
(0.868)
amp 19p13 3 120 (25%) 352 0.627
(0.86) 		0.0446
(0.211) 		0.831
(0.957) 		0.631
(0.86) 		1e-05
(0.000208) 		0.594
(0.853) 		0.803
(0.945) 		0.789
(0.943)
amp 19p13 2 113 (24%) 359 0.806
(0.945) 		0.0115
(0.0796) 		0.277
(0.641) 		0.315
(0.668) 		1e-05
(0.000208) 		0.892
(0.991) 		0.707
(0.897) 		0.78
(0.942)
del 3p21 31 44 (9%) 428 0.323
(0.668) 		0.493
(0.779) 		0.874
(0.982) 		0.00609
(0.0445) 		0.48
(0.779) 		0.322
(0.668) 		0.443
(0.749) 		0.0194
(0.126)
del 6p25 3 44 (9%) 428 4.75e-07
(2.2e-05) 		0.345
(0.681) 		0.874
(0.982) 		0.0275
(0.155) 		0.369
(0.704) 		0.843
(0.961) 		0.0785
(0.298) 		0.233
(0.564)
del 11p15 5 94 (20%) 378 0.331
(0.672) 		0.0273
(0.155) 		0.081
(0.298) 		0.0996
(0.343) 		1e-05
(0.000208) 		0.467
(0.774) 		0.559
(0.833) 		0.77
(0.941)
del 11p15 1 66 (14%) 406 0.0684
(0.271) 		0.23
(0.564) 		0.0613
(0.26) 		0.0356
(0.177) 		0.00083
(0.00909) 		0.315
(0.668) 		0.67
(0.874) 		0.739
(0.918)
del 12p13 1 35 (7%) 437 0.00339
(0.0307) 		0.366
(0.704) 		1
(1.00) 		0.492
(0.779) 		0.0421
(0.206) 		0.374
(0.704) 		0.808
(0.945) 		0.384
(0.712)
del 14q24 3 108 (23%) 364 0.00016
(0.00215) 		0.0556
(0.249) 		0.151
(0.44) 		0.441
(0.749) 		0.191
(0.499) 		0.783
(0.942) 		0.189
(0.497) 		1
(1.00)
del 19q13 42 255 (54%) 217 0.000722
(0.00812) 		0.133
(0.416) 		0.78
(0.942) 		0.666
(0.874) 		1e-05
(0.000208) 		0.727
(0.914) 		0.389
(0.713) 		0.811
(0.945)
amp 1q22 39 (8%) 433 0.111
(0.37) 		0.00054
(0.00641) 		1
(1.00) 		0.505
(0.789) 		0.345
(0.681) 		0.297
(0.661) 		0.257
(0.612) 		0.385
(0.712)
amp 9q34 3 43 (9%) 429 0.999
(1.00) 		0.833
(0.957) 		0.107
(0.364) 		0.108
(0.364) 		0.0274
(0.155) 		0.545
(0.828) 		0.128
(0.408) 		0.222
(0.556)
amp 12p13 32 64 (14%) 408 0.633
(0.86) 		0.0239
(0.144) 		0.222
(0.556) 		0.81
(0.945) 		0.122
(0.395) 		0.0879
(0.318) 		1
(1.00) 		0.489
(0.779)
amp 15q26 3 15 (3%) 457 4.89e-05
(0.000783) 		0.558
(0.833) 		0.799
(0.945) 		0.14
(0.423) 		0.0866
(0.316) 		0.506
(0.789) 		1
(1.00) 		0.45
(0.755)
amp xp11 22 41 (9%) 431 0.473
(0.779) 		0.445
(0.749) 		1
(1.00) 		0.668
(0.874) 		0.0084
(0.0602) 		0.218
(0.554) 		0.291
(0.659) 		1
(1.00)
amp xp11 22 57 (12%) 415 0.913
(0.995) 		0.914
(0.995) 		0.156
(0.445) 		0.991
(1.00) 		0.00011
(0.00158) 		0.48
(0.779) 		0.897
(0.991) 		1
(1.00)
del 2q37 3 69 (15%) 403 0.542
(0.828) 		0.098
(0.342) 		0.434
(0.745) 		0.701
(0.892) 		0.0216
(0.132) 		0.412
(0.726) 		0.686
(0.884) 		0.176
(0.472)
del 3q13 31 35 (7%) 437 0.00534
(0.0419) 		0.62
(0.86) 		0.29
(0.659) 		0.487
(0.779) 		0.566
(0.841) 		0.374
(0.704) 		0.671
(0.874) 		0.633
(0.86)
del 3q29 40 (8%) 432 0.021
(0.132) 		0.73
(0.915) 		0.739
(0.918) 		0.404
(0.72) 		0.132
(0.416) 		0.676
(0.874) 		0.396
(0.713) 		0.652
(0.873)
del 5q34 60 (13%) 412 0.0989
(0.343) 		0.608
(0.86) 		0.889
(0.991) 		0.31
(0.668) 		2e-05
(0.000362) 		0.161
(0.449) 		0.343
(0.681) 		0.49
(0.779)
del 12q12 66 (14%) 406 0.638
(0.865) 		0.395
(0.713) 		0.423
(0.734) 		0.602
(0.857) 		0.00016
(0.00215) 		0.868
(0.982) 		0.31
(0.668) 		0.154
(0.442)
del 13q14 2 129 (27%) 343 0.075
(0.292) 		0.904
(0.991) 		0.145
(0.434) 		0.00576
(0.0443) 		0.14
(0.423) 		0.0897
(0.322) 		0.343
(0.681) 		1
(1.00)
del 13q14 2 131 (28%) 341 0.0973
(0.342) 		0.895
(0.991) 		0.148
(0.438) 		0.00597
(0.0443) 		0.109
(0.364) 		0.119
(0.389) 		0.347
(0.681) 		1
(1.00)
del 18q23 74 (16%) 398 0.558
(0.833) 		0.0291
(0.155) 		0.308
(0.668) 		0.902
(0.991) 		0.496
(0.782) 		0.873
(0.982) 		0.136
(0.419) 		0.168
(0.457)
del xq21 1 66 (14%) 406 0.0302
(0.157) 		0.0599
(0.259) 		0.594
(0.853) 		0.902
(0.991) 		0.503
(0.789) 		1
(1.00) 		0.378
(0.707) 		1
(1.00)
amp 2p24 3 22 (5%) 450 0.068
(0.271) 		0.784
(0.942) 		0.661
(0.874) 		0.479
(0.779) 		0.123
(0.395) 		0.592
(0.853) 		1
(1.00) 		0.181
(0.483)
amp 11q24 1 82 (17%) 390 0.906
(0.991) 		0.248
(0.597) 		0.463
(0.771) 		0.887
(0.991) 		0.52
(0.804) 		0.878
(0.985) 		0.577
(0.843) 		0.75
(0.926)
amp 13q34 21 (4%) 451 0.272
(0.641) 		0.742
(0.919) 		0.658
(0.874) 		0.117
(0.386) 		0.586
(0.853) 		0.578
(0.843) 		0.664
(0.874) 		0.577
(0.843)
del 1q43 27 (6%) 445 0.676
(0.874) 		0.276
(0.641) 		0.427
(0.736) 		0.801
(0.945) 		0.283
(0.647) 		1
(1.00) 		0.223
(0.556) 		0.307
(0.668)
del 4q34 3 125 (26%) 347 0.826
(0.957) 		0.151
(0.44) 		0.754
(0.928) 		0.476
(0.779) 		0.831
(0.957) 		0.148
(0.438) 		0.589
(0.853) 		1
(1.00)
del 7p22 3 19 (4%) 453 0.167
(0.457) 		0.923
(0.999) 		1
(1.00) 		0.76
(0.932) 		0.916
(0.995) 		0.773
(0.941) 		0.405
(0.72) 		1
(1.00)
del 8q24 3 26 (6%) 446 0.842
(0.961) 		0.62
(0.86) 		0.545
(0.828) 		0.955
(1.00) 		0.158
(0.446) 		0.314
(0.668) 		0.413
(0.726) 		0.0619
(0.26)
del 13q34 99 (21%) 373 0.0792
(0.298) 		0.72
(0.91) 		0.255
(0.611) 		0.138
(0.423) 		0.989
(1.00) 		0.318
(0.668) 		0.394
(0.713) 		0.557
(0.833)
'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.00054 (Wilcoxon-test), Q value = 0.0064

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

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 1(1Q22) MUTATED 39 50.2 (13.2)
AMP PEAK 1(1Q22) WILD-TYPE 432 42.4 (13.3)

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 = 0.00121 (logrank test), Q value = 0.012

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

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 2(1Q32.1) MUTATED 39 17 0.2 - 211.2 (18.4)
AMP PEAK 2(1Q32.1) WILD-TYPE 431 77 0.0 - 182.3 (18.7)

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 = 9.21e-07 (Wilcoxon-test), Q value = 3.5e-05

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

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 2(1Q32.1) MUTATED 39 53.5 (12.3)
AMP PEAK 2(1Q32.1) WILD-TYPE 432 42.1 (13.1)

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

'amp_3q26.33' versus 'Time to Death'

P value = 1.85e-05 (logrank test), Q value = 0.00035

Table S4.  Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 4(3Q26.33) MUTATED 18 8 0.2 - 47.8 (17.6)
AMP PEAK 4(3Q26.33) WILD-TYPE 452 86 0.0 - 211.2 (18.7)

Figure S4.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00447 (Fisher's exact test), Q value = 0.036

Table S5.  Gene #4: 'amp_3q26.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 4(3Q26.33) MUTATED 14 1 4
AMP PEAK 4(3Q26.33) WILD-TYPE 162 117 174

Figure S5.  Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_4q12' versus 'Time to Death'

P value = 0.014 (logrank test), Q value = 0.095

Table S6.  Gene #5: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 5(4Q12) MUTATED 27 8 2.8 - 60.3 (15.1)
AMP PEAK 5(4Q12) WILD-TYPE 443 86 0.0 - 211.2 (18.7)

Figure S6.  Get High-res Image Gene #5: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00385 (Fisher's exact test), Q value = 0.034

Table S7.  Gene #5: 'amp_4q12' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 5(4Q12) MUTATED 18 2 7
AMP PEAK 5(4Q12) WILD-TYPE 158 116 171

Figure S7.  Get High-res Image Gene #5: 'amp_4q12' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

P value = 3.98e-08 (logrank test), Q value = 3.3e-06

Table S8.  Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 6(7P11.2) MUTATED 117 42 0.1 - 211.2 (16.5)
AMP PEAK 6(7P11.2) WILD-TYPE 353 52 0.0 - 182.3 (19.6)

Figure S8.  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 = 8.98e-10 (Wilcoxon-test), Q value = 1.2e-07

Table S9.  Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 6(7P11.2) MUTATED 117 49.8 (13.4)
AMP PEAK 6(7P11.2) WILD-TYPE 354 40.8 (12.7)

Figure S9.  Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'Time to Death'

P value = 0.00109 (logrank test), Q value = 0.012

Table S10.  Gene #7: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 7(7Q31.2) MUTATED 164 47 0.1 - 211.2 (17.3)
AMP PEAK 7(7Q31.2) WILD-TYPE 306 47 0.0 - 182.3 (19.9)

Figure S10.  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 = 6.09e-07 (Wilcoxon-test), Q value = 2.5e-05

Table S11.  Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 7(7Q31.2) MUTATED 164 47.3 (13.3)
AMP PEAK 7(7Q31.2) WILD-TYPE 307 40.8 (12.9)

Figure S11.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'GENDER'

P value = 0.0511 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #7: 'amp_7q31.2' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 206 266
AMP PEAK 7(7Q31.2) MUTATED 82 82
AMP PEAK 7(7Q31.2) WILD-TYPE 124 184

Figure S12.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #3: 'GENDER'

'amp_7q31.2' versus 'RACE'

P value = 0.0555 (Fisher's exact test), Q value = 0.25

Table S13.  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 15 437
AMP PEAK 7(7Q31.2) MUTATED 1 4 9 149
AMP PEAK 7(7Q31.2) WILD-TYPE 0 4 6 288

Figure S13.  Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #7: 'RACE'

'amp_7q32.3' versus 'Time to Death'

P value = 0.0017 (logrank test), Q value = 0.017

Table S14.  Gene #8: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 8(7Q32.3) MUTATED 170 48 0.1 - 211.2 (17.1)
AMP PEAK 8(7Q32.3) WILD-TYPE 300 46 0.0 - 182.3 (20.0)

Figure S14.  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 = 1.17e-07 (Wilcoxon-test), Q value = 8.1e-06

Table S15.  Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 8(7Q32.3) MUTATED 170 47.4 (13.2)
AMP PEAK 8(7Q32.3) WILD-TYPE 301 40.6 (13.0)

Figure S15.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q32.3' versus 'GENDER'

P value = 0.0262 (Fisher's exact test), Q value = 0.15

Table S16.  Gene #8: 'amp_7q32.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 206 266
AMP PEAK 8(7Q32.3) MUTATED 86 84
AMP PEAK 8(7Q32.3) WILD-TYPE 120 182

Figure S16.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #3: 'GENDER'

'amp_7q32.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0538 (Fisher's exact test), Q value = 0.25

Table S17.  Gene #8: 'amp_7q32.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 8(7Q32.3) MUTATED 71 47 52
AMP PEAK 8(7Q32.3) WILD-TYPE 105 71 126

Figure S17.  Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_8q24.13' versus 'YEARS_TO_BIRTH'

P value = 0.0466 (Wilcoxon-test), Q value = 0.22

Table S18.  Gene #9: 'amp_8q24.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 9(8Q24.13) MUTATED 93 40.8 (13.3)
AMP PEAK 9(8Q24.13) WILD-TYPE 378 43.6 (13.4)

Figure S18.  Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00204 (Fisher's exact test), Q value = 0.02

Table S19.  Gene #9: 'amp_8q24.13' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 9(8Q24.13) MUTATED 45 27 21
AMP PEAK 9(8Q24.13) WILD-TYPE 131 91 157

Figure S19.  Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0274 (Fisher's exact test), Q value = 0.15

Table S20.  Gene #10: 'amp_9q34.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 10(9Q34.3) MUTATED 23 11 9
AMP PEAK 10(9Q34.3) WILD-TYPE 153 107 169

Figure S20.  Get High-res Image Gene #10: 'amp_9q34.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 0.000326 (Wilcoxon-test), Q value = 0.004

Table S21.  Gene #11: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 11(10P15.3) MUTATED 66 37.0 (10.4)
AMP PEAK 11(10P15.3) WILD-TYPE 405 44.0 (13.6)

Figure S21.  Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p15.3' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0011

Table S22.  Gene #11: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 11(10P15.3) MUTATED 34 23 9
AMP PEAK 11(10P15.3) WILD-TYPE 142 95 169

Figure S22.  Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_12p13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0239 (Wilcoxon-test), Q value = 0.14

Table S23.  Gene #13: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 13(12P13.32) MUTATED 64 40.0 (12.7)
AMP PEAK 13(12P13.32) WILD-TYPE 407 43.5 (13.5)

Figure S23.  Get High-res Image Gene #13: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'Time to Death'

P value = 3.62e-08 (logrank test), Q value = 3.3e-06

Table S24.  Gene #14: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 14(12Q14.1) MUTATED 34 16 0.2 - 80.0 (14.8)
AMP PEAK 14(12Q14.1) WILD-TYPE 436 78 0.0 - 211.2 (18.8)

Figure S24.  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 = 0.00504 (Wilcoxon-test), Q value = 0.04

Table S25.  Gene #14: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 14(12Q14.1) MUTATED 34 49.9 (14.8)
AMP PEAK 14(12Q14.1) WILD-TYPE 437 42.5 (13.2)

Figure S25.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0337 (Fisher's exact test), Q value = 0.17

Table S26.  Gene #14: 'amp_12q14.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 14(12Q14.1) MUTATED 20 5 9
AMP PEAK 14(12Q14.1) WILD-TYPE 156 113 169

Figure S26.  Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_15q26.3' versus 'Time to Death'

P value = 4.89e-05 (logrank test), Q value = 0.00078

Table S27.  Gene #16: 'amp_15q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 16(15Q26.3) MUTATED 15 8 2.5 - 50.9 (21.7)
AMP PEAK 16(15Q26.3) WILD-TYPE 455 86 0.0 - 211.2 (18.6)

Figure S27.  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 = 0.00926 (logrank test), Q value = 0.065

Table S28.  Gene #17: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
AMP PEAK 17(17Q25.1) MUTATED 39 13 0.2 - 80.1 (20.0)
AMP PEAK 17(17Q25.1) WILD-TYPE 431 81 0.0 - 211.2 (18.6)

Figure S28.  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 = 0.0302 (Wilcoxon-test), Q value = 0.16

Table S29.  Gene #17: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 17(17Q25.1) MUTATED 39 47.1 (12.6)
AMP PEAK 17(17Q25.1) WILD-TYPE 432 42.7 (13.5)

Figure S29.  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 = 0.0446 (Wilcoxon-test), Q value = 0.21

Table S30.  Gene #18: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 18(19P13.3) MUTATED 119 45.1 (13.8)
AMP PEAK 18(19P13.3) WILD-TYPE 352 42.4 (13.3)

Figure S30.  Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S31.  Gene #18: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 18(19P13.3) MUTATED 24 27 69
AMP PEAK 18(19P13.3) WILD-TYPE 152 91 109

Figure S31.  Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_19p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0115 (Wilcoxon-test), Q value = 0.08

Table S32.  Gene #19: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
AMP PEAK 19(19P13.2) MUTATED 112 45.9 (13.7)
AMP PEAK 19(19P13.2) WILD-TYPE 359 42.2 (13.3)

Figure S32.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S33.  Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 19(19P13.2) MUTATED 22 23 68
AMP PEAK 19(19P13.2) WILD-TYPE 154 95 110

Figure S33.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_xp11.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.0084 (Fisher's exact test), Q value = 0.06

Table S34.  Gene #20: 'amp_xp11.22' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 20(XP11.22) MUTATED 24 9 8
AMP PEAK 20(XP11.22) WILD-TYPE 152 109 170

Figure S34.  Get High-res Image Gene #20: 'amp_xp11.22' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_xp11.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0016

Table S35.  Gene #21: 'amp_xp11.22' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
AMP PEAK 21(XP11.22) MUTATED 35 13 9
AMP PEAK 21(XP11.22) WILD-TYPE 141 105 169

Figure S35.  Get High-res Image Gene #21: 'amp_xp11.22' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_1p36.32' versus 'YEARS_TO_BIRTH'

P value = 3.25e-07 (Wilcoxon-test), Q value = 1.7e-05

Table S36.  Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 1(1P36.32) MUTATED 190 46.6 (12.7)
DEL PEAK 1(1P36.32) WILD-TYPE 281 40.6 (13.4)

Figure S36.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S37.  Gene #22: 'del_1p36.32' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 1(1P36.32) MUTATED 19 41 131
DEL PEAK 1(1P36.32) WILD-TYPE 157 77 47

Figure S37.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_1p36.32' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.033 (Fisher's exact test), Q value = 0.17

Table S38.  Gene #22: 'del_1p36.32' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
DEL PEAK 1(1P36.32) MUTATED 28 163
DEL PEAK 1(1P36.32) WILD-TYPE 64 217

Figure S38.  Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_1p32.3' versus 'Time to Death'

P value = 0.0214 (logrank test), Q value = 0.13

Table S39.  Gene #23: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 2(1P32.3) MUTATED 180 27 0.1 - 182.3 (18.7)
DEL PEAK 2(1P32.3) WILD-TYPE 290 67 0.0 - 211.2 (18.7)

Figure S39.  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 = 1.47e-06 (Wilcoxon-test), Q value = 5.1e-05

Table S40.  Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 2(1P32.3) MUTATED 180 46.7 (13.1)
DEL PEAK 2(1P32.3) WILD-TYPE 291 40.8 (13.2)

Figure S40.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p32.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S41.  Gene #23: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 2(1P32.3) MUTATED 13 37 131
DEL PEAK 2(1P32.3) WILD-TYPE 163 81 47

Figure S41.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_1p32.3' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00396 (Fisher's exact test), Q value = 0.034

Table S42.  Gene #23: 'del_1p32.3' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
DEL PEAK 2(1P32.3) MUTATED 23 158
DEL PEAK 2(1P32.3) WILD-TYPE 69 222

Figure S42.  Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0216 (Fisher's exact test), Q value = 0.13

Table S43.  Gene #25: 'del_2q37.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 4(2Q37.3) MUTATED 32 21 16
DEL PEAK 4(2Q37.3) WILD-TYPE 144 97 162

Figure S43.  Get High-res Image Gene #25: 'del_2q37.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00609 (Wilcoxon-test), Q value = 0.044

Table S44.  Gene #26: 'del_3p21.31' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 5(3P21.31) MUTATED 28 81.1 (15.5)
DEL PEAK 5(3P21.31) WILD-TYPE 241 88.5 (11.3)

Figure S44.  Get High-res Image Gene #26: 'del_3p21.31' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.31' versus 'ETHNICITY'

P value = 0.0194 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #26: 'del_3p21.31' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 18 419
DEL PEAK 5(3P21.31) MUTATED 5 36
DEL PEAK 5(3P21.31) WILD-TYPE 13 383

Figure S45.  Get High-res Image Gene #26: 'del_3p21.31' versus Clinical Feature #8: 'ETHNICITY'

'del_3q13.31' versus 'Time to Death'

P value = 0.00534 (logrank test), Q value = 0.042

Table S46.  Gene #27: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 6(3Q13.31) MUTATED 35 13 0.2 - 117.4 (19.0)
DEL PEAK 6(3Q13.31) WILD-TYPE 435 81 0.0 - 211.2 (18.6)

Figure S46.  Get High-res Image Gene #27: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

'del_3q29' versus 'Time to Death'

P value = 0.021 (logrank test), Q value = 0.13

Table S47.  Gene #28: 'del_3q29' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 7(3Q29) MUTATED 40 15 0.0 - 122.5 (23.0)
DEL PEAK 7(3Q29) WILD-TYPE 430 79 0.1 - 211.2 (18.3)

Figure S47.  Get High-res Image Gene #28: 'del_3q29' versus Clinical Feature #1: 'Time to Death'

'del_5p15.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0326 (Wilcoxon-test), Q value = 0.17

Table S48.  Gene #30: 'del_5p15.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 9(5P15.33) MUTATED 27 83.3 (13.0)
DEL PEAK 9(5P15.33) WILD-TYPE 242 88.2 (11.8)

Figure S48.  Get High-res Image Gene #30: 'del_5p15.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00291 (Fisher's exact test), Q value = 0.027

Table S49.  Gene #30: 'del_5p15.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 9(5P15.33) MUTATED 19 19 8
DEL PEAK 9(5P15.33) WILD-TYPE 157 99 170

Figure S49.  Get High-res Image Gene #30: 'del_5p15.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_5p15.33' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0291 (Fisher's exact test), Q value = 0.16

Table S50.  Gene #30: 'del_5p15.33' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
DEL PEAK 9(5P15.33) MUTATED 15 31
DEL PEAK 9(5P15.33) WILD-TYPE 77 349

Figure S50.  Get High-res Image Gene #30: 'del_5p15.33' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_5q34' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00036

Table S51.  Gene #31: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 10(5Q34) MUTATED 39 12 9
DEL PEAK 10(5Q34) WILD-TYPE 137 106 169

Figure S51.  Get High-res Image Gene #31: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 4.75e-07 (logrank test), Q value = 2.2e-05

Table S52.  Gene #32: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 11(6P25.3) MUTATED 43 17 0.2 - 94.5 (18.8)
DEL PEAK 11(6P25.3) WILD-TYPE 427 77 0.0 - 211.2 (18.6)

Figure S52.  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 = 0.0275 (Wilcoxon-test), Q value = 0.15

Table S53.  Gene #32: 'del_6p25.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 11(6P25.3) MUTATED 28 83.2 (12.8)
DEL PEAK 11(6P25.3) WILD-TYPE 241 88.3 (11.8)

Figure S53.  Get High-res Image Gene #32: 'del_6p25.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'Time to Death'

P value = 1.28e-05 (logrank test), Q value = 0.00025

Table S54.  Gene #33: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 12(6Q22.31) MUTATED 68 23 0.1 - 117.4 (17.9)
DEL PEAK 12(6Q22.31) WILD-TYPE 402 71 0.0 - 211.2 (18.8)

Figure S54.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0442 (Wilcoxon-test), Q value = 0.21

Table S55.  Gene #33: 'del_6q22.31' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 12(6Q22.31) MUTATED 44 84.3 (13.2)
DEL PEAK 12(6Q22.31) WILD-TYPE 225 88.4 (11.7)

Figure S55.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 5e-04

Table S56.  Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 12(6Q22.31) MUTATED 44 11 14
DEL PEAK 12(6Q22.31) WILD-TYPE 132 107 164

Figure S56.  Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_6q24.3' versus 'Time to Death'

P value = 0.00021 (logrank test), Q value = 0.0027

Table S57.  Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 13(6Q24.3) MUTATED 71 23 0.0 - 130.8 (17.9)
DEL PEAK 13(6Q24.3) WILD-TYPE 399 71 0.1 - 211.2 (18.8)

Figure S57.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

'del_6q24.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0442 (Wilcoxon-test), Q value = 0.21

Table S58.  Gene #34: 'del_6q24.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 13(6Q24.3) MUTATED 44 84.3 (13.2)
DEL PEAK 13(6Q24.3) WILD-TYPE 225 88.4 (11.7)

Figure S58.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0012

Table S59.  Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 13(6Q24.3) MUTATED 44 12 16
DEL PEAK 13(6Q24.3) WILD-TYPE 132 106 162

Figure S59.  Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.000222 (logrank test), Q value = 0.0028

Table S60.  Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 16(9P23) MUTATED 133 38 0.1 - 169.8 (18.4)
DEL PEAK 16(9P23) WILD-TYPE 337 56 0.0 - 211.2 (18.7)

Figure S60.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.00424 (Wilcoxon-test), Q value = 0.036

Table S61.  Gene #37: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 16(9P23) MUTATED 133 45.8 (13.4)
DEL PEAK 16(9P23) WILD-TYPE 338 42.0 (13.3)

Figure S61.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0162 (Wilcoxon-test), Q value = 0.11

Table S62.  Gene #37: 'del_9p23' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 16(9P23) MUTATED 83 85.2 (12.9)
DEL PEAK 16(9P23) WILD-TYPE 186 88.9 (11.4)

Figure S62.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 0.0286 (Fisher's exact test), Q value = 0.16

Table S63.  Gene #37: 'del_9p23' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 16(9P23) MUTATED 62 32 40
DEL PEAK 16(9P23) WILD-TYPE 114 86 138

Figure S63.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0281 (Fisher's exact test), Q value = 0.16

Table S64.  Gene #37: 'del_9p23' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
DEL PEAK 16(9P23) MUTATED 35 99
DEL PEAK 16(9P23) WILD-TYPE 57 281

Figure S64.  Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_9p21.3' versus 'Time to Death'

P value = 6.44e-10 (logrank test), Q value = 1.2e-07

Table S65.  Gene #38: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 17(9P21.3) MUTATED 160 52 0.1 - 169.8 (17.9)
DEL PEAK 17(9P21.3) WILD-TYPE 310 42 0.0 - 211.2 (19.0)

Figure S65.  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 = 3.11e-06 (Wilcoxon-test), Q value = 1e-04

Table S66.  Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 17(9P21.3) MUTATED 160 47.2 (14.0)
DEL PEAK 17(9P21.3) WILD-TYPE 311 40.9 (12.6)

Figure S66.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00441 (Wilcoxon-test), Q value = 0.036

Table S67.  Gene #38: 'del_9p21.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 17(9P21.3) MUTATED 93 84.6 (13.6)
DEL PEAK 17(9P21.3) WILD-TYPE 176 89.4 (10.7)

Figure S67.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00592 (Fisher's exact test), Q value = 0.044

Table S68.  Gene #38: 'del_9p21.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 17(9P21.3) MUTATED 76 35 50
DEL PEAK 17(9P21.3) WILD-TYPE 100 83 128

Figure S68.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0203 (Fisher's exact test), Q value = 0.13

Table S69.  Gene #38: 'del_9p21.3' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 92 380
DEL PEAK 17(9P21.3) MUTATED 41 120
DEL PEAK 17(9P21.3) WILD-TYPE 51 260

Figure S69.  Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #6: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_10q26.3' versus 'Time to Death'

P value = 3.75e-12 (logrank test), Q value = 1.6e-09

Table S70.  Gene #39: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 18(10Q26.3) MUTATED 134 53 0.1 - 172.8 (16.4)
DEL PEAK 18(10Q26.3) WILD-TYPE 336 41 0.0 - 211.2 (20.2)

Figure S70.  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 = 2.23e-07 (Wilcoxon-test), Q value = 1.3e-05

Table S71.  Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 18(10Q26.3) MUTATED 135 48.3 (13.9)
DEL PEAK 18(10Q26.3) WILD-TYPE 336 40.9 (12.7)

Figure S71.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 5e-04

Table S72.  Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 18(10Q26.3) MUTATED 72 29 34
DEL PEAK 18(10Q26.3) WILD-TYPE 104 89 144

Figure S72.  Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.0273 (Wilcoxon-test), Q value = 0.15

Table S73.  Gene #40: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 19(11P15.5) MUTATED 94 40.4 (11.6)
DEL PEAK 19(11P15.5) WILD-TYPE 377 43.7 (13.8)

Figure S73.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S74.  Gene #40: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 19(11P15.5) MUTATED 50 27 17
DEL PEAK 19(11P15.5) WILD-TYPE 126 91 161

Figure S74.  Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_11p15.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0356 (Wilcoxon-test), Q value = 0.18

Table S75.  Gene #41: 'del_11p15.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 20(11P15.1) MUTATED 45 85.6 (10.6)
DEL PEAK 20(11P15.1) WILD-TYPE 224 88.2 (12.2)

Figure S75.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00083 (Fisher's exact test), Q value = 0.0091

Table S76.  Gene #41: 'del_11p15.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 20(11P15.1) MUTATED 38 14 14
DEL PEAK 20(11P15.1) WILD-TYPE 138 104 164

Figure S76.  Get High-res Image Gene #41: 'del_11p15.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'Time to Death'

P value = 0.00339 (logrank test), Q value = 0.031

Table S77.  Gene #42: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 21(12P13.1) MUTATED 34 12 0.1 - 78.0 (20.5)
DEL PEAK 21(12P13.1) WILD-TYPE 436 82 0.0 - 211.2 (18.6)

Figure S77.  Get High-res Image Gene #42: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0421 (Fisher's exact test), Q value = 0.21

Table S78.  Gene #42: 'del_12p13.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 21(12P13.1) MUTATED 19 9 7
DEL PEAK 21(12P13.1) WILD-TYPE 157 109 171

Figure S78.  Get High-res Image Gene #42: 'del_12p13.1' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_12q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0021

Table S79.  Gene #43: 'del_12q12' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 22(12Q12) MUTATED 39 15 12
DEL PEAK 22(12Q12) WILD-TYPE 137 103 166

Figure S79.  Get High-res Image Gene #43: 'del_12q12' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00576 (Wilcoxon-test), Q value = 0.044

Table S80.  Gene #44: 'del_13q14.2' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 23(13Q14.2) MUTATED 80 84.9 (12.6)
DEL PEAK 23(13Q14.2) WILD-TYPE 189 88.9 (11.5)

Figure S80.  Get High-res Image Gene #44: 'del_13q14.2' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00597 (Wilcoxon-test), Q value = 0.044

Table S81.  Gene #45: 'del_13q14.2' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 269 87.7 (12.0)
DEL PEAK 24(13Q14.2) MUTATED 81 84.9 (12.6)
DEL PEAK 24(13Q14.2) WILD-TYPE 188 88.9 (11.6)

Figure S81.  Get High-res Image Gene #45: 'del_13q14.2' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q24.3' versus 'Time to Death'

P value = 0.00016 (logrank test), Q value = 0.0021

Table S82.  Gene #47: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 26(14Q24.3) MUTATED 107 35 0.1 - 130.8 (19.9)
DEL PEAK 26(14Q24.3) WILD-TYPE 363 59 0.0 - 211.2 (18.4)

Figure S82.  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 = 0.0556 (Wilcoxon-test), Q value = 0.25

Table S83.  Gene #47: 'del_14q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 26(14Q24.3) MUTATED 108 45.2 (13.1)
DEL PEAK 26(14Q24.3) WILD-TYPE 363 42.4 (13.5)

Figure S83.  Get High-res Image Gene #47: 'del_14q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'YEARS_TO_BIRTH'

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

Table S84.  Gene #48: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 27(18Q23) MUTATED 74 46.6 (14.3)
DEL PEAK 27(18Q23) WILD-TYPE 397 42.4 (13.2)

Figure S84.  Get High-res Image Gene #48: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'Time to Death'

P value = 0.0192 (logrank test), Q value = 0.13

Table S85.  Gene #49: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 28(19Q13.41) MUTATED 245 41 0.0 - 182.3 (19.9)
DEL PEAK 28(19Q13.41) WILD-TYPE 225 53 0.1 - 211.2 (18.0)

Figure S85.  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 = 0.0247 (Wilcoxon-test), Q value = 0.15

Table S86.  Gene #49: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 28(19Q13.41) MUTATED 246 44.2 (12.6)
DEL PEAK 28(19Q13.41) WILD-TYPE 225 41.8 (14.2)

Figure S86.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S87.  Gene #49: 'del_19q13.41' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 28(19Q13.41) MUTATED 50 53 144
DEL PEAK 28(19Q13.41) WILD-TYPE 126 65 34

Figure S87.  Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_19q13.42' versus 'Time to Death'

P value = 0.000722 (logrank test), Q value = 0.0081

Table S88.  Gene #50: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 29(19Q13.42) MUTATED 253 40 0.0 - 182.3 (20.1)
DEL PEAK 29(19Q13.42) WILD-TYPE 217 54 0.1 - 211.2 (17.6)

Figure S88.  Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00021

Table S89.  Gene #50: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 29(19Q13.42) MUTATED 53 57 145
DEL PEAK 29(19Q13.42) WILD-TYPE 123 61 33

Figure S89.  Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_22q13.31' versus 'Time to Death'

P value = 0.000626 (logrank test), Q value = 0.0072

Table S90.  Gene #51: 'del_22q13.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 30(22Q13.31) MUTATED 68 26 0.1 - 156.2 (19.0)
DEL PEAK 30(22Q13.31) WILD-TYPE 402 68 0.0 - 211.2 (18.6)

Figure S90.  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 = 0.00252 (Wilcoxon-test), Q value = 0.024

Table S91.  Gene #51: 'del_22q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 471 43.1 (13.4)
DEL PEAK 30(22Q13.31) MUTATED 68 48.2 (14.9)
DEL PEAK 30(22Q13.31) WILD-TYPE 403 42.2 (13.0)

Figure S91.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00121 (Fisher's exact test), Q value = 0.012

Table S92.  Gene #51: 'del_22q13.31' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 176 118 178
DEL PEAK 30(22Q13.31) MUTATED 39 13 16
DEL PEAK 30(22Q13.31) WILD-TYPE 137 105 162

Figure S92.  Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_xq21.1' versus 'Time to Death'

P value = 0.0302 (logrank test), Q value = 0.16

Table S93.  Gene #52: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 470 94 0.0 - 211.2 (18.7)
DEL PEAK 31(XQ21.1) MUTATED 65 20 0.1 - 156.2 (16.7)
DEL PEAK 31(XQ21.1) WILD-TYPE 405 74 0.0 - 211.2 (18.8)

Figure S93.  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/15087635/transformed.cor.cli.txt

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

  • Number of patients = 472

  • Number of significantly 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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