Correlation between copy number variations of arm-level result and selected clinical features
Glioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1X929G9
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1X929G9
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 9 clinical features across 1083 patients, 359 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 1q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 2p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 2q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

  • 3q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 4p gain cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • 4q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • 5q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • 6p gain cnv correlated to 'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 6q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

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

  • 8q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 9p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 9q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 10p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 10q gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 11p gain cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 11q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 12p gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'RADIATION_THERAPY'.

  • 12q gain cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 13q gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 14q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

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

  • 16p gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 16q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • 17q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 18p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 18q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 19p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 19q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 20p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

  • 21q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

  • xq gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

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

  • 1q loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 2p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 2q loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'RADIATION_THERAPY' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 3q loss cnv correlated to 'RADIATION_THERAPY'.

  • 4p loss cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 4q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • 5q loss cnv correlated to 'RADIATION_THERAPY'.

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

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

  • 7q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 8p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 8q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 9p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

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

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

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

  • 11q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 12p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • 12q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 13q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 14q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • 15q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

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

  • 16q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • 17q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • 18p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

  • 20p loss cnv correlated to 'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY', and 'RACE'.

  • 20q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 21q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • xp loss cnv correlated to 'ETHNICITY'.

  • xq loss cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 359 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		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 Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
10p loss 557 (51%) 526 0
(0) 		4.56e-74
(2.59e-72) 		5.18e-116
(3.82e-114) 		0.0843
(0.188) 		1.95e-15
(4.64e-14) 		6.54e-19
(1.86e-17) 		1e-05
(7.31e-05) 		0.00286
(0.0109) 		0.003
(0.0113)
7p gain 590 (54%) 493 0
(0) 		1.9e-54
(8.76e-53) 		2.4e-83
(1.47e-81) 		0.621
(0.756) 		1.19e-11
(2.14e-10) 		5.29e-13
(1.12e-11) 		1e-05
(7.31e-05) 		0.00205
(0.00818) 		0.0299
(0.0833)
7q gain 625 (58%) 458 0
(0) 		2.24e-51
(9.7e-50) 		5.81e-70
(3.06e-68) 		0.35
(0.524) 		1.02e-10
(1.75e-09) 		6.99e-12
(1.29e-10) 		1e-05
(7.31e-05) 		0.00095
(0.00415) 		0.00748
(0.0249)
20p gain 264 (24%) 819 0
(0) 		6.15e-28
(1.97e-26) 		1.86e-32
(6.53e-31) 		0.72
(0.84) 		2.5e-05
(0.000161) 		2.7e-05
(0.00017) 		1e-05
(7.31e-05) 		0.0836
(0.188) 		0.106
(0.226)
20q gain 261 (24%) 822 0
(0) 		1.29e-26
(3.97e-25) 		2.17e-32
(7.29e-31) 		0.472
(0.632) 		1.58e-05
(0.00011) 		8.81e-06
(7.31e-05) 		1e-05
(7.31e-05) 		0.0756
(0.174) 		0.106
(0.226)
6q loss 187 (17%) 896 1.86e-08
(2.65e-07) 		0.000893
(0.00395) 		5.23e-05
(0.000301) 		0.221
(0.396) 		0.0683
(0.163) 		0.0043
(0.0155) 		3e-05
(0.000188) 		0.0165
(0.0496) 		0.0951
(0.206)
9p loss 315 (29%) 768 3.06e-05
(0.00019) 		0.000103
(0.000537) 		2.32e-05
(0.000152) 		0.946
(0.989) 		0.000619
(0.00282) 		0.0417
(0.11) 		8e-05
(0.000434) 		0.119
(0.247) 		0.0603
(0.147)
10q loss 585 (54%) 498 0
(0) 		4.63e-68
(2.28e-66) 		3.12e-115
(2.1e-113) 		0.174
(0.328) 		1.37e-18
(3.74e-17) 		1.65e-20
(4.88e-19) 		1e-05
(7.31e-05) 		0.00344
(0.0128) 		0.000958
(0.00416)
19q gain 221 (20%) 862 0
(0) 		2.16e-16
(5.3e-15) 		1.25e-34
(4.62e-33) 		0.541
(0.7) 		2.74e-06
(3.07e-05) 		4.17e-05
(0.000246) 		1e-05
(7.31e-05) 		0.013
(0.0405) 		1
(1.00)
21q gain 87 (8%) 996 0.00555
(0.0195) 		1.59e-06
(1.9e-05) 		0.000121
(0.000623) 		0.91
(0.963) 		0.0175
(0.0524) 		0.156
(0.307) 		0.00162
(0.00668) 		0.0927
(0.203) 		0.044
(0.115)
xq gain 58 (5%) 1025 0.00655
(0.0223) 		0.000332
(0.00158) 		0.000357
(0.00168) 		0.0748
(0.173) 		0.747
(0.857) 		0.036
(0.0983) 		6e-05
(0.000333) 		0.721
(0.84) 		0.000948
(0.00415)
1p loss 198 (18%) 885 0
(0) 		5.33e-05
(0.000303) 		3.49e-50
(1.43e-48) 		0.425
(0.589) 		2.29e-18
(6.02e-17) 		5e-06
(4.86e-05) 		1e-05
(7.31e-05) 		0.0889
(0.196) 		0.173
(0.328)
9q loss 142 (13%) 941 0.00353
(0.0131) 		0.00298
(0.0113) 		0.00678
(0.0227) 		0.784
(0.874) 		0.000688
(0.00308) 		0.00113
(0.00476) 		0.0628
(0.153) 		0.0386
(0.103) 		0.258
(0.443)
11q loss 113 (10%) 970 1.07e-09
(1.76e-08) 		5.43e-06
(5.2e-05) 		1.34e-10
(2.25e-09) 		0.763
(0.864) 		0.0186
(0.0551) 		0.0448
(0.117) 		1e-05
(7.31e-05) 		1
(1.00) 		0.117
(0.245)
14q loss 224 (21%) 859 2.68e-05
(0.00017) 		3.71e-05
(0.000224) 		6.43e-05
(0.000354) 		0.595
(0.736) 		0.29
(0.478) 		0.0287
(0.0805) 		0.00109
(0.00462) 		0.0506
(0.128) 		0.0803
(0.182)
19q loss 244 (23%) 839 0
(0) 		1.17e-08
(1.73e-07) 		5.61e-46
(2.18e-44) 		0.302
(0.489) 		1.05e-13
(2.29e-12) 		3.53e-06
(3.72e-05) 		1e-05
(7.31e-05) 		0.484
(0.642) 		0.0096
(0.0307)
1p gain 94 (9%) 989 1.12e-09
(1.79e-08) 		2.54e-06
(2.89e-05) 		1.41e-12
(2.74e-11) 		0.585
(0.729) 		0.0781
(0.178) 		0.00178
(0.00726) 		1e-05
(7.31e-05) 		0.774
(0.87) 		0.571
(0.719)
3q gain 70 (6%) 1013 1.43e-06
(1.74e-05) 		1.04e-06
(1.28e-05) 		8.52e-11
(1.5e-09) 		0.381
(0.554) 		0.0572
(0.141) 		0.0824
(0.186) 		1e-05
(7.31e-05) 		0.72
(0.84) 		0.511
(0.669)
9q gain 95 (9%) 988 0.00737
(0.0246) 		0.00674
(0.0227) 		4.99e-06
(4.86e-05) 		0.0163
(0.0492) 		0.0568
(0.141) 		0.155
(0.306) 		2e-05
(0.000134) 		0.594
(0.736) 		0.784
(0.874)
10p gain 70 (6%) 1013 4.29e-06
(4.33e-05) 		5.44e-12
(1.03e-10) 		1.66e-09
(2.55e-08) 		0.9
(0.958) 		0.238
(0.416) 		0.00425
(0.0154) 		1e-05
(7.31e-05) 		0.564
(0.715) 		0.0221
(0.0641)
18q gain 74 (7%) 1009 1.63e-05
(0.000113) 		0.00213
(0.00842) 		3.11e-06
(3.32e-05) 		0.465
(0.627) 		0.0484
(0.124) 		0.0374
(0.1) 		2e-05
(0.000134) 		0.502
(0.661) 		0.356
(0.531)
19p gain 320 (30%) 763 1.11e-05
(8.05e-05) 		3.16e-07
(4.09e-06) 		1.08e-12
(2.15e-11) 		0.544
(0.702) 		0.0828
(0.187) 		0.0246
(0.0706) 		1e-05
(7.31e-05) 		0.128
(0.26) 		0.311
(0.497)
6p loss 116 (11%) 967 6.18e-13
(1.27e-11) 		5.53e-05
(0.000309) 		2.83e-06
(3.12e-05) 		0.766
(0.865) 		0.29
(0.478) 		0.0529
(0.133) 		8e-05
(0.000434) 		0.0411
(0.109) 		0.31
(0.497)
8p loss 74 (7%) 1009 8.86e-05
(0.000471) 		0.000135
(0.00068) 		3.11e-06
(3.32e-05) 		0.33
(0.514) 		0.006
(0.0208) 		0.437
(0.603) 		0.00016
(0.000798) 		0.00588
(0.0205) 		0.763
(0.864)
13q loss 297 (27%) 786 0.00301
(0.0113) 		0.0579
(0.142) 		0.000129
(0.000653) 		0.3
(0.489) 		0.0203
(0.0592) 		0.11
(0.233) 		0.00362
(0.0133) 		0.541
(0.7) 		0.224
(0.398)
22q loss 240 (22%) 843 1.51e-14
(3.48e-13) 		4.7e-14
(1.05e-12) 		4.14e-17
(1.05e-15) 		1
(1.00) 		0.00133
(0.00551) 		0.0064
(0.022) 		1e-05
(7.31e-05) 		0.428
(0.591) 		0.195
(0.356)
1q gain 111 (10%) 972 4.83e-05
(0.000281) 		3.97e-06
(4.07e-05) 		1.47e-09
(2.31e-08) 		0.361
(0.538) 		0.29
(0.478) 		0.00268
(0.0103) 		1e-05
(7.31e-05) 		0.376
(0.549) 		0.424
(0.588)
2p gain 51 (5%) 1032 0.00354
(0.0131) 		0.0247
(0.0707) 		0.00384
(0.014) 		0.191
(0.351) 		0.394
(0.561) 		0.0834
(0.188) 		0.0712
(0.167) 		0.503
(0.661) 		0.716
(0.84)
2q gain 48 (4%) 1035 0.00486
(0.0172) 		0.015
(0.046) 		0.00461
(0.0165) 		0.374
(0.549) 		0.16
(0.312) 		0.0544
(0.136) 		0.0703
(0.166) 		0.348
(0.524) 		1
(1.00)
4q gain 40 (4%) 1043 0.00284
(0.0108) 		0.0229
(0.0662) 		8.1e-05
(0.000436) 		0.514
(0.672) 		0.0885
(0.196) 		0.812
(0.897) 		0.00182
(0.00738) 		0.262
(0.446) 		0.412
(0.576)
9p gain 64 (6%) 1019 0.00892
(0.0289) 		0.0124
(0.039) 		0.000688
(0.00308) 		0.067
(0.16) 		0.127
(0.259) 		0.254
(0.441) 		0.00188
(0.00758) 		0.39
(0.561) 		0.735
(0.854)
11q gain 74 (7%) 1009 1.87e-05
(0.000128) 		0.0131
(0.0405) 		4.58e-09
(6.89e-08) 		0.465
(0.627) 		0.124
(0.255) 		0.0076
(0.0252) 		1e-05
(7.31e-05) 		0.468
(0.628) 		0.224
(0.398)
12q gain 65 (6%) 1018 0.00225
(0.00882) 		0.138
(0.275) 		0.000464
(0.00215) 		0.897
(0.955) 		0.00953
(0.0306) 		0.184
(0.342) 		0.01
(0.0318) 		0.119
(0.247) 		0.168
(0.32)
17p gain 71 (7%) 1012 3.13e-05
(0.000192) 		1.37e-05
(9.73e-05) 		0.00202
(0.00809) 		0.0343
(0.094) 		1
(1.00) 		0.744
(0.855) 		0.00426
(0.0154) 		0.42
(0.584) 		0.762
(0.864)
17q gain 85 (8%) 998 6.65e-07
(8.32e-06) 		1.15e-05
(8.21e-05) 		0.000625
(0.00283) 		0.108
(0.23) 		0.693
(0.823) 		0.65
(0.783) 		0.00585
(0.0205) 		0.715
(0.84) 		0.77
(0.868)
18p gain 77 (7%) 1006 4.48e-05
(0.000263) 		0.0203
(0.0592) 		8.31e-05
(0.000444) 		0.719
(0.84) 		0.334
(0.517) 		0.0284
(0.08) 		0.00034
(0.00161) 		0.657
(0.788) 		0.763
(0.864)
4q loss 150 (14%) 933 5.27e-05
(0.000302) 		0.0336
(0.0926) 		0.000102
(0.000536) 		0.328
(0.512) 		0.0747
(0.173) 		0.416
(0.58) 		0.00011
(0.000568) 		0.747
(0.857) 		0.653
(0.785)
8q loss 52 (5%) 1031 4.89e-06
(4.86e-05) 		0.000298
(0.00147) 		9.16e-05
(0.000483) 		0.388
(0.56) 		0.016
(0.0489) 		0.778
(0.872) 		0.00516
(0.0182) 		0.165
(0.316) 		1
(1.00)
11p loss 163 (15%) 920 0.12
(0.248) 		0.935
(0.979) 		0.0271
(0.0766) 		0.031
(0.086) 		0.00885
(0.0288) 		0.718
(0.84) 		0.00032
(0.00155) 		0.576
(0.72) 		0.384
(0.557)
16q loss 104 (10%) 979 1.44e-07
(1.89e-06) 		2.45e-05
(0.000159) 		1.2e-08
(1.74e-07) 		1
(1.00) 		0.037
(0.0998) 		0.125
(0.256) 		1e-05
(7.31e-05) 		0.263
(0.447) 		1
(1.00)
17p loss 75 (7%) 1008 2.09e-05
(0.000139) 		0.000391
(0.00183) 		2.92e-08
(4.07e-07) 		0.397
(0.563) 		0.161
(0.312) 		0.00669
(0.0226) 		1e-05
(7.31e-05) 		1
(1.00) 		0.536
(0.698)
17q loss 49 (5%) 1034 3.34e-05
(0.000204) 		0.000848
(0.00377) 		5.86e-06
(5.55e-05) 		0.659
(0.789) 		0.392
(0.561) 		0.0691
(0.164) 		0.00047
(0.00217) 		0.916
(0.966) 		0.441
(0.606)
3p gain 66 (6%) 1017 2.33e-05
(0.000152) 		2.21e-06
(2.55e-05) 		3.06e-08
(4.19e-07) 		0.303
(0.489) 		0.364
(0.541) 		0.241
(0.42) 		1e-05
(7.31e-05) 		1
(1.00) 		0.508
(0.666)
5p gain 60 (6%) 1023 5.44e-05
(0.000306) 		0.0108
(0.0342) 		2.01e-06
(2.35e-05) 		0.285
(0.473) 		0.348
(0.524) 		0.93
(0.974) 		1e-05
(7.31e-05) 		0.417
(0.58) 		1
(1.00)
5q gain 50 (5%) 1033 3.99e-05
(0.000239) 		0.00116
(0.00486) 		1.58e-05
(0.00011) 		0.143
(0.284) 		0.865
(0.93) 		0.398
(0.564) 		0.00024
(0.00119) 		0.203
(0.369) 		0.26
(0.445)
10q gain 12 (1%) 1071 0.835
(0.912) 		0.0534
(0.134) 		0.0784
(0.178) 		0.255
(0.441) 		0.308
(0.496) 		0.163
(0.313) 		0.0428
(0.112) 		0.172
(0.327) 		0.0864
(0.193)
11p gain 50 (5%) 1033 0.0525
(0.133) 		0.795
(0.884) 		0.00851
(0.0278) 		0.38
(0.554) 		0.129
(0.26) 		0.0778
(0.178) 		0.012
(0.0379) 		0.349
(0.524) 		0.271
(0.455)
14q gain 26 (2%) 1057 0.000507
(0.00233) 		0.00033
(0.00158) 		0.00104
(0.00447) 		0.316
(0.502) 		0.475
(0.633) 		0.177
(0.331) 		0.00617
(0.0213) 		1
(1.00) 		0.624
(0.759)
15q gain 36 (3%) 1047 0.0128
(0.0401) 		0.0463
(0.119) 		0.0926
(0.203) 		0.735
(0.854) 		0.698
(0.828) 		0.00253
(0.00978) 		0.259
(0.444) 		1
(1.00) 		0.394
(0.561)
16p gain 54 (5%) 1029 0.612
(0.749) 		0.0546
(0.136) 		0.00783
(0.0257) 		0.257
(0.443) 		0.0489
(0.124) 		0.348
(0.524) 		0.0423
(0.111) 		0.347
(0.524) 		0.162
(0.312)
22q gain 55 (5%) 1028 0.321
(0.505) 		0.111
(0.234) 		0.489
(0.645) 		1
(1.00) 		0.626
(0.76) 		0.0365
(0.0991) 		0.0163
(0.0492) 		0.918
(0.966) 		0.0577
(0.142)
4p loss 126 (12%) 957 0.0465
(0.12) 		0.705
(0.834) 		0.0365
(0.0991) 		0.0163
(0.0492) 		0.309
(0.496) 		0.902
(0.958) 		0.00033
(0.00158) 		0.439
(0.605) 		0.472
(0.632)
12p loss 86 (8%) 997 0.00955
(0.0306) 		0.108
(0.23) 		0.00475
(0.0169) 		0.569
(0.719) 		0.235
(0.414) 		0.474
(0.633) 		0.0156
(0.0478) 		0.187
(0.346) 		0.571
(0.719)
15q loss 156 (14%) 927 0.00238
(0.00928) 		0.000125
(0.000636) 		4.17e-05
(0.000246) 		1
(1.00) 		0.837
(0.912) 		0.229
(0.404) 		0.00098
(0.00423) 		0.917
(0.966) 		1
(1.00)
16p loss 78 (7%) 1005 4.29e-07
(5.45e-06) 		3.84e-06
(4e-05) 		1.21e-07
(1.63e-06) 		0.475
(0.633) 		0.161
(0.312) 		0.407
(0.573) 		1e-05
(7.31e-05) 		0.888
(0.949) 		1
(1.00)
20p loss 26 (2%) 1057 0.319
(0.502) 		0.753
(0.86) 		0.0455
(0.118) 		0.109
(0.231) 		0.115
(0.241) 		0.559
(0.714) 		0.254
(0.441) 		0.0667
(0.16) 		0.301
(0.489)
4p gain 47 (4%) 1036 0.0368
(0.0994) 		0.257
(0.443) 		0.00252
(0.00978) 		0.763
(0.864) 		0.16
(0.312) 		0.3
(0.489) 		0.00643
(0.022) 		0.214
(0.387) 		0.716
(0.84)
6p gain 35 (3%) 1048 0.22
(0.395) 		0.783
(0.874) 		0.0256
(0.073) 		0.864
(0.93) 		0.0258
(0.0732) 		0.317
(0.502) 		0.0961
(0.207) 		0.55
(0.706) 		0.634
(0.768)
6q gain 28 (3%) 1055 0.191
(0.351) 		0.861
(0.929) 		0.00169
(0.00691) 		0.848
(0.921) 		0.114
(0.241) 		0.267
(0.451) 		0.0325
(0.0897) 		0.484
(0.642) 		0.619
(0.756)
13q gain 17 (2%) 1066 0.269
(0.453) 		0.0727
(0.17) 		0.635
(0.768) 		0.458
(0.624) 		0.0696
(0.165) 		0.0198
(0.0583) 		0.81
(0.897) 		1
(1.00) 		1
(1.00)
16q gain 56 (5%) 1027 0.448
(0.615) 		0.393
(0.561) 		0.0535
(0.134) 		0.488
(0.645) 		0.0771
(0.177) 		0.606
(0.744) 		0.0232
(0.0669) 		0.396
(0.563) 		0.163
(0.312)
20q loss 21 (2%) 1062 0.221
(0.396) 		0.373
(0.549) 		0.0132
(0.0409) 		0.0733
(0.171) 		0.619
(0.756) 		0.818
(0.903) 		0.0731
(0.171) 		0.37
(0.548) 		0.592
(0.735)
xq loss 174 (16%) 909 0.0939
(0.204) 		0.223
(0.398) 		0.0467
(0.12) 		0.867
(0.931) 		0.323
(0.506) 		0.0972
(0.209) 		0.349
(0.524) 		0.454
(0.621) 		1
(1.00)
12p gain 93 (9%) 990 0.285
(0.473) 		0.575
(0.719) 		0.0386
(0.103) 		0.913
(0.965) 		0.000305
(0.00149) 		0.741
(0.855) 		0.214
(0.387) 		0.906
(0.96) 		0.572
(0.719)
1q loss 43 (4%) 1040 0.127
(0.258) 		0.374
(0.549) 		0.00777
(0.0256) 		0.347
(0.524) 		0.358
(0.534) 		0.274
(0.458) 		0.00126
(0.00525) 		0.796
(0.884) 		1
(1.00)
2q loss 52 (5%) 1031 0.195
(0.356) 		0.191
(0.351) 		0.119
(0.247) 		0.388
(0.56) 		0.738
(0.855) 		0.344
(0.524) 		0.0645
(0.155) 		0.641
(0.773) 		0.263
(0.447)
3p loss 71 (7%) 1012 0.4
(0.565) 		0.349
(0.524) 		0.392
(0.561) 		0.536
(0.698) 		0.02
(0.0587) 		0.0289
(0.0807) 		0.859
(0.929) 		0.821
(0.904) 		0.207
(0.375)
5p loss 79 (7%) 1004 0.41
(0.575) 		0.857
(0.928) 		0.64
(0.773) 		1
(1.00) 		0.00209
(0.00827) 		0.188
(0.348) 		0.0621
(0.151) 		0.461
(0.625) 		0.764
(0.864)
12q loss 109 (10%) 974 0.925
(0.971) 		0.872
(0.935) 		0.84
(0.913) 		0.539
(0.699) 		0.72
(0.84) 		0.688
(0.821) 		0.0177
(0.0527) 		0.0399
(0.106) 		0.612
(0.749)
8q gain 118 (11%) 965 0.176
(0.33) 		0.0877
(0.195) 		0.559
(0.714) 		0.767
(0.866) 		0.161
(0.312) 		0.832
(0.912) 		0.258
(0.443) 		0.588
(0.73) 		0.13
(0.261)
2p loss 54 (5%) 1029 0.174
(0.328) 		0.0632
(0.153) 		0.332
(0.516) 		0.326
(0.51) 		0.41
(0.575) 		0.336
(0.518) 		0.45
(0.616) 		0.601
(0.742) 		0.267
(0.451)
3q loss 64 (6%) 1019 0.35
(0.524) 		0.891
(0.95) 		0.797
(0.884) 		1
(1.00) 		0.088
(0.195) 		0.344
(0.524) 		0.995
(1.00) 		0.538
(0.699) 		0.741
(0.855)
5q loss 78 (7%) 1005 0.949
(0.991) 		0.774
(0.87) 		0.41
(0.575) 		0.554
(0.71) 		0.00106
(0.00453) 		0.375
(0.549) 		0.129
(0.26) 		0.838
(0.912) 		0.549
(0.706)
7q loss 9 (1%) 1074 0.924
(0.971) 		0.0928
(0.203) 		1
(1.00) 		0.742
(0.855) 		0.687
(0.821) 		0.205
(0.372) 		0.744
(0.855) 		0.568
(0.719) 		1
(1.00)
18p loss 137 (13%) 946 0.374
(0.549) 		0.0942
(0.204) 		0.855
(0.926) 		0.139
(0.276) 		0.586
(0.73) 		0.46
(0.625) 		0.403
(0.569) 		0.218
(0.392) 		1
(1.00)
19p loss 57 (5%) 1026 0.297
(0.487) 		0.228
(0.403) 		0.279
(0.466) 		0.68
(0.813) 		0.87
(0.933) 		0.118
(0.246) 		0.742
(0.855) 		0.393
(0.561) 		0.28
(0.467)
21q loss 79 (7%) 1004 0.998
(1.00) 		0.268
(0.452) 		1
(1.00) 		0.346
(0.524) 		0.324
(0.507) 		0.811
(0.897) 		0.0646
(0.155) 		0.705
(0.834) 		0.564
(0.715)
xp loss 212 (20%) 871 0.835
(0.912) 		0.372
(0.549) 		0.878
(0.939) 		0.314
(0.5) 		0.465
(0.627) 		0.383
(0.557) 		0.956
(0.997) 		0.573
(0.719) 		0.121
(0.248)
8p gain 101 (9%) 982 0.605
(0.744) 		0.691
(0.823) 		0.835
(0.912) 		0.833
(0.912) 		0.317
(0.502) 		0.34
(0.524) 		0.476
(0.633) 		0.302
(0.489) 		0.291
(0.478)
xp gain 35 (3%) 1048 0.182
(0.34) 		0.177
(0.331) 		0.302
(0.489) 		0.163
(0.312) 		0.226
(0.4) 		0.238
(0.416) 		0.159
(0.311) 		0.549
(0.706) 		0.318
(0.502)
7p loss 10 (1%) 1073 0.564
(0.715) 		0.136
(0.273) 		0.349
(0.524) 		0.75
(0.858) 		0.463
(0.627) 		0.835
(0.912) 		0.779
(0.872) 		0.603
(0.743) 		1
(1.00)
18q loss 123 (11%) 960 0.152
(0.3) 		0.455
(0.621) 		0.502
(0.661) 		0.561
(0.715) 		0.306
(0.494) 		0.573
(0.719) 		0.138
(0.275) 		0.166
(0.317) 		0.334
(0.517)
'1p gain' versus 'Time to Death'

P value = 1.12e-09 (logrank test), Q value = 1.8e-08

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

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
1P GAIN MUTATED 94 72 0.2 - 92.7 (12.5)
1P GAIN WILD-TYPE 985 519 0.0 - 211.2 (16.2)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 2.54e-06 (Wilcoxon-test), Q value = 2.9e-05

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

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
1P GAIN MUTATED 94 57.8 (13.9)
1P GAIN WILD-TYPE 988 50.1 (15.8)

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

'1p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.41e-12 (Fisher's exact test), Q value = 2.7e-11

Table S3.  Gene #1: '1p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
1P GAIN MUTATED 81 13
1P GAIN WILD-TYPE 490 499

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0781 (Fisher's exact test), Q value = 0.18

Table S4.  Gene #1: '1p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
1P GAIN MUTATED 16 76
1P GAIN WILD-TYPE 242 691

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00178 (Wilcoxon-test), Q value = 0.0073

Table S5.  Gene #1: '1p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
1P GAIN MUTATED 66 76.2 (14.5)
1P GAIN WILD-TYPE 664 81.8 (14.6)

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S6.  Gene #1: '1p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
1P GAIN MUTATED 10 0 0 3 1 80
1P GAIN WILD-TYPE 184 28 129 186 17 445

Figure S6.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'Time to Death'

P value = 4.83e-05 (logrank test), Q value = 0.00028

Table S7.  Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
1Q GAIN MUTATED 111 78 0.1 - 211.2 (13.5)
1Q GAIN WILD-TYPE 968 513 0.0 - 182.3 (16.0)

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 3.97e-06 (Wilcoxon-test), Q value = 4.1e-05

Table S8.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
1Q GAIN MUTATED 111 56.9 (15.1)
1Q GAIN WILD-TYPE 971 50.1 (15.7)

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.47e-09 (Fisher's exact test), Q value = 2.3e-08

Table S9.  Gene #2: '1q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
1Q GAIN MUTATED 88 23
1Q GAIN WILD-TYPE 483 489

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00268 (Wilcoxon-test), Q value = 0.01

Table S10.  Gene #2: '1q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
1Q GAIN MUTATED 75 76.9 (14.3)
1Q GAIN WILD-TYPE 655 81.8 (14.7)

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S11.  Gene #2: '1q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
1Q GAIN MUTATED 13 1 2 8 2 85
1Q GAIN WILD-TYPE 181 27 127 181 16 440

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'Time to Death'

P value = 0.00354 (logrank test), Q value = 0.013

Table S12.  Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
2P GAIN MUTATED 51 37 0.2 - 92.7 (14.3)
2P GAIN WILD-TYPE 1028 554 0.0 - 211.2 (15.9)

Figure S12.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

'2p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0247 (Wilcoxon-test), Q value = 0.071

Table S13.  Gene #3: '2p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
2P GAIN MUTATED 51 55.4 (16.2)
2P GAIN WILD-TYPE 1031 50.5 (15.7)

Figure S13.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00384 (Fisher's exact test), Q value = 0.014

Table S14.  Gene #3: '2p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
2P GAIN MUTATED 37 14
2P GAIN WILD-TYPE 534 498

Figure S14.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0834 (Wilcoxon-test), Q value = 0.19

Table S15.  Gene #3: '2p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
2P GAIN MUTATED 36 77.8 (13.3)
2P GAIN WILD-TYPE 694 81.5 (14.7)

Figure S15.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0712 (Fisher's exact test), Q value = 0.17

Table S16.  Gene #3: '2p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
2P GAIN MUTATED 7 1 2 5 1 35
2P GAIN WILD-TYPE 187 27 127 184 17 490

Figure S16.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'Time to Death'

P value = 0.00486 (logrank test), Q value = 0.017

Table S17.  Gene #4: '2q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
2Q GAIN MUTATED 48 34 0.2 - 92.7 (14.1)
2Q GAIN WILD-TYPE 1031 557 0.0 - 211.2 (15.9)

Figure S17.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #1: 'Time to Death'

'2q gain' versus 'YEARS_TO_BIRTH'

P value = 0.015 (Wilcoxon-test), Q value = 0.046

Table S18.  Gene #4: '2q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
2Q GAIN MUTATED 48 55.9 (16.2)
2Q GAIN WILD-TYPE 1034 50.5 (15.7)

Figure S18.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00461 (Fisher's exact test), Q value = 0.017

Table S19.  Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
2Q GAIN MUTATED 35 13
2Q GAIN WILD-TYPE 536 499

Figure S19.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0544 (Wilcoxon-test), Q value = 0.14

Table S20.  Gene #4: '2q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
2Q GAIN MUTATED 36 77.2 (13.7)
2Q GAIN WILD-TYPE 694 81.5 (14.7)

Figure S20.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0703 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #4: '2q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
2Q GAIN MUTATED 7 1 2 4 1 33
2Q GAIN WILD-TYPE 187 27 127 185 17 492

Figure S21.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'Time to Death'

P value = 2.33e-05 (logrank test), Q value = 0.00015

Table S22.  Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
3P GAIN MUTATED 66 50 0.2 - 127.6 (10.8)
3P GAIN WILD-TYPE 1013 541 0.0 - 211.2 (16.0)

Figure S22.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 2.21e-06 (Wilcoxon-test), Q value = 2.5e-05

Table S23.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
3P GAIN MUTATED 66 59.5 (13.8)
3P GAIN WILD-TYPE 1016 50.2 (15.7)

Figure S23.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'TUMOR_TISSUE_SITE'

P value = 3.06e-08 (Fisher's exact test), Q value = 4.2e-07

Table S24.  Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
3P GAIN MUTATED 56 10
3P GAIN WILD-TYPE 515 502

Figure S24.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S25.  Gene #5: '3p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
3P GAIN MUTATED 7 1 0 3 1 54
3P GAIN WILD-TYPE 187 27 129 186 17 471

Figure S25.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 1.43e-06 (logrank test), Q value = 1.7e-05

Table S26.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
3Q GAIN MUTATED 70 54 0.2 - 127.6 (10.8)
3Q GAIN WILD-TYPE 1009 537 0.0 - 211.2 (16.0)

Figure S26.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 1.04e-06 (Wilcoxon-test), Q value = 1.3e-05

Table S27.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
3Q GAIN MUTATED 70 59.5 (14.0)
3Q GAIN WILD-TYPE 1012 50.2 (15.7)

Figure S27.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'TUMOR_TISSUE_SITE'

P value = 8.52e-11 (Fisher's exact test), Q value = 1.5e-09

Table S28.  Gene #6: '3q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
3Q GAIN MUTATED 62 8
3Q GAIN WILD-TYPE 509 504

Figure S28.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3q gain' versus 'RADIATION_THERAPY'

P value = 0.0572 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #6: '3q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
3Q GAIN MUTATED 10 57
3Q GAIN WILD-TYPE 248 710

Figure S29.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'3q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0824 (Wilcoxon-test), Q value = 0.19

Table S30.  Gene #6: '3q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
3Q GAIN MUTATED 50 79.0 (12.2)
3Q GAIN WILD-TYPE 680 81.5 (14.9)

Figure S30.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S31.  Gene #6: '3q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
3Q GAIN MUTATED 6 1 0 2 1 60
3Q GAIN WILD-TYPE 188 27 129 187 17 465

Figure S31.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'4p gain' versus 'Time to Death'

P value = 0.0368 (logrank test), Q value = 0.099

Table S32.  Gene #7: '4p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
4P GAIN MUTATED 47 32 0.2 - 92.7 (12.9)
4P GAIN WILD-TYPE 1032 559 0.0 - 211.2 (15.8)

Figure S32.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #1: 'Time to Death'

'4p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00252 (Fisher's exact test), Q value = 0.0098

Table S33.  Gene #7: '4p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
4P GAIN MUTATED 35 12
4P GAIN WILD-TYPE 536 500

Figure S33.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00643 (Fisher's exact test), Q value = 0.022

Table S34.  Gene #7: '4p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
4P GAIN MUTATED 8 1 0 4 1 33
4P GAIN WILD-TYPE 186 27 129 185 17 492

Figure S34.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'Time to Death'

P value = 0.00284 (logrank test), Q value = 0.011

Table S35.  Gene #8: '4q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
4Q GAIN MUTATED 40 30 0.2 - 92.7 (12.9)
4Q GAIN WILD-TYPE 1039 561 0.0 - 211.2 (15.8)

Figure S35.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #1: 'Time to Death'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0229 (Wilcoxon-test), Q value = 0.066

Table S36.  Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
4Q GAIN MUTATED 40 55.8 (16.4)
4Q GAIN WILD-TYPE 1042 50.6 (15.7)

Figure S36.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'TUMOR_TISSUE_SITE'

P value = 8.1e-05 (Fisher's exact test), Q value = 0.00044

Table S37.  Gene #8: '4q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
4Q GAIN MUTATED 33 7
4Q GAIN WILD-TYPE 538 505

Figure S37.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q gain' versus 'RADIATION_THERAPY'

P value = 0.0885 (Fisher's exact test), Q value = 0.2

Table S38.  Gene #8: '4q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
4Q GAIN MUTATED 5 33
4Q GAIN WILD-TYPE 253 734

Figure S38.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00182 (Fisher's exact test), Q value = 0.0074

Table S39.  Gene #8: '4q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
4Q GAIN MUTATED 5 1 0 2 1 31
4Q GAIN WILD-TYPE 189 27 129 187 17 494

Figure S39.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'Time to Death'

P value = 5.44e-05 (logrank test), Q value = 0.00031

Table S40.  Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
5P GAIN MUTATED 60 49 1.1 - 92.7 (12.4)
5P GAIN WILD-TYPE 1019 542 0.0 - 211.2 (16.0)

Figure S40.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0108 (Wilcoxon-test), Q value = 0.034

Table S41.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
5P GAIN MUTATED 60 55.7 (15.1)
5P GAIN WILD-TYPE 1022 50.5 (15.8)

Figure S41.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.01e-06 (Fisher's exact test), Q value = 2.4e-05

Table S42.  Gene #9: '5p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
5P GAIN MUTATED 49 11
5P GAIN WILD-TYPE 522 501

Figure S42.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S43.  Gene #9: '5p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
5P GAIN MUTATED 7 3 2 2 4 42
5P GAIN WILD-TYPE 187 25 127 187 14 483

Figure S43.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'Time to Death'

P value = 3.99e-05 (logrank test), Q value = 0.00024

Table S44.  Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
5Q GAIN MUTATED 50 40 1.1 - 92.7 (9.1)
5Q GAIN WILD-TYPE 1029 551 0.0 - 211.2 (16.0)

Figure S44.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00116 (Wilcoxon-test), Q value = 0.0049

Table S45.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
5Q GAIN MUTATED 50 57.8 (13.8)
5Q GAIN WILD-TYPE 1032 50.4 (15.8)

Figure S45.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.00011

Table S46.  Gene #10: '5q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
5Q GAIN MUTATED 41 9
5Q GAIN WILD-TYPE 530 503

Figure S46.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S47.  Gene #10: '5q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
5Q GAIN MUTATED 5 3 2 2 3 35
5Q GAIN WILD-TYPE 189 25 127 187 15 490

Figure S47.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0256 (Fisher's exact test), Q value = 0.073

Table S48.  Gene #11: '6p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
6P GAIN MUTATED 25 10
6P GAIN WILD-TYPE 546 502

Figure S48.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6p gain' versus 'RADIATION_THERAPY'

P value = 0.0258 (Fisher's exact test), Q value = 0.073

Table S49.  Gene #11: '6p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
6P GAIN MUTATED 3 31
6P GAIN WILD-TYPE 255 736

Figure S49.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0961 (Fisher's exact test), Q value = 0.21

Table S50.  Gene #11: '6p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
6P GAIN MUTATED 7 1 1 2 0 24
6P GAIN WILD-TYPE 187 27 128 187 18 501

Figure S50.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00169 (Fisher's exact test), Q value = 0.0069

Table S51.  Gene #12: '6q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
6Q GAIN MUTATED 23 5
6Q GAIN WILD-TYPE 548 507

Figure S51.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6q gain' versus 'RADIATION_THERAPY'

P value = 0.114 (Fisher's exact test), Q value = 0.24

Table S52.  Gene #12: '6q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
6Q GAIN MUTATED 3 24
6Q GAIN WILD-TYPE 255 743

Figure S52.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0325 (Fisher's exact test), Q value = 0.09

Table S53.  Gene #12: '6q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
6Q GAIN MUTATED 3 1 0 2 0 22
6Q GAIN WILD-TYPE 191 27 129 187 18 503

Figure S53.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'Time to Death'

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

Table S54.  Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
7P GAIN MUTATED 589 444 0.1 - 211.2 (12.8)
7P GAIN WILD-TYPE 490 147 0.0 - 182.3 (20.5)

Figure S54.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 1.9e-54 (Wilcoxon-test), Q value = 8.8e-53

Table S55.  Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
7P GAIN MUTATED 590 57.5 (13.1)
7P GAIN WILD-TYPE 492 42.7 (14.9)

Figure S55.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.4e-83 (Fisher's exact test), Q value = 1.5e-81

Table S56.  Gene #13: '7p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
7P GAIN MUTATED 465 125
7P GAIN WILD-TYPE 106 387

Figure S56.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'7p gain' versus 'RADIATION_THERAPY'

P value = 1.19e-11 (Fisher's exact test), Q value = 2.1e-10

Table S57.  Gene #13: '7p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
7P GAIN MUTATED 94 467
7P GAIN WILD-TYPE 164 300

Figure S57.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5.29e-13 (Wilcoxon-test), Q value = 1.1e-11

Table S58.  Gene #13: '7p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
7P GAIN MUTATED 421 78.2 (15.3)
7P GAIN WILD-TYPE 309 85.5 (12.7)

Figure S58.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S59.  Gene #13: '7p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
7P GAIN MUTATED 53 20 31 41 12 433
7P GAIN WILD-TYPE 141 8 98 148 6 92

Figure S59.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'RACE'

P value = 0.00205 (Fisher's exact test), Q value = 0.0082

Table S60.  Gene #13: '7p gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
7P GAIN MUTATED 1 9 52 507
7P GAIN WILD-TYPE 0 12 19 450

Figure S60.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #8: 'RACE'

'7p gain' versus 'ETHNICITY'

P value = 0.0299 (Fisher's exact test), Q value = 0.083

Table S61.  Gene #13: '7p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
7P GAIN MUTATED 16 493
7P GAIN WILD-TYPE 28 426

Figure S61.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'ETHNICITY'

'7q gain' versus 'Time to Death'

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

Table S62.  Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
7Q GAIN MUTATED 624 451 0.1 - 211.2 (12.9)
7Q GAIN WILD-TYPE 455 140 0.0 - 182.3 (21.0)

Figure S62.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 2.24e-51 (Wilcoxon-test), Q value = 9.7e-50

Table S63.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
7Q GAIN MUTATED 625 56.9 (13.3)
7Q GAIN WILD-TYPE 457 42.3 (15.0)

Figure S63.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'TUMOR_TISSUE_SITE'

P value = 5.81e-70 (Fisher's exact test), Q value = 3.1e-68

Table S64.  Gene #14: '7q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
7Q GAIN MUTATED 470 155
7Q GAIN WILD-TYPE 101 357

Figure S64.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'7q gain' versus 'RADIATION_THERAPY'

P value = 1.02e-10 (Fisher's exact test), Q value = 1.7e-09

Table S65.  Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
7Q GAIN MUTATED 104 488
7Q GAIN WILD-TYPE 154 279

Figure S65.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.99e-12 (Wilcoxon-test), Q value = 1.3e-10

Table S66.  Gene #14: '7q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
7Q GAIN MUTATED 437 78.4 (15.3)
7Q GAIN WILD-TYPE 293 85.5 (12.7)

Figure S66.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S67.  Gene #14: '7q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
7Q GAIN MUTATED 68 21 39 48 12 437
7Q GAIN WILD-TYPE 126 7 90 141 6 88

Figure S67.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'RACE'

P value = 0.00095 (Fisher's exact test), Q value = 0.0041

Table S68.  Gene #14: '7q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
7Q GAIN MUTATED 1 10 55 538
7Q GAIN WILD-TYPE 0 11 16 419

Figure S68.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #8: 'RACE'

'7q gain' versus 'ETHNICITY'

P value = 0.00748 (Fisher's exact test), Q value = 0.025

Table S69.  Gene #14: '7q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
7Q GAIN MUTATED 16 530
7Q GAIN WILD-TYPE 28 389

Figure S69.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'ETHNICITY'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0877 (Wilcoxon-test), Q value = 0.19

Table S70.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
8Q GAIN MUTATED 118 48.2 (16.4)
8Q GAIN WILD-TYPE 964 51.1 (15.7)

Figure S70.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'Time to Death'

P value = 0.00892 (logrank test), Q value = 0.029

Table S71.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
9P GAIN MUTATED 64 44 0.4 - 172.8 (12.9)
9P GAIN WILD-TYPE 1015 547 0.0 - 211.2 (15.9)

Figure S71.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0124 (Wilcoxon-test), Q value = 0.039

Table S72.  Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
9P GAIN MUTATED 64 54.8 (16.9)
9P GAIN WILD-TYPE 1018 50.5 (15.7)

Figure S72.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000688 (Fisher's exact test), Q value = 0.0031

Table S73.  Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
9P GAIN MUTATED 47 17
9P GAIN WILD-TYPE 524 495

Figure S73.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p gain' versus 'GENDER'

P value = 0.067 (Fisher's exact test), Q value = 0.16

Table S74.  Gene #17: '9p gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
9P GAIN MUTATED 34 30
9P GAIN WILD-TYPE 418 601

Figure S74.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'GENDER'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00188 (Fisher's exact test), Q value = 0.0076

Table S75.  Gene #17: '9p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
9P GAIN MUTATED 8 0 6 3 0 47
9P GAIN WILD-TYPE 186 28 123 186 18 478

Figure S75.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'Time to Death'

P value = 0.00737 (logrank test), Q value = 0.025

Table S76.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
9Q GAIN MUTATED 95 67 0.4 - 172.8 (13.8)
9Q GAIN WILD-TYPE 984 524 0.0 - 211.2 (15.9)

Figure S76.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00674 (Wilcoxon-test), Q value = 0.023

Table S77.  Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
9Q GAIN MUTATED 95 54.6 (15.6)
9Q GAIN WILD-TYPE 987 50.4 (15.8)

Figure S77.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'TUMOR_TISSUE_SITE'

P value = 4.99e-06 (Fisher's exact test), Q value = 4.9e-05

Table S78.  Gene #18: '9q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
9Q GAIN MUTATED 71 24
9Q GAIN WILD-TYPE 500 488

Figure S78.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q gain' versus 'GENDER'

P value = 0.0163 (Fisher's exact test), Q value = 0.049

Table S79.  Gene #18: '9q gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
9Q GAIN MUTATED 51 44
9Q GAIN WILD-TYPE 401 587

Figure S79.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'GENDER'

'9q gain' versus 'RADIATION_THERAPY'

P value = 0.0568 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #18: '9q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
9Q GAIN MUTATED 15 76
9Q GAIN WILD-TYPE 243 691

Figure S80.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S81.  Gene #18: '9q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
9Q GAIN MUTATED 13 1 7 4 2 68
9Q GAIN WILD-TYPE 181 27 122 185 16 457

Figure S81.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 4.29e-06 (logrank test), Q value = 4.3e-05

Table S82.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
10P GAIN MUTATED 70 21 0.1 - 172.8 (23.5)
10P GAIN WILD-TYPE 1009 570 0.0 - 211.2 (15.2)

Figure S82.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 5.44e-12 (Wilcoxon-test), Q value = 1e-10

Table S83.  Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
10P GAIN MUTATED 70 38.3 (12.2)
10P GAIN WILD-TYPE 1012 51.6 (15.6)

Figure S83.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.66e-09 (Fisher's exact test), Q value = 2.6e-08

Table S84.  Gene #19: '10p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
10P GAIN MUTATED 13 57
10P GAIN WILD-TYPE 558 455

Figure S84.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00425 (Wilcoxon-test), Q value = 0.015

Table S85.  Gene #19: '10p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
10P GAIN MUTATED 44 87.0 (10.7)
10P GAIN WILD-TYPE 686 80.9 (14.8)

Figure S85.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S86.  Gene #19: '10p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
10P GAIN MUTATED 32 1 17 8 1 11
10P GAIN WILD-TYPE 162 27 112 181 17 514

Figure S86.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'ETHNICITY'

P value = 0.0221 (Fisher's exact test), Q value = 0.064

Table S87.  Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
10P GAIN MUTATED 7 57
10P GAIN WILD-TYPE 37 862

Figure S87.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0534 (Wilcoxon-test), Q value = 0.13

Table S88.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
10Q GAIN MUTATED 12 42.1 (17.6)
10Q GAIN WILD-TYPE 1070 50.9 (15.7)

Figure S88.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0784 (Fisher's exact test), Q value = 0.18

Table S89.  Gene #20: '10q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
10Q GAIN MUTATED 3 9
10Q GAIN WILD-TYPE 568 503

Figure S89.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0428 (Fisher's exact test), Q value = 0.11

Table S90.  Gene #20: '10q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
10Q GAIN MUTATED 7 0 0 2 0 3
10Q GAIN WILD-TYPE 187 28 129 187 18 522

Figure S90.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'ETHNICITY'

P value = 0.0864 (Fisher's exact test), Q value = 0.19

Table S91.  Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
10Q GAIN MUTATED 2 9
10Q GAIN WILD-TYPE 42 910

Figure S91.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

'11p gain' versus 'Time to Death'

P value = 0.0525 (logrank test), Q value = 0.13

Table S92.  Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
11P GAIN MUTATED 50 20 1.2 - 211.2 (18.5)
11P GAIN WILD-TYPE 1029 571 0.0 - 182.3 (15.4)

Figure S92.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00851 (Fisher's exact test), Q value = 0.028

Table S93.  Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
11P GAIN MUTATED 17 33
11P GAIN WILD-TYPE 554 479

Figure S93.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0778 (Wilcoxon-test), Q value = 0.18

Table S94.  Gene #21: '11p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
11P GAIN MUTATED 36 85.3 (13.6)
11P GAIN WILD-TYPE 694 81.1 (14.7)

Figure S94.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.012 (Fisher's exact test), Q value = 0.038

Table S95.  Gene #21: '11p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
11P GAIN MUTATED 6 0 10 17 0 17
11P GAIN WILD-TYPE 188 28 119 172 18 508

Figure S95.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'Time to Death'

P value = 1.87e-05 (logrank test), Q value = 0.00013

Table S96.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
11Q GAIN MUTATED 74 23 1.2 - 211.2 (21.9)
11Q GAIN WILD-TYPE 1005 568 0.0 - 172.8 (15.2)

Figure S96.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0131 (Wilcoxon-test), Q value = 0.04

Table S97.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
11Q GAIN MUTATED 74 46.5 (14.1)
11Q GAIN WILD-TYPE 1008 51.1 (15.9)

Figure S97.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'TUMOR_TISSUE_SITE'

P value = 4.58e-09 (Fisher's exact test), Q value = 6.9e-08

Table S98.  Gene #22: '11q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
11Q GAIN MUTATED 15 59
11Q GAIN WILD-TYPE 556 453

Figure S98.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0076 (Wilcoxon-test), Q value = 0.025

Table S99.  Gene #22: '11q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
11Q GAIN MUTATED 47 86.8 (11.2)
11Q GAIN WILD-TYPE 683 80.9 (14.8)

Figure S99.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S100.  Gene #22: '11q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
11Q GAIN MUTATED 18 0 14 27 1 14
11Q GAIN WILD-TYPE 176 28 115 162 17 511

Figure S100.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0386 (Fisher's exact test), Q value = 0.1

Table S101.  Gene #23: '12p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
12P GAIN MUTATED 59 34
12P GAIN WILD-TYPE 512 478

Figure S101.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.000305 (Fisher's exact test), Q value = 0.0015

Table S102.  Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
12P GAIN MUTATED 9 80
12P GAIN WILD-TYPE 249 687

Figure S102.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'Time to Death'

P value = 0.00225 (logrank test), Q value = 0.0088

Table S103.  Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
12Q GAIN MUTATED 65 49 1.1 - 84.3 (14.9)
12Q GAIN WILD-TYPE 1014 542 0.0 - 211.2 (15.8)

Figure S103.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000464 (Fisher's exact test), Q value = 0.0022

Table S104.  Gene #24: '12q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
12Q GAIN MUTATED 48 17
12Q GAIN WILD-TYPE 523 495

Figure S104.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.00953 (Fisher's exact test), Q value = 0.031

Table S105.  Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
12Q GAIN MUTATED 7 55
12Q GAIN WILD-TYPE 251 712

Figure S105.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.01 (Fisher's exact test), Q value = 0.032

Table S106.  Gene #24: '12q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
12Q GAIN MUTATED 5 2 4 8 0 46
12Q GAIN WILD-TYPE 189 26 125 181 18 479

Figure S106.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RACE'

P value = 0.119 (Fisher's exact test), Q value = 0.25

Table S107.  Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
12Q GAIN MUTATED 0 4 4 54
12Q GAIN WILD-TYPE 1 17 67 903

Figure S107.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

'13q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0727 (Wilcoxon-test), Q value = 0.17

Table S108.  Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
13Q GAIN MUTATED 17 57.6 (17.7)
13Q GAIN WILD-TYPE 1065 50.7 (15.7)

Figure S108.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0696 (Fisher's exact test), Q value = 0.16

Table S109.  Gene #25: '13q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
13Q GAIN MUTATED 7 8
13Q GAIN WILD-TYPE 251 759

Figure S109.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0198 (Wilcoxon-test), Q value = 0.058

Table S110.  Gene #25: '13q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
13Q GAIN MUTATED 14 72.1 (14.8)
13Q GAIN WILD-TYPE 716 81.5 (14.6)

Figure S110.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q gain' versus 'Time to Death'

P value = 0.000507 (logrank test), Q value = 0.0023

Table S111.  Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
14Q GAIN MUTATED 26 22 0.4 - 46.6 (10.4)
14Q GAIN WILD-TYPE 1053 569 0.0 - 211.2 (15.8)

Figure S111.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00033 (Wilcoxon-test), Q value = 0.0016

Table S112.  Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
14Q GAIN MUTATED 26 61.4 (14.5)
14Q GAIN WILD-TYPE 1056 50.5 (15.7)

Figure S112.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00104 (Fisher's exact test), Q value = 0.0045

Table S113.  Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
14Q GAIN MUTATED 22 4
14Q GAIN WILD-TYPE 549 508

Figure S113.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00617 (Fisher's exact test), Q value = 0.021

Table S114.  Gene #26: '14q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
14Q GAIN MUTATED 2 2 1 1 2 18
14Q GAIN WILD-TYPE 192 26 128 188 16 507

Figure S114.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'Time to Death'

P value = 0.0128 (logrank test), Q value = 0.04

Table S115.  Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
15Q GAIN MUTATED 36 28 0.2 - 117.4 (13.7)
15Q GAIN WILD-TYPE 1043 563 0.0 - 211.2 (15.7)

Figure S115.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0463 (Wilcoxon-test), Q value = 0.12

Table S116.  Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
15Q GAIN MUTATED 36 55.3 (13.3)
15Q GAIN WILD-TYPE 1046 50.6 (15.8)

Figure S116.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0926 (Fisher's exact test), Q value = 0.2

Table S117.  Gene #27: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
15Q GAIN MUTATED 24 12
15Q GAIN WILD-TYPE 547 500

Figure S117.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00253 (Wilcoxon-test), Q value = 0.0098

Table S118.  Gene #27: '15q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
15Q GAIN MUTATED 28 72.9 (15.1)
15Q GAIN WILD-TYPE 702 81.6 (14.6)

Figure S118.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0546 (Wilcoxon-test), Q value = 0.14

Table S119.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
16P GAIN MUTATED 54 54.5 (14.8)
16P GAIN WILD-TYPE 1028 50.6 (15.8)

Figure S119.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00783 (Fisher's exact test), Q value = 0.026

Table S120.  Gene #28: '16p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
16P GAIN MUTATED 38 16
16P GAIN WILD-TYPE 533 496

Figure S120.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16p gain' versus 'RADIATION_THERAPY'

P value = 0.0489 (Fisher's exact test), Q value = 0.12

Table S121.  Gene #28: '16p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
16P GAIN MUTATED 7 45
16P GAIN WILD-TYPE 251 722

Figure S121.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0423 (Fisher's exact test), Q value = 0.11

Table S122.  Gene #28: '16p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
16P GAIN MUTATED 10 1 2 4 1 36
16P GAIN WILD-TYPE 184 27 127 185 17 489

Figure S122.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0535 (Fisher's exact test), Q value = 0.13

Table S123.  Gene #29: '16q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
16Q GAIN MUTATED 37 19
16Q GAIN WILD-TYPE 534 493

Figure S123.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16q gain' versus 'RADIATION_THERAPY'

P value = 0.0771 (Fisher's exact test), Q value = 0.18

Table S124.  Gene #29: '16q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
16Q GAIN MUTATED 8 46
16Q GAIN WILD-TYPE 250 721

Figure S124.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0232 (Fisher's exact test), Q value = 0.067

Table S125.  Gene #29: '16q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
16Q GAIN MUTATED 13 1 1 5 1 35
16Q GAIN WILD-TYPE 181 27 128 184 17 490

Figure S125.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 3.13e-05 (logrank test), Q value = 0.00019

Table S126.  Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
17P GAIN MUTATED 71 52 0.2 - 72.4 (12.9)
17P GAIN WILD-TYPE 1008 539 0.0 - 211.2 (15.9)

Figure S126.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 1.37e-05 (Wilcoxon-test), Q value = 9.7e-05

Table S127.  Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
17P GAIN MUTATED 71 58.4 (15.0)
17P GAIN WILD-TYPE 1011 50.2 (15.7)

Figure S127.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00202 (Fisher's exact test), Q value = 0.0081

Table S128.  Gene #30: '17p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
17P GAIN MUTATED 50 21
17P GAIN WILD-TYPE 521 491

Figure S128.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p gain' versus 'GENDER'

P value = 0.0343 (Fisher's exact test), Q value = 0.094

Table S129.  Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
17P GAIN MUTATED 21 50
17P GAIN WILD-TYPE 431 581

Figure S129.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00426 (Fisher's exact test), Q value = 0.015

Table S130.  Gene #30: '17p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
17P GAIN MUTATED 11 4 1 9 1 45
17P GAIN WILD-TYPE 183 24 128 180 17 480

Figure S130.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 6.65e-07 (logrank test), Q value = 8.3e-06

Table S131.  Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
17Q GAIN MUTATED 85 64 0.2 - 72.4 (12.9)
17Q GAIN WILD-TYPE 994 527 0.0 - 211.2 (16.0)

Figure S131.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'YEARS_TO_BIRTH'

P value = 1.15e-05 (Wilcoxon-test), Q value = 8.2e-05

Table S132.  Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
17Q GAIN MUTATED 85 57.8 (15.3)
17Q GAIN WILD-TYPE 997 50.2 (15.7)

Figure S132.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000625 (Fisher's exact test), Q value = 0.0028

Table S133.  Gene #31: '17q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
17Q GAIN MUTATED 60 25
17Q GAIN WILD-TYPE 511 487

Figure S133.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17q gain' versus 'GENDER'

P value = 0.108 (Fisher's exact test), Q value = 0.23

Table S134.  Gene #31: '17q gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
17Q GAIN MUTATED 28 57
17Q GAIN WILD-TYPE 424 574

Figure S134.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'GENDER'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00585 (Fisher's exact test), Q value = 0.02

Table S135.  Gene #31: '17q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
17Q GAIN MUTATED 13 4 3 9 2 54
17Q GAIN WILD-TYPE 181 24 126 180 16 471

Figure S135.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'Time to Death'

P value = 4.48e-05 (logrank test), Q value = 0.00026

Table S136.  Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
18P GAIN MUTATED 77 56 0.1 - 65.0 (13.3)
18P GAIN WILD-TYPE 1002 535 0.0 - 211.2 (15.9)

Figure S136.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0203 (Wilcoxon-test), Q value = 0.059

Table S137.  Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
18P GAIN MUTATED 77 54.8 (17.1)
18P GAIN WILD-TYPE 1005 50.5 (15.6)

Figure S137.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'TUMOR_TISSUE_SITE'

P value = 8.31e-05 (Fisher's exact test), Q value = 0.00044

Table S138.  Gene #32: '18p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
18P GAIN MUTATED 57 20
18P GAIN WILD-TYPE 514 492

Figure S138.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0284 (Wilcoxon-test), Q value = 0.08

Table S139.  Gene #32: '18p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
18P GAIN MUTATED 48 75.8 (17.6)
18P GAIN WILD-TYPE 682 81.7 (14.4)

Figure S139.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0016

Table S140.  Gene #32: '18p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
18P GAIN MUTATED 11 0 4 5 0 57
18P GAIN WILD-TYPE 183 28 125 184 18 468

Figure S140.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'Time to Death'

P value = 1.63e-05 (logrank test), Q value = 0.00011

Table S141.  Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
18Q GAIN MUTATED 74 56 0.1 - 65.0 (13.3)
18Q GAIN WILD-TYPE 1005 535 0.0 - 211.2 (15.9)

Figure S141.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00213 (Wilcoxon-test), Q value = 0.0084

Table S142.  Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
18Q GAIN MUTATED 74 56.1 (16.4)
18Q GAIN WILD-TYPE 1008 50.4 (15.7)

Figure S142.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q gain' versus 'TUMOR_TISSUE_SITE'

P value = 3.11e-06 (Fisher's exact test), Q value = 3.3e-05

Table S143.  Gene #33: '18q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
18Q GAIN MUTATED 58 16
18Q GAIN WILD-TYPE 513 496

Figure S143.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18q gain' versus 'RADIATION_THERAPY'

P value = 0.0484 (Fisher's exact test), Q value = 0.12

Table S144.  Gene #33: '18q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
18Q GAIN MUTATED 11 61
18Q GAIN WILD-TYPE 247 706

Figure S144.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0374 (Wilcoxon-test), Q value = 0.1

Table S145.  Gene #33: '18q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
18Q GAIN MUTATED 48 76.7 (16.5)
18Q GAIN WILD-TYPE 682 81.6 (14.5)

Figure S145.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S146.  Gene #33: '18q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
18Q GAIN MUTATED 10 0 3 3 0 58
18Q GAIN WILD-TYPE 184 28 126 186 18 467

Figure S146.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'Time to Death'

P value = 1.11e-05 (logrank test), Q value = 8.1e-05

Table S147.  Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
19P GAIN MUTATED 317 205 0.1 - 169.8 (15.3)
19P GAIN WILD-TYPE 762 386 0.0 - 211.2 (16.0)

Figure S147.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 3.16e-07 (Wilcoxon-test), Q value = 4.1e-06

Table S148.  Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
19P GAIN MUTATED 319 54.5 (14.3)
19P GAIN WILD-TYPE 763 49.2 (16.1)

Figure S148.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.08e-12 (Fisher's exact test), Q value = 2.1e-11

Table S149.  Gene #34: '19p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
19P GAIN MUTATED 222 98
19P GAIN WILD-TYPE 349 414

Figure S149.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19p gain' versus 'RADIATION_THERAPY'

P value = 0.0828 (Fisher's exact test), Q value = 0.19

Table S150.  Gene #34: '19p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
19P GAIN MUTATED 65 238
19P GAIN WILD-TYPE 193 529

Figure S150.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0246 (Wilcoxon-test), Q value = 0.071

Table S151.  Gene #34: '19p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
19P GAIN MUTATED 211 79.8 (14.4)
19P GAIN WILD-TYPE 519 81.9 (14.8)

Figure S151.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S152.  Gene #34: '19p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
19P GAIN MUTATED 21 12 19 58 9 201
19P GAIN WILD-TYPE 173 16 110 131 9 324

Figure S152.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'Time to Death'

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

Table S153.  Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
19Q GAIN MUTATED 220 172 0.1 - 92.7 (14.1)
19Q GAIN WILD-TYPE 859 419 0.0 - 211.2 (16.2)

Figure S153.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 2.16e-16 (Wilcoxon-test), Q value = 5.3e-15

Table S154.  Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
19Q GAIN MUTATED 221 58.5 (12.3)
19Q GAIN WILD-TYPE 861 48.8 (16.0)

Figure S154.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.25e-34 (Fisher's exact test), Q value = 4.6e-33

Table S155.  Gene #35: '19q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
19Q GAIN MUTATED 194 27
19Q GAIN WILD-TYPE 377 485

Figure S155.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19q gain' versus 'RADIATION_THERAPY'

P value = 2.74e-06 (Fisher's exact test), Q value = 3.1e-05

Table S156.  Gene #35: '19q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
19Q GAIN MUTATED 27 180
19Q GAIN WILD-TYPE 231 587

Figure S156.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 4.17e-05 (Wilcoxon-test), Q value = 0.00025

Table S157.  Gene #35: '19q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
19Q GAIN MUTATED 152 77.6 (14.4)
19Q GAIN WILD-TYPE 578 82.2 (14.6)

Figure S157.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S158.  Gene #35: '19q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
19Q GAIN MUTATED 13 11 9 5 7 176
19Q GAIN WILD-TYPE 181 17 120 184 11 349

Figure S158.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'RACE'

P value = 0.013 (Fisher's exact test), Q value = 0.04

Table S159.  Gene #35: '19q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
19Q GAIN MUTATED 0 8 22 184
19Q GAIN WILD-TYPE 1 13 49 773

Figure S159.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #8: 'RACE'

'20p gain' versus 'Time to Death'

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

Table S160.  Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
20P GAIN MUTATED 264 212 0.1 - 94.8 (13.7)
20P GAIN WILD-TYPE 815 379 0.0 - 211.2 (16.9)

Figure S160.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 6.15e-28 (Wilcoxon-test), Q value = 2e-26

Table S161.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
20P GAIN MUTATED 264 59.9 (13.0)
20P GAIN WILD-TYPE 818 47.8 (15.5)

Figure S161.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.86e-32 (Fisher's exact test), Q value = 6.5e-31

Table S162.  Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
20P GAIN MUTATED 220 44
20P GAIN WILD-TYPE 351 468

Figure S162.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p gain' versus 'RADIATION_THERAPY'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.00016

Table S163.  Gene #36: '20p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
20P GAIN MUTATED 38 210
20P GAIN WILD-TYPE 220 557

Figure S163.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.7e-05 (Wilcoxon-test), Q value = 0.00017

Table S164.  Gene #36: '20p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
20P GAIN MUTATED 190 77.9 (14.5)
20P GAIN WILD-TYPE 540 82.5 (14.6)

Figure S164.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S165.  Gene #36: '20p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
20P GAIN MUTATED 23 9 8 13 9 202
20P GAIN WILD-TYPE 171 19 121 176 9 323

Figure S165.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'RACE'

P value = 0.0836 (Fisher's exact test), Q value = 0.19

Table S166.  Gene #36: '20p gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
20P GAIN MUTATED 0 10 18 230
20P GAIN WILD-TYPE 1 11 53 727

Figure S166.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'RACE'

'20p gain' versus 'ETHNICITY'

P value = 0.106 (Fisher's exact test), Q value = 0.23

Table S167.  Gene #36: '20p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
20P GAIN MUTATED 6 229
20P GAIN WILD-TYPE 38 690

Figure S167.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'ETHNICITY'

'20q gain' versus 'Time to Death'

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

Table S168.  Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
20Q GAIN MUTATED 261 209 0.1 - 94.8 (13.5)
20Q GAIN WILD-TYPE 818 382 0.0 - 211.2 (16.7)

Figure S168.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 1.29e-26 (Wilcoxon-test), Q value = 4e-25

Table S169.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
20Q GAIN MUTATED 261 59.8 (13.2)
20Q GAIN WILD-TYPE 821 47.9 (15.5)

Figure S169.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.17e-32 (Fisher's exact test), Q value = 7.3e-31

Table S170.  Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
20Q GAIN MUTATED 218 43
20Q GAIN WILD-TYPE 353 469

Figure S170.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q gain' versus 'RADIATION_THERAPY'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.00011

Table S171.  Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
20Q GAIN MUTATED 37 210
20Q GAIN WILD-TYPE 221 557

Figure S171.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 8.81e-06 (Wilcoxon-test), Q value = 7.3e-05

Table S172.  Gene #37: '20q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
20Q GAIN MUTATED 189 77.8 (14.3)
20Q GAIN WILD-TYPE 541 82.5 (14.6)

Figure S172.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S173.  Gene #37: '20q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
20Q GAIN MUTATED 22 9 7 14 9 200
20Q GAIN WILD-TYPE 172 19 122 175 9 325

Figure S173.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'RACE'

P value = 0.0756 (Fisher's exact test), Q value = 0.17

Table S174.  Gene #37: '20q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
20Q GAIN MUTATED 0 10 18 227
20Q GAIN WILD-TYPE 1 11 53 730

Figure S174.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'RACE'

'20q gain' versus 'ETHNICITY'

P value = 0.106 (Fisher's exact test), Q value = 0.23

Table S175.  Gene #37: '20q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
20Q GAIN MUTATED 6 228
20Q GAIN WILD-TYPE 38 691

Figure S175.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'ETHNICITY'

'21q gain' versus 'Time to Death'

P value = 0.00555 (logrank test), Q value = 0.019

Table S176.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
21Q GAIN MUTATED 87 64 0.2 - 211.2 (14.4)
21Q GAIN WILD-TYPE 992 527 0.0 - 182.3 (15.9)

Figure S176.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 1.59e-06 (Wilcoxon-test), Q value = 1.9e-05

Table S177.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
21Q GAIN MUTATED 87 58.6 (14.4)
21Q GAIN WILD-TYPE 995 50.1 (15.7)

Figure S177.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000121 (Fisher's exact test), Q value = 0.00062

Table S178.  Gene #38: '21q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
21Q GAIN MUTATED 63 24
21Q GAIN WILD-TYPE 508 488

Figure S178.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'21q gain' versus 'RADIATION_THERAPY'

P value = 0.0175 (Fisher's exact test), Q value = 0.052

Table S179.  Gene #38: '21q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
21Q GAIN MUTATED 12 71
21Q GAIN WILD-TYPE 246 696

Figure S179.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00162 (Fisher's exact test), Q value = 0.0067

Table S180.  Gene #38: '21q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
21Q GAIN MUTATED 9 6 5 10 1 56
21Q GAIN WILD-TYPE 185 22 124 179 17 469

Figure S180.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RACE'

P value = 0.0927 (Fisher's exact test), Q value = 0.2

Table S181.  Gene #38: '21q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
21Q GAIN MUTATED 0 5 6 75
21Q GAIN WILD-TYPE 1 16 65 882

Figure S181.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'RACE'

'21q gain' versus 'ETHNICITY'

P value = 0.044 (Fisher's exact test), Q value = 0.11

Table S182.  Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
21Q GAIN MUTATED 0 80
21Q GAIN WILD-TYPE 44 839

Figure S182.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.111 (Wilcoxon-test), Q value = 0.23

Table S183.  Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
22Q GAIN MUTATED 55 54.3 (15.0)
22Q GAIN WILD-TYPE 1027 50.6 (15.8)

Figure S183.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0365 (Wilcoxon-test), Q value = 0.099

Table S184.  Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
22Q GAIN MUTATED 32 76.9 (12.0)
22Q GAIN WILD-TYPE 698 81.5 (14.8)

Figure S184.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0163 (Fisher's exact test), Q value = 0.049

Table S185.  Gene #39: '22q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
22Q GAIN MUTATED 3 0 4 16 0 32
22Q GAIN WILD-TYPE 191 28 125 173 18 493

Figure S185.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'ETHNICITY'

P value = 0.0577 (Fisher's exact test), Q value = 0.14

Table S186.  Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
22Q GAIN MUTATED 5 42
22Q GAIN WILD-TYPE 39 877

Figure S186.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

'xq gain' versus 'Time to Death'

P value = 0.00655 (logrank test), Q value = 0.022

Table S187.  Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
XQ GAIN MUTATED 58 22 0.1 - 130.8 (20.0)
XQ GAIN WILD-TYPE 1021 569 0.0 - 211.2 (15.3)

Figure S187.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.000332 (Wilcoxon-test), Q value = 0.0016

Table S188.  Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
XQ GAIN MUTATED 58 43.6 (16.0)
XQ GAIN WILD-TYPE 1024 51.2 (15.7)

Figure S188.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000357 (Fisher's exact test), Q value = 0.0017

Table S189.  Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
XQ GAIN MUTATED 17 41
XQ GAIN WILD-TYPE 554 471

Figure S189.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq gain' versus 'GENDER'

P value = 0.0748 (Fisher's exact test), Q value = 0.17

Table S190.  Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
XQ GAIN MUTATED 31 27
XQ GAIN WILD-TYPE 421 604

Figure S190.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.036 (Wilcoxon-test), Q value = 0.098

Table S191.  Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
XQ GAIN MUTATED 32 86.2 (12.6)
XQ GAIN WILD-TYPE 698 81.1 (14.7)

Figure S191.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S192.  Gene #41: 'xq gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
XQ GAIN MUTATED 20 1 15 6 1 15
XQ GAIN WILD-TYPE 174 27 114 183 17 510

Figure S192.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.000948 (Fisher's exact test), Q value = 0.0041

Table S193.  Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
XQ GAIN MUTATED 8 40
XQ GAIN WILD-TYPE 36 879

Figure S193.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

'1p loss' versus 'Time to Death'

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

Table S194.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
1P LOSS MUTATED 196 40 0.1 - 182.3 (21.5)
1P LOSS WILD-TYPE 883 551 0.0 - 211.2 (14.9)

Figure S194.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 5.33e-05 (Wilcoxon-test), Q value = 3e-04

Table S195.  Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
1P LOSS MUTATED 197 46.8 (13.6)
1P LOSS WILD-TYPE 885 51.7 (16.1)

Figure S195.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.49e-50 (Fisher's exact test), Q value = 1.4e-48

Table S196.  Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
1P LOSS MUTATED 15 183
1P LOSS WILD-TYPE 556 329

Figure S196.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1p loss' versus 'RADIATION_THERAPY'

P value = 2.29e-18 (Fisher's exact test), Q value = 6e-17

Table S197.  Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
1P LOSS MUTATED 96 89
1P LOSS WILD-TYPE 162 678

Figure S197.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5e-06 (Wilcoxon-test), Q value = 4.9e-05

Table S198.  Gene #42: '1p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
1P LOSS MUTATED 120 86.4 (13.0)
1P LOSS WILD-TYPE 610 80.3 (14.8)

Figure S198.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S199.  Gene #42: '1p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
1P LOSS MUTATED 10 0 40 133 1 14
1P LOSS WILD-TYPE 184 28 89 56 17 511

Figure S199.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'RACE'

P value = 0.0889 (Fisher's exact test), Q value = 0.2

Table S200.  Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
1P LOSS MUTATED 0 5 6 180
1P LOSS WILD-TYPE 1 16 65 777

Figure S200.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

'1q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00777 (Fisher's exact test), Q value = 0.026

Table S201.  Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
1Q LOSS MUTATED 14 29
1Q LOSS WILD-TYPE 557 483

Figure S201.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00126 (Fisher's exact test), Q value = 0.0053

Table S202.  Gene #43: '1q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
1Q LOSS MUTATED 4 0 6 19 0 14
1Q LOSS WILD-TYPE 190 28 123 170 18 511

Figure S202.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0632 (Wilcoxon-test), Q value = 0.15

Table S203.  Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
2P LOSS MUTATED 54 54.5 (17.0)
2P LOSS WILD-TYPE 1028 50.6 (15.7)

Figure S203.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.119 (Fisher's exact test), Q value = 0.25

Table S204.  Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
2Q LOSS MUTATED 33 19
2Q LOSS WILD-TYPE 538 493

Figure S204.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0645 (Fisher's exact test), Q value = 0.16

Table S205.  Gene #45: '2q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
2Q LOSS MUTATED 12 3 4 3 1 29
2Q LOSS WILD-TYPE 182 25 125 186 17 496

Figure S205.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RADIATION_THERAPY'

P value = 0.02 (Fisher's exact test), Q value = 0.059

Table S206.  Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
3P LOSS MUTATED 9 58
3P LOSS WILD-TYPE 249 709

Figure S206.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0289 (Wilcoxon-test), Q value = 0.081

Table S207.  Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
3P LOSS MUTATED 53 77.7 (13.1)
3P LOSS WILD-TYPE 677 81.6 (14.8)

Figure S207.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'RADIATION_THERAPY'

P value = 0.088 (Fisher's exact test), Q value = 0.2

Table S208.  Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
3Q LOSS MUTATED 9 50
3Q LOSS WILD-TYPE 249 717

Figure S208.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4p loss' versus 'Time to Death'

P value = 0.0465 (logrank test), Q value = 0.12

Table S209.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
4P LOSS MUTATED 126 63 0.1 - 139.0 (17.9)
4P LOSS WILD-TYPE 953 528 0.0 - 211.2 (15.2)

Figure S209.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0365 (Fisher's exact test), Q value = 0.099

Table S210.  Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
4P LOSS MUTATED 55 71
4P LOSS WILD-TYPE 516 441

Figure S210.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4p loss' versus 'GENDER'

P value = 0.0163 (Fisher's exact test), Q value = 0.049

Table S211.  Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
4P LOSS MUTATED 40 86
4P LOSS WILD-TYPE 412 545

Figure S211.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0016

Table S212.  Gene #48: '4p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
4P LOSS MUTATED 13 2 19 39 0 53
4P LOSS WILD-TYPE 181 26 110 150 18 472

Figure S212.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 5.27e-05 (logrank test), Q value = 3e-04

Table S213.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
4Q LOSS MUTATED 150 62 0.1 - 156.2 (20.9)
4Q LOSS WILD-TYPE 929 529 0.0 - 211.2 (15.0)

Figure S213.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0336 (Wilcoxon-test), Q value = 0.093

Table S214.  Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
4Q LOSS MUTATED 150 48.3 (14.4)
4Q LOSS WILD-TYPE 932 51.2 (16.0)

Figure S214.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000102 (Fisher's exact test), Q value = 0.00054

Table S215.  Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
4Q LOSS MUTATED 57 93
4Q LOSS WILD-TYPE 514 419

Figure S215.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.0747 (Fisher's exact test), Q value = 0.17

Table S216.  Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
4Q LOSS MUTATED 44 96
4Q LOSS WILD-TYPE 214 671

Figure S216.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.00057

Table S217.  Gene #49: '4q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
4Q LOSS MUTATED 24 3 23 46 1 53
4Q LOSS WILD-TYPE 170 25 106 143 17 472

Figure S217.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00209 (Fisher's exact test), Q value = 0.0083

Table S218.  Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
5P LOSS MUTATED 8 66
5P LOSS WILD-TYPE 250 701

Figure S218.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0621 (Fisher's exact test), Q value = 0.15

Table S219.  Gene #50: '5p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
5P LOSS MUTATED 19 1 11 5 1 42
5P LOSS WILD-TYPE 175 27 118 184 17 483

Figure S219.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00106 (Fisher's exact test), Q value = 0.0045

Table S220.  Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
5Q LOSS MUTATED 7 65
5Q LOSS WILD-TYPE 251 702

Figure S220.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6p loss' versus 'Time to Death'

P value = 6.18e-13 (logrank test), Q value = 1.3e-11

Table S221.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
6P LOSS MUTATED 116 89 0.2 - 92.7 (10.7)
6P LOSS WILD-TYPE 963 502 0.0 - 211.2 (16.4)

Figure S221.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 5.53e-05 (Wilcoxon-test), Q value = 0.00031

Table S222.  Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
6P LOSS MUTATED 116 56.2 (14.8)
6P LOSS WILD-TYPE 966 50.1 (15.8)

Figure S222.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.83e-06 (Fisher's exact test), Q value = 3.1e-05

Table S223.  Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
6P LOSS MUTATED 85 31
6P LOSS WILD-TYPE 486 481

Figure S223.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0529 (Wilcoxon-test), Q value = 0.13

Table S224.  Gene #52: '6p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
6P LOSS MUTATED 85 78.6 (15.1)
6P LOSS WILD-TYPE 645 81.6 (14.6)

Figure S224.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00043

Table S225.  Gene #52: '6p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
6P LOSS MUTATED 15 3 4 12 3 79
6P LOSS WILD-TYPE 179 25 125 177 15 446

Figure S225.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RACE'

P value = 0.0411 (Fisher's exact test), Q value = 0.11

Table S226.  Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
6P LOSS MUTATED 1 4 10 98
6P LOSS WILD-TYPE 0 17 61 859

Figure S226.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'Time to Death'

P value = 1.86e-08 (logrank test), Q value = 2.6e-07

Table S227.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
6Q LOSS MUTATED 186 125 0.1 - 94.8 (13.4)
6Q LOSS WILD-TYPE 893 466 0.0 - 211.2 (16.5)

Figure S227.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000893 (Wilcoxon-test), Q value = 0.0039

Table S228.  Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
6Q LOSS MUTATED 187 54.2 (15.0)
6Q LOSS WILD-TYPE 895 50.1 (15.9)

Figure S228.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.23e-05 (Fisher's exact test), Q value = 3e-04

Table S229.  Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
6Q LOSS MUTATED 124 63
6Q LOSS WILD-TYPE 447 449

Figure S229.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0683 (Fisher's exact test), Q value = 0.16

Table S230.  Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
6Q LOSS MUTATED 34 140
6Q LOSS WILD-TYPE 224 627

Figure S230.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0043 (Wilcoxon-test), Q value = 0.015

Table S231.  Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
6Q LOSS MUTATED 135 78.6 (14.1)
6Q LOSS WILD-TYPE 595 81.9 (14.8)

Figure S231.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S232.  Gene #53: '6q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
6Q LOSS MUTATED 37 5 10 16 4 115
6Q LOSS WILD-TYPE 157 23 119 173 14 410

Figure S232.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0165 (Fisher's exact test), Q value = 0.05

Table S233.  Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
6Q LOSS MUTATED 1 6 18 156
6Q LOSS WILD-TYPE 0 15 53 801

Figure S233.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'ETHNICITY'

P value = 0.0951 (Fisher's exact test), Q value = 0.21

Table S234.  Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
6Q LOSS MUTATED 3 158
6Q LOSS WILD-TYPE 41 761

Figure S234.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

'7q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0928 (Wilcoxon-test), Q value = 0.2

Table S235.  Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
7Q LOSS MUTATED 9 41.6 (17.8)
7Q LOSS WILD-TYPE 1073 50.9 (15.8)

Figure S235.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'Time to Death'

P value = 8.86e-05 (logrank test), Q value = 0.00047

Table S236.  Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
8P LOSS MUTATED 73 51 0.2 - 120.6 (11.7)
8P LOSS WILD-TYPE 1006 540 0.0 - 211.2 (16.0)

Figure S236.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000135 (Wilcoxon-test), Q value = 0.00068

Table S237.  Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
8P LOSS MUTATED 74 57.4 (14.2)
8P LOSS WILD-TYPE 1008 50.3 (15.8)

Figure S237.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.11e-06 (Fisher's exact test), Q value = 3.3e-05

Table S238.  Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
8P LOSS MUTATED 58 16
8P LOSS WILD-TYPE 513 496

Figure S238.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8p loss' versus 'RADIATION_THERAPY'

P value = 0.006 (Fisher's exact test), Q value = 0.021

Table S239.  Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
8P LOSS MUTATED 8 61
8P LOSS WILD-TYPE 250 706

Figure S239.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 8e-04

Table S240.  Gene #56: '8p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
8P LOSS MUTATED 8 1 4 4 1 56
8P LOSS WILD-TYPE 186 27 125 185 17 469

Figure S240.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.00588 (Fisher's exact test), Q value = 0.02

Table S241.  Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
8P LOSS MUTATED 0 6 4 59
8P LOSS WILD-TYPE 1 15 67 898

Figure S241.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

'8q loss' versus 'Time to Death'

P value = 4.89e-06 (logrank test), Q value = 4.9e-05

Table S242.  Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
8Q LOSS MUTATED 52 38 0.2 - 58.8 (11.6)
8Q LOSS WILD-TYPE 1027 553 0.0 - 211.2 (16.0)

Figure S242.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000298 (Wilcoxon-test), Q value = 0.0015

Table S243.  Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
8Q LOSS MUTATED 52 58.5 (12.7)
8Q LOSS WILD-TYPE 1030 50.4 (15.8)

Figure S243.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.16e-05 (Fisher's exact test), Q value = 0.00048

Table S244.  Gene #57: '8q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
8Q LOSS MUTATED 41 11
8Q LOSS WILD-TYPE 530 501

Figure S244.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8q loss' versus 'RADIATION_THERAPY'

P value = 0.016 (Fisher's exact test), Q value = 0.049

Table S245.  Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
8Q LOSS MUTATED 5 43
8Q LOSS WILD-TYPE 253 724

Figure S245.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00516 (Fisher's exact test), Q value = 0.018

Table S246.  Gene #57: '8q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
8Q LOSS MUTATED 5 1 3 3 1 39
8Q LOSS WILD-TYPE 189 27 126 186 17 486

Figure S246.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'Time to Death'

P value = 3.06e-05 (logrank test), Q value = 0.00019

Table S247.  Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
9P LOSS MUTATED 313 205 0.1 - 169.8 (14.9)
9P LOSS WILD-TYPE 766 386 0.0 - 211.2 (16.0)

Figure S247.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000103 (Wilcoxon-test), Q value = 0.00054

Table S248.  Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
9P LOSS MUTATED 314 53.7 (15.3)
9P LOSS WILD-TYPE 768 49.6 (15.8)

Figure S248.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.00015

Table S249.  Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
9P LOSS MUTATED 198 117
9P LOSS WILD-TYPE 373 395

Figure S249.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000619 (Fisher's exact test), Q value = 0.0028

Table S250.  Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
9P LOSS MUTATED 53 243
9P LOSS WILD-TYPE 205 524

Figure S250.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0417 (Wilcoxon-test), Q value = 0.11

Table S251.  Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
9P LOSS MUTATED 212 79.3 (16.0)
9P LOSS WILD-TYPE 518 82.1 (14.1)

Figure S251.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00043

Table S252.  Gene #58: '9p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
9P LOSS MUTATED 56 11 23 38 5 182
9P LOSS WILD-TYPE 138 17 106 151 13 343

Figure S252.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RACE'

P value = 0.119 (Fisher's exact test), Q value = 0.25

Table S253.  Gene #58: '9p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
9P LOSS MUTATED 0 8 28 270
9P LOSS WILD-TYPE 1 13 43 687

Figure S253.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #8: 'RACE'

'9p loss' versus 'ETHNICITY'

P value = 0.0603 (Fisher's exact test), Q value = 0.15

Table S254.  Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
9P LOSS MUTATED 7 272
9P LOSS WILD-TYPE 37 647

Figure S254.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

'9q loss' versus 'Time to Death'

P value = 0.00353 (logrank test), Q value = 0.013

Table S255.  Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
9Q LOSS MUTATED 141 95 0.1 - 169.8 (14.5)
9Q LOSS WILD-TYPE 938 496 0.0 - 211.2 (16.0)

Figure S255.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00298 (Wilcoxon-test), Q value = 0.011

Table S256.  Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
9Q LOSS MUTATED 142 54.1 (15.6)
9Q LOSS WILD-TYPE 940 50.3 (15.8)

Figure S256.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00678 (Fisher's exact test), Q value = 0.023

Table S257.  Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
9Q LOSS MUTATED 90 52
9Q LOSS WILD-TYPE 481 460

Figure S257.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q loss' versus 'RADIATION_THERAPY'

P value = 0.000688 (Fisher's exact test), Q value = 0.0031

Table S258.  Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
9Q LOSS MUTATED 17 110
9Q LOSS WILD-TYPE 241 657

Figure S258.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00113 (Wilcoxon-test), Q value = 0.0048

Table S259.  Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
9Q LOSS MUTATED 95 76.8 (14.7)
9Q LOSS WILD-TYPE 635 82.0 (14.6)

Figure S259.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0628 (Fisher's exact test), Q value = 0.15

Table S260.  Gene #59: '9q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
9Q LOSS MUTATED 22 7 11 19 3 80
9Q LOSS WILD-TYPE 172 21 118 170 15 445

Figure S260.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

P value = 0.0386 (Fisher's exact test), Q value = 0.1

Table S261.  Gene #59: '9q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
9Q LOSS MUTATED 0 3 17 117
9Q LOSS WILD-TYPE 1 18 54 840

Figure S261.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'Time to Death'

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

Table S262.  Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
10P LOSS MUTATED 556 446 0.1 - 134.3 (12.3)
10P LOSS WILD-TYPE 523 145 0.0 - 211.2 (21.1)

Figure S262.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 4.56e-74 (Wilcoxon-test), Q value = 2.6e-72

Table S263.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
10P LOSS MUTATED 557 59.1 (12.4)
10P LOSS WILD-TYPE 525 42.0 (14.1)

Figure S263.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.18e-116 (Fisher's exact test), Q value = 3.8e-114

Table S264.  Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
10P LOSS MUTATED 474 83
10P LOSS WILD-TYPE 97 429

Figure S264.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10p loss' versus 'GENDER'

P value = 0.0843 (Fisher's exact test), Q value = 0.19

Table S265.  Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
10P LOSS MUTATED 218 339
10P LOSS WILD-TYPE 234 292

Figure S265.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

'10p loss' versus 'RADIATION_THERAPY'

P value = 1.95e-15 (Fisher's exact test), Q value = 4.6e-14

Table S266.  Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
10P LOSS MUTATED 78 451
10P LOSS WILD-TYPE 180 316

Figure S266.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.54e-19 (Wilcoxon-test), Q value = 1.9e-17

Table S267.  Gene #60: '10p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
10P LOSS MUTATED 407 77.3 (15.3)
10P LOSS WILD-TYPE 323 86.3 (12.1)

Figure S267.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S268.  Gene #60: '10p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
10P LOSS MUTATED 49 21 16 18 10 443
10P LOSS WILD-TYPE 145 7 113 171 8 82

Figure S268.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00286 (Fisher's exact test), Q value = 0.011

Table S269.  Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
10P LOSS MUTATED 1 9 50 476
10P LOSS WILD-TYPE 0 12 21 481

Figure S269.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'ETHNICITY'

P value = 0.003 (Fisher's exact test), Q value = 0.011

Table S270.  Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
10P LOSS MUTATED 12 465
10P LOSS WILD-TYPE 32 454

Figure S270.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

'10q loss' versus 'Time to Death'

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

Table S271.  Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
10Q LOSS MUTATED 584 461 0.1 - 172.8 (12.6)
10Q LOSS WILD-TYPE 495 130 0.0 - 211.2 (21.4)

Figure S271.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 4.63e-68 (Wilcoxon-test), Q value = 2.3e-66

Table S272.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
10Q LOSS MUTATED 585 58.3 (13.1)
10Q LOSS WILD-TYPE 497 41.9 (13.9)

Figure S272.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.12e-115 (Fisher's exact test), Q value = 2.1e-113

Table S273.  Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
10Q LOSS MUTATED 488 97
10Q LOSS WILD-TYPE 83 415

Figure S273.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10q loss' versus 'RADIATION_THERAPY'

P value = 1.37e-18 (Fisher's exact test), Q value = 3.7e-17

Table S274.  Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
10Q LOSS MUTATED 79 477
10Q LOSS WILD-TYPE 179 290

Figure S274.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.65e-20 (Wilcoxon-test), Q value = 4.9e-19

Table S275.  Gene #61: '10q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
10Q LOSS MUTATED 426 77.3 (15.3)
10Q LOSS WILD-TYPE 304 86.9 (11.6)

Figure S275.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S276.  Gene #61: '10q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
10Q LOSS MUTATED 57 21 19 21 13 454
10Q LOSS WILD-TYPE 137 7 110 168 5 71

Figure S276.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.00344 (Fisher's exact test), Q value = 0.013

Table S277.  Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
10Q LOSS MUTATED 1 9 51 502
10Q LOSS WILD-TYPE 0 12 20 455

Figure S277.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

'10q loss' versus 'ETHNICITY'

P value = 0.000958 (Fisher's exact test), Q value = 0.0042

Table S278.  Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
10Q LOSS MUTATED 12 492
10Q LOSS WILD-TYPE 32 427

Figure S278.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

'11p loss' versus 'Time to Death'

P value = 0.12 (logrank test), Q value = 0.25

Table S279.  Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
11P LOSS MUTATED 163 106 0.2 - 156.2 (16.5)
11P LOSS WILD-TYPE 916 485 0.0 - 211.2 (15.4)

Figure S279.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0271 (Fisher's exact test), Q value = 0.077

Table S280.  Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
11P LOSS MUTATED 99 64
11P LOSS WILD-TYPE 472 448

Figure S280.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p loss' versus 'GENDER'

P value = 0.031 (Fisher's exact test), Q value = 0.086

Table S281.  Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
11P LOSS MUTATED 81 82
11P LOSS WILD-TYPE 371 549

Figure S281.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.00885 (Fisher's exact test), Q value = 0.029

Table S282.  Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
11P LOSS MUTATED 26 129
11P LOSS WILD-TYPE 232 638

Figure S282.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0016

Table S283.  Gene #62: '11p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
11P LOSS MUTATED 38 4 14 12 5 90
11P LOSS WILD-TYPE 156 24 115 177 13 435

Figure S283.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 1.07e-09 (logrank test), Q value = 1.8e-08

Table S284.  Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
11Q LOSS MUTATED 113 90 0.2 - 92.7 (13.3)
11Q LOSS WILD-TYPE 966 501 0.0 - 211.2 (16.0)

Figure S284.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 5.43e-06 (Wilcoxon-test), Q value = 5.2e-05

Table S285.  Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
11Q LOSS MUTATED 113 57.0 (14.2)
11Q LOSS WILD-TYPE 969 50.1 (15.8)

Figure S285.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.34e-10 (Fisher's exact test), Q value = 2.3e-09

Table S286.  Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
11Q LOSS MUTATED 91 22
11Q LOSS WILD-TYPE 480 490

Figure S286.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.0186 (Fisher's exact test), Q value = 0.055

Table S287.  Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
11Q LOSS MUTATED 17 91
11Q LOSS WILD-TYPE 241 676

Figure S287.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0448 (Wilcoxon-test), Q value = 0.12

Table S288.  Gene #63: '11q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
11Q LOSS MUTATED 87 78.9 (13.9)
11Q LOSS WILD-TYPE 643 81.6 (14.8)

Figure S288.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S289.  Gene #63: '11q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
11Q LOSS MUTATED 14 3 6 2 3 85
11Q LOSS WILD-TYPE 180 25 123 187 15 440

Figure S289.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'ETHNICITY'

P value = 0.117 (Fisher's exact test), Q value = 0.25

Table S290.  Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
11Q LOSS MUTATED 1 96
11Q LOSS WILD-TYPE 43 823

Figure S290.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

'12p loss' versus 'Time to Death'

P value = 0.00955 (logrank test), Q value = 0.031

Table S291.  Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
12P LOSS MUTATED 85 57 0.1 - 95.1 (14.9)
12P LOSS WILD-TYPE 994 534 0.0 - 211.2 (15.8)

Figure S291.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'YEARS_TO_BIRTH'

P value = 0.108 (Wilcoxon-test), Q value = 0.23

Table S292.  Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
12P LOSS MUTATED 86 53.3 (16.6)
12P LOSS WILD-TYPE 996 50.6 (15.7)

Figure S292.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00475 (Fisher's exact test), Q value = 0.017

Table S293.  Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
12P LOSS MUTATED 58 28
12P LOSS WILD-TYPE 513 484

Figure S293.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0156 (Fisher's exact test), Q value = 0.048

Table S294.  Gene #64: '12p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
12P LOSS MUTATED 16 1 5 7 2 55
12P LOSS WILD-TYPE 178 27 124 182 16 470

Figure S294.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0177 (Fisher's exact test), Q value = 0.053

Table S295.  Gene #65: '12q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
12Q LOSS MUTATED 30 1 13 10 3 52
12Q LOSS WILD-TYPE 164 27 116 179 15 473

Figure S295.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.0399 (Fisher's exact test), Q value = 0.11

Table S296.  Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
12Q LOSS MUTATED 0 0 2 104
12Q LOSS WILD-TYPE 1 21 69 853

Figure S296.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

'13q loss' versus 'Time to Death'

P value = 0.00301 (logrank test), Q value = 0.011

Table S297.  Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
13Q LOSS MUTATED 297 188 0.1 - 211.2 (15.0)
13Q LOSS WILD-TYPE 782 403 0.0 - 182.3 (16.2)

Figure S297.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0579 (Wilcoxon-test), Q value = 0.14

Table S298.  Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
13Q LOSS MUTATED 297 52.2 (15.7)
13Q LOSS WILD-TYPE 785 50.2 (15.8)

Figure S298.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000129 (Fisher's exact test), Q value = 0.00065

Table S299.  Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
13Q LOSS MUTATED 185 112
13Q LOSS WILD-TYPE 386 400

Figure S299.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.0203 (Fisher's exact test), Q value = 0.059

Table S300.  Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
13Q LOSS MUTATED 58 231
13Q LOSS WILD-TYPE 200 536

Figure S300.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.11 (Wilcoxon-test), Q value = 0.23

Table S301.  Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
13Q LOSS MUTATED 211 80.0 (14.6)
13Q LOSS WILD-TYPE 519 81.8 (14.7)

Figure S301.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00362 (Fisher's exact test), Q value = 0.013

Table S302.  Gene #66: '13q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
13Q LOSS MUTATED 48 8 25 39 4 173
13Q LOSS WILD-TYPE 146 20 104 150 14 352

Figure S302.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 2.68e-05 (logrank test), Q value = 0.00017

Table S303.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
14Q LOSS MUTATED 223 148 0.1 - 130.8 (14.7)
14Q LOSS WILD-TYPE 856 443 0.0 - 211.2 (16.2)

Figure S303.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 3.71e-05 (Wilcoxon-test), Q value = 0.00022

Table S304.  Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
14Q LOSS MUTATED 224 54.6 (14.9)
14Q LOSS WILD-TYPE 858 49.8 (15.9)

Figure S304.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'TUMOR_TISSUE_SITE'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.00035

Table S305.  Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
14Q LOSS MUTATED 145 79
14Q LOSS WILD-TYPE 426 433

Figure S305.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0287 (Wilcoxon-test), Q value = 0.081

Table S306.  Gene #67: '14q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
14Q LOSS MUTATED 164 79.6 (14.1)
14Q LOSS WILD-TYPE 566 81.8 (14.8)

Figure S306.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00109 (Fisher's exact test), Q value = 0.0046

Table S307.  Gene #67: '14q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
14Q LOSS MUTATED 36 5 18 25 6 134
14Q LOSS WILD-TYPE 158 23 111 164 12 391

Figure S307.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 0.0506 (Fisher's exact test), Q value = 0.13

Table S308.  Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
14Q LOSS MUTATED 1 5 21 190
14Q LOSS WILD-TYPE 0 16 50 767

Figure S308.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

'14q loss' versus 'ETHNICITY'

P value = 0.0803 (Fisher's exact test), Q value = 0.18

Table S309.  Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
14Q LOSS MUTATED 4 187
14Q LOSS WILD-TYPE 40 732

Figure S309.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

'15q loss' versus 'Time to Death'

P value = 0.00238 (logrank test), Q value = 0.0093

Table S310.  Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
15Q LOSS MUTATED 154 102 0.2 - 134.3 (15.2)
15Q LOSS WILD-TYPE 925 489 0.0 - 211.2 (15.8)

Figure S310.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000125 (Wilcoxon-test), Q value = 0.00064

Table S311.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
15Q LOSS MUTATED 155 55.3 (15.9)
15Q LOSS WILD-TYPE 927 50.0 (15.6)

Figure S311.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.00025

Table S312.  Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
15Q LOSS MUTATED 106 50
15Q LOSS WILD-TYPE 465 462

Figure S312.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00098 (Fisher's exact test), Q value = 0.0042

Table S313.  Gene #68: '15q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
15Q LOSS MUTATED 16 7 12 22 2 97
15Q LOSS WILD-TYPE 178 21 117 167 16 428

Figure S313.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 4.29e-07 (logrank test), Q value = 5.5e-06

Table S314.  Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
16P LOSS MUTATED 78 63 0.4 - 78.3 (13.9)
16P LOSS WILD-TYPE 1001 528 0.0 - 211.2 (15.9)

Figure S314.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 3.84e-06 (Wilcoxon-test), Q value = 4e-05

Table S315.  Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
16P LOSS MUTATED 78 58.6 (14.2)
16P LOSS WILD-TYPE 1004 50.2 (15.7)

Figure S315.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.21e-07 (Fisher's exact test), Q value = 1.6e-06

Table S316.  Gene #69: '16p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
16P LOSS MUTATED 63 15
16P LOSS WILD-TYPE 508 497

Figure S316.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S317.  Gene #69: '16p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
16P LOSS MUTATED 8 1 3 4 0 62
16P LOSS WILD-TYPE 186 27 126 185 18 463

Figure S317.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 1.44e-07 (logrank test), Q value = 1.9e-06

Table S318.  Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
16Q LOSS MUTATED 104 83 0.2 - 120.6 (14.3)
16Q LOSS WILD-TYPE 975 508 0.0 - 211.2 (16.0)

Figure S318.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 2.45e-05 (Wilcoxon-test), Q value = 0.00016

Table S319.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
16Q LOSS MUTATED 104 56.9 (14.4)
16Q LOSS WILD-TYPE 978 50.1 (15.8)

Figure S319.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.2e-08 (Fisher's exact test), Q value = 1.7e-07

Table S320.  Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
16Q LOSS MUTATED 82 22
16Q LOSS WILD-TYPE 489 490

Figure S320.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.037 (Fisher's exact test), Q value = 0.1

Table S321.  Gene #70: '16q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
16Q LOSS MUTATED 16 82
16Q LOSS WILD-TYPE 242 685

Figure S321.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S322.  Gene #70: '16q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
16Q LOSS MUTATED 11 2 5 6 1 79
16Q LOSS WILD-TYPE 183 26 124 183 17 446

Figure S322.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'Time to Death'

P value = 2.09e-05 (logrank test), Q value = 0.00014

Table S323.  Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
17P LOSS MUTATED 75 53 0.1 - 92.7 (12.2)
17P LOSS WILD-TYPE 1004 538 0.0 - 211.2 (16.0)

Figure S323.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000391 (Wilcoxon-test), Q value = 0.0018

Table S324.  Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
17P LOSS MUTATED 75 57.0 (14.4)
17P LOSS WILD-TYPE 1007 50.3 (15.8)

Figure S324.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.92e-08 (Fisher's exact test), Q value = 4.1e-07

Table S325.  Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
17P LOSS MUTATED 62 13
17P LOSS WILD-TYPE 509 499

Figure S325.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00669 (Wilcoxon-test), Q value = 0.023

Table S326.  Gene #71: '17p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
17P LOSS MUTATED 53 77.4 (12.3)
17P LOSS WILD-TYPE 677 81.6 (14.8)

Figure S326.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S327.  Gene #71: '17p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
17P LOSS MUTATED 6 3 2 5 1 58
17P LOSS WILD-TYPE 188 25 127 184 17 467

Figure S327.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 3.34e-05 (logrank test), Q value = 2e-04

Table S328.  Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
17Q LOSS MUTATED 49 36 0.1 - 92.7 (11.7)
17Q LOSS WILD-TYPE 1030 555 0.0 - 211.2 (16.0)

Figure S328.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000848 (Wilcoxon-test), Q value = 0.0038

Table S329.  Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
17Q LOSS MUTATED 49 57.9 (13.6)
17Q LOSS WILD-TYPE 1033 50.4 (15.8)

Figure S329.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.86e-06 (Fisher's exact test), Q value = 5.5e-05

Table S330.  Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
17Q LOSS MUTATED 41 8
17Q LOSS WILD-TYPE 530 504

Figure S330.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0691 (Wilcoxon-test), Q value = 0.16

Table S331.  Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
17Q LOSS MUTATED 33 78.2 (11.8)
17Q LOSS WILD-TYPE 697 81.4 (14.8)

Figure S331.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0022

Table S332.  Gene #72: '17q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
17Q LOSS MUTATED 3 2 1 4 1 38
17Q LOSS WILD-TYPE 191 26 128 185 17 487

Figure S332.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0942 (Wilcoxon-test), Q value = 0.2

Table S333.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
18P LOSS MUTATED 137 52.8 (15.8)
18P LOSS WILD-TYPE 945 50.5 (15.8)

Figure S333.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.118 (Wilcoxon-test), Q value = 0.25

Table S334.  Gene #75: '19p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
19P LOSS MUTATED 44 85.0 (13.0)
19P LOSS WILD-TYPE 686 81.0 (14.8)

Figure S334.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q loss' versus 'Time to Death'

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

Table S335.  Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
19Q LOSS MUTATED 242 68 0.1 - 182.3 (21.0)
19Q LOSS WILD-TYPE 837 523 0.0 - 211.2 (14.5)

Figure S335.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 1.17e-08 (Wilcoxon-test), Q value = 1.7e-07

Table S336.  Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
19Q LOSS MUTATED 243 45.9 (13.5)
19Q LOSS WILD-TYPE 839 52.2 (16.1)

Figure S336.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.61e-46 (Fisher's exact test), Q value = 2.2e-44

Table S337.  Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
19Q LOSS MUTATED 34 210
19Q LOSS WILD-TYPE 537 302

Figure S337.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19q loss' versus 'RADIATION_THERAPY'

P value = 1.05e-13 (Fisher's exact test), Q value = 2.3e-12

Table S338.  Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
19Q LOSS MUTATED 102 125
19Q LOSS WILD-TYPE 156 642

Figure S338.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.53e-06 (Wilcoxon-test), Q value = 3.7e-05

Table S339.  Gene #76: '19q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
19Q LOSS MUTATED 158 85.6 (13.2)
19Q LOSS WILD-TYPE 572 80.1 (14.9)

Figure S339.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S340.  Gene #76: '19q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
19Q LOSS MUTATED 23 2 44 143 2 30
19Q LOSS WILD-TYPE 171 26 85 46 16 495

Figure S340.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'ETHNICITY'

P value = 0.0096 (Fisher's exact test), Q value = 0.031

Table S341.  Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
19Q LOSS MUTATED 18 208
19Q LOSS WILD-TYPE 26 711

Figure S341.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

'20p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0455 (Fisher's exact test), Q value = 0.12

Table S342.  Gene #77: '20p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
20P LOSS MUTATED 19 7
20P LOSS WILD-TYPE 552 505

Figure S342.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p loss' versus 'GENDER'

P value = 0.109 (Fisher's exact test), Q value = 0.23

Table S343.  Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
20P LOSS MUTATED 15 11
20P LOSS WILD-TYPE 437 620

Figure S343.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.115 (Fisher's exact test), Q value = 0.24

Table S344.  Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
20P LOSS MUTATED 3 23
20P LOSS WILD-TYPE 255 744

Figure S344.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'RACE'

P value = 0.0667 (Fisher's exact test), Q value = 0.16

Table S345.  Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 957
20P LOSS MUTATED 0 2 3 21
20P LOSS WILD-TYPE 1 19 68 936

Figure S345.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

'20q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0132 (Fisher's exact test), Q value = 0.041

Table S346.  Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
20Q LOSS MUTATED 17 4
20Q LOSS WILD-TYPE 554 508

Figure S346.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q loss' versus 'GENDER'

P value = 0.0733 (Fisher's exact test), Q value = 0.17

Table S347.  Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 452 631
20Q LOSS MUTATED 13 8
20Q LOSS WILD-TYPE 439 623

Figure S347.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0731 (Fisher's exact test), Q value = 0.17

Table S348.  Gene #78: '20q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
20Q LOSS MUTATED 2 1 2 0 0 16
20Q LOSS WILD-TYPE 192 27 127 189 18 509

Figure S348.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0646 (Fisher's exact test), Q value = 0.16

Table S349.  Gene #79: '21q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
21Q LOSS MUTATED 23 2 7 7 1 39
21Q LOSS WILD-TYPE 171 26 122 182 17 486

Figure S349.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 1.51e-14 (logrank test), Q value = 3.5e-13

Table S350.  Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
22Q LOSS MUTATED 240 182 0.1 - 156.2 (13.7)
22Q LOSS WILD-TYPE 839 409 0.0 - 211.2 (16.4)

Figure S350.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 4.7e-14 (Wilcoxon-test), Q value = 1.1e-12

Table S351.  Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1082 50.8 (15.8)
22Q LOSS MUTATED 240 57.4 (14.8)
22Q LOSS WILD-TYPE 842 48.9 (15.6)

Figure S351.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.14e-17 (Fisher's exact test), Q value = 1.1e-15

Table S352.  Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
22Q LOSS MUTATED 183 57
22Q LOSS WILD-TYPE 388 455

Figure S352.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.00133 (Fisher's exact test), Q value = 0.0055

Table S353.  Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 767
22Q LOSS MUTATED 39 189
22Q LOSS WILD-TYPE 219 578

Figure S353.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0064 (Wilcoxon-test), Q value = 0.022

Table S354.  Gene #80: '22q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
22Q LOSS MUTATED 169 79.1 (15.0)
22Q LOSS WILD-TYPE 561 82.0 (14.6)

Figure S354.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.3e-05

Table S355.  Gene #80: '22q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 28 129 189 18 525
22Q LOSS MUTATED 29 9 11 17 6 168
22Q LOSS WILD-TYPE 165 19 118 172 12 357

Figure S355.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'ETHNICITY'

P value = 0.121 (Fisher's exact test), Q value = 0.25

Table S356.  Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 919
XP LOSS MUTATED 13 179
XP LOSS WILD-TYPE 31 740

Figure S356.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

'xq loss' versus 'Time to Death'

P value = 0.0939 (logrank test), Q value = 0.2

Table S357.  Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1079 591 0.0 - 211.2 (15.7)
XQ LOSS MUTATED 173 101 0.1 - 134.3 (15.0)
XQ LOSS WILD-TYPE 906 490 0.0 - 211.2 (15.9)

Figure S357.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0467 (Fisher's exact test), Q value = 0.12

Table S358.  Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 571 512
XQ LOSS MUTATED 104 70
XQ LOSS WILD-TYPE 467 442

Figure S358.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0972 (Wilcoxon-test), Q value = 0.21

Table S359.  Gene #82: 'xq loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 730 81.3 (14.7)
XQ LOSS MUTATED 123 79.1 (15.9)
XQ LOSS WILD-TYPE 607 81.7 (14.4)

Figure S359.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/19791524/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/19775190/GBMLGG-TP.merged_data.txt

  • Number of patients = 1083

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 9

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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