Correlation between copy number variations of arm-level result and selected clinical features
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1FB5299
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1FB5299
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 1085 patients, 363 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',  'KARNOFSKY_PERFORMANCE_SCORE', 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',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  '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' 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',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

  • xp gain cnv correlated to 'Time to Death'.

  • 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 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', 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' and 'HISTOLOGICAL_TYPE'.

  • 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 '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', 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, 363 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 559 (52%) 526 0
(0) 		2.02e-74
(1.14e-72) 		1.94e-116
(1.43e-114) 		0.0846
(0.188) 		1.23e-15
(2.93e-14) 		2.7e-19
(7.65e-18) 		1e-05
(6.9e-05) 		0.00228
(0.00887) 		0.00298
(0.0113)
7p gain 591 (54%) 494 0
(0) 		3.29e-55
(1.52e-53) 		4.91e-84
(3.02e-82) 		0.665
(0.791) 		1.24e-11
(2.24e-10) 		2.45e-13
(5.17e-12) 		1e-05
(6.9e-05) 		0.00203
(0.00801) 		0.0299
(0.0821)
7q gain 627 (58%) 458 0
(0) 		1.25e-52
(5.45e-51) 		2.1e-71
(1.11e-69) 		0.35
(0.531) 		1.78e-10
(3.06e-09) 		1.53e-12
(2.89e-11) 		1e-05
(6.9e-05) 		0.00133
(0.00555) 		0.00749
(0.0248)
20p gain 265 (24%) 820 0
(0) 		4.89e-28
(1.57e-26) 		1.82e-32
(6.39e-31) 		0.667
(0.792) 		2.51e-05
(0.000158) 		2.08e-05
(0.000132) 		1e-05
(6.9e-05) 		0.0859
(0.19) 		0.106
(0.222)
20q gain 262 (24%) 823 0
(0) 		1.01e-26
(3.12e-25) 		2.26e-32
(7.58e-31) 		0.429
(0.601) 		1.61e-05
(0.000107) 		6.72e-06
(6.28e-05) 		1e-05
(6.9e-05) 		0.0777
(0.177) 		0.106
(0.222)
21q gain 88 (8%) 997 0.00316
(0.0119) 		9.77e-07
(1.16e-05) 		8.45e-05
(0.000455) 		0.822
(0.908) 		0.0177
(0.0527) 		0.109
(0.228) 		0.00082
(0.00358) 		0.096
(0.205) 		0.0446
(0.115)
6q loss 188 (17%) 897 1.41e-08
(2.03e-07) 		0.000709
(0.00315) 		3.86e-05
(0.000234) 		0.224
(0.394) 		0.0686
(0.162) 		0.00389
(0.0142) 		2e-05
(0.000128) 		0.0176
(0.0527) 		0.0954
(0.205)
9p loss 316 (29%) 769 5.34e-06
(5.12e-05) 		9.23e-05
(0.00049) 		9.65e-06
(6.9e-05) 		1
(1.00) 		0.000449
(0.00206) 		0.0355
(0.0957) 		6e-05
(0.000341) 		0.119
(0.244) 		0.0603
(0.145)
10q loss 587 (54%) 498 0
(0) 		2.15e-68
(1.06e-66) 		9.59e-116
(6.43e-114) 		0.175
(0.323) 		1.4e-18
(3.69e-17) 		6.88e-21
(2.03e-19) 		1e-05
(6.9e-05) 		0.004
(0.0145) 		0.000617
(0.00278)
9q gain 95 (9%) 990 0.00943
(0.0304) 		0.00733
(0.0244) 		7.65e-06
(6.88e-05) 		0.0163
(0.0494) 		0.0564
(0.138) 		0.111
(0.231) 		6e-05
(0.000341) 		0.618
(0.756) 		0.784
(0.876)
12q gain 65 (6%) 1020 0.00123
(0.0052) 		0.0694
(0.163) 		0.000165
(0.000835) 		1
(1.00) 		0.00943
(0.0304) 		0.0739
(0.17) 		0.00525
(0.0184) 		0.118
(0.243) 		0.168
(0.313)
19q gain 222 (20%) 863 0
(0) 		5.33e-16
(1.31e-14) 		7.04e-35
(2.6e-33) 		0.594
(0.735) 		2.74e-06
(2.98e-05) 		5.35e-05
(0.000316) 		1e-05
(6.9e-05) 		0.0134
(0.0417) 		0.849
(0.918)
xq gain 57 (5%) 1028 0.00236
(0.00912) 		0.000335
(0.00162) 		0.000358
(0.0017) 		0.0534
(0.133) 		0.623
(0.757) 		0.028
(0.0772) 		0.00019
(0.000954) 		0.716
(0.836) 		0.00399
(0.0145)
1p loss 200 (18%) 885 0
(0) 		3.46e-05
(0.000213) 		4.74e-51
(1.95e-49) 		0.384
(0.565) 		1.16e-18
(3.16e-17) 		2.88e-06
(3.08e-05) 		1e-05
(6.9e-05) 		0.0844
(0.188) 		0.241
(0.417)
9q loss 141 (13%) 944 0.00188
(0.00746) 		0.00228
(0.00887) 		0.00505
(0.0178) 		0.855
(0.92) 		0.000949
(0.00412) 		0.00123
(0.0052) 		0.0506
(0.127) 		0.0927
(0.199) 		0.257
(0.439)
11q loss 112 (10%) 973 1.4e-09
(2.23e-08) 		8.94e-06
(6.9e-05) 		2.35e-10
(3.95e-09) 		0.686
(0.81) 		0.0187
(0.0549) 		0.033
(0.09) 		1e-05
(6.9e-05) 		1
(1.00) 		0.116
(0.239)
14q loss 226 (21%) 859 5.44e-05
(0.000319) 		7.32e-05
(0.000409) 		0.000129
(0.000658) 		0.496
(0.655) 		0.29
(0.475) 		0.0403
(0.106) 		0.00109
(0.00465) 		0.0564
(0.138) 		0.0805
(0.181)
19q loss 244 (22%) 841 0
(0) 		1.65e-08
(2.34e-07) 		2.55e-46
(9.91e-45) 		0.377
(0.561) 		1.16e-13
(2.6e-12) 		3.01e-06
(3.17e-05) 		1e-05
(6.9e-05) 		0.482
(0.642) 		0.00952
(0.0305)
1p gain 95 (9%) 990 1.42e-09
(2.23e-08) 		1.61e-06
(1.88e-05) 		8.26e-13
(1.65e-11) 		0.514
(0.67) 		0.0783
(0.177) 		0.00102
(0.00438) 		1e-05
(6.9e-05) 		0.777
(0.871) 		0.571
(0.719)
3q gain 71 (7%) 1014 1.1e-07
(1.45e-06) 		3.38e-07
(4.16e-06) 		4.75e-11
(8.35e-10) 		0.455
(0.629) 		0.0426
(0.112) 		0.0842
(0.188) 		1e-05
(6.9e-05) 		0.476
(0.636) 		0.513
(0.67)
10p gain 70 (6%) 1015 2.05e-06
(2.32e-05) 		4.94e-12
(9.12e-11) 		1.58e-09
(2.43e-08) 		0.9
(0.953) 		0.297
(0.481) 		0.00406
(0.0146) 		1e-05
(6.9e-05) 		0.563
(0.712) 		0.0218
(0.0632)
18q gain 75 (7%) 1010 2.6e-06
(2.9e-05) 		0.00142
(0.00584) 		2.03e-06
(2.32e-05) 		0.397
(0.573) 		0.0485
(0.123) 		0.022
(0.0635) 		2e-05
(0.000128) 		0.505
(0.663) 		0.357
(0.539)
19p gain 322 (30%) 763 5.1e-06
(4.97e-05) 		3.12e-07
(3.9e-06) 		4.73e-13
(9.7e-12) 		0.501
(0.66) 		0.0585
(0.142) 		0.0229
(0.0656) 		1e-05
(6.9e-05) 		0.139
(0.276) 		0.313
(0.497)
6p loss 117 (11%) 968 1.14e-12
(2.22e-11) 		0.000125
(0.000639) 		5.11e-06
(4.97e-05) 		0.692
(0.813) 		0.411
(0.585) 		0.0865
(0.19) 		8e-05
(0.000441) 		0.0437
(0.114) 		0.218
(0.389)
8p loss 75 (7%) 1010 0.000115
(0.000598) 		0.000279
(0.00138) 		7.01e-06
(6.39e-05) 		0.397
(0.573) 		0.00613
(0.0209) 		0.457
(0.631) 		0.00031
(0.00152) 		0.00581
(0.02) 		0.762
(0.864)
13q loss 298 (27%) 787 0.00152
(0.00618) 		0.0534
(0.133) 		0.000101
(0.000529) 		0.334
(0.519) 		0.0162
(0.0492) 		0.0959
(0.205) 		0.00337
(0.0126) 		0.536
(0.69) 		0.224
(0.394)
22q loss 240 (22%) 845 2.15e-14
(4.97e-13) 		2.04e-13
(4.43e-12) 		4.56e-17
(1.16e-15) 		0.941
(0.985) 		0.00135
(0.00559) 		0.00647
(0.0219) 		1e-05
(6.9e-05) 		0.424
(0.598) 		0.195
(0.355)
1q gain 112 (10%) 973 4.62e-05
(0.000277) 		2.63e-06
(2.9e-05) 		9.44e-10
(1.55e-08) 		0.312
(0.496) 		0.29
(0.475) 		0.00161
(0.00651) 		1e-05
(6.9e-05) 		0.404
(0.579) 		0.425
(0.599)
2p gain 51 (5%) 1034 0.00562
(0.0196) 		0.026
(0.0727) 		0.00388
(0.0142) 		0.191
(0.349) 		0.394
(0.572) 		0.0893
(0.194) 		0.0701
(0.164) 		0.505
(0.663) 		0.716
(0.836)
2q gain 48 (4%) 1037 0.00786
(0.0258) 		0.0158
(0.0483) 		0.00465
(0.0165) 		0.374
(0.56) 		0.16
(0.308) 		0.0587
(0.142) 		0.0728
(0.169) 		0.346
(0.531) 		1
(1.00)
4q gain 43 (4%) 1042 0.00352
(0.0131) 		0.0157
(0.0482) 		0.000466
(0.00213) 		0.531
(0.686) 		0.0643
(0.154) 		0.746
(0.853) 		0.00358
(0.0133) 		0.287
(0.473) 		0.253
(0.436)
9p gain 64 (6%) 1021 0.0254
(0.0721) 		0.0133
(0.0413) 		0.000694
(0.00311) 		0.0671
(0.159) 		0.128
(0.258) 		0.269
(0.449) 		0.00153
(0.0062) 		0.388
(0.568) 		0.734
(0.849)
11q gain 74 (7%) 1011 1.79e-05
(0.000118) 		0.0123
(0.0387) 		4.43e-09
(6.67e-08) 		0.465
(0.633) 		0.163
(0.308) 		0.00725
(0.0242) 		1e-05
(6.9e-05) 		0.47
(0.636) 		0.223
(0.394)
17p gain 72 (7%) 1013 2.65e-05
(0.000166) 		7.01e-06
(6.39e-05) 		0.00144
(0.00592) 		0.0261
(0.0727) 		1
(1.00) 		0.735
(0.849) 		0.00382
(0.0141) 		0.427
(0.599) 		0.762
(0.864)
17q gain 86 (8%) 999 5.63e-07
(6.81e-06) 		6.2e-06
(5.87e-05) 		0.000445
(0.00206) 		0.087
(0.19) 		0.792
(0.884) 		0.647
(0.776) 		0.00571
(0.0198) 		0.719
(0.837) 		0.772
(0.869)
18p gain 78 (7%) 1007 5.89e-05
(0.00034) 		0.0145
(0.0449) 		8.22e-05
(0.000446) 		0.634
(0.766) 		0.334
(0.519) 		0.0164
(0.0494) 		0.00074
(0.00325) 		0.662
(0.788) 		0.763
(0.864)
4q loss 149 (14%) 936 9.07e-05
(0.000485) 		0.0177
(0.0527) 		6.59e-05
(0.000371) 		0.475
(0.636) 		0.046
(0.118) 		0.588
(0.732) 		8e-05
(0.000441) 		0.743
(0.852) 		0.651
(0.778)
8q loss 52 (5%) 1033 4.28e-06
(4.33e-05) 		0.000324
(0.00157) 		9.33e-05
(0.000492) 		0.388
(0.568) 		0.016
(0.0489) 		0.799
(0.89) 		0.00489
(0.0173) 		0.151
(0.296) 		1
(1.00)
16q loss 104 (10%) 981 5.86e-08
(7.87e-07) 		2.94e-05
(0.000182) 		1.23e-08
(1.81e-07) 		0.835
(0.913) 		0.0196
(0.0573) 		0.124
(0.251) 		1e-05
(6.9e-05) 		0.261
(0.441) 		1
(1.00)
17p loss 78 (7%) 1007 7.82e-06
(6.9e-05) 		0.000118
(0.000611) 		2.98e-08
(4.07e-07) 		0.34
(0.526) 		0.161
(0.308) 		0.0027
(0.0104) 		1e-05
(6.9e-05) 		1
(1.00) 		0.548
(0.703)
17q loss 51 (5%) 1034 1.11e-05
(7.61e-05) 		0.000383
(0.0018) 		9.74e-06
(6.9e-05) 		0.468
(0.635) 		0.392
(0.572) 		0.0277
(0.0765) 		0.00061
(0.00276) 		0.635
(0.766) 		0.454
(0.629)
3p gain 67 (6%) 1018 1.42e-05
(9.63e-05) 		3.45e-06
(3.53e-05) 		1.79e-08
(2.49e-07) 		0.309
(0.494) 		0.295
(0.481) 		0.241
(0.417) 		1e-05
(6.9e-05) 		1
(1.00) 		0.509
(0.665)
5p gain 60 (6%) 1025 4.69e-05
(0.000279) 		0.0115
(0.0364) 		3.35e-06
(3.48e-05) 		0.346
(0.531) 		0.348
(0.531) 		0.951
(0.993) 		2e-05
(0.000128) 		0.413
(0.586) 		1
(1.00)
5q gain 50 (5%) 1035 3.51e-05
(0.000214) 		0.00124
(0.00522) 		1.61e-05
(0.000107) 		0.143
(0.284) 		0.865
(0.926) 		0.414
(0.586) 		0.0003
(0.00148) 		0.201
(0.364) 		0.26
(0.441)
10q gain 12 (1%) 1073 0.842
(0.918) 		0.0527
(0.132) 		0.0781
(0.177) 		0.255
(0.439) 		0.309
(0.494) 		0.162
(0.308) 		0.0434
(0.113) 		0.171
(0.318) 		0.0861
(0.19)
11p gain 49 (5%) 1036 0.0561
(0.138) 		0.704
(0.826) 		0.0122
(0.0383) 		0.462
(0.632) 		0.128
(0.258) 		0.12
(0.244) 		0.0184
(0.0543) 		0.378
(0.561) 		0.161
(0.308)
14q gain 26 (2%) 1059 0.00183
(0.0073) 		0.00035
(0.00168) 		0.00105
(0.0045) 		0.316
(0.5) 		0.475
(0.636) 		0.185
(0.339) 		0.0066
(0.0222) 		1
(1.00) 		0.624
(0.757)
15q gain 37 (3%) 1048 0.00596
(0.0204) 		0.064
(0.154) 		0.0926
(0.199) 		0.867
(0.926) 		0.847
(0.918) 		0.00771
(0.0254) 		0.237
(0.412) 		1
(1.00) 		0.394
(0.572)
16p gain 54 (5%) 1031 0.589
(0.732) 		0.0572
(0.139) 		0.00793
(0.0259) 		0.257
(0.439) 		0.049
(0.123) 		0.363
(0.546) 		0.0411
(0.108) 		0.344
(0.531) 		0.162
(0.308)
1q loss 46 (4%) 1039 0.0571
(0.139) 		0.463
(0.632) 		0.00616
(0.021) 		0.647
(0.776) 		0.0719
(0.167) 		0.522
(0.675) 		0.00024
(0.0012) 		0.816
(0.906) 		0.717
(0.836)
4p loss 127 (12%) 958 0.0548
(0.136) 		0.884
(0.941) 		0.0378
(0.101) 		0.0355
(0.0957) 		0.261
(0.441) 		0.766
(0.865) 		0.00037
(0.00175) 		0.256
(0.439) 		0.473
(0.636)
11p loss 162 (15%) 923 0.151
(0.295) 		0.847
(0.918) 		0.0404
(0.106) 		0.0246
(0.07) 		0.0115
(0.0364) 		0.651
(0.778) 		0.00042
(0.00196) 		0.588
(0.732) 		0.384
(0.565)
12p loss 84 (8%) 1001 0.00662
(0.0222) 		0.0461
(0.118) 		0.00431
(0.0155) 		0.647
(0.776) 		0.347
(0.531) 		0.279
(0.461) 		0.0178
(0.0528) 		0.222
(0.393) 		0.571
(0.719)
15q loss 154 (14%) 931 0.00288
(0.0109) 		5.8e-05
(0.000337) 		8.13e-05
(0.000444) 		0.93
(0.975) 		0.757
(0.862) 		0.187
(0.342) 		0.00275
(0.0105) 		0.916
(0.964) 		0.825
(0.908)
16p loss 78 (7%) 1007 1.82e-07
(2.32e-06) 		4.4e-06
(4.39e-05) 		1.27e-07
(1.65e-06) 		0.407
(0.583) 		0.161
(0.308) 		0.427
(0.599) 		1e-05
(6.9e-05) 		0.885
(0.941) 		1
(1.00)
4p gain 48 (4%) 1037 0.0376
(0.101) 		0.159
(0.308) 		0.00465
(0.0165) 		1
(1.00) 		0.162
(0.308) 		0.291
(0.476) 		0.0111
(0.0354) 		0.269
(0.449) 		0.717
(0.836)
6p gain 35 (3%) 1050 0.303
(0.487) 		0.772
(0.869) 		0.0258
(0.0725) 		0.864
(0.926) 		0.0258
(0.0725) 		0.328
(0.515) 		0.098
(0.208) 		0.549
(0.703) 		0.634
(0.766)
6q gain 28 (3%) 1057 0.277
(0.459) 		0.852
(0.919) 		0.0017
(0.00681) 		0.848
(0.918) 		0.114
(0.237) 		0.277
(0.459) 		0.0328
(0.0896) 		0.484
(0.644) 		0.619
(0.756)
13q gain 17 (2%) 1068 0.263
(0.442) 		0.0741
(0.17) 		0.807
(0.899) 		0.458
(0.631) 		0.069
(0.162) 		0.021
(0.0611) 		0.832
(0.913) 		1
(1.00) 		1
(1.00)
22q gain 57 (5%) 1028 0.275
(0.458) 		0.176
(0.324) 		0.496
(0.655) 		0.891
(0.944) 		0.522
(0.675) 		0.076
(0.173) 		0.00903
(0.0294) 		0.923
(0.97) 		0.0665
(0.158)
20p loss 26 (2%) 1059 0.223
(0.394) 		0.765
(0.864) 		0.0456
(0.118) 		0.109
(0.228) 		0.166
(0.311) 		0.573
(0.719) 		0.26
(0.441) 		0.0664
(0.158) 		0.3
(0.485)
20q loss 21 (2%) 1064 0.214
(0.383) 		0.381
(0.564) 		0.0132
(0.0413) 		0.0734
(0.169) 		0.62
(0.756) 		0.832
(0.913) 		0.076
(0.173) 		0.37
(0.554) 		0.592
(0.734)
xq loss 174 (16%) 911 0.0895
(0.194) 		0.212
(0.382) 		0.047
(0.12) 		0.867
(0.926) 		0.376
(0.561) 		0.0881
(0.192) 		0.381
(0.564) 		0.451
(0.626) 		0.675
(0.8)
12p gain 93 (9%) 992 0.226
(0.395) 		0.777
(0.871) 		0.0221
(0.0636) 		0.742
(0.852) 		0.000447
(0.00206) 		0.46
(0.632) 		0.14
(0.278) 		0.906
(0.957) 		0.572
(0.719)
16q gain 57 (5%) 1028 0.339
(0.526) 		0.301
(0.486) 		0.0401
(0.106) 		0.409
(0.584) 		0.15
(0.295) 		0.475
(0.636) 		0.0189
(0.0552) 		0.435
(0.607) 		0.163
(0.308)
2q loss 52 (5%) 1033 0.183
(0.336) 		0.198
(0.358) 		0.12
(0.244) 		0.388
(0.568) 		0.738
(0.851) 		0.359
(0.542) 		0.073
(0.169) 		0.642
(0.773) 		0.263
(0.442)
3p loss 70 (6%) 1015 0.36
(0.543) 		0.351
(0.531) 		0.461
(0.632) 		0.618
(0.756) 		0.0272
(0.0755) 		0.0339
(0.0919) 		0.882
(0.94) 		0.82
(0.907) 		0.201
(0.363)
5p loss 80 (7%) 1005 0.491
(0.651) 		0.997
(1.00) 		0.728
(0.845) 		1
(1.00) 		0.0021
(0.00825) 		0.242
(0.418) 		0.0472
(0.12) 		0.466
(0.633) 		0.764
(0.864)
5q loss 80 (7%) 1005 0.847
(0.918) 		0.979
(1.00) 		0.416
(0.589) 		0.557
(0.709) 		0.00073
(0.00322) 		0.436
(0.607) 		0.0847
(0.188) 		0.841
(0.918) 		0.558
(0.709)
12q loss 108 (10%) 977 0.951
(0.993) 		0.996
(1.00) 		0.686
(0.81) 		0.539
(0.693) 		0.81
(0.9) 		0.962
(1.00) 		0.0257
(0.0725) 		0.0486
(0.123) 		0.613
(0.752)
8q gain 117 (11%) 968 0.256
(0.439) 		0.0974
(0.207) 		0.624
(0.757) 		0.692
(0.813) 		0.161
(0.308) 		0.863
(0.926) 		0.296
(0.481) 		0.583
(0.729) 		0.127
(0.257)
xp gain 35 (3%) 1050 0.0866
(0.19) 		0.173
(0.32) 		0.302
(0.486) 		0.163
(0.308) 		0.226
(0.395) 		0.233
(0.406) 		0.164
(0.309) 		0.55
(0.703) 		0.317
(0.501)
2p loss 54 (5%) 1031 0.165
(0.31) 		0.0661
(0.158) 		0.402
(0.577) 		0.326
(0.514) 		0.41
(0.585) 		0.351
(0.531) 		0.472
(0.636) 		0.601
(0.741) 		0.267
(0.447)
3q loss 62 (6%) 1023 0.391
(0.571) 		0.994
(1.00) 		1
(1.00) 		1
(1.00) 		0.115
(0.239) 		0.4
(0.575) 		0.997
(1.00) 		0.479
(0.639) 		0.734
(0.849)
7q loss 9 (1%) 1076 0.93
(0.975) 		0.0919
(0.199) 		1
(1.00) 		0.742
(0.852) 		0.687
(0.81) 		0.203
(0.365) 		0.747
(0.853) 		0.563
(0.712) 		1
(1.00)
18p loss 137 (13%) 948 0.333
(0.519) 		0.101
(0.214) 		0.855
(0.92) 		0.139
(0.276) 		0.515
(0.671) 		0.488
(0.648) 		0.436
(0.607) 		0.219
(0.389) 		1
(1.00)
19p loss 57 (5%) 1028 0.145
(0.285) 		0.159
(0.308) 		0.175
(0.323) 		0.891
(0.944) 		1
(1.00) 		0.102
(0.215) 		0.589
(0.732) 		0.394
(0.572) 		0.28
(0.462)
21q loss 78 (7%) 1007 0.728
(0.845) 		0.334
(0.519) 		0.906
(0.957) 		0.34
(0.526) 		0.322
(0.508) 		0.835
(0.913) 		0.0358
(0.0962) 		0.743
(0.852) 		0.558
(0.709)
xp loss 211 (19%) 874 0.823
(0.908) 		0.398
(0.574) 		0.818
(0.907) 		0.312
(0.496) 		0.521
(0.675) 		0.376
(0.561) 		0.969
(1.00) 		0.558
(0.709) 		0.119
(0.244)
8p gain 101 (9%) 984 0.602
(0.741) 		0.661
(0.788) 		0.834
(0.913) 		0.916
(0.964) 		0.453
(0.629) 		0.581
(0.728) 		0.519
(0.674) 		0.217
(0.388) 		0.29
(0.475)
7p loss 10 (1%) 1075 0.623
(0.757) 		0.135
(0.271) 		0.349
(0.531) 		0.75
(0.855) 		0.463
(0.632) 		0.844
(0.918) 		0.781
(0.875) 		0.607
(0.747) 		1
(1.00)
18q loss 123 (11%) 962 0.13
(0.261) 		0.473
(0.636) 		0.502
(0.661) 		0.561
(0.711) 		0.306
(0.491) 		0.601
(0.741) 		0.146
(0.287) 		0.166
(0.311) 		0.334
(0.519)
'1p gain' versus 'Time to Death'

P value = 1.42e-09 (logrank test), Q value = 2.2e-08

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
1P GAIN MUTATED 95 73 0.2 - 92.7 (12.6)
1P GAIN WILD-TYPE 983 525 0.0 - 211.2 (16.6)

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 = 1.61e-06 (Wilcoxon-test), Q value = 1.9e-05

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
1P GAIN MUTATED 95 57.9 (13.9)
1P GAIN WILD-TYPE 989 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 = 8.26e-13 (Fisher's exact test), Q value = 1.6e-11

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
1P GAIN MUTATED 82 13
1P GAIN WILD-TYPE 491 499

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

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0783 (Fisher's exact test), Q value = 0.18

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

nPatients NO YES
ALL 258 770
1P GAIN MUTATED 16 76
1P GAIN WILD-TYPE 242 694

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

'1p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00102 (Wilcoxon-test), Q value = 0.0044

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
1P GAIN MUTATED 67 75.1 (17.2)
1P GAIN WILD-TYPE 665 81.7 (15.0)

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 = 6.9e-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 30 129 189 18 525
1P GAIN MUTATED 10 1 0 3 1 80
1P GAIN WILD-TYPE 184 29 129 186 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 = 4.62e-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 1078 598 0.0 - 211.2 (16.0)
1Q GAIN MUTATED 112 79 0.1 - 211.2 (13.6)
1Q GAIN WILD-TYPE 966 519 0.0 - 182.3 (16.5)

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 = 2.63e-06 (Wilcoxon-test), Q value = 2.9e-05

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
1Q GAIN MUTATED 112 57.1 (15.1)
1Q GAIN WILD-TYPE 972 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 = 9.44e-10 (Fisher's exact test), Q value = 1.5e-08

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
1Q GAIN MUTATED 89 23
1Q GAIN WILD-TYPE 484 489

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 = 0.00161 (Wilcoxon-test), Q value = 0.0065

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
1Q GAIN MUTATED 76 75.9 (16.7)
1Q GAIN WILD-TYPE 656 81.7 (15.0)

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 = 6.9e-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 30 129 189 18 525
1Q GAIN MUTATED 13 2 2 8 2 85
1Q GAIN WILD-TYPE 181 28 127 181 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 = 0.00562 (logrank test), Q value = 0.02

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
2P GAIN MUTATED 50 36 0.2 - 92.7 (14.3)
2P GAIN WILD-TYPE 1028 562 0.0 - 211.2 (16.2)

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 = 0.026 (Wilcoxon-test), Q value = 0.073

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
2P GAIN MUTATED 51 55.4 (16.2)
2P GAIN WILD-TYPE 1033 50.6 (15.8)

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 = 0.00388 (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 573 512
2P GAIN MUTATED 37 14
2P GAIN WILD-TYPE 536 498

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 = 0.0893 (Wilcoxon-test), Q value = 0.19

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
2P GAIN MUTATED 36 77.8 (13.3)
2P GAIN WILD-TYPE 696 81.2 (15.4)

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

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0701 (Fisher's exact test), Q value = 0.16

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 30 129 189 18 525
2P GAIN MUTATED 7 1 2 5 1 35
2P GAIN WILD-TYPE 187 29 127 184 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 = 0.00786 (logrank test), Q value = 0.026

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
2Q GAIN MUTATED 47 33 0.2 - 92.7 (14.3)
2Q GAIN WILD-TYPE 1031 565 0.0 - 211.2 (16.2)

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 = 0.0158 (Wilcoxon-test), Q value = 0.048

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
2Q GAIN MUTATED 48 55.9 (16.2)
2Q GAIN WILD-TYPE 1036 50.6 (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 = 0.00465 (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 573 512
2Q GAIN MUTATED 35 13
2Q GAIN WILD-TYPE 538 499

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 = 0.0587 (Wilcoxon-test), Q value = 0.14

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
2Q GAIN MUTATED 36 77.2 (13.7)
2Q GAIN WILD-TYPE 696 81.3 (15.4)

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

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0728 (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 30 129 189 18 525
2Q GAIN MUTATED 7 1 2 4 1 33
2Q GAIN WILD-TYPE 187 29 127 185 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 = 1.42e-05 (logrank test), Q value = 9.6e-05

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
3P GAIN MUTATED 67 51 0.2 - 127.6 (11.0)
3P GAIN WILD-TYPE 1011 547 0.0 - 211.2 (16.2)

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 = 3.45e-06 (Wilcoxon-test), Q value = 3.5e-05

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
3P GAIN MUTATED 67 59.4 (13.8)
3P GAIN WILD-TYPE 1017 50.3 (15.8)

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 = 1.79e-08 (Fisher's exact test), Q value = 2.5e-07

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
3P GAIN MUTATED 57 10
3P GAIN WILD-TYPE 516 502

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 = 6.9e-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 30 129 189 18 525
3P GAIN MUTATED 7 1 0 3 1 55
3P GAIN WILD-TYPE 187 29 129 186 17 470

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

'3q gain' versus 'Time to Death'

P value = 1.1e-07 (logrank test), Q value = 1.4e-06

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
3Q GAIN MUTATED 71 56 0.2 - 127.6 (10.6)
3Q GAIN WILD-TYPE 1007 542 0.0 - 211.2 (16.4)

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 = 3.38e-07 (Wilcoxon-test), Q value = 4.2e-06

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
3Q GAIN MUTATED 71 59.8 (13.6)
3Q GAIN WILD-TYPE 1013 50.2 (15.8)

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 = 4.75e-11 (Fisher's exact test), Q value = 8.3e-10

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
3Q GAIN MUTATED 63 8
3Q GAIN WILD-TYPE 510 504

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

'3q gain' versus 'RADIATION_THERAPY'

P value = 0.0426 (Fisher's exact test), Q value = 0.11

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

nPatients NO YES
ALL 258 770
3Q GAIN MUTATED 10 58
3Q GAIN WILD-TYPE 248 712

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

'3q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0842 (Wilcoxon-test), Q value = 0.19

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
3Q GAIN MUTATED 51 79.0 (12.0)
3Q GAIN WILD-TYPE 681 81.2 (15.5)

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 = 6.9e-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 30 129 189 18 525
3Q GAIN MUTATED 6 1 0 2 1 61
3Q GAIN WILD-TYPE 188 29 129 187 17 464

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

'4p gain' versus 'Time to Death'

P value = 0.0376 (logrank test), Q value = 0.1

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
4P GAIN MUTATED 48 33 0.2 - 92.7 (13.4)
4P GAIN WILD-TYPE 1030 565 0.0 - 211.2 (16.0)

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 = 0.00465 (Fisher's exact test), Q value = 0.017

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
4P GAIN MUTATED 35 13
4P GAIN WILD-TYPE 538 499

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

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0111 (Fisher's exact test), Q value = 0.035

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 30 129 189 18 525
4P GAIN MUTATED 8 1 0 5 1 33
4P GAIN WILD-TYPE 186 29 129 184 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 = 0.00352 (logrank test), Q value = 0.013

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
4Q GAIN MUTATED 43 31 0.2 - 92.7 (12.8)
4Q GAIN WILD-TYPE 1035 567 0.0 - 211.2 (16.1)

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 = 0.0157 (Wilcoxon-test), Q value = 0.048

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
4Q GAIN MUTATED 43 56.0 (15.8)
4Q GAIN WILD-TYPE 1041 50.6 (15.8)

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 = 0.000466 (Fisher's exact test), Q value = 0.0021

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
4Q GAIN MUTATED 34 9
4Q GAIN WILD-TYPE 539 503

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

'4q gain' versus 'RADIATION_THERAPY'

P value = 0.0643 (Fisher's exact test), Q value = 0.15

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

nPatients NO YES
ALL 258 770
4Q GAIN MUTATED 5 36
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 = 0.00358 (Fisher's exact test), Q value = 0.013

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 30 129 189 18 525
4Q GAIN MUTATED 6 1 0 3 1 32
4Q GAIN WILD-TYPE 188 29 129 186 17 493

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

'5p gain' versus 'Time to Death'

P value = 4.69e-05 (logrank test), Q value = 0.00028

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
5P GAIN MUTATED 60 49 1.1 - 92.7 (12.4)
5P GAIN WILD-TYPE 1018 549 0.0 - 211.2 (16.2)

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 = 0.0115 (Wilcoxon-test), Q value = 0.036

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
5P GAIN MUTATED 60 55.7 (15.1)
5P GAIN WILD-TYPE 1024 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 = 3.35e-06 (Fisher's exact test), Q value = 3.5e-05

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
5P GAIN MUTATED 49 11
5P GAIN WILD-TYPE 524 501

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

'5p gain' versus 'HISTOLOGICAL_TYPE'

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

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 30 129 189 18 525
5P GAIN MUTATED 7 3 2 2 4 42
5P GAIN WILD-TYPE 187 27 127 187 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 = 3.51e-05 (logrank test), Q value = 0.00021

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
5Q GAIN MUTATED 50 40 1.1 - 92.7 (9.1)
5Q GAIN WILD-TYPE 1028 558 0.0 - 211.2 (16.3)

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 = 0.00124 (Wilcoxon-test), Q value = 0.0052

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
5Q GAIN MUTATED 50 57.8 (13.8)
5Q GAIN WILD-TYPE 1034 50.5 (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 = 1.61e-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 573 512
5Q GAIN MUTATED 41 9
5Q GAIN WILD-TYPE 532 503

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

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0015

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 30 129 189 18 525
5Q GAIN MUTATED 5 3 2 2 3 35
5Q GAIN WILD-TYPE 189 27 127 187 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 = 0.0258 (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 573 512
6P GAIN MUTATED 25 10
6P GAIN WILD-TYPE 548 502

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 258 770
6P GAIN MUTATED 3 31
6P GAIN WILD-TYPE 255 739

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

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.098 (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 30 129 189 18 525
6P GAIN MUTATED 7 1 1 2 0 24
6P GAIN WILD-TYPE 187 29 128 187 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 = 0.0017 (Fisher's exact test), Q value = 0.0068

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
6Q GAIN MUTATED 23 5
6Q GAIN WILD-TYPE 550 507

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 258 770
6Q GAIN MUTATED 3 24
6Q GAIN WILD-TYPE 255 746

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

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0328 (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 30 129 189 18 525
6Q GAIN MUTATED 3 1 0 2 0 22
6Q GAIN WILD-TYPE 191 29 129 187 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 1078 598 0.0 - 211.2 (16.0)
7P GAIN MUTATED 588 445 0.1 - 211.2 (13.0)
7P GAIN WILD-TYPE 490 153 0.0 - 182.3 (21.3)

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 = 3.29e-55 (Wilcoxon-test), Q value = 1.5e-53

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
7P GAIN MUTATED 591 57.6 (13.1)
7P GAIN WILD-TYPE 493 42.6 (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 = 4.91e-84 (Fisher's exact test), Q value = 3e-82

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
7P GAIN MUTATED 467 124
7P GAIN WILD-TYPE 106 388

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

'7p gain' versus 'RADIATION_THERAPY'

P value = 1.24e-11 (Fisher's exact test), Q value = 2.2e-10

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

nPatients NO YES
ALL 258 770
7P GAIN MUTATED 93 466
7P GAIN WILD-TYPE 165 304

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

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.45e-13 (Wilcoxon-test), Q value = 5.2e-12

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
7P GAIN MUTATED 423 77.8 (16.1)
7P GAIN WILD-TYPE 309 85.6 (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 = 6.9e-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 30 129 189 18 525
7P GAIN MUTATED 52 22 31 41 12 433
7P GAIN WILD-TYPE 142 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 = 0.00203 (Fisher's exact test), Q value = 0.008

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 71 959
7P GAIN MUTATED 1 9 52 508
7P GAIN WILD-TYPE 0 12 19 451

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 = 0.082

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

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
7P GAIN MUTATED 16 494
7P GAIN WILD-TYPE 28 427

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 1078 598 0.0 - 211.2 (16.0)
7Q GAIN MUTATED 624 456 0.1 - 211.2 (13.5)
7Q GAIN WILD-TYPE 454 142 0.0 - 182.3 (22.3)

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 = 1.25e-52 (Wilcoxon-test), Q value = 5.4e-51

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
7Q GAIN MUTATED 627 57.0 (13.2)
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 = 2.1e-71 (Fisher's exact test), Q value = 1.1e-69

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
7Q GAIN MUTATED 473 154
7Q GAIN WILD-TYPE 100 358

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

'7q gain' versus 'RADIATION_THERAPY'

P value = 1.78e-10 (Fisher's exact test), Q value = 3.1e-09

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

nPatients NO YES
ALL 258 770
7Q GAIN MUTATED 104 487
7Q GAIN WILD-TYPE 154 283

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

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.53e-12 (Wilcoxon-test), Q value = 2.9e-11

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

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
7Q GAIN MUTATED 440 78.0 (16.1)
7Q GAIN WILD-TYPE 292 85.7 (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 = 6.9e-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 30 129 189 18 525
7Q GAIN MUTATED 67 23 39 48 12 438
7Q GAIN WILD-TYPE 127 7 90 141 6 87

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

'7q gain' versus 'RACE'

P value = 0.00133 (Fisher's exact test), Q value = 0.0055

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 71 959
7Q GAIN MUTATED 1 10 55 540
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 = 0.00749 (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 44 921
7Q GAIN MUTATED 16 531
7Q GAIN WILD-TYPE 28 390

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

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0974 (Wilcoxon-test), Q value = 0.21

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
8Q GAIN MUTATED 117 48.3 (16.5)
8Q GAIN WILD-TYPE 967 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 = 0.0254 (logrank test), Q value = 0.072

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
9P GAIN MUTATED 64 44 0.4 - 172.8 (13.7)
9P GAIN WILD-TYPE 1014 554 0.0 - 211.2 (16.2)

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 = 0.0133 (Wilcoxon-test), Q value = 0.041

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
9P GAIN MUTATED 64 54.8 (16.9)
9P GAIN WILD-TYPE 1020 50.6 (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 = 0.000694 (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 573 512
9P GAIN MUTATED 47 17
9P GAIN WILD-TYPE 526 495

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

'9p gain' versus 'GENDER'

P value = 0.0671 (Fisher's exact test), Q value = 0.16

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

nPatients FEMALE MALE
ALL 453 632
9P GAIN MUTATED 34 30
9P GAIN WILD-TYPE 419 602

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

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00153 (Fisher's exact test), Q value = 0.0062

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 30 129 189 18 525
9P GAIN MUTATED 8 0 6 3 0 47
9P GAIN WILD-TYPE 186 30 123 186 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 = 0.00943 (logrank test), Q value = 0.03

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

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
9Q GAIN MUTATED 95 68 0.4 - 172.8 (15.0)
9Q GAIN WILD-TYPE 983 530 0.0 - 211.2 (16.1)

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 = 0.00733 (Wilcoxon-test), Q value = 0.024

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

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
9Q GAIN MUTATED 95 54.6 (15.7)
9Q GAIN WILD-TYPE 989 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 = 7.65e-06 (Fisher's exact test), Q value = 6.9e-05

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

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
9Q GAIN MUTATED 71 24
9Q GAIN WILD-TYPE 502 488

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 453 632
9Q GAIN MUTATED 51 44
9Q GAIN WILD-TYPE 402 588

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

'9q gain' versus 'RADIATION_THERAPY'

P value = 0.0564 (Fisher's exact test), Q value = 0.14

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

nPatients NO YES
ALL 258 770
9Q GAIN MUTATED 15 75
9Q GAIN WILD-TYPE 243 695

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

'9q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.111 (Wilcoxon-test), Q value = 0.23

Table S81.  Gene #18: '9q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
9Q GAIN MUTATED 73 78.1 (17.4)
9Q GAIN WILD-TYPE 659 81.4 (15.0)

Figure S81.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S82.  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 30 129 189 18 525
9Q GAIN MUTATED 13 2 7 4 2 67
9Q GAIN WILD-TYPE 181 28 122 185 16 458

Figure S82.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 2.05e-06 (logrank test), Q value = 2.3e-05

Table S83.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
10P GAIN MUTATED 70 21 0.1 - 172.8 (27.4)
10P GAIN WILD-TYPE 1008 577 0.0 - 211.2 (15.4)

Figure S83.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 4.94e-12 (Wilcoxon-test), Q value = 9.1e-11

Table S84.  Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
10P GAIN MUTATED 70 38.3 (12.2)
10P GAIN WILD-TYPE 1014 51.7 (15.7)

Figure S84.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.58e-09 (Fisher's exact test), Q value = 2.4e-08

Table S85.  Gene #19: '10p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
10P GAIN MUTATED 13 57
10P GAIN WILD-TYPE 560 455

Figure S85.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00406 (Wilcoxon-test), Q value = 0.015

Table S86.  Gene #19: '10p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
10P GAIN MUTATED 44 87.0 (10.7)
10P GAIN WILD-TYPE 688 80.7 (15.5)

Figure S86.  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 = 6.9e-05

Table S87.  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 30 129 189 18 525
10P GAIN MUTATED 32 1 17 8 1 11
10P GAIN WILD-TYPE 162 29 112 181 17 514

Figure S87.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'ETHNICITY'

P value = 0.0218 (Fisher's exact test), Q value = 0.063

Table S88.  Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
10P GAIN MUTATED 7 57
10P GAIN WILD-TYPE 37 864

Figure S88.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0527 (Wilcoxon-test), Q value = 0.13

Table S89.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
10Q GAIN MUTATED 12 42.1 (17.6)
10Q GAIN WILD-TYPE 1072 50.9 (15.8)

Figure S89.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'TUMOR_TISSUE_SITE'

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

Table S90.  Gene #20: '10q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
10Q GAIN MUTATED 3 9
10Q GAIN WILD-TYPE 570 503

Figure S90.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0434 (Fisher's exact test), Q value = 0.11

Table S91.  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 30 129 189 18 525
10Q GAIN MUTATED 7 0 0 2 0 3
10Q GAIN WILD-TYPE 187 30 129 187 18 522

Figure S91.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'ETHNICITY'

P value = 0.0861 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
10Q GAIN MUTATED 2 9
10Q GAIN WILD-TYPE 42 912

Figure S92.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

'11p gain' versus 'Time to Death'

P value = 0.0561 (logrank test), Q value = 0.14

Table S93.  Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
11P GAIN MUTATED 49 21 1.2 - 211.2 (19.8)
11P GAIN WILD-TYPE 1029 577 0.0 - 182.3 (15.9)

Figure S93.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0122 (Fisher's exact test), Q value = 0.038

Table S94.  Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
11P GAIN MUTATED 17 32
11P GAIN WILD-TYPE 556 480

Figure S94.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.12 (Wilcoxon-test), Q value = 0.24

Table S95.  Gene #21: '11p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
11P GAIN MUTATED 35 84.9 (13.6)
11P GAIN WILD-TYPE 697 80.9 (15.4)

Figure S95.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0184 (Fisher's exact test), Q value = 0.054

Table S96.  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 30 129 189 18 525
11P GAIN MUTATED 6 0 9 17 0 17
11P GAIN WILD-TYPE 188 30 120 172 18 508

Figure S96.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'Time to Death'

P value = 1.79e-05 (logrank test), Q value = 0.00012

Table S97.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
11Q GAIN MUTATED 74 24 1.2 - 211.2 (23.0)
11Q GAIN WILD-TYPE 1004 574 0.0 - 172.8 (15.4)

Figure S97.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0123 (Wilcoxon-test), Q value = 0.039

Table S98.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
11Q GAIN MUTATED 74 46.5 (14.1)
11Q GAIN WILD-TYPE 1010 51.1 (15.9)

Figure S98.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'TUMOR_TISSUE_SITE'

P value = 4.43e-09 (Fisher's exact test), Q value = 6.7e-08

Table S99.  Gene #22: '11q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
11Q GAIN MUTATED 15 59
11Q GAIN WILD-TYPE 558 453

Figure S99.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00725 (Wilcoxon-test), Q value = 0.024

Table S100.  Gene #22: '11q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
11Q GAIN MUTATED 47 86.8 (11.2)
11Q GAIN WILD-TYPE 685 80.7 (15.5)

Figure S100.  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 = 6.9e-05

Table S101.  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 30 129 189 18 525
11Q GAIN MUTATED 18 0 14 27 1 14
11Q GAIN WILD-TYPE 176 30 115 162 17 511

Figure S101.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'TUMOR_TISSUE_SITE'

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

Table S102.  Gene #23: '12p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
12P GAIN MUTATED 60 33
12P GAIN WILD-TYPE 513 479

Figure S102.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.000447 (Fisher's exact test), Q value = 0.0021

Table S103.  Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
12P GAIN MUTATED 9 79
12P GAIN WILD-TYPE 249 691

Figure S103.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'Time to Death'

P value = 0.00123 (logrank test), Q value = 0.0052

Table S104.  Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
12Q GAIN MUTATED 64 49 1.1 - 84.3 (14.7)
12Q GAIN WILD-TYPE 1014 549 0.0 - 211.2 (16.1)

Figure S104.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0694 (Wilcoxon-test), Q value = 0.16

Table S105.  Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
12Q GAIN MUTATED 65 53.9 (15.9)
12Q GAIN WILD-TYPE 1019 50.6 (15.8)

Figure S105.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000165 (Fisher's exact test), Q value = 0.00084

Table S106.  Gene #24: '12q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
12Q GAIN MUTATED 49 16
12Q GAIN WILD-TYPE 524 496

Figure S106.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.00943 (Fisher's exact test), Q value = 0.03

Table S107.  Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
12Q GAIN MUTATED 7 54
12Q GAIN WILD-TYPE 251 716

Figure S107.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0739 (Wilcoxon-test), Q value = 0.17

Table S108.  Gene #24: '12q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
12Q GAIN MUTATED 46 76.7 (18.1)
12Q GAIN WILD-TYPE 686 81.4 (15.0)

Figure S108.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00525 (Fisher's exact test), Q value = 0.018

Table S109.  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 30 129 189 18 525
12Q GAIN MUTATED 5 3 4 7 0 46
12Q GAIN WILD-TYPE 189 27 125 182 18 479

Figure S109.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RACE'

P value = 0.118 (Fisher's exact test), Q value = 0.24

Table S110.  Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
12Q GAIN MUTATED 0 4 4 54
12Q GAIN WILD-TYPE 1 17 67 905

Figure S110.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

'13q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0741 (Wilcoxon-test), Q value = 0.17

Table S111.  Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
13Q GAIN MUTATED 17 57.6 (17.7)
13Q GAIN WILD-TYPE 1067 50.7 (15.7)

Figure S111.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.069 (Fisher's exact test), Q value = 0.16

Table S112.  Gene #25: '13q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
13Q GAIN MUTATED 7 8
13Q GAIN WILD-TYPE 251 762

Figure S112.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.021 (Wilcoxon-test), Q value = 0.061

Table S113.  Gene #25: '13q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
13Q GAIN MUTATED 14 72.1 (14.8)
13Q GAIN WILD-TYPE 718 81.3 (15.3)

Figure S113.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q gain' versus 'Time to Death'

P value = 0.00183 (logrank test), Q value = 0.0073

Table S114.  Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
14Q GAIN MUTATED 26 22 0.4 - 51.5 (10.4)
14Q GAIN WILD-TYPE 1052 576 0.0 - 211.2 (16.0)

Figure S114.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00035 (Wilcoxon-test), Q value = 0.0017

Table S115.  Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
14Q GAIN MUTATED 26 61.4 (14.5)
14Q GAIN WILD-TYPE 1058 50.6 (15.7)

Figure S115.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00105 (Fisher's exact test), Q value = 0.0045

Table S116.  Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
14Q GAIN MUTATED 22 4
14Q GAIN WILD-TYPE 551 508

Figure S116.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0066 (Fisher's exact test), Q value = 0.022

Table S117.  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 30 129 189 18 525
14Q GAIN MUTATED 2 2 1 1 2 18
14Q GAIN WILD-TYPE 192 28 128 188 16 507

Figure S117.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'Time to Death'

P value = 0.00596 (logrank test), Q value = 0.02

Table S118.  Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
15Q GAIN MUTATED 37 30 0.2 - 117.4 (14.5)
15Q GAIN WILD-TYPE 1041 568 0.0 - 211.2 (16.0)

Figure S118.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.064 (Wilcoxon-test), Q value = 0.15

Table S119.  Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
15Q GAIN MUTATED 37 55.0 (13.3)
15Q GAIN WILD-TYPE 1047 50.7 (15.9)

Figure S119.  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 S120.  Gene #27: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
15Q GAIN MUTATED 25 12
15Q GAIN WILD-TYPE 548 500

Figure S120.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00771 (Wilcoxon-test), Q value = 0.025

Table S121.  Gene #27: '15q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
15Q GAIN MUTATED 29 73.8 (15.7)
15Q GAIN WILD-TYPE 703 81.4 (15.2)

Figure S121.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0572 (Wilcoxon-test), Q value = 0.14

Table S122.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
16P GAIN MUTATED 54 54.5 (14.8)
16P GAIN WILD-TYPE 1030 50.6 (15.8)

Figure S122.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00793 (Fisher's exact test), Q value = 0.026

Table S123.  Gene #28: '16p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
16P GAIN MUTATED 38 16
16P GAIN WILD-TYPE 535 496

Figure S123.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16p gain' versus 'RADIATION_THERAPY'

P value = 0.049 (Fisher's exact test), Q value = 0.12

Table S124.  Gene #28: '16p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
16P GAIN MUTATED 7 45
16P GAIN WILD-TYPE 251 725

Figure S124.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0411 (Fisher's exact test), Q value = 0.11

Table S125.  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 30 129 189 18 525
16P GAIN MUTATED 10 1 2 4 1 36
16P GAIN WILD-TYPE 184 29 127 185 17 489

Figure S125.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0401 (Fisher's exact test), Q value = 0.11

Table S126.  Gene #29: '16q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
16Q GAIN MUTATED 38 19
16Q GAIN WILD-TYPE 535 493

Figure S126.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0189 (Fisher's exact test), Q value = 0.055

Table S127.  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 30 129 189 18 525
16Q GAIN MUTATED 13 1 1 5 1 36
16Q GAIN WILD-TYPE 181 29 128 184 17 489

Figure S127.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 2.65e-05 (logrank test), Q value = 0.00017

Table S128.  Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
17P GAIN MUTATED 72 54 0.2 - 72.4 (14.2)
17P GAIN WILD-TYPE 1006 544 0.0 - 211.2 (16.2)

Figure S128.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 7.01e-06 (Wilcoxon-test), Q value = 6.4e-05

Table S129.  Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
17P GAIN MUTATED 72 58.6 (15.0)
17P GAIN WILD-TYPE 1012 50.3 (15.7)

Figure S129.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00144 (Fisher's exact test), Q value = 0.0059

Table S130.  Gene #30: '17p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
17P GAIN MUTATED 51 21
17P GAIN WILD-TYPE 522 491

Figure S130.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p gain' versus 'GENDER'

P value = 0.0261 (Fisher's exact test), Q value = 0.073

Table S131.  Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
17P GAIN MUTATED 21 51
17P GAIN WILD-TYPE 432 581

Figure S131.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00382 (Fisher's exact test), Q value = 0.014

Table S132.  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 30 129 189 18 525
17P GAIN MUTATED 11 4 1 9 1 46
17P GAIN WILD-TYPE 183 26 128 180 17 479

Figure S132.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 5.63e-07 (logrank test), Q value = 6.8e-06

Table S133.  Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
17Q GAIN MUTATED 86 66 0.2 - 72.4 (13.6)
17Q GAIN WILD-TYPE 992 532 0.0 - 211.2 (16.2)

Figure S133.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'YEARS_TO_BIRTH'

P value = 6.2e-06 (Wilcoxon-test), Q value = 5.9e-05

Table S134.  Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
17Q GAIN MUTATED 86 58.0 (15.4)
17Q GAIN WILD-TYPE 998 50.2 (15.7)

Figure S134.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000445 (Fisher's exact test), Q value = 0.0021

Table S135.  Gene #31: '17q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
17Q GAIN MUTATED 61 25
17Q GAIN WILD-TYPE 512 487

Figure S135.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17q gain' versus 'GENDER'

P value = 0.087 (Fisher's exact test), Q value = 0.19

Table S136.  Gene #31: '17q gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
17Q GAIN MUTATED 28 58
17Q GAIN WILD-TYPE 425 574

Figure S136.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'GENDER'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00571 (Fisher's exact test), Q value = 0.02

Table S137.  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 30 129 189 18 525
17Q GAIN MUTATED 13 4 3 9 2 55
17Q GAIN WILD-TYPE 181 26 126 180 16 470

Figure S137.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'Time to Death'

P value = 5.89e-05 (logrank test), Q value = 0.00034

Table S138.  Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
18P GAIN MUTATED 78 59 0.1 - 117.5 (14.3)
18P GAIN WILD-TYPE 1000 539 0.0 - 211.2 (16.2)

Figure S138.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0145 (Wilcoxon-test), Q value = 0.045

Table S139.  Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
18P GAIN MUTATED 78 55.0 (17.1)
18P GAIN WILD-TYPE 1006 50.5 (15.7)

Figure S139.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'TUMOR_TISSUE_SITE'

P value = 8.22e-05 (Fisher's exact test), Q value = 0.00045

Table S140.  Gene #32: '18p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
18P GAIN MUTATED 58 20
18P GAIN WILD-TYPE 515 492

Figure S140.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0164 (Wilcoxon-test), Q value = 0.049

Table S141.  Gene #32: '18p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
18P GAIN MUTATED 49 74.3 (20.5)
18P GAIN WILD-TYPE 683 81.6 (14.7)

Figure S141.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00074 (Fisher's exact test), Q value = 0.0033

Table S142.  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 30 129 189 18 525
18P GAIN MUTATED 11 1 4 5 0 57
18P GAIN WILD-TYPE 183 29 125 184 18 468

Figure S142.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'Time to Death'

P value = 2.6e-06 (logrank test), Q value = 2.9e-05

Table S143.  Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
18Q GAIN MUTATED 75 59 0.1 - 65.0 (13.3)
18Q GAIN WILD-TYPE 1003 539 0.0 - 211.2 (16.2)

Figure S143.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00142 (Wilcoxon-test), Q value = 0.0058

Table S144.  Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
18Q GAIN MUTATED 75 56.3 (16.4)
18Q GAIN WILD-TYPE 1009 50.4 (15.7)

Figure S144.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.03e-06 (Fisher's exact test), Q value = 2.3e-05

Table S145.  Gene #33: '18q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
18Q GAIN MUTATED 59 16
18Q GAIN WILD-TYPE 514 496

Figure S145.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18q gain' versus 'RADIATION_THERAPY'

P value = 0.0485 (Fisher's exact test), Q value = 0.12

Table S146.  Gene #33: '18q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
18Q GAIN MUTATED 11 61
18Q GAIN WILD-TYPE 247 709

Figure S146.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.022 (Wilcoxon-test), Q value = 0.064

Table S147.  Gene #33: '18q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
18Q GAIN MUTATED 49 75.1 (19.7)
18Q GAIN WILD-TYPE 683 81.5 (14.8)

Figure S147.  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 S148.  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 30 129 189 18 525
18Q GAIN MUTATED 10 1 3 3 0 58
18Q GAIN WILD-TYPE 184 29 126 186 18 467

Figure S148.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'Time to Death'

P value = 5.1e-06 (logrank test), Q value = 5e-05

Table S149.  Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
19P GAIN MUTATED 318 209 0.1 - 169.8 (15.4)
19P GAIN WILD-TYPE 760 389 0.0 - 211.2 (16.3)

Figure S149.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 3.12e-07 (Wilcoxon-test), Q value = 3.9e-06

Table S150.  Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
19P GAIN MUTATED 321 54.6 (14.3)
19P GAIN WILD-TYPE 763 49.2 (16.1)

Figure S150.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'TUMOR_TISSUE_SITE'

P value = 4.73e-13 (Fisher's exact test), Q value = 9.7e-12

Table S151.  Gene #34: '19p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
19P GAIN MUTATED 224 98
19P GAIN WILD-TYPE 349 414

Figure S151.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19p gain' versus 'RADIATION_THERAPY'

P value = 0.0585 (Fisher's exact test), Q value = 0.14

Table S152.  Gene #34: '19p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
19P GAIN MUTATED 64 240
19P GAIN WILD-TYPE 194 530

Figure S152.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

Table S153.  Gene #34: '19p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
19P GAIN MUTATED 213 79.5 (15.4)
19P GAIN WILD-TYPE 519 81.7 (15.2)

Figure S153.  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 = 6.9e-05

Table S154.  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 30 129 189 18 525
19P GAIN MUTATED 21 13 19 58 10 201
19P GAIN WILD-TYPE 173 17 110 131 8 324

Figure S154.  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 S155.  Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
19Q GAIN MUTATED 220 173 0.1 - 92.7 (14.5)
19Q GAIN WILD-TYPE 858 425 0.0 - 211.2 (16.6)

Figure S155.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 5.33e-16 (Wilcoxon-test), Q value = 1.3e-14

Table S156.  Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
19Q GAIN MUTATED 222 58.4 (12.4)
19Q GAIN WILD-TYPE 862 48.9 (16.0)

Figure S156.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'TUMOR_TISSUE_SITE'

P value = 7.04e-35 (Fisher's exact test), Q value = 2.6e-33

Table S157.  Gene #35: '19q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
19Q GAIN MUTATED 195 27
19Q GAIN WILD-TYPE 378 485

Figure S157.  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 = 3e-05

Table S158.  Gene #35: '19q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
19Q GAIN MUTATED 27 181
19Q GAIN WILD-TYPE 231 589

Figure S158.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5.35e-05 (Wilcoxon-test), Q value = 0.00032

Table S159.  Gene #35: '19q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
19Q GAIN MUTATED 153 77.6 (14.3)
19Q GAIN WILD-TYPE 579 82.0 (15.4)

Figure S159.  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 = 6.9e-05

Table S160.  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 30 129 189 18 525
19Q GAIN MUTATED 13 11 9 5 7 177
19Q GAIN WILD-TYPE 181 19 120 184 11 348

Figure S160.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'RACE'

P value = 0.0134 (Fisher's exact test), Q value = 0.042

Table S161.  Gene #35: '19q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
19Q GAIN MUTATED 0 8 22 185
19Q GAIN WILD-TYPE 1 13 49 774

Figure S161.  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 S162.  Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
20P GAIN MUTATED 263 213 0.1 - 94.8 (13.9)
20P GAIN WILD-TYPE 815 385 0.0 - 211.2 (17.3)

Figure S162.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 4.89e-28 (Wilcoxon-test), Q value = 1.6e-26

Table S163.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
20P GAIN MUTATED 265 59.9 (13.0)
20P GAIN WILD-TYPE 819 47.9 (15.5)

Figure S163.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'TUMOR_TISSUE_SITE'

P value = 1.82e-32 (Fisher's exact test), Q value = 6.4e-31

Table S164.  Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
20P GAIN MUTATED 221 44
20P GAIN WILD-TYPE 352 468

Figure S164.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p gain' versus 'RADIATION_THERAPY'

P value = 2.51e-05 (Fisher's exact test), Q value = 0.00016

Table S165.  Gene #36: '20p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
20P GAIN MUTATED 38 211
20P GAIN WILD-TYPE 220 559

Figure S165.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.08e-05 (Wilcoxon-test), Q value = 0.00013

Table S166.  Gene #36: '20p gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
20P GAIN MUTATED 191 77.5 (15.5)
20P GAIN WILD-TYPE 541 82.3 (15.0)

Figure S166.  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 = 6.9e-05

Table S167.  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 30 129 189 18 525
20P GAIN MUTATED 23 10 8 13 9 202
20P GAIN WILD-TYPE 171 20 121 176 9 323

Figure S167.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'RACE'

P value = 0.0859 (Fisher's exact test), Q value = 0.19

Table S168.  Gene #36: '20p gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
20P GAIN MUTATED 0 10 18 231
20P GAIN WILD-TYPE 1 11 53 728

Figure S168.  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 = 0.22

Table S169.  Gene #36: '20p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
20P GAIN MUTATED 6 230
20P GAIN WILD-TYPE 38 691

Figure S169.  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 S170.  Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
20Q GAIN MUTATED 261 211 0.1 - 117.5 (13.9)
20Q GAIN WILD-TYPE 817 387 0.0 - 211.2 (17.2)

Figure S170.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 1.01e-26 (Wilcoxon-test), Q value = 3.1e-25

Table S171.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
20Q GAIN MUTATED 262 59.8 (13.2)
20Q GAIN WILD-TYPE 822 47.9 (15.5)

Figure S171.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.26e-32 (Fisher's exact test), Q value = 7.6e-31

Table S172.  Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
20Q GAIN MUTATED 219 43
20Q GAIN WILD-TYPE 354 469

Figure S172.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q gain' versus 'RADIATION_THERAPY'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.00011

Table S173.  Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
20Q GAIN MUTATED 37 211
20Q GAIN WILD-TYPE 221 559

Figure S173.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.72e-06 (Wilcoxon-test), Q value = 6.3e-05

Table S174.  Gene #37: '20q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
20Q GAIN MUTATED 190 77.4 (15.3)
20Q GAIN WILD-TYPE 542 82.4 (15.1)

Figure S174.  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 = 6.9e-05

Table S175.  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 30 129 189 18 525
20Q GAIN MUTATED 22 10 7 14 9 200
20Q GAIN WILD-TYPE 172 20 122 175 9 325

Figure S175.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'RACE'

P value = 0.0777 (Fisher's exact test), Q value = 0.18

Table S176.  Gene #37: '20q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
20Q GAIN MUTATED 0 10 18 228
20Q GAIN WILD-TYPE 1 11 53 731

Figure S176.  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 = 0.22

Table S177.  Gene #37: '20q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
20Q GAIN MUTATED 6 229
20Q GAIN WILD-TYPE 38 692

Figure S177.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'ETHNICITY'

'21q gain' versus 'Time to Death'

P value = 0.00316 (logrank test), Q value = 0.012

Table S178.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
21Q GAIN MUTATED 88 65 0.2 - 211.2 (14.4)
21Q GAIN WILD-TYPE 990 533 0.0 - 182.3 (16.2)

Figure S178.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 9.77e-07 (Wilcoxon-test), Q value = 1.2e-05

Table S179.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
21Q GAIN MUTATED 88 58.8 (14.4)
21Q GAIN WILD-TYPE 996 50.1 (15.7)

Figure S179.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'TUMOR_TISSUE_SITE'

P value = 8.45e-05 (Fisher's exact test), Q value = 0.00046

Table S180.  Gene #38: '21q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
21Q GAIN MUTATED 64 24
21Q GAIN WILD-TYPE 509 488

Figure S180.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'21q gain' versus 'RADIATION_THERAPY'

P value = 0.0177 (Fisher's exact test), Q value = 0.053

Table S181.  Gene #38: '21q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
21Q GAIN MUTATED 12 71
21Q GAIN WILD-TYPE 246 699

Figure S181.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'21q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.109 (Wilcoxon-test), Q value = 0.23

Table S182.  Gene #38: '21q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
21Q GAIN MUTATED 66 78.0 (17.1)
21Q GAIN WILD-TYPE 666 81.4 (15.1)

Figure S182.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00082 (Fisher's exact test), Q value = 0.0036

Table S183.  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 30 129 189 18 525
21Q GAIN MUTATED 9 7 5 10 1 56
21Q GAIN WILD-TYPE 185 23 124 179 17 469

Figure S183.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RACE'

P value = 0.096 (Fisher's exact test), Q value = 0.2

Table S184.  Gene #38: '21q gain' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
21Q GAIN MUTATED 0 5 6 76
21Q GAIN WILD-TYPE 1 16 65 883

Figure S184.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'RACE'

'21q gain' versus 'ETHNICITY'

P value = 0.0446 (Fisher's exact test), Q value = 0.12

Table S185.  Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
21Q GAIN MUTATED 0 81
21Q GAIN WILD-TYPE 44 840

Figure S185.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

'22q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.076 (Wilcoxon-test), Q value = 0.17

Table S186.  Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
22Q GAIN MUTATED 33 77.6 (12.5)
22Q GAIN WILD-TYPE 699 81.2 (15.4)

Figure S186.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00903 (Fisher's exact test), Q value = 0.029

Table S187.  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 30 129 189 18 525
22Q GAIN MUTATED 3 0 4 17 0 33
22Q GAIN WILD-TYPE 191 30 125 172 18 492

Figure S187.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'ETHNICITY'

P value = 0.0665 (Fisher's exact test), Q value = 0.16

Table S188.  Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
22Q GAIN MUTATED 5 44
22Q GAIN WILD-TYPE 39 877

Figure S188.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

'xp gain' versus 'Time to Death'

P value = 0.0866 (logrank test), Q value = 0.19

Table S189.  Gene #40: 'xp gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
XP GAIN MUTATED 35 15 0.9 - 69.3 (20.0)
XP GAIN WILD-TYPE 1043 583 0.0 - 211.2 (15.9)

Figure S189.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'Time to Death'

P value = 0.00236 (logrank test), Q value = 0.0091

Table S190.  Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
XQ GAIN MUTATED 57 22 0.1 - 130.8 (20.8)
XQ GAIN WILD-TYPE 1021 576 0.0 - 211.2 (15.8)

Figure S190.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.000335 (Wilcoxon-test), Q value = 0.0016

Table S191.  Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
XQ GAIN MUTATED 57 43.6 (16.2)
XQ GAIN WILD-TYPE 1027 51.2 (15.7)

Figure S191.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000358 (Fisher's exact test), Q value = 0.0017

Table S192.  Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
XQ GAIN MUTATED 17 40
XQ GAIN WILD-TYPE 556 472

Figure S192.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq gain' versus 'GENDER'

P value = 0.0534 (Fisher's exact test), Q value = 0.13

Table S193.  Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
XQ GAIN MUTATED 31 26
XQ GAIN WILD-TYPE 422 606

Figure S193.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.028 (Wilcoxon-test), Q value = 0.077

Table S194.  Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
XQ GAIN MUTATED 31 86.5 (12.8)
XQ GAIN WILD-TYPE 701 80.8 (15.4)

Figure S194.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.00095

Table S195.  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 30 129 189 18 525
XQ GAIN MUTATED 19 1 15 6 1 15
XQ GAIN WILD-TYPE 175 29 114 183 17 510

Figure S195.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.00399 (Fisher's exact test), Q value = 0.014

Table S196.  Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
XQ GAIN MUTATED 7 40
XQ GAIN WILD-TYPE 37 881

Figure S196.  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 S197.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
1P LOSS MUTATED 197 41 0.1 - 182.3 (22.5)
1P LOSS WILD-TYPE 881 557 0.0 - 211.2 (15.0)

Figure S197.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 3.46e-05 (Wilcoxon-test), Q value = 0.00021

Table S198.  Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
1P LOSS MUTATED 199 46.8 (13.6)
1P LOSS WILD-TYPE 885 51.7 (16.1)

Figure S198.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.74e-51 (Fisher's exact test), Q value = 1.9e-49

Table S199.  Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
1P LOSS MUTATED 15 185
1P LOSS WILD-TYPE 558 327

Figure S199.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1p loss' versus 'RADIATION_THERAPY'

P value = 1.16e-18 (Fisher's exact test), Q value = 3.2e-17

Table S200.  Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
1P LOSS MUTATED 97 90
1P LOSS WILD-TYPE 161 680

Figure S200.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.88e-06 (Wilcoxon-test), Q value = 3.1e-05

Table S201.  Gene #42: '1p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
1P LOSS MUTATED 121 86.0 (15.0)
1P LOSS WILD-TYPE 611 80.1 (15.2)

Figure S201.  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 = 6.9e-05

Table S202.  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 30 129 189 18 525
1P LOSS MUTATED 10 1 40 135 1 13
1P LOSS WILD-TYPE 184 29 89 54 17 512

Figure S202.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'RACE'

P value = 0.0844 (Fisher's exact test), Q value = 0.19

Table S203.  Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
1P LOSS MUTATED 0 5 6 182
1P LOSS WILD-TYPE 1 16 65 777

Figure S203.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

'1q loss' versus 'Time to Death'

P value = 0.0571 (logrank test), Q value = 0.14

Table S204.  Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
1Q LOSS MUTATED 46 22 0.2 - 169.8 (18.4)
1Q LOSS WILD-TYPE 1032 576 0.0 - 211.2 (16.0)

Figure S204.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

'1q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00616 (Fisher's exact test), Q value = 0.021

Table S205.  Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
1Q LOSS MUTATED 15 31
1Q LOSS WILD-TYPE 558 481

Figure S205.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1q loss' versus 'RADIATION_THERAPY'

P value = 0.0719 (Fisher's exact test), Q value = 0.17

Table S206.  Gene #43: '1q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
1Q LOSS MUTATED 16 27
1Q LOSS WILD-TYPE 242 743

Figure S206.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S207.  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 30 129 189 18 525
1Q LOSS MUTATED 4 1 6 21 0 14
1Q LOSS WILD-TYPE 190 29 123 168 18 511

Figure S207.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0661 (Wilcoxon-test), Q value = 0.16

Table S208.  Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
2P LOSS MUTATED 54 54.5 (17.0)
2P LOSS WILD-TYPE 1030 50.6 (15.7)

Figure S208.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.12 (Fisher's exact test), Q value = 0.24

Table S209.  Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
2Q LOSS MUTATED 33 19
2Q LOSS WILD-TYPE 540 493

Figure S209.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.073 (Fisher's exact test), Q value = 0.17

Table S210.  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 30 129 189 18 525
2Q LOSS MUTATED 12 3 4 3 1 29
2Q LOSS WILD-TYPE 182 27 125 186 17 496

Figure S210.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RADIATION_THERAPY'

P value = 0.0272 (Fisher's exact test), Q value = 0.075

Table S211.  Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
3P LOSS MUTATED 9 57
3P LOSS WILD-TYPE 249 713

Figure S211.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0339 (Wilcoxon-test), Q value = 0.092

Table S212.  Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
3P LOSS MUTATED 52 77.7 (13.2)
3P LOSS WILD-TYPE 680 81.3 (15.4)

Figure S212.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'RADIATION_THERAPY'

P value = 0.115 (Fisher's exact test), Q value = 0.24

Table S213.  Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
3Q LOSS MUTATED 9 48
3Q LOSS WILD-TYPE 249 722

Figure S213.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4p loss' versus 'Time to Death'

P value = 0.0548 (logrank test), Q value = 0.14

Table S214.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
4P LOSS MUTATED 127 64 0.1 - 139.0 (18.0)
4P LOSS WILD-TYPE 951 534 0.0 - 211.2 (15.7)

Figure S214.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0378 (Fisher's exact test), Q value = 0.1

Table S215.  Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
4P LOSS MUTATED 56 71
4P LOSS WILD-TYPE 517 441

Figure S215.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4p loss' versus 'GENDER'

P value = 0.0355 (Fisher's exact test), Q value = 0.096

Table S216.  Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
4P LOSS MUTATED 42 85
4P LOSS WILD-TYPE 411 547

Figure S216.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0018

Table S217.  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 30 129 189 18 525
4P LOSS MUTATED 13 3 19 39 0 53
4P LOSS WILD-TYPE 181 27 110 150 18 472

Figure S217.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 9.07e-05 (logrank test), Q value = 0.00048

Table S218.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
4Q LOSS MUTATED 149 63 0.1 - 156.2 (21.3)
4Q LOSS WILD-TYPE 929 535 0.0 - 211.2 (15.3)

Figure S218.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0177 (Wilcoxon-test), Q value = 0.053

Table S219.  Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
4Q LOSS MUTATED 149 48.0 (14.4)
4Q LOSS WILD-TYPE 935 51.3 (16.0)

Figure S219.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'TUMOR_TISSUE_SITE'

P value = 6.59e-05 (Fisher's exact test), Q value = 0.00037

Table S220.  Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
4Q LOSS MUTATED 56 93
4Q LOSS WILD-TYPE 517 419

Figure S220.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.046 (Fisher's exact test), Q value = 0.12

Table S221.  Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
4Q LOSS MUTATED 45 95
4Q LOSS WILD-TYPE 213 675

Figure S221.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S222.  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 30 129 189 18 525
4Q LOSS MUTATED 24 4 23 46 1 51
4Q LOSS WILD-TYPE 170 26 106 143 17 474

Figure S222.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.0021 (Fisher's exact test), Q value = 0.0083

Table S223.  Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
5P LOSS MUTATED 8 67
5P LOSS WILD-TYPE 250 703

Figure S223.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0472 (Fisher's exact test), Q value = 0.12

Table S224.  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 30 129 189 18 525
5P LOSS MUTATED 20 1 11 5 1 42
5P LOSS WILD-TYPE 174 29 118 184 17 483

Figure S224.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00073 (Fisher's exact test), Q value = 0.0032

Table S225.  Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
5Q LOSS MUTATED 7 67
5Q LOSS WILD-TYPE 251 703

Figure S225.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0847 (Fisher's exact test), Q value = 0.19

Table S226.  Gene #51: '5q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA OLIGODENDROGLIOMA TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 194 30 129 189 18 525
5Q LOSS MUTATED 20 1 7 7 0 45
5Q LOSS WILD-TYPE 174 29 122 182 18 480

Figure S226.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'Time to Death'

P value = 1.14e-12 (logrank test), Q value = 2.2e-11

Table S227.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
6P LOSS MUTATED 117 90 0.2 - 92.7 (11.7)
6P LOSS WILD-TYPE 961 508 0.0 - 211.2 (16.8)

Figure S227.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000125 (Wilcoxon-test), Q value = 0.00064

Table S228.  Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
6P LOSS MUTATED 117 56.0 (15.0)
6P LOSS WILD-TYPE 967 50.2 (15.8)

Figure S228.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.11e-06 (Fisher's exact test), Q value = 5e-05

Table S229.  Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
6P LOSS MUTATED 85 32
6P LOSS WILD-TYPE 488 480

Figure S229.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0865 (Wilcoxon-test), Q value = 0.19

Table S230.  Gene #52: '6p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
6P LOSS MUTATED 86 78.8 (15.1)
6P LOSS WILD-TYPE 646 81.4 (15.3)

Figure S230.  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 = 0.00044

Table S231.  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 30 129 189 18 525
6P LOSS MUTATED 15 3 4 13 3 79
6P LOSS WILD-TYPE 179 27 125 176 15 446

Figure S231.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RACE'

P value = 0.0437 (Fisher's exact test), Q value = 0.11

Table S232.  Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
6P LOSS MUTATED 1 4 10 99
6P LOSS WILD-TYPE 0 17 61 860

Figure S232.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'Time to Death'

P value = 1.41e-08 (logrank test), Q value = 2e-07

Table S233.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
6Q LOSS MUTATED 186 127 0.1 - 94.8 (13.9)
6Q LOSS WILD-TYPE 892 471 0.0 - 211.2 (16.8)

Figure S233.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000709 (Wilcoxon-test), Q value = 0.0032

Table S234.  Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
6Q LOSS MUTATED 188 54.3 (15.0)
6Q LOSS WILD-TYPE 896 50.1 (15.9)

Figure S234.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.86e-05 (Fisher's exact test), Q value = 0.00023

Table S235.  Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
6Q LOSS MUTATED 125 63
6Q LOSS WILD-TYPE 448 449

Figure S235.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0686 (Fisher's exact test), Q value = 0.16

Table S236.  Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
6Q LOSS MUTATED 34 141
6Q LOSS WILD-TYPE 224 629

Figure S236.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00389 (Wilcoxon-test), Q value = 0.014

Table S237.  Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
6Q LOSS MUTATED 136 78.1 (15.7)
6Q LOSS WILD-TYPE 596 81.8 (15.1)

Figure S237.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S238.  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 30 129 189 18 525
6Q LOSS MUTATED 37 6 10 16 4 115
6Q LOSS WILD-TYPE 157 24 119 173 14 410

Figure S238.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0176 (Fisher's exact test), Q value = 0.053

Table S239.  Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
6Q LOSS MUTATED 1 6 18 157
6Q LOSS WILD-TYPE 0 15 53 802

Figure S239.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'ETHNICITY'

P value = 0.0954 (Fisher's exact test), Q value = 0.2

Table S240.  Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
6Q LOSS MUTATED 3 159
6Q LOSS WILD-TYPE 41 762

Figure S240.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

'7q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0919 (Wilcoxon-test), Q value = 0.2

Table S241.  Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
7Q LOSS MUTATED 9 41.6 (17.8)
7Q LOSS WILD-TYPE 1075 50.9 (15.8)

Figure S241.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'Time to Death'

P value = 0.000115 (logrank test), Q value = 6e-04

Table S242.  Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
8P LOSS MUTATED 74 52 0.2 - 120.6 (11.8)
8P LOSS WILD-TYPE 1004 546 0.0 - 211.2 (16.4)

Figure S242.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000279 (Wilcoxon-test), Q value = 0.0014

Table S243.  Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
8P LOSS MUTATED 75 57.1 (14.4)
8P LOSS WILD-TYPE 1009 50.3 (15.8)

Figure S243.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'TUMOR_TISSUE_SITE'

P value = 7.01e-06 (Fisher's exact test), Q value = 6.4e-05

Table S244.  Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
8P LOSS MUTATED 58 17
8P LOSS WILD-TYPE 515 495

Figure S244.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8p loss' versus 'RADIATION_THERAPY'

P value = 0.00613 (Fisher's exact test), Q value = 0.021

Table S245.  Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
8P LOSS MUTATED 8 62
8P LOSS WILD-TYPE 250 708

Figure S245.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00031 (Fisher's exact test), Q value = 0.0015

Table S246.  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 30 129 189 18 525
8P LOSS MUTATED 9 1 4 4 1 56
8P LOSS WILD-TYPE 185 29 125 185 17 469

Figure S246.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.00581 (Fisher's exact test), Q value = 0.02

Table S247.  Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
8P LOSS MUTATED 0 6 4 60
8P LOSS WILD-TYPE 1 15 67 899

Figure S247.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

'8q loss' versus 'Time to Death'

P value = 4.28e-06 (logrank test), Q value = 4.3e-05

Table S248.  Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
8Q LOSS MUTATED 52 38 0.2 - 58.8 (11.6)
8Q LOSS WILD-TYPE 1026 560 0.0 - 211.2 (16.4)

Figure S248.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000324 (Wilcoxon-test), Q value = 0.0016

Table S249.  Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
8Q LOSS MUTATED 52 58.5 (12.7)
8Q LOSS WILD-TYPE 1032 50.4 (15.8)

Figure S249.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.33e-05 (Fisher's exact test), Q value = 0.00049

Table S250.  Gene #57: '8q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
8Q LOSS MUTATED 41 11
8Q LOSS WILD-TYPE 532 501

Figure S250.  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 S251.  Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
8Q LOSS MUTATED 5 43
8Q LOSS WILD-TYPE 253 727

Figure S251.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00489 (Fisher's exact test), Q value = 0.017

Table S252.  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 30 129 189 18 525
8Q LOSS MUTATED 5 1 3 3 1 39
8Q LOSS WILD-TYPE 189 29 126 186 17 486

Figure S252.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'Time to Death'

P value = 5.34e-06 (logrank test), Q value = 5.1e-05

Table S253.  Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
9P LOSS MUTATED 313 211 0.1 - 169.8 (15.3)
9P LOSS WILD-TYPE 765 387 0.0 - 211.2 (16.4)

Figure S253.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 9.23e-05 (Wilcoxon-test), Q value = 0.00049

Table S254.  Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
9P LOSS MUTATED 315 53.8 (15.3)
9P LOSS WILD-TYPE 769 49.6 (15.8)

Figure S254.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.65e-06 (Fisher's exact test), Q value = 6.9e-05

Table S255.  Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
9P LOSS MUTATED 200 116
9P LOSS WILD-TYPE 373 396

Figure S255.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000449 (Fisher's exact test), Q value = 0.0021

Table S256.  Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
9P LOSS MUTATED 52 243
9P LOSS WILD-TYPE 206 527

Figure S256.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0355 (Wilcoxon-test), Q value = 0.096

Table S257.  Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
9P LOSS MUTATED 213 78.9 (16.9)
9P LOSS WILD-TYPE 519 82.0 (14.5)

Figure S257.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S258.  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 30 129 189 18 525
9P LOSS MUTATED 55 12 23 38 6 182
9P LOSS WILD-TYPE 139 18 106 151 12 343

Figure S258.  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 = 0.24

Table S259.  Gene #58: '9p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
9P LOSS MUTATED 0 8 28 271
9P LOSS WILD-TYPE 1 13 43 688

Figure S259.  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 S260.  Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
9P LOSS MUTATED 7 273
9P LOSS WILD-TYPE 37 648

Figure S260.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

'9q loss' versus 'Time to Death'

P value = 0.00188 (logrank test), Q value = 0.0075

Table S261.  Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
9Q LOSS MUTATED 140 96 0.1 - 169.8 (14.6)
9Q LOSS WILD-TYPE 938 502 0.0 - 211.2 (16.2)

Figure S261.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00228 (Wilcoxon-test), Q value = 0.0089

Table S262.  Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
9Q LOSS MUTATED 141 54.3 (15.6)
9Q LOSS WILD-TYPE 943 50.3 (15.8)

Figure S262.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00505 (Fisher's exact test), Q value = 0.018

Table S263.  Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
9Q LOSS MUTATED 90 51
9Q LOSS WILD-TYPE 483 461

Figure S263.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q loss' versus 'RADIATION_THERAPY'

P value = 0.000949 (Fisher's exact test), Q value = 0.0041

Table S264.  Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
9Q LOSS MUTATED 17 109
9Q LOSS WILD-TYPE 241 661

Figure S264.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00123 (Wilcoxon-test), Q value = 0.0052

Table S265.  Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
9Q LOSS MUTATED 93 76.8 (14.5)
9Q LOSS WILD-TYPE 639 81.7 (15.3)

Figure S265.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0506 (Fisher's exact test), Q value = 0.13

Table S266.  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 30 129 189 18 525
9Q LOSS MUTATED 21 7 11 19 4 79
9Q LOSS WILD-TYPE 173 23 118 170 14 446

Figure S266.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

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

Table S267.  Gene #59: '9q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
9Q LOSS MUTATED 0 3 16 118
9Q LOSS WILD-TYPE 1 18 55 841

Figure S267.  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 S268.  Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
10P LOSS MUTATED 557 450 0.1 - 134.3 (12.6)
10P LOSS WILD-TYPE 521 148 0.0 - 211.2 (22.7)

Figure S268.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 2.02e-74 (Wilcoxon-test), Q value = 1.1e-72

Table S269.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
10P LOSS MUTATED 559 59.1 (12.4)
10P LOSS WILD-TYPE 525 42.0 (14.1)

Figure S269.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.94e-116 (Fisher's exact test), Q value = 1.4e-114

Table S270.  Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
10P LOSS MUTATED 476 83
10P LOSS WILD-TYPE 97 429

Figure S270.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10p loss' versus 'GENDER'

P value = 0.0846 (Fisher's exact test), Q value = 0.19

Table S271.  Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
10P LOSS MUTATED 219 340
10P LOSS WILD-TYPE 234 292

Figure S271.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

'10p loss' versus 'RADIATION_THERAPY'

P value = 1.23e-15 (Fisher's exact test), Q value = 2.9e-14

Table S272.  Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
10P LOSS MUTATED 78 453
10P LOSS WILD-TYPE 180 317

Figure S272.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.7e-19 (Wilcoxon-test), Q value = 7.7e-18

Table S273.  Gene #60: '10p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
10P LOSS MUTATED 409 76.9 (16.2)
10P LOSS WILD-TYPE 323 86.3 (12.1)

Figure S273.  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 = 6.9e-05

Table S274.  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 30 129 189 18 525
10P LOSS MUTATED 49 23 16 18 10 443
10P LOSS WILD-TYPE 145 7 113 171 8 82

Figure S274.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00228 (Fisher's exact test), Q value = 0.0089

Table S275.  Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
10P LOSS MUTATED 1 9 50 478
10P LOSS WILD-TYPE 0 12 21 481

Figure S275.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'ETHNICITY'

P value = 0.00298 (Fisher's exact test), Q value = 0.011

Table S276.  Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
10P LOSS MUTATED 12 467
10P LOSS WILD-TYPE 32 454

Figure S276.  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 S277.  Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
10Q LOSS MUTATED 585 465 0.1 - 172.8 (12.6)
10Q LOSS WILD-TYPE 493 133 0.0 - 211.2 (23.2)

Figure S277.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 2.15e-68 (Wilcoxon-test), Q value = 1.1e-66

Table S278.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
10Q LOSS MUTATED 587 58.4 (13.1)
10Q LOSS WILD-TYPE 497 41.9 (13.9)

Figure S278.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.59e-116 (Fisher's exact test), Q value = 6.4e-114

Table S279.  Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
10Q LOSS MUTATED 490 97
10Q LOSS WILD-TYPE 83 415

Figure S279.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10q loss' versus 'RADIATION_THERAPY'

P value = 1.4e-18 (Fisher's exact test), Q value = 3.7e-17

Table S280.  Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
10Q LOSS MUTATED 79 479
10Q LOSS WILD-TYPE 179 291

Figure S280.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.88e-21 (Wilcoxon-test), Q value = 2e-19

Table S281.  Gene #61: '10q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
10Q LOSS MUTATED 428 76.9 (16.2)
10Q LOSS WILD-TYPE 304 86.9 (11.6)

Figure S281.  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 = 6.9e-05

Table S282.  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 30 129 189 18 525
10Q LOSS MUTATED 57 23 19 21 13 454
10Q LOSS WILD-TYPE 137 7 110 168 5 71

Figure S282.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.004 (Fisher's exact test), Q value = 0.014

Table S283.  Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
10Q LOSS MUTATED 1 9 51 504
10Q LOSS WILD-TYPE 0 12 20 455

Figure S283.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

'10q loss' versus 'ETHNICITY'

P value = 0.000617 (Fisher's exact test), Q value = 0.0028

Table S284.  Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
10Q LOSS MUTATED 12 494
10Q LOSS WILD-TYPE 32 427

Figure S284.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

'11p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0404 (Fisher's exact test), Q value = 0.11

Table S285.  Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
11P LOSS MUTATED 98 64
11P LOSS WILD-TYPE 475 448

Figure S285.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p loss' versus 'GENDER'

P value = 0.0246 (Fisher's exact test), Q value = 0.07

Table S286.  Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
11P LOSS MUTATED 81 81
11P LOSS WILD-TYPE 372 551

Figure S286.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.0115 (Fisher's exact test), Q value = 0.036

Table S287.  Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
11P LOSS MUTATED 26 128
11P LOSS WILD-TYPE 232 642

Figure S287.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00042 (Fisher's exact test), Q value = 0.002

Table S288.  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 30 129 189 18 525
11P LOSS MUTATED 38 4 14 12 5 89
11P LOSS WILD-TYPE 156 26 115 177 13 436

Figure S288.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 1.4e-09 (logrank test), Q value = 2.2e-08

Table S289.  Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
11Q LOSS MUTATED 112 89 0.2 - 92.7 (13.5)
11Q LOSS WILD-TYPE 966 509 0.0 - 211.2 (16.5)

Figure S289.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 8.94e-06 (Wilcoxon-test), Q value = 6.9e-05

Table S290.  Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
11Q LOSS MUTATED 112 56.9 (14.2)
11Q LOSS WILD-TYPE 972 50.1 (15.8)

Figure S290.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.35e-10 (Fisher's exact test), Q value = 3.9e-09

Table S291.  Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
11Q LOSS MUTATED 90 22
11Q LOSS WILD-TYPE 483 490

Figure S291.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.0187 (Fisher's exact test), Q value = 0.055

Table S292.  Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
11Q LOSS MUTATED 17 90
11Q LOSS WILD-TYPE 241 680

Figure S292.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.033 (Wilcoxon-test), Q value = 0.09

Table S293.  Gene #63: '11q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
11Q LOSS MUTATED 86 78.6 (13.8)
11Q LOSS WILD-TYPE 646 81.4 (15.5)

Figure S293.  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 = 6.9e-05

Table S294.  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 30 129 189 18 525
11Q LOSS MUTATED 14 3 6 2 3 84
11Q LOSS WILD-TYPE 180 27 123 187 15 441

Figure S294.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'ETHNICITY'

P value = 0.116 (Fisher's exact test), Q value = 0.24

Table S295.  Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
11Q LOSS MUTATED 1 95
11Q LOSS WILD-TYPE 43 826

Figure S295.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

'12p loss' versus 'Time to Death'

P value = 0.00662 (logrank test), Q value = 0.022

Table S296.  Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
12P LOSS MUTATED 83 57 0.1 - 95.1 (14.9)
12P LOSS WILD-TYPE 995 541 0.0 - 211.2 (16.1)

Figure S296.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0461 (Wilcoxon-test), Q value = 0.12

Table S297.  Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
12P LOSS MUTATED 84 54.0 (16.3)
12P LOSS WILD-TYPE 1000 50.5 (15.7)

Figure S297.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00431 (Fisher's exact test), Q value = 0.015

Table S298.  Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
12P LOSS MUTATED 57 27
12P LOSS WILD-TYPE 516 485

Figure S298.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0178 (Fisher's exact test), Q value = 0.053

Table S299.  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 30 129 189 18 525
12P LOSS MUTATED 15 1 5 7 1 55
12P LOSS WILD-TYPE 179 29 124 182 17 470

Figure S299.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0257 (Fisher's exact test), Q value = 0.073

Table S300.  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 30 129 189 18 525
12Q LOSS MUTATED 30 1 13 10 2 52
12Q LOSS WILD-TYPE 164 29 116 179 16 473

Figure S300.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.0486 (Fisher's exact test), Q value = 0.12

Table S301.  Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
12Q LOSS MUTATED 0 0 2 103
12Q LOSS WILD-TYPE 1 21 69 856

Figure S301.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

'13q loss' versus 'Time to Death'

P value = 0.00152 (logrank test), Q value = 0.0062

Table S302.  Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
13Q LOSS MUTATED 298 192 0.1 - 211.2 (15.0)
13Q LOSS WILD-TYPE 780 406 0.0 - 182.3 (16.8)

Figure S302.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

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

Table S303.  Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
13Q LOSS MUTATED 298 52.3 (15.7)
13Q LOSS WILD-TYPE 786 50.3 (15.8)

Figure S303.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000101 (Fisher's exact test), Q value = 0.00053

Table S304.  Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
13Q LOSS MUTATED 186 112
13Q LOSS WILD-TYPE 387 400

Figure S304.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.0162 (Fisher's exact test), Q value = 0.049

Table S305.  Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
13Q LOSS MUTATED 57 230
13Q LOSS WILD-TYPE 201 540

Figure S305.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0959 (Wilcoxon-test), Q value = 0.2

Table S306.  Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
13Q LOSS MUTATED 212 79.7 (15.5)
13Q LOSS WILD-TYPE 520 81.7 (15.2)

Figure S306.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00337 (Fisher's exact test), Q value = 0.013

Table S307.  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 30 129 189 18 525
13Q LOSS MUTATED 48 9 25 39 4 173
13Q LOSS WILD-TYPE 146 21 104 150 14 352

Figure S307.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 5.44e-05 (logrank test), Q value = 0.00032

Table S308.  Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
14Q LOSS MUTATED 224 149 0.1 - 130.8 (14.8)
14Q LOSS WILD-TYPE 854 449 0.0 - 211.2 (16.5)

Figure S308.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 7.32e-05 (Wilcoxon-test), Q value = 0.00041

Table S309.  Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
14Q LOSS MUTATED 226 54.5 (14.9)
14Q LOSS WILD-TYPE 858 49.9 (15.9)

Figure S309.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000129 (Fisher's exact test), Q value = 0.00066

Table S310.  Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
14Q LOSS MUTATED 145 81
14Q LOSS WILD-TYPE 428 431

Figure S310.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0403 (Wilcoxon-test), Q value = 0.11

Table S311.  Gene #67: '14q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
14Q LOSS MUTATED 165 79.6 (14.1)
14Q LOSS WILD-TYPE 567 81.5 (15.6)

Figure S311.  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 S312.  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 30 129 189 18 525
14Q LOSS MUTATED 38 5 18 25 6 134
14Q LOSS WILD-TYPE 156 25 111 164 12 391

Figure S312.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 0.0564 (Fisher's exact test), Q value = 0.14

Table S313.  Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
14Q LOSS MUTATED 1 5 21 192
14Q LOSS WILD-TYPE 0 16 50 767

Figure S313.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

'14q loss' versus 'ETHNICITY'

P value = 0.0805 (Fisher's exact test), Q value = 0.18

Table S314.  Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
14Q LOSS MUTATED 4 189
14Q LOSS WILD-TYPE 40 732

Figure S314.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

'15q loss' versus 'Time to Death'

P value = 0.00288 (logrank test), Q value = 0.011

Table S315.  Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
15Q LOSS MUTATED 152 100 0.2 - 134.3 (15.2)
15Q LOSS WILD-TYPE 926 498 0.0 - 211.2 (16.2)

Figure S315.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 5.8e-05 (Wilcoxon-test), Q value = 0.00034

Table S316.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
15Q LOSS MUTATED 153 55.6 (15.7)
15Q LOSS WILD-TYPE 931 50.0 (15.7)

Figure S316.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'TUMOR_TISSUE_SITE'

P value = 8.13e-05 (Fisher's exact test), Q value = 0.00044

Table S317.  Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
15Q LOSS MUTATED 104 50
15Q LOSS WILD-TYPE 469 462

Figure S317.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00275 (Fisher's exact test), Q value = 0.011

Table S318.  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 30 129 189 18 525
15Q LOSS MUTATED 16 7 12 22 2 95
15Q LOSS WILD-TYPE 178 23 117 167 16 430

Figure S318.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 1.82e-07 (logrank test), Q value = 2.3e-06

Table S319.  Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
16P LOSS MUTATED 78 64 0.4 - 78.3 (14.4)
16P LOSS WILD-TYPE 1000 534 0.0 - 211.2 (16.2)

Figure S319.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 4.4e-06 (Wilcoxon-test), Q value = 4.4e-05

Table S320.  Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
16P LOSS MUTATED 78 58.6 (14.2)
16P LOSS WILD-TYPE 1006 50.2 (15.8)

Figure S320.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.27e-07 (Fisher's exact test), Q value = 1.6e-06

Table S321.  Gene #69: '16p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
16P LOSS MUTATED 63 15
16P LOSS WILD-TYPE 510 497

Figure S321.  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 = 6.9e-05

Table S322.  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 30 129 189 18 525
16P LOSS MUTATED 8 1 3 4 0 62
16P LOSS WILD-TYPE 186 29 126 185 18 463

Figure S322.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 5.86e-08 (logrank test), Q value = 7.9e-07

Table S323.  Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
16Q LOSS MUTATED 104 84 0.2 - 120.6 (14.4)
16Q LOSS WILD-TYPE 974 514 0.0 - 211.2 (16.3)

Figure S323.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 2.94e-05 (Wilcoxon-test), Q value = 0.00018

Table S324.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
16Q LOSS MUTATED 104 56.8 (14.4)
16Q LOSS WILD-TYPE 980 50.2 (15.8)

Figure S324.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.23e-08 (Fisher's exact test), Q value = 1.8e-07

Table S325.  Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
16Q LOSS MUTATED 82 22
16Q LOSS WILD-TYPE 491 490

Figure S325.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.0196 (Fisher's exact test), Q value = 0.057

Table S326.  Gene #70: '16q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
16Q LOSS MUTATED 15 82
16Q LOSS WILD-TYPE 243 688

Figure S326.  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 = 6.9e-05

Table S327.  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 30 129 189 18 525
16Q LOSS MUTATED 11 3 5 6 1 78
16Q LOSS WILD-TYPE 183 27 124 183 17 447

Figure S327.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'Time to Death'

P value = 7.82e-06 (logrank test), Q value = 6.9e-05

Table S328.  Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
17P LOSS MUTATED 78 55 0.1 - 92.7 (12.0)
17P LOSS WILD-TYPE 1000 543 0.0 - 211.2 (16.5)

Figure S328.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000118 (Wilcoxon-test), Q value = 0.00061

Table S329.  Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
17P LOSS MUTATED 78 57.4 (14.3)
17P LOSS WILD-TYPE 1006 50.3 (15.8)

Figure S329.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.98e-08 (Fisher's exact test), Q value = 4.1e-07

Table S330.  Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
17P LOSS MUTATED 64 14
17P LOSS WILD-TYPE 509 498

Figure S330.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0027 (Wilcoxon-test), Q value = 0.01

Table S331.  Gene #71: '17p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
17P LOSS MUTATED 56 74.8 (18.9)
17P LOSS WILD-TYPE 676 81.6 (14.9)

Figure S331.  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 = 6.9e-05

Table S332.  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 30 129 189 18 525
17P LOSS MUTATED 7 5 2 5 1 58
17P LOSS WILD-TYPE 187 25 127 184 17 467

Figure S332.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 1.11e-05 (logrank test), Q value = 7.6e-05

Table S333.  Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
17Q LOSS MUTATED 51 38 0.1 - 92.7 (11.7)
17Q LOSS WILD-TYPE 1027 560 0.0 - 211.2 (16.3)

Figure S333.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000383 (Wilcoxon-test), Q value = 0.0018

Table S334.  Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
17Q LOSS MUTATED 51 58.3 (13.5)
17Q LOSS WILD-TYPE 1033 50.4 (15.8)

Figure S334.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.74e-06 (Fisher's exact test), Q value = 6.9e-05

Table S335.  Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
17Q LOSS MUTATED 42 9
17Q LOSS WILD-TYPE 531 503

Figure S335.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0277 (Wilcoxon-test), Q value = 0.077

Table S336.  Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
17Q LOSS MUTATED 36 74.2 (21.6)
17Q LOSS WILD-TYPE 696 81.4 (14.8)

Figure S336.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00061 (Fisher's exact test), Q value = 0.0028

Table S337.  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 30 129 189 18 525
17Q LOSS MUTATED 4 3 1 4 1 38
17Q LOSS WILD-TYPE 190 27 128 185 17 487

Figure S337.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.101 (Wilcoxon-test), Q value = 0.21

Table S338.  Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
18P LOSS MUTATED 137 52.8 (15.8)
18P LOSS WILD-TYPE 947 50.5 (15.8)

Figure S338.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.102 (Wilcoxon-test), Q value = 0.22

Table S339.  Gene #75: '19p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
19P LOSS MUTATED 44 85.0 (12.8)
19P LOSS WILD-TYPE 688 80.8 (15.4)

Figure S339.  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 S340.  Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
19Q LOSS MUTATED 241 70 0.1 - 182.3 (22.3)
19Q LOSS WILD-TYPE 837 528 0.0 - 211.2 (14.9)

Figure S340.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 1.65e-08 (Wilcoxon-test), Q value = 2.3e-07

Table S341.  Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
19Q LOSS MUTATED 243 45.9 (13.5)
19Q LOSS WILD-TYPE 841 52.2 (16.1)

Figure S341.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.55e-46 (Fisher's exact test), Q value = 9.9e-45

Table S342.  Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
19Q LOSS MUTATED 34 210
19Q LOSS WILD-TYPE 539 302

Figure S342.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19q loss' versus 'RADIATION_THERAPY'

P value = 1.16e-13 (Fisher's exact test), Q value = 2.6e-12

Table S343.  Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
19Q LOSS MUTATED 102 126
19Q LOSS WILD-TYPE 156 644

Figure S343.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.01e-06 (Wilcoxon-test), Q value = 3.2e-05

Table S344.  Gene #76: '19q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
19Q LOSS MUTATED 158 85.6 (13.2)
19Q LOSS WILD-TYPE 574 79.8 (15.6)

Figure S344.  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 = 6.9e-05

Table S345.  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 30 129 189 18 525
19Q LOSS MUTATED 23 2 44 143 2 30
19Q LOSS WILD-TYPE 171 28 85 46 16 495

Figure S345.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'ETHNICITY'

P value = 0.00952 (Fisher's exact test), Q value = 0.031

Table S346.  Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
19Q LOSS MUTATED 18 208
19Q LOSS WILD-TYPE 26 713

Figure S346.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

'20p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0456 (Fisher's exact test), Q value = 0.12

Table S347.  Gene #77: '20p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
20P LOSS MUTATED 19 7
20P LOSS WILD-TYPE 554 505

Figure S347.  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 S348.  Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
20P LOSS MUTATED 15 11
20P LOSS WILD-TYPE 438 621

Figure S348.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

'20p loss' versus 'RACE'

P value = 0.0664 (Fisher's exact test), Q value = 0.16

Table S349.  Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
20P LOSS MUTATED 0 2 3 21
20P LOSS WILD-TYPE 1 19 68 938

Figure S349.  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 S350.  Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
20Q LOSS MUTATED 17 4
20Q LOSS WILD-TYPE 556 508

Figure S350.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q loss' versus 'GENDER'

P value = 0.0734 (Fisher's exact test), Q value = 0.17

Table S351.  Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
20Q LOSS MUTATED 13 8
20Q LOSS WILD-TYPE 440 624

Figure S351.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.076 (Fisher's exact test), Q value = 0.17

Table S352.  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 30 129 189 18 525
20Q LOSS MUTATED 2 1 2 0 0 16
20Q LOSS WILD-TYPE 192 29 127 189 18 509

Figure S352.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0358 (Fisher's exact test), Q value = 0.096

Table S353.  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 30 129 189 18 525
21Q LOSS MUTATED 23 2 7 6 1 39
21Q LOSS WILD-TYPE 171 28 122 183 17 486

Figure S353.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 2.15e-14 (logrank test), Q value = 5e-13

Table S354.  Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
22Q LOSS MUTATED 240 182 0.1 - 156.2 (13.9)
22Q LOSS WILD-TYPE 838 416 0.0 - 211.2 (16.7)

Figure S354.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 2.04e-13 (Wilcoxon-test), Q value = 4.4e-12

Table S355.  Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
22Q LOSS MUTATED 240 57.2 (14.8)
22Q LOSS WILD-TYPE 844 49.0 (15.6)

Figure S355.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.56e-17 (Fisher's exact test), Q value = 1.2e-15

Table S356.  Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
22Q LOSS MUTATED 183 57
22Q LOSS WILD-TYPE 390 455

Figure S356.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.00135 (Fisher's exact test), Q value = 0.0056

Table S357.  Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
22Q LOSS MUTATED 39 189
22Q LOSS WILD-TYPE 219 581

Figure S357.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00647 (Wilcoxon-test), Q value = 0.022

Table S358.  Gene #80: '22q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
22Q LOSS MUTATED 169 79.0 (15.0)
22Q LOSS WILD-TYPE 563 81.7 (15.3)

Figure S358.  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 = 6.9e-05

Table S359.  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 30 129 189 18 525
22Q LOSS MUTATED 29 9 11 17 6 168
22Q LOSS WILD-TYPE 165 21 118 172 12 357

Figure S359.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'ETHNICITY'

P value = 0.119 (Fisher's exact test), Q value = 0.24

Table S360.  Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
XP LOSS MUTATED 13 178
XP LOSS WILD-TYPE 31 743

Figure S360.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

'xq loss' versus 'Time to Death'

P value = 0.0895 (logrank test), Q value = 0.19

Table S361.  Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
XQ LOSS MUTATED 172 101 0.1 - 134.3 (15.1)
XQ LOSS WILD-TYPE 906 497 0.0 - 211.2 (16.2)

Figure S361.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.047 (Fisher's exact test), Q value = 0.12

Table S362.  Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
XQ LOSS MUTATED 104 70
XQ LOSS WILD-TYPE 469 442

Figure S362.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0881 (Wilcoxon-test), Q value = 0.19

Table S363.  Gene #82: 'xq loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
XQ LOSS MUTATED 123 79.0 (15.9)
XQ LOSS WILD-TYPE 609 81.5 (15.1)

Figure S363.  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/22534382/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/22506567/GBMLGG-TP.merged_data.txt

  • Number of patients = 1085

  • 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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