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

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

Summary

Testing the association between copy number variation 75 focal events and 9 clinical features across 1085 patients, 398 significant findings detected with Q value < 0.25.

  • amp_1p36.21 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • amp_1q22 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

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

  • amp_1q44 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • amp_2p24.3 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

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

  • amp_4p16.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • amp_5p15.33 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • amp_7q11.21 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • amp_7q21.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

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

  • amp_8q24.21 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • amp_9q34.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • amp_10p15.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • amp_11p13 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_11q24.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

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

  • amp_12q15 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • amp_13q34 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • amp_14q32.33 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • amp_17p13.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • amp_17q25.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • amp_19p13.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • amp_19q12 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_19q13.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • amp_xp11.21 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_1p36.32 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_1p36.23 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_1p32.3 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_1p22.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_1q42.11 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_2q22.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_2q37.1 cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • del_3p21.31 cnv correlated to 'RADIATION_THERAPY'.

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

  • del_4q34.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

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

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

  • del_6p25.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

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

  • del_6q26 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_8p23.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_8q24.3 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • del_10p15.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • del_10p13 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • del_10q23.31 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

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

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

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

  • del_11p11.2 cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

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

  • del_12q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_12q15 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • del_13q22.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_14q13.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE',  'RACE', and 'ETHNICITY'.

  • del_14q24.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • del_14q31.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_15q14 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_16p12.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • del_16q23.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_17p13.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'GENDER',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_17q11.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

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

  • del_19q13.43 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • del_22q13.32 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • del_xq21.1 cnv correlated to 'YEARS_TO_BIRTH' and 'KARNOFSKY_PERFORMANCE_SCORE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 focal events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 398 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
del 6q22 31 239 (22%) 846 2.97e-12
(2.67e-11) 		1.22e-05
(4.66e-05) 		1.61e-07
(9.37e-07) 		0.138
(0.236) 		0.0233
(0.0516) 		0.00855
(0.0211) 		1e-05
(3.86e-05) 		0.116
(0.204) 		0.0947
(0.17)
del 10p15 3 549 (51%) 536 0
(0) 		9.83e-72
(2.77e-70) 		9.83e-110
(3.69e-108) 		0.0649
(0.124) 		1.13e-15
(1.42e-14) 		2.81e-18
(4.22e-17) 		1e-05
(3.86e-05) 		0.00725
(0.0184) 		0.00497
(0.0132)
del 10p13 549 (51%) 536 0
(0) 		6.25e-72
(1.83e-70) 		4.32e-111
(1.72e-109) 		0.0267
(0.0572) 		9.5e-17
(1.36e-15) 		1.11e-16
(1.56e-15) 		1e-05
(3.86e-05) 		0.0168
(0.0387) 		0.00497
(0.0132)
amp 7p11 2 630 (58%) 455 0
(0) 		2.8e-69
(7.56e-68) 		3.16e-105
(1.12e-103) 		0.319
(0.461) 		6.09e-14
(6.33e-13) 		9.91e-20
(1.59e-18) 		1e-05
(3.86e-05) 		0.00536
(0.014) 		0.00772
(0.0194)
amp 7q11 21 577 (53%) 508 0
(0) 		7.26e-56
(1.69e-54) 		2.7e-85
(8.67e-84) 		0.355
(0.5) 		4.12e-11
(3.43e-10) 		3.89e-14
(4.23e-13) 		1e-05
(3.86e-05) 		0.00277
(0.00782) 		0.00829
(0.0205)
amp 7q21 2 631 (58%) 454 0
(0) 		9.66e-51
(2.17e-49) 		1.36e-72
(4.18e-71) 		0.803
(0.885) 		1.29e-11
(1.09e-10) 		1.64e-12
(1.49e-11) 		1e-05
(3.86e-05) 		0.00147
(0.00445) 		0.00265
(0.00751)
amp 7q31 2 641 (59%) 444 0
(0) 		1.27e-40
(2.52e-39) 		1.12e-59
(2.81e-58) 		0.851
(0.912) 		1.05e-09
(7.23e-09) 		1.54e-09
(1.05e-08) 		1e-05
(3.86e-05) 		0.00796
(0.0199) 		0.00286
(0.00804)
amp 7q32 3 654 (60%) 431 0
(0) 		3.08e-41
(6.31e-40) 		9.51e-59
(2.29e-57) 		0.753
(0.85) 		1.19e-10
(9.33e-10) 		2.22e-09
(1.47e-08) 		1e-05
(3.86e-05) 		0.006
(0.0155) 		0.00154
(0.00462)
amp xp11 21 104 (10%) 981 9.97e-05
(0.000341) 		2.91e-06
(1.52e-05) 		1.86e-05
(6.93e-05) 		0.0284
(0.06) 		0.00966
(0.0235) 		0.0239
(0.0527) 		1e-05
(3.86e-05) 		0.568
(0.69) 		0.0303
(0.0637)
del 9p21 3 592 (55%) 493 0
(0) 		1.65e-30
(2.85e-29) 		1.31e-38
(2.53e-37) 		0.422
(0.563) 		4.09e-10
(3e-09) 		2.15e-13
(2.13e-12) 		1e-05
(3.86e-05) 		0.0155
(0.0356) 		0.063
(0.121)
del 10q23 31 624 (58%) 461 0
(0) 		4.02e-64
(1.04e-62) 		7.82e-119
(3.3e-117) 		0.663
(0.772) 		3.56e-19
(5.58e-18) 		9.71e-19
(1.49e-17) 		1e-05
(3.86e-05) 		0.00814
(0.0203) 		0.00819
(0.0203)
del 10q26 3 661 (61%) 424 0
(0) 		2.56e-50
(5.57e-49) 		2.98e-97
(1.01e-95) 		0.95
(0.986) 		5.32e-17
(7.81e-16) 		1.5e-16
(2.03e-15) 		1e-05
(3.86e-05) 		0.00919
(0.0225) 		0.0269
(0.0573)
del 14q13 1 244 (22%) 841 5.84e-11
(4.81e-10) 		1.67e-09
(1.12e-08) 		4.67e-12
(4.1e-11) 		0.377
(0.525) 		0.0205
(0.0456) 		0.00749
(0.0189) 		1e-05
(3.86e-05) 		0.0442
(0.0887) 		0.0568
(0.111)
amp 1q32 1 204 (19%) 881 7.89e-13
(7.4e-12) 		2.59e-13
(2.54e-12) 		3.43e-16
(4.54e-15) 		0.753
(0.85) 		0.0171
(0.0391) 		0.000114
(0.000385) 		1e-05
(3.86e-05) 		0.39
(0.54) 		0.0147
(0.034)
amp 9q34 3 141 (13%) 944 0.0388
(0.0792) 		0.0265
(0.057) 		0.000199
(0.000655) 		0.0675
(0.129) 		0.0859
(0.157) 		0.0747
(0.141) 		0.00048
(0.00153) 		0.251
(0.391) 		0.818
(0.894)
amp 12q14 1 171 (16%) 914 5.66e-15
(6.48e-14) 		9.7e-06
(3.86e-05) 		7.86e-14
(8.04e-13) 		0.673
(0.781) 		0.0104
(0.025) 		0.13
(0.225) 		1e-05
(3.86e-05) 		0.316
(0.459) 		0.0337
(0.0702)
amp 12q15 111 (10%) 974 1.7e-10
(1.31e-09) 		3.2e-05
(0.000117) 		8.88e-13
(8.21e-12) 		0.155
(0.262) 		0.0443
(0.0887) 		0.0251
(0.0546) 		1e-05
(3.86e-05) 		0.362
(0.509) 		0.0174
(0.0395)
amp 19q12 246 (23%) 839 0
(0) 		3.68e-16
(4.78e-15) 		1.93e-38
(3.62e-37) 		0.419
(0.561) 		1.04e-07
(6.16e-07) 		7.05e-05
(0.000247) 		1e-05
(3.86e-05) 		0.0404
(0.0821) 		0.582
(0.699)
amp 19q13 2 230 (21%) 855 0
(0) 		2.86e-15
(3.45e-14) 		2.11e-33
(3.74e-32) 		0.407
(0.554) 		6.05e-07
(3.35e-06) 		0.000511
(0.00162) 		1e-05
(3.86e-05) 		0.0336
(0.0702) 		0.567
(0.69)
del 1p22 1 234 (22%) 851 0
(0) 		0.00479
(0.0128) 		6.19e-30
(1.04e-28) 		0.55
(0.676) 		4.4e-14
(4.72e-13) 		0.000183
(0.000607) 		1e-05
(3.86e-05) 		0.42
(0.561) 		0.14
(0.239)
del 13q22 1 365 (34%) 720 4.66e-06
(2.4e-05) 		0.0122
(0.0287) 		6.38e-06
(3.21e-05) 		0.297
(0.442) 		0.0122
(0.0287) 		0.00181
(0.00531) 		0.0001
(0.000341) 		0.561
(0.687) 		0.142
(0.242)
del 17p13 1 116 (11%) 969 2.65e-10
(1.97e-09) 		1.71e-07
(9.85e-07) 		5.36e-14
(5.66e-13) 		0.136
(0.234) 		0.0345
(0.0714) 		0.00479
(0.0128) 		1e-05
(3.86e-05) 		0.606
(0.723) 		0.466
(0.607)
del 17q11 2 93 (9%) 992 5.28e-09
(3.33e-08) 		7.99e-05
(0.000276) 		3.94e-07
(2.22e-06) 		0.913
(0.966) 		0.117
(0.204) 		0.00354
(0.00973) 		5e-05
(0.00018) 		0.0931
(0.168) 		0.408
(0.554)
del 19q13 41 364 (34%) 721 0
(0) 		2.55e-09
(1.66e-08) 		2.93e-35
(5.35e-34) 		0.193
(0.315) 		3.32e-08
(2.02e-07) 		2.52e-05
(9.28e-05) 		1e-05
(3.86e-05) 		0.817
(0.894) 		0.144
(0.245)
del 22q13 32 289 (27%) 796 3.85e-12
(3.42e-11) 		1.92e-10
(1.45e-09) 		1.32e-16
(1.82e-15) 		0.531
(0.664) 		0.000175
(0.000581) 		0.004
(0.0109) 		1e-05
(3.86e-05) 		0.303
(0.448) 		0.118
(0.205)
amp 1p36 21 104 (10%) 981 1.2e-13
(1.21e-12) 		2.2e-08
(1.36e-07) 		5.77e-16
(7.35e-15) 		0.466
(0.607) 		0.0522
(0.103) 		0.00153
(0.00461) 		1e-05
(3.86e-05) 		0.376
(0.524) 		0.791
(0.878)
amp 1q22 144 (13%) 941 0.0189
(0.0424) 		0.00105
(0.00323) 		2.71e-06
(1.44e-05) 		0.318
(0.461) 		0.171
(0.284) 		0.0347
(0.0717) 		6e-05
(0.000213) 		0.343
(0.489) 		0.107
(0.188)
amp 1q44 129 (12%) 956 2.63e-06
(1.41e-05) 		3.28e-06
(1.7e-05) 		3.34e-09
(2.13e-08) 		0.255
(0.393) 		0.123
(0.213) 		0.00191
(0.00559) 		1e-05
(3.86e-05) 		0.414
(0.56) 		0.809
(0.889)
amp 3q26 33 130 (12%) 955 1.44e-15
(1.77e-14) 		5.2e-10
(3.69e-09) 		4.87e-15
(5.66e-14) 		0.344
(0.489) 		0.187
(0.308) 		0.00041
(0.00132) 		1e-05
(3.86e-05) 		0.344
(0.489) 		0.0774
(0.145)
amp 4q12 138 (13%) 947 6.98e-10
(4.86e-09) 		5.29e-06
(2.68e-05) 		7.12e-11
(5.79e-10) 		0.167
(0.278) 		0.0859
(0.157) 		0.0547
(0.107) 		1e-05
(3.86e-05) 		0.47
(0.608) 		0.35
(0.494)
amp 10p15 1 88 (8%) 997 4.74e-07
(2.64e-06) 		3.94e-15
(4.67e-14) 		5.83e-10
(4.1e-09) 		0.736
(0.838) 		1
(1.00) 		0.000762
(0.00238) 		1e-05
(3.86e-05) 		1
(1.00) 		0.0843
(0.156)
amp 14q32 33 44 (4%) 1041 0.00179
(0.00528) 		9.57e-06
(3.86e-05) 		7.59e-05
(0.000264) 		0.212
(0.338) 		0.0643
(0.124) 		0.09
(0.164) 		0.00226
(0.00652) 		1
(1.00) 		0.254
(0.393)
del 1p36 32 315 (29%) 770 7.08e-09
(4.43e-08) 		0.582
(0.699) 		1.44e-14
(1.62e-13) 		0.588
(0.703) 		6.2e-08
(3.74e-07) 		0.0272
(0.0576) 		1e-05
(3.86e-05) 		0.0217
(0.0481) 		0.736
(0.838)
del 1p36 23 344 (32%) 741 1.29e-05
(4.87e-05) 		0.182
(0.301) 		8.52e-11
(6.78e-10) 		0.467
(0.608) 		2.97e-07
(1.7e-06) 		0.00252
(0.00718) 		1e-05
(3.86e-05) 		0.0996
(0.177) 		1
(1.00)
del 1p32 3 257 (24%) 828 3.19e-13
(3.08e-12) 		0.232
(0.369) 		2.5e-27
(4.12e-26) 		1
(1.00) 		3.31e-13
(3.14e-12) 		0.00217
(0.00629) 		1e-05
(3.86e-05) 		0.036
(0.0742) 		0.279
(0.424)
del 2q22 1 68 (6%) 1017 0.00355
(0.00973) 		0.0179
(0.0404) 		0.00564
(0.0147) 		0.899
(0.953) 		0.297
(0.442) 		0.0834
(0.155) 		0.00489
(0.013) 		0.345
(0.489) 		0.105
(0.185)
del 6q26 260 (24%) 825 5.75e-12
(4.91e-11) 		0.00012
(0.000402) 		2.66e-09
(1.71e-08) 		0.194
(0.315) 		0.00228
(0.00655) 		0.00302
(0.00838) 		1e-05
(3.86e-05) 		0.225
(0.359) 		0.276
(0.42)
del 8p23 2 88 (8%) 997 5.96e-05
(0.000213) 		6.92e-05
(0.000243) 		1.09e-05
(4.2e-05) 		0.822
(0.895) 		0.0111
(0.0264) 		0.319
(0.461) 		0.00014
(0.000468) 		0.0146
(0.0339) 		0.571
(0.691)
del 13q14 2 382 (35%) 703 1.29e-05
(4.87e-05) 		0.0577
(0.112) 		1.24e-06
(6.81e-06) 		0.156
(0.263) 		0.00206
(0.00599) 		0.00413
(0.0112) 		1e-05
(3.86e-05) 		0.575
(0.693) 		0.263
(0.403)
del 14q31 3 275 (25%) 810 0.00451
(0.0122) 		0.0999
(0.177) 		0.0591
(0.115) 		0.0477
(0.0946) 		0.324
(0.467) 		0.309
(0.453) 		0.0768
(0.144) 		0.0962
(0.172) 		0.859
(0.919)
del 16q23 1 128 (12%) 957 2.54e-10
(1.9e-09) 		4.11e-05
(0.000149) 		4.36e-10
(3.16e-09) 		0.924
(0.968) 		0.0911
(0.165) 		0.00745
(0.0188) 		1e-05
(3.86e-05) 		0.345
(0.489) 		0.811
(0.889)
del 19q13 43 355 (33%) 730 0
(0) 		2.98e-14
(3.29e-13) 		2.72e-41
(5.74e-40) 		0.265
(0.405) 		2.52e-09
(1.65e-08) 		2.85e-06
(1.5e-05) 		1e-05
(3.86e-05) 		0.3
(0.445) 		0.193
(0.315)
amp 4p16 3 69 (6%) 1016 0.01
(0.0242) 		0.0341
(0.0708) 		0.00405
(0.011) 		0.45
(0.591) 		0.0272
(0.0576) 		0.569
(0.691) 		0.0409
(0.0826) 		0.489
(0.622) 		1
(1.00)
amp 5p15 33 76 (7%) 1009 0.000777
(0.00241) 		0.0388
(0.0792) 		1.28e-06
(6.95e-06) 		0.47
(0.608) 		0.118
(0.205) 		0.841
(0.906) 		1e-05
(3.86e-05) 		0.272
(0.415) 		1
(1.00)
amp 11q24 1 112 (10%) 973 1.68e-06
(9.06e-06) 		0.000446
(0.00143) 		5.41e-12
(4.68e-11) 		0.84
(0.906) 		0.162
(0.271) 		0.0109
(0.0261) 		1e-05
(3.86e-05) 		0.288
(0.434) 		0.45
(0.591)
amp 17p13 2 74 (7%) 1011 0.00293
(0.00819) 		0.0115
(0.0271) 		0.00522
(0.0137) 		0.0664
(0.127) 		0.575
(0.693) 		0.787
(0.877) 		0.0051
(0.0134) 		0.489
(0.622) 		0.762
(0.855)
amp 17q25 1 127 (12%) 958 5.13e-06
(2.62e-05) 		1.31e-05
(4.92e-05) 		0.00171
(0.0051) 		0.0858
(0.157) 		1
(1.00) 		0.794
(0.88) 		0.0154
(0.0356) 		0.721
(0.825) 		0.628
(0.74)
del 4q34 3 230 (21%) 855 0.000118
(0.000398) 		0.0175
(0.0397) 		2.89e-05
(0.000106) 		0.0983
(0.175) 		0.251
(0.391) 		0.245
(0.385) 		0.00164
(0.0049) 		0.55
(0.676) 		0.346
(0.49)
del 6p25 3 138 (13%) 947 7.99e-08
(4.77e-07) 		0.0376
(0.0771) 		0.00613
(0.0157) 		0.927
(0.968) 		0.51
(0.645) 		0.144
(0.245) 		0.057
(0.111) 		0.198
(0.319) 		0.489
(0.622)
del 11p15 1 176 (16%) 909 0.0967
(0.173) 		0.653
(0.762) 		0.0701
(0.133) 		0.0448
(0.0895) 		0.0243
(0.0532) 		0.333
(0.479) 		0.00036
(0.00117) 		0.468
(0.608) 		0.528
(0.661)
del 14q24 2 291 (27%) 794 0.00327
(0.00905) 		0.0938
(0.169) 		0.0196
(0.0437) 		0.0516
(0.102) 		0.42
(0.561) 		0.249
(0.388) 		0.0405
(0.0821) 		0.165
(0.276) 		0.483
(0.617)
del 15q14 215 (20%) 870 2.78e-08
(1.71e-07) 		3.15e-07
(1.78e-06) 		4.6e-10
(3.3e-09) 		0.396
(0.543) 		0.528
(0.661) 		0.0244
(0.0532) 		1e-05
(3.86e-05) 		0.628
(0.74) 		0.567
(0.69)
del 16p12 2 114 (11%) 971 1.63e-10
(1.26e-09) 		1.28e-07
(7.49e-07) 		8.54e-11
(6.78e-10) 		0.368
(0.515) 		0.0609
(0.118) 		0.447
(0.59) 		1e-05
(3.86e-05) 		0.571
(0.691) 		1
(1.00)
amp 8q24 21 169 (16%) 916 0.000897
(0.00276) 		6.65e-05
(0.000235) 		0.000773
(0.00241) 		0.8
(0.884) 		0.425
(0.565) 		0.198
(0.319) 		0.00064
(0.00201) 		0.447
(0.59) 		0.203
(0.326)
amp 19p13 3 373 (34%) 712 0.0104
(0.025) 		4.65e-05
(0.000168) 		1.6e-09
(1.08e-08) 		0.4
(0.546) 		0.763
(0.855) 		0.956
(0.991) 		1e-05
(3.86e-05) 		0.357
(0.501) 		0.521
(0.657)
del 1q42 11 78 (7%) 1007 0.0181
(0.0407) 		0.024
(0.0528) 		0.045
(0.0895) 		0.634
(0.744) 		0.48
(0.616) 		0.00912
(0.0224) 		0.311
(0.454) 		0.212
(0.338) 		0.763
(0.855)
del 8q24 3 78 (7%) 1007 0.0117
(0.0277) 		0.194
(0.315) 		0.0249
(0.0542) 		0.34
(0.488) 		0.0128
(0.0298) 		0.845
(0.908) 		0.082
(0.152) 		0.248
(0.388) 		1
(1.00)
del 11p15 5 234 (22%) 851 0.609
(0.723) 		0.000556
(0.00175) 		0.46
(0.601) 		0.0516
(0.102) 		0.0111
(0.0264) 		0.537
(0.668) 		2e-05
(7.42e-05) 		0.796
(0.881) 		1
(1.00)
del 11p11 2 159 (15%) 926 0.00242
(0.00692) 		0.396
(0.543) 		0.000295
(0.000962) 		0.259
(0.398) 		0.00294
(0.00819) 		0.672
(0.78) 		9e-05
(0.00031) 		0.654
(0.763) 		0.825
(0.896)
del 12p13 1 110 (10%) 975 0.0432
(0.087) 		0.419
(0.561) 		0.00632
(0.0162) 		0.542
(0.671) 		0.154
(0.261) 		0.712
(0.816) 		0.0171
(0.0391) 		0.288
(0.434) 		0.116
(0.204)
amp 2p24 3 72 (7%) 1013 0.0928
(0.168) 		0.705
(0.809) 		0.00724
(0.0184) 		0.537
(0.668) 		0.31
(0.454) 		0.391
(0.54) 		0.0689
(0.131) 		0.823
(0.895) 		0.757
(0.853)
del 2q37 1 121 (11%) 964 0.472
(0.609) 		0.0265
(0.057) 		0.1
(0.177) 		0.496
(0.629) 		0.298
(0.443) 		0.475
(0.612) 		0.00601
(0.0155) 		0.389
(0.54) 		1
(1.00)
del 5q34 132 (12%) 953 0.366
(0.513) 		0.0878
(0.16) 		0.926
(0.968) 		0.158
(0.265) 		0.00179
(0.00528) 		0.524
(0.659) 		0.00021
(0.000688) 		0.698
(0.802) 		1
(1.00)
amp 12p13 32 152 (14%) 933 0.81
(0.889) 		0.0268
(0.0573) 		0.54
(0.67) 		0.287
(0.434) 		0.00973
(0.0236) 		0.875
(0.93) 		0.308
(0.452) 		0.742
(0.843) 		0.823
(0.895)
del 3q13 31 95 (9%) 990 0.0798
(0.149) 		0.723
(0.825) 		0.237
(0.374) 		1
(1.00) 		0.0724
(0.137) 		0.452
(0.593) 		0.683
(0.788) 		0.481
(0.616) 		1
(1.00)
del 5p15 33 106 (10%) 979 0.394
(0.542) 		0.627
(0.74) 		1
(1.00) 		0.679
(0.786) 		0.000381
(0.00123) 		0.296
(0.442) 		0.0259
(0.0559) 		0.743
(0.843) 		1
(1.00)
del xq21 1 183 (17%) 902 0.477
(0.613) 		0.0306
(0.0641) 		0.194
(0.315) 		0.682
(0.788) 		0.564
(0.69) 		0.0818
(0.152) 		0.633
(0.744) 		0.696
(0.802) 		1
(1.00)
amp 11p13 59 (5%) 1026 0.645
(0.755) 		0.918
(0.968) 		0.79
(0.878) 		0.416
(0.56) 		0.438
(0.581) 		0.413
(0.56) 		0.124
(0.215) 		0.926
(0.968) 		0.309
(0.453)
amp 13q34 54 (5%) 1031 0.549
(0.676) 		0.99
(1.00) 		0.402
(0.548) 		0.396
(0.543) 		1
(1.00) 		0.0856
(0.157) 		0.587
(0.703) 		0.778
(0.87) 		1
(1.00)
del 3p21 31 109 (10%) 976 0.866
(0.924) 		0.236
(0.373) 		1
(1.00) 		0.919
(0.968) 		0.00121
(0.00369) 		0.242
(0.38) 		0.593
(0.709) 		0.781
(0.872) 		0.203
(0.326)
del 12q12 147 (14%) 938 0.828
(0.897) 		0.84
(0.906) 		0.929
(0.968) 		0.788
(0.877) 		0.29
(0.435) 		0.611
(0.724) 		0.00123
(0.00374) 		0.197
(0.318) 		0.257
(0.396)
del 12q15 142 (13%) 943 0.87
(0.927) 		0.839
(0.906) 		0.528
(0.661) 		0.927
(0.968) 		0.392
(0.541) 		0.928
(0.968) 		0.00575
(0.0149) 		0.17
(0.283) 		1
(1.00)
del 1q44 69 (6%) 1016 0.545
(0.674) 		0.642
(0.752) 		0.803
(0.885) 		0.45
(0.591) 		0.557
(0.683) 		0.86
(0.919) 		0.848
(0.91) 		0.931
(0.968) 		1
(1.00)
del 3q29 107 (10%) 978 0.291
(0.436) 		0.914
(0.966) 		0.415
(0.56) 		0.607
(0.723) 		0.335
(0.482) 		0.181
(0.299) 		0.51
(0.645) 		0.879
(0.933) 		0.609
(0.723)
del 18q23 155 (14%) 930 0.193
(0.315) 		0.283
(0.428) 		0.434
(0.577) 		0.253
(0.393) 		0.305
(0.449) 		0.748
(0.847) 		0.533
(0.665) 		0.238
(0.376) 		0.263
(0.403)
'amp_1p36.21' versus 'Time to Death'

P value = 1.2e-13 (logrank test), Q value = 1.2e-12

Table S1.  Gene #1: 'amp_1p36.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 1(1P36.21) MUTATED 104 86 0.1 - 92.7 (12.5)
AMP PEAK 1(1P36.21) WILD-TYPE 974 512 0.0 - 211.2 (16.6)

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #1: 'Time to Death'

'amp_1p36.21' versus 'YEARS_TO_BIRTH'

P value = 2.2e-08 (Wilcoxon-test), Q value = 1.4e-07

Table S2.  Gene #1: 'amp_1p36.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 1(1P36.21) MUTATED 104 58.7 (13.0)
AMP PEAK 1(1P36.21) WILD-TYPE 980 50.0 (15.8)

Figure S2.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1p36.21' versus 'TUMOR_TISSUE_SITE'

P value = 5.77e-16 (Fisher's exact test), Q value = 7.3e-15

Table S3.  Gene #1: 'amp_1p36.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 1(1P36.21) MUTATED 92 12
AMP PEAK 1(1P36.21) WILD-TYPE 481 500

Figure S3.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1p36.21' versus 'RADIATION_THERAPY'

P value = 0.0522 (Fisher's exact test), Q value = 0.1

Table S4.  Gene #1: 'amp_1p36.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 1(1P36.21) MUTATED 17 83
AMP PEAK 1(1P36.21) WILD-TYPE 241 687

Figure S4.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1p36.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00153 (Wilcoxon-test), Q value = 0.0046

Table S5.  Gene #1: 'amp_1p36.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 1(1P36.21) MUTATED 67 75.5 (16.7)
AMP PEAK 1(1P36.21) WILD-TYPE 665 81.6 (15.0)

Figure S5.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_1p36.21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S6.  Gene #1: 'amp_1p36.21' 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
AMP PEAK 1(1P36.21) MUTATED 9 1 0 3 1 90
AMP PEAK 1(1P36.21) WILD-TYPE 185 29 129 186 17 435

Figure S6.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_1q22' versus 'Time to Death'

P value = 0.0189 (logrank test), Q value = 0.042

Table S7.  Gene #2: 'amp_1q22' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 2(1Q22) MUTATED 144 95 0.1 - 211.2 (14.7)
AMP PEAK 2(1Q22) WILD-TYPE 934 503 0.0 - 182.3 (16.3)

Figure S7.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #1: 'Time to Death'

'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.00105 (Wilcoxon-test), Q value = 0.0032

Table S8.  Gene #2: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 2(1Q22) MUTATED 144 54.5 (15.5)
AMP PEAK 2(1Q22) WILD-TYPE 940 50.2 (15.8)

Figure S8.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q22' versus 'TUMOR_TISSUE_SITE'

P value = 2.71e-06 (Fisher's exact test), Q value = 1.4e-05

Table S9.  Gene #2: 'amp_1q22' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 2(1Q22) MUTATED 102 42
AMP PEAK 2(1Q22) WILD-TYPE 471 470

Figure S9.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1q22' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0347 (Wilcoxon-test), Q value = 0.072

Table S10.  Gene #2: 'amp_1q22' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 2(1Q22) MUTATED 99 78.0 (16.5)
AMP PEAK 2(1Q22) WILD-TYPE 633 81.6 (15.1)

Figure S10.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_1q22' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00021

Table S11.  Gene #2: 'amp_1q22' 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
AMP PEAK 2(1Q22) MUTATED 19 2 6 17 3 97
AMP PEAK 2(1Q22) WILD-TYPE 175 28 123 172 15 428

Figure S11.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_1q22' versus 'ETHNICITY'

P value = 0.107 (Fisher's exact test), Q value = 0.19

Table S12.  Gene #2: 'amp_1q22' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 2(1Q22) MUTATED 2 122
AMP PEAK 2(1Q22) WILD-TYPE 42 799

Figure S12.  Get High-res Image Gene #2: 'amp_1q22' versus Clinical Feature #9: 'ETHNICITY'

'amp_1q32.1' versus 'Time to Death'

P value = 7.89e-13 (logrank test), Q value = 7.4e-12

Table S13.  Gene #3: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 3(1Q32.1) MUTATED 202 153 0.1 - 211.2 (13.4)
AMP PEAK 3(1Q32.1) WILD-TYPE 876 445 0.0 - 182.3 (16.9)

Figure S13.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 2.59e-13 (Wilcoxon-test), Q value = 2.5e-12

Table S14.  Gene #3: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 3(1Q32.1) MUTATED 204 57.9 (14.0)
AMP PEAK 3(1Q32.1) WILD-TYPE 880 49.2 (15.7)

Figure S14.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q32.1' versus 'TUMOR_TISSUE_SITE'

P value = 3.43e-16 (Fisher's exact test), Q value = 4.5e-15

Table S15.  Gene #3: 'amp_1q32.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 3(1Q32.1) MUTATED 159 45
AMP PEAK 3(1Q32.1) WILD-TYPE 414 467

Figure S15.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1q32.1' versus 'RADIATION_THERAPY'

P value = 0.0171 (Fisher's exact test), Q value = 0.039

Table S16.  Gene #3: 'amp_1q32.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 3(1Q32.1) MUTATED 36 159
AMP PEAK 3(1Q32.1) WILD-TYPE 222 611

Figure S16.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000114 (Wilcoxon-test), Q value = 0.00039

Table S17.  Gene #3: 'amp_1q32.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 3(1Q32.1) MUTATED 139 76.6 (16.3)
AMP PEAK 3(1Q32.1) WILD-TYPE 593 82.1 (14.9)

Figure S17.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_1q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S18.  Gene #3: 'amp_1q32.1' 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
AMP PEAK 3(1Q32.1) MUTATED 23 8 7 15 5 146
AMP PEAK 3(1Q32.1) WILD-TYPE 171 22 122 174 13 379

Figure S18.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_1q32.1' versus 'ETHNICITY'

P value = 0.0147 (Fisher's exact test), Q value = 0.034

Table S19.  Gene #3: 'amp_1q32.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 3(1Q32.1) MUTATED 2 173
AMP PEAK 3(1Q32.1) WILD-TYPE 42 748

Figure S19.  Get High-res Image Gene #3: 'amp_1q32.1' versus Clinical Feature #9: 'ETHNICITY'

'amp_1q44' versus 'Time to Death'

P value = 2.63e-06 (logrank test), Q value = 1.4e-05

Table S20.  Gene #4: 'amp_1q44' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 4(1Q44) MUTATED 129 93 0.1 - 211.2 (14.3)
AMP PEAK 4(1Q44) WILD-TYPE 949 505 0.0 - 182.3 (16.5)

Figure S20.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #1: 'Time to Death'

'amp_1q44' versus 'YEARS_TO_BIRTH'

P value = 3.28e-06 (Wilcoxon-test), Q value = 1.7e-05

Table S21.  Gene #4: 'amp_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 4(1Q44) MUTATED 129 56.6 (14.5)
AMP PEAK 4(1Q44) WILD-TYPE 955 50.0 (15.8)

Figure S21.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q44' versus 'TUMOR_TISSUE_SITE'

P value = 3.34e-09 (Fisher's exact test), Q value = 2.1e-08

Table S22.  Gene #4: 'amp_1q44' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 4(1Q44) MUTATED 99 30
AMP PEAK 4(1Q44) WILD-TYPE 474 482

Figure S22.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1q44' versus 'RADIATION_THERAPY'

P value = 0.123 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #4: 'amp_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 4(1Q44) MUTATED 24 100
AMP PEAK 4(1Q44) WILD-TYPE 234 670

Figure S23.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q44' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00191 (Wilcoxon-test), Q value = 0.0056

Table S24.  Gene #4: 'amp_1q44' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 4(1Q44) MUTATED 85 76.5 (16.5)
AMP PEAK 4(1Q44) WILD-TYPE 647 81.7 (15.0)

Figure S24.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S25.  Gene #4: 'amp_1q44' 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
AMP PEAK 4(1Q44) MUTATED 15 2 5 10 3 94
AMP PEAK 4(1Q44) WILD-TYPE 179 28 124 179 15 431

Figure S25.  Get High-res Image Gene #4: 'amp_1q44' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_2p24.3' versus 'Time to Death'

P value = 0.0928 (logrank test), Q value = 0.17

Table S26.  Gene #5: 'amp_2p24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 5(2P24.3) MUTATED 71 48 0.1 - 94.5 (16.4)
AMP PEAK 5(2P24.3) WILD-TYPE 1007 550 0.0 - 211.2 (16.0)

Figure S26.  Get High-res Image Gene #5: 'amp_2p24.3' versus Clinical Feature #1: 'Time to Death'

'amp_2p24.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00724 (Fisher's exact test), Q value = 0.018

Table S27.  Gene #5: 'amp_2p24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 5(2P24.3) MUTATED 49 23
AMP PEAK 5(2P24.3) WILD-TYPE 524 489

Figure S27.  Get High-res Image Gene #5: 'amp_2p24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_2p24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0689 (Fisher's exact test), Q value = 0.13

Table S28.  Gene #5: 'amp_2p24.3' 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
AMP PEAK 5(2P24.3) MUTATED 12 2 3 8 1 46
AMP PEAK 5(2P24.3) WILD-TYPE 182 28 126 181 17 479

Figure S28.  Get High-res Image Gene #5: 'amp_2p24.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_3q26.33' versus 'Time to Death'

P value = 1.44e-15 (logrank test), Q value = 1.8e-14

Table S29.  Gene #6: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 6(3Q26.33) MUTATED 129 101 0.1 - 127.6 (10.6)
AMP PEAK 6(3Q26.33) WILD-TYPE 949 497 0.0 - 211.2 (16.9)

Figure S29.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

'amp_3q26.33' versus 'YEARS_TO_BIRTH'

P value = 5.2e-10 (Wilcoxon-test), Q value = 3.7e-09

Table S30.  Gene #6: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 6(3Q26.33) MUTATED 130 58.7 (12.9)
AMP PEAK 6(3Q26.33) WILD-TYPE 954 49.7 (15.8)

Figure S30.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.33' versus 'TUMOR_TISSUE_SITE'

P value = 4.87e-15 (Fisher's exact test), Q value = 5.7e-14

Table S31.  Gene #6: 'amp_3q26.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 6(3Q26.33) MUTATED 109 21
AMP PEAK 6(3Q26.33) WILD-TYPE 464 491

Figure S31.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_3q26.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00041 (Wilcoxon-test), Q value = 0.0013

Table S32.  Gene #6: 'amp_3q26.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 6(3Q26.33) MUTATED 96 76.6 (15.3)
AMP PEAK 6(3Q26.33) WILD-TYPE 636 81.8 (15.2)

Figure S32.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S33.  Gene #6: 'amp_3q26.33' 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
AMP PEAK 6(3Q26.33) MUTATED 15 1 1 5 0 108
AMP PEAK 6(3Q26.33) WILD-TYPE 179 29 128 184 18 417

Figure S33.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_3q26.33' versus 'ETHNICITY'

P value = 0.0774 (Fisher's exact test), Q value = 0.15

Table S34.  Gene #6: 'amp_3q26.33' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 6(3Q26.33) MUTATED 1 103
AMP PEAK 6(3Q26.33) WILD-TYPE 43 818

Figure S34.  Get High-res Image Gene #6: 'amp_3q26.33' versus Clinical Feature #9: 'ETHNICITY'

'amp_4p16.3' versus 'Time to Death'

P value = 0.01 (logrank test), Q value = 0.024

Table S35.  Gene #7: 'amp_4p16.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 7(4P16.3) MUTATED 69 48 0.2 - 94.5 (14.1)
AMP PEAK 7(4P16.3) WILD-TYPE 1009 550 0.0 - 211.2 (16.1)

Figure S35.  Get High-res Image Gene #7: 'amp_4p16.3' versus Clinical Feature #1: 'Time to Death'

'amp_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0341 (Wilcoxon-test), Q value = 0.071

Table S36.  Gene #7: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 7(4P16.3) MUTATED 69 54.5 (14.5)
AMP PEAK 7(4P16.3) WILD-TYPE 1015 50.6 (15.9)

Figure S36.  Get High-res Image Gene #7: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4p16.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00405 (Fisher's exact test), Q value = 0.011

Table S37.  Gene #7: 'amp_4p16.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 7(4P16.3) MUTATED 48 21
AMP PEAK 7(4P16.3) WILD-TYPE 525 491

Figure S37.  Get High-res Image Gene #7: 'amp_4p16.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_4p16.3' versus 'RADIATION_THERAPY'

P value = 0.0272 (Fisher's exact test), Q value = 0.058

Table S38.  Gene #7: 'amp_4p16.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 7(4P16.3) MUTATED 9 57
AMP PEAK 7(4P16.3) WILD-TYPE 249 713

Figure S38.  Get High-res Image Gene #7: 'amp_4p16.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_4p16.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0409 (Fisher's exact test), Q value = 0.083

Table S39.  Gene #7: 'amp_4p16.3' 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
AMP PEAK 7(4P16.3) MUTATED 11 1 3 7 1 46
AMP PEAK 7(4P16.3) WILD-TYPE 183 29 126 182 17 479

Figure S39.  Get High-res Image Gene #7: 'amp_4p16.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_4q12' versus 'Time to Death'

P value = 6.98e-10 (logrank test), Q value = 4.9e-09

Table S40.  Gene #8: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 8(4Q12) MUTATED 138 102 0.1 - 92.7 (11.9)
AMP PEAK 8(4Q12) WILD-TYPE 940 496 0.0 - 211.2 (16.7)

Figure S40.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

'amp_4q12' versus 'YEARS_TO_BIRTH'

P value = 5.29e-06 (Wilcoxon-test), Q value = 2.7e-05

Table S41.  Gene #8: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 8(4Q12) MUTATED 138 56.2 (15.1)
AMP PEAK 8(4Q12) WILD-TYPE 946 50.0 (15.7)

Figure S41.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4q12' versus 'TUMOR_TISSUE_SITE'

P value = 7.12e-11 (Fisher's exact test), Q value = 5.8e-10

Table S42.  Gene #8: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 8(4Q12) MUTATED 108 30
AMP PEAK 8(4Q12) WILD-TYPE 465 482

Figure S42.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_4q12' versus 'RADIATION_THERAPY'

P value = 0.0859 (Fisher's exact test), Q value = 0.16

Table S43.  Gene #8: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 8(4Q12) MUTATED 25 108
AMP PEAK 8(4Q12) WILD-TYPE 233 662

Figure S43.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_4q12' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0547 (Wilcoxon-test), Q value = 0.11

Table S44.  Gene #8: 'amp_4q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 8(4Q12) MUTATED 100 78.7 (15.4)
AMP PEAK 8(4Q12) WILD-TYPE 632 81.5 (15.2)

Figure S44.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S45.  Gene #8: 'amp_4q12' 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
AMP PEAK 8(4Q12) MUTATED 21 4 2 7 2 102
AMP PEAK 8(4Q12) WILD-TYPE 173 26 127 182 16 423

Figure S45.  Get High-res Image Gene #8: 'amp_4q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'Time to Death'

P value = 0.000777 (logrank test), Q value = 0.0024

Table S46.  Gene #9: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 9(5P15.33) MUTATED 76 57 0.2 - 92.7 (12.9)
AMP PEAK 9(5P15.33) WILD-TYPE 1002 541 0.0 - 211.2 (16.2)

Figure S46.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.0388 (Wilcoxon-test), Q value = 0.079

Table S47.  Gene #9: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 9(5P15.33) MUTATED 76 54.2 (16.4)
AMP PEAK 9(5P15.33) WILD-TYPE 1008 50.6 (15.7)

Figure S47.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p15.33' versus 'TUMOR_TISSUE_SITE'

P value = 1.28e-06 (Fisher's exact test), Q value = 6.9e-06

Table S48.  Gene #9: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 9(5P15.33) MUTATED 60 16
AMP PEAK 9(5P15.33) WILD-TYPE 513 496

Figure S48.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.118 (Fisher's exact test), Q value = 0.21

Table S49.  Gene #9: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 9(5P15.33) MUTATED 12 59
AMP PEAK 9(5P15.33) WILD-TYPE 246 711

Figure S49.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S50.  Gene #9: 'amp_5p15.33' 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
AMP PEAK 9(5P15.33) MUTATED 10 3 4 2 4 53
AMP PEAK 9(5P15.33) WILD-TYPE 184 27 125 187 14 472

Figure S50.  Get High-res Image Gene #9: 'amp_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

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

Table S51.  Gene #10: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 10(7P11.2) MUTATED 627 478 0.1 - 211.2 (12.8)
AMP PEAK 10(7P11.2) WILD-TYPE 451 120 0.0 - 182.3 (23.2)

Figure S51.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'YEARS_TO_BIRTH'

P value = 2.8e-69 (Wilcoxon-test), Q value = 7.6e-68

Table S52.  Gene #10: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 10(7P11.2) MUTATED 630 57.9 (13.2)
AMP PEAK 10(7P11.2) WILD-TYPE 454 41.0 (13.7)

Figure S52.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7p11.2' versus 'TUMOR_TISSUE_SITE'

P value = 3.16e-105 (Fisher's exact test), Q value = 1.1e-103

Table S53.  Gene #10: 'amp_7p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 10(7P11.2) MUTATED 503 127
AMP PEAK 10(7P11.2) WILD-TYPE 70 385

Figure S53.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7p11.2' versus 'RADIATION_THERAPY'

P value = 6.09e-14 (Fisher's exact test), Q value = 6.3e-13

Table S54.  Gene #10: 'amp_7p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 10(7P11.2) MUTATED 98 499
AMP PEAK 10(7P11.2) WILD-TYPE 160 271

Figure S54.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7p11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 9.91e-20 (Wilcoxon-test), Q value = 1.6e-18

Table S55.  Gene #10: 'amp_7p11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 10(7P11.2) MUTATED 451 77.3 (16.1)
AMP PEAK 10(7P11.2) WILD-TYPE 281 87.1 (11.6)

Figure S55.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S56.  Gene #10: 'amp_7p11.2' 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
AMP PEAK 10(7P11.2) MUTATED 57 25 33 37 13 465
AMP PEAK 10(7P11.2) WILD-TYPE 137 5 96 152 5 60

Figure S56.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'RACE'

P value = 0.00536 (Fisher's exact test), Q value = 0.014

Table S57.  Gene #10: 'amp_7p11.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 10(7P11.2) MUTATED 1 12 54 541
AMP PEAK 10(7P11.2) WILD-TYPE 0 9 17 418

Figure S57.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #8: 'RACE'

'amp_7p11.2' versus 'ETHNICITY'

P value = 0.00772 (Fisher's exact test), Q value = 0.019

Table S58.  Gene #10: 'amp_7p11.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 10(7P11.2) MUTATED 16 528
AMP PEAK 10(7P11.2) WILD-TYPE 28 393

Figure S58.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q11.21' versus 'Time to Death'

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

Table S59.  Gene #11: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 11(7Q11.21) MUTATED 574 434 0.1 - 211.2 (12.7)
AMP PEAK 11(7Q11.21) WILD-TYPE 504 164 0.0 - 182.3 (22.3)

Figure S59.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

'amp_7q11.21' versus 'YEARS_TO_BIRTH'

P value = 7.26e-56 (Wilcoxon-test), Q value = 1.7e-54

Table S60.  Gene #11: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 11(7Q11.21) MUTATED 577 57.9 (13.2)
AMP PEAK 11(7Q11.21) WILD-TYPE 507 42.8 (14.6)

Figure S60.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q11.21' versus 'TUMOR_TISSUE_SITE'

P value = 2.7e-85 (Fisher's exact test), Q value = 8.7e-84

Table S61.  Gene #11: 'amp_7q11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 11(7Q11.21) MUTATED 461 116
AMP PEAK 11(7Q11.21) WILD-TYPE 112 396

Figure S61.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q11.21' versus 'RADIATION_THERAPY'

P value = 4.12e-11 (Fisher's exact test), Q value = 3.4e-10

Table S62.  Gene #11: 'amp_7q11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 11(7Q11.21) MUTATED 91 454
AMP PEAK 11(7Q11.21) WILD-TYPE 167 316

Figure S62.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q11.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.89e-14 (Wilcoxon-test), Q value = 4.2e-13

Table S63.  Gene #11: 'amp_7q11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 11(7Q11.21) MUTATED 409 77.6 (16.2)
AMP PEAK 11(7Q11.21) WILD-TYPE 323 85.5 (12.7)

Figure S63.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q11.21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S64.  Gene #11: 'amp_7q11.21' 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
AMP PEAK 11(7Q11.21) MUTATED 50 22 31 35 10 429
AMP PEAK 11(7Q11.21) WILD-TYPE 144 8 98 154 8 96

Figure S64.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q11.21' versus 'RACE'

P value = 0.00277 (Fisher's exact test), Q value = 0.0078

Table S65.  Gene #11: 'amp_7q11.21' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 11(7Q11.21) MUTATED 1 10 51 493
AMP PEAK 11(7Q11.21) WILD-TYPE 0 11 20 466

Figure S65.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #8: 'RACE'

'amp_7q11.21' versus 'ETHNICITY'

P value = 0.00829 (Fisher's exact test), Q value = 0.021

Table S66.  Gene #11: 'amp_7q11.21' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 11(7Q11.21) MUTATED 14 484
AMP PEAK 11(7Q11.21) WILD-TYPE 30 437

Figure S66.  Get High-res Image Gene #11: 'amp_7q11.21' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q21.2' versus 'Time to Death'

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

Table S67.  Gene #12: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 12(7Q21.2) MUTATED 628 459 0.1 - 211.2 (13.8)
AMP PEAK 12(7Q21.2) WILD-TYPE 450 139 0.0 - 182.3 (22.3)

Figure S67.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.2' versus 'YEARS_TO_BIRTH'

P value = 9.66e-51 (Wilcoxon-test), Q value = 2.2e-49

Table S68.  Gene #12: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 12(7Q21.2) MUTATED 631 56.9 (13.5)
AMP PEAK 12(7Q21.2) WILD-TYPE 453 42.4 (14.9)

Figure S68.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q21.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.36e-72 (Fisher's exact test), Q value = 4.2e-71

Table S69.  Gene #12: 'amp_7q21.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 12(7Q21.2) MUTATED 476 155
AMP PEAK 12(7Q21.2) WILD-TYPE 97 357

Figure S69.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q21.2' versus 'RADIATION_THERAPY'

P value = 1.29e-11 (Fisher's exact test), Q value = 1.1e-10

Table S70.  Gene #12: 'amp_7q21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 12(7Q21.2) MUTATED 103 495
AMP PEAK 12(7Q21.2) WILD-TYPE 155 275

Figure S70.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q21.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.64e-12 (Wilcoxon-test), Q value = 1.5e-11

Table S71.  Gene #12: 'amp_7q21.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 12(7Q21.2) MUTATED 443 78.0 (16.3)
AMP PEAK 12(7Q21.2) WILD-TYPE 289 85.8 (12.1)

Figure S71.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q21.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S72.  Gene #12: 'amp_7q21.2' 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
AMP PEAK 12(7Q21.2) MUTATED 67 24 40 48 12 440
AMP PEAK 12(7Q21.2) WILD-TYPE 127 6 89 141 6 85

Figure S72.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q21.2' versus 'RACE'

P value = 0.00147 (Fisher's exact test), Q value = 0.0044

Table S73.  Gene #12: 'amp_7q21.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 12(7Q21.2) MUTATED 1 10 55 543
AMP PEAK 12(7Q21.2) WILD-TYPE 0 11 16 416

Figure S73.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #8: 'RACE'

'amp_7q21.2' versus 'ETHNICITY'

P value = 0.00265 (Fisher's exact test), Q value = 0.0075

Table S74.  Gene #12: 'amp_7q21.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 12(7Q21.2) MUTATED 15 536
AMP PEAK 12(7Q21.2) WILD-TYPE 29 385

Figure S74.  Get High-res Image Gene #12: 'amp_7q21.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q31.2' versus 'Time to Death'

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

Table S75.  Gene #13: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 13(7Q31.2) MUTATED 638 453 0.1 - 211.2 (14.0)
AMP PEAK 13(7Q31.2) WILD-TYPE 440 145 0.0 - 182.3 (21.3)

Figure S75.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 1.27e-40 (Wilcoxon-test), Q value = 2.5e-39

Table S76.  Gene #13: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 13(7Q31.2) MUTATED 641 56.1 (13.8)
AMP PEAK 13(7Q31.2) WILD-TYPE 443 43.1 (15.4)

Figure S76.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.12e-59 (Fisher's exact test), Q value = 2.8e-58

Table S77.  Gene #13: 'amp_7q31.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 13(7Q31.2) MUTATED 468 173
AMP PEAK 13(7Q31.2) WILD-TYPE 105 339

Figure S77.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 1.05e-09 (Fisher's exact test), Q value = 7.2e-09

Table S78.  Gene #13: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 13(7Q31.2) MUTATED 110 496
AMP PEAK 13(7Q31.2) WILD-TYPE 148 274

Figure S78.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.54e-09 (Wilcoxon-test), Q value = 1.1e-08

Table S79.  Gene #13: 'amp_7q31.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 13(7Q31.2) MUTATED 446 78.5 (16.0)
AMP PEAK 13(7Q31.2) WILD-TYPE 286 85.0 (13.1)

Figure S79.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S80.  Gene #13: 'amp_7q31.2' 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
AMP PEAK 13(7Q31.2) MUTATED 74 23 47 52 13 432
AMP PEAK 13(7Q31.2) WILD-TYPE 120 7 82 137 5 93

Figure S80.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'RACE'

P value = 0.00796 (Fisher's exact test), Q value = 0.02

Table S81.  Gene #13: 'amp_7q31.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 13(7Q31.2) MUTATED 1 11 54 554
AMP PEAK 13(7Q31.2) WILD-TYPE 0 10 17 405

Figure S81.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #8: 'RACE'

'amp_7q31.2' versus 'ETHNICITY'

P value = 0.00286 (Fisher's exact test), Q value = 0.008

Table S82.  Gene #13: 'amp_7q31.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 13(7Q31.2) MUTATED 16 547
AMP PEAK 13(7Q31.2) WILD-TYPE 28 374

Figure S82.  Get High-res Image Gene #13: 'amp_7q31.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q32.3' versus 'Time to Death'

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

Table S83.  Gene #14: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 14(7Q32.3) MUTATED 651 459 0.1 - 211.2 (14.0)
AMP PEAK 14(7Q32.3) WILD-TYPE 427 139 0.0 - 182.3 (21.4)

Figure S83.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

'amp_7q32.3' versus 'YEARS_TO_BIRTH'

P value = 3.08e-41 (Wilcoxon-test), Q value = 6.3e-40

Table S84.  Gene #14: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 14(7Q32.3) MUTATED 654 56.1 (13.8)
AMP PEAK 14(7Q32.3) WILD-TYPE 430 42.8 (15.4)

Figure S84.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q32.3' versus 'TUMOR_TISSUE_SITE'

P value = 9.51e-59 (Fisher's exact test), Q value = 2.3e-57

Table S85.  Gene #14: 'amp_7q32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 14(7Q32.3) MUTATED 473 181
AMP PEAK 14(7Q32.3) WILD-TYPE 100 331

Figure S85.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q32.3' versus 'RADIATION_THERAPY'

P value = 1.19e-10 (Fisher's exact test), Q value = 9.3e-10

Table S86.  Gene #14: 'amp_7q32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 14(7Q32.3) MUTATED 111 508
AMP PEAK 14(7Q32.3) WILD-TYPE 147 262

Figure S86.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q32.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.22e-09 (Wilcoxon-test), Q value = 1.5e-08

Table S87.  Gene #14: 'amp_7q32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 14(7Q32.3) MUTATED 456 78.6 (16.2)
AMP PEAK 14(7Q32.3) WILD-TYPE 276 85.2 (12.7)

Figure S87.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q32.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S88.  Gene #14: 'amp_7q32.3' 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
AMP PEAK 14(7Q32.3) MUTATED 77 23 49 55 12 438
AMP PEAK 14(7Q32.3) WILD-TYPE 117 7 80 134 6 87

Figure S88.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q32.3' versus 'RACE'

P value = 0.006 (Fisher's exact test), Q value = 0.015

Table S89.  Gene #14: 'amp_7q32.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 14(7Q32.3) MUTATED 1 11 55 566
AMP PEAK 14(7Q32.3) WILD-TYPE 0 10 16 393

Figure S89.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #8: 'RACE'

'amp_7q32.3' versus 'ETHNICITY'

P value = 0.00154 (Fisher's exact test), Q value = 0.0046

Table S90.  Gene #14: 'amp_7q32.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 14(7Q32.3) MUTATED 16 560
AMP PEAK 14(7Q32.3) WILD-TYPE 28 361

Figure S90.  Get High-res Image Gene #14: 'amp_7q32.3' versus Clinical Feature #9: 'ETHNICITY'

'amp_8q24.21' versus 'Time to Death'

P value = 0.000897 (logrank test), Q value = 0.0028

Table S91.  Gene #15: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 15(8Q24.21) MUTATED 169 82 0.1 - 146.1 (20.0)
AMP PEAK 15(8Q24.21) WILD-TYPE 909 516 0.0 - 211.2 (15.3)

Figure S91.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 6.65e-05 (Wilcoxon-test), Q value = 0.00024

Table S92.  Gene #15: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 15(8Q24.21) MUTATED 169 46.2 (16.2)
AMP PEAK 15(8Q24.21) WILD-TYPE 915 51.7 (15.6)

Figure S92.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'TUMOR_TISSUE_SITE'

P value = 0.000773 (Fisher's exact test), Q value = 0.0024

Table S93.  Gene #15: 'amp_8q24.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 15(8Q24.21) MUTATED 69 100
AMP PEAK 15(8Q24.21) WILD-TYPE 504 412

Figure S93.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00064 (Fisher's exact test), Q value = 0.002

Table S94.  Gene #15: 'amp_8q24.21' 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
AMP PEAK 15(8Q24.21) MUTATED 47 2 29 24 2 65
AMP PEAK 15(8Q24.21) WILD-TYPE 147 28 100 165 16 460

Figure S94.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_9q34.3' versus 'Time to Death'

P value = 0.0388 (logrank test), Q value = 0.079

Table S95.  Gene #16: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 16(9Q34.3) MUTATED 141 90 0.1 - 172.8 (15.0)
AMP PEAK 16(9Q34.3) WILD-TYPE 937 508 0.0 - 211.2 (16.2)

Figure S95.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

'amp_9q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0265 (Wilcoxon-test), Q value = 0.057

Table S96.  Gene #16: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 16(9Q34.3) MUTATED 141 53.2 (16.7)
AMP PEAK 16(9Q34.3) WILD-TYPE 943 50.5 (15.6)

Figure S96.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_9q34.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.000199 (Fisher's exact test), Q value = 0.00066

Table S97.  Gene #16: 'amp_9q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 16(9Q34.3) MUTATED 95 46
AMP PEAK 16(9Q34.3) WILD-TYPE 478 466

Figure S97.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_9q34.3' versus 'GENDER'

P value = 0.0675 (Fisher's exact test), Q value = 0.13

Table S98.  Gene #16: 'amp_9q34.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
AMP PEAK 16(9Q34.3) MUTATED 69 72
AMP PEAK 16(9Q34.3) WILD-TYPE 384 560

Figure S98.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #4: 'GENDER'

'amp_9q34.3' versus 'RADIATION_THERAPY'

P value = 0.0859 (Fisher's exact test), Q value = 0.16

Table S99.  Gene #16: 'amp_9q34.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 16(9Q34.3) MUTATED 25 108
AMP PEAK 16(9Q34.3) WILD-TYPE 233 662

Figure S99.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_9q34.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0747 (Wilcoxon-test), Q value = 0.14

Table S100.  Gene #16: 'amp_9q34.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 16(9Q34.3) MUTATED 104 78.3 (16.9)
AMP PEAK 16(9Q34.3) WILD-TYPE 628 81.5 (15.0)

Figure S100.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00048 (Fisher's exact test), Q value = 0.0015

Table S101.  Gene #16: 'amp_9q34.3' 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
AMP PEAK 16(9Q34.3) MUTATED 24 4 13 9 2 89
AMP PEAK 16(9Q34.3) WILD-TYPE 170 26 116 180 16 436

Figure S101.  Get High-res Image Gene #16: 'amp_9q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'Time to Death'

P value = 4.74e-07 (logrank test), Q value = 2.6e-06

Table S102.  Gene #17: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 17(10P15.1) MUTATED 88 31 0.1 - 172.8 (28.6)
AMP PEAK 17(10P15.1) WILD-TYPE 990 567 0.0 - 211.2 (15.3)

Figure S102.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

'amp_10p15.1' versus 'YEARS_TO_BIRTH'

P value = 3.94e-15 (Wilcoxon-test), Q value = 4.7e-14

Table S103.  Gene #17: 'amp_10p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 17(10P15.1) MUTATED 88 38.2 (12.4)
AMP PEAK 17(10P15.1) WILD-TYPE 996 51.9 (15.6)

Figure S103.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p15.1' versus 'TUMOR_TISSUE_SITE'

P value = 5.83e-10 (Fisher's exact test), Q value = 4.1e-09

Table S104.  Gene #17: 'amp_10p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 17(10P15.1) MUTATED 19 69
AMP PEAK 17(10P15.1) WILD-TYPE 554 443

Figure S104.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_10p15.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000762 (Wilcoxon-test), Q value = 0.0024

Table S105.  Gene #17: 'amp_10p15.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 17(10P15.1) MUTATED 58 86.9 (11.9)
AMP PEAK 17(10P15.1) WILD-TYPE 674 80.6 (15.5)

Figure S105.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_10p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S106.  Gene #17: 'amp_10p15.1' 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
AMP PEAK 17(10P15.1) MUTATED 37 1 23 9 1 17
AMP PEAK 17(10P15.1) WILD-TYPE 157 29 106 180 17 508

Figure S106.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'ETHNICITY'

P value = 0.0843 (Fisher's exact test), Q value = 0.16

Table S107.  Gene #17: 'amp_10p15.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 17(10P15.1) MUTATED 7 73
AMP PEAK 17(10P15.1) WILD-TYPE 37 848

Figure S107.  Get High-res Image Gene #17: 'amp_10p15.1' versus Clinical Feature #9: 'ETHNICITY'

'amp_11p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.124 (Fisher's exact test), Q value = 0.21

Table S108.  Gene #18: 'amp_11p13' 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
AMP PEAK 18(11P13) MUTATED 5 2 7 17 1 27
AMP PEAK 18(11P13) WILD-TYPE 189 28 122 172 17 498

Figure S108.  Get High-res Image Gene #18: 'amp_11p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_11q24.1' versus 'Time to Death'

P value = 1.68e-06 (logrank test), Q value = 9.1e-06

Table S109.  Gene #19: 'amp_11q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 19(11Q24.1) MUTATED 111 40 0.2 - 211.2 (24.2)
AMP PEAK 19(11Q24.1) WILD-TYPE 967 558 0.0 - 172.8 (15.3)

Figure S109.  Get High-res Image Gene #19: 'amp_11q24.1' versus Clinical Feature #1: 'Time to Death'

'amp_11q24.1' versus 'YEARS_TO_BIRTH'

P value = 0.000446 (Wilcoxon-test), Q value = 0.0014

Table S110.  Gene #19: 'amp_11q24.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 19(11Q24.1) MUTATED 112 46.0 (14.0)
AMP PEAK 19(11Q24.1) WILD-TYPE 972 51.4 (15.9)

Figure S110.  Get High-res Image Gene #19: 'amp_11q24.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11q24.1' versus 'TUMOR_TISSUE_SITE'

P value = 5.41e-12 (Fisher's exact test), Q value = 4.7e-11

Table S111.  Gene #19: 'amp_11q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 19(11Q24.1) MUTATED 25 87
AMP PEAK 19(11Q24.1) WILD-TYPE 548 425

Figure S111.  Get High-res Image Gene #19: 'amp_11q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_11q24.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0109 (Wilcoxon-test), Q value = 0.026

Table S112.  Gene #19: 'amp_11q24.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 19(11Q24.1) MUTATED 74 85.0 (13.3)
AMP PEAK 19(11Q24.1) WILD-TYPE 658 80.6 (15.4)

Figure S112.  Get High-res Image Gene #19: 'amp_11q24.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_11q24.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S113.  Gene #19: 'amp_11q24.1' 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
AMP PEAK 19(11Q24.1) MUTATED 33 0 18 36 1 24
AMP PEAK 19(11Q24.1) WILD-TYPE 161 30 111 153 17 501

Figure S113.  Get High-res Image Gene #19: 'amp_11q24.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12p13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0268 (Wilcoxon-test), Q value = 0.057

Table S114.  Gene #20: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 20(12P13.32) MUTATED 152 48.1 (16.5)
AMP PEAK 20(12P13.32) WILD-TYPE 932 51.3 (15.6)

Figure S114.  Get High-res Image Gene #20: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p13.32' versus 'RADIATION_THERAPY'

P value = 0.00973 (Fisher's exact test), Q value = 0.024

Table S115.  Gene #20: 'amp_12p13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 20(12P13.32) MUTATED 24 122
AMP PEAK 20(12P13.32) WILD-TYPE 234 648

Figure S115.  Get High-res Image Gene #20: 'amp_12p13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'Time to Death'

P value = 5.66e-15 (logrank test), Q value = 6.5e-14

Table S116.  Gene #21: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 21(12Q14.1) MUTATED 169 133 0.1 - 84.3 (14.3)
AMP PEAK 21(12Q14.1) WILD-TYPE 909 465 0.0 - 211.2 (16.6)

Figure S116.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_12q14.1' versus 'YEARS_TO_BIRTH'

P value = 9.7e-06 (Wilcoxon-test), Q value = 3.9e-05

Table S117.  Gene #21: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 21(12Q14.1) MUTATED 171 55.7 (15.3)
AMP PEAK 21(12Q14.1) WILD-TYPE 913 49.9 (15.7)

Figure S117.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'TUMOR_TISSUE_SITE'

P value = 7.86e-14 (Fisher's exact test), Q value = 8e-13

Table S118.  Gene #21: 'amp_12q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 21(12Q14.1) MUTATED 134 37
AMP PEAK 21(12Q14.1) WILD-TYPE 439 475

Figure S118.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q14.1' versus 'RADIATION_THERAPY'

P value = 0.0104 (Fisher's exact test), Q value = 0.025

Table S119.  Gene #21: 'amp_12q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 21(12Q14.1) MUTATED 28 136
AMP PEAK 21(12Q14.1) WILD-TYPE 230 634

Figure S119.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.13 (Wilcoxon-test), Q value = 0.22

Table S120.  Gene #21: 'amp_12q14.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 21(12Q14.1) MUTATED 119 79.2 (15.5)
AMP PEAK 21(12Q14.1) WILD-TYPE 613 81.5 (15.2)

Figure S120.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_12q14.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S121.  Gene #21: 'amp_12q14.1' 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
AMP PEAK 21(12Q14.1) MUTATED 22 5 5 10 3 126
AMP PEAK 21(12Q14.1) WILD-TYPE 172 25 124 179 15 399

Figure S121.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12q14.1' versus 'ETHNICITY'

P value = 0.0337 (Fisher's exact test), Q value = 0.07

Table S122.  Gene #21: 'amp_12q14.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 21(12Q14.1) MUTATED 2 150
AMP PEAK 21(12Q14.1) WILD-TYPE 42 771

Figure S122.  Get High-res Image Gene #21: 'amp_12q14.1' versus Clinical Feature #9: 'ETHNICITY'

'amp_12q15' versus 'Time to Death'

P value = 1.7e-10 (logrank test), Q value = 1.3e-09

Table S123.  Gene #22: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 22(12Q15) MUTATED 110 89 0.2 - 84.3 (14.0)
AMP PEAK 22(12Q15) WILD-TYPE 968 509 0.0 - 211.2 (16.4)

Figure S123.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 3.2e-05 (Wilcoxon-test), Q value = 0.00012

Table S124.  Gene #22: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 22(12Q15) MUTATED 111 56.8 (14.3)
AMP PEAK 22(12Q15) WILD-TYPE 973 50.1 (15.8)

Figure S124.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'TUMOR_TISSUE_SITE'

P value = 8.88e-13 (Fisher's exact test), Q value = 8.2e-12

Table S125.  Gene #22: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 22(12Q15) MUTATED 93 18
AMP PEAK 22(12Q15) WILD-TYPE 480 494

Figure S125.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q15' versus 'RADIATION_THERAPY'

P value = 0.0443 (Fisher's exact test), Q value = 0.089

Table S126.  Gene #22: 'amp_12q15' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 22(12Q15) MUTATED 18 88
AMP PEAK 22(12Q15) WILD-TYPE 240 682

Figure S126.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q15' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0251 (Wilcoxon-test), Q value = 0.055

Table S127.  Gene #22: 'amp_12q15' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 22(12Q15) MUTATED 87 77.6 (16.7)
AMP PEAK 22(12Q15) WILD-TYPE 645 81.6 (15.0)

Figure S127.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S128.  Gene #22: 'amp_12q15' 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
AMP PEAK 22(12Q15) MUTATED 8 4 2 8 2 87
AMP PEAK 22(12Q15) WILD-TYPE 186 26 127 181 16 438

Figure S128.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'ETHNICITY'

P value = 0.0174 (Fisher's exact test), Q value = 0.04

Table S129.  Gene #22: 'amp_12q15' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 22(12Q15) MUTATED 0 97
AMP PEAK 22(12Q15) WILD-TYPE 44 824

Figure S129.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #9: 'ETHNICITY'

'amp_13q34' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0856 (Wilcoxon-test), Q value = 0.16

Table S130.  Gene #23: 'amp_13q34' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 23(13Q34) MUTATED 36 76.9 (15.8)
AMP PEAK 23(13Q34) WILD-TYPE 696 81.3 (15.2)

Figure S130.  Get High-res Image Gene #23: 'amp_13q34' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_14q32.33' versus 'Time to Death'

P value = 0.00179 (logrank test), Q value = 0.0053

Table S131.  Gene #24: 'amp_14q32.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 24(14Q32.33) MUTATED 44 34 0.4 - 72.9 (13.8)
AMP PEAK 24(14Q32.33) WILD-TYPE 1034 564 0.0 - 211.2 (16.1)

Figure S131.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #1: 'Time to Death'

'amp_14q32.33' versus 'YEARS_TO_BIRTH'

P value = 9.57e-06 (Wilcoxon-test), Q value = 3.9e-05

Table S132.  Gene #24: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 24(14Q32.33) MUTATED 44 61.0 (14.9)
AMP PEAK 24(14Q32.33) WILD-TYPE 1040 50.4 (15.7)

Figure S132.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_14q32.33' versus 'TUMOR_TISSUE_SITE'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.00026

Table S133.  Gene #24: 'amp_14q32.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 24(14Q32.33) MUTATED 36 8
AMP PEAK 24(14Q32.33) WILD-TYPE 537 504

Figure S133.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_14q32.33' versus 'RADIATION_THERAPY'

P value = 0.0643 (Fisher's exact test), Q value = 0.12

Table S134.  Gene #24: 'amp_14q32.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 24(14Q32.33) MUTATED 5 36
AMP PEAK 24(14Q32.33) WILD-TYPE 253 734

Figure S134.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_14q32.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.09 (Wilcoxon-test), Q value = 0.16

Table S135.  Gene #24: 'amp_14q32.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 24(14Q32.33) MUTATED 33 76.7 (16.7)
AMP PEAK 24(14Q32.33) WILD-TYPE 699 81.3 (15.2)

Figure S135.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_14q32.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00226 (Fisher's exact test), Q value = 0.0065

Table S136.  Gene #24: 'amp_14q32.33' 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
AMP PEAK 24(14Q32.33) MUTATED 2 2 3 3 2 32
AMP PEAK 24(14Q32.33) WILD-TYPE 192 28 126 186 16 493

Figure S136.  Get High-res Image Gene #24: 'amp_14q32.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_17p13.2' versus 'Time to Death'

P value = 0.00293 (logrank test), Q value = 0.0082

Table S137.  Gene #25: 'amp_17p13.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 25(17P13.2) MUTATED 74 54 0.2 - 72.4 (15.3)
AMP PEAK 25(17P13.2) WILD-TYPE 1004 544 0.0 - 211.2 (16.0)

Figure S137.  Get High-res Image Gene #25: 'amp_17p13.2' versus Clinical Feature #1: 'Time to Death'

'amp_17p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0115 (Wilcoxon-test), Q value = 0.027

Table S138.  Gene #25: 'amp_17p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 25(17P13.2) MUTATED 74 55.0 (16.1)
AMP PEAK 25(17P13.2) WILD-TYPE 1010 50.5 (15.7)

Figure S138.  Get High-res Image Gene #25: 'amp_17p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p13.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.00522 (Fisher's exact test), Q value = 0.014

Table S139.  Gene #25: 'amp_17p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 25(17P13.2) MUTATED 51 23
AMP PEAK 25(17P13.2) WILD-TYPE 522 489

Figure S139.  Get High-res Image Gene #25: 'amp_17p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17p13.2' versus 'GENDER'

P value = 0.0664 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #25: 'amp_17p13.2' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
AMP PEAK 25(17P13.2) MUTATED 23 51
AMP PEAK 25(17P13.2) WILD-TYPE 430 581

Figure S140.  Get High-res Image Gene #25: 'amp_17p13.2' versus Clinical Feature #4: 'GENDER'

'amp_17p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0051 (Fisher's exact test), Q value = 0.013

Table S141.  Gene #25: 'amp_17p13.2' 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
AMP PEAK 25(17P13.2) MUTATED 10 4 1 12 1 46
AMP PEAK 25(17P13.2) WILD-TYPE 184 26 128 177 17 479

Figure S141.  Get High-res Image Gene #25: 'amp_17p13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_17q25.1' versus 'Time to Death'

P value = 5.13e-06 (logrank test), Q value = 2.6e-05

Table S142.  Gene #26: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 26(17Q25.1) MUTATED 127 91 0.1 - 91.8 (14.0)
AMP PEAK 26(17Q25.1) WILD-TYPE 951 507 0.0 - 211.2 (16.3)

Figure S142.  Get High-res Image Gene #26: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

'amp_17q25.1' versus 'YEARS_TO_BIRTH'

P value = 1.31e-05 (Wilcoxon-test), Q value = 4.9e-05

Table S143.  Gene #26: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 26(17Q25.1) MUTATED 127 56.4 (14.9)
AMP PEAK 26(17Q25.1) WILD-TYPE 957 50.1 (15.8)

Figure S143.  Get High-res Image Gene #26: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q25.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00171 (Fisher's exact test), Q value = 0.0051

Table S144.  Gene #26: 'amp_17q25.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 26(17Q25.1) MUTATED 84 43
AMP PEAK 26(17Q25.1) WILD-TYPE 489 469

Figure S144.  Get High-res Image Gene #26: 'amp_17q25.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17q25.1' versus 'GENDER'

P value = 0.0858 (Fisher's exact test), Q value = 0.16

Table S145.  Gene #26: 'amp_17q25.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
AMP PEAK 26(17Q25.1) MUTATED 44 83
AMP PEAK 26(17Q25.1) WILD-TYPE 409 549

Figure S145.  Get High-res Image Gene #26: 'amp_17q25.1' versus Clinical Feature #4: 'GENDER'

'amp_17q25.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0154 (Fisher's exact test), Q value = 0.036

Table S146.  Gene #26: 'amp_17q25.1' 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
AMP PEAK 26(17Q25.1) MUTATED 21 6 8 14 2 76
AMP PEAK 26(17Q25.1) WILD-TYPE 173 24 121 175 16 449

Figure S146.  Get High-res Image Gene #26: 'amp_17q25.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19p13.3' versus 'Time to Death'

P value = 0.0104 (logrank test), Q value = 0.025

Table S147.  Gene #27: 'amp_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 27(19P13.3) MUTATED 369 231 0.0 - 172.8 (16.2)
AMP PEAK 27(19P13.3) WILD-TYPE 709 367 0.1 - 211.2 (15.9)

Figure S147.  Get High-res Image Gene #27: 'amp_19p13.3' versus Clinical Feature #1: 'Time to Death'

'amp_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 4.65e-05 (Wilcoxon-test), Q value = 0.00017

Table S148.  Gene #27: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 27(19P13.3) MUTATED 372 53.5 (14.7)
AMP PEAK 27(19P13.3) WILD-TYPE 712 49.4 (16.2)

Figure S148.  Get High-res Image Gene #27: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.3' versus 'TUMOR_TISSUE_SITE'

P value = 1.6e-09 (Fisher's exact test), Q value = 1.1e-08

Table S149.  Gene #27: 'amp_19p13.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 27(19P13.3) MUTATED 244 129
AMP PEAK 27(19P13.3) WILD-TYPE 329 383

Figure S149.  Get High-res Image Gene #27: 'amp_19p13.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S150.  Gene #27: 'amp_19p13.3' 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
AMP PEAK 27(19P13.3) MUTATED 26 13 29 74 10 221
AMP PEAK 27(19P13.3) WILD-TYPE 168 17 100 115 8 304

Figure S150.  Get High-res Image Gene #27: 'amp_19p13.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'Time to Death'

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

Table S151.  Gene #28: 'amp_19q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 28(19Q12) MUTATED 244 192 0.0 - 92.7 (14.5)
AMP PEAK 28(19Q12) WILD-TYPE 834 406 0.1 - 211.2 (16.8)

Figure S151.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #1: 'Time to Death'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 3.68e-16 (Wilcoxon-test), Q value = 4.8e-15

Table S152.  Gene #28: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 28(19Q12) MUTATED 246 58.0 (12.9)
AMP PEAK 28(19Q12) WILD-TYPE 838 48.7 (16.0)

Figure S152.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q12' versus 'TUMOR_TISSUE_SITE'

P value = 1.93e-38 (Fisher's exact test), Q value = 3.6e-37

Table S153.  Gene #28: 'amp_19q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 28(19Q12) MUTATED 215 31
AMP PEAK 28(19Q12) WILD-TYPE 358 481

Figure S153.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19q12' versus 'RADIATION_THERAPY'

P value = 1.04e-07 (Fisher's exact test), Q value = 6.2e-07

Table S154.  Gene #28: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 28(19Q12) MUTATED 28 202
AMP PEAK 28(19Q12) WILD-TYPE 230 568

Figure S154.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q12' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 7.05e-05 (Wilcoxon-test), Q value = 0.00025

Table S155.  Gene #28: 'amp_19q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 28(19Q12) MUTATED 167 77.4 (15.8)
AMP PEAK 28(19Q12) WILD-TYPE 565 82.2 (15.0)

Figure S155.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S156.  Gene #28: 'amp_19q12' 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
AMP PEAK 28(19Q12) MUTATED 16 14 9 6 8 193
AMP PEAK 28(19Q12) WILD-TYPE 178 16 120 183 10 332

Figure S156.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'RACE'

P value = 0.0404 (Fisher's exact test), Q value = 0.082

Table S157.  Gene #28: 'amp_19q12' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 28(19Q12) MUTATED 0 8 23 207
AMP PEAK 28(19Q12) WILD-TYPE 1 13 48 752

Figure S157.  Get High-res Image Gene #28: 'amp_19q12' versus Clinical Feature #8: 'RACE'

'amp_19q13.2' versus 'Time to Death'

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

Table S158.  Gene #29: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 29(19Q13.2) MUTATED 228 176 0.1 - 92.7 (14.5)
AMP PEAK 29(19Q13.2) WILD-TYPE 850 422 0.0 - 211.2 (16.6)

Figure S158.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

'amp_19q13.2' versus 'YEARS_TO_BIRTH'

P value = 2.86e-15 (Wilcoxon-test), Q value = 3.4e-14

Table S159.  Gene #29: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 29(19Q13.2) MUTATED 230 58.0 (12.4)
AMP PEAK 29(19Q13.2) WILD-TYPE 854 48.9 (16.1)

Figure S159.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q13.2' versus 'TUMOR_TISSUE_SITE'

P value = 2.11e-33 (Fisher's exact test), Q value = 3.7e-32

Table S160.  Gene #29: 'amp_19q13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 29(19Q13.2) MUTATED 199 31
AMP PEAK 29(19Q13.2) WILD-TYPE 374 481

Figure S160.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19q13.2' versus 'RADIATION_THERAPY'

P value = 6.05e-07 (Fisher's exact test), Q value = 3.3e-06

Table S161.  Gene #29: 'amp_19q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 29(19Q13.2) MUTATED 27 189
AMP PEAK 29(19Q13.2) WILD-TYPE 231 581

Figure S161.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q13.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000511 (Wilcoxon-test), Q value = 0.0016

Table S162.  Gene #29: 'amp_19q13.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 29(19Q13.2) MUTATED 160 78.2 (14.7)
AMP PEAK 29(19Q13.2) WILD-TYPE 572 81.9 (15.4)

Figure S162.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_19q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S163.  Gene #29: 'amp_19q13.2' 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
AMP PEAK 29(19Q13.2) MUTATED 18 12 7 6 6 181
AMP PEAK 29(19Q13.2) WILD-TYPE 176 18 122 183 12 344

Figure S163.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q13.2' versus 'RACE'

P value = 0.0336 (Fisher's exact test), Q value = 0.07

Table S164.  Gene #29: 'amp_19q13.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
AMP PEAK 29(19Q13.2) MUTATED 0 7 23 193
AMP PEAK 29(19Q13.2) WILD-TYPE 1 14 48 766

Figure S164.  Get High-res Image Gene #29: 'amp_19q13.2' versus Clinical Feature #8: 'RACE'

'amp_xp11.21' versus 'Time to Death'

P value = 9.97e-05 (logrank test), Q value = 0.00034

Table S165.  Gene #30: 'amp_xp11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
AMP PEAK 30(XP11.21) MUTATED 104 41 0.1 - 145.1 (20.2)
AMP PEAK 30(XP11.21) WILD-TYPE 974 557 0.0 - 211.2 (15.7)

Figure S165.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #1: 'Time to Death'

'amp_xp11.21' versus 'YEARS_TO_BIRTH'

P value = 2.91e-06 (Wilcoxon-test), Q value = 1.5e-05

Table S166.  Gene #30: 'amp_xp11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
AMP PEAK 30(XP11.21) MUTATED 104 43.9 (15.7)
AMP PEAK 30(XP11.21) WILD-TYPE 980 51.5 (15.6)

Figure S166.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp11.21' versus 'TUMOR_TISSUE_SITE'

P value = 1.86e-05 (Fisher's exact test), Q value = 6.9e-05

Table S167.  Gene #30: 'amp_xp11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
AMP PEAK 30(XP11.21) MUTATED 34 70
AMP PEAK 30(XP11.21) WILD-TYPE 539 442

Figure S167.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_xp11.21' versus 'GENDER'

P value = 0.0284 (Fisher's exact test), Q value = 0.06

Table S168.  Gene #30: 'amp_xp11.21' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
AMP PEAK 30(XP11.21) MUTATED 54 50
AMP PEAK 30(XP11.21) WILD-TYPE 399 582

Figure S168.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #4: 'GENDER'

'amp_xp11.21' versus 'RADIATION_THERAPY'

P value = 0.00966 (Fisher's exact test), Q value = 0.024

Table S169.  Gene #30: 'amp_xp11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
AMP PEAK 30(XP11.21) MUTATED 14 83
AMP PEAK 30(XP11.21) WILD-TYPE 244 687

Figure S169.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_xp11.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0239 (Wilcoxon-test), Q value = 0.053

Table S170.  Gene #30: 'amp_xp11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
AMP PEAK 30(XP11.21) MUTATED 67 84.3 (15.1)
AMP PEAK 30(XP11.21) WILD-TYPE 665 80.8 (15.3)

Figure S170.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xp11.21' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S171.  Gene #30: 'amp_xp11.21' 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
AMP PEAK 30(XP11.21) MUTATED 44 3 17 9 2 29
AMP PEAK 30(XP11.21) WILD-TYPE 150 27 112 180 16 496

Figure S171.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_xp11.21' versus 'ETHNICITY'

P value = 0.0303 (Fisher's exact test), Q value = 0.064

Table S172.  Gene #30: 'amp_xp11.21' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
AMP PEAK 30(XP11.21) MUTATED 9 84
AMP PEAK 30(XP11.21) WILD-TYPE 35 837

Figure S172.  Get High-res Image Gene #30: 'amp_xp11.21' versus Clinical Feature #9: 'ETHNICITY'

'del_1p36.32' versus 'Time to Death'

P value = 7.08e-09 (logrank test), Q value = 4.4e-08

Table S173.  Gene #31: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 1(1P36.32) MUTATED 311 130 0.1 - 182.3 (18.0)
DEL PEAK 1(1P36.32) WILD-TYPE 767 468 0.0 - 211.2 (15.0)

Figure S173.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'TUMOR_TISSUE_SITE'

P value = 1.44e-14 (Fisher's exact test), Q value = 1.6e-13

Table S174.  Gene #31: 'del_1p36.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 1(1P36.32) MUTATED 109 206
DEL PEAK 1(1P36.32) WILD-TYPE 464 306

Figure S174.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p36.32' versus 'RADIATION_THERAPY'

P value = 6.2e-08 (Fisher's exact test), Q value = 3.7e-07

Table S175.  Gene #31: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 1(1P36.32) MUTATED 110 189
DEL PEAK 1(1P36.32) WILD-TYPE 148 581

Figure S175.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p36.32' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0272 (Wilcoxon-test), Q value = 0.058

Table S176.  Gene #31: 'del_1p36.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 1(1P36.32) MUTATED 216 82.3 (16.8)
DEL PEAK 1(1P36.32) WILD-TYPE 516 80.6 (14.6)

Figure S176.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S177.  Gene #31: 'del_1p36.32' 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
DEL PEAK 1(1P36.32) MUTATED 22 2 46 138 4 103
DEL PEAK 1(1P36.32) WILD-TYPE 172 28 83 51 14 422

Figure S177.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p36.32' versus 'RACE'

P value = 0.0217 (Fisher's exact test), Q value = 0.048

Table S178.  Gene #31: 'del_1p36.32' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 1(1P36.32) MUTATED 1 10 14 282
DEL PEAK 1(1P36.32) WILD-TYPE 0 11 57 677

Figure S178.  Get High-res Image Gene #31: 'del_1p36.32' versus Clinical Feature #8: 'RACE'

'del_1p36.23' versus 'Time to Death'

P value = 1.29e-05 (logrank test), Q value = 4.9e-05

Table S179.  Gene #32: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 2(1P36.23) MUTATED 340 156 0.1 - 182.3 (17.1)
DEL PEAK 2(1P36.23) WILD-TYPE 738 442 0.0 - 211.2 (15.2)

Figure S179.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

'del_1p36.23' versus 'TUMOR_TISSUE_SITE'

P value = 8.52e-11 (Fisher's exact test), Q value = 6.8e-10

Table S180.  Gene #32: 'del_1p36.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 2(1P36.23) MUTATED 132 212
DEL PEAK 2(1P36.23) WILD-TYPE 441 300

Figure S180.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p36.23' versus 'RADIATION_THERAPY'

P value = 2.97e-07 (Fisher's exact test), Q value = 1.7e-06

Table S181.  Gene #32: 'del_1p36.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 2(1P36.23) MUTATED 116 211
DEL PEAK 2(1P36.23) WILD-TYPE 142 559

Figure S181.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p36.23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00252 (Wilcoxon-test), Q value = 0.0072

Table S182.  Gene #32: 'del_1p36.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 2(1P36.23) MUTATED 234 82.8 (16.9)
DEL PEAK 2(1P36.23) WILD-TYPE 498 80.3 (14.4)

Figure S182.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S183.  Gene #32: 'del_1p36.23' 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
DEL PEAK 2(1P36.23) MUTATED 24 5 48 140 3 124
DEL PEAK 2(1P36.23) WILD-TYPE 170 25 81 49 15 401

Figure S183.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p36.23' versus 'RACE'

P value = 0.0996 (Fisher's exact test), Q value = 0.18

Table S184.  Gene #32: 'del_1p36.23' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 2(1P36.23) MUTATED 1 10 18 305
DEL PEAK 2(1P36.23) WILD-TYPE 0 11 53 654

Figure S184.  Get High-res Image Gene #32: 'del_1p36.23' versus Clinical Feature #8: 'RACE'

'del_1p32.3' versus 'Time to Death'

P value = 3.19e-13 (logrank test), Q value = 3.1e-12

Table S185.  Gene #33: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 3(1P32.3) MUTATED 254 85 0.1 - 182.3 (18.2)
DEL PEAK 3(1P32.3) WILD-TYPE 824 513 0.0 - 211.2 (15.3)

Figure S185.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

'del_1p32.3' versus 'TUMOR_TISSUE_SITE'

P value = 2.5e-27 (Fisher's exact test), Q value = 4.1e-26

Table S186.  Gene #33: 'del_1p32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 3(1P32.3) MUTATED 61 196
DEL PEAK 3(1P32.3) WILD-TYPE 512 316

Figure S186.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p32.3' versus 'RADIATION_THERAPY'

P value = 3.31e-13 (Fisher's exact test), Q value = 3.1e-12

Table S187.  Gene #33: 'del_1p32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 3(1P32.3) MUTATED 105 135
DEL PEAK 3(1P32.3) WILD-TYPE 153 635

Figure S187.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p32.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00217 (Wilcoxon-test), Q value = 0.0063

Table S188.  Gene #33: 'del_1p32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 3(1P32.3) MUTATED 162 84.0 (14.9)
DEL PEAK 3(1P32.3) WILD-TYPE 570 80.3 (15.3)

Figure S188.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p32.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S189.  Gene #33: 'del_1p32.3' 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
DEL PEAK 3(1P32.3) MUTATED 16 2 42 138 2 57
DEL PEAK 3(1P32.3) WILD-TYPE 178 28 87 51 16 468

Figure S189.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p32.3' versus 'RACE'

P value = 0.036 (Fisher's exact test), Q value = 0.074

Table S190.  Gene #33: 'del_1p32.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 3(1P32.3) MUTATED 1 7 10 231
DEL PEAK 3(1P32.3) WILD-TYPE 0 14 61 728

Figure S190.  Get High-res Image Gene #33: 'del_1p32.3' versus Clinical Feature #8: 'RACE'

'del_1p22.1' versus 'Time to Death'

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

Table S191.  Gene #34: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 4(1P22.1) MUTATED 231 68 0.1 - 182.3 (20.9)
DEL PEAK 4(1P22.1) WILD-TYPE 847 530 0.0 - 211.2 (15.0)

Figure S191.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

'del_1p22.1' versus 'YEARS_TO_BIRTH'

P value = 0.00479 (Wilcoxon-test), Q value = 0.013

Table S192.  Gene #34: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 4(1P22.1) MUTATED 233 48.4 (14.0)
DEL PEAK 4(1P22.1) WILD-TYPE 851 51.5 (16.2)

Figure S192.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p22.1' versus 'TUMOR_TISSUE_SITE'

P value = 6.19e-30 (Fisher's exact test), Q value = 1e-28

Table S193.  Gene #34: 'del_1p22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 4(1P22.1) MUTATED 48 186
DEL PEAK 4(1P22.1) WILD-TYPE 525 326

Figure S193.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p22.1' versus 'RADIATION_THERAPY'

P value = 4.4e-14 (Fisher's exact test), Q value = 4.7e-13

Table S194.  Gene #34: 'del_1p22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 4(1P22.1) MUTATED 100 119
DEL PEAK 4(1P22.1) WILD-TYPE 158 651

Figure S194.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000183 (Wilcoxon-test), Q value = 0.00061

Table S195.  Gene #34: 'del_1p22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 4(1P22.1) MUTATED 149 84.4 (16.1)
DEL PEAK 4(1P22.1) WILD-TYPE 583 80.2 (15.0)

Figure S195.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S196.  Gene #34: 'del_1p22.1' 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
DEL PEAK 4(1P22.1) MUTATED 11 2 39 136 4 42
DEL PEAK 4(1P22.1) WILD-TYPE 183 28 90 53 14 483

Figure S196.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p22.1' versus 'ETHNICITY'

P value = 0.14 (Fisher's exact test), Q value = 0.24

Table S197.  Gene #34: 'del_1p22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 4(1P22.1) MUTATED 14 203
DEL PEAK 4(1P22.1) WILD-TYPE 30 718

Figure S197.  Get High-res Image Gene #34: 'del_1p22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_1q42.11' versus 'Time to Death'

P value = 0.0181 (logrank test), Q value = 0.041

Table S198.  Gene #35: 'del_1q42.11' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 5(1Q42.11) MUTATED 78 51 0.1 - 146.1 (12.6)
DEL PEAK 5(1Q42.11) WILD-TYPE 1000 547 0.0 - 211.2 (16.3)

Figure S198.  Get High-res Image Gene #35: 'del_1q42.11' versus Clinical Feature #1: 'Time to Death'

'del_1q42.11' versus 'YEARS_TO_BIRTH'

P value = 0.024 (Wilcoxon-test), Q value = 0.053

Table S199.  Gene #35: 'del_1q42.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 5(1Q42.11) MUTATED 78 54.9 (15.0)
DEL PEAK 5(1Q42.11) WILD-TYPE 1006 50.5 (15.8)

Figure S199.  Get High-res Image Gene #35: 'del_1q42.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q42.11' versus 'TUMOR_TISSUE_SITE'

P value = 0.045 (Fisher's exact test), Q value = 0.09

Table S200.  Gene #35: 'del_1q42.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 5(1Q42.11) MUTATED 50 28
DEL PEAK 5(1Q42.11) WILD-TYPE 523 484

Figure S200.  Get High-res Image Gene #35: 'del_1q42.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1q42.11' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00912 (Wilcoxon-test), Q value = 0.022

Table S201.  Gene #35: 'del_1q42.11' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 5(1Q42.11) MUTATED 62 74.7 (20.3)
DEL PEAK 5(1Q42.11) WILD-TYPE 670 81.7 (14.6)

Figure S201.  Get High-res Image Gene #35: 'del_1q42.11' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q22.1' versus 'Time to Death'

P value = 0.00355 (logrank test), Q value = 0.0097

Table S202.  Gene #37: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 7(2Q22.1) MUTATED 68 51 1.3 - 117.4 (15.2)
DEL PEAK 7(2Q22.1) WILD-TYPE 1010 547 0.0 - 211.2 (16.1)

Figure S202.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0179 (Wilcoxon-test), Q value = 0.04

Table S203.  Gene #37: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 7(2Q22.1) MUTATED 68 55.0 (16.8)
DEL PEAK 7(2Q22.1) WILD-TYPE 1016 50.5 (15.7)

Figure S203.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00564 (Fisher's exact test), Q value = 0.015

Table S204.  Gene #37: 'del_2q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 7(2Q22.1) MUTATED 47 21
DEL PEAK 7(2Q22.1) WILD-TYPE 526 491

Figure S204.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0834 (Wilcoxon-test), Q value = 0.15

Table S205.  Gene #37: 'del_2q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 7(2Q22.1) MUTATED 48 78.3 (13.1)
DEL PEAK 7(2Q22.1) WILD-TYPE 684 81.3 (15.4)

Figure S205.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00489 (Fisher's exact test), Q value = 0.013

Table S206.  Gene #37: 'del_2q22.1' 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
DEL PEAK 7(2Q22.1) MUTATED 13 5 3 5 2 40
DEL PEAK 7(2Q22.1) WILD-TYPE 181 25 126 184 16 485

Figure S206.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_2q22.1' versus 'ETHNICITY'

P value = 0.105 (Fisher's exact test), Q value = 0.18

Table S207.  Gene #37: 'del_2q22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 7(2Q22.1) MUTATED 0 60
DEL PEAK 7(2Q22.1) WILD-TYPE 44 861

Figure S207.  Get High-res Image Gene #37: 'del_2q22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_2q37.1' versus 'YEARS_TO_BIRTH'

P value = 0.0265 (Wilcoxon-test), Q value = 0.057

Table S208.  Gene #38: 'del_2q37.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 8(2Q37.1) MUTATED 121 47.9 (17.0)
DEL PEAK 8(2Q37.1) WILD-TYPE 963 51.2 (15.6)

Figure S208.  Get High-res Image Gene #38: 'del_2q37.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.1 (Fisher's exact test), Q value = 0.18

Table S209.  Gene #38: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 8(2Q37.1) MUTATED 55 66
DEL PEAK 8(2Q37.1) WILD-TYPE 518 446

Figure S209.  Get High-res Image Gene #38: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00601 (Fisher's exact test), Q value = 0.015

Table S210.  Gene #38: 'del_2q37.1' 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
DEL PEAK 8(2Q37.1) MUTATED 34 3 20 12 1 51
DEL PEAK 8(2Q37.1) WILD-TYPE 160 27 109 177 17 474

Figure S210.  Get High-res Image Gene #38: 'del_2q37.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.00121 (Fisher's exact test), Q value = 0.0037

Table S211.  Gene #39: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 9(3P21.31) MUTATED 13 91
DEL PEAK 9(3P21.31) WILD-TYPE 245 679

Figure S211.  Get High-res Image Gene #39: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3q13.31' versus 'Time to Death'

P value = 0.0798 (logrank test), Q value = 0.15

Table S212.  Gene #40: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 10(3Q13.31) MUTATED 95 64 0.1 - 117.4 (15.9)
DEL PEAK 10(3Q13.31) WILD-TYPE 983 534 0.0 - 211.2 (16.0)

Figure S212.  Get High-res Image Gene #40: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

'del_3q13.31' versus 'RADIATION_THERAPY'

P value = 0.0724 (Fisher's exact test), Q value = 0.14

Table S213.  Gene #40: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 10(3Q13.31) MUTATED 15 73
DEL PEAK 10(3Q13.31) WILD-TYPE 243 697

Figure S213.  Get High-res Image Gene #40: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q34.3' versus 'Time to Death'

P value = 0.000118 (logrank test), Q value = 4e-04

Table S214.  Gene #42: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 12(4Q34.3) MUTATED 229 104 0.1 - 156.2 (20.0)
DEL PEAK 12(4Q34.3) WILD-TYPE 849 494 0.0 - 211.2 (15.0)

Figure S214.  Get High-res Image Gene #42: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0175 (Wilcoxon-test), Q value = 0.04

Table S215.  Gene #42: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 12(4Q34.3) MUTATED 230 48.7 (14.6)
DEL PEAK 12(4Q34.3) WILD-TYPE 854 51.4 (16.1)

Figure S215.  Get High-res Image Gene #42: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'TUMOR_TISSUE_SITE'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.00011

Table S216.  Gene #42: 'del_4q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 12(4Q34.3) MUTATED 93 137
DEL PEAK 12(4Q34.3) WILD-TYPE 480 375

Figure S216.  Get High-res Image Gene #42: 'del_4q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_4q34.3' versus 'GENDER'

P value = 0.0983 (Fisher's exact test), Q value = 0.18

Table S217.  Gene #42: 'del_4q34.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 12(4Q34.3) MUTATED 85 145
DEL PEAK 12(4Q34.3) WILD-TYPE 368 487

Figure S217.  Get High-res Image Gene #42: 'del_4q34.3' versus Clinical Feature #4: 'GENDER'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00164 (Fisher's exact test), Q value = 0.0049

Table S218.  Gene #42: 'del_4q34.3' 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
DEL PEAK 12(4Q34.3) MUTATED 48 6 36 53 2 85
DEL PEAK 12(4Q34.3) WILD-TYPE 146 24 93 136 16 440

Figure S218.  Get High-res Image Gene #42: 'del_4q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.000381 (Fisher's exact test), Q value = 0.0012

Table S219.  Gene #43: 'del_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 13(5P15.33) MUTATED 11 88
DEL PEAK 13(5P15.33) WILD-TYPE 247 682

Figure S219.  Get High-res Image Gene #43: 'del_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0259 (Fisher's exact test), Q value = 0.056

Table S220.  Gene #43: 'del_5p15.33' 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
DEL PEAK 13(5P15.33) MUTATED 23 3 19 8 1 52
DEL PEAK 13(5P15.33) WILD-TYPE 171 27 110 181 17 473

Figure S220.  Get High-res Image Gene #43: 'del_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_5q34' versus 'YEARS_TO_BIRTH'

P value = 0.0878 (Wilcoxon-test), Q value = 0.16

Table S221.  Gene #44: 'del_5q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 14(5Q34) MUTATED 132 48.5 (17.7)
DEL PEAK 14(5Q34) WILD-TYPE 952 51.1 (15.5)

Figure S221.  Get High-res Image Gene #44: 'del_5q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q34' versus 'RADIATION_THERAPY'

P value = 0.00179 (Fisher's exact test), Q value = 0.0053

Table S222.  Gene #44: 'del_5q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 14(5Q34) MUTATED 17 106
DEL PEAK 14(5Q34) WILD-TYPE 241 664

Figure S222.  Get High-res Image Gene #44: 'del_5q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.00069

Table S223.  Gene #44: 'del_5q34' 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
DEL PEAK 14(5Q34) MUTATED 40 6 13 10 1 62
DEL PEAK 14(5Q34) WILD-TYPE 154 24 116 179 17 463

Figure S223.  Get High-res Image Gene #44: 'del_5q34' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 7.99e-08 (logrank test), Q value = 4.8e-07

Table S224.  Gene #45: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 15(6P25.3) MUTATED 137 97 0.1 - 145.1 (12.1)
DEL PEAK 15(6P25.3) WILD-TYPE 941 501 0.0 - 211.2 (16.7)

Figure S224.  Get High-res Image Gene #45: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0376 (Wilcoxon-test), Q value = 0.077

Table S225.  Gene #45: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 15(6P25.3) MUTATED 138 53.3 (15.9)
DEL PEAK 15(6P25.3) WILD-TYPE 946 50.4 (15.7)

Figure S225.  Get High-res Image Gene #45: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00613 (Fisher's exact test), Q value = 0.016

Table S226.  Gene #45: 'del_6p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 15(6P25.3) MUTATED 88 50
DEL PEAK 15(6P25.3) WILD-TYPE 485 462

Figure S226.  Get High-res Image Gene #45: 'del_6p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6p25.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.144 (Wilcoxon-test), Q value = 0.24

Table S227.  Gene #45: 'del_6p25.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 15(6P25.3) MUTATED 99 79.7 (13.9)
DEL PEAK 15(6P25.3) WILD-TYPE 633 81.3 (15.5)

Figure S227.  Get High-res Image Gene #45: 'del_6p25.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.057 (Fisher's exact test), Q value = 0.11

Table S228.  Gene #45: 'del_6p25.3' 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
DEL PEAK 15(6P25.3) MUTATED 24 3 10 16 2 83
DEL PEAK 15(6P25.3) WILD-TYPE 170 27 119 173 16 442

Figure S228.  Get High-res Image Gene #45: 'del_6p25.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'Time to Death'

P value = 2.97e-12 (logrank test), Q value = 2.7e-11

Table S229.  Gene #46: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 16(6Q22.31) MUTATED 237 167 0.1 - 117.4 (13.0)
DEL PEAK 16(6Q22.31) WILD-TYPE 841 431 0.0 - 211.2 (17.2)

Figure S229.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'YEARS_TO_BIRTH'

P value = 1.22e-05 (Wilcoxon-test), Q value = 4.7e-05

Table S230.  Gene #46: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 16(6Q22.31) MUTATED 239 54.8 (15.3)
DEL PEAK 16(6Q22.31) WILD-TYPE 845 49.7 (15.7)

Figure S230.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q22.31' versus 'TUMOR_TISSUE_SITE'

P value = 1.61e-07 (Fisher's exact test), Q value = 9.4e-07

Table S231.  Gene #46: 'del_6q22.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 16(6Q22.31) MUTATED 162 77
DEL PEAK 16(6Q22.31) WILD-TYPE 411 435

Figure S231.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q22.31' versus 'GENDER'

P value = 0.138 (Fisher's exact test), Q value = 0.24

Table S232.  Gene #46: 'del_6q22.31' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 16(6Q22.31) MUTATED 110 129
DEL PEAK 16(6Q22.31) WILD-TYPE 343 503

Figure S232.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #4: 'GENDER'

'del_6q22.31' versus 'RADIATION_THERAPY'

P value = 0.0233 (Fisher's exact test), Q value = 0.052

Table S233.  Gene #46: 'del_6q22.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 16(6Q22.31) MUTATED 43 181
DEL PEAK 16(6Q22.31) WILD-TYPE 215 589

Figure S233.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00855 (Wilcoxon-test), Q value = 0.021

Table S234.  Gene #46: 'del_6q22.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 16(6Q22.31) MUTATED 173 78.7 (15.9)
DEL PEAK 16(6Q22.31) WILD-TYPE 559 81.8 (15.0)

Figure S234.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S235.  Gene #46: 'del_6q22.31' 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
DEL PEAK 16(6Q22.31) MUTATED 47 7 11 19 7 148
DEL PEAK 16(6Q22.31) WILD-TYPE 147 23 118 170 11 377

Figure S235.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'RACE'

P value = 0.116 (Fisher's exact test), Q value = 0.2

Table S236.  Gene #46: 'del_6q22.31' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 16(6Q22.31) MUTATED 1 6 20 205
DEL PEAK 16(6Q22.31) WILD-TYPE 0 15 51 754

Figure S236.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #8: 'RACE'

'del_6q22.31' versus 'ETHNICITY'

P value = 0.0947 (Fisher's exact test), Q value = 0.17

Table S237.  Gene #46: 'del_6q22.31' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 16(6Q22.31) MUTATED 5 204
DEL PEAK 16(6Q22.31) WILD-TYPE 39 717

Figure S237.  Get High-res Image Gene #46: 'del_6q22.31' versus Clinical Feature #9: 'ETHNICITY'

'del_6q26' versus 'Time to Death'

P value = 5.75e-12 (logrank test), Q value = 4.9e-11

Table S238.  Gene #47: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 17(6Q26) MUTATED 258 181 0.0 - 145.1 (13.9)
DEL PEAK 17(6Q26) WILD-TYPE 820 417 0.1 - 211.2 (17.2)

Figure S238.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

'del_6q26' versus 'YEARS_TO_BIRTH'

P value = 0.00012 (Wilcoxon-test), Q value = 4e-04

Table S239.  Gene #47: 'del_6q26' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 17(6Q26) MUTATED 260 54.0 (14.9)
DEL PEAK 17(6Q26) WILD-TYPE 824 49.8 (15.9)

Figure S239.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q26' versus 'TUMOR_TISSUE_SITE'

P value = 2.66e-09 (Fisher's exact test), Q value = 1.7e-08

Table S240.  Gene #47: 'del_6q26' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 17(6Q26) MUTATED 179 81
DEL PEAK 17(6Q26) WILD-TYPE 394 431

Figure S240.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q26' versus 'RADIATION_THERAPY'

P value = 0.00228 (Fisher's exact test), Q value = 0.0065

Table S241.  Gene #47: 'del_6q26' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 17(6Q26) MUTATED 43 199
DEL PEAK 17(6Q26) WILD-TYPE 215 571

Figure S241.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_6q26' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00302 (Wilcoxon-test), Q value = 0.0084

Table S242.  Gene #47: 'del_6q26' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 17(6Q26) MUTATED 187 78.7 (15.5)
DEL PEAK 17(6Q26) WILD-TYPE 545 81.9 (15.1)

Figure S242.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S243.  Gene #47: 'del_6q26' 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
DEL PEAK 17(6Q26) MUTATED 48 8 12 21 9 162
DEL PEAK 17(6Q26) WILD-TYPE 146 22 117 168 9 363

Figure S243.  Get High-res Image Gene #47: 'del_6q26' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'Time to Death'

P value = 5.96e-05 (logrank test), Q value = 0.00021

Table S244.  Gene #48: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 18(8P23.2) MUTATED 87 61 0.1 - 120.6 (13.1)
DEL PEAK 18(8P23.2) WILD-TYPE 991 537 0.0 - 211.2 (16.4)

Figure S244.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'YEARS_TO_BIRTH'

P value = 6.92e-05 (Wilcoxon-test), Q value = 0.00024

Table S245.  Gene #48: 'del_8p23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 18(8P23.2) MUTATED 88 57.1 (14.5)
DEL PEAK 18(8P23.2) WILD-TYPE 996 50.3 (15.8)

Figure S245.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_8p23.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.09e-05 (Fisher's exact test), Q value = 4.2e-05

Table S246.  Gene #48: 'del_8p23.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 18(8P23.2) MUTATED 66 22
DEL PEAK 18(8P23.2) WILD-TYPE 507 490

Figure S246.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_8p23.2' versus 'RADIATION_THERAPY'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S247.  Gene #48: 'del_8p23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 18(8P23.2) MUTATED 11 71
DEL PEAK 18(8P23.2) WILD-TYPE 247 699

Figure S247.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00014 (Fisher's exact test), Q value = 0.00047

Table S248.  Gene #48: 'del_8p23.2' 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
DEL PEAK 18(8P23.2) MUTATED 13 3 5 4 1 62
DEL PEAK 18(8P23.2) WILD-TYPE 181 27 124 185 17 463

Figure S248.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.0146 (Fisher's exact test), Q value = 0.034

Table S249.  Gene #48: 'del_8p23.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 18(8P23.2) MUTATED 0 6 6 72
DEL PEAK 18(8P23.2) WILD-TYPE 1 15 65 887

Figure S249.  Get High-res Image Gene #48: 'del_8p23.2' versus Clinical Feature #8: 'RACE'

'del_8q24.3' versus 'Time to Death'

P value = 0.0117 (logrank test), Q value = 0.028

Table S250.  Gene #49: 'del_8q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 19(8Q24.3) MUTATED 78 49 0.2 - 82.6 (14.3)
DEL PEAK 19(8Q24.3) WILD-TYPE 1000 549 0.0 - 211.2 (16.2)

Figure S250.  Get High-res Image Gene #49: 'del_8q24.3' versus Clinical Feature #1: 'Time to Death'

'del_8q24.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0249 (Fisher's exact test), Q value = 0.054

Table S251.  Gene #49: 'del_8q24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 19(8Q24.3) MUTATED 51 27
DEL PEAK 19(8Q24.3) WILD-TYPE 522 485

Figure S251.  Get High-res Image Gene #49: 'del_8q24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_8q24.3' versus 'RADIATION_THERAPY'

P value = 0.0128 (Fisher's exact test), Q value = 0.03

Table S252.  Gene #49: 'del_8q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 19(8Q24.3) MUTATED 10 65
DEL PEAK 19(8Q24.3) WILD-TYPE 248 705

Figure S252.  Get High-res Image Gene #49: 'del_8q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.082 (Fisher's exact test), Q value = 0.15

Table S253.  Gene #49: 'del_8q24.3' 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
DEL PEAK 19(8Q24.3) MUTATED 12 1 9 6 2 48
DEL PEAK 19(8Q24.3) WILD-TYPE 182 29 120 183 16 477

Figure S253.  Get High-res Image Gene #49: 'del_8q24.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'Time to Death'

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

Table S254.  Gene #50: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 20(9P21.3) MUTATED 588 415 0.1 - 169.8 (13.8)
DEL PEAK 20(9P21.3) WILD-TYPE 490 183 0.0 - 211.2 (19.3)

Figure S254.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 1.65e-30 (Wilcoxon-test), Q value = 2.9e-29

Table S255.  Gene #50: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 20(9P21.3) MUTATED 591 55.7 (14.8)
DEL PEAK 20(9P21.3) WILD-TYPE 493 45.0 (14.9)

Figure S255.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'TUMOR_TISSUE_SITE'

P value = 1.31e-38 (Fisher's exact test), Q value = 2.5e-37

Table S256.  Gene #50: 'del_9p21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 20(9P21.3) MUTATED 418 174
DEL PEAK 20(9P21.3) WILD-TYPE 155 338

Figure S256.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_9p21.3' versus 'RADIATION_THERAPY'

P value = 4.09e-10 (Fisher's exact test), Q value = 3e-09

Table S257.  Gene #50: 'del_9p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 20(9P21.3) MUTATED 96 460
DEL PEAK 20(9P21.3) WILD-TYPE 162 310

Figure S257.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.15e-13 (Wilcoxon-test), Q value = 2.1e-12

Table S258.  Gene #50: 'del_9p21.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 20(9P21.3) MUTATED 412 77.7 (15.9)
DEL PEAK 20(9P21.3) WILD-TYPE 320 85.4 (13.3)

Figure S258.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S259.  Gene #50: 'del_9p21.3' 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
DEL PEAK 20(9P21.3) MUTATED 85 22 36 53 15 381
DEL PEAK 20(9P21.3) WILD-TYPE 109 8 93 136 3 144

Figure S259.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RACE'

P value = 0.0155 (Fisher's exact test), Q value = 0.036

Table S260.  Gene #50: 'del_9p21.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 20(9P21.3) MUTATED 0 12 50 511
DEL PEAK 20(9P21.3) WILD-TYPE 1 9 21 448

Figure S260.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #8: 'RACE'

'del_9p21.3' versus 'ETHNICITY'

P value = 0.063 (Fisher's exact test), Q value = 0.12

Table S261.  Gene #50: 'del_9p21.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 20(9P21.3) MUTATED 17 494
DEL PEAK 20(9P21.3) WILD-TYPE 27 427

Figure S261.  Get High-res Image Gene #50: 'del_9p21.3' versus Clinical Feature #9: 'ETHNICITY'

'del_10p15.3' versus 'Time to Death'

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

Table S262.  Gene #51: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 21(10P15.3) MUTATED 547 440 0.1 - 134.3 (12.4)
DEL PEAK 21(10P15.3) WILD-TYPE 531 158 0.0 - 211.2 (22.5)

Figure S262.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 9.83e-72 (Wilcoxon-test), Q value = 2.8e-70

Table S263.  Gene #51: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 21(10P15.3) MUTATED 549 59.2 (12.4)
DEL PEAK 21(10P15.3) WILD-TYPE 535 42.2 (14.2)

Figure S263.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'TUMOR_TISSUE_SITE'

P value = 9.83e-110 (Fisher's exact test), Q value = 3.7e-108

Table S264.  Gene #51: 'del_10p15.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 21(10P15.3) MUTATED 466 83
DEL PEAK 21(10P15.3) WILD-TYPE 107 429

Figure S264.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10p15.3' versus 'GENDER'

P value = 0.0649 (Fisher's exact test), Q value = 0.12

Table S265.  Gene #51: 'del_10p15.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 21(10P15.3) MUTATED 214 335
DEL PEAK 21(10P15.3) WILD-TYPE 239 297

Figure S265.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #4: 'GENDER'

'del_10p15.3' versus 'RADIATION_THERAPY'

P value = 1.13e-15 (Fisher's exact test), Q value = 1.4e-14

Table S266.  Gene #51: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 21(10P15.3) MUTATED 75 445
DEL PEAK 21(10P15.3) WILD-TYPE 183 325

Figure S266.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p15.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.81e-18 (Wilcoxon-test), Q value = 4.2e-17

Table S267.  Gene #51: 'del_10p15.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 21(10P15.3) MUTATED 400 77.0 (16.2)
DEL PEAK 21(10P15.3) WILD-TYPE 332 86.0 (12.5)

Figure S267.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10p15.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S268.  Gene #51: 'del_10p15.3' 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
DEL PEAK 21(10P15.3) MUTATED 50 22 15 18 11 433
DEL PEAK 21(10P15.3) WILD-TYPE 144 8 114 171 7 92

Figure S268.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10p15.3' versus 'RACE'

P value = 0.00725 (Fisher's exact test), Q value = 0.018

Table S269.  Gene #51: 'del_10p15.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 21(10P15.3) MUTATED 1 9 48 470
DEL PEAK 21(10P15.3) WILD-TYPE 0 12 23 489

Figure S269.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #8: 'RACE'

'del_10p15.3' versus 'ETHNICITY'

P value = 0.00497 (Fisher's exact test), Q value = 0.013

Table S270.  Gene #51: 'del_10p15.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 21(10P15.3) MUTATED 12 455
DEL PEAK 21(10P15.3) WILD-TYPE 32 466

Figure S270.  Get High-res Image Gene #51: 'del_10p15.3' versus Clinical Feature #9: 'ETHNICITY'

'del_10p13' versus 'Time to Death'

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

Table S271.  Gene #52: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 22(10P13) MUTATED 547 443 0.1 - 134.3 (12.5)
DEL PEAK 22(10P13) WILD-TYPE 531 155 0.0 - 211.2 (22.6)

Figure S271.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'YEARS_TO_BIRTH'

P value = 6.25e-72 (Wilcoxon-test), Q value = 1.8e-70

Table S272.  Gene #52: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 22(10P13) MUTATED 549 59.2 (12.3)
DEL PEAK 22(10P13) WILD-TYPE 535 42.2 (14.4)

Figure S272.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'TUMOR_TISSUE_SITE'

P value = 4.32e-111 (Fisher's exact test), Q value = 1.7e-109

Table S273.  Gene #52: 'del_10p13' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 22(10P13) MUTATED 467 82
DEL PEAK 22(10P13) WILD-TYPE 106 430

Figure S273.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10p13' versus 'GENDER'

P value = 0.0267 (Fisher's exact test), Q value = 0.057

Table S274.  Gene #52: 'del_10p13' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 22(10P13) MUTATED 211 338
DEL PEAK 22(10P13) WILD-TYPE 242 294

Figure S274.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #4: 'GENDER'

'del_10p13' versus 'RADIATION_THERAPY'

P value = 9.5e-17 (Fisher's exact test), Q value = 1.4e-15

Table S275.  Gene #52: 'del_10p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 22(10P13) MUTATED 73 447
DEL PEAK 22(10P13) WILD-TYPE 185 323

Figure S275.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p13' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.11e-16 (Wilcoxon-test), Q value = 1.6e-15

Table S276.  Gene #52: 'del_10p13' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 22(10P13) MUTATED 401 77.2 (16.2)
DEL PEAK 22(10P13) WILD-TYPE 331 85.8 (12.6)

Figure S276.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10p13' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S277.  Gene #52: 'del_10p13' 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
DEL PEAK 22(10P13) MUTATED 50 21 15 17 11 435
DEL PEAK 22(10P13) WILD-TYPE 144 9 114 172 7 90

Figure S277.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10p13' versus 'RACE'

P value = 0.0168 (Fisher's exact test), Q value = 0.039

Table S278.  Gene #52: 'del_10p13' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 22(10P13) MUTATED 1 9 47 471
DEL PEAK 22(10P13) WILD-TYPE 0 12 24 488

Figure S278.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #8: 'RACE'

'del_10p13' versus 'ETHNICITY'

P value = 0.00497 (Fisher's exact test), Q value = 0.013

Table S279.  Gene #52: 'del_10p13' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 22(10P13) MUTATED 12 455
DEL PEAK 22(10P13) WILD-TYPE 32 466

Figure S279.  Get High-res Image Gene #52: 'del_10p13' versus Clinical Feature #9: 'ETHNICITY'

'del_10q23.31' versus 'Time to Death'

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

Table S280.  Gene #53: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 23(10Q23.31) MUTATED 621 488 0.1 - 156.2 (12.7)
DEL PEAK 23(10Q23.31) WILD-TYPE 457 110 0.0 - 211.2 (24.6)

Figure S280.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 4.02e-64 (Wilcoxon-test), Q value = 1e-62

Table S281.  Gene #53: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 23(10Q23.31) MUTATED 624 57.7 (13.6)
DEL PEAK 23(10Q23.31) WILD-TYPE 460 41.5 (13.7)

Figure S281.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'TUMOR_TISSUE_SITE'

P value = 7.82e-119 (Fisher's exact test), Q value = 3.3e-117

Table S282.  Gene #53: 'del_10q23.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 23(10Q23.31) MUTATED 510 114
DEL PEAK 23(10Q23.31) WILD-TYPE 63 398

Figure S282.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 3.56e-19 (Fisher's exact test), Q value = 5.6e-18

Table S283.  Gene #53: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 23(10Q23.31) MUTATED 87 506
DEL PEAK 23(10Q23.31) WILD-TYPE 171 264

Figure S283.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q23.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 9.71e-19 (Wilcoxon-test), Q value = 1.5e-17

Table S284.  Gene #53: 'del_10q23.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 23(10Q23.31) MUTATED 446 77.4 (16.1)
DEL PEAK 23(10Q23.31) WILD-TYPE 286 86.8 (11.9)

Figure S284.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S285.  Gene #53: 'del_10q23.31' 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
DEL PEAK 23(10Q23.31) MUTATED 68 25 19 27 13 472
DEL PEAK 23(10Q23.31) WILD-TYPE 126 5 110 162 5 53

Figure S285.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'RACE'

P value = 0.00814 (Fisher's exact test), Q value = 0.02

Table S286.  Gene #53: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 23(10Q23.31) MUTATED 1 11 53 537
DEL PEAK 23(10Q23.31) WILD-TYPE 0 10 18 422

Figure S286.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

'del_10q23.31' versus 'ETHNICITY'

P value = 0.00819 (Fisher's exact test), Q value = 0.02

Table S287.  Gene #53: 'del_10q23.31' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 23(10Q23.31) MUTATED 16 524
DEL PEAK 23(10Q23.31) WILD-TYPE 28 397

Figure S287.  Get High-res Image Gene #53: 'del_10q23.31' versus Clinical Feature #9: 'ETHNICITY'

'del_10q26.3' versus 'Time to Death'

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

Table S288.  Gene #54: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 24(10Q26.3) MUTATED 657 494 0.1 - 172.8 (13.6)
DEL PEAK 24(10Q26.3) WILD-TYPE 421 104 0.0 - 211.2 (23.7)

Figure S288.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 2.56e-50 (Wilcoxon-test), Q value = 5.6e-49

Table S289.  Gene #54: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 24(10Q26.3) MUTATED 661 56.5 (14.3)
DEL PEAK 24(10Q26.3) WILD-TYPE 423 42.0 (13.9)

Figure S289.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'TUMOR_TISSUE_SITE'

P value = 2.98e-97 (Fisher's exact test), Q value = 1e-95

Table S290.  Gene #54: 'del_10q26.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 24(10Q26.3) MUTATED 511 150
DEL PEAK 24(10Q26.3) WILD-TYPE 62 362

Figure S290.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10q26.3' versus 'RADIATION_THERAPY'

P value = 5.32e-17 (Fisher's exact test), Q value = 7.8e-16

Table S291.  Gene #54: 'del_10q26.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 24(10Q26.3) MUTATED 101 530
DEL PEAK 24(10Q26.3) WILD-TYPE 157 240

Figure S291.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q26.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.5e-16 (Wilcoxon-test), Q value = 2e-15

Table S292.  Gene #54: 'del_10q26.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 24(10Q26.3) MUTATED 471 77.8 (16.2)
DEL PEAK 24(10Q26.3) WILD-TYPE 261 87.0 (11.4)

Figure S292.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S293.  Gene #54: 'del_10q26.3' 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
DEL PEAK 24(10Q26.3) MUTATED 81 25 32 37 14 472
DEL PEAK 24(10Q26.3) WILD-TYPE 113 5 97 152 4 53

Figure S293.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'RACE'

P value = 0.00919 (Fisher's exact test), Q value = 0.022

Table S294.  Gene #54: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 24(10Q26.3) MUTATED 1 11 55 572
DEL PEAK 24(10Q26.3) WILD-TYPE 0 10 16 387

Figure S294.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

'del_10q26.3' versus 'ETHNICITY'

P value = 0.0269 (Fisher's exact test), Q value = 0.057

Table S295.  Gene #54: 'del_10q26.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 24(10Q26.3) MUTATED 19 558
DEL PEAK 24(10Q26.3) WILD-TYPE 25 363

Figure S295.  Get High-res Image Gene #54: 'del_10q26.3' versus Clinical Feature #9: 'ETHNICITY'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.000556 (Wilcoxon-test), Q value = 0.0018

Table S296.  Gene #55: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 25(11P15.5) MUTATED 234 47.8 (15.9)
DEL PEAK 25(11P15.5) WILD-TYPE 850 51.7 (15.7)

Figure S296.  Get High-res Image Gene #55: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'GENDER'

P value = 0.0516 (Fisher's exact test), Q value = 0.1

Table S297.  Gene #55: 'del_11p15.5' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 25(11P15.5) MUTATED 111 123
DEL PEAK 25(11P15.5) WILD-TYPE 342 509

Figure S297.  Get High-res Image Gene #55: 'del_11p15.5' versus Clinical Feature #4: 'GENDER'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S298.  Gene #55: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 25(11P15.5) MUTATED 41 180
DEL PEAK 25(11P15.5) WILD-TYPE 217 590

Figure S298.  Get High-res Image Gene #55: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 7.4e-05

Table S299.  Gene #55: 'del_11p15.5' 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
DEL PEAK 25(11P15.5) MUTATED 59 6 29 17 6 117
DEL PEAK 25(11P15.5) WILD-TYPE 135 24 100 172 12 408

Figure S299.  Get High-res Image Gene #55: 'del_11p15.5' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_11p15.1' versus 'Time to Death'

P value = 0.0967 (logrank test), Q value = 0.17

Table S300.  Gene #56: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 26(11P15.1) MUTATED 175 112 0.2 - 156.2 (16.8)
DEL PEAK 26(11P15.1) WILD-TYPE 903 486 0.0 - 211.2 (15.9)

Figure S300.  Get High-res Image Gene #56: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

'del_11p15.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0701 (Fisher's exact test), Q value = 0.13

Table S301.  Gene #56: 'del_11p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 26(11P15.1) MUTATED 104 72
DEL PEAK 26(11P15.1) WILD-TYPE 469 440

Figure S301.  Get High-res Image Gene #56: 'del_11p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_11p15.1' versus 'GENDER'

P value = 0.0448 (Fisher's exact test), Q value = 0.09

Table S302.  Gene #56: 'del_11p15.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 26(11P15.1) MUTATED 86 90
DEL PEAK 26(11P15.1) WILD-TYPE 367 542

Figure S302.  Get High-res Image Gene #56: 'del_11p15.1' versus Clinical Feature #4: 'GENDER'

'del_11p15.1' versus 'RADIATION_THERAPY'

P value = 0.0243 (Fisher's exact test), Q value = 0.053

Table S303.  Gene #56: 'del_11p15.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 26(11P15.1) MUTATED 30 136
DEL PEAK 26(11P15.1) WILD-TYPE 228 634

Figure S303.  Get High-res Image Gene #56: 'del_11p15.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0012

Table S304.  Gene #56: 'del_11p15.1' 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
DEL PEAK 26(11P15.1) MUTATED 43 5 15 14 5 94
DEL PEAK 26(11P15.1) WILD-TYPE 151 25 114 175 13 431

Figure S304.  Get High-res Image Gene #56: 'del_11p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_11p11.2' versus 'Time to Death'

P value = 0.00242 (logrank test), Q value = 0.0069

Table S305.  Gene #57: 'del_11p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 27(11P11.2) MUTATED 158 112 0.2 - 117.4 (16.4)
DEL PEAK 27(11P11.2) WILD-TYPE 920 486 0.0 - 211.2 (16.0)

Figure S305.  Get High-res Image Gene #57: 'del_11p11.2' versus Clinical Feature #1: 'Time to Death'

'del_11p11.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.000295 (Fisher's exact test), Q value = 0.00096

Table S306.  Gene #57: 'del_11p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 27(11P11.2) MUTATED 105 54
DEL PEAK 27(11P11.2) WILD-TYPE 468 458

Figure S306.  Get High-res Image Gene #57: 'del_11p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_11p11.2' versus 'RADIATION_THERAPY'

P value = 0.00294 (Fisher's exact test), Q value = 0.0082

Table S307.  Gene #57: 'del_11p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 27(11P11.2) MUTATED 23 126
DEL PEAK 27(11P11.2) WILD-TYPE 235 644

Figure S307.  Get High-res Image Gene #57: 'del_11p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00031

Table S308.  Gene #57: 'del_11p11.2' 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
DEL PEAK 27(11P11.2) MUTATED 30 5 13 11 6 94
DEL PEAK 27(11P11.2) WILD-TYPE 164 25 116 178 12 431

Figure S308.  Get High-res Image Gene #57: 'del_11p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'Time to Death'

P value = 0.0432 (logrank test), Q value = 0.087

Table S309.  Gene #58: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 28(12P13.1) MUTATED 108 70 0.1 - 95.1 (15.8)
DEL PEAK 28(12P13.1) WILD-TYPE 970 528 0.0 - 211.2 (16.0)

Figure S309.  Get High-res Image Gene #58: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

'del_12p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00632 (Fisher's exact test), Q value = 0.016

Table S310.  Gene #58: 'del_12p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 28(12P13.1) MUTATED 72 38
DEL PEAK 28(12P13.1) WILD-TYPE 501 474

Figure S310.  Get High-res Image Gene #58: 'del_12p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0171 (Fisher's exact test), Q value = 0.039

Table S311.  Gene #58: 'del_12p13.1' 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
DEL PEAK 28(12P13.1) MUTATED 20 2 9 9 1 69
DEL PEAK 28(12P13.1) WILD-TYPE 174 28 120 180 17 456

Figure S311.  Get High-res Image Gene #58: 'del_12p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'ETHNICITY'

P value = 0.116 (Fisher's exact test), Q value = 0.2

Table S312.  Gene #58: 'del_12p13.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 28(12P13.1) MUTATED 1 95
DEL PEAK 28(12P13.1) WILD-TYPE 43 826

Figure S312.  Get High-res Image Gene #58: 'del_12p13.1' versus Clinical Feature #9: 'ETHNICITY'

'del_12q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00123 (Fisher's exact test), Q value = 0.0037

Table S313.  Gene #59: 'del_12q12' 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
DEL PEAK 29(12Q12) MUTATED 42 4 16 12 2 71
DEL PEAK 29(12Q12) WILD-TYPE 152 26 113 177 16 454

Figure S313.  Get High-res Image Gene #59: 'del_12q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 0.00575 (Fisher's exact test), Q value = 0.015

Table S314.  Gene #60: 'del_12q15' 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
DEL PEAK 30(12Q15) MUTATED 37 5 14 12 3 71
DEL PEAK 30(12Q15) WILD-TYPE 157 25 115 177 15 454

Figure S314.  Get High-res Image Gene #60: 'del_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'Time to Death'

P value = 1.29e-05 (logrank test), Q value = 4.9e-05

Table S315.  Gene #61: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 31(13Q14.2) MUTATED 381 251 0.1 - 211.2 (15.1)
DEL PEAK 31(13Q14.2) WILD-TYPE 697 347 0.0 - 182.3 (16.7)

Figure S315.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.0577 (Wilcoxon-test), Q value = 0.11

Table S316.  Gene #61: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 31(13Q14.2) MUTATED 382 52.0 (16.2)
DEL PEAK 31(13Q14.2) WILD-TYPE 702 50.2 (15.6)

Figure S316.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.24e-06 (Fisher's exact test), Q value = 6.8e-06

Table S317.  Gene #61: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 31(13Q14.2) MUTATED 240 142
DEL PEAK 31(13Q14.2) WILD-TYPE 333 370

Figure S317.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.00206 (Fisher's exact test), Q value = 0.006

Table S318.  Gene #61: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 31(13Q14.2) MUTATED 71 293
DEL PEAK 31(13Q14.2) WILD-TYPE 187 477

Figure S318.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00413 (Wilcoxon-test), Q value = 0.011

Table S319.  Gene #61: 'del_13q14.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 31(13Q14.2) MUTATED 270 79.1 (15.5)
DEL PEAK 31(13Q14.2) WILD-TYPE 462 82.2 (15.1)

Figure S319.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S320.  Gene #61: 'del_13q14.2' 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
DEL PEAK 31(13Q14.2) MUTATED 63 10 36 43 6 224
DEL PEAK 31(13Q14.2) WILD-TYPE 131 20 93 146 12 301

Figure S320.  Get High-res Image Gene #61: 'del_13q14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q22.1' versus 'Time to Death'

P value = 4.66e-06 (logrank test), Q value = 2.4e-05

Table S321.  Gene #62: 'del_13q22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 32(13Q22.1) MUTATED 364 240 0.1 - 211.2 (15.0)
DEL PEAK 32(13Q22.1) WILD-TYPE 714 358 0.0 - 182.3 (16.8)

Figure S321.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #1: 'Time to Death'

'del_13q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0122 (Wilcoxon-test), Q value = 0.029

Table S322.  Gene #62: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 32(13Q22.1) MUTATED 365 52.5 (15.6)
DEL PEAK 32(13Q22.1) WILD-TYPE 719 50.0 (15.9)

Figure S322.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q22.1' versus 'TUMOR_TISSUE_SITE'

P value = 6.38e-06 (Fisher's exact test), Q value = 3.2e-05

Table S323.  Gene #62: 'del_13q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 32(13Q22.1) MUTATED 228 137
DEL PEAK 32(13Q22.1) WILD-TYPE 345 375

Figure S323.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q22.1' versus 'RADIATION_THERAPY'

P value = 0.0122 (Fisher's exact test), Q value = 0.029

Table S324.  Gene #62: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 32(13Q22.1) MUTATED 71 278
DEL PEAK 32(13Q22.1) WILD-TYPE 187 492

Figure S324.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00181 (Wilcoxon-test), Q value = 0.0053

Table S325.  Gene #62: 'del_13q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 32(13Q22.1) MUTATED 256 78.9 (15.4)
DEL PEAK 32(13Q22.1) WILD-TYPE 476 82.3 (15.1)

Figure S325.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.00034

Table S326.  Gene #62: 'del_13q22.1' 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
DEL PEAK 32(13Q22.1) MUTATED 59 10 34 44 5 213
DEL PEAK 32(13Q22.1) WILD-TYPE 135 20 95 145 13 312

Figure S326.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q22.1' versus 'ETHNICITY'

P value = 0.142 (Fisher's exact test), Q value = 0.24

Table S327.  Gene #62: 'del_13q22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 32(13Q22.1) MUTATED 10 314
DEL PEAK 32(13Q22.1) WILD-TYPE 34 607

Figure S327.  Get High-res Image Gene #62: 'del_13q22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_14q13.1' versus 'Time to Death'

P value = 5.84e-11 (logrank test), Q value = 4.8e-10

Table S328.  Gene #63: 'del_14q13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 33(14Q13.1) MUTATED 243 170 0.1 - 130.8 (13.8)
DEL PEAK 33(14Q13.1) WILD-TYPE 835 428 0.0 - 211.2 (16.9)

Figure S328.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #1: 'Time to Death'

'del_14q13.1' versus 'YEARS_TO_BIRTH'

P value = 1.67e-09 (Wilcoxon-test), Q value = 1.1e-08

Table S329.  Gene #63: 'del_14q13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 33(14Q13.1) MUTATED 244 56.1 (14.3)
DEL PEAK 33(14Q13.1) WILD-TYPE 840 49.3 (15.9)

Figure S329.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q13.1' versus 'TUMOR_TISSUE_SITE'

P value = 4.67e-12 (Fisher's exact test), Q value = 4.1e-11

Table S330.  Gene #63: 'del_14q13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 33(14Q13.1) MUTATED 176 68
DEL PEAK 33(14Q13.1) WILD-TYPE 397 444

Figure S330.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q13.1' versus 'RADIATION_THERAPY'

P value = 0.0205 (Fisher's exact test), Q value = 0.046

Table S331.  Gene #63: 'del_14q13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 33(14Q13.1) MUTATED 45 188
DEL PEAK 33(14Q13.1) WILD-TYPE 213 582

Figure S331.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_14q13.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00749 (Wilcoxon-test), Q value = 0.019

Table S332.  Gene #63: 'del_14q13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 33(14Q13.1) MUTATED 178 79.6 (13.1)
DEL PEAK 33(14Q13.1) WILD-TYPE 554 81.6 (15.9)

Figure S332.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q13.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S333.  Gene #63: 'del_14q13.1' 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
DEL PEAK 33(14Q13.1) MUTATED 31 6 15 22 6 164
DEL PEAK 33(14Q13.1) WILD-TYPE 163 24 114 167 12 361

Figure S333.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q13.1' versus 'RACE'

P value = 0.0442 (Fisher's exact test), Q value = 0.089

Table S334.  Gene #63: 'del_14q13.1' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 33(14Q13.1) MUTATED 1 4 23 205
DEL PEAK 33(14Q13.1) WILD-TYPE 0 17 48 754

Figure S334.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #8: 'RACE'

'del_14q13.1' versus 'ETHNICITY'

P value = 0.0568 (Fisher's exact test), Q value = 0.11

Table S335.  Gene #63: 'del_14q13.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 33(14Q13.1) MUTATED 4 201
DEL PEAK 33(14Q13.1) WILD-TYPE 40 720

Figure S335.  Get High-res Image Gene #63: 'del_14q13.1' versus Clinical Feature #9: 'ETHNICITY'

'del_14q24.2' versus 'Time to Death'

P value = 0.00327 (logrank test), Q value = 0.009

Table S336.  Gene #64: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 34(14Q24.2) MUTATED 289 183 0.1 - 130.8 (15.3)
DEL PEAK 34(14Q24.2) WILD-TYPE 789 415 0.0 - 211.2 (16.2)

Figure S336.  Get High-res Image Gene #64: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

'del_14q24.2' versus 'YEARS_TO_BIRTH'

P value = 0.0938 (Wilcoxon-test), Q value = 0.17

Table S337.  Gene #64: 'del_14q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 34(14Q24.2) MUTATED 291 52.1 (15.7)
DEL PEAK 34(14Q24.2) WILD-TYPE 793 50.3 (15.8)

Figure S337.  Get High-res Image Gene #64: 'del_14q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q24.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.0196 (Fisher's exact test), Q value = 0.044

Table S338.  Gene #64: 'del_14q24.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 34(14Q24.2) MUTATED 171 120
DEL PEAK 34(14Q24.2) WILD-TYPE 402 392

Figure S338.  Get High-res Image Gene #64: 'del_14q24.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q24.2' versus 'GENDER'

P value = 0.0516 (Fisher's exact test), Q value = 0.1

Table S339.  Gene #64: 'del_14q24.2' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 34(14Q24.2) MUTATED 136 155
DEL PEAK 34(14Q24.2) WILD-TYPE 317 477

Figure S339.  Get High-res Image Gene #64: 'del_14q24.2' versus Clinical Feature #4: 'GENDER'

'del_14q24.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0405 (Fisher's exact test), Q value = 0.082

Table S340.  Gene #64: 'del_14q24.2' 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
DEL PEAK 34(14Q24.2) MUTATED 53 5 28 39 7 159
DEL PEAK 34(14Q24.2) WILD-TYPE 141 25 101 150 11 366

Figure S340.  Get High-res Image Gene #64: 'del_14q24.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q31.3' versus 'Time to Death'

P value = 0.00451 (logrank test), Q value = 0.012

Table S341.  Gene #65: 'del_14q31.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 35(14Q31.3) MUTATED 273 171 0.1 - 130.8 (15.7)
DEL PEAK 35(14Q31.3) WILD-TYPE 805 427 0.0 - 211.2 (16.1)

Figure S341.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #1: 'Time to Death'

'del_14q31.3' versus 'YEARS_TO_BIRTH'

P value = 0.0999 (Wilcoxon-test), Q value = 0.18

Table S342.  Gene #65: 'del_14q31.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 35(14Q31.3) MUTATED 275 52.1 (15.6)
DEL PEAK 35(14Q31.3) WILD-TYPE 809 50.4 (15.8)

Figure S342.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q31.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0591 (Fisher's exact test), Q value = 0.11

Table S343.  Gene #65: 'del_14q31.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 35(14Q31.3) MUTATED 159 116
DEL PEAK 35(14Q31.3) WILD-TYPE 414 396

Figure S343.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q31.3' versus 'GENDER'

P value = 0.0477 (Fisher's exact test), Q value = 0.095

Table S344.  Gene #65: 'del_14q31.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 35(14Q31.3) MUTATED 129 146
DEL PEAK 35(14Q31.3) WILD-TYPE 324 486

Figure S344.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #4: 'GENDER'

'del_14q31.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0768 (Fisher's exact test), Q value = 0.14

Table S345.  Gene #65: 'del_14q31.3' 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
DEL PEAK 35(14Q31.3) MUTATED 51 6 29 36 8 145
DEL PEAK 35(14Q31.3) WILD-TYPE 143 24 100 153 10 380

Figure S345.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q31.3' versus 'RACE'

P value = 0.0962 (Fisher's exact test), Q value = 0.17

Table S346.  Gene #65: 'del_14q31.3' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 35(14Q31.3) MUTATED 1 6 24 235
DEL PEAK 35(14Q31.3) WILD-TYPE 0 15 47 724

Figure S346.  Get High-res Image Gene #65: 'del_14q31.3' versus Clinical Feature #8: 'RACE'

'del_15q14' versus 'Time to Death'

P value = 2.78e-08 (logrank test), Q value = 1.7e-07

Table S347.  Gene #66: 'del_15q14' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 36(15Q14) MUTATED 213 150 0.2 - 134.3 (14.2)
DEL PEAK 36(15Q14) WILD-TYPE 865 448 0.0 - 211.2 (16.8)

Figure S347.  Get High-res Image Gene #66: 'del_15q14' versus Clinical Feature #1: 'Time to Death'

'del_15q14' versus 'YEARS_TO_BIRTH'

P value = 3.15e-07 (Wilcoxon-test), Q value = 1.8e-06

Table S348.  Gene #66: 'del_15q14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 36(15Q14) MUTATED 214 55.9 (15.8)
DEL PEAK 36(15Q14) WILD-TYPE 870 49.6 (15.5)

Figure S348.  Get High-res Image Gene #66: 'del_15q14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q14' versus 'TUMOR_TISSUE_SITE'

P value = 4.6e-10 (Fisher's exact test), Q value = 3.3e-09

Table S349.  Gene #66: 'del_15q14' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 36(15Q14) MUTATED 154 61
DEL PEAK 36(15Q14) WILD-TYPE 419 451

Figure S349.  Get High-res Image Gene #66: 'del_15q14' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_15q14' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0244 (Wilcoxon-test), Q value = 0.053

Table S350.  Gene #66: 'del_15q14' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 36(15Q14) MUTATED 134 78.5 (16.8)
DEL PEAK 36(15Q14) WILD-TYPE 598 81.7 (14.9)

Figure S350.  Get High-res Image Gene #66: 'del_15q14' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_15q14' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S351.  Gene #66: 'del_15q14' 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
DEL PEAK 36(15Q14) MUTATED 25 10 14 22 4 140
DEL PEAK 36(15Q14) WILD-TYPE 169 20 115 167 14 385

Figure S351.  Get High-res Image Gene #66: 'del_15q14' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16p12.2' versus 'Time to Death'

P value = 1.63e-10 (logrank test), Q value = 1.3e-09

Table S352.  Gene #67: 'del_16p12.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 37(16P12.2) MUTATED 113 93 0.4 - 78.3 (15.0)
DEL PEAK 37(16P12.2) WILD-TYPE 965 505 0.0 - 211.2 (16.2)

Figure S352.  Get High-res Image Gene #67: 'del_16p12.2' versus Clinical Feature #1: 'Time to Death'

'del_16p12.2' versus 'YEARS_TO_BIRTH'

P value = 1.28e-07 (Wilcoxon-test), Q value = 7.5e-07

Table S353.  Gene #67: 'del_16p12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 37(16P12.2) MUTATED 114 58.3 (14.3)
DEL PEAK 37(16P12.2) WILD-TYPE 970 49.9 (15.7)

Figure S353.  Get High-res Image Gene #67: 'del_16p12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16p12.2' versus 'TUMOR_TISSUE_SITE'

P value = 8.54e-11 (Fisher's exact test), Q value = 6.8e-10

Table S354.  Gene #67: 'del_16p12.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 37(16P12.2) MUTATED 92 22
DEL PEAK 37(16P12.2) WILD-TYPE 481 490

Figure S354.  Get High-res Image Gene #67: 'del_16p12.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16p12.2' versus 'RADIATION_THERAPY'

P value = 0.0609 (Fisher's exact test), Q value = 0.12

Table S355.  Gene #67: 'del_16p12.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 37(16P12.2) MUTATED 19 90
DEL PEAK 37(16P12.2) WILD-TYPE 239 680

Figure S355.  Get High-res Image Gene #67: 'del_16p12.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_16p12.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S356.  Gene #67: 'del_16p12.2' 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
DEL PEAK 37(16P12.2) MUTATED 14 3 3 5 1 88
DEL PEAK 37(16P12.2) WILD-TYPE 180 27 126 184 17 437

Figure S356.  Get High-res Image Gene #67: 'del_16p12.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16q23.1' versus 'Time to Death'

P value = 2.54e-10 (logrank test), Q value = 1.9e-09

Table S357.  Gene #68: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 38(16Q23.1) MUTATED 128 102 0.1 - 127.6 (13.1)
DEL PEAK 38(16Q23.1) WILD-TYPE 950 496 0.0 - 211.2 (16.6)

Figure S357.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 4.11e-05 (Wilcoxon-test), Q value = 0.00015

Table S358.  Gene #68: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 38(16Q23.1) MUTATED 128 56.0 (14.9)
DEL PEAK 38(16Q23.1) WILD-TYPE 956 50.1 (15.8)

Figure S358.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'TUMOR_TISSUE_SITE'

P value = 4.36e-10 (Fisher's exact test), Q value = 3.2e-09

Table S359.  Gene #68: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 38(16Q23.1) MUTATED 100 28
DEL PEAK 38(16Q23.1) WILD-TYPE 473 484

Figure S359.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16q23.1' versus 'RADIATION_THERAPY'

P value = 0.0911 (Fisher's exact test), Q value = 0.17

Table S360.  Gene #68: 'del_16q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 38(16Q23.1) MUTATED 22 96
DEL PEAK 38(16Q23.1) WILD-TYPE 236 674

Figure S360.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_16q23.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00745 (Wilcoxon-test), Q value = 0.019

Table S361.  Gene #68: 'del_16q23.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 38(16Q23.1) MUTATED 89 76.5 (18.3)
DEL PEAK 38(16Q23.1) WILD-TYPE 643 81.7 (14.7)

Figure S361.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S362.  Gene #68: 'del_16q23.1' 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
DEL PEAK 38(16Q23.1) MUTATED 15 4 6 7 2 94
DEL PEAK 38(16Q23.1) WILD-TYPE 179 26 123 182 16 431

Figure S362.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17p13.1' versus 'Time to Death'

P value = 2.65e-10 (logrank test), Q value = 2e-09

Table S363.  Gene #69: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 39(17P13.1) MUTATED 116 86 0.1 - 92.7 (11.7)
DEL PEAK 39(17P13.1) WILD-TYPE 962 512 0.0 - 211.2 (16.8)

Figure S363.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

'del_17p13.1' versus 'YEARS_TO_BIRTH'

P value = 1.71e-07 (Wilcoxon-test), Q value = 9.9e-07

Table S364.  Gene #69: 'del_17p13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 39(17P13.1) MUTATED 116 58.0 (14.9)
DEL PEAK 39(17P13.1) WILD-TYPE 968 50.0 (15.7)

Figure S364.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 5.36e-14 (Fisher's exact test), Q value = 5.7e-13

Table S365.  Gene #69: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 39(17P13.1) MUTATED 98 18
DEL PEAK 39(17P13.1) WILD-TYPE 475 494

Figure S365.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17p13.1' versus 'GENDER'

P value = 0.136 (Fisher's exact test), Q value = 0.23

Table S366.  Gene #69: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 453 632
DEL PEAK 39(17P13.1) MUTATED 56 60
DEL PEAK 39(17P13.1) WILD-TYPE 397 572

Figure S366.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0345 (Fisher's exact test), Q value = 0.071

Table S367.  Gene #69: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 39(17P13.1) MUTATED 18 90
DEL PEAK 39(17P13.1) WILD-TYPE 240 680

Figure S367.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17p13.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00479 (Wilcoxon-test), Q value = 0.013

Table S368.  Gene #69: 'del_17p13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 39(17P13.1) MUTATED 81 76.4 (17.9)
DEL PEAK 39(17P13.1) WILD-TYPE 651 81.7 (14.8)

Figure S368.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_17p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S369.  Gene #69: 'del_17p13.1' 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
DEL PEAK 39(17P13.1) MUTATED 6 6 4 8 3 89
DEL PEAK 39(17P13.1) WILD-TYPE 188 24 125 181 15 436

Figure S369.  Get High-res Image Gene #69: 'del_17p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'Time to Death'

P value = 5.28e-09 (logrank test), Q value = 3.3e-08

Table S370.  Gene #70: 'del_17q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 40(17Q11.2) MUTATED 93 68 0.1 - 92.7 (11.8)
DEL PEAK 40(17Q11.2) WILD-TYPE 985 530 0.0 - 211.2 (16.6)

Figure S370.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #1: 'Time to Death'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 7.99e-05 (Wilcoxon-test), Q value = 0.00028

Table S371.  Gene #70: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 40(17Q11.2) MUTATED 93 56.8 (13.5)
DEL PEAK 40(17Q11.2) WILD-TYPE 991 50.3 (15.9)

Figure S371.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 3.94e-07 (Fisher's exact test), Q value = 2.2e-06

Table S372.  Gene #70: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 40(17Q11.2) MUTATED 72 21
DEL PEAK 40(17Q11.2) WILD-TYPE 501 491

Figure S372.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17q11.2' versus 'RADIATION_THERAPY'

P value = 0.117 (Fisher's exact test), Q value = 0.2

Table S373.  Gene #70: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 40(17Q11.2) MUTATED 15 69
DEL PEAK 40(17Q11.2) WILD-TYPE 243 701

Figure S373.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17q11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00354 (Wilcoxon-test), Q value = 0.0097

Table S374.  Gene #70: 'del_17q11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 40(17Q11.2) MUTATED 69 74.1 (21.6)
DEL PEAK 40(17Q11.2) WILD-TYPE 663 81.8 (14.3)

Figure S374.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_17q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00018

Table S375.  Gene #70: 'del_17q11.2' 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
DEL PEAK 40(17Q11.2) MUTATED 11 5 4 6 2 65
DEL PEAK 40(17Q11.2) WILD-TYPE 183 25 125 183 16 460

Figure S375.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'RACE'

P value = 0.0931 (Fisher's exact test), Q value = 0.17

Table S376.  Gene #70: 'del_17q11.2' versus Clinical Feature #8: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 21 71 959
DEL PEAK 40(17Q11.2) MUTATED 1 2 8 80
DEL PEAK 40(17Q11.2) WILD-TYPE 0 19 63 879

Figure S376.  Get High-res Image Gene #70: 'del_17q11.2' versus Clinical Feature #8: 'RACE'

'del_19q13.41' versus 'Time to Death'

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

Table S377.  Gene #72: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 42(19Q13.41) MUTATED 359 133 0.0 - 182.3 (20.2)
DEL PEAK 42(19Q13.41) WILD-TYPE 719 465 0.1 - 211.2 (14.4)

Figure S377.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

'del_19q13.41' versus 'YEARS_TO_BIRTH'

P value = 2.55e-09 (Wilcoxon-test), Q value = 1.7e-08

Table S378.  Gene #72: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 42(19Q13.41) MUTATED 363 47.0 (14.3)
DEL PEAK 42(19Q13.41) WILD-TYPE 721 52.8 (16.1)

Figure S378.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'TUMOR_TISSUE_SITE'

P value = 2.93e-35 (Fisher's exact test), Q value = 5.4e-34

Table S379.  Gene #72: 'del_19q13.41' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 42(19Q13.41) MUTATED 97 267
DEL PEAK 42(19Q13.41) WILD-TYPE 476 245

Figure S379.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_19q13.41' versus 'RADIATION_THERAPY'

P value = 3.32e-08 (Fisher's exact test), Q value = 2e-07

Table S380.  Gene #72: 'del_19q13.41' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 42(19Q13.41) MUTATED 123 220
DEL PEAK 42(19Q13.41) WILD-TYPE 135 550

Figure S380.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.41' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.52e-05 (Wilcoxon-test), Q value = 9.3e-05

Table S381.  Gene #72: 'del_19q13.41' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 42(19Q13.41) MUTATED 237 84.4 (13.2)
DEL PEAK 42(19Q13.41) WILD-TYPE 495 79.5 (16.0)

Figure S381.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.41' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S382.  Gene #72: 'del_19q13.41' 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
DEL PEAK 42(19Q13.41) MUTATED 54 3 60 153 4 90
DEL PEAK 42(19Q13.41) WILD-TYPE 140 27 69 36 14 435

Figure S382.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_19q13.41' versus 'ETHNICITY'

P value = 0.144 (Fisher's exact test), Q value = 0.24

Table S383.  Gene #72: 'del_19q13.41' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 42(19Q13.41) MUTATED 20 314
DEL PEAK 42(19Q13.41) WILD-TYPE 24 607

Figure S383.  Get High-res Image Gene #72: 'del_19q13.41' versus Clinical Feature #9: 'ETHNICITY'

'del_19q13.43' versus 'Time to Death'

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

Table S384.  Gene #73: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 43(19Q13.43) MUTATED 350 120 0.0 - 182.3 (21.3)
DEL PEAK 43(19Q13.43) WILD-TYPE 728 478 0.1 - 211.2 (14.3)

Figure S384.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

'del_19q13.43' versus 'YEARS_TO_BIRTH'

P value = 2.98e-14 (Wilcoxon-test), Q value = 3.3e-13

Table S385.  Gene #73: 'del_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 43(19Q13.43) MUTATED 354 45.7 (14.4)
DEL PEAK 43(19Q13.43) WILD-TYPE 730 53.3 (15.8)

Figure S385.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.43' versus 'TUMOR_TISSUE_SITE'

P value = 2.72e-41 (Fisher's exact test), Q value = 5.7e-40

Table S386.  Gene #73: 'del_19q13.43' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 43(19Q13.43) MUTATED 85 270
DEL PEAK 43(19Q13.43) WILD-TYPE 488 242

Figure S386.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_19q13.43' versus 'RADIATION_THERAPY'

P value = 2.52e-09 (Fisher's exact test), Q value = 1.6e-08

Table S387.  Gene #73: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 43(19Q13.43) MUTATED 124 211
DEL PEAK 43(19Q13.43) WILD-TYPE 134 559

Figure S387.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.43' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.85e-06 (Wilcoxon-test), Q value = 1.5e-05

Table S388.  Gene #73: 'del_19q13.43' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 43(19Q13.43) MUTATED 235 84.7 (13.4)
DEL PEAK 43(19Q13.43) WILD-TYPE 497 79.4 (15.8)

Figure S388.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.43' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S389.  Gene #73: 'del_19q13.43' 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
DEL PEAK 43(19Q13.43) MUTATED 58 4 62 150 4 77
DEL PEAK 43(19Q13.43) WILD-TYPE 136 26 67 39 14 448

Figure S389.  Get High-res Image Gene #73: 'del_19q13.43' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'Time to Death'

P value = 3.85e-12 (logrank test), Q value = 3.4e-11

Table S390.  Gene #74: 'del_22q13.32' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 1078 598 0.0 - 211.2 (16.0)
DEL PEAK 44(22Q13.32) MUTATED 289 215 0.1 - 156.2 (15.3)
DEL PEAK 44(22Q13.32) WILD-TYPE 789 383 0.0 - 211.2 (16.4)

Figure S390.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #1: 'Time to Death'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 1.92e-10 (Wilcoxon-test), Q value = 1.5e-09

Table S391.  Gene #74: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 44(22Q13.32) MUTATED 289 55.7 (15.6)
DEL PEAK 44(22Q13.32) WILD-TYPE 795 49.0 (15.5)

Figure S391.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'TUMOR_TISSUE_SITE'

P value = 1.32e-16 (Fisher's exact test), Q value = 1.8e-15

Table S392.  Gene #74: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients BRAIN CENTRAL NERVOUS SYSTEM
ALL 573 512
DEL PEAK 44(22Q13.32) MUTATED 212 77
DEL PEAK 44(22Q13.32) WILD-TYPE 361 435

Figure S392.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_22q13.32' versus 'RADIATION_THERAPY'

P value = 0.000175 (Fisher's exact test), Q value = 0.00058

Table S393.  Gene #74: 'del_22q13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 258 770
DEL PEAK 44(22Q13.32) MUTATED 46 228
DEL PEAK 44(22Q13.32) WILD-TYPE 212 542

Figure S393.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_22q13.32' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.004 (Wilcoxon-test), Q value = 0.011

Table S394.  Gene #74: 'del_22q13.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 44(22Q13.32) MUTATED 205 79.2 (14.9)
DEL PEAK 44(22Q13.32) WILD-TYPE 527 81.8 (15.4)

Figure S394.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 3.9e-05

Table S395.  Gene #74: 'del_22q13.32' 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
DEL PEAK 44(22Q13.32) MUTATED 43 10 16 18 6 196
DEL PEAK 44(22Q13.32) WILD-TYPE 151 20 113 171 12 329

Figure S395.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'ETHNICITY'

P value = 0.118 (Fisher's exact test), Q value = 0.2

Table S396.  Gene #74: 'del_22q13.32' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 44 921
DEL PEAK 44(22Q13.32) MUTATED 7 247
DEL PEAK 44(22Q13.32) WILD-TYPE 37 674

Figure S396.  Get High-res Image Gene #74: 'del_22q13.32' versus Clinical Feature #9: 'ETHNICITY'

'del_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0306 (Wilcoxon-test), Q value = 0.064

Table S397.  Gene #75: 'del_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 1084 50.8 (15.8)
DEL PEAK 45(XQ21.1) MUTATED 183 52.9 (16.0)
DEL PEAK 45(XQ21.1) WILD-TYPE 901 50.4 (15.7)

Figure S397.  Get High-res Image Gene #75: 'del_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xq21.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0818 (Wilcoxon-test), Q value = 0.15

Table S398.  Gene #75: 'del_xq21.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 732 81.1 (15.3)
DEL PEAK 45(XQ21.1) MUTATED 128 78.3 (17.6)
DEL PEAK 45(XQ21.1) WILD-TYPE 604 81.7 (14.7)

Figure S398.  Get High-res Image Gene #75: 'del_xq21.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/22534381/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 focal cnvs = 75

  • Number of selected clinical features = 9

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

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