Correlation between copy number variations of arm-level result and selected clinical features

Overview

Introduction

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

Summary

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

1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
1q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
2p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
2q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
3p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
3q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
4p gain cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
4q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
5p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
5q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
6p gain cnv correlated to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
6q gain cnv correlated to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
7p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
7q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
8q gain cnv correlated to 'YEARS_TO_BIRTH'.
9p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
9q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
10p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
10q gain cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
11p gain cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
11q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
12p gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'RADIATION_THERAPY'.
12q gain cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
13q gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.
14q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
15q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'KARNOFSKY_PERFORMANCE_SCORE'.
16p gain cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
16q gain cnv correlated to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
17p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
17q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
18p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
18q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
19p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
19q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
20p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
20q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
21q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
22q gain cnv correlated to 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
xq gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
1p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
1q loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.
2p loss cnv correlated to 'YEARS_TO_BIRTH'.
2q loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.
3p loss cnv correlated to 'RADIATION_THERAPY' and 'KARNOFSKY_PERFORMANCE_SCORE'.
3q loss cnv correlated to 'RADIATION_THERAPY'.
4p loss cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
4q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
5p loss cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
5q loss cnv correlated to 'RADIATION_THERAPY'.
6p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
6q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
7q loss cnv correlated to 'YEARS_TO_BIRTH'.
8p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
8q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
9p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
9q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
10p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
10q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
11p loss cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
11q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
12p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
12q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
13q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
14q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
15q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
16p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
16q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
17p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
17q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
18p loss cnv correlated to 'YEARS_TO_BIRTH'.
19p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
19q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
20p loss cnv correlated to 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'RACE'.
20q loss cnv correlated to 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
21q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
22q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
xp loss cnv correlated to 'ETHNICITY'.
xq loss cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', and 'KARNOFSKY_PERFORMANCE_SCORE'.

Results

Overview of the results

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


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

'1p gain' versus 'Time to Death'

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

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

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

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

'1p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'1p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'1p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'1p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'1q gain' versus 'Time to Death'

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

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

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

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

'1q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'1q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'1q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'2p gain' versus 'Time to Death'

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

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

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

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

'2p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'2p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'2p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'2p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'2q gain' versus 'Time to Death'

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

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

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

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

'2q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'2q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'2q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'2q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'3p gain' versus 'Time to Death'

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

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

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

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

'3p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'3p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'3p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'3q gain' versus 'Time to Death'

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

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

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

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

'3q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'3q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'3q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'3q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'3q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'4p gain' versus 'Time to Death'

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

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

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

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

'4p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'4p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'4q gain' versus 'Time to Death'

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

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

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

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

'4q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'4q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'4q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'4q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'5p gain' versus 'Time to Death'

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

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

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

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

'5p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'5p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'5p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'5q gain' versus 'Time to Death'

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

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

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

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

'5q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'5q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'5q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'6p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'6p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'6p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'6q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'6q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'6q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'7p gain' versus 'Time to Death'

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

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

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

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

'7p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'7p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'7p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'7p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'7p gain' versus 'RACE'

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

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

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

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

'7p gain' versus 'ETHNICITY'

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

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

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

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

'7q gain' versus 'Time to Death'

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

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

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

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

'7q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'7q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'7q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'7q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'7q gain' versus 'RACE'

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

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

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

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

'7q gain' versus 'ETHNICITY'

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

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

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

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

'8q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'9p gain' versus 'Time to Death'

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

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

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

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

'9p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'9p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'9p gain' versus 'GENDER'

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

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

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

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

'9p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'9q gain' versus 'Time to Death'

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

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

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

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

'9q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'9q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'9q gain' versus 'GENDER'

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

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

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

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

'9q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'9q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'10p gain' versus 'Time to Death'

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

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

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

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

'10p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'10p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'10p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'10p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'10p gain' versus 'ETHNICITY'

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

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

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

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

'10q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'10q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'10q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'10q gain' versus 'ETHNICITY'

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

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

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

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

'11p gain' versus 'Time to Death'

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

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

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

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

'11p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'11p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'11p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'11q gain' versus 'Time to Death'

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

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

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

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

'11q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'11q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'11q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'11q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'12p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'12p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'12q gain' versus 'Time to Death'

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

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

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

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

'12q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'12q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'12q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'12q gain' versus 'RACE'

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

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

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

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

'13q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'13q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'13q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'14q gain' versus 'Time to Death'

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

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

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

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

'14q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'14q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'14q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'15q gain' versus 'Time to Death'

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

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

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

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

'15q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'15q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'16p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'16p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'16p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'16p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'16q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'16q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'16q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'17p gain' versus 'Time to Death'

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

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

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

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

'17p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'17p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'17p gain' versus 'GENDER'

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

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

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

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

'17p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'17q gain' versus 'Time to Death'

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

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

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

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

'17q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'17q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'17q gain' versus 'GENDER'

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

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

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

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

'17q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'18p gain' versus 'Time to Death'

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

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

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

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

'18p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'18p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'18p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'18p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'18q gain' versus 'Time to Death'

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

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

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

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

'18q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'18q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'18q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'18q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'19p gain' versus 'Time to Death'

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

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

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

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

'19p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'19p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'19p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'19p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'19p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'19q gain' versus 'Time to Death'

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

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

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

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

'19q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'19q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'19q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'19q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'19q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'19q gain' versus 'RACE'

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

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

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

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

'20p gain' versus 'Time to Death'

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

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

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

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

'20p gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'20p gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'20p gain' versus 'RADIATION_THERAPY'

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

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

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

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

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'20p gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'20p gain' versus 'RACE'

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

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

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

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

'20p gain' versus 'ETHNICITY'

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

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

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

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

'20q gain' versus 'Time to Death'

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

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

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

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

'20q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'20q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'20q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

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

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

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

'20q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'20q gain' versus 'RACE'

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

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

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

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

'20q gain' versus 'ETHNICITY'

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

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

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

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

'21q gain' versus 'Time to Death'

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

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

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

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

'21q gain' versus 'YEARS_TO_BIRTH'

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

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

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

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

'21q gain' versus 'TUMOR_TISSUE_SITE'

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

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

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

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

'21q gain' versus 'RADIATION_THERAPY'

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

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

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

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

'21q gain' versus 'HISTOLOGICAL_TYPE'

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

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

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

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

'21q gain' versus 'RACE'

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

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

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

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

'21q gain' versus 'ETHNICITY'

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

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

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
21Q GAIN MUTATED	0	80
21Q GAIN WILD-TYPE	44	839

Figure S182. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

'22q gain' versus 'YEARS_TO_BIRTH'

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

Table S183. Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
22Q GAIN MUTATED	55	54.3 (15.0)
22Q GAIN WILD-TYPE	1027	50.6 (15.8)

Figure S183. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0365 (Wilcoxon-test), Q value = 0.099

Table S184. Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
22Q GAIN MUTATED	32	76.9 (12.0)
22Q GAIN WILD-TYPE	698	81.5 (14.8)

Figure S184. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

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

Table S185. Gene #39: '22q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
22Q GAIN MUTATED	3	0	4	16	0	32
22Q GAIN WILD-TYPE	191	28	125	173	18	493

Figure S185. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'ETHNICITY'

P value = 0.0577 (Fisher's exact test), Q value = 0.14

Table S186. Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
22Q GAIN MUTATED	5	42
22Q GAIN WILD-TYPE	39	877

Figure S186. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'ETHNICITY'

'xq gain' versus 'Time to Death'

P value = 0.00655 (logrank test), Q value = 0.022

Table S187. Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
XQ GAIN MUTATED	58	22	0.1 - 130.8 (20.0)
XQ GAIN WILD-TYPE	1021	569	0.0 - 211.2 (15.3)

Figure S187. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.000332 (Wilcoxon-test), Q value = 0.0016

Table S188. Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
XQ GAIN MUTATED	58	43.6 (16.0)
XQ GAIN WILD-TYPE	1024	51.2 (15.7)

Figure S188. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.000357 (Fisher's exact test), Q value = 0.0017

Table S189. Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
XQ GAIN MUTATED	17	41
XQ GAIN WILD-TYPE	554	471

Figure S189. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq gain' versus 'GENDER'

P value = 0.0748 (Fisher's exact test), Q value = 0.17

Table S190. Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
XQ GAIN MUTATED	31	27
XQ GAIN WILD-TYPE	421	604

Figure S190. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.036 (Wilcoxon-test), Q value = 0.098

Table S191. Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
XQ GAIN MUTATED	32	86.2 (12.6)
XQ GAIN WILD-TYPE	698	81.1 (14.7)

Figure S191. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00033

Table S192. Gene #41: 'xq gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
XQ GAIN MUTATED	20	1	15	6	1	15
XQ GAIN WILD-TYPE	174	27	114	183	17	510

Figure S192. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.000948 (Fisher's exact test), Q value = 0.0041

Table S193. Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
XQ GAIN MUTATED	8	40
XQ GAIN WILD-TYPE	36	879

Figure S193. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

'1p loss' versus 'Time to Death'

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

Table S194. Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
1P LOSS MUTATED	196	40	0.1 - 182.3 (21.5)
1P LOSS WILD-TYPE	883	551	0.0 - 211.2 (14.9)

Figure S194. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 5.33e-05 (Wilcoxon-test), Q value = 3e-04

Table S195. Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
1P LOSS MUTATED	197	46.8 (13.6)
1P LOSS WILD-TYPE	885	51.7 (16.1)

Figure S195. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.49e-50 (Fisher's exact test), Q value = 1.4e-48

Table S196. Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
1P LOSS MUTATED	15	183
1P LOSS WILD-TYPE	556	329

Figure S196. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1p loss' versus 'RADIATION_THERAPY'

P value = 2.29e-18 (Fisher's exact test), Q value = 6e-17

Table S197. Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
1P LOSS MUTATED	96	89
1P LOSS WILD-TYPE	162	678

Figure S197. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5e-06 (Wilcoxon-test), Q value = 4.9e-05

Table S198. Gene #42: '1p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
1P LOSS MUTATED	120	86.4 (13.0)
1P LOSS WILD-TYPE	610	80.3 (14.8)

Figure S198. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S199. Gene #42: '1p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
1P LOSS MUTATED	10	0	40	133	1	14
1P LOSS WILD-TYPE	184	28	89	56	17	511

Figure S199. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'RACE'

P value = 0.0889 (Fisher's exact test), Q value = 0.2

Table S200. Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
1P LOSS MUTATED	0	5	6	180
1P LOSS WILD-TYPE	1	16	65	777

Figure S200. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

'1q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00777 (Fisher's exact test), Q value = 0.026

Table S201. Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
1Q LOSS MUTATED	14	29
1Q LOSS WILD-TYPE	557	483

Figure S201. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00126 (Fisher's exact test), Q value = 0.0053

Table S202. Gene #43: '1q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
1Q LOSS MUTATED	4	0	6	19	0	14
1Q LOSS WILD-TYPE	190	28	123	170	18	511

Figure S202. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0632 (Wilcoxon-test), Q value = 0.15

Table S203. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
2P LOSS MUTATED	54	54.5 (17.0)
2P LOSS WILD-TYPE	1028	50.6 (15.7)

Figure S203. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q loss' versus 'TUMOR_TISSUE_SITE'

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

Table S204. Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
2Q LOSS MUTATED	33	19
2Q LOSS WILD-TYPE	538	493

Figure S204. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0645 (Fisher's exact test), Q value = 0.16

Table S205. Gene #45: '2q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
2Q LOSS MUTATED	12	3	4	3	1	29
2Q LOSS WILD-TYPE	182	25	125	186	17	496

Figure S205. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RADIATION_THERAPY'

P value = 0.02 (Fisher's exact test), Q value = 0.059

Table S206. Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
3P LOSS MUTATED	9	58
3P LOSS WILD-TYPE	249	709

Figure S206. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0289 (Wilcoxon-test), Q value = 0.081

Table S207. Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
3P LOSS MUTATED	53	77.7 (13.1)
3P LOSS WILD-TYPE	677	81.6 (14.8)

Figure S207. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'RADIATION_THERAPY'

P value = 0.088 (Fisher's exact test), Q value = 0.2

Table S208. Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
3Q LOSS MUTATED	9	50
3Q LOSS WILD-TYPE	249	717

Figure S208. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4p loss' versus 'Time to Death'

P value = 0.0465 (logrank test), Q value = 0.12

Table S209. Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
4P LOSS MUTATED	126	63	0.1 - 139.0 (17.9)
4P LOSS WILD-TYPE	953	528	0.0 - 211.2 (15.2)

Figure S209. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0365 (Fisher's exact test), Q value = 0.099

Table S210. Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
4P LOSS MUTATED	55	71
4P LOSS WILD-TYPE	516	441

Figure S210. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4p loss' versus 'GENDER'

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

Table S211. Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
4P LOSS MUTATED	40	86
4P LOSS WILD-TYPE	412	545

Figure S211. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0016

Table S212. Gene #48: '4p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
4P LOSS MUTATED	13	2	19	39	0	53
4P LOSS WILD-TYPE	181	26	110	150	18	472

Figure S212. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 5.27e-05 (logrank test), Q value = 3e-04

Table S213. Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
4Q LOSS MUTATED	150	62	0.1 - 156.2 (20.9)
4Q LOSS WILD-TYPE	929	529	0.0 - 211.2 (15.0)

Figure S213. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0336 (Wilcoxon-test), Q value = 0.093

Table S214. Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
4Q LOSS MUTATED	150	48.3 (14.4)
4Q LOSS WILD-TYPE	932	51.2 (16.0)

Figure S214. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000102 (Fisher's exact test), Q value = 0.00054

Table S215. Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
4Q LOSS MUTATED	57	93
4Q LOSS WILD-TYPE	514	419

Figure S215. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.0747 (Fisher's exact test), Q value = 0.17

Table S216. Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
4Q LOSS MUTATED	44	96
4Q LOSS WILD-TYPE	214	671

Figure S216. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.00057

Table S217. Gene #49: '4q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
4Q LOSS MUTATED	24	3	23	46	1	53
4Q LOSS WILD-TYPE	170	25	106	143	17	472

Figure S217. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00209 (Fisher's exact test), Q value = 0.0083

Table S218. Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
5P LOSS MUTATED	8	66
5P LOSS WILD-TYPE	250	701

Figure S218. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0621 (Fisher's exact test), Q value = 0.15

Table S219. Gene #50: '5p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
5P LOSS MUTATED	19	1	11	5	1	42
5P LOSS WILD-TYPE	175	27	118	184	17	483

Figure S219. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00106 (Fisher's exact test), Q value = 0.0045

Table S220. Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
5Q LOSS MUTATED	7	65
5Q LOSS WILD-TYPE	251	702

Figure S220. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6p loss' versus 'Time to Death'

P value = 6.18e-13 (logrank test), Q value = 1.3e-11

Table S221. Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
6P LOSS MUTATED	116	89	0.2 - 92.7 (10.7)
6P LOSS WILD-TYPE	963	502	0.0 - 211.2 (16.4)

Figure S221. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 5.53e-05 (Wilcoxon-test), Q value = 0.00031

Table S222. Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
6P LOSS MUTATED	116	56.2 (14.8)
6P LOSS WILD-TYPE	966	50.1 (15.8)

Figure S222. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.83e-06 (Fisher's exact test), Q value = 3.1e-05

Table S223. Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
6P LOSS MUTATED	85	31
6P LOSS WILD-TYPE	486	481

Figure S223. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0529 (Wilcoxon-test), Q value = 0.13

Table S224. Gene #52: '6p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
6P LOSS MUTATED	85	78.6 (15.1)
6P LOSS WILD-TYPE	645	81.6 (14.6)

Figure S224. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00043

Table S225. Gene #52: '6p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
6P LOSS MUTATED	15	3	4	12	3	79
6P LOSS WILD-TYPE	179	25	125	177	15	446

Figure S225. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RACE'

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

Table S226. Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
6P LOSS MUTATED	1	4	10	98
6P LOSS WILD-TYPE	0	17	61	859

Figure S226. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'Time to Death'

P value = 1.86e-08 (logrank test), Q value = 2.6e-07

Table S227. Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
6Q LOSS MUTATED	186	125	0.1 - 94.8 (13.4)
6Q LOSS WILD-TYPE	893	466	0.0 - 211.2 (16.5)

Figure S227. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000893 (Wilcoxon-test), Q value = 0.0039

Table S228. Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
6Q LOSS MUTATED	187	54.2 (15.0)
6Q LOSS WILD-TYPE	895	50.1 (15.9)

Figure S228. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.23e-05 (Fisher's exact test), Q value = 3e-04

Table S229. Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
6Q LOSS MUTATED	124	63
6Q LOSS WILD-TYPE	447	449

Figure S229. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0683 (Fisher's exact test), Q value = 0.16

Table S230. Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
6Q LOSS MUTATED	34	140
6Q LOSS WILD-TYPE	224	627

Figure S230. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0043 (Wilcoxon-test), Q value = 0.015

Table S231. Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
6Q LOSS MUTATED	135	78.6 (14.1)
6Q LOSS WILD-TYPE	595	81.9 (14.8)

Figure S231. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S232. Gene #53: '6q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
6Q LOSS MUTATED	37	5	10	16	4	115
6Q LOSS WILD-TYPE	157	23	119	173	14	410

Figure S232. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0165 (Fisher's exact test), Q value = 0.05

Table S233. Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
6Q LOSS MUTATED	1	6	18	156
6Q LOSS WILD-TYPE	0	15	53	801

Figure S233. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'ETHNICITY'

P value = 0.0951 (Fisher's exact test), Q value = 0.21

Table S234. Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
6Q LOSS MUTATED	3	158
6Q LOSS WILD-TYPE	41	761

Figure S234. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'ETHNICITY'

'7q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0928 (Wilcoxon-test), Q value = 0.2

Table S235. Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
7Q LOSS MUTATED	9	41.6 (17.8)
7Q LOSS WILD-TYPE	1073	50.9 (15.8)

Figure S235. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'Time to Death'

P value = 8.86e-05 (logrank test), Q value = 0.00047

Table S236. Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
8P LOSS MUTATED	73	51	0.2 - 120.6 (11.7)
8P LOSS WILD-TYPE	1006	540	0.0 - 211.2 (16.0)

Figure S236. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000135 (Wilcoxon-test), Q value = 0.00068

Table S237. Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
8P LOSS MUTATED	74	57.4 (14.2)
8P LOSS WILD-TYPE	1008	50.3 (15.8)

Figure S237. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'TUMOR_TISSUE_SITE'

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

Table S238. Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
8P LOSS MUTATED	58	16
8P LOSS WILD-TYPE	513	496

Figure S238. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8p loss' versus 'RADIATION_THERAPY'

P value = 0.006 (Fisher's exact test), Q value = 0.021

Table S239. Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
8P LOSS MUTATED	8	61
8P LOSS WILD-TYPE	250	706

Figure S239. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 8e-04

Table S240. Gene #56: '8p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
8P LOSS MUTATED	8	1	4	4	1	56
8P LOSS WILD-TYPE	186	27	125	185	17	469

Figure S240. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.00588 (Fisher's exact test), Q value = 0.02

Table S241. Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
8P LOSS MUTATED	0	6	4	59
8P LOSS WILD-TYPE	1	15	67	898

Figure S241. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

'8q loss' versus 'Time to Death'

P value = 4.89e-06 (logrank test), Q value = 4.9e-05

Table S242. Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
8Q LOSS MUTATED	52	38	0.2 - 58.8 (11.6)
8Q LOSS WILD-TYPE	1027	553	0.0 - 211.2 (16.0)

Figure S242. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000298 (Wilcoxon-test), Q value = 0.0015

Table S243. Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
8Q LOSS MUTATED	52	58.5 (12.7)
8Q LOSS WILD-TYPE	1030	50.4 (15.8)

Figure S243. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'TUMOR_TISSUE_SITE'

P value = 9.16e-05 (Fisher's exact test), Q value = 0.00048

Table S244. Gene #57: '8q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
8Q LOSS MUTATED	41	11
8Q LOSS WILD-TYPE	530	501

Figure S244. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8q loss' versus 'RADIATION_THERAPY'

P value = 0.016 (Fisher's exact test), Q value = 0.049

Table S245. Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
8Q LOSS MUTATED	5	43
8Q LOSS WILD-TYPE	253	724

Figure S245. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00516 (Fisher's exact test), Q value = 0.018

Table S246. Gene #57: '8q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
8Q LOSS MUTATED	5	1	3	3	1	39
8Q LOSS WILD-TYPE	189	27	126	186	17	486

Figure S246. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'Time to Death'

P value = 3.06e-05 (logrank test), Q value = 0.00019

Table S247. Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
9P LOSS MUTATED	313	205	0.1 - 169.8 (14.9)
9P LOSS WILD-TYPE	766	386	0.0 - 211.2 (16.0)

Figure S247. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000103 (Wilcoxon-test), Q value = 0.00054

Table S248. Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
9P LOSS MUTATED	314	53.7 (15.3)
9P LOSS WILD-TYPE	768	49.6 (15.8)

Figure S248. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.00015

Table S249. Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
9P LOSS MUTATED	198	117
9P LOSS WILD-TYPE	373	395

Figure S249. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000619 (Fisher's exact test), Q value = 0.0028

Table S250. Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
9P LOSS MUTATED	53	243
9P LOSS WILD-TYPE	205	524

Figure S250. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0417 (Wilcoxon-test), Q value = 0.11

Table S251. Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
9P LOSS MUTATED	212	79.3 (16.0)
9P LOSS WILD-TYPE	518	82.1 (14.1)

Figure S251. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00043

Table S252. Gene #58: '9p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
9P LOSS MUTATED	56	11	23	38	5	182
9P LOSS WILD-TYPE	138	17	106	151	13	343

Figure S252. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RACE'

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

Table S253. Gene #58: '9p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
9P LOSS MUTATED	0	8	28	270
9P LOSS WILD-TYPE	1	13	43	687

Figure S253. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #8: 'RACE'

'9p loss' versus 'ETHNICITY'

P value = 0.0603 (Fisher's exact test), Q value = 0.15

Table S254. Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
9P LOSS MUTATED	7	272
9P LOSS WILD-TYPE	37	647

Figure S254. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'ETHNICITY'

'9q loss' versus 'Time to Death'

P value = 0.00353 (logrank test), Q value = 0.013

Table S255. Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
9Q LOSS MUTATED	141	95	0.1 - 169.8 (14.5)
9Q LOSS WILD-TYPE	938	496	0.0 - 211.2 (16.0)

Figure S255. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00298 (Wilcoxon-test), Q value = 0.011

Table S256. Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
9Q LOSS MUTATED	142	54.1 (15.6)
9Q LOSS WILD-TYPE	940	50.3 (15.8)

Figure S256. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00678 (Fisher's exact test), Q value = 0.023

Table S257. Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
9Q LOSS MUTATED	90	52
9Q LOSS WILD-TYPE	481	460

Figure S257. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q loss' versus 'RADIATION_THERAPY'

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

Table S258. Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
9Q LOSS MUTATED	17	110
9Q LOSS WILD-TYPE	241	657

Figure S258. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00113 (Wilcoxon-test), Q value = 0.0048

Table S259. Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
9Q LOSS MUTATED	95	76.8 (14.7)
9Q LOSS WILD-TYPE	635	82.0 (14.6)

Figure S259. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0628 (Fisher's exact test), Q value = 0.15

Table S260. Gene #59: '9q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
9Q LOSS MUTATED	22	7	11	19	3	80
9Q LOSS WILD-TYPE	172	21	118	170	15	445

Figure S260. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

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

Table S261. Gene #59: '9q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
9Q LOSS MUTATED	0	3	17	117
9Q LOSS WILD-TYPE	1	18	54	840

Figure S261. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'Time to Death'

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

Table S262. Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
10P LOSS MUTATED	556	446	0.1 - 134.3 (12.3)
10P LOSS WILD-TYPE	523	145	0.0 - 211.2 (21.1)

Figure S262. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 4.56e-74 (Wilcoxon-test), Q value = 2.6e-72

Table S263. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
10P LOSS MUTATED	557	59.1 (12.4)
10P LOSS WILD-TYPE	525	42.0 (14.1)

Figure S263. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.18e-116 (Fisher's exact test), Q value = 3.8e-114

Table S264. Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
10P LOSS MUTATED	474	83
10P LOSS WILD-TYPE	97	429

Figure S264. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10p loss' versus 'GENDER'

P value = 0.0843 (Fisher's exact test), Q value = 0.19

Table S265. Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
10P LOSS MUTATED	218	339
10P LOSS WILD-TYPE	234	292

Figure S265. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

'10p loss' versus 'RADIATION_THERAPY'

P value = 1.95e-15 (Fisher's exact test), Q value = 4.6e-14

Table S266. Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
10P LOSS MUTATED	78	451
10P LOSS WILD-TYPE	180	316

Figure S266. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.54e-19 (Wilcoxon-test), Q value = 1.9e-17

Table S267. Gene #60: '10p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
10P LOSS MUTATED	407	77.3 (15.3)
10P LOSS WILD-TYPE	323	86.3 (12.1)

Figure S267. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S268. Gene #60: '10p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
10P LOSS MUTATED	49	21	16	18	10	443
10P LOSS WILD-TYPE	145	7	113	171	8	82

Figure S268. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00286 (Fisher's exact test), Q value = 0.011

Table S269. Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
10P LOSS MUTATED	1	9	50	476
10P LOSS WILD-TYPE	0	12	21	481

Figure S269. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'ETHNICITY'

P value = 0.003 (Fisher's exact test), Q value = 0.011

Table S270. Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
10P LOSS MUTATED	12	465
10P LOSS WILD-TYPE	32	454

Figure S270. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

'10q loss' versus 'Time to Death'

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

Table S271. Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
10Q LOSS MUTATED	584	461	0.1 - 172.8 (12.6)
10Q LOSS WILD-TYPE	495	130	0.0 - 211.2 (21.4)

Figure S271. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 4.63e-68 (Wilcoxon-test), Q value = 2.3e-66

Table S272. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
10Q LOSS MUTATED	585	58.3 (13.1)
10Q LOSS WILD-TYPE	497	41.9 (13.9)

Figure S272. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'TUMOR_TISSUE_SITE'

P value = 3.12e-115 (Fisher's exact test), Q value = 2.1e-113

Table S273. Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
10Q LOSS MUTATED	488	97
10Q LOSS WILD-TYPE	83	415

Figure S273. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'10q loss' versus 'RADIATION_THERAPY'

P value = 1.37e-18 (Fisher's exact test), Q value = 3.7e-17

Table S274. Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
10Q LOSS MUTATED	79	477
10Q LOSS WILD-TYPE	179	290

Figure S274. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.65e-20 (Wilcoxon-test), Q value = 4.9e-19

Table S275. Gene #61: '10q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
10Q LOSS MUTATED	426	77.3 (15.3)
10Q LOSS WILD-TYPE	304	86.9 (11.6)

Figure S275. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S276. Gene #61: '10q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
10Q LOSS MUTATED	57	21	19	21	13	454
10Q LOSS WILD-TYPE	137	7	110	168	5	71

Figure S276. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.00344 (Fisher's exact test), Q value = 0.013

Table S277. Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
10Q LOSS MUTATED	1	9	51	502
10Q LOSS WILD-TYPE	0	12	20	455

Figure S277. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

'10q loss' versus 'ETHNICITY'

P value = 0.000958 (Fisher's exact test), Q value = 0.0042

Table S278. Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
10Q LOSS MUTATED	12	492
10Q LOSS WILD-TYPE	32	427

Figure S278. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

'11p loss' versus 'Time to Death'

P value = 0.12 (logrank test), Q value = 0.25

Table S279. Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
11P LOSS MUTATED	163	106	0.2 - 156.2 (16.5)
11P LOSS WILD-TYPE	916	485	0.0 - 211.2 (15.4)

Figure S279. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0271 (Fisher's exact test), Q value = 0.077

Table S280. Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
11P LOSS MUTATED	99	64
11P LOSS WILD-TYPE	472	448

Figure S280. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p loss' versus 'GENDER'

P value = 0.031 (Fisher's exact test), Q value = 0.086

Table S281. Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
11P LOSS MUTATED	81	82
11P LOSS WILD-TYPE	371	549

Figure S281. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.00885 (Fisher's exact test), Q value = 0.029

Table S282. Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
11P LOSS MUTATED	26	129
11P LOSS WILD-TYPE	232	638

Figure S282. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0016

Table S283. Gene #62: '11p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
11P LOSS MUTATED	38	4	14	12	5	90
11P LOSS WILD-TYPE	156	24	115	177	13	435

Figure S283. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 1.07e-09 (logrank test), Q value = 1.8e-08

Table S284. Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
11Q LOSS MUTATED	113	90	0.2 - 92.7 (13.3)
11Q LOSS WILD-TYPE	966	501	0.0 - 211.2 (16.0)

Figure S284. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 5.43e-06 (Wilcoxon-test), Q value = 5.2e-05

Table S285. Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
11Q LOSS MUTATED	113	57.0 (14.2)
11Q LOSS WILD-TYPE	969	50.1 (15.8)

Figure S285. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.34e-10 (Fisher's exact test), Q value = 2.3e-09

Table S286. Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
11Q LOSS MUTATED	91	22
11Q LOSS WILD-TYPE	480	490

Figure S286. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.0186 (Fisher's exact test), Q value = 0.055

Table S287. Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
11Q LOSS MUTATED	17	91
11Q LOSS WILD-TYPE	241	676

Figure S287. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0448 (Wilcoxon-test), Q value = 0.12

Table S288. Gene #63: '11q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
11Q LOSS MUTATED	87	78.9 (13.9)
11Q LOSS WILD-TYPE	643	81.6 (14.8)

Figure S288. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S289. Gene #63: '11q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
11Q LOSS MUTATED	14	3	6	2	3	85
11Q LOSS WILD-TYPE	180	25	123	187	15	440

Figure S289. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'ETHNICITY'

P value = 0.117 (Fisher's exact test), Q value = 0.25

Table S290. Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
11Q LOSS MUTATED	1	96
11Q LOSS WILD-TYPE	43	823

Figure S290. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #9: 'ETHNICITY'

'12p loss' versus 'Time to Death'

P value = 0.00955 (logrank test), Q value = 0.031

Table S291. Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
12P LOSS MUTATED	85	57	0.1 - 95.1 (14.9)
12P LOSS WILD-TYPE	994	534	0.0 - 211.2 (15.8)

Figure S291. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'YEARS_TO_BIRTH'

P value = 0.108 (Wilcoxon-test), Q value = 0.23

Table S292. Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
12P LOSS MUTATED	86	53.3 (16.6)
12P LOSS WILD-TYPE	996	50.6 (15.7)

Figure S292. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00475 (Fisher's exact test), Q value = 0.017

Table S293. Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
12P LOSS MUTATED	58	28
12P LOSS WILD-TYPE	513	484

Figure S293. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0156 (Fisher's exact test), Q value = 0.048

Table S294. Gene #64: '12p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
12P LOSS MUTATED	16	1	5	7	2	55
12P LOSS WILD-TYPE	178	27	124	182	16	470

Figure S294. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S295. Gene #65: '12q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
12Q LOSS MUTATED	30	1	13	10	3	52
12Q LOSS WILD-TYPE	164	27	116	179	15	473

Figure S295. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.0399 (Fisher's exact test), Q value = 0.11

Table S296. Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
12Q LOSS MUTATED	0	0	2	104
12Q LOSS WILD-TYPE	1	21	69	853

Figure S296. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

'13q loss' versus 'Time to Death'

P value = 0.00301 (logrank test), Q value = 0.011

Table S297. Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
13Q LOSS MUTATED	297	188	0.1 - 211.2 (15.0)
13Q LOSS WILD-TYPE	782	403	0.0 - 182.3 (16.2)

Figure S297. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0579 (Wilcoxon-test), Q value = 0.14

Table S298. Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
13Q LOSS MUTATED	297	52.2 (15.7)
13Q LOSS WILD-TYPE	785	50.2 (15.8)

Figure S298. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.000129 (Fisher's exact test), Q value = 0.00065

Table S299. Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
13Q LOSS MUTATED	185	112
13Q LOSS WILD-TYPE	386	400

Figure S299. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.0203 (Fisher's exact test), Q value = 0.059

Table S300. Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
13Q LOSS MUTATED	58	231
13Q LOSS WILD-TYPE	200	536

Figure S300. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.11 (Wilcoxon-test), Q value = 0.23

Table S301. Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
13Q LOSS MUTATED	211	80.0 (14.6)
13Q LOSS WILD-TYPE	519	81.8 (14.7)

Figure S301. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00362 (Fisher's exact test), Q value = 0.013

Table S302. Gene #66: '13q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
13Q LOSS MUTATED	48	8	25	39	4	173
13Q LOSS WILD-TYPE	146	20	104	150	14	352

Figure S302. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 2.68e-05 (logrank test), Q value = 0.00017

Table S303. Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
14Q LOSS MUTATED	223	148	0.1 - 130.8 (14.7)
14Q LOSS WILD-TYPE	856	443	0.0 - 211.2 (16.2)

Figure S303. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 3.71e-05 (Wilcoxon-test), Q value = 0.00022

Table S304. Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
14Q LOSS MUTATED	224	54.6 (14.9)
14Q LOSS WILD-TYPE	858	49.8 (15.9)

Figure S304. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'TUMOR_TISSUE_SITE'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.00035

Table S305. Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
14Q LOSS MUTATED	145	79
14Q LOSS WILD-TYPE	426	433

Figure S305. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0287 (Wilcoxon-test), Q value = 0.081

Table S306. Gene #67: '14q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
14Q LOSS MUTATED	164	79.6 (14.1)
14Q LOSS WILD-TYPE	566	81.8 (14.8)

Figure S306. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00109 (Fisher's exact test), Q value = 0.0046

Table S307. Gene #67: '14q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
14Q LOSS MUTATED	36	5	18	25	6	134
14Q LOSS WILD-TYPE	158	23	111	164	12	391

Figure S307. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RACE'

P value = 0.0506 (Fisher's exact test), Q value = 0.13

Table S308. Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
14Q LOSS MUTATED	1	5	21	190
14Q LOSS WILD-TYPE	0	16	50	767

Figure S308. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

'14q loss' versus 'ETHNICITY'

P value = 0.0803 (Fisher's exact test), Q value = 0.18

Table S309. Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
14Q LOSS MUTATED	4	187
14Q LOSS WILD-TYPE	40	732

Figure S309. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

'15q loss' versus 'Time to Death'

P value = 0.00238 (logrank test), Q value = 0.0093

Table S310. Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
15Q LOSS MUTATED	154	102	0.2 - 134.3 (15.2)
15Q LOSS WILD-TYPE	925	489	0.0 - 211.2 (15.8)

Figure S310. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

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

Table S311. Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
15Q LOSS MUTATED	155	55.3 (15.9)
15Q LOSS WILD-TYPE	927	50.0 (15.6)

Figure S311. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.00025

Table S312. Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
15Q LOSS MUTATED	106	50
15Q LOSS WILD-TYPE	465	462

Figure S312. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00098 (Fisher's exact test), Q value = 0.0042

Table S313. Gene #68: '15q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
15Q LOSS MUTATED	16	7	12	22	2	97
15Q LOSS WILD-TYPE	178	21	117	167	16	428

Figure S313. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 4.29e-07 (logrank test), Q value = 5.5e-06

Table S314. Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
16P LOSS MUTATED	78	63	0.4 - 78.3 (13.9)
16P LOSS WILD-TYPE	1001	528	0.0 - 211.2 (15.9)

Figure S314. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 3.84e-06 (Wilcoxon-test), Q value = 4e-05

Table S315. Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
16P LOSS MUTATED	78	58.6 (14.2)
16P LOSS WILD-TYPE	1004	50.2 (15.7)

Figure S315. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.21e-07 (Fisher's exact test), Q value = 1.6e-06

Table S316. Gene #69: '16p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
16P LOSS MUTATED	63	15
16P LOSS WILD-TYPE	508	497

Figure S316. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S317. Gene #69: '16p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
16P LOSS MUTATED	8	1	3	4	0	62
16P LOSS WILD-TYPE	186	27	126	185	18	463

Figure S317. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 1.44e-07 (logrank test), Q value = 1.9e-06

Table S318. Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
16Q LOSS MUTATED	104	83	0.2 - 120.6 (14.3)
16Q LOSS WILD-TYPE	975	508	0.0 - 211.2 (16.0)

Figure S318. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 2.45e-05 (Wilcoxon-test), Q value = 0.00016

Table S319. Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
16Q LOSS MUTATED	104	56.9 (14.4)
16Q LOSS WILD-TYPE	978	50.1 (15.8)

Figure S319. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'TUMOR_TISSUE_SITE'

P value = 1.2e-08 (Fisher's exact test), Q value = 1.7e-07

Table S320. Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
16Q LOSS MUTATED	82	22
16Q LOSS WILD-TYPE	489	490

Figure S320. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.037 (Fisher's exact test), Q value = 0.1

Table S321. Gene #70: '16q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
16Q LOSS MUTATED	16	82
16Q LOSS WILD-TYPE	242	685

Figure S321. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'16q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S322. Gene #70: '16q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
16Q LOSS MUTATED	11	2	5	6	1	79
16Q LOSS WILD-TYPE	183	26	124	183	17	446

Figure S322. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'Time to Death'

P value = 2.09e-05 (logrank test), Q value = 0.00014

Table S323. Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
17P LOSS MUTATED	75	53	0.1 - 92.7 (12.2)
17P LOSS WILD-TYPE	1004	538	0.0 - 211.2 (16.0)

Figure S323. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000391 (Wilcoxon-test), Q value = 0.0018

Table S324. Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
17P LOSS MUTATED	75	57.0 (14.4)
17P LOSS WILD-TYPE	1007	50.3 (15.8)

Figure S324. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'TUMOR_TISSUE_SITE'

P value = 2.92e-08 (Fisher's exact test), Q value = 4.1e-07

Table S325. Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
17P LOSS MUTATED	62	13
17P LOSS WILD-TYPE	509	499

Figure S325. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00669 (Wilcoxon-test), Q value = 0.023

Table S326. Gene #71: '17p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
17P LOSS MUTATED	53	77.4 (12.3)
17P LOSS WILD-TYPE	677	81.6 (14.8)

Figure S326. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

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

Table S327. Gene #71: '17p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
17P LOSS MUTATED	6	3	2	5	1	58
17P LOSS WILD-TYPE	188	25	127	184	17	467

Figure S327. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 3.34e-05 (logrank test), Q value = 2e-04

Table S328. Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
17Q LOSS MUTATED	49	36	0.1 - 92.7 (11.7)
17Q LOSS WILD-TYPE	1030	555	0.0 - 211.2 (16.0)

Figure S328. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000848 (Wilcoxon-test), Q value = 0.0038

Table S329. Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
17Q LOSS MUTATED	49	57.9 (13.6)
17Q LOSS WILD-TYPE	1033	50.4 (15.8)

Figure S329. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.86e-06 (Fisher's exact test), Q value = 5.5e-05

Table S330. Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
17Q LOSS MUTATED	41	8
17Q LOSS WILD-TYPE	530	504

Figure S330. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0691 (Wilcoxon-test), Q value = 0.16

Table S331. Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
17Q LOSS MUTATED	33	78.2 (11.8)
17Q LOSS WILD-TYPE	697	81.4 (14.8)

Figure S331. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0022

Table S332. Gene #72: '17q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
17Q LOSS MUTATED	3	2	1	4	1	38
17Q LOSS WILD-TYPE	191	26	128	185	17	487

Figure S332. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0942 (Wilcoxon-test), Q value = 0.2

Table S333. Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
18P LOSS MUTATED	137	52.8 (15.8)
18P LOSS WILD-TYPE	945	50.5 (15.8)

Figure S333. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.118 (Wilcoxon-test), Q value = 0.25

Table S334. Gene #75: '19p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
19P LOSS MUTATED	44	85.0 (13.0)
19P LOSS WILD-TYPE	686	81.0 (14.8)

Figure S334. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q loss' versus 'Time to Death'

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

Table S335. Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
19Q LOSS MUTATED	242	68	0.1 - 182.3 (21.0)
19Q LOSS WILD-TYPE	837	523	0.0 - 211.2 (14.5)

Figure S335. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 1.17e-08 (Wilcoxon-test), Q value = 1.7e-07

Table S336. Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
19Q LOSS MUTATED	243	45.9 (13.5)
19Q LOSS WILD-TYPE	839	52.2 (16.1)

Figure S336. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'TUMOR_TISSUE_SITE'

P value = 5.61e-46 (Fisher's exact test), Q value = 2.2e-44

Table S337. Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
19Q LOSS MUTATED	34	210
19Q LOSS WILD-TYPE	537	302

Figure S337. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'19q loss' versus 'RADIATION_THERAPY'

P value = 1.05e-13 (Fisher's exact test), Q value = 2.3e-12

Table S338. Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
19Q LOSS MUTATED	102	125
19Q LOSS WILD-TYPE	156	642

Figure S338. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.53e-06 (Wilcoxon-test), Q value = 3.7e-05

Table S339. Gene #76: '19q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
19Q LOSS MUTATED	158	85.6 (13.2)
19Q LOSS WILD-TYPE	572	80.1 (14.9)

Figure S339. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S340. Gene #76: '19q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
19Q LOSS MUTATED	23	2	44	143	2	30
19Q LOSS WILD-TYPE	171	26	85	46	16	495

Figure S340. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'ETHNICITY'

P value = 0.0096 (Fisher's exact test), Q value = 0.031

Table S341. Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
19Q LOSS MUTATED	18	208
19Q LOSS WILD-TYPE	26	711

Figure S341. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #9: 'ETHNICITY'

'20p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0455 (Fisher's exact test), Q value = 0.12

Table S342. Gene #77: '20p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
20P LOSS MUTATED	19	7
20P LOSS WILD-TYPE	552	505

Figure S342. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p loss' versus 'GENDER'

P value = 0.109 (Fisher's exact test), Q value = 0.23

Table S343. Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
20P LOSS MUTATED	15	11
20P LOSS WILD-TYPE	437	620

Figure S343. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #4: 'GENDER'

'20p loss' versus 'RADIATION_THERAPY'

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

Table S344. Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
20P LOSS MUTATED	3	23
20P LOSS WILD-TYPE	255	744

Figure S344. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'RACE'

P value = 0.0667 (Fisher's exact test), Q value = 0.16

Table S345. Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
20P LOSS MUTATED	0	2	3	21
20P LOSS WILD-TYPE	1	19	68	936

Figure S345. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

'20q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0132 (Fisher's exact test), Q value = 0.041

Table S346. Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
20Q LOSS MUTATED	17	4
20Q LOSS WILD-TYPE	554	508

Figure S346. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q loss' versus 'GENDER'

P value = 0.0733 (Fisher's exact test), Q value = 0.17

Table S347. Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
20Q LOSS MUTATED	13	8
20Q LOSS WILD-TYPE	439	623

Figure S347. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0731 (Fisher's exact test), Q value = 0.17

Table S348. Gene #78: '20q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
20Q LOSS MUTATED	2	1	2	0	0	16
20Q LOSS WILD-TYPE	192	27	127	189	18	509

Figure S348. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0646 (Fisher's exact test), Q value = 0.16

Table S349. Gene #79: '21q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
21Q LOSS MUTATED	23	2	7	7	1	39
21Q LOSS WILD-TYPE	171	26	122	182	17	486

Figure S349. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 1.51e-14 (logrank test), Q value = 3.5e-13

Table S350. Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
22Q LOSS MUTATED	240	182	0.1 - 156.2 (13.7)
22Q LOSS WILD-TYPE	839	409	0.0 - 211.2 (16.4)

Figure S350. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 4.7e-14 (Wilcoxon-test), Q value = 1.1e-12

Table S351. Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
22Q LOSS MUTATED	240	57.4 (14.8)
22Q LOSS WILD-TYPE	842	48.9 (15.6)

Figure S351. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.14e-17 (Fisher's exact test), Q value = 1.1e-15

Table S352. Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
22Q LOSS MUTATED	183	57
22Q LOSS WILD-TYPE	388	455

Figure S352. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'22q loss' versus 'RADIATION_THERAPY'

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

Table S353. Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
22Q LOSS MUTATED	39	189
22Q LOSS WILD-TYPE	219	578

Figure S353. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0064 (Wilcoxon-test), Q value = 0.022

Table S354. Gene #80: '22q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
22Q LOSS MUTATED	169	79.1 (15.0)
22Q LOSS WILD-TYPE	561	82.0 (14.6)

Figure S354. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

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

Table S355. Gene #80: '22q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
22Q LOSS MUTATED	29	9	11	17	6	168
22Q LOSS WILD-TYPE	165	19	118	172	12	357

Figure S355. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'ETHNICITY'

P value = 0.121 (Fisher's exact test), Q value = 0.25

Table S356. Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
XP LOSS MUTATED	13	179
XP LOSS WILD-TYPE	31	740

Figure S356. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #9: 'ETHNICITY'

'xq loss' versus 'Time to Death'

P value = 0.0939 (logrank test), Q value = 0.2

Table S357. Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
XQ LOSS MUTATED	173	101	0.1 - 134.3 (15.0)
XQ LOSS WILD-TYPE	906	490	0.0 - 211.2 (15.9)

Figure S357. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0467 (Fisher's exact test), Q value = 0.12

Table S358. Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
XQ LOSS MUTATED	104	70
XQ LOSS WILD-TYPE	467	442

Figure S358. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0972 (Wilcoxon-test), Q value = 0.21

Table S359. Gene #82: 'xq loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
XQ LOSS MUTATED	123	79.1 (15.9)
XQ LOSS WILD-TYPE	607	81.7 (14.4)

Figure S359. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/19791524/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/19775190/GBMLGG-TP.merged_data.txt
Number of patients = 1083
Number of significantly arm-level cnvs = 82
Number of selected clinical features = 9
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

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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