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

Glioma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1057DXH

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 1042 patients, 339 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
1q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
2p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
2q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
3p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
3q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
4p gain cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
4q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
5p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
5q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
6p gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
6q gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
7p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
7q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
9p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
9q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
10p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
10q gain cnv correlated to 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', and 'ETHNICITY'.
11p gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
11q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
12p gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE'.
12q gain cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
13q gain cnv correlated to 'YEARS_TO_BIRTH' and 'KARNOFSKY_PERFORMANCE_SCORE'.
14q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
15q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'KARNOFSKY_PERFORMANCE_SCORE'.
16p gain cnv correlated to 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
16q gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
17p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
17q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
18p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
18q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
19p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
19q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
20p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
20q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
21q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.
22q gain cnv correlated to 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
xp gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
xq gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
1p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
1q loss cnv correlated to 'PRIMARY_SITE_OF_DISEASE' and 'HISTOLOGICAL_TYPE'.
2p loss cnv correlated to 'YEARS_TO_BIRTH'.
3p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'ETHNICITY'.
4p loss cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
4q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
5p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
5q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
6p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
6q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
7q loss cnv correlated to 'YEARS_TO_BIRTH'.
8p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
8q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
9p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
9q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
10p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', 'RACE', and 'ETHNICITY'.
10q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', 'RACE', and 'ETHNICITY'.
11p loss cnv correlated to 'PRIMARY_SITE_OF_DISEASE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
11q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
12p loss cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', and 'RACE'.
12q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
13q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
14q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RADIATIONS_RADIATION_REGIMENINDICATION', 'RACE', and 'ETHNICITY'.
15q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
16p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', and 'HISTOLOGICAL_TYPE'.
16q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
17p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
17q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
18q loss cnv correlated to 'Time to Death'.
19q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
20p loss cnv correlated to 'PRIMARY_SITE_OF_DISEASE' and 'RACE'.
20q loss cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
22q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PRIMARY_SITE_OF_DISEASE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RADIATIONS_RADIATION_REGIMENINDICATION'.
xq loss cnv correlated to 'Time to Death', 'PRIMARY_SITE_OF_DISEASE', 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, 339 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PRIMARY SITE OF DISEASE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
10p loss	547 (52%)	495	0 (0)	5.7e-69 (3.24e-67)	7.17e-113 (5.29e-111)	0.148 (0.3)	1.05e-18 (2.77e-17)	1e-05 (7.38e-05)	1.24e-22 (3.51e-21)	0.0013 (0.00571)	0.0632 (0.158)
10q loss	575 (55%)	467	0 (0)	5.55e-63 (2.73e-61)	1.35e-111 (9.04e-110)	0.312 (0.503)	7.29e-20 (1.99e-18)	1e-05 (7.38e-05)	3.37e-24 (9.94e-23)	0.0018 (0.00759)	0.0259 (0.0727)
14q loss	214 (21%)	828	3.44e-05 (0.000221)	0.000156 (0.000824)	1.53e-05 (0.000108)	0.586 (0.759)	0.0988 (0.222)	0.00027 (0.00136)	0.0544 (0.14)	0.0579 (0.145)	0.0985 (0.222)
7p gain	578 (55%)	464	0 (0)	4.61e-50 (2.13e-48)	1.57e-80 (9.65e-79)	0.752 (0.885)	4.48e-11 (8.06e-10)	1e-05 (7.38e-05)	3.4e-17 (8.09e-16)	0.00217 (0.00876)	0.266 (0.464)
7q gain	613 (59%)	429	0 (0)	4.24e-47 (1.74e-45)	1.24e-66 (6.55e-65)	0.482 (0.676)	6.42e-10 (1.1e-08)	1e-05 (7.38e-05)	2.48e-14 (5.38e-13)	0.00234 (0.00927)	0.259 (0.458)
19q gain	217 (21%)	825	0 (0)	6.42e-15 (1.48e-13)	2.13e-33 (7.86e-32)	0.877 (0.956)	5.51e-05 (0.000336)	1e-05 (7.38e-05)	3.83e-07 (4.79e-06)	0.0221 (0.064)	0.649 (0.807)
20p gain	259 (25%)	783	0 (0)	2.61e-26 (8.37e-25)	6.71e-32 (2.36e-30)	0.561 (0.731)	0.000355 (0.00172)	1e-05 (7.38e-05)	1.06e-08 (1.53e-07)	0.0924 (0.211)	0.669 (0.82)
20q gain	256 (25%)	786	0 (0)	4.92e-25 (1.51e-23)	7.39e-32 (2.48e-30)	0.381 (0.58)	0.000101 (0.000575)	1e-05 (7.38e-05)	2.47e-09 (3.88e-08)	0.081 (0.192)	0.669 (0.82)
xq gain	54 (5%)	988	0.0314 (0.0872)	0.00159 (0.00686)	0.000624 (0.00283)	0.065 (0.161)	0.00811 (0.0266)	0.00038 (0.00181)	0.125 (0.266)	0.915 (0.989)	0.0127 (0.0387)
1p loss	186 (18%)	856	0 (0)	0.00012 (0.000652)	1.66e-49 (7.22e-48)	0.511 (0.699)	2.19e-06 (2.41e-05)	1e-05 (7.38e-05)	4.92e-18 (1.25e-16)	0.034 (0.093)	0.813 (0.903)
6p loss	110 (11%)	932	4.94e-13 (1.01e-11)	0.000111 (0.000622)	2.89e-07 (3.67e-06)	0.919 (0.99)	0.0782 (0.186)	3e-05 (0.000194)	0.0849 (0.198)	0.0571 (0.144)	0.761 (0.887)
6q loss	180 (17%)	862	5.51e-08 (7.52e-07)	0.00208 (0.00852)	2.49e-05 (0.000164)	0.28 (0.472)	0.0121 (0.0376)	2e-05 (0.000137)	0.00849 (0.0276)	0.0243 (0.0691)	0.456 (0.656)
1p gain	92 (9%)	950	4.5e-09 (6.78e-08)	8.75e-06 (7.38e-05)	1.43e-12 (2.85e-11)	0.508 (0.696)	0.00397 (0.0144)	1e-05 (7.38e-05)	1.45e-05 (0.000103)	0.855 (0.938)	1 (1.00)
1q gain	108 (10%)	934	4.67e-05 (0.000287)	1.01e-05 (7.39e-05)	1.35e-09 (2.22e-08)	0.409 (0.605)	0.00716 (0.024)	1e-05 (7.38e-05)	0.000143 (0.000759)	0.484 (0.677)	0.76 (0.887)
3q gain	70 (7%)	972	5.64e-06 (5.55e-05)	2.41e-06 (2.62e-05)	5.09e-10 (8.94e-09)	0.316 (0.509)	0.0892 (0.206)	1e-05 (7.38e-05)	0.000469 (0.0022)	0.547 (0.72)	1 (1.00)
9q gain	93 (9%)	949	0.00679 (0.0229)	0.0061 (0.0211)	9.56e-06 (7.38e-05)	0.0206 (0.0609)	0.177 (0.346)	9e-05 (0.000522)	0.0382 (0.104)	0.563 (0.733)	0.74 (0.88)
10p gain	66 (6%)	976	3.08e-06 (3.29e-05)	7.22e-12 (1.33e-10)	2.41e-09 (3.86e-08)	0.897 (0.974)	0.000956 (0.00428)	1e-05 (7.38e-05)	0.205 (0.381)	0.538 (0.715)	0.0103 (0.0326)
11q gain	71 (7%)	971	4.66e-05 (0.000287)	0.0205 (0.0608)	3.7e-09 (5.69e-08)	0.533 (0.712)	0.00813 (0.0266)	1e-05 (7.38e-05)	0.0478 (0.125)	0.517 (0.702)	0.464 (0.659)
18p gain	75 (7%)	967	0.000113 (0.000627)	0.0235 (0.0674)	9.91e-05 (0.000567)	0.809 (0.902)	0.0106 (0.0335)	0.00029 (0.00144)	0.0402 (0.107)	0.641 (0.804)	1 (1.00)
18q gain	71 (7%)	971	2.73e-05 (0.000178)	0.0019 (0.00786)	1.54e-06 (1.74e-05)	0.533 (0.712)	0.0214 (0.0623)	1e-05 (7.38e-05)	0.00194 (0.00798)	0.592 (0.76)	0.715 (0.857)
19p gain	310 (30%)	732	1.7e-05 (0.000118)	9.6e-07 (1.16e-05)	1.7e-12 (3.3e-11)	0.836 (0.923)	0.00576 (0.0202)	1e-05 (7.38e-05)	0.00217 (0.00876)	0.202 (0.377)	0.685 (0.834)
21q gain	86 (8%)	956	0.00781 (0.0259)	4.74e-06 (4.86e-05)	0.000272 (0.00136)	0.909 (0.984)	0.584 (0.757)	0.00344 (0.0128)	0.0896 (0.206)	0.116 (0.25)	0.102 (0.226)
8p loss	72 (7%)	970	0.000114 (0.000627)	0.000194 (0.000994)	3.52e-06 (3.72e-05)	0.321 (0.512)	0.412 (0.605)	0.00016 (0.000837)	0.0031 (0.0118)	0.00585 (0.0204)	0.715 (0.857)
11q loss	112 (11%)	930	1e-07 (1.32e-06)	1.21e-05 (8.67e-05)	7.36e-10 (1.23e-08)	0.612 (0.779)	0.0259 (0.0727)	1e-05 (7.38e-05)	0.109 (0.239)	1 (1.00)	0.355 (0.556)
13q loss	285 (27%)	757	0.00539 (0.019)	0.0785 (0.186)	9.05e-05 (0.000522)	0.231 (0.419)	0.0364 (0.0991)	0.00234 (0.00927)	0.00796 (0.0262)	0.436 (0.629)	0.413 (0.605)
19q loss	228 (22%)	814	0 (0)	4.55e-08 (6.46e-07)	1.1e-44 (4.26e-43)	0.403 (0.6)	8.39e-06 (7.38e-05)	1e-05 (7.38e-05)	7.33e-15 (1.64e-13)	0.246 (0.441)	0.373 (0.575)
22q loss	233 (22%)	809	2.8e-12 (5.31e-11)	4.43e-13 (9.33e-12)	1.96e-17 (4.82e-16)	1 (1.00)	0.00358 (0.0133)	1e-05 (7.38e-05)	0.000759 (0.00342)	0.428 (0.621)	0.828 (0.917)
2q gain	47 (5%)	995	0.0159 (0.0478)	0.0236 (0.0675)	0.00642 (0.0219)	0.291 (0.485)	0.0813 (0.192)	0.108 (0.237)	0.179 (0.348)	0.297 (0.49)	1 (1.00)
3p gain	66 (6%)	976	2.43e-05 (0.000161)	4.91e-06 (4.97e-05)	1.39e-07 (1.81e-06)	0.245 (0.441)	0.219 (0.403)	1e-05 (7.38e-05)	0.0147 (0.0446)	1 (1.00)	1 (1.00)
4q gain	38 (4%)	1004	0.00328 (0.0123)	0.0388 (0.105)	3.67e-05 (0.000233)	0.503 (0.694)	0.792 (0.893)	0.0006 (0.00273)	0.0124 (0.0382)	0.391 (0.592)	0.626 (0.79)
5p gain	58 (6%)	984	0.000173 (0.000895)	0.0213 (0.0623)	1.12e-06 (1.32e-05)	0.275 (0.469)	0.972 (1.00)	1e-05 (7.38e-05)	0.0786 (0.186)	0.523 (0.706)	0.684 (0.834)
9p gain	63 (6%)	979	0.00471 (0.0169)	0.0141 (0.0431)	0.00101 (0.00447)	0.0854 (0.198)	0.231 (0.419)	0.00304 (0.0116)	0.192 (0.367)	0.412 (0.605)	0.694 (0.841)
14q gain	26 (2%)	1016	0.00125 (0.00551)	0.000468 (0.0022)	0.00213 (0.00867)	0.317 (0.509)	0.15 (0.302)	0.00999 (0.0318)	0.112 (0.244)	1 (1.00)	1 (1.00)
17p gain	69 (7%)	973	0.000141 (0.000756)	5.81e-05 (0.000349)	0.00246 (0.00959)	0.0758 (0.183)	0.666 (0.82)	0.00637 (0.0219)	0.534 (0.712)	0.546 (0.72)	1 (1.00)
8q loss	50 (5%)	992	2.1e-06 (2.34e-05)	0.000351 (0.00172)	5.73e-05 (0.000346)	0.377 (0.578)	0.779 (0.889)	0.00243 (0.00954)	0.0412 (0.109)	0.137 (0.286)	1 (1.00)
9p loss	301 (29%)	741	0.00011 (0.000618)	0.000525 (0.00242)	1.05e-05 (7.61e-05)	1 (1.00)	0.167 (0.329)	0.00025 (0.00126)	0.000361 (0.00174)	0.498 (0.692)	0.155 (0.309)
9q loss	134 (13%)	908	0.00362 (0.0134)	0.0158 (0.0477)	0.00386 (0.0141)	0.639 (0.803)	0.00445 (0.016)	0.0681 (0.168)	0.195 (0.369)	0.263 (0.463)	0.412 (0.605)
12p loss	83 (8%)	959	0.00896 (0.029)	0.15 (0.303)	0.00394 (0.0143)	0.643 (0.806)	0.23 (0.419)	0.0091 (0.0293)	0.0214 (0.0623)	0.106 (0.233)	0.504 (0.694)
16q loss	101 (10%)	941	4.86e-07 (5.98e-06)	3.72e-05 (0.000234)	6.68e-09 (9.87e-08)	0.751 (0.885)	0.0393 (0.105)	1e-05 (7.38e-05)	0.209 (0.386)	0.282 (0.475)	1 (1.00)
17p loss	74 (7%)	968	6.78e-05 (4e-04)	0.000473 (0.0022)	8.27e-08 (1.11e-06)	0.395 (0.593)	0.00235 (0.00927)	2e-05 (0.000137)	0.333 (0.526)	0.94 (1.00)	0.464 (0.659)
17q loss	49 (5%)	993	0.000139 (0.000751)	0.00144 (0.0063)	2.32e-05 (0.000156)	0.656 (0.815)	0.0504 (0.13)	0.00171 (0.00734)	1 (1.00)	0.836 (0.923)	0.16 (0.318)
2p gain	50 (5%)	992	0.0122 (0.0379)	0.0387 (0.104)	0.00534 (0.0189)	0.14 (0.29)	0.12 (0.259)	0.105 (0.232)	0.384 (0.584)	0.361 (0.561)	1 (1.00)
4p gain	45 (4%)	997	0.0197 (0.0586)	0.373 (0.575)	0.00188 (0.00783)	0.647 (0.807)	0.303 (0.496)	0.00634 (0.0219)	0.0946 (0.215)	0.306 (0.499)	1 (1.00)
5q gain	48 (5%)	994	9.03e-05 (0.000522)	0.00247 (0.00959)	5.2e-06 (5.18e-05)	0.134 (0.281)	0.481 (0.676)	6e-05 (0.000357)	0.237 (0.427)	0.279 (0.472)	0.393 (0.592)
12q gain	63 (6%)	979	0.00253 (0.00979)	0.148 (0.301)	0.000367 (0.00176)	0.793 (0.893)	0.231 (0.419)	0.0094 (0.0302)	0.0672 (0.166)	0.117 (0.253)	0.407 (0.603)
15q gain	34 (3%)	1008	0.00984 (0.0314)	0.0547 (0.14)	0.0786 (0.186)	1 (1.00)	0.0434 (0.114)	0.14 (0.29)	1 (1.00)	0.869 (0.95)	0.62 (0.783)
16p gain	53 (5%)	989	0.802 (0.899)	0.0847 (0.198)	0.0108 (0.0339)	0.153 (0.307)	0.285 (0.479)	0.0718 (0.174)	0.00669 (0.0227)	0.275 (0.469)	0.397 (0.596)
17q gain	82 (8%)	960	1.31e-06 (1.51e-05)	2.24e-05 (0.000152)	0.000471 (0.0022)	0.199 (0.375)	0.497 (0.692)	0.00286 (0.011)	0.42 (0.613)	0.794 (0.893)	0.504 (0.694)
4p loss	117 (11%)	925	0.0549 (0.14)	0.662 (0.818)	0.0607 (0.152)	0.0281 (0.0785)	0.463 (0.659)	0.00054 (0.00248)	0.768 (0.888)	0.185 (0.356)	1 (1.00)
4q loss	139 (13%)	903	0.000118 (0.000646)	0.0309 (0.0862)	0.000332 (0.00164)	0.459 (0.658)	0.737 (0.88)	0.00017 (0.000884)	0.361 (0.561)	0.537 (0.715)	0.787 (0.893)
15q loss	150 (14%)	892	0.0072 (0.0241)	0.000205 (0.00104)	4.23e-05 (0.000265)	0.858 (0.94)	0.13 (0.274)	0.00153 (0.00664)	0.929 (0.997)	0.969 (1.00)	0.792 (0.893)
16p loss	75 (7%)	967	1.09e-06 (1.3e-05)	4.17e-06 (4.34e-05)	4.93e-08 (6.86e-07)	0.273 (0.468)	0.164 (0.324)	1e-05 (7.38e-05)	0.279 (0.472)	0.939 (1.00)	1 (1.00)
20q loss	18 (2%)	1024	0.0715 (0.174)	0.355 (0.556)	0.00316 (0.012)	0.0948 (0.215)	0.513 (0.7)	0.0672 (0.166)	0.476 (0.67)	0.549 (0.722)	1 (1.00)
6q gain	28 (3%)	1014	0.204 (0.381)	0.785 (0.892)	0.00327 (0.0123)	1 (1.00)	0.23 (0.419)	0.0538 (0.139)	0.00174 (0.00736)	0.576 (0.749)	1 (1.00)
10q gain	10 (1%)	1032	0.663 (0.818)	0.103 (0.228)	0.2 (0.375)	0.749 (0.885)	0.102 (0.226)	0.165 (0.325)	0.763 (0.887)	0.126 (0.267)	0.032 (0.0882)
11p gain	49 (5%)	993	0.124 (0.266)	0.763 (0.887)	0.00488 (0.0174)	0.299 (0.491)	0.114 (0.247)	0.0124 (0.0382)	0.379 (0.58)	0.503 (0.694)	0.193 (0.369)
16q gain	55 (5%)	987	0.619 (0.783)	0.514 (0.7)	0.0696 (0.17)	0.399 (0.597)	0.522 (0.706)	0.0424 (0.112)	0.00769 (0.0256)	0.294 (0.486)	0.399 (0.597)
22q gain	49 (5%)	993	0.185 (0.356)	0.056 (0.142)	0.143 (0.293)	0.768 (0.888)	0.0322 (0.0884)	0.0119 (0.0372)	0.305 (0.499)	1 (1.00)	0.137 (0.286)
3p loss	67 (6%)	975	0.374 (0.575)	0.291 (0.485)	0.311 (0.503)	0.372 (0.575)	0.0253 (0.0714)	0.802 (0.899)	0.101 (0.226)	1 (1.00)	0.04 (0.107)
5p loss	76 (7%)	966	0.361 (0.561)	0.928 (0.997)	0.811 (0.903)	0.904 (0.98)	0.0785 (0.186)	0.0483 (0.125)	0.00172 (0.00734)	0.473 (0.668)	1 (1.00)
11p loss	157 (15%)	885	0.354 (0.556)	0.999 (1.00)	0.0238 (0.0677)	0.0222 (0.064)	0.523 (0.706)	0.00182 (0.00763)	0.259 (0.458)	0.487 (0.679)	0.605 (0.773)
xq loss	166 (16%)	876	0.0768 (0.185)	0.264 (0.463)	0.0413 (0.109)	0.668 (0.82)	0.0691 (0.169)	0.354 (0.556)	0.271 (0.467)	0.509 (0.697)	0.804 (0.899)
6p gain	35 (3%)	1007	0.266 (0.464)	0.698 (0.844)	0.0562 (0.142)	1 (1.00)	0.272 (0.467)	0.129 (0.274)	0.00569 (0.02)	0.554 (0.724)	1 (1.00)
13q gain	17 (2%)	1025	0.344 (0.543)	0.0841 (0.197)	0.809 (0.902)	0.333 (0.526)	0.0162 (0.0486)	0.841 (0.926)	0.223 (0.409)	1 (1.00)	1 (1.00)
1q loss	42 (4%)	1000	0.18 (0.349)	0.322 (0.512)	0.0065 (0.0221)	0.426 (0.62)	0.313 (0.504)	0.0022 (0.00882)	0.209 (0.386)	0.89 (0.967)	1 (1.00)
5q loss	76 (7%)	966	0.692 (0.841)	0.934 (1.00)	0.633 (0.797)	0.546 (0.72)	0.248 (0.442)	0.0943 (0.215)	0.00385 (0.0141)	0.884 (0.962)	0.268 (0.465)
12q loss	104 (10%)	938	0.976 (1.00)	0.776 (0.889)	0.917 (0.99)	0.753 (0.885)	0.45 (0.648)	0.0222 (0.064)	0.756 (0.886)	0.0188 (0.0561)	0.76 (0.887)
20p loss	23 (2%)	1019	0.132 (0.279)	0.77 (0.888)	0.032 (0.0882)	0.14 (0.29)	0.308 (0.499)	0.254 (0.451)	0.144 (0.294)	0.1 (0.225)	0.505 (0.694)
12p gain	91 (9%)	951	0.376 (0.577)	0.499 (0.692)	0.0471 (0.123)	1 (1.00)	0.722 (0.863)	0.199 (0.375)	0.153 (0.307)	0.952 (1.00)	1 (1.00)
xp gain	33 (3%)	1009	0.405 (0.602)	0.247 (0.441)	0.292 (0.485)	0.15 (0.302)	0.0557 (0.142)	0.266 (0.464)	1 (1.00)	0.533 (0.712)	0.553 (0.724)
2p loss	51 (5%)	991	0.116 (0.25)	0.0861 (0.199)	0.391 (0.592)	0.307 (0.499)	0.646 (0.807)	0.713 (0.857)	0.774 (0.889)	0.327 (0.519)	0.393 (0.592)
7q loss	9 (1%)	1033	0.845 (0.928)	0.0819 (0.193)	1 (1.00)	0.744 (0.884)	0.218 (0.401)	0.709 (0.855)	0.739 (0.88)	0.554 (0.724)	1 (1.00)
18q loss	119 (11%)	923	0.0909 (0.208)	0.59 (0.759)	0.435 (0.629)	0.555 (0.724)	0.685 (0.834)	0.293 (0.485)	0.172 (0.337)	0.176 (0.344)	0.147 (0.3)
8p gain	98 (9%)	944	0.769 (0.888)	0.756 (0.886)	0.75 (0.885)	0.829 (0.918)	0.776 (0.889)	0.467 (0.663)	0.596 (0.764)	0.321 (0.512)	0.52 (0.706)
8q gain	113 (11%)	929	0.486 (0.679)	0.144 (0.294)	0.617 (0.783)	1 (1.00)	0.713 (0.857)	0.184 (0.356)	0.842 (0.926)	0.589 (0.759)	0.362 (0.562)
2q loss	49 (5%)	993	0.133 (0.279)	0.244 (0.44)	0.143 (0.293)	0.299 (0.491)	0.248 (0.442)	0.197 (0.372)	0.77 (0.888)	0.428 (0.621)	0.393 (0.592)
3q loss	61 (6%)	981	0.293 (0.485)	0.93 (0.997)	0.693 (0.841)	0.79 (0.893)	0.618 (0.783)	0.988 (1.00)	0.29 (0.485)	0.599 (0.766)	0.413 (0.605)
7p loss	10 (1%)	1032	0.647 (0.807)	0.124 (0.266)	0.526 (0.707)	0.749 (0.885)	0.791 (0.893)	0.804 (0.899)	0.526 (0.707)	0.59 (0.759)	1 (1.00)
18p loss	131 (13%)	911	0.276 (0.47)	0.16 (0.318)	0.779 (0.889)	0.186 (0.356)	0.699 (0.844)	0.661 (0.818)	0.779 (0.889)	0.207 (0.383)	0.406 (0.602)
19p loss	55 (5%)	987	0.307 (0.499)	0.27 (0.467)	0.268 (0.465)	0.675 (0.826)	0.201 (0.376)	0.607 (0.773)	0.783 (0.892)	0.775 (0.889)	0.662 (0.818)
21q loss	72 (7%)	970	0.463 (0.659)	0.47 (0.664)	0.542 (0.718)	0.457 (0.656)	0.321 (0.512)	0.194 (0.369)	0.541 (0.718)	0.876 (0.956)	0.469 (0.664)
xp loss	201 (19%)	841	0.936 (1.00)	0.423 (0.617)	0.753 (0.885)	0.265 (0.464)	0.272 (0.467)	0.976 (1.00)	0.813 (0.903)	0.591 (0.759)	0.161 (0.318)

'1p gain' versus 'Time to Death'

P value = 4.5e-09 (logrank test), Q value = 6.8e-08

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
1P GAIN MUTATED	92	70	0.2 - 92.7 (12.1)
1P GAIN WILD-TYPE	947	489	0.0 - 211.2 (15.0)

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 = 8.75e-06 (Wilcoxon-test), Q value = 7.4e-05

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

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
1P GAIN MUTATED	92	57.8 (14.1)
1P GAIN WILD-TYPE	949	50.4 (15.8)

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

'1p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.43e-12 (Fisher's exact test), Q value = 2.8e-11

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
1P GAIN MUTATED	81	11
1P GAIN WILD-TYPE	489	461

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

'1p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00397 (Wilcoxon-test), Q value = 0.014

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

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
1P GAIN MUTATED	64	77.0 (14.3)
1P GAIN WILD-TYPE	625	82.0 (14.5)

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

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

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
1P GAIN MUTATED	9	0	0	2	1	80
1P GAIN WILD-TYPE	167	27	118	176	17	445

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

'1p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 1.45e-05 (Fisher's exact test), Q value = 1e-04

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

nPatients	NO	YES
ALL	474	568
1P GAIN MUTATED	62	30
1P GAIN WILD-TYPE	412	538

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

'1q gain' versus 'Time to Death'

P value = 4.67e-05 (logrank test), Q value = 0.00029

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
1Q GAIN MUTATED	108	76	0.1 - 211.2 (12.8)
1Q GAIN WILD-TYPE	931	483	0.0 - 182.3 (15.0)

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 = 1.01e-05 (Wilcoxon-test), Q value = 7.4e-05

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

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
1Q GAIN MUTATED	108	57.0 (15.2)
1Q GAIN WILD-TYPE	933	50.4 (15.7)

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

'1q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.35e-09 (Fisher's exact test), Q value = 2.2e-08

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
1Q GAIN MUTATED	88	20
1Q GAIN WILD-TYPE	482	452

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

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00716 (Wilcoxon-test), Q value = 0.024

Table S10. Gene #2: '1q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
1Q GAIN MUTATED	73	77.7 (14.4)
1Q GAIN WILD-TYPE	616	82.0 (14.5)

Figure S10. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S11. Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
1Q GAIN MUTATED	11	1	2	7	2	85
1Q GAIN WILD-TYPE	165	26	116	171	16	440

Figure S11. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000143 (Fisher's exact test), Q value = 0.00076

Table S12. Gene #2: '1q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
1Q GAIN MUTATED	68	40
1Q GAIN WILD-TYPE	406	528

Figure S12. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'2p gain' versus 'Time to Death'

P value = 0.0122 (logrank test), Q value = 0.038

Table S13. Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
2P GAIN MUTATED	50	36	0.2 - 92.7 (14.1)
2P GAIN WILD-TYPE	989	523	0.0 - 211.2 (14.9)

Figure S13. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

'2p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0387 (Wilcoxon-test), Q value = 0.1

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

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
2P GAIN MUTATED	50	55.3 (16.3)
2P GAIN WILD-TYPE	991	50.9 (15.8)

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

'2p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00534 (Fisher's exact test), Q value = 0.019

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
2P GAIN MUTATED	37	13
2P GAIN WILD-TYPE	533	459

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

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.105 (Fisher's exact test), Q value = 0.23

Table S16. Gene #3: '2p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
2P GAIN MUTATED	6	1	2	5	1	35
2P GAIN WILD-TYPE	170	26	116	173	17	490

Figure S16. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'Time to Death'

P value = 0.0159 (logrank test), Q value = 0.048

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
2Q GAIN MUTATED	47	33	0.2 - 92.7 (13.9)
2Q GAIN WILD-TYPE	992	526	0.0 - 211.2 (14.9)

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 = 0.0236 (Wilcoxon-test), Q value = 0.068

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

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
2Q GAIN MUTATED	47	55.9 (16.4)
2Q GAIN WILD-TYPE	994	50.9 (15.8)

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

'2q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00642 (Fisher's exact test), Q value = 0.022

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
2Q GAIN MUTATED	35	12
2Q GAIN WILD-TYPE	535	460

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

'2q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0813 (Wilcoxon-test), Q value = 0.19

Table S20. Gene #4: '2q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
2Q GAIN MUTATED	36	78.1 (13.7)
2Q GAIN WILD-TYPE	653	81.7 (14.6)

Figure S20. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.108 (Fisher's exact test), Q value = 0.24

Table S21. Gene #4: '2q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
2Q GAIN MUTATED	6	1	2	4	1	33
2Q GAIN WILD-TYPE	170	26	116	174	17	492

Figure S21. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'Time to Death'

P value = 2.43e-05 (logrank test), Q value = 0.00016

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
3P GAIN MUTATED	66	50	0.2 - 127.6 (10.3)
3P GAIN WILD-TYPE	973	509	0.0 - 211.2 (14.9)

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 = 4.91e-06 (Wilcoxon-test), Q value = 5e-05

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

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
3P GAIN MUTATED	66	59.5 (13.8)
3P GAIN WILD-TYPE	975	50.5 (15.8)

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

'3p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.39e-07 (Fisher's exact test), Q value = 1.8e-06

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
3P GAIN MUTATED	56	10
3P GAIN WILD-TYPE	514	462

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

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S25. Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
3P GAIN MUTATED	7	1	0	3	1	54
3P GAIN WILD-TYPE	169	26	118	175	17	471

Figure S25. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0147 (Fisher's exact test), Q value = 0.045

Table S26. Gene #5: '3p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
3P GAIN MUTATED	40	26
3P GAIN WILD-TYPE	434	542

Figure S26. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'3q gain' versus 'Time to Death'

P value = 5.64e-06 (logrank test), Q value = 5.5e-05

Table S27. Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
3Q GAIN MUTATED	70	54	0.2 - 127.6 (10.5)
3Q GAIN WILD-TYPE	969	505	0.0 - 211.2 (15.0)

Figure S27. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 2.41e-06 (Wilcoxon-test), Q value = 2.6e-05

Table S28. Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
3Q GAIN MUTATED	70	59.5 (14.0)
3Q GAIN WILD-TYPE	971	50.5 (15.8)

Figure S28. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 5.09e-10 (Fisher's exact test), Q value = 8.9e-09

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
3Q GAIN MUTATED	62	8
3Q GAIN WILD-TYPE	508	464

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

'3q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0892 (Wilcoxon-test), Q value = 0.21

Table S30. Gene #6: '3q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
3Q GAIN MUTATED	49	79.4 (12.7)
3Q GAIN WILD-TYPE	640	81.7 (14.7)

Figure S30. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

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

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
3Q GAIN MUTATED	6	1	0	2	1	60
3Q GAIN WILD-TYPE	170	26	118	176	17	465

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

'3q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000469 (Fisher's exact test), Q value = 0.0022

Table S32. Gene #6: '3q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
3Q GAIN MUTATED	46	24
3Q GAIN WILD-TYPE	428	544

Figure S32. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4p gain' versus 'Time to Death'

P value = 0.0197 (logrank test), Q value = 0.059

Table S33. Gene #7: '4p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
4P GAIN MUTATED	45	30	0.2 - 92.7 (12.1)
4P GAIN WILD-TYPE	994	529	0.0 - 211.2 (14.9)

Figure S33. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #1: 'Time to Death'

'4p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00188 (Fisher's exact test), Q value = 0.0078

Table S34. Gene #7: '4p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
4P GAIN MUTATED	35	10
4P GAIN WILD-TYPE	535	462

Figure S34. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00634 (Fisher's exact test), Q value = 0.022

Table S35. Gene #7: '4p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
4P GAIN MUTATED	7	1	0	3	1	33
4P GAIN WILD-TYPE	169	26	118	175	17	492

Figure S35. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0946 (Fisher's exact test), Q value = 0.21

Table S36. Gene #7: '4p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
4P GAIN MUTATED	26	19
4P GAIN WILD-TYPE	448	549

Figure S36. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4q gain' versus 'Time to Death'

P value = 0.00328 (logrank test), Q value = 0.012

Table S37. Gene #8: '4q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
4Q GAIN MUTATED	38	28	0.2 - 92.7 (11.0)
4Q GAIN WILD-TYPE	1001	531	0.0 - 211.2 (14.9)

Figure S37. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #1: 'Time to Death'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0388 (Wilcoxon-test), Q value = 0.1

Table S38. Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
4Q GAIN MUTATED	38	55.7 (16.8)
4Q GAIN WILD-TYPE	1003	50.9 (15.8)

Figure S38. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.67e-05 (Fisher's exact test), Q value = 0.00023

Table S39. Gene #8: '4q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
4Q GAIN MUTATED	33	5
4Q GAIN WILD-TYPE	537	467

Figure S39. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-04 (Fisher's exact test), Q value = 0.0027

Table S40. Gene #8: '4q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
4Q GAIN MUTATED	4	1	0	1	1	31
4Q GAIN WILD-TYPE	172	26	118	177	17	494

Figure S40. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0124 (Fisher's exact test), Q value = 0.038

Table S41. Gene #8: '4q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
4Q GAIN MUTATED	25	13
4Q GAIN WILD-TYPE	449	555

Figure S41. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5p gain' versus 'Time to Death'

P value = 0.000173 (logrank test), Q value = 9e-04

Table S42. Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
5P GAIN MUTATED	58	46	1.1 - 92.7 (11.7)
5P GAIN WILD-TYPE	981	513	0.0 - 211.2 (14.9)

Figure S42. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0213 (Wilcoxon-test), Q value = 0.062

Table S43. Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
5P GAIN MUTATED	58	55.6 (15.4)
5P GAIN WILD-TYPE	983	50.8 (15.8)

Figure S43. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.12e-06 (Fisher's exact test), Q value = 1.3e-05

Table S44. Gene #9: '5p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
5P GAIN MUTATED	49	9
5P GAIN WILD-TYPE	521	463

Figure S44. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S45. Gene #9: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
5P GAIN MUTATED	6	3	2	1	4	42
5P GAIN WILD-TYPE	170	24	116	177	14	483

Figure S45. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0786 (Fisher's exact test), Q value = 0.19

Table S46. Gene #9: '5p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
5P GAIN MUTATED	33	25
5P GAIN WILD-TYPE	441	543

Figure S46. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5q gain' versus 'Time to Death'

P value = 9.03e-05 (logrank test), Q value = 0.00052

Table S47. Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
5Q GAIN MUTATED	48	37	1.1 - 92.7 (8.8)
5Q GAIN WILD-TYPE	991	522	0.0 - 211.2 (14.9)

Figure S47. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00247 (Wilcoxon-test), Q value = 0.0096

Table S48. Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
5Q GAIN MUTATED	48	57.8 (14.1)
5Q GAIN WILD-TYPE	993	50.8 (15.8)

Figure S48. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 5.2e-06 (Fisher's exact test), Q value = 5.2e-05

Table S49. Gene #10: '5q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
5Q GAIN MUTATED	41	7
5Q GAIN WILD-TYPE	529	465

Figure S49. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S50. Gene #10: '5q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
5Q GAIN MUTATED	4	3	2	1	3	35
5Q GAIN WILD-TYPE	172	24	116	177	15	490

Figure S50. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0562 (Fisher's exact test), Q value = 0.14

Table S51. Gene #11: '6p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
6P GAIN MUTATED	25	10
6P GAIN WILD-TYPE	545	462

Figure S51. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'6p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00569 (Fisher's exact test), Q value = 0.02

Table S52. Gene #11: '6p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
6P GAIN MUTATED	24	11
6P GAIN WILD-TYPE	450	557

Figure S52. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00327 (Fisher's exact test), Q value = 0.012

Table S53. Gene #12: '6q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
6Q GAIN MUTATED	23	5
6Q GAIN WILD-TYPE	547	467

Figure S53. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0538 (Fisher's exact test), Q value = 0.14

Table S54. Gene #12: '6q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
6Q GAIN MUTATED	3	1	0	2	0	22
6Q GAIN WILD-TYPE	173	26	118	176	18	503

Figure S54. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00174 (Fisher's exact test), Q value = 0.0074

Table S55. Gene #12: '6q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
6Q GAIN MUTATED	21	7
6Q GAIN WILD-TYPE	453	561

Figure S55. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'7p gain' versus 'Time to Death'

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

Table S56. Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
7P GAIN MUTATED	577	427	0.1 - 211.2 (12.3)
7P GAIN WILD-TYPE	462	132	0.0 - 182.3 (18.0)

Figure S56. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 4.61e-50 (Wilcoxon-test), Q value = 2.1e-48

Table S57. Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
7P GAIN MUTATED	578	57.6 (13.1)
7P GAIN WILD-TYPE	463	43.0 (15.1)

Figure S57. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.57e-80 (Fisher's exact test), Q value = 9.6e-79

Table S58. Gene #13: '7p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
7P GAIN MUTATED	464	114
7P GAIN WILD-TYPE	106	358

Figure S58. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 4.48e-11 (Wilcoxon-test), Q value = 8.1e-10

Table S59. Gene #13: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
7P GAIN MUTATED	410	78.8 (15.1)
7P GAIN WILD-TYPE	279	85.6 (12.8)

Figure S59. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S60. Gene #13: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
7P GAIN MUTATED	47	19	29	38	12	433
7P GAIN WILD-TYPE	129	8	89	140	6	92

Figure S60. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 3.4e-17 (Fisher's exact test), Q value = 8.1e-16

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

nPatients	NO	YES
ALL	474	568
7P GAIN MUTATED	330	248
7P GAIN WILD-TYPE	144	320

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

'7p gain' versus 'RACE'

P value = 0.00217 (Fisher's exact test), Q value = 0.0088

Table S62. Gene #13: '7p gain' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
7P GAIN MUTATED	1	9	48	498
7P GAIN WILD-TYPE	0	12	16	424

Figure S62. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #8: 'RACE'

'7q gain' versus 'Time to Death'

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

Table S63. Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
7Q GAIN MUTATED	612	432	0.1 - 211.2 (12.5)
7Q GAIN WILD-TYPE	427	127	0.0 - 182.3 (18.7)

Figure S63. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 4.24e-47 (Wilcoxon-test), Q value = 1.7e-45

Table S64. Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
7Q GAIN MUTATED	613	57.0 (13.3)
7Q GAIN WILD-TYPE	428	42.6 (15.3)

Figure S64. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.24e-66 (Fisher's exact test), Q value = 6.5e-65

Table S65. Gene #14: '7q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
7Q GAIN MUTATED	469	144
7Q GAIN WILD-TYPE	101	328

Figure S65. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.42e-10 (Wilcoxon-test), Q value = 1.1e-08

Table S66. Gene #14: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
7Q GAIN MUTATED	427	79.1 (15.1)
7Q GAIN WILD-TYPE	262	85.5 (12.8)

Figure S66. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S67. Gene #14: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
7Q GAIN MUTATED	61	20	38	45	12	437
7Q GAIN WILD-TYPE	115	7	80	133	6	88

Figure S67. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 2.48e-14 (Fisher's exact test), Q value = 5.4e-13

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

nPatients	NO	YES
ALL	474	568
7Q GAIN MUTATED	339	274
7Q GAIN WILD-TYPE	135	294

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

'7q gain' versus 'RACE'

P value = 0.00234 (Fisher's exact test), Q value = 0.0093

Table S69. Gene #14: '7q gain' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
7Q GAIN MUTATED	1	10	50	530
7Q GAIN WILD-TYPE	0	11	14	392

Figure S69. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #8: 'RACE'

'9p gain' versus 'Time to Death'

P value = 0.00471 (logrank test), Q value = 0.017

Table S70. Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
9P GAIN MUTATED	63	44	0.4 - 172.8 (12.4)
9P GAIN WILD-TYPE	976	515	0.0 - 211.2 (14.9)

Figure S70. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0141 (Wilcoxon-test), Q value = 0.043

Table S71. Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
9P GAIN MUTATED	63	55.0 (16.9)
9P GAIN WILD-TYPE	978	50.8 (15.7)

Figure S71. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00101 (Fisher's exact test), Q value = 0.0045

Table S72. Gene #17: '9p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
9P GAIN MUTATED	47	16
9P GAIN WILD-TYPE	523	456

Figure S72. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'9p gain' versus 'GENDER'

P value = 0.0854 (Fisher's exact test), Q value = 0.2

Table S73. Gene #17: '9p gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
9P GAIN MUTATED	33	30
9P GAIN WILD-TYPE	397	582

Figure S73. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'GENDER'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00304 (Fisher's exact test), Q value = 0.012

Table S74. Gene #17: '9p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
9P GAIN MUTATED	8	0	5	3	0	47
9P GAIN WILD-TYPE	168	27	113	175	18	478

Figure S74. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'Time to Death'

P value = 0.00679 (logrank test), Q value = 0.023

Table S75. Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
9Q GAIN MUTATED	93	64	0.4 - 172.8 (12.6)
9Q GAIN WILD-TYPE	946	495	0.0 - 211.2 (14.9)

Figure S75. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0061 (Wilcoxon-test), Q value = 0.021

Table S76. Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
9Q GAIN MUTATED	93	55.0 (15.5)
9Q GAIN WILD-TYPE	948	50.7 (15.8)

Figure S76. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 9.56e-06 (Fisher's exact test), Q value = 7.4e-05

Table S77. Gene #18: '9q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
9Q GAIN MUTATED	71	22
9Q GAIN WILD-TYPE	499	450

Figure S77. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'9q gain' versus 'GENDER'

P value = 0.0206 (Fisher's exact test), Q value = 0.061

Table S78. Gene #18: '9q gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
9Q GAIN MUTATED	49	44
9Q GAIN WILD-TYPE	381	568

Figure S78. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'GENDER'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00052

Table S79. Gene #18: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
9Q GAIN MUTATED	12	1	6	4	2	68
9Q GAIN WILD-TYPE	164	26	112	174	16	457

Figure S79. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0382 (Fisher's exact test), Q value = 0.1

Table S80. Gene #18: '9q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
9Q GAIN MUTATED	52	41
9Q GAIN WILD-TYPE	422	527

Figure S80. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10p gain' versus 'Time to Death'

P value = 3.08e-06 (logrank test), Q value = 3.3e-05

Table S81. Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
10P GAIN MUTATED	66	19	0.1 - 172.8 (22.1)
10P GAIN WILD-TYPE	973	540	0.0 - 211.2 (14.5)

Figure S81. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 7.22e-12 (Wilcoxon-test), Q value = 1.3e-10

Table S82. Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
10P GAIN MUTATED	66	38.2 (12.3)
10P GAIN WILD-TYPE	975	52.0 (15.7)

Figure S82. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.41e-09 (Fisher's exact test), Q value = 3.9e-08

Table S83. Gene #19: '10p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
10P GAIN MUTATED	13	53
10P GAIN WILD-TYPE	557	419

Figure S83. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'10p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000956 (Wilcoxon-test), Q value = 0.0043

Table S84. Gene #19: '10p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
10P GAIN MUTATED	40	88.5 (9.5)
10P GAIN WILD-TYPE	649	81.1 (14.7)

Figure S84. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

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

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
10P GAIN MUTATED	28	1	17	8	1	11
10P GAIN WILD-TYPE	148	26	101	170	17	514

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

'10p gain' versus 'ETHNICITY'

P value = 0.0103 (Fisher's exact test), Q value = 0.033

Table S86. Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
10P GAIN MUTATED	6	54
10P GAIN WILD-TYPE	24	837

Figure S86. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'ETHNICITY'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.103 (Wilcoxon-test), Q value = 0.23

Table S87. Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
10Q GAIN MUTATED	10	42.8 (19.2)
10Q GAIN WILD-TYPE	1031	51.2 (15.8)

Figure S87. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.102 (Wilcoxon-test), Q value = 0.23

Table S88. Gene #20: '10q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
10Q GAIN MUTATED	5	92.0 (11.0)
10Q GAIN WILD-TYPE	684	81.4 (14.6)

Figure S88. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q gain' versus 'ETHNICITY'

P value = 0.032 (Fisher's exact test), Q value = 0.088

Table S89. Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
10Q GAIN MUTATED	2	7
10Q GAIN WILD-TYPE	28	884

Figure S89. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'ETHNICITY'

'11p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00488 (Fisher's exact test), Q value = 0.017

Table S90. Gene #21: '11p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
11P GAIN MUTATED	17	32
11P GAIN WILD-TYPE	553	440

Figure S90. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'11p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.114 (Wilcoxon-test), Q value = 0.25

Table S91. Gene #21: '11p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
11P GAIN MUTATED	35	85.1 (13.8)
11P GAIN WILD-TYPE	654	81.3 (14.6)

Figure S91. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0124 (Fisher's exact test), Q value = 0.038

Table S92. Gene #21: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
11P GAIN MUTATED	6	0	10	16	0	17
11P GAIN WILD-TYPE	170	27	108	162	18	508

Figure S92. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'Time to Death'

P value = 4.66e-05 (logrank test), Q value = 0.00029

Table S93. Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
11Q GAIN MUTATED	71	21	1.2 - 211.2 (18.0)
11Q GAIN WILD-TYPE	968	538	0.0 - 172.8 (14.5)

Figure S93. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0205 (Wilcoxon-test), Q value = 0.061

Table S94. Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
11Q GAIN MUTATED	71	47.1 (14.0)
11Q GAIN WILD-TYPE	970	51.4 (15.9)

Figure S94. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.7e-09 (Fisher's exact test), Q value = 5.7e-08

Table S95. Gene #22: '11q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
11Q GAIN MUTATED	15	56
11Q GAIN WILD-TYPE	555	416

Figure S95. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'11q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00813 (Wilcoxon-test), Q value = 0.027

Table S96. Gene #22: '11q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
11Q GAIN MUTATED	45	87.1 (10.6)
11Q GAIN WILD-TYPE	644	81.1 (14.7)

Figure S96. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S97. Gene #22: '11q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
11Q GAIN MUTATED	17	0	13	26	1	14
11Q GAIN WILD-TYPE	159	27	105	152	17	511

Figure S97. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0478 (Fisher's exact test), Q value = 0.12

Table S98. Gene #22: '11q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
11Q GAIN MUTATED	24	47
11Q GAIN WILD-TYPE	450	521

Figure S98. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'12p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0471 (Fisher's exact test), Q value = 0.12

Table S99. Gene #23: '12p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
12P GAIN MUTATED	59	32
12P GAIN WILD-TYPE	511	440

Figure S99. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'12q gain' versus 'Time to Death'

P value = 0.00253 (logrank test), Q value = 0.0098

Table S100. Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
12Q GAIN MUTATED	63	46	1.1 - 77.9 (13.8)
12Q GAIN WILD-TYPE	976	513	0.0 - 211.2 (14.9)

Figure S100. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000367 (Fisher's exact test), Q value = 0.0018

Table S101. Gene #24: '12q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
12Q GAIN MUTATED	48	15
12Q GAIN WILD-TYPE	522	457

Figure S101. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0094 (Fisher's exact test), Q value = 0.03

Table S102. Gene #24: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
12Q GAIN MUTATED	4	2	4	7	0	46
12Q GAIN WILD-TYPE	172	25	114	171	18	479

Figure S102. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0672 (Fisher's exact test), Q value = 0.17

Table S103. Gene #24: '12q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
12Q GAIN MUTATED	36	27
12Q GAIN WILD-TYPE	438	541

Figure S103. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'13q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0841 (Wilcoxon-test), Q value = 0.2

Table S104. Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
13Q GAIN MUTATED	17	57.6 (17.7)
13Q GAIN WILD-TYPE	1024	51.0 (15.8)

Figure S104. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0162 (Wilcoxon-test), Q value = 0.049

Table S105. Gene #25: '13q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
13Q GAIN MUTATED	13	71.5 (15.2)
13Q GAIN WILD-TYPE	676	81.7 (14.5)

Figure S105. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q gain' versus 'Time to Death'

P value = 0.00125 (logrank test), Q value = 0.0055

Table S106. Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
14Q GAIN MUTATED	26	22	0.4 - 46.6 (10.4)
14Q GAIN WILD-TYPE	1013	537	0.0 - 211.2 (14.9)

Figure S106. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000468 (Wilcoxon-test), Q value = 0.0022

Table S107. Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
14Q GAIN MUTATED	26	61.4 (14.5)
14Q GAIN WILD-TYPE	1015	50.8 (15.8)

Figure S107. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00213 (Fisher's exact test), Q value = 0.0087

Table S108. Gene #26: '14q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
14Q GAIN MUTATED	22	4
14Q GAIN WILD-TYPE	548	468

Figure S108. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00999 (Fisher's exact test), Q value = 0.032

Table S109. Gene #26: '14q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
14Q GAIN MUTATED	2	2	1	1	2	18
14Q GAIN WILD-TYPE	174	25	117	177	16	507

Figure S109. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.112 (Fisher's exact test), Q value = 0.24

Table S110. Gene #26: '14q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
14Q GAIN MUTATED	16	10
14Q GAIN WILD-TYPE	458	558

Figure S110. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'15q gain' versus 'Time to Death'

P value = 0.00984 (logrank test), Q value = 0.031

Table S111. Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
15Q GAIN MUTATED	34	27	0.2 - 117.4 (12.3)
15Q GAIN WILD-TYPE	1005	532	0.0 - 211.2 (14.9)

Figure S111. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #1: 'Time to Death'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0547 (Wilcoxon-test), Q value = 0.14

Table S112. Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
15Q GAIN MUTATED	34	55.6 (13.6)
15Q GAIN WILD-TYPE	1007	50.9 (15.9)

Figure S112. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0786 (Fisher's exact test), Q value = 0.19

Table S113. Gene #27: '15q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
15Q GAIN MUTATED	24	10
15Q GAIN WILD-TYPE	546	462

Figure S113. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0434 (Wilcoxon-test), Q value = 0.11

Table S114. Gene #27: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
15Q GAIN MUTATED	27	76.3 (14.5)
15Q GAIN WILD-TYPE	662	81.7 (14.6)

Figure S114. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0847 (Wilcoxon-test), Q value = 0.2

Table S115. Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
16P GAIN MUTATED	53	54.5 (14.9)
16P GAIN WILD-TYPE	988	50.9 (15.9)

Figure S115. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S116. Gene #28: '16p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
16P GAIN MUTATED	38	15
16P GAIN WILD-TYPE	532	457

Figure S116. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0718 (Fisher's exact test), Q value = 0.17

Table S117. Gene #28: '16p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
16P GAIN MUTATED	9	1	2	4	1	36
16P GAIN WILD-TYPE	167	26	116	174	17	489

Figure S117. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00669 (Fisher's exact test), Q value = 0.023

Table S118. Gene #28: '16p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
16P GAIN MUTATED	34	19
16P GAIN WILD-TYPE	440	549

Figure S118. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'16q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0696 (Fisher's exact test), Q value = 0.17

Table S119. Gene #29: '16q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
16Q GAIN MUTATED	37	18
16Q GAIN WILD-TYPE	533	454

Figure S119. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0424 (Fisher's exact test), Q value = 0.11

Table S120. Gene #29: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
16Q GAIN MUTATED	12	1	1	5	1	35
16Q GAIN WILD-TYPE	164	26	117	173	17	490

Figure S120. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00769 (Fisher's exact test), Q value = 0.026

Table S121. Gene #29: '16q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
16Q GAIN MUTATED	35	20
16Q GAIN WILD-TYPE	439	548

Figure S121. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'17p gain' versus 'Time to Death'

P value = 0.000141 (logrank test), Q value = 0.00076

Table S122. Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
17P GAIN MUTATED	69	50	0.2 - 72.4 (11.8)
17P GAIN WILD-TYPE	970	509	0.0 - 211.2 (14.9)

Figure S122. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 5.81e-05 (Wilcoxon-test), Q value = 0.00035

Table S123. Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
17P GAIN MUTATED	69	58.2 (15.1)
17P GAIN WILD-TYPE	972	50.6 (15.8)

Figure S123. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00246 (Fisher's exact test), Q value = 0.0096

Table S124. Gene #30: '17p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
17P GAIN MUTATED	50	19
17P GAIN WILD-TYPE	520	453

Figure S124. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'17p gain' versus 'GENDER'

P value = 0.0758 (Fisher's exact test), Q value = 0.18

Table S125. Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
17P GAIN MUTATED	21	48
17P GAIN WILD-TYPE	409	564

Figure S125. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'GENDER'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00637 (Fisher's exact test), Q value = 0.022

Table S126. Gene #30: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
17P GAIN MUTATED	10	4	1	8	1	45
17P GAIN WILD-TYPE	166	23	117	170	17	480

Figure S126. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 1.31e-06 (logrank test), Q value = 1.5e-05

Table S127. Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
17Q GAIN MUTATED	82	62	0.2 - 72.4 (11.8)
17Q GAIN WILD-TYPE	957	497	0.0 - 211.2 (14.9)

Figure S127. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'YEARS_TO_BIRTH'

P value = 2.24e-05 (Wilcoxon-test), Q value = 0.00015

Table S128. Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
17Q GAIN MUTATED	82	58.0 (15.2)
17Q GAIN WILD-TYPE	959	50.5 (15.7)

Figure S128. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000471 (Fisher's exact test), Q value = 0.0022

Table S129. Gene #31: '17q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
17Q GAIN MUTATED	60	22
17Q GAIN WILD-TYPE	510	450

Figure S129. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00286 (Fisher's exact test), Q value = 0.011

Table S130. Gene #31: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
17Q GAIN MUTATED	12	4	2	8	2	54
17Q GAIN WILD-TYPE	164	23	116	170	16	471

Figure S130. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'Time to Death'

P value = 0.000113 (logrank test), Q value = 0.00063

Table S131. Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
18P GAIN MUTATED	75	51	0.1 - 65.0 (12.7)
18P GAIN WILD-TYPE	964	508	0.0 - 211.2 (14.9)

Figure S131. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0235 (Wilcoxon-test), Q value = 0.067

Table S132. Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
18P GAIN MUTATED	75	55.1 (17.1)
18P GAIN WILD-TYPE	966	50.8 (15.7)

Figure S132. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 9.91e-05 (Fisher's exact test), Q value = 0.00057

Table S133. Gene #32: '18p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
18P GAIN MUTATED	57	18
18P GAIN WILD-TYPE	513	454

Figure S133. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'18p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0106 (Wilcoxon-test), Q value = 0.033

Table S134. Gene #32: '18p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
18P GAIN MUTATED	45	75.3 (17.7)
18P GAIN WILD-TYPE	644	82.0 (14.3)

Figure S134. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00029 (Fisher's exact test), Q value = 0.0014

Table S135. Gene #32: '18p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
18P GAIN MUTATED	10	0	4	4	0	57
18P GAIN WILD-TYPE	166	27	114	174	18	468

Figure S135. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0402 (Fisher's exact test), Q value = 0.11

Table S136. Gene #32: '18p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
18P GAIN MUTATED	43	32
18P GAIN WILD-TYPE	431	536

Figure S136. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'18q gain' versus 'Time to Death'

P value = 2.73e-05 (logrank test), Q value = 0.00018

Table S137. Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
18Q GAIN MUTATED	71	51	0.1 - 65.0 (12.7)
18Q GAIN WILD-TYPE	968	508	0.0 - 211.2 (14.9)

Figure S137. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0019 (Wilcoxon-test), Q value = 0.0079

Table S138. Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
18Q GAIN MUTATED	71	56.6 (16.5)
18Q GAIN WILD-TYPE	970	50.7 (15.7)

Figure S138. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.54e-06 (Fisher's exact test), Q value = 1.7e-05

Table S139. Gene #33: '18q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
18Q GAIN MUTATED	58	13
18Q GAIN WILD-TYPE	512	459

Figure S139. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0214 (Wilcoxon-test), Q value = 0.062

Table S140. Gene #33: '18q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
18Q GAIN MUTATED	44	76.4 (16.7)
18Q GAIN WILD-TYPE	645	81.9 (14.4)

Figure S140. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S141. Gene #33: '18q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
18Q GAIN MUTATED	8	0	3	2	0	58
18Q GAIN WILD-TYPE	168	27	115	176	18	467

Figure S141. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00194 (Fisher's exact test), Q value = 0.008

Table S142. Gene #33: '18q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
18Q GAIN MUTATED	45	26
18Q GAIN WILD-TYPE	429	542

Figure S142. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'19p gain' versus 'Time to Death'

P value = 1.7e-05 (logrank test), Q value = 0.00012

Table S143. Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
19P GAIN MUTATED	308	198	0.1 - 169.8 (14.6)
19P GAIN WILD-TYPE	731	361	0.0 - 211.2 (14.9)

Figure S143. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 9.6e-07 (Wilcoxon-test), Q value = 1.2e-05

Table S144. Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
19P GAIN MUTATED	309	54.8 (14.2)
19P GAIN WILD-TYPE	732	49.5 (16.2)

Figure S144. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.7e-12 (Fisher's exact test), Q value = 3.3e-11

Table S145. Gene #34: '19p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
19P GAIN MUTATED	221	89
19P GAIN WILD-TYPE	349	383

Figure S145. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'19p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00576 (Wilcoxon-test), Q value = 0.02

Table S146. Gene #34: '19p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
19P GAIN MUTATED	201	79.6 (14.4)
19P GAIN WILD-TYPE	488	82.3 (14.6)

Figure S146. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S147. Gene #34: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
19P GAIN MUTATED	19	11	17	53	9	201
19P GAIN WILD-TYPE	157	16	101	125	9	324

Figure S147. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00217 (Fisher's exact test), Q value = 0.0088

Table S148. Gene #34: '19p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
19P GAIN MUTATED	164	146
19P GAIN WILD-TYPE	310	422

Figure S148. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'19q gain' versus 'Time to Death'

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

Table S149. Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
19Q GAIN MUTATED	216	167	0.1 - 92.7 (13.7)
19Q GAIN WILD-TYPE	823	392	0.0 - 211.2 (15.0)

Figure S149. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 6.42e-15 (Wilcoxon-test), Q value = 1.5e-13

Table S150. Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
19Q GAIN MUTATED	217	58.5 (12.4)
19Q GAIN WILD-TYPE	824	49.1 (16.0)

Figure S150. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.13e-33 (Fisher's exact test), Q value = 7.9e-32

Table S151. Gene #35: '19q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
19Q GAIN MUTATED	193	24
19Q GAIN WILD-TYPE	377	448

Figure S151. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'19q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5.51e-05 (Wilcoxon-test), Q value = 0.00034

Table S152. Gene #35: '19q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
19Q GAIN MUTATED	148	77.9 (14.5)
19Q GAIN WILD-TYPE	541	82.5 (14.5)

Figure S152. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S153. Gene #35: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
19Q GAIN MUTATED	11	10	8	5	7	176
19Q GAIN WILD-TYPE	165	17	110	173	11	349

Figure S153. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 3.83e-07 (Fisher's exact test), Q value = 4.8e-06

Table S154. Gene #35: '19q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
19Q GAIN MUTATED	132	85
19Q GAIN WILD-TYPE	342	483

Figure S154. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'19q gain' versus 'RACE'

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

Table S155. Gene #35: '19q gain' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
19Q GAIN MUTATED	0	8	20	182
19Q GAIN WILD-TYPE	1	13	44	740

Figure S155. 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 S156. Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
20P GAIN MUTATED	259	202	0.1 - 94.8 (12.8)
20P GAIN WILD-TYPE	780	357	0.0 - 211.2 (15.2)

Figure S156. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 2.61e-26 (Wilcoxon-test), Q value = 8.4e-25

Table S157. Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
20P GAIN MUTATED	259	60.0 (13.1)
20P GAIN WILD-TYPE	782	48.2 (15.5)

Figure S157. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 6.71e-32 (Fisher's exact test), Q value = 2.4e-30

Table S158. Gene #36: '20p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
20P GAIN MUTATED	220	39
20P GAIN WILD-TYPE	350	433

Figure S158. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000355 (Wilcoxon-test), Q value = 0.0017

Table S159. Gene #36: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
20P GAIN MUTATED	185	78.8 (14.2)
20P GAIN WILD-TYPE	504	82.5 (14.6)

Figure S159. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S160. Gene #36: '20p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
20P GAIN MUTATED	20	9	8	11	9	202
20P GAIN WILD-TYPE	156	18	110	167	9	323

Figure S160. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 1.06e-08 (Fisher's exact test), Q value = 1.5e-07

Table S161. Gene #36: '20p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
20P GAIN MUTATED	158	101
20P GAIN WILD-TYPE	316	467

Figure S161. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'20p gain' versus 'RACE'

P value = 0.0924 (Fisher's exact test), Q value = 0.21

Table S162. Gene #36: '20p gain' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
20P GAIN MUTATED	0	10	17	226
20P GAIN WILD-TYPE	1	11	47	696

Figure S162. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'RACE'

'20q gain' versus 'Time to Death'

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

Table S163. Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
20Q GAIN MUTATED	256	199	0.1 - 94.8 (12.6)
20Q GAIN WILD-TYPE	783	360	0.0 - 211.2 (15.2)

Figure S163. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 4.92e-25 (Wilcoxon-test), Q value = 1.5e-23

Table S164. Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
20Q GAIN MUTATED	256	59.9 (13.3)
20Q GAIN WILD-TYPE	785	48.2 (15.5)

Figure S164. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 7.39e-32 (Fisher's exact test), Q value = 2.5e-30

Table S165. Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
20Q GAIN MUTATED	218	38
20Q GAIN WILD-TYPE	352	434

Figure S165. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000101 (Wilcoxon-test), Q value = 0.00058

Table S166. Gene #37: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
20Q GAIN MUTATED	184	78.6 (14.0)
20Q GAIN WILD-TYPE	505	82.6 (14.7)

Figure S166. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S167. Gene #37: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
20Q GAIN MUTATED	19	9	7	12	9	200
20Q GAIN WILD-TYPE	157	18	111	166	9	325

Figure S167. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 2.47e-09 (Fisher's exact test), Q value = 3.9e-08

Table S168. Gene #37: '20q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
20Q GAIN MUTATED	158	98
20Q GAIN WILD-TYPE	316	470

Figure S168. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'20q gain' versus 'RACE'

P value = 0.081 (Fisher's exact test), Q value = 0.19

Table S169. Gene #37: '20q gain' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
20Q GAIN MUTATED	0	10	17	223
20Q GAIN WILD-TYPE	1	11	47	699

Figure S169. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'RACE'

'21q gain' versus 'Time to Death'

P value = 0.00781 (logrank test), Q value = 0.026

Table S170. Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
21Q GAIN MUTATED	86	62	0.2 - 211.2 (13.3)
21Q GAIN WILD-TYPE	953	497	0.0 - 182.3 (14.9)

Figure S170. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 4.74e-06 (Wilcoxon-test), Q value = 4.9e-05

Table S171. Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
21Q GAIN MUTATED	86	58.6 (14.5)
21Q GAIN WILD-TYPE	955	50.4 (15.8)

Figure S171. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000272 (Fisher's exact test), Q value = 0.0014

Table S172. Gene #38: '21q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
21Q GAIN MUTATED	63	23
21Q GAIN WILD-TYPE	507	449

Figure S172. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00344 (Fisher's exact test), Q value = 0.013

Table S173. Gene #38: '21q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
21Q GAIN MUTATED	9	6	5	9	1	56
21Q GAIN WILD-TYPE	167	21	113	169	17	469

Figure S173. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0896 (Fisher's exact test), Q value = 0.21

Table S174. Gene #38: '21q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
21Q GAIN MUTATED	47	39
21Q GAIN WILD-TYPE	427	529

Figure S174. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'21q gain' versus 'ETHNICITY'

P value = 0.102 (Fisher's exact test), Q value = 0.23

Table S175. Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
21Q GAIN MUTATED	0	79
21Q GAIN WILD-TYPE	30	812

Figure S175. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'ETHNICITY'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.056 (Wilcoxon-test), Q value = 0.14

Table S176. Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
22Q GAIN MUTATED	49	55.5 (15.1)
22Q GAIN WILD-TYPE	992	50.9 (15.8)

Figure S176. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0322 (Wilcoxon-test), Q value = 0.088

Table S177. Gene #39: '22q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
22Q GAIN MUTATED	30	77.0 (11.8)
22Q GAIN WILD-TYPE	659	81.7 (14.7)

Figure S177. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0119 (Fisher's exact test), Q value = 0.037

Table S178. Gene #39: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
22Q GAIN MUTATED	2	0	2	13	0	32
22Q GAIN WILD-TYPE	174	27	116	165	18	493

Figure S178. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0557 (Wilcoxon-test), Q value = 0.14

Table S179. Gene #40: 'xp gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
XP GAIN MUTATED	18	87.2 (13.2)
XP GAIN WILD-TYPE	671	81.4 (14.6)

Figure S179. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'Time to Death'

P value = 0.0314 (logrank test), Q value = 0.087

Table S180. Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
XQ GAIN MUTATED	54	22	0.1 - 130.8 (15.9)
XQ GAIN WILD-TYPE	985	537	0.0 - 211.2 (14.7)

Figure S180. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.00159 (Wilcoxon-test), Q value = 0.0069

Table S181. Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
XQ GAIN MUTATED	54	44.5 (16.1)
XQ GAIN WILD-TYPE	987	51.5 (15.7)

Figure S181. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000624 (Fisher's exact test), Q value = 0.0028

Table S182. Gene #41: 'xq gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
XQ GAIN MUTATED	17	37
XQ GAIN WILD-TYPE	553	435

Figure S182. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'xq gain' versus 'GENDER'

P value = 0.065 (Fisher's exact test), Q value = 0.16

Table S183. Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
XQ GAIN MUTATED	29	25
XQ GAIN WILD-TYPE	401	587

Figure S183. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00811 (Wilcoxon-test), Q value = 0.027

Table S184. Gene #41: 'xq gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
XQ GAIN MUTATED	27	87.8 (12.8)
XQ GAIN WILD-TYPE	662	81.3 (14.6)

Figure S184. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00038 (Fisher's exact test), Q value = 0.0018

Table S185. Gene #41: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
XQ GAIN MUTATED	18	1	13	6	1	15
XQ GAIN WILD-TYPE	158	26	105	172	17	510

Figure S185. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0127 (Fisher's exact test), Q value = 0.039

Table S186. Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
XQ GAIN MUTATED	5	40
XQ GAIN WILD-TYPE	25	851

Figure S186. 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 S187. Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
1P LOSS MUTATED	185	37	0.1 - 182.3 (20.1)
1P LOSS WILD-TYPE	854	522	0.0 - 211.2 (14.0)

Figure S187. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00012 (Wilcoxon-test), Q value = 0.00065

Table S188. Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
1P LOSS MUTATED	185	47.2 (13.6)
1P LOSS WILD-TYPE	856	51.9 (16.1)

Figure S188. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.66e-49 (Fisher's exact test), Q value = 7.2e-48

Table S189. Gene #42: '1p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
1P LOSS MUTATED	15	171
1P LOSS WILD-TYPE	555	301

Figure S189. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'1p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.19e-06 (Wilcoxon-test), Q value = 2.4e-05

Table S190. Gene #42: '1p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
1P LOSS MUTATED	108	86.9 (12.6)
1P LOSS WILD-TYPE	581	80.5 (14.7)

Figure S190. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S191. Gene #42: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
1P LOSS MUTATED	9	0	35	127	1	14
1P LOSS WILD-TYPE	167	27	83	51	17	511

Figure S191. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 4.92e-18 (Fisher's exact test), Q value = 1.3e-16

Table S192. Gene #42: '1p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
1P LOSS MUTATED	33	153
1P LOSS WILD-TYPE	441	415

Figure S192. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'1p loss' versus 'RACE'

P value = 0.034 (Fisher's exact test), Q value = 0.093

Table S193. Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
1P LOSS MUTATED	0	5	4	170
1P LOSS WILD-TYPE	1	16	60	752

Figure S193. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #8: 'RACE'

'1q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0065 (Fisher's exact test), Q value = 0.022

Table S194. Gene #43: '1q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
1Q LOSS MUTATED	14	28
1Q LOSS WILD-TYPE	556	444

Figure S194. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0022 (Fisher's exact test), Q value = 0.0088

Table S195. Gene #43: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
1Q LOSS MUTATED	4	0	6	18	0	14
1Q LOSS WILD-TYPE	172	27	112	160	18	511

Figure S195. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0861 (Wilcoxon-test), Q value = 0.2

Table S196. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
2P LOSS MUTATED	51	54.5 (17.4)
2P LOSS WILD-TYPE	990	50.9 (15.7)

Figure S196. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0253 (Wilcoxon-test), Q value = 0.071

Table S197. Gene #46: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
3P LOSS MUTATED	51	77.8 (12.9)
3P LOSS WILD-TYPE	638	81.8 (14.7)

Figure S197. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'3p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.101 (Fisher's exact test), Q value = 0.23

Table S198. Gene #46: '3p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
3P LOSS MUTATED	37	30
3P LOSS WILD-TYPE	437	538

Figure S198. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'3p loss' versus 'ETHNICITY'

P value = 0.04 (Fisher's exact test), Q value = 0.11

Table S199. Gene #46: '3p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
3P LOSS MUTATED	5	55
3P LOSS WILD-TYPE	25	836

Figure S199. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'ETHNICITY'

'4p loss' versus 'Time to Death'

P value = 0.0549 (logrank test), Q value = 0.14

Table S200. Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
4P LOSS MUTATED	117	60	0.1 - 134.3 (17.6)
4P LOSS WILD-TYPE	922	499	0.0 - 211.2 (14.4)

Figure S200. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0607 (Fisher's exact test), Q value = 0.15

Table S201. Gene #48: '4p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
4P LOSS MUTATED	54	63
4P LOSS WILD-TYPE	516	409

Figure S201. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'4p loss' versus 'GENDER'

P value = 0.0281 (Fisher's exact test), Q value = 0.079

Table S202. Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
4P LOSS MUTATED	37	80
4P LOSS WILD-TYPE	393	532

Figure S202. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.0025

Table S203. Gene #48: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
4P LOSS MUTATED	12	1	14	37	0	53
4P LOSS WILD-TYPE	164	26	104	141	18	472

Figure S203. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 0.000118 (logrank test), Q value = 0.00065

Table S204. Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
4Q LOSS MUTATED	139	59	0.1 - 156.2 (19.1)
4Q LOSS WILD-TYPE	900	500	0.0 - 211.2 (14.3)

Figure S204. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0309 (Wilcoxon-test), Q value = 0.086

Table S205. Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
4Q LOSS MUTATED	139	48.4 (14.6)
4Q LOSS WILD-TYPE	902	51.5 (16.0)

Figure S205. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.000332 (Fisher's exact test), Q value = 0.0016

Table S206. Gene #49: '4q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
4Q LOSS MUTATED	56	83
4Q LOSS WILD-TYPE	514	389

Figure S206. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00017 (Fisher's exact test), Q value = 0.00088

Table S207. Gene #49: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
4Q LOSS MUTATED	21	2	18	44	1	53
4Q LOSS WILD-TYPE	155	25	100	134	17	472

Figure S207. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0785 (Wilcoxon-test), Q value = 0.19

Table S208. Gene #50: '5p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
5P LOSS MUTATED	55	79.1 (12.9)
5P LOSS WILD-TYPE	634	81.7 (14.7)

Figure S208. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0483 (Fisher's exact test), Q value = 0.13

Table S209. Gene #50: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
5P LOSS MUTATED	17	0	11	5	1	42
5P LOSS WILD-TYPE	159	27	107	173	17	483

Figure S209. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00172 (Fisher's exact test), Q value = 0.0073

Table S210. Gene #50: '5p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
5P LOSS MUTATED	48	28
5P LOSS WILD-TYPE	426	540

Figure S210. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0943 (Fisher's exact test), Q value = 0.21

Table S211. Gene #51: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
5Q LOSS MUTATED	18	0	7	7	0	44
5Q LOSS WILD-TYPE	158	27	111	171	18	481

Figure S211. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00385 (Fisher's exact test), Q value = 0.014

Table S212. Gene #51: '5q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
5Q LOSS MUTATED	47	29
5Q LOSS WILD-TYPE	427	539

Figure S212. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6p loss' versus 'Time to Death'

P value = 4.94e-13 (logrank test), Q value = 1e-11

Table S213. Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
6P LOSS MUTATED	110	86	0.2 - 92.7 (10.4)
6P LOSS WILD-TYPE	929	473	0.0 - 211.2 (15.0)

Figure S213. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000111 (Wilcoxon-test), Q value = 0.00062

Table S214. Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
6P LOSS MUTATED	110	56.5 (14.8)
6P LOSS WILD-TYPE	931	50.5 (15.8)

Figure S214. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.89e-07 (Fisher's exact test), Q value = 3.7e-06

Table S215. Gene #52: '6p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
6P LOSS MUTATED	85	25
6P LOSS WILD-TYPE	485	447

Figure S215. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'6p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0782 (Wilcoxon-test), Q value = 0.19

Table S216. Gene #52: '6p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
6P LOSS MUTATED	80	79.1 (15.0)
6P LOSS WILD-TYPE	609	81.8 (14.5)

Figure S216. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S217. Gene #52: '6p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
6P LOSS MUTATED	13	3	4	8	3	79
6P LOSS WILD-TYPE	163	24	114	170	15	446

Figure S217. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0849 (Fisher's exact test), Q value = 0.2

Table S218. Gene #52: '6p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
6P LOSS MUTATED	59	51
6P LOSS WILD-TYPE	415	517

Figure S218. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6p loss' versus 'RACE'

P value = 0.0571 (Fisher's exact test), Q value = 0.14

Table S219. Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
6P LOSS MUTATED	1	4	8	94
6P LOSS WILD-TYPE	0	17	56	828

Figure S219. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'RACE'

'6q loss' versus 'Time to Death'

P value = 5.51e-08 (logrank test), Q value = 7.5e-07

Table S220. Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
6Q LOSS MUTATED	179	122	0.1 - 94.8 (13.0)
6Q LOSS WILD-TYPE	860	437	0.0 - 211.2 (14.9)

Figure S220. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00208 (Wilcoxon-test), Q value = 0.0085

Table S221. Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
6Q LOSS MUTATED	180	54.4 (15.0)
6Q LOSS WILD-TYPE	861	50.4 (15.9)

Figure S221. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.49e-05 (Fisher's exact test), Q value = 0.00016

Table S222. Gene #53: '6q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
6Q LOSS MUTATED	124	56
6Q LOSS WILD-TYPE	446	416

Figure S222. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0121 (Wilcoxon-test), Q value = 0.038

Table S223. Gene #53: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
6Q LOSS MUTATED	129	79.2 (14.0)
6Q LOSS WILD-TYPE	560	82.1 (14.7)

Figure S223. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S224. Gene #53: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
6Q LOSS MUTATED	34	5	10	12	4	115
6Q LOSS WILD-TYPE	142	22	108	166	14	410

Figure S224. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00849 (Fisher's exact test), Q value = 0.028

Table S225. Gene #53: '6q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
6Q LOSS MUTATED	98	82
6Q LOSS WILD-TYPE	376	486

Figure S225. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6q loss' versus 'RACE'

P value = 0.0243 (Fisher's exact test), Q value = 0.069

Table S226. Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
6Q LOSS MUTATED	1	6	16	151
6Q LOSS WILD-TYPE	0	15	48	771

Figure S226. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'RACE'

'7q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0819 (Wilcoxon-test), Q value = 0.19

Table S227. Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
7Q LOSS MUTATED	9	41.6 (17.8)
7Q LOSS WILD-TYPE	1032	51.2 (15.8)

Figure S227. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'Time to Death'

P value = 0.000114 (logrank test), Q value = 0.00063

Table S228. Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
8P LOSS MUTATED	71	50	0.2 - 120.6 (11.7)
8P LOSS WILD-TYPE	968	509	0.0 - 211.2 (14.9)

Figure S228. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000194 (Wilcoxon-test), Q value = 0.00099

Table S229. Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
8P LOSS MUTATED	72	57.6 (14.2)
8P LOSS WILD-TYPE	969	50.6 (15.8)

Figure S229. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.52e-06 (Fisher's exact test), Q value = 3.7e-05

Table S230. Gene #56: '8p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
8P LOSS MUTATED	58	14
8P LOSS WILD-TYPE	512	458

Figure S230. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.00084

Table S231. Gene #56: '8p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
8P LOSS MUTATED	8	1	3	3	1	56
8P LOSS WILD-TYPE	168	26	115	175	17	469

Figure S231. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0031 (Fisher's exact test), Q value = 0.012

Table S232. Gene #56: '8p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
8P LOSS MUTATED	45	27
8P LOSS WILD-TYPE	429	541

Figure S232. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'8p loss' versus 'RACE'

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

Table S233. Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
8P LOSS MUTATED	0	6	3	58
8P LOSS WILD-TYPE	1	15	61	864

Figure S233. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #8: 'RACE'

'8q loss' versus 'Time to Death'

P value = 2.1e-06 (logrank test), Q value = 2.3e-05

Table S234. Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
8Q LOSS MUTATED	50	37	0.2 - 58.8 (11.2)
8Q LOSS WILD-TYPE	989	522	0.0 - 211.2 (14.9)

Figure S234. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000351 (Wilcoxon-test), Q value = 0.0017

Table S235. Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
8Q LOSS MUTATED	50	58.9 (12.6)
8Q LOSS WILD-TYPE	991	50.7 (15.9)

Figure S235. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 5.73e-05 (Fisher's exact test), Q value = 0.00035

Table S236. Gene #57: '8q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
8Q LOSS MUTATED	41	9
8Q LOSS WILD-TYPE	529	463

Figure S236. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'8q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00243 (Fisher's exact test), Q value = 0.0095

Table S237. Gene #57: '8q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
8Q LOSS MUTATED	5	1	2	2	1	39
8Q LOSS WILD-TYPE	171	26	116	176	17	486

Figure S237. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0412 (Fisher's exact test), Q value = 0.11

Table S238. Gene #57: '8q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
8Q LOSS MUTATED	30	20
8Q LOSS WILD-TYPE	444	548

Figure S238. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'9p loss' versus 'Time to Death'

P value = 0.00011 (logrank test), Q value = 0.00062

Table S239. Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
9P LOSS MUTATED	299	193	0.1 - 169.8 (14.0)
9P LOSS WILD-TYPE	740	366	0.0 - 211.2 (15.0)

Figure S239. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000525 (Wilcoxon-test), Q value = 0.0024

Table S240. Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
9P LOSS MUTATED	300	53.8 (15.4)
9P LOSS WILD-TYPE	741	50.0 (15.9)

Figure S240. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.05e-05 (Fisher's exact test), Q value = 7.6e-05

Table S241. Gene #58: '9p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
9P LOSS MUTATED	197	104
9P LOSS WILD-TYPE	373	368

Figure S241. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0013

Table S242. Gene #58: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
9P LOSS MUTATED	47	10	22	35	5	182
9P LOSS WILD-TYPE	129	17	96	143	13	343

Figure S242. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000361 (Fisher's exact test), Q value = 0.0017

Table S243. Gene #58: '9p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
9P LOSS MUTATED	163	138
9P LOSS WILD-TYPE	311	430

Figure S243. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'9q loss' versus 'Time to Death'

P value = 0.00362 (logrank test), Q value = 0.013

Table S244. Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
9Q LOSS MUTATED	133	89	0.1 - 169.8 (13.9)
9Q LOSS WILD-TYPE	906	470	0.0 - 211.2 (14.9)

Figure S244. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

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

Table S245. Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
9Q LOSS MUTATED	134	53.9 (15.8)
9Q LOSS WILD-TYPE	907	50.7 (15.8)

Figure S245. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00386 (Fisher's exact test), Q value = 0.014

Table S246. Gene #59: '9q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
9Q LOSS MUTATED	89	45
9Q LOSS WILD-TYPE	481	427

Figure S246. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00445 (Wilcoxon-test), Q value = 0.016

Table S247. Gene #59: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
9Q LOSS MUTATED	88	77.5 (15.0)
9Q LOSS WILD-TYPE	601	82.1 (14.4)

Figure S247. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0681 (Fisher's exact test), Q value = 0.17

Table S248. Gene #59: '9q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
9Q LOSS MUTATED	18	6	10	17	3	80
9Q LOSS WILD-TYPE	158	21	108	161	15	445

Figure S248. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'Time to Death'

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

Table S249. Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
10P LOSS MUTATED	546	430	0.1 - 134.3 (12.0)
10P LOSS WILD-TYPE	493	129	0.0 - 211.2 (18.6)

Figure S249. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 5.7e-69 (Wilcoxon-test), Q value = 3.2e-67

Table S250. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
10P LOSS MUTATED	547	59.1 (12.5)
10P LOSS WILD-TYPE	494	42.2 (14.3)

Figure S250. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 7.17e-113 (Fisher's exact test), Q value = 5.3e-111

Table S251. Gene #60: '10p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
10P LOSS MUTATED	473	74
10P LOSS WILD-TYPE	97	398

Figure S251. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 1.05e-18 (Wilcoxon-test), Q value = 2.8e-17

Table S252. Gene #60: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
10P LOSS MUTATED	396	77.7 (15.1)
10P LOSS WILD-TYPE	293	86.7 (12.1)

Figure S252. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S253. Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
10P LOSS MUTATED	44	20	14	16	10	443
10P LOSS WILD-TYPE	132	7	104	162	8	82

Figure S253. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 1.24e-22 (Fisher's exact test), Q value = 3.5e-21

Table S254. Gene #60: '10p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
10P LOSS MUTATED	327	220
10P LOSS WILD-TYPE	147	348

Figure S254. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10p loss' versus 'RACE'

P value = 0.0013 (Fisher's exact test), Q value = 0.0057

Table S255. Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
10P LOSS MUTATED	1	9	47	469
10P LOSS WILD-TYPE	0	12	17	453

Figure S255. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #8: 'RACE'

'10p loss' versus 'ETHNICITY'

P value = 0.0632 (Fisher's exact test), Q value = 0.16

Table S256. Gene #60: '10p loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
10P LOSS MUTATED	10	457
10P LOSS WILD-TYPE	20	434

Figure S256. 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 S257. Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
10Q LOSS MUTATED	574	445	0.1 - 172.8 (12.2)
10Q LOSS WILD-TYPE	465	114	0.0 - 211.2 (18.6)

Figure S257. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 5.55e-63 (Wilcoxon-test), Q value = 2.7e-61

Table S258. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
10Q LOSS MUTATED	575	58.4 (13.2)
10Q LOSS WILD-TYPE	466	42.1 (14.1)

Figure S258. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.35e-111 (Fisher's exact test), Q value = 9e-110

Table S259. Gene #61: '10q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
10Q LOSS MUTATED	487	88
10Q LOSS WILD-TYPE	83	384

Figure S259. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 7.29e-20 (Wilcoxon-test), Q value = 2e-18

Table S260. Gene #61: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
10Q LOSS MUTATED	415	77.8 (15.1)
10Q LOSS WILD-TYPE	274	87.2 (11.7)

Figure S260. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S261. Gene #61: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
10Q LOSS MUTATED	52	20	17	19	13	454
10Q LOSS WILD-TYPE	124	7	101	159	5	71

Figure S261. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 3.37e-24 (Fisher's exact test), Q value = 9.9e-23

Table S262. Gene #61: '10q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
10Q LOSS MUTATED	342	233
10Q LOSS WILD-TYPE	132	335

Figure S262. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10q loss' versus 'RACE'

P value = 0.0018 (Fisher's exact test), Q value = 0.0076

Table S263. Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
10Q LOSS MUTATED	1	9	48	495
10Q LOSS WILD-TYPE	0	12	16	427

Figure S263. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #8: 'RACE'

'10q loss' versus 'ETHNICITY'

P value = 0.0259 (Fisher's exact test), Q value = 0.073

Table S264. Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
10Q LOSS MUTATED	10	484
10Q LOSS WILD-TYPE	20	407

Figure S264. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'ETHNICITY'

'11p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0238 (Fisher's exact test), Q value = 0.068

Table S265. Gene #62: '11p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
11P LOSS MUTATED	99	58
11P LOSS WILD-TYPE	471	414

Figure S265. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'11p loss' versus 'GENDER'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S266. Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
11P LOSS MUTATED	78	79
11P LOSS WILD-TYPE	352	533

Figure S266. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'GENDER'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00182 (Fisher's exact test), Q value = 0.0076

Table S267. Gene #62: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
11P LOSS MUTATED	33	4	13	12	5	90
11P LOSS WILD-TYPE	143	23	105	166	13	435

Figure S267. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 1e-07 (logrank test), Q value = 1.3e-06

Table S268. Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
11Q LOSS MUTATED	112	87	0.2 - 92.7 (13.1)
11Q LOSS WILD-TYPE	927	472	0.0 - 211.2 (14.9)

Figure S268. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 1.21e-05 (Wilcoxon-test), Q value = 8.7e-05

Table S269. Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
11Q LOSS MUTATED	112	57.1 (14.2)
11Q LOSS WILD-TYPE	929	50.4 (15.9)

Figure S269. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 7.36e-10 (Fisher's exact test), Q value = 1.2e-08

Table S270. Gene #63: '11q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
11Q LOSS MUTATED	91	21
11Q LOSS WILD-TYPE	479	451

Figure S270. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0259 (Wilcoxon-test), Q value = 0.073

Table S271. Gene #63: '11q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
11Q LOSS MUTATED	85	78.8 (14.1)
11Q LOSS WILD-TYPE	604	81.9 (14.6)

Figure S271. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S272. Gene #63: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
11Q LOSS MUTATED	13	3	6	2	3	85
11Q LOSS WILD-TYPE	163	24	112	176	15	440

Figure S272. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.109 (Fisher's exact test), Q value = 0.24

Table S273. Gene #63: '11q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
11Q LOSS MUTATED	59	53
11Q LOSS WILD-TYPE	415	515

Figure S273. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'12p loss' versus 'Time to Death'

P value = 0.00896 (logrank test), Q value = 0.029

Table S274. Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
12P LOSS MUTATED	82	55	0.1 - 92.7 (14.5)
12P LOSS WILD-TYPE	957	504	0.0 - 211.2 (14.8)

Figure S274. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #1: 'Time to Death'

'12p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00394 (Fisher's exact test), Q value = 0.014

Table S275. Gene #64: '12p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
12P LOSS MUTATED	58	25
12P LOSS WILD-TYPE	512	447

Figure S275. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0091 (Fisher's exact test), Q value = 0.029

Table S276. Gene #64: '12p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
12P LOSS MUTATED	15	1	4	6	2	55
12P LOSS WILD-TYPE	161	26	114	172	16	470

Figure S276. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0214 (Fisher's exact test), Q value = 0.062

Table S277. Gene #64: '12p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
12P LOSS MUTATED	48	35
12P LOSS WILD-TYPE	426	533

Figure S277. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'12p loss' versus 'RACE'

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

Table S278. Gene #64: '12p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
12P LOSS MUTATED	0	0	1	78
12P LOSS WILD-TYPE	1	21	63	844

Figure S278. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #8: 'RACE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0222 (Fisher's exact test), Q value = 0.064

Table S279. Gene #65: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
12Q LOSS MUTATED	27	1	12	9	3	52
12Q LOSS WILD-TYPE	149	26	106	169	15	473

Figure S279. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.0188 (Fisher's exact test), Q value = 0.056

Table S280. Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
12Q LOSS MUTATED	0	0	1	100
12Q LOSS WILD-TYPE	1	21	63	822

Figure S280. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #8: 'RACE'

'13q loss' versus 'Time to Death'

P value = 0.00539 (logrank test), Q value = 0.019

Table S281. Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
13Q LOSS MUTATED	285	173	0.1 - 211.2 (14.5)
13Q LOSS WILD-TYPE	754	386	0.0 - 182.3 (14.9)

Figure S281. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0785 (Wilcoxon-test), Q value = 0.19

Table S282. Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
13Q LOSS MUTATED	285	52.5 (15.7)
13Q LOSS WILD-TYPE	756	50.6 (15.8)

Figure S282. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 9.05e-05 (Fisher's exact test), Q value = 0.00052

Table S283. Gene #66: '13q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
13Q LOSS MUTATED	184	101
13Q LOSS WILD-TYPE	386	371

Figure S283. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'13q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0364 (Wilcoxon-test), Q value = 0.099

Table S284. Gene #66: '13q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
13Q LOSS MUTATED	202	80.0 (14.5)
13Q LOSS WILD-TYPE	487	82.2 (14.6)

Figure S284. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00234 (Fisher's exact test), Q value = 0.0093

Table S285. Gene #66: '13q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
13Q LOSS MUTATED	43	7	22	36	4	173
13Q LOSS WILD-TYPE	133	20	96	142	14	352

Figure S285. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00796 (Fisher's exact test), Q value = 0.026

Table S286. Gene #66: '13q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
13Q LOSS MUTATED	149	136
13Q LOSS WILD-TYPE	325	432

Figure S286. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'14q loss' versus 'Time to Death'

P value = 3.44e-05 (logrank test), Q value = 0.00022

Table S287. Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
14Q LOSS MUTATED	213	139	0.1 - 130.8 (13.6)
14Q LOSS WILD-TYPE	826	420	0.0 - 211.2 (15.0)

Figure S287. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000156 (Wilcoxon-test), Q value = 0.00082

Table S288. Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
14Q LOSS MUTATED	214	54.7 (15.0)
14Q LOSS WILD-TYPE	827	50.2 (15.9)

Figure S288. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.00011

Table S289. Gene #67: '14q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
14Q LOSS MUTATED	145	69
14Q LOSS WILD-TYPE	425	403

Figure S289. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0988 (Wilcoxon-test), Q value = 0.22

Table S290. Gene #67: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
14Q LOSS MUTATED	156	80.3 (13.7)
14Q LOSS WILD-TYPE	533	81.9 (14.8)

Figure S290. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00027 (Fisher's exact test), Q value = 0.0014

Table S291. Gene #67: '14q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
14Q LOSS MUTATED	32	5	16	21	6	134
14Q LOSS WILD-TYPE	144	22	102	157	12	391

Figure S291. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0544 (Fisher's exact test), Q value = 0.14

Table S292. Gene #67: '14q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
14Q LOSS MUTATED	110	104
14Q LOSS WILD-TYPE	364	464

Figure S292. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'14q loss' versus 'RACE'

P value = 0.0579 (Fisher's exact test), Q value = 0.15

Table S293. Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
14Q LOSS MUTATED	1	5	19	182
14Q LOSS WILD-TYPE	0	16	45	740

Figure S293. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #8: 'RACE'

'14q loss' versus 'ETHNICITY'

P value = 0.0985 (Fisher's exact test), Q value = 0.22

Table S294. Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	30	891
14Q LOSS MUTATED	2	180
14Q LOSS WILD-TYPE	28	711

Figure S294. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'ETHNICITY'

'15q loss' versus 'Time to Death'

P value = 0.0072 (logrank test), Q value = 0.024

Table S295. Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
15Q LOSS MUTATED	148	96	0.2 - 134.3 (13.3)
15Q LOSS WILD-TYPE	891	463	0.0 - 211.2 (14.9)

Figure S295. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000205 (Wilcoxon-test), Q value = 0.001

Table S296. Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
15Q LOSS MUTATED	149	55.5 (16.0)
15Q LOSS WILD-TYPE	892	50.4 (15.7)

Figure S296. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.00026

Table S297. Gene #68: '15q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
15Q LOSS MUTATED	105	45
15Q LOSS WILD-TYPE	465	427

Figure S297. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00153 (Fisher's exact test), Q value = 0.0066

Table S298. Gene #68: '15q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
15Q LOSS MUTATED	14	6	10	21	2	97
15Q LOSS WILD-TYPE	162	21	108	157	16	428

Figure S298. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 1.09e-06 (logrank test), Q value = 1.3e-05

Table S299. Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
16P LOSS MUTATED	75	61	0.4 - 78.3 (13.6)
16P LOSS WILD-TYPE	964	498	0.0 - 211.2 (14.9)

Figure S299. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 4.17e-06 (Wilcoxon-test), Q value = 4.3e-05

Table S300. Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
16P LOSS MUTATED	75	59.0 (14.2)
16P LOSS WILD-TYPE	966	50.5 (15.8)

Figure S300. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 4.93e-08 (Fisher's exact test), Q value = 6.9e-07

Table S301. Gene #69: '16p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
16P LOSS MUTATED	63	12
16P LOSS WILD-TYPE	507	460

Figure S301. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S302. Gene #69: '16p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
16P LOSS MUTATED	7	1	2	3	0	62
16P LOSS WILD-TYPE	169	26	116	175	18	463

Figure S302. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 4.86e-07 (logrank test), Q value = 6e-06

Table S303. Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
16Q LOSS MUTATED	101	81	0.2 - 120.6 (13.6)
16Q LOSS WILD-TYPE	938	478	0.0 - 211.2 (14.9)

Figure S303. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 3.72e-05 (Wilcoxon-test), Q value = 0.00023

Table S304. Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
16Q LOSS MUTATED	101	57.1 (14.5)
16Q LOSS WILD-TYPE	940	50.4 (15.8)

Figure S304. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 6.68e-09 (Fisher's exact test), Q value = 9.9e-08

Table S305. Gene #70: '16q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
16Q LOSS MUTATED	82	19
16Q LOSS WILD-TYPE	488	453

Figure S305. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'16q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0393 (Wilcoxon-test), Q value = 0.11

Table S306. Gene #70: '16q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
16Q LOSS MUTATED	66	78.0 (16.3)
16Q LOSS WILD-TYPE	623	81.9 (14.4)

Figure S306. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S307. Gene #70: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
16Q LOSS MUTATED	10	2	4	5	1	79
16Q LOSS WILD-TYPE	166	25	114	173	17	446

Figure S307. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'Time to Death'

P value = 6.78e-05 (logrank test), Q value = 4e-04

Table S308. Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
17P LOSS MUTATED	74	52	0.1 - 92.7 (12.0)
17P LOSS WILD-TYPE	965	507	0.0 - 211.2 (14.9)

Figure S308. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000473 (Wilcoxon-test), Q value = 0.0022

Table S309. Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
17P LOSS MUTATED	74	57.3 (14.3)
17P LOSS WILD-TYPE	967	50.6 (15.8)

Figure S309. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 8.27e-08 (Fisher's exact test), Q value = 1.1e-06

Table S310. Gene #71: '17p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
17P LOSS MUTATED	62	12
17P LOSS WILD-TYPE	508	460

Figure S310. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00235 (Wilcoxon-test), Q value = 0.0093

Table S311. Gene #71: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
17P LOSS MUTATED	53	77.4 (11.6)
17P LOSS WILD-TYPE	636	81.9 (14.8)

Figure S311. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S312. Gene #71: '17p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
17P LOSS MUTATED	6	3	2	4	1	58
17P LOSS WILD-TYPE	170	24	116	174	17	467

Figure S312. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 0.000139 (logrank test), Q value = 0.00075

Table S313. Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
17Q LOSS MUTATED	49	36	0.1 - 92.7 (11.7)
17Q LOSS WILD-TYPE	990	523	0.0 - 211.2 (14.9)

Figure S313. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00144 (Wilcoxon-test), Q value = 0.0063

Table S314. Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
17Q LOSS MUTATED	49	57.9 (13.6)
17Q LOSS WILD-TYPE	992	50.8 (15.8)

Figure S314. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.00016

Table S315. Gene #72: '17q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
17Q LOSS MUTATED	41	8
17Q LOSS WILD-TYPE	529	464

Figure S315. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0504 (Wilcoxon-test), Q value = 0.13

Table S316. Gene #72: '17q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
17Q LOSS MUTATED	33	78.5 (10.9)
17Q LOSS WILD-TYPE	656	81.7 (14.7)

Figure S316. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00171 (Fisher's exact test), Q value = 0.0073

Table S317. Gene #72: '17q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
17Q LOSS MUTATED	3	2	1	4	1	38
17Q LOSS WILD-TYPE	173	25	117	174	17	487

Figure S317. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'Time to Death'

P value = 0.0909 (logrank test), Q value = 0.21

Table S318. Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
18Q LOSS MUTATED	119	59	0.1 - 182.3 (15.3)
18Q LOSS WILD-TYPE	920	500	0.0 - 211.2 (14.5)

Figure S318. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'Time to Death'

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

Table S319. Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
19Q LOSS MUTATED	227	62	0.1 - 182.3 (18.6)
19Q LOSS WILD-TYPE	812	497	0.0 - 211.2 (13.6)

Figure S319. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 4.55e-08 (Wilcoxon-test), Q value = 6.5e-07

Table S320. Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
19Q LOSS MUTATED	227	46.2 (13.5)
19Q LOSS WILD-TYPE	814	52.5 (16.1)

Figure S320. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.1e-44 (Fisher's exact test), Q value = 4.3e-43

Table S321. Gene #76: '19q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
19Q LOSS MUTATED	34	194
19Q LOSS WILD-TYPE	536	278

Figure S321. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'19q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 8.39e-06 (Wilcoxon-test), Q value = 7.4e-05

Table S322. Gene #76: '19q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
19Q LOSS MUTATED	143	85.8 (13.0)
19Q LOSS WILD-TYPE	546	80.4 (14.8)

Figure S322. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S323. Gene #76: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
19Q LOSS MUTATED	21	2	38	135	2	30
19Q LOSS WILD-TYPE	155	25	80	43	16	495

Figure S323. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 7.33e-15 (Fisher's exact test), Q value = 1.6e-13

Table S324. Gene #76: '19q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
19Q LOSS MUTATED	53	175
19Q LOSS WILD-TYPE	421	393

Figure S324. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'20p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.032 (Fisher's exact test), Q value = 0.088

Table S325. Gene #77: '20p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
20P LOSS MUTATED	18	5
20P LOSS WILD-TYPE	552	467

Figure S325. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20p loss' versus 'RACE'

P value = 0.1 (Fisher's exact test), Q value = 0.22

Table S326. Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	64	922
20P LOSS MUTATED	0	2	2	19
20P LOSS WILD-TYPE	1	19	62	903

Figure S326. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #8: 'RACE'

'20q loss' versus 'Time to Death'

P value = 0.0715 (logrank test), Q value = 0.17

Table S327. Gene #78: '20q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
20Q LOSS MUTATED	18	14	2.0 - 44.6 (16.0)
20Q LOSS WILD-TYPE	1021	545	0.0 - 211.2 (14.8)

Figure S327. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #1: 'Time to Death'

'20q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00316 (Fisher's exact test), Q value = 0.012

Table S328. Gene #78: '20q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
20Q LOSS MUTATED	16	2
20Q LOSS WILD-TYPE	554	470

Figure S328. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20q loss' versus 'GENDER'

P value = 0.0948 (Fisher's exact test), Q value = 0.21

Table S329. Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	430	612
20Q LOSS MUTATED	11	7
20Q LOSS WILD-TYPE	419	605

Figure S329. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #4: 'GENDER'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0672 (Fisher's exact test), Q value = 0.17

Table S330. Gene #78: '20q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
20Q LOSS MUTATED	1	0	1	0	0	16
20Q LOSS WILD-TYPE	175	27	117	178	18	509

Figure S330. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 2.8e-12 (logrank test), Q value = 5.3e-11

Table S331. Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
22Q LOSS MUTATED	233	174	0.1 - 156.2 (12.7)
22Q LOSS WILD-TYPE	806	385	0.0 - 211.2 (15.0)

Figure S331. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 4.43e-13 (Wilcoxon-test), Q value = 9.3e-12

Table S332. Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1041	51.1 (15.8)
22Q LOSS MUTATED	233	57.5 (14.8)
22Q LOSS WILD-TYPE	808	49.2 (15.6)

Figure S332. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.96e-17 (Fisher's exact test), Q value = 4.8e-16

Table S333. Gene #80: '22q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
22Q LOSS MUTATED	183	50
22Q LOSS WILD-TYPE	387	422

Figure S333. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00358 (Wilcoxon-test), Q value = 0.013

Table S334. Gene #80: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
22Q LOSS MUTATED	162	79.2 (14.7)
22Q LOSS WILD-TYPE	527	82.2 (14.5)

Figure S334. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.4e-05

Table S335. Gene #80: '22q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	176	27	118	178	18	525
22Q LOSS MUTATED	24	9	11	15	6	168
22Q LOSS WILD-TYPE	152	18	107	163	12	357

Figure S335. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000759 (Fisher's exact test), Q value = 0.0034

Table S336. Gene #80: '22q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients	NO	YES
ALL	474	568
22Q LOSS MUTATED	129	104
22Q LOSS WILD-TYPE	345	464

Figure S336. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'xq loss' versus 'Time to Death'

P value = 0.0768 (logrank test), Q value = 0.19

Table S337. Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1039	559	0.0 - 211.2 (14.8)
XQ LOSS MUTATED	165	97	0.1 - 134.3 (14.4)
XQ LOSS WILD-TYPE	874	462	0.0 - 211.2 (14.8)

Figure S337. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0413 (Fisher's exact test), Q value = 0.11

Table S338. Gene #82: 'xq loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	570	472
XQ LOSS MUTATED	103	63
XQ LOSS WILD-TYPE	467	409

Figure S338. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'xq loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0691 (Wilcoxon-test), Q value = 0.17

Table S339. Gene #82: 'xq loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	689	81.5 (14.6)
XQ LOSS MUTATED	116	79.0 (16.0)
XQ LOSS WILD-TYPE	573	82.0 (14.2)

Figure S339. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #5: '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/15101903/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/15078950/GBMLGG-TP.merged_data.txt
Number of patients = 1042
Number of significantly arm-level cnvs = 82
Number of selected clinical features = 9
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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