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

Overview

Introduction

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

Summary

Testing the association between copy number variation 79 focal events and 9 clinical features across 1083 patients, 418 significant findings detected with Q value < 0.25.

amp_1p36.21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_1q22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_1q32.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_1q44 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_2p24.3 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
amp_3p25.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
amp_3q26.33 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_4p16.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_4q12 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_5p15.33 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_7p11.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
amp_7q11.21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
amp_7q21.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
amp_7q31.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
amp_7q32.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
amp_8q24.21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
amp_9q34.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_10p15.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_11p13 cnv correlated to 'HISTOLOGICAL_TYPE'.
amp_11q24.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_12p13.32 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
amp_12q14.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_12q15 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
amp_13q34 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.
amp_14q32.33 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
amp_17p13.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
amp_17q25.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
amp_19p13.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
amp_19p13.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
amp_19q12 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_19q13.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_xp11.21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_1p36.32 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_1p36.23 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_1p32.3 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_1p22.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_1q42.11 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'KARNOFSKY_PERFORMANCE_SCORE'.
del_2q22.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_2q37.1 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
del_3p21.31 cnv correlated to 'RADIATION_THERAPY'.
del_3q13.31 cnv correlated to 'Time to Death' and 'RADIATION_THERAPY'.
del_4q34.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
del_5p15.33 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
del_5q34 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_6p25.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_6q22.31 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_6q26 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_8p23.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_8q24.3 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_10p15.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_10p13 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_10p11.23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_10q23.31 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_10q26.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_11p15.1 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_11p11.2 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_12p13.1 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_12q12 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_12q15 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_13q14.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_13q22.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_14q13.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
del_14q24.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
del_14q31.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_15q14 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_16p12.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_16q23.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_17p13.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_17q11.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_18q23 cnv correlated to 'YEARS_TO_BIRTH'.
del_19q13.41 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_19q13.43 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_22q13.32 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_xq21.1 cnv correlated to 'YEARS_TO_BIRTH' and 'KARNOFSKY_PERFORMANCE_SCORE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 focal events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 418 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	TUMOR TISSUE SITE	GENDER	RADIATION THERAPY	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 6q22 31	234 (22%)	849	9.96e-12 (8.64e-11)	4.01e-05 (0.000147)	6.44e-07 (3.61e-06)	0.0995 (0.178)	0.0351 (0.0736)	0.00692 (0.0178)	1e-05 (3.91e-05)	0.0988 (0.178)	0.13 (0.223)
del 10p15 3	547 (51%)	536	0 (0)	2.28e-71 (6e-70)	1.4e-109 (4.98e-108)	0.0645 (0.124)	1.12e-15 (1.33e-14)	6.84e-18 (9.93e-17)	1e-05 (3.91e-05)	0.00766 (0.0195)	0.00501 (0.0133)
del 10p13	547 (51%)	536	0 (0)	1.44e-71 (3.93e-70)	6.21e-111 (2.32e-109)	0.0265 (0.058)	9.39e-17 (1.31e-15)	2.63e-16 (3.53e-15)	1e-05 (3.91e-05)	0.016 (0.0366)	0.00501 (0.0133)
del 10p11 23	552 (51%)	531	0 (0)	3.67e-75 (1.09e-73)	4.92e-114 (1.94e-112)	0.0485 (0.097)	6.1e-16 (7.6e-15)	2.49e-19 (3.84e-18)	1e-05 (3.91e-05)	0.00155 (0.00461)	0.00325 (0.00897)
amp 7p11 2	629 (58%)	454	0 (0)	1.71e-68 (4.34e-67)	3.58e-104 (1.21e-102)	0.289 (0.431)	8.74e-14 (8.75e-13)	2.26e-19 (3.56e-18)	1e-05 (3.91e-05)	0.00508 (0.0135)	0.0077 (0.0195)
amp 7q11 21	576 (53%)	507	0 (0)	4.47e-55 (9.94e-54)	1.36e-84 (4.2e-83)	0.323 (0.466)	5.95e-11 (4.81e-10)	8.71e-14 (8.75e-13)	1e-05 (3.91e-05)	0.00298 (0.00837)	0.00829 (0.0208)
amp 7q21 2	630 (58%)	453	0 (0)	4.83e-50 (1.01e-48)	9.69e-72 (2.75e-70)	0.755 (0.851)	1.19e-11 (1.02e-10)	3.39e-12 (3.02e-11)	1e-05 (3.91e-05)	0.00132 (0.00399)	0.00264 (0.00757)
amp 7q31 2	640 (59%)	443	0 (0)	5.49e-40 (1.05e-38)	3.92e-59 (9.29e-58)	0.802 (0.886)	1.49e-09 (1.02e-08)	2.97e-09 (1.95e-08)	1e-05 (3.91e-05)	0.00839 (0.0209)	0.00285 (0.00806)
amp 7q32 3	653 (60%)	430	0 (0)	1.31e-40 (2.59e-39)	5.3e-58 (1.22e-56)	0.801 (0.886)	1.74e-10 (1.33e-09)	4.21e-09 (2.72e-08)	1e-05 (3.91e-05)	0.00604 (0.0158)	0.00153 (0.00457)
amp xp11 21	104 (10%)	979	0.000448 (0.00144)	3.21e-06 (1.71e-05)	1.89e-05 (7.2e-05)	0.0284 (0.0613)	0.00971 (0.024)	0.0254 (0.0559)	1e-05 (3.91e-05)	0.568 (0.692)	0.0304 (0.0654)
del 9p21 3	589 (54%)	494	0 (0)	3.58e-30 (5.91e-29)	5.89e-38 (1.07e-36)	0.387 (0.535)	4.11e-10 (3.04e-09)	4.66e-13 (4.36e-12)	1e-05 (3.91e-05)	0.015 (0.0348)	0.0636 (0.123)
del 10q23 31	622 (57%)	461	0 (0)	8.17e-64 (2e-62)	2.51e-118 (1.05e-116)	0.663 (0.773)	3.55e-19 (5.37e-18)	2.2e-18 (3.26e-17)	1e-05 (3.91e-05)	0.00702 (0.018)	0.00831 (0.0208)
del 10q26 3	659 (61%)	424	0 (0)	4.8e-50 (1.01e-48)	7.75e-97 (2.5e-95)	0.9 (0.955)	8.23e-17 (1.17e-15)	3.22e-16 (4.24e-15)	1e-05 (3.91e-05)	0.00837 (0.0209)	0.0271 (0.0592)
del 14q13 1	244 (23%)	839	1.86e-10 (1.4e-09)	1.2e-09 (8.46e-09)	2.96e-12 (2.66e-11)	0.377 (0.523)	0.0203 (0.0459)	0.00597 (0.0157)	1e-05 (3.91e-05)	0.0466 (0.0938)	0.0569 (0.112)
amp 1q32 1	203 (19%)	880	2.28e-12 (2.08e-11)	3.54e-13 (3.36e-12)	5.39e-16 (6.85e-15)	0.693 (0.796)	0.017 (0.0388)	0.000164 (0.000552)	1e-05 (3.91e-05)	0.39 (0.538)	0.0146 (0.034)
amp 9q34 3	139 (13%)	944	0.0254 (0.0559)	0.0443 (0.0903)	0.000364 (0.00119)	0.0798 (0.149)	0.0856 (0.157)	0.124 (0.214)	0.00056 (0.00179)	0.222 (0.35)	0.816 (0.894)
amp 12q14 1	171 (16%)	912	6.66e-16 (8.17e-15)	7.97e-06 (3.91e-05)	7.18e-14 (7.51e-13)	0.673 (0.781)	0.00811 (0.0204)	0.117 (0.204)	1e-05 (3.91e-05)	0.316 (0.457)	0.0336 (0.0714)
amp 12q15	110 (10%)	973	2.55e-10 (1.91e-09)	4.78e-05 (0.000174)	1.49e-12 (1.38e-11)	0.185 (0.303)	0.0442 (0.0902)	0.0364 (0.0761)	1e-05 (3.91e-05)	0.359 (0.506)	0.0172 (0.0391)
amp 19q12	245 (23%)	838	0 (0)	4.86e-16 (6.28e-15)	3.12e-38 (5.83e-37)	0.462 (0.605)	6.89e-08 (4.15e-07)	9.53e-05 (0.000334)	1e-05 (3.91e-05)	0.0403 (0.0829)	0.582 (0.701)
amp 19q13 2	230 (21%)	853	0 (0)	1.81e-15 (2.11e-14)	9.95e-34 (1.73e-32)	0.407 (0.554)	5.99e-07 (3.38e-06)	0.000304 (0.000995)	1e-05 (3.91e-05)	0.0337 (0.0714)	0.567 (0.692)
del 1p22 1	233 (22%)	850	0 (0)	0.00387 (0.0106)	2.27e-30 (3.85e-29)	0.5 (0.637)	2.08e-14 (2.28e-13)	0.000136 (0.000467)	1e-05 (3.91e-05)	0.423 (0.569)	0.139 (0.237)
del 13q14 2	381 (35%)	702	3.31e-05 (0.000122)	0.0605 (0.118)	1.23e-06 (6.72e-06)	0.122 (0.212)	0.00263 (0.00757)	0.00468 (0.0126)	1e-05 (3.91e-05)	0.573 (0.693)	0.264 (0.403)
del 13q22 1	364 (34%)	719	1.74e-05 (6.64e-05)	0.013 (0.0306)	6.34e-06 (3.24e-05)	0.268 (0.407)	0.0151 (0.0349)	0.00209 (0.0061)	0.0001 (0.000349)	0.56 (0.689)	0.142 (0.242)
del 17q11 2	91 (8%)	992	3.78e-08 (2.34e-07)	0.000205 (0.000684)	9.35e-07 (5.19e-06)	0.912 (0.964)	0.116 (0.204)	0.0111 (0.027)	6e-05 (0.000214)	0.0845 (0.156)	0.398 (0.542)
del 19q13 41	366 (34%)	717	0 (0)	4.16e-08 (2.55e-07)	3.95e-34 (7.02e-33)	0.193 (0.312)	1.35e-08 (8.5e-08)	5.97e-05 (0.000214)	1e-05 (3.91e-05)	0.808 (0.89)	0.146 (0.248)
del 22q13 32	289 (27%)	794	1.61e-11 (1.36e-10)	1.31e-10 (1.02e-09)	1.22e-16 (1.67e-15)	0.531 (0.663)	0.000173 (0.000581)	0.00307 (0.00855)	1e-05 (3.91e-05)	0.308 (0.45)	0.117 (0.204)
amp 1p36 21	103 (10%)	980	8.52e-14 (8.75e-13)	3.52e-08 (2.2e-07)	9.73e-16 (1.17e-14)	0.53 (0.663)	0.052 (0.103)	0.00265 (0.00757)	1e-05 (3.91e-05)	0.437 (0.578)	1 (1.00)
amp 1q22	143 (13%)	940	0.0214 (0.0481)	0.00137 (0.00413)	3.81e-06 (2.01e-05)	0.363 (0.509)	0.171 (0.285)	0.0481 (0.0966)	3e-05 (0.000112)	0.342 (0.486)	0.107 (0.19)
amp 1q44	128 (12%)	955	2.82e-06 (1.51e-05)	4.72e-06 (2.43e-05)	5.06e-09 (3.24e-08)	0.295 (0.436)	0.123 (0.212)	0.00305 (0.00853)	1e-05 (3.91e-05)	0.415 (0.563)	0.809 (0.89)
amp 3q26 33	129 (12%)	954	3.64e-14 (3.92e-13)	8.37e-10 (5.95e-09)	8.32e-15 (9.39e-14)	0.392 (0.539)	0.186 (0.304)	0.000652 (0.00206)	1e-05 (3.91e-05)	0.34 (0.485)	0.077 (0.144)
amp 4q12	138 (13%)	945	4.93e-10 (3.61e-09)	4.41e-06 (2.29e-05)	4.38e-11 (3.58e-10)	0.167 (0.279)	0.086 (0.157)	0.0486 (0.097)	1e-05 (3.91e-05)	0.468 (0.609)	0.35 (0.496)
amp 10p15 1	88 (8%)	995	3.31e-07 (1.93e-06)	4.45e-15 (5.11e-14)	6.15e-10 (4.46e-09)	0.736 (0.835)	0.895 (0.953)	0.000808 (0.00251)	1e-05 (3.91e-05)	1 (1.00)	0.0847 (0.156)
amp 11q24 1	112 (10%)	971	1.57e-06 (8.5e-06)	0.000491 (0.00157)	5.68e-12 (4.99e-11)	0.84 (0.91)	0.13 (0.223)	0.0117 (0.028)	1e-05 (3.91e-05)	0.289 (0.431)	0.451 (0.595)
amp 14q32 33	44 (4%)	1039	0.000792 (0.00247)	8.78e-06 (3.91e-05)	7.54e-05 (0.000267)	0.212 (0.335)	0.0644 (0.124)	0.0844 (0.156)	0.00182 (0.00533)	1 (1.00)	0.254 (0.393)
del 1p36 32	314 (29%)	769	5.51e-09 (3.5e-08)	0.555 (0.685)	1.26e-14 (1.39e-13)	0.588 (0.704)	5.48e-08 (3.33e-07)	0.0215 (0.0481)	1e-05 (3.91e-05)	0.022 (0.0493)	0.736 (0.835)
del 1p36 23	344 (32%)	739	1.37e-05 (5.3e-05)	0.18 (0.295)	1.23e-10 (9.74e-10)	0.467 (0.609)	4.42e-07 (2.55e-06)	0.00254 (0.00733)	1e-05 (3.91e-05)	0.046 (0.0933)	1 (1.00)
del 1p32 3	256 (24%)	827	9.31e-14 (9.2e-13)	0.211 (0.335)	1.69e-27 (2.73e-26)	1 (1.00)	3.12e-13 (3e-12)	0.00142 (0.00425)	1e-05 (3.91e-05)	0.0379 (0.0783)	0.279 (0.42)
del 2q22 1	68 (6%)	1015	0.00412 (0.0111)	0.0169 (0.0386)	0.00558 (0.0147)	0.899 (0.955)	0.297 (0.438)	0.0771 (0.144)	0.00396 (0.0107)	0.369 (0.516)	0.105 (0.187)
del 6q26	259 (24%)	824	1.63e-11 (1.36e-10)	0.000142 (0.000486)	2.65e-09 (1.76e-08)	0.17 (0.283)	0.00225 (0.00652)	0.00312 (0.00865)	1e-05 (3.91e-05)	0.23 (0.361)	0.276 (0.418)
del 8p23 2	88 (8%)	995	0.000161 (0.000544)	6.13e-05 (0.000218)	1.07e-05 (4.16e-05)	0.822 (0.896)	0.0111 (0.027)	0.301 (0.441)	0.00012 (0.000414)	0.0141 (0.0331)	0.571 (0.693)
del 14q31 3	274 (25%)	809	0.00337 (0.00924)	0.0713 (0.135)	0.0427 (0.0874)	0.0559 (0.11)	0.323 (0.466)	0.25 (0.39)	0.0872 (0.159)	0.0921 (0.167)	0.859 (0.924)
del 16q23 1	127 (12%)	956	1.29e-09 (8.97e-09)	5.91e-05 (0.000213)	6.77e-10 (4.86e-09)	0.849 (0.916)	0.0909 (0.165)	0.0112 (0.0271)	1e-05 (3.91e-05)	0.326 (0.469)	0.811 (0.89)
del 17p13 1	114 (11%)	969	1.88e-09 (1.27e-08)	4.99e-07 (2.84e-06)	1.57e-13 (1.53e-12)	0.16 (0.27)	0.0344 (0.0727)	0.0134 (0.0315)	1e-05 (3.91e-05)	0.598 (0.711)	0.458 (0.602)
del 19q13 43	354 (33%)	729	0 (0)	4.72e-14 (5e-13)	2.06e-41 (4.18e-40)	0.293 (0.435)	1.43e-09 (9.88e-09)	4.12e-06 (2.15e-05)	1e-05 (3.91e-05)	0.176 (0.291)	0.193 (0.312)
amp 3p25 3	84 (8%)	999	0.0319 (0.068)	0.0366 (0.0764)	0.000888 (0.00273)	0.0835 (0.155)	0.687 (0.792)	0.451 (0.595)	0.00972 (0.024)	0.894 (0.953)	0.559 (0.688)
amp 4p16 3	70 (6%)	1013	0.0115 (0.0277)	0.0463 (0.0934)	0.00633 (0.0164)	0.531 (0.663)	0.02 (0.0452)	0.588 (0.704)	0.0451 (0.0917)	0.491 (0.63)	0.763 (0.851)
amp 5p15 33	76 (7%)	1007	0.000888 (0.00273)	0.0368 (0.0765)	1.23e-06 (6.72e-06)	0.47 (0.611)	0.118 (0.205)	0.865 (0.928)	2e-05 (7.52e-05)	0.273 (0.414)	1 (1.00)
amp 17p13 2	74 (7%)	1009	0.00322 (0.00891)	0.0107 (0.0261)	0.00377 (0.0103)	0.0664 (0.127)	0.576 (0.696)	0.809 (0.89)	0.0044 (0.0118)	0.52 (0.657)	0.762 (0.851)
amp 17q25 1	126 (12%)	957	9.1e-06 (3.91e-05)	1.93e-05 (7.28e-05)	0.0017 (0.00503)	0.103 (0.184)	0.912 (0.964)	0.923 (0.967)	0.0224 (0.0499)	0.716 (0.817)	0.626 (0.737)
del 4q34 3	230 (21%)	853	3.46e-05 (0.000127)	0.0122 (0.0291)	1.5e-05 (5.77e-05)	0.114 (0.201)	0.252 (0.39)	0.202 (0.324)	0.00123 (0.00374)	0.552 (0.682)	0.347 (0.492)
del 6p25 3	138 (13%)	945	1.65e-07 (9.75e-07)	0.0347 (0.0729)	0.00607 (0.0159)	0.927 (0.967)	0.51 (0.647)	0.131 (0.225)	0.0577 (0.113)	0.198 (0.32)	0.49 (0.63)
del 11p15 1	176 (16%)	907	0.0903 (0.164)	0.679 (0.785)	0.0697 (0.132)	0.0372 (0.0771)	0.0243 (0.0541)	0.305 (0.447)	0.00023 (0.000764)	0.463 (0.605)	0.528 (0.662)
del 14q24 2	290 (27%)	793	0.00176 (0.00519)	0.0667 (0.127)	0.0134 (0.0315)	0.0602 (0.117)	0.42 (0.566)	0.178 (0.293)	0.0504 (0.1)	0.162 (0.272)	0.483 (0.623)
del 15q14	212 (20%)	871	2.76e-07 (1.62e-06)	2.63e-06 (1.42e-05)	4.08e-09 (2.66e-08)	0.351 (0.497)	0.586 (0.704)	0.0318 (0.068)	1e-05 (3.91e-05)	0.603 (0.716)	0.568 (0.692)
del 16p12 2	114 (11%)	969	1.53e-10 (1.19e-09)	1.07e-07 (6.4e-07)	8.05e-11 (6.43e-10)	0.368 (0.516)	0.0611 (0.118)	0.421 (0.567)	1e-05 (3.91e-05)	0.572 (0.693)	1 (1.00)
amp 8q24 21	169 (16%)	914	0.000447 (0.00144)	7.58e-05 (0.000267)	0.000788 (0.00247)	0.865 (0.928)	0.424 (0.569)	0.212 (0.335)	0.00058 (0.00184)	0.452 (0.595)	0.204 (0.326)
amp 19p13 3	372 (34%)	711	0.0101 (0.0247)	5.05e-05 (0.000183)	2.19e-09 (1.47e-08)	0.437 (0.578)	0.763 (0.851)	0.994 (1.00)	1e-05 (3.91e-05)	0.354 (0.499)	0.52 (0.657)
amp 19p13 2	368 (34%)	715	0.000258 (0.000855)	4.93e-07 (2.82e-06)	1.98e-11 (1.64e-10)	0.173 (0.286)	0.595 (0.709)	0.301 (0.441)	1e-05 (3.91e-05)	0.497 (0.635)	0.516 (0.654)
del 1q42 11	77 (7%)	1006	0.0283 (0.0613)	0.0334 (0.0711)	0.0576 (0.113)	0.549 (0.68)	0.481 (0.623)	0.0152 (0.0349)	0.432 (0.576)	0.211 (0.335)	0.763 (0.851)
del 8q24 3	78 (7%)	1005	0.0126 (0.0301)	0.185 (0.303)	0.0248 (0.055)	0.34 (0.485)	0.0127 (0.0301)	0.868 (0.93)	0.0845 (0.156)	0.251 (0.39)	1 (1.00)
del 11p15 5	234 (22%)	849	0.673 (0.781)	0.000747 (0.00235)	0.417 (0.563)	0.0515 (0.102)	0.0146 (0.034)	0.595 (0.709)	3e-05 (0.000112)	0.798 (0.885)	1 (1.00)
del 11p11 2	159 (15%)	924	0.00283 (0.00806)	0.377 (0.523)	0.000289 (0.000952)	0.258 (0.398)	0.00293 (0.00827)	0.635 (0.747)	0.00012 (0.000414)	0.657 (0.769)	0.825 (0.897)
del 12p13 1	109 (10%)	974	0.0581 (0.113)	0.483 (0.623)	0.00631 (0.0164)	0.61 (0.721)	0.154 (0.261)	0.844 (0.912)	0.0114 (0.0275)	0.287 (0.43)	0.115 (0.203)
amp 2p24 3	72 (7%)	1011	0.0739 (0.139)	0.689 (0.793)	0.00715 (0.0182)	0.462 (0.605)	0.311 (0.451)	0.372 (0.519)	0.0675 (0.128)	0.821 (0.896)	0.758 (0.851)
del 2q37 1	121 (11%)	962	0.383 (0.53)	0.0283 (0.0613)	0.1 (0.18)	0.495 (0.635)	0.25 (0.39)	0.497 (0.635)	0.00613 (0.016)	0.393 (0.539)	1 (1.00)
del 5q34	132 (12%)	951	0.396 (0.54)	0.0929 (0.168)	0.926 (0.967)	0.158 (0.267)	0.00179 (0.00527)	0.549 (0.68)	0.00016 (0.000544)	0.697 (0.798)	1 (1.00)
amp 12p13 32	152 (14%)	931	0.833 (0.904)	0.0291 (0.0626)	0.54 (0.671)	0.287 (0.43)	0.00976 (0.024)	0.841 (0.91)	0.321 (0.464)	0.745 (0.841)	0.823 (0.896)
del 3q13 31	95 (9%)	988	0.114 (0.201)	0.742 (0.84)	0.237 (0.371)	1 (1.00)	0.0722 (0.136)	0.43 (0.574)	0.665 (0.773)	0.481 (0.623)	1 (1.00)
del 5p15 33	106 (10%)	977	0.281 (0.422)	0.647 (0.757)	1 (1.00)	0.679 (0.785)	0.000375 (0.00122)	0.278 (0.419)	0.0255 (0.0559)	0.745 (0.841)	1 (1.00)
del xq21 1	183 (17%)	900	0.49 (0.63)	0.0388 (0.0799)	0.169 (0.281)	0.681 (0.787)	0.564 (0.692)	0.0989 (0.178)	0.638 (0.749)	0.694 (0.796)	1 (1.00)
amp 11p13	59 (5%)	1024	0.707 (0.808)	0.904 (0.958)	0.79 (0.877)	0.416 (0.563)	0.432 (0.576)	0.427 (0.571)	0.114 (0.201)	0.926 (0.967)	0.31 (0.451)
amp 13q34	54 (5%)	1029	0.578 (0.697)	0.976 (1.00)	0.332 (0.476)	0.396 (0.54)	1 (1.00)	0.0801 (0.149)	0.583 (0.701)	0.778 (0.866)	1 (1.00)
del 3p21 31	108 (10%)	975	0.937 (0.973)	0.259 (0.398)	1 (1.00)	0.918 (0.967)	0.0012 (0.00366)	0.19 (0.31)	0.589 (0.704)	0.721 (0.82)	0.2 (0.322)
del 12q12	146 (13%)	937	0.8 (0.886)	0.766 (0.854)	0.929 (0.967)	0.719 (0.819)	0.29 (0.431)	0.502 (0.638)	0.00116 (0.00355)	0.201 (0.323)	0.257 (0.397)
del 12q15	141 (13%)	942	0.983 (1.00)	0.762 (0.851)	0.528 (0.662)	0.855 (0.921)	0.392 (0.539)	0.948 (0.983)	0.00702 (0.018)	0.175 (0.29)	1 (1.00)
del 18q23	151 (14%)	932	0.565 (0.692)	0.0625 (0.121)	0.661 (0.772)	0.534 (0.664)	0.297 (0.438)	0.522 (0.657)	0.264 (0.403)	0.227 (0.357)	0.262 (0.402)
del 1q44	69 (6%)	1014	0.203 (0.325)	0.207 (0.33)	0.619 (0.729)	1 (1.00)	0.309 (0.45)	0.392 (0.539)	0.928 (0.967)	0.931 (0.967)	1 (1.00)
del 3q29	107 (10%)	976	0.434 (0.577)	0.891 (0.951)	0.361 (0.507)	0.607 (0.719)	0.334 (0.478)	0.167 (0.279)	0.522 (0.657)	0.917 (0.967)	0.609 (0.721)
del xp22 2	227 (21%)	856	0.93 (0.967)	0.273 (0.414)	0.823 (0.896)	0.289 (0.431)	0.25 (0.39)	0.166 (0.279)	0.876 (0.936)	0.923 (0.967)	0.571 (0.693)

'amp_1p36.21' versus 'Time to Death'

P value = 8.52e-14 (logrank test), Q value = 8.8e-13

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 1(1P36.21) MUTATED	103	85	0.1 - 92.7 (12.5)
AMP PEAK 1(1P36.21) WILD-TYPE	976	506	0.0 - 211.2 (16.2)

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

'amp_1p36.21' versus 'YEARS_TO_BIRTH'

P value = 3.52e-08 (Wilcoxon-test), Q value = 2.2e-07

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

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 1(1P36.21) MUTATED	103	58.6 (13.0)
AMP PEAK 1(1P36.21) WILD-TYPE	979	49.9 (15.8)

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

'amp_1p36.21' versus 'TUMOR_TISSUE_SITE'

P value = 9.73e-16 (Fisher's exact test), Q value = 1.2e-14

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 1(1P36.21) MUTATED	91	12
AMP PEAK 1(1P36.21) WILD-TYPE	480	500

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

'amp_1p36.21' versus 'RADIATION_THERAPY'

P value = 0.052 (Fisher's exact test), Q value = 0.1

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

nPatients	NO	YES
ALL	258	767
AMP PEAK 1(1P36.21) MUTATED	17	83
AMP PEAK 1(1P36.21) WILD-TYPE	241	684

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

'amp_1p36.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00265 (Wilcoxon-test), Q value = 0.0076

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

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 1(1P36.21) MUTATED	66	76.7 (14.0)
AMP PEAK 1(1P36.21) WILD-TYPE	664	81.7 (14.7)

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

'amp_1p36.21' versus 'HISTOLOGICAL_TYPE'

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

Table S6. Gene #1: 'amp_1p36.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 1(1P36.21) MUTATED	9	0	0	3	1	90
AMP PEAK 1(1P36.21) WILD-TYPE	185	28	129	186	17	435

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

'amp_1q22' versus 'Time to Death'

P value = 0.0214 (logrank test), Q value = 0.048

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 2(1Q22) MUTATED	143	94	0.1 - 211.2 (14.6)
AMP PEAK 2(1Q22) WILD-TYPE	936	497	0.0 - 182.3 (16.0)

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

'amp_1q22' versus 'YEARS_TO_BIRTH'

P value = 0.00137 (Wilcoxon-test), Q value = 0.0041

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

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 2(1Q22) MUTATED	143	54.4 (15.5)
AMP PEAK 2(1Q22) WILD-TYPE	939	50.2 (15.8)

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

'amp_1q22' versus 'TUMOR_TISSUE_SITE'

P value = 3.81e-06 (Fisher's exact test), Q value = 2e-05

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 2(1Q22) MUTATED	101	42
AMP PEAK 2(1Q22) WILD-TYPE	470	470

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

'amp_1q22' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0481 (Wilcoxon-test), Q value = 0.097

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

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 2(1Q22) MUTATED	98	78.8 (14.5)
AMP PEAK 2(1Q22) WILD-TYPE	632	81.7 (14.7)

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

'amp_1q22' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S11. Gene #2: 'amp_1q22' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 2(1Q22) MUTATED	19	1	6	17	3	97
AMP PEAK 2(1Q22) WILD-TYPE	175	27	123	172	15	428

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

'amp_1q22' versus 'ETHNICITY'

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

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

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 2(1Q22) MUTATED	2	121
AMP PEAK 2(1Q22) WILD-TYPE	42	798

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

'amp_1q32.1' versus 'Time to Death'

P value = 2.28e-12 (logrank test), Q value = 2.1e-11

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 3(1Q32.1) MUTATED	202	151	0.1 - 211.2 (13.3)
AMP PEAK 3(1Q32.1) WILD-TYPE	877	440	0.0 - 182.3 (16.6)

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

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 3.54e-13 (Wilcoxon-test), Q value = 3.4e-12

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

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 3(1Q32.1) MUTATED	203	57.8 (14.0)
AMP PEAK 3(1Q32.1) WILD-TYPE	879	49.1 (15.7)

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

'amp_1q32.1' versus 'TUMOR_TISSUE_SITE'

P value = 5.39e-16 (Fisher's exact test), Q value = 6.8e-15

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 3(1Q32.1) MUTATED	158	45
AMP PEAK 3(1Q32.1) WILD-TYPE	413	467

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

'amp_1q32.1' versus 'RADIATION_THERAPY'

P value = 0.017 (Fisher's exact test), Q value = 0.039

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

nPatients	NO	YES
ALL	258	767
AMP PEAK 3(1Q32.1) MUTATED	36	159
AMP PEAK 3(1Q32.1) WILD-TYPE	222	608

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

'amp_1q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000164 (Wilcoxon-test), Q value = 0.00055

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

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 3(1Q32.1) MUTATED	138	77.2 (15.0)
AMP PEAK 3(1Q32.1) WILD-TYPE	592	82.2 (14.5)

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

'amp_1q32.1' versus 'HISTOLOGICAL_TYPE'

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

Table S18. Gene #3: 'amp_1q32.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 3(1Q32.1) MUTATED	23	7	7	15	5	146
AMP PEAK 3(1Q32.1) WILD-TYPE	171	21	122	174	13	379

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

'amp_1q32.1' versus 'ETHNICITY'

P value = 0.0146 (Fisher's exact test), Q value = 0.034

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

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 3(1Q32.1) MUTATED	2	172
AMP PEAK 3(1Q32.1) WILD-TYPE	42	747

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

'amp_1q44' versus 'Time to Death'

P value = 2.82e-06 (logrank test), Q value = 1.5e-05

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 4(1Q44) MUTATED	128	92	0.1 - 211.2 (14.3)
AMP PEAK 4(1Q44) WILD-TYPE	951	499	0.0 - 182.3 (16.1)

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

'amp_1q44' versus 'YEARS_TO_BIRTH'

P value = 4.72e-06 (Wilcoxon-test), Q value = 2.4e-05

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

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 4(1Q44) MUTATED	128	56.5 (14.5)
AMP PEAK 4(1Q44) WILD-TYPE	954	50.0 (15.8)

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

'amp_1q44' versus 'TUMOR_TISSUE_SITE'

P value = 5.06e-09 (Fisher's exact test), Q value = 3.2e-08

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 4(1Q44) MUTATED	98	30
AMP PEAK 4(1Q44) WILD-TYPE	473	482

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

'amp_1q44' versus 'RADIATION_THERAPY'

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

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

nPatients	NO	YES
ALL	258	767
AMP PEAK 4(1Q44) MUTATED	24	100
AMP PEAK 4(1Q44) WILD-TYPE	234	667

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

'amp_1q44' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00305 (Wilcoxon-test), Q value = 0.0085

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

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 4(1Q44) MUTATED	84	77.4 (14.2)
AMP PEAK 4(1Q44) WILD-TYPE	646	81.8 (14.7)

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

'amp_1q44' versus 'HISTOLOGICAL_TYPE'

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

Table S25. Gene #4: 'amp_1q44' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 4(1Q44) MUTATED	15	1	5	10	3	94
AMP PEAK 4(1Q44) WILD-TYPE	179	27	124	179	15	431

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

'amp_2p24.3' versus 'Time to Death'

P value = 0.0739 (logrank test), Q value = 0.14

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 5(2P24.3) MUTATED	72	49	0.1 - 94.5 (16.0)
AMP PEAK 5(2P24.3) WILD-TYPE	1007	542	0.0 - 211.2 (15.7)

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

'amp_2p24.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00715 (Fisher's exact test), Q value = 0.018

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

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 5(2P24.3) MUTATED	49	23
AMP PEAK 5(2P24.3) WILD-TYPE	522	489

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

'amp_2p24.3' versus 'HISTOLOGICAL_TYPE'

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

Table S28. Gene #5: 'amp_2p24.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 5(2P24.3) MUTATED	12	2	3	8	1	46
AMP PEAK 5(2P24.3) WILD-TYPE	182	26	126	181	17	479

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

'amp_3p25.3' versus 'Time to Death'

P value = 0.0319 (logrank test), Q value = 0.068

Table S29. Gene #6: 'amp_3p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 6(3P25.3) MUTATED	84	56	0.2 - 127.6 (12.7)
AMP PEAK 6(3P25.3) WILD-TYPE	995	535	0.0 - 211.2 (15.8)

Figure S29. Get High-res Image Gene #6: 'amp_3p25.3' versus Clinical Feature #1: 'Time to Death'

'amp_3p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0366 (Wilcoxon-test), Q value = 0.076

Table S30. Gene #6: 'amp_3p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 6(3P25.3) MUTATED	84	54.2 (15.8)
AMP PEAK 6(3P25.3) WILD-TYPE	998	50.5 (15.8)

Figure S30. Get High-res Image Gene #6: 'amp_3p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p25.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.000888 (Fisher's exact test), Q value = 0.0027

Table S31. Gene #6: 'amp_3p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 6(3P25.3) MUTATED	59	25
AMP PEAK 6(3P25.3) WILD-TYPE	512	487

Figure S31. Get High-res Image Gene #6: 'amp_3p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_3p25.3' versus 'GENDER'

P value = 0.0835 (Fisher's exact test), Q value = 0.15

Table S32. Gene #6: 'amp_3p25.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
AMP PEAK 6(3P25.3) MUTATED	43	41
AMP PEAK 6(3P25.3) WILD-TYPE	409	590

Figure S32. Get High-res Image Gene #6: 'amp_3p25.3' versus Clinical Feature #4: 'GENDER'

'amp_3p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00972 (Fisher's exact test), Q value = 0.024

Table S33. Gene #6: 'amp_3p25.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 6(3P25.3) MUTATED	13	1	5	7	1	57
AMP PEAK 6(3P25.3) WILD-TYPE	181	27	124	182	17	468

Figure S33. Get High-res Image Gene #6: 'amp_3p25.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_3q26.33' versus 'Time to Death'

P value = 3.64e-14 (logrank test), Q value = 3.9e-13

Table S34. Gene #7: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 7(3Q26.33) MUTATED	128	98	0.1 - 127.6 (10.5)
AMP PEAK 7(3Q26.33) WILD-TYPE	951	493	0.0 - 211.2 (16.5)

Figure S34. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

'amp_3q26.33' versus 'YEARS_TO_BIRTH'

P value = 8.37e-10 (Wilcoxon-test), Q value = 5.9e-09

Table S35. Gene #7: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 7(3Q26.33) MUTATED	129	58.6 (12.9)
AMP PEAK 7(3Q26.33) WILD-TYPE	953	49.7 (15.8)

Figure S35. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.33' versus 'TUMOR_TISSUE_SITE'

P value = 8.32e-15 (Fisher's exact test), Q value = 9.4e-14

Table S36. Gene #7: 'amp_3q26.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 7(3Q26.33) MUTATED	108	21
AMP PEAK 7(3Q26.33) WILD-TYPE	463	491

Figure S36. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_3q26.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000652 (Wilcoxon-test), Q value = 0.0021

Table S37. Gene #7: 'amp_3q26.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 7(3Q26.33) MUTATED	95	77.4 (13.1)
AMP PEAK 7(3Q26.33) WILD-TYPE	635	81.9 (14.8)

Figure S37. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

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

Table S38. Gene #7: 'amp_3q26.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 7(3Q26.33) MUTATED	15	0	1	5	0	108
AMP PEAK 7(3Q26.33) WILD-TYPE	179	28	128	184	18	417

Figure S38. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_3q26.33' versus 'ETHNICITY'

P value = 0.077 (Fisher's exact test), Q value = 0.14

Table S39. Gene #7: 'amp_3q26.33' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 7(3Q26.33) MUTATED	1	102
AMP PEAK 7(3Q26.33) WILD-TYPE	43	817

Figure S39. Get High-res Image Gene #7: 'amp_3q26.33' versus Clinical Feature #9: 'ETHNICITY'

'amp_4p16.3' versus 'Time to Death'

P value = 0.0115 (logrank test), Q value = 0.028

Table S40. Gene #8: 'amp_4p16.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 8(4P16.3) MUTATED	70	48	0.2 - 94.5 (13.9)
AMP PEAK 8(4P16.3) WILD-TYPE	1009	543	0.0 - 211.2 (15.8)

Figure S40. Get High-res Image Gene #8: 'amp_4p16.3' versus Clinical Feature #1: 'Time to Death'

'amp_4p16.3' versus 'YEARS_TO_BIRTH'

P value = 0.0463 (Wilcoxon-test), Q value = 0.093

Table S41. Gene #8: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 8(4P16.3) MUTATED	70	54.2 (14.6)
AMP PEAK 8(4P16.3) WILD-TYPE	1012	50.5 (15.8)

Figure S41. Get High-res Image Gene #8: 'amp_4p16.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4p16.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00633 (Fisher's exact test), Q value = 0.016

Table S42. Gene #8: 'amp_4p16.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 8(4P16.3) MUTATED	48	22
AMP PEAK 8(4P16.3) WILD-TYPE	523	490

Figure S42. Get High-res Image Gene #8: 'amp_4p16.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_4p16.3' versus 'RADIATION_THERAPY'

P value = 0.02 (Fisher's exact test), Q value = 0.045

Table S43. Gene #8: 'amp_4p16.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 8(4P16.3) MUTATED	9	58
AMP PEAK 8(4P16.3) WILD-TYPE	249	709

Figure S43. Get High-res Image Gene #8: 'amp_4p16.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_4p16.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0451 (Fisher's exact test), Q value = 0.092

Table S44. Gene #8: 'amp_4p16.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 8(4P16.3) MUTATED	12	1	3	7	1	46
AMP PEAK 8(4P16.3) WILD-TYPE	182	27	126	182	17	479

Figure S44. Get High-res Image Gene #8: 'amp_4p16.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_4q12' versus 'Time to Death'

P value = 4.93e-10 (logrank test), Q value = 3.6e-09

Table S45. Gene #9: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 9(4Q12) MUTATED	138	101	0.1 - 92.7 (11.9)
AMP PEAK 9(4Q12) WILD-TYPE	941	490	0.0 - 211.2 (16.2)

Figure S45. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #1: 'Time to Death'

'amp_4q12' versus 'YEARS_TO_BIRTH'

P value = 4.41e-06 (Wilcoxon-test), Q value = 2.3e-05

Table S46. Gene #9: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 9(4Q12) MUTATED	138	56.2 (15.1)
AMP PEAK 9(4Q12) WILD-TYPE	944	50.0 (15.7)

Figure S46. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4q12' versus 'TUMOR_TISSUE_SITE'

P value = 4.38e-11 (Fisher's exact test), Q value = 3.6e-10

Table S47. Gene #9: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 9(4Q12) MUTATED	108	30
AMP PEAK 9(4Q12) WILD-TYPE	463	482

Figure S47. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_4q12' versus 'RADIATION_THERAPY'

P value = 0.086 (Fisher's exact test), Q value = 0.16

Table S48. Gene #9: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 9(4Q12) MUTATED	25	108
AMP PEAK 9(4Q12) WILD-TYPE	233	659

Figure S48. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_4q12' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0486 (Wilcoxon-test), Q value = 0.097

Table S49. Gene #9: 'amp_4q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 9(4Q12) MUTATED	100	78.7 (15.4)
AMP PEAK 9(4Q12) WILD-TYPE	630	81.7 (14.5)

Figure S49. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

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

Table S50. Gene #9: 'amp_4q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 9(4Q12) MUTATED	21	4	2	7	2	102
AMP PEAK 9(4Q12) WILD-TYPE	173	24	127	182	16	423

Figure S50. Get High-res Image Gene #9: 'amp_4q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'Time to Death'

P value = 0.000888 (logrank test), Q value = 0.0027

Table S51. Gene #10: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 10(5P15.33) MUTATED	76	57	0.2 - 92.7 (12.9)
AMP PEAK 10(5P15.33) WILD-TYPE	1003	534	0.0 - 211.2 (15.9)

Figure S51. Get High-res Image Gene #10: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.0368 (Wilcoxon-test), Q value = 0.076

Table S52. Gene #10: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 10(5P15.33) MUTATED	76	54.2 (16.4)
AMP PEAK 10(5P15.33) WILD-TYPE	1006	50.5 (15.7)

Figure S52. Get High-res Image Gene #10: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p15.33' versus 'TUMOR_TISSUE_SITE'

P value = 1.23e-06 (Fisher's exact test), Q value = 6.7e-06

Table S53. Gene #10: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 10(5P15.33) MUTATED	60	16
AMP PEAK 10(5P15.33) WILD-TYPE	511	496

Figure S53. Get High-res Image Gene #10: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_5p15.33' versus 'RADIATION_THERAPY'

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

Table S54. Gene #10: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 10(5P15.33) MUTATED	12	59
AMP PEAK 10(5P15.33) WILD-TYPE	246	708

Figure S54. Get High-res Image Gene #10: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 7.5e-05

Table S55. Gene #10: 'amp_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 10(5P15.33) MUTATED	10	3	4	2	4	53
AMP PEAK 10(5P15.33) WILD-TYPE	184	25	125	187	14	472

Figure S55. Get High-res Image Gene #10: 'amp_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

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

Table S56. Gene #11: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 11(7P11.2) MUTATED	628	476	0.1 - 211.2 (12.6)
AMP PEAK 11(7P11.2) WILD-TYPE	451	115	0.0 - 182.3 (22.1)

Figure S56. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'YEARS_TO_BIRTH'

P value = 1.71e-68 (Wilcoxon-test), Q value = 4.3e-67

Table S57. Gene #11: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 11(7P11.2) MUTATED	629	57.8 (13.2)
AMP PEAK 11(7P11.2) WILD-TYPE	453	41.0 (13.7)

Figure S57. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7p11.2' versus 'TUMOR_TISSUE_SITE'

P value = 3.58e-104 (Fisher's exact test), Q value = 1.2e-102

Table S58. Gene #11: 'amp_7p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 11(7P11.2) MUTATED	501	128
AMP PEAK 11(7P11.2) WILD-TYPE	70	384

Figure S58. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7p11.2' versus 'RADIATION_THERAPY'

P value = 8.74e-14 (Fisher's exact test), Q value = 8.8e-13

Table S59. Gene #11: 'amp_7p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 11(7P11.2) MUTATED	99	500
AMP PEAK 11(7P11.2) WILD-TYPE	159	267

Figure S59. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7p11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.26e-19 (Wilcoxon-test), Q value = 3.6e-18

Table S60. Gene #11: 'amp_7p11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 11(7P11.2) MUTATED	449	77.7 (15.3)
AMP PEAK 11(7P11.2) WILD-TYPE	281	87.1 (11.5)

Figure S60. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7p11.2' versus 'HISTOLOGICAL_TYPE'

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

Table S61. Gene #11: 'amp_7p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 11(7P11.2) MUTATED	58	23	33	37	13	465
AMP PEAK 11(7P11.2) WILD-TYPE	136	5	96	152	5	60

Figure S61. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'RACE'

P value = 0.00508 (Fisher's exact test), Q value = 0.013

Table S62. Gene #11: 'amp_7p11.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 11(7P11.2) MUTATED	1	12	54	540
AMP PEAK 11(7P11.2) WILD-TYPE	0	9	17	417

Figure S62. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #8: 'RACE'

'amp_7p11.2' versus 'ETHNICITY'

P value = 0.0077 (Fisher's exact test), Q value = 0.019

Table S63. Gene #11: 'amp_7p11.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 11(7P11.2) MUTATED	16	527
AMP PEAK 11(7P11.2) WILD-TYPE	28	392

Figure S63. Get High-res Image Gene #11: 'amp_7p11.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q11.21' versus 'Time to Death'

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

Table S64. Gene #12: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 12(7Q11.21) MUTATED	575	432	0.1 - 211.2 (12.6)
AMP PEAK 12(7Q11.21) WILD-TYPE	504	159	0.0 - 182.3 (20.9)

Figure S64. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

'amp_7q11.21' versus 'YEARS_TO_BIRTH'

P value = 4.47e-55 (Wilcoxon-test), Q value = 9.9e-54

Table S65. Gene #12: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 12(7Q11.21) MUTATED	576	57.8 (13.2)
AMP PEAK 12(7Q11.21) WILD-TYPE	506	42.8 (14.6)

Figure S65. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q11.21' versus 'TUMOR_TISSUE_SITE'

P value = 1.36e-84 (Fisher's exact test), Q value = 4.2e-83

Table S66. Gene #12: 'amp_7q11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 12(7Q11.21) MUTATED	459	117
AMP PEAK 12(7Q11.21) WILD-TYPE	112	395

Figure S66. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q11.21' versus 'RADIATION_THERAPY'

P value = 5.95e-11 (Fisher's exact test), Q value = 4.8e-10

Table S67. Gene #12: 'amp_7q11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 12(7Q11.21) MUTATED	92	455
AMP PEAK 12(7Q11.21) WILD-TYPE	166	312

Figure S67. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q11.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 8.71e-14 (Wilcoxon-test), Q value = 8.8e-13

Table S68. Gene #12: 'amp_7q11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 12(7Q11.21) MUTATED	407	77.9 (15.3)
AMP PEAK 12(7Q11.21) WILD-TYPE	323	85.5 (12.7)

Figure S68. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q11.21' versus 'HISTOLOGICAL_TYPE'

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

Table S69. Gene #12: 'amp_7q11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 12(7Q11.21) MUTATED	51	20	31	35	10	429
AMP PEAK 12(7Q11.21) WILD-TYPE	143	8	98	154	8	96

Figure S69. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q11.21' versus 'RACE'

P value = 0.00298 (Fisher's exact test), Q value = 0.0084

Table S70. Gene #12: 'amp_7q11.21' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 12(7Q11.21) MUTATED	1	10	51	492
AMP PEAK 12(7Q11.21) WILD-TYPE	0	11	20	465

Figure S70. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #8: 'RACE'

'amp_7q11.21' versus 'ETHNICITY'

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

Table S71. Gene #12: 'amp_7q11.21' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 12(7Q11.21) MUTATED	14	483
AMP PEAK 12(7Q11.21) WILD-TYPE	30	436

Figure S71. Get High-res Image Gene #12: 'amp_7q11.21' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q21.2' versus 'Time to Death'

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

Table S72. Gene #13: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 13(7Q21.2) MUTATED	629	455	0.1 - 211.2 (13.1)
AMP PEAK 13(7Q21.2) WILD-TYPE	450	136	0.0 - 182.3 (21.1)

Figure S72. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.2' versus 'YEARS_TO_BIRTH'

P value = 4.83e-50 (Wilcoxon-test), Q value = 1e-48

Table S73. Gene #13: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 13(7Q21.2) MUTATED	630	56.8 (13.5)
AMP PEAK 13(7Q21.2) WILD-TYPE	452	42.4 (14.9)

Figure S73. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q21.2' versus 'TUMOR_TISSUE_SITE'

P value = 9.69e-72 (Fisher's exact test), Q value = 2.8e-70

Table S74. Gene #13: 'amp_7q21.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 13(7Q21.2) MUTATED	474	156
AMP PEAK 13(7Q21.2) WILD-TYPE	97	356

Figure S74. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q21.2' versus 'RADIATION_THERAPY'

P value = 1.19e-11 (Fisher's exact test), Q value = 1e-10

Table S75. Gene #13: 'amp_7q21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 13(7Q21.2) MUTATED	104	496
AMP PEAK 13(7Q21.2) WILD-TYPE	154	271

Figure S75. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q21.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.39e-12 (Wilcoxon-test), Q value = 3e-11

Table S76. Gene #13: 'amp_7q21.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 13(7Q21.2) MUTATED	441	78.4 (15.5)
AMP PEAK 13(7Q21.2) WILD-TYPE	289	85.7 (12.1)

Figure S76. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q21.2' versus 'HISTOLOGICAL_TYPE'

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

Table S77. Gene #13: 'amp_7q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 13(7Q21.2) MUTATED	68	22	40	48	12	440
AMP PEAK 13(7Q21.2) WILD-TYPE	126	6	89	141	6	85

Figure S77. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q21.2' versus 'RACE'

P value = 0.00132 (Fisher's exact test), Q value = 0.004

Table S78. Gene #13: 'amp_7q21.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 13(7Q21.2) MUTATED	1	10	55	542
AMP PEAK 13(7Q21.2) WILD-TYPE	0	11	16	415

Figure S78. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #8: 'RACE'

'amp_7q21.2' versus 'ETHNICITY'

P value = 0.00264 (Fisher's exact test), Q value = 0.0076

Table S79. Gene #13: 'amp_7q21.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 13(7Q21.2) MUTATED	15	535
AMP PEAK 13(7Q21.2) WILD-TYPE	29	384

Figure S79. Get High-res Image Gene #13: 'amp_7q21.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q31.2' versus 'Time to Death'

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

Table S80. Gene #14: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 14(7Q31.2) MUTATED	639	450	0.1 - 211.2 (13.6)
AMP PEAK 14(7Q31.2) WILD-TYPE	440	141	0.0 - 182.3 (20.7)

Figure S80. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 5.49e-40 (Wilcoxon-test), Q value = 1.1e-38

Table S81. Gene #14: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 14(7Q31.2) MUTATED	640	56.1 (13.8)
AMP PEAK 14(7Q31.2) WILD-TYPE	442	43.1 (15.4)

Figure S81. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'TUMOR_TISSUE_SITE'

P value = 3.92e-59 (Fisher's exact test), Q value = 9.3e-58

Table S82. Gene #14: 'amp_7q31.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 14(7Q31.2) MUTATED	466	174
AMP PEAK 14(7Q31.2) WILD-TYPE	105	338

Figure S82. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 1.49e-09 (Fisher's exact test), Q value = 1e-08

Table S83. Gene #14: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 14(7Q31.2) MUTATED	111	496
AMP PEAK 14(7Q31.2) WILD-TYPE	147	271

Figure S83. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.97e-09 (Wilcoxon-test), Q value = 2e-08

Table S84. Gene #14: 'amp_7q31.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 14(7Q31.2) MUTATED	444	78.9 (15.2)
AMP PEAK 14(7Q31.2) WILD-TYPE	286	85.0 (13.1)

Figure S84. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

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

Table S85. Gene #14: 'amp_7q31.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 14(7Q31.2) MUTATED	75	21	47	52	13	432
AMP PEAK 14(7Q31.2) WILD-TYPE	119	7	82	137	5	93

Figure S85. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'RACE'

P value = 0.00839 (Fisher's exact test), Q value = 0.021

Table S86. Gene #14: 'amp_7q31.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 14(7Q31.2) MUTATED	1	11	54	553
AMP PEAK 14(7Q31.2) WILD-TYPE	0	10	17	404

Figure S86. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #8: 'RACE'

'amp_7q31.2' versus 'ETHNICITY'

P value = 0.00285 (Fisher's exact test), Q value = 0.0081

Table S87. Gene #14: 'amp_7q31.2' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 14(7Q31.2) MUTATED	16	546
AMP PEAK 14(7Q31.2) WILD-TYPE	28	373

Figure S87. Get High-res Image Gene #14: 'amp_7q31.2' versus Clinical Feature #9: 'ETHNICITY'

'amp_7q32.3' versus 'Time to Death'

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

Table S88. Gene #15: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 15(7Q32.3) MUTATED	652	456	0.1 - 211.2 (13.7)
AMP PEAK 15(7Q32.3) WILD-TYPE	427	135	0.0 - 182.3 (20.7)

Figure S88. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #1: 'Time to Death'

'amp_7q32.3' versus 'YEARS_TO_BIRTH'

P value = 1.31e-40 (Wilcoxon-test), Q value = 2.6e-39

Table S89. Gene #15: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 15(7Q32.3) MUTATED	653	56.0 (13.8)
AMP PEAK 15(7Q32.3) WILD-TYPE	429	42.9 (15.4)

Figure S89. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q32.3' versus 'TUMOR_TISSUE_SITE'

P value = 5.3e-58 (Fisher's exact test), Q value = 1.2e-56

Table S90. Gene #15: 'amp_7q32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 15(7Q32.3) MUTATED	471	182
AMP PEAK 15(7Q32.3) WILD-TYPE	100	330

Figure S90. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_7q32.3' versus 'RADIATION_THERAPY'

P value = 1.74e-10 (Fisher's exact test), Q value = 1.3e-09

Table S91. Gene #15: 'amp_7q32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 15(7Q32.3) MUTATED	112	508
AMP PEAK 15(7Q32.3) WILD-TYPE	146	259

Figure S91. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q32.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 4.21e-09 (Wilcoxon-test), Q value = 2.7e-08

Table S92. Gene #15: 'amp_7q32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 15(7Q32.3) MUTATED	454	78.9 (15.3)
AMP PEAK 15(7Q32.3) WILD-TYPE	276	85.1 (12.7)

Figure S92. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q32.3' versus 'HISTOLOGICAL_TYPE'

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

Table S93. Gene #15: 'amp_7q32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 15(7Q32.3) MUTATED	78	21	49	55	12	438
AMP PEAK 15(7Q32.3) WILD-TYPE	116	7	80	134	6	87

Figure S93. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_7q32.3' versus 'RACE'

P value = 0.00604 (Fisher's exact test), Q value = 0.016

Table S94. Gene #15: 'amp_7q32.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 15(7Q32.3) MUTATED	1	11	55	565
AMP PEAK 15(7Q32.3) WILD-TYPE	0	10	16	392

Figure S94. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #8: 'RACE'

'amp_7q32.3' versus 'ETHNICITY'

P value = 0.00153 (Fisher's exact test), Q value = 0.0046

Table S95. Gene #15: 'amp_7q32.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 15(7Q32.3) MUTATED	16	559
AMP PEAK 15(7Q32.3) WILD-TYPE	28	360

Figure S95. Get High-res Image Gene #15: 'amp_7q32.3' versus Clinical Feature #9: 'ETHNICITY'

'amp_8q24.21' versus 'Time to Death'

P value = 0.000447 (logrank test), Q value = 0.0014

Table S96. Gene #16: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 16(8Q24.21) MUTATED	169	79	0.1 - 146.1 (18.9)
AMP PEAK 16(8Q24.21) WILD-TYPE	910	512	0.0 - 211.2 (15.0)

Figure S96. Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 7.58e-05 (Wilcoxon-test), Q value = 0.00027

Table S97. Gene #16: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 16(8Q24.21) MUTATED	169	46.2 (16.2)
AMP PEAK 16(8Q24.21) WILD-TYPE	913	51.6 (15.6)

Figure S97. Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'TUMOR_TISSUE_SITE'

P value = 0.000788 (Fisher's exact test), Q value = 0.0025

Table S98. Gene #16: 'amp_8q24.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 16(8Q24.21) MUTATED	69	100
AMP PEAK 16(8Q24.21) WILD-TYPE	502	412

Figure S98. Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_8q24.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00058 (Fisher's exact test), Q value = 0.0018

Table S99. Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 16(8Q24.21) MUTATED	47	2	29	24	2	65
AMP PEAK 16(8Q24.21) WILD-TYPE	147	26	100	165	16	460

Figure S99. Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_9q34.3' versus 'Time to Death'

P value = 0.0254 (logrank test), Q value = 0.056

Table S100. Gene #17: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 17(9Q34.3) MUTATED	139	88	0.1 - 172.8 (14.2)
AMP PEAK 17(9Q34.3) WILD-TYPE	940	503	0.0 - 211.2 (15.9)

Figure S100. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #1: 'Time to Death'

'amp_9q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0443 (Wilcoxon-test), Q value = 0.09

Table S101. Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 17(9Q34.3) MUTATED	139	52.9 (16.6)
AMP PEAK 17(9Q34.3) WILD-TYPE	943	50.5 (15.6)

Figure S101. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_9q34.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.000364 (Fisher's exact test), Q value = 0.0012

Table S102. Gene #17: 'amp_9q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 17(9Q34.3) MUTATED	93	46
AMP PEAK 17(9Q34.3) WILD-TYPE	478	466

Figure S102. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_9q34.3' versus 'GENDER'

P value = 0.0798 (Fisher's exact test), Q value = 0.15

Table S103. Gene #17: 'amp_9q34.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
AMP PEAK 17(9Q34.3) MUTATED	68	71
AMP PEAK 17(9Q34.3) WILD-TYPE	384	560

Figure S103. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #4: 'GENDER'

'amp_9q34.3' versus 'RADIATION_THERAPY'

P value = 0.0856 (Fisher's exact test), Q value = 0.16

Table S104. Gene #17: 'amp_9q34.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 17(9Q34.3) MUTATED	25	107
AMP PEAK 17(9Q34.3) WILD-TYPE	233	660

Figure S104. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_9q34.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.124 (Wilcoxon-test), Q value = 0.21

Table S105. Gene #17: 'amp_9q34.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 17(9Q34.3) MUTATED	102	79.1 (15.2)
AMP PEAK 17(9Q34.3) WILD-TYPE	628	81.6 (14.6)

Figure S105. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00056 (Fisher's exact test), Q value = 0.0018

Table S106. Gene #17: 'amp_9q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 17(9Q34.3) MUTATED	24	3	13	9	2	88
AMP PEAK 17(9Q34.3) WILD-TYPE	170	25	116	180	16	437

Figure S106. Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'Time to Death'

P value = 3.31e-07 (logrank test), Q value = 1.9e-06

Table S107. Gene #18: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 18(10P15.1) MUTATED	88	29	0.1 - 172.8 (24.0)
AMP PEAK 18(10P15.1) WILD-TYPE	991	562	0.0 - 211.2 (15.1)

Figure S107. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

'amp_10p15.1' versus 'YEARS_TO_BIRTH'

P value = 4.45e-15 (Wilcoxon-test), Q value = 5.1e-14

Table S108. Gene #18: 'amp_10p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 18(10P15.1) MUTATED	88	38.2 (12.4)
AMP PEAK 18(10P15.1) WILD-TYPE	994	51.9 (15.6)

Figure S108. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p15.1' versus 'TUMOR_TISSUE_SITE'

P value = 6.15e-10 (Fisher's exact test), Q value = 4.5e-09

Table S109. Gene #18: 'amp_10p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 18(10P15.1) MUTATED	19	69
AMP PEAK 18(10P15.1) WILD-TYPE	552	443

Figure S109. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_10p15.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000808 (Wilcoxon-test), Q value = 0.0025

Table S110. Gene #18: 'amp_10p15.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 18(10P15.1) MUTATED	58	86.9 (11.9)
AMP PEAK 18(10P15.1) WILD-TYPE	672	80.8 (14.8)

Figure S110. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_10p15.1' versus 'HISTOLOGICAL_TYPE'

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

Table S111. Gene #18: 'amp_10p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 18(10P15.1) MUTATED	37	1	23	9	1	17
AMP PEAK 18(10P15.1) WILD-TYPE	157	27	106	180	17	508

Figure S111. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_10p15.1' versus 'ETHNICITY'

P value = 0.0847 (Fisher's exact test), Q value = 0.16

Table S112. Gene #18: 'amp_10p15.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 18(10P15.1) MUTATED	7	73
AMP PEAK 18(10P15.1) WILD-TYPE	37	846

Figure S112. Get High-res Image Gene #18: 'amp_10p15.1' versus Clinical Feature #9: 'ETHNICITY'

'amp_11p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.114 (Fisher's exact test), Q value = 0.2

Table S113. Gene #19: 'amp_11p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 19(11P13) MUTATED	5	2	7	17	1	27
AMP PEAK 19(11P13) WILD-TYPE	189	26	122	172	17	498

Figure S113. Get High-res Image Gene #19: 'amp_11p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_11q24.1' versus 'Time to Death'

P value = 1.57e-06 (logrank test), Q value = 8.5e-06

Table S114. Gene #20: 'amp_11q24.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 20(11Q24.1) MUTATED	112	39	0.2 - 211.2 (23.0)
AMP PEAK 20(11Q24.1) WILD-TYPE	967	552	0.0 - 172.8 (15.1)

Figure S114. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #1: 'Time to Death'

'amp_11q24.1' versus 'YEARS_TO_BIRTH'

P value = 0.000491 (Wilcoxon-test), Q value = 0.0016

Table S115. Gene #20: 'amp_11q24.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 20(11Q24.1) MUTATED	112	46.0 (14.0)
AMP PEAK 20(11Q24.1) WILD-TYPE	970	51.3 (15.9)

Figure S115. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11q24.1' versus 'TUMOR_TISSUE_SITE'

P value = 5.68e-12 (Fisher's exact test), Q value = 5e-11

Table S116. Gene #20: 'amp_11q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 20(11Q24.1) MUTATED	25	87
AMP PEAK 20(11Q24.1) WILD-TYPE	546	425

Figure S116. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_11q24.1' versus 'RADIATION_THERAPY'

P value = 0.13 (Fisher's exact test), Q value = 0.22

Table S117. Gene #20: 'amp_11q24.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 20(11Q24.1) MUTATED	34	75
AMP PEAK 20(11Q24.1) WILD-TYPE	224	692

Figure S117. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_11q24.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0117 (Wilcoxon-test), Q value = 0.028

Table S118. Gene #20: 'amp_11q24.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 20(11Q24.1) MUTATED	74	85.0 (13.3)
AMP PEAK 20(11Q24.1) WILD-TYPE	656	80.9 (14.8)

Figure S118. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_11q24.1' versus 'HISTOLOGICAL_TYPE'

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

Table S119. Gene #20: 'amp_11q24.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 20(11Q24.1) MUTATED	33	0	18	36	1	24
AMP PEAK 20(11Q24.1) WILD-TYPE	161	28	111	153	17	501

Figure S119. Get High-res Image Gene #20: 'amp_11q24.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12p13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0291 (Wilcoxon-test), Q value = 0.063

Table S120. Gene #21: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 21(12P13.32) MUTATED	152	48.1 (16.5)
AMP PEAK 21(12P13.32) WILD-TYPE	930	51.2 (15.6)

Figure S120. Get High-res Image Gene #21: 'amp_12p13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p13.32' versus 'RADIATION_THERAPY'

P value = 0.00976 (Fisher's exact test), Q value = 0.024

Table S121. Gene #21: 'amp_12p13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 21(12P13.32) MUTATED	24	122
AMP PEAK 21(12P13.32) WILD-TYPE	234	645

Figure S121. Get High-res Image Gene #21: 'amp_12p13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'Time to Death'

P value = 6.66e-16 (logrank test), Q value = 8.2e-15

Table S122. Gene #22: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 22(12Q14.1) MUTATED	170	134	0.1 - 84.3 (13.9)
AMP PEAK 22(12Q14.1) WILD-TYPE	909	457	0.0 - 211.2 (16.2)

Figure S122. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_12q14.1' versus 'YEARS_TO_BIRTH'

P value = 7.97e-06 (Wilcoxon-test), Q value = 3.9e-05

Table S123. Gene #22: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 22(12Q14.1) MUTATED	171	55.7 (15.3)
AMP PEAK 22(12Q14.1) WILD-TYPE	911	49.9 (15.7)

Figure S123. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q14.1' versus 'TUMOR_TISSUE_SITE'

P value = 7.18e-14 (Fisher's exact test), Q value = 7.5e-13

Table S124. Gene #22: 'amp_12q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 22(12Q14.1) MUTATED	134	37
AMP PEAK 22(12Q14.1) WILD-TYPE	437	475

Figure S124. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q14.1' versus 'RADIATION_THERAPY'

P value = 0.00811 (Fisher's exact test), Q value = 0.02

Table S125. Gene #22: 'amp_12q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 22(12Q14.1) MUTATED	28	136
AMP PEAK 22(12Q14.1) WILD-TYPE	230	631

Figure S125. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q14.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.117 (Wilcoxon-test), Q value = 0.2

Table S126. Gene #22: 'amp_12q14.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 22(12Q14.1) MUTATED	119	79.2 (15.5)
AMP PEAK 22(12Q14.1) WILD-TYPE	611	81.7 (14.5)

Figure S126. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_12q14.1' versus 'HISTOLOGICAL_TYPE'

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

Table S127. Gene #22: 'amp_12q14.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 22(12Q14.1) MUTATED	22	5	5	10	3	126
AMP PEAK 22(12Q14.1) WILD-TYPE	172	23	124	179	15	399

Figure S127. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12q14.1' versus 'ETHNICITY'

P value = 0.0336 (Fisher's exact test), Q value = 0.071

Table S128. Gene #22: 'amp_12q14.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 22(12Q14.1) MUTATED	2	150
AMP PEAK 22(12Q14.1) WILD-TYPE	42	769

Figure S128. Get High-res Image Gene #22: 'amp_12q14.1' versus Clinical Feature #9: 'ETHNICITY'

'amp_12q15' versus 'Time to Death'

P value = 2.55e-10 (logrank test), Q value = 1.9e-09

Table S129. Gene #23: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 23(12Q15) MUTATED	110	89	0.2 - 84.3 (14.0)
AMP PEAK 23(12Q15) WILD-TYPE	969	502	0.0 - 211.2 (16.0)

Figure S129. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 4.78e-05 (Wilcoxon-test), Q value = 0.00017

Table S130. Gene #23: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 23(12Q15) MUTATED	110	56.6 (14.3)
AMP PEAK 23(12Q15) WILD-TYPE	972	50.1 (15.8)

Figure S130. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'TUMOR_TISSUE_SITE'

P value = 1.49e-12 (Fisher's exact test), Q value = 1.4e-11

Table S131. Gene #23: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 23(12Q15) MUTATED	92	18
AMP PEAK 23(12Q15) WILD-TYPE	479	494

Figure S131. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q15' versus 'RADIATION_THERAPY'

P value = 0.0442 (Fisher's exact test), Q value = 0.09

Table S132. Gene #23: 'amp_12q15' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 23(12Q15) MUTATED	18	88
AMP PEAK 23(12Q15) WILD-TYPE	240	679

Figure S132. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_12q15' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0364 (Wilcoxon-test), Q value = 0.076

Table S133. Gene #23: 'amp_12q15' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 23(12Q15) MUTATED	86	78.5 (14.5)
AMP PEAK 23(12Q15) WILD-TYPE	644	81.7 (14.7)

Figure S133. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

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

Table S134. Gene #23: 'amp_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 23(12Q15) MUTATED	8	3	2	8	2	87
AMP PEAK 23(12Q15) WILD-TYPE	186	25	127	181	16	438

Figure S134. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'ETHNICITY'

P value = 0.0172 (Fisher's exact test), Q value = 0.039

Table S135. Gene #23: 'amp_12q15' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 23(12Q15) MUTATED	0	96
AMP PEAK 23(12Q15) WILD-TYPE	44	823

Figure S135. Get High-res Image Gene #23: 'amp_12q15' versus Clinical Feature #9: 'ETHNICITY'

'amp_13q34' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0801 (Wilcoxon-test), Q value = 0.15

Table S136. Gene #24: 'amp_13q34' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 24(13Q34) MUTATED	36	76.9 (15.8)
AMP PEAK 24(13Q34) WILD-TYPE	694	81.5 (14.6)

Figure S136. Get High-res Image Gene #24: 'amp_13q34' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_14q32.33' versus 'Time to Death'

P value = 0.000792 (logrank test), Q value = 0.0025

Table S137. Gene #25: 'amp_14q32.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 25(14Q32.33) MUTATED	44	34	0.4 - 72.9 (13.0)
AMP PEAK 25(14Q32.33) WILD-TYPE	1035	557	0.0 - 211.2 (15.8)

Figure S137. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #1: 'Time to Death'

'amp_14q32.33' versus 'YEARS_TO_BIRTH'

P value = 8.78e-06 (Wilcoxon-test), Q value = 3.9e-05

Table S138. Gene #25: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 25(14Q32.33) MUTATED	44	61.0 (14.9)
AMP PEAK 25(14Q32.33) WILD-TYPE	1038	50.3 (15.7)

Figure S138. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_14q32.33' versus 'TUMOR_TISSUE_SITE'

P value = 7.54e-05 (Fisher's exact test), Q value = 0.00027

Table S139. Gene #25: 'amp_14q32.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 25(14Q32.33) MUTATED	36	8
AMP PEAK 25(14Q32.33) WILD-TYPE	535	504

Figure S139. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_14q32.33' versus 'RADIATION_THERAPY'

P value = 0.0644 (Fisher's exact test), Q value = 0.12

Table S140. Gene #25: 'amp_14q32.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 25(14Q32.33) MUTATED	5	36
AMP PEAK 25(14Q32.33) WILD-TYPE	253	731

Figure S140. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_14q32.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0844 (Wilcoxon-test), Q value = 0.16

Table S141. Gene #25: 'amp_14q32.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 25(14Q32.33) MUTATED	33	76.7 (16.7)
AMP PEAK 25(14Q32.33) WILD-TYPE	697	81.5 (14.6)

Figure S141. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_14q32.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00182 (Fisher's exact test), Q value = 0.0053

Table S142. Gene #25: 'amp_14q32.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 25(14Q32.33) MUTATED	2	2	3	3	2	32
AMP PEAK 25(14Q32.33) WILD-TYPE	192	26	126	186	16	493

Figure S142. Get High-res Image Gene #25: 'amp_14q32.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_17p13.2' versus 'Time to Death'

P value = 0.00322 (logrank test), Q value = 0.0089

Table S143. Gene #26: 'amp_17p13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 26(17P13.2) MUTATED	74	52	0.2 - 72.4 (14.5)
AMP PEAK 26(17P13.2) WILD-TYPE	1005	539	0.0 - 211.2 (15.8)

Figure S143. Get High-res Image Gene #26: 'amp_17p13.2' versus Clinical Feature #1: 'Time to Death'

'amp_17p13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0107 (Wilcoxon-test), Q value = 0.026

Table S144. Gene #26: 'amp_17p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 26(17P13.2) MUTATED	74	55.0 (16.1)
AMP PEAK 26(17P13.2) WILD-TYPE	1008	50.5 (15.7)

Figure S144. Get High-res Image Gene #26: 'amp_17p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p13.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.00377 (Fisher's exact test), Q value = 0.01

Table S145. Gene #26: 'amp_17p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 26(17P13.2) MUTATED	51	23
AMP PEAK 26(17P13.2) WILD-TYPE	520	489

Figure S145. Get High-res Image Gene #26: 'amp_17p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17p13.2' versus 'GENDER'

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

Table S146. Gene #26: 'amp_17p13.2' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
AMP PEAK 26(17P13.2) MUTATED	23	51
AMP PEAK 26(17P13.2) WILD-TYPE	429	580

Figure S146. Get High-res Image Gene #26: 'amp_17p13.2' versus Clinical Feature #4: 'GENDER'

'amp_17p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0044 (Fisher's exact test), Q value = 0.012

Table S147. Gene #26: 'amp_17p13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 26(17P13.2) MUTATED	10	4	1	12	1	46
AMP PEAK 26(17P13.2) WILD-TYPE	184	24	128	177	17	479

Figure S147. Get High-res Image Gene #26: 'amp_17p13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_17q25.1' versus 'Time to Death'

P value = 9.1e-06 (logrank test), Q value = 3.9e-05

Table S148. Gene #27: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 27(17Q25.1) MUTATED	126	89	0.1 - 91.8 (13.6)
AMP PEAK 27(17Q25.1) WILD-TYPE	953	502	0.0 - 211.2 (16.0)

Figure S148. Get High-res Image Gene #27: 'amp_17q25.1' versus Clinical Feature #1: 'Time to Death'

'amp_17q25.1' versus 'YEARS_TO_BIRTH'

P value = 1.93e-05 (Wilcoxon-test), Q value = 7.3e-05

Table S149. Gene #27: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 27(17Q25.1) MUTATED	126	56.3 (14.9)
AMP PEAK 27(17Q25.1) WILD-TYPE	956	50.1 (15.8)

Figure S149. Get High-res Image Gene #27: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q25.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0017 (Fisher's exact test), Q value = 0.005

Table S150. Gene #27: 'amp_17q25.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 27(17Q25.1) MUTATED	83	43
AMP PEAK 27(17Q25.1) WILD-TYPE	488	469

Figure S150. Get High-res Image Gene #27: 'amp_17q25.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17q25.1' versus 'GENDER'

P value = 0.103 (Fisher's exact test), Q value = 0.18

Table S151. Gene #27: 'amp_17q25.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
AMP PEAK 27(17Q25.1) MUTATED	44	82
AMP PEAK 27(17Q25.1) WILD-TYPE	408	549

Figure S151. Get High-res Image Gene #27: 'amp_17q25.1' versus Clinical Feature #4: 'GENDER'

'amp_17q25.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0224 (Fisher's exact test), Q value = 0.05

Table S152. Gene #27: 'amp_17q25.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 27(17Q25.1) MUTATED	21	5	8	14	2	76
AMP PEAK 27(17Q25.1) WILD-TYPE	173	23	121	175	16	449

Figure S152. Get High-res Image Gene #27: 'amp_17q25.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19p13.3' versus 'Time to Death'

P value = 0.0101 (logrank test), Q value = 0.025

Table S153. Gene #28: 'amp_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 28(19P13.3) MUTATED	370	229	0.0 - 172.8 (15.8)
AMP PEAK 28(19P13.3) WILD-TYPE	709	362	0.1 - 211.2 (15.3)

Figure S153. Get High-res Image Gene #28: 'amp_19p13.3' versus Clinical Feature #1: 'Time to Death'

'amp_19p13.3' versus 'YEARS_TO_BIRTH'

P value = 5.05e-05 (Wilcoxon-test), Q value = 0.00018

Table S154. Gene #28: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 28(19P13.3) MUTATED	371	53.4 (14.6)
AMP PEAK 28(19P13.3) WILD-TYPE	711	49.4 (16.2)

Figure S154. Get High-res Image Gene #28: 'amp_19p13.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.3' versus 'TUMOR_TISSUE_SITE'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.5e-08

Table S155. Gene #28: 'amp_19p13.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 28(19P13.3) MUTATED	243	129
AMP PEAK 28(19P13.3) WILD-TYPE	328	383

Figure S155. Get High-res Image Gene #28: 'amp_19p13.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19p13.3' versus 'HISTOLOGICAL_TYPE'

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

Table S156. Gene #28: 'amp_19p13.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 28(19P13.3) MUTATED	26	12	29	74	10	221
AMP PEAK 28(19P13.3) WILD-TYPE	168	16	100	115	8	304

Figure S156. Get High-res Image Gene #28: 'amp_19p13.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19p13.2' versus 'Time to Death'

P value = 0.000258 (logrank test), Q value = 0.00085

Table S157. Gene #29: 'amp_19p13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 29(19P13.2) MUTATED	365	230	0.1 - 169.8 (15.4)
AMP PEAK 29(19P13.2) WILD-TYPE	714	361	0.0 - 211.2 (15.9)

Figure S157. Get High-res Image Gene #29: 'amp_19p13.2' versus Clinical Feature #1: 'Time to Death'

'amp_19p13.2' versus 'YEARS_TO_BIRTH'

P value = 4.93e-07 (Wilcoxon-test), Q value = 2.8e-06

Table S158. Gene #29: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 29(19P13.2) MUTATED	367	54.2 (14.4)
AMP PEAK 29(19P13.2) WILD-TYPE	715	49.0 (16.2)

Figure S158. Get High-res Image Gene #29: 'amp_19p13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19p13.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.98e-11 (Fisher's exact test), Q value = 1.6e-10

Table S159. Gene #29: 'amp_19p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 29(19P13.2) MUTATED	246	122
AMP PEAK 29(19P13.2) WILD-TYPE	325	390

Figure S159. Get High-res Image Gene #29: 'amp_19p13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

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

Table S160. Gene #29: 'amp_19p13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 29(19P13.2) MUTATED	24	11	25	73	10	225
AMP PEAK 29(19P13.2) WILD-TYPE	170	17	104	116	8	300

Figure S160. Get High-res Image Gene #29: 'amp_19p13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'Time to Death'

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

Table S161. Gene #30: 'amp_19q12' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 30(19Q12) MUTATED	244	190	0.0 - 92.7 (14.1)
AMP PEAK 30(19Q12) WILD-TYPE	835	401	0.1 - 211.2 (16.4)

Figure S161. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #1: 'Time to Death'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 4.86e-16 (Wilcoxon-test), Q value = 6.3e-15

Table S162. Gene #30: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 30(19Q12) MUTATED	245	57.9 (12.8)
AMP PEAK 30(19Q12) WILD-TYPE	837	48.7 (16.0)

Figure S162. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q12' versus 'TUMOR_TISSUE_SITE'

P value = 3.12e-38 (Fisher's exact test), Q value = 5.8e-37

Table S163. Gene #30: 'amp_19q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 30(19Q12) MUTATED	214	31
AMP PEAK 30(19Q12) WILD-TYPE	357	481

Figure S163. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19q12' versus 'RADIATION_THERAPY'

P value = 6.89e-08 (Fisher's exact test), Q value = 4.2e-07

Table S164. Gene #30: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 30(19Q12) MUTATED	28	202
AMP PEAK 30(19Q12) WILD-TYPE	230	565

Figure S164. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q12' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 9.53e-05 (Wilcoxon-test), Q value = 0.00033

Table S165. Gene #30: 'amp_19q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 30(19Q12) MUTATED	166	77.9 (14.7)
AMP PEAK 30(19Q12) WILD-TYPE	564	82.3 (14.6)

Figure S165. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

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

Table S166. Gene #30: 'amp_19q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 30(19Q12) MUTATED	16	13	9	6	8	193
AMP PEAK 30(19Q12) WILD-TYPE	178	15	120	183	10	332

Figure S166. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'RACE'

P value = 0.0403 (Fisher's exact test), Q value = 0.083

Table S167. Gene #30: 'amp_19q12' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 30(19Q12) MUTATED	0	8	23	206
AMP PEAK 30(19Q12) WILD-TYPE	1	13	48	751

Figure S167. Get High-res Image Gene #30: 'amp_19q12' versus Clinical Feature #8: 'RACE'

'amp_19q13.2' versus 'Time to Death'

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

Table S168. Gene #31: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 31(19Q13.2) MUTATED	229	175	0.1 - 92.7 (14.2)
AMP PEAK 31(19Q13.2) WILD-TYPE	850	416	0.0 - 211.2 (16.3)

Figure S168. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

'amp_19q13.2' versus 'YEARS_TO_BIRTH'

P value = 1.81e-15 (Wilcoxon-test), Q value = 2.1e-14

Table S169. Gene #31: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 31(19Q13.2) MUTATED	230	58.0 (12.4)
AMP PEAK 31(19Q13.2) WILD-TYPE	852	48.8 (16.0)

Figure S169. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q13.2' versus 'TUMOR_TISSUE_SITE'

P value = 9.95e-34 (Fisher's exact test), Q value = 1.7e-32

Table S170. Gene #31: 'amp_19q13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 31(19Q13.2) MUTATED	199	31
AMP PEAK 31(19Q13.2) WILD-TYPE	372	481

Figure S170. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_19q13.2' versus 'RADIATION_THERAPY'

P value = 5.99e-07 (Fisher's exact test), Q value = 3.4e-06

Table S171. Gene #31: 'amp_19q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 31(19Q13.2) MUTATED	27	188
AMP PEAK 31(19Q13.2) WILD-TYPE	231	579

Figure S171. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q13.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000304 (Wilcoxon-test), Q value = 0.00099

Table S172. Gene #31: 'amp_19q13.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 31(19Q13.2) MUTATED	160	78.2 (14.6)
AMP PEAK 31(19Q13.2) WILD-TYPE	570	82.2 (14.6)

Figure S172. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_19q13.2' versus 'HISTOLOGICAL_TYPE'

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

Table S173. Gene #31: 'amp_19q13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 31(19Q13.2) MUTATED	18	12	7	6	6	181
AMP PEAK 31(19Q13.2) WILD-TYPE	176	16	122	183	12	344

Figure S173. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_19q13.2' versus 'RACE'

P value = 0.0337 (Fisher's exact test), Q value = 0.071

Table S174. Gene #31: 'amp_19q13.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
AMP PEAK 31(19Q13.2) MUTATED	0	7	23	193
AMP PEAK 31(19Q13.2) WILD-TYPE	1	14	48	764

Figure S174. Get High-res Image Gene #31: 'amp_19q13.2' versus Clinical Feature #8: 'RACE'

'amp_xp11.21' versus 'Time to Death'

P value = 0.000448 (logrank test), Q value = 0.0014

Table S175. Gene #32: 'amp_xp11.21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
AMP PEAK 32(XP11.21) MUTATED	104	41	0.1 - 145.1 (19.5)
AMP PEAK 32(XP11.21) WILD-TYPE	975	550	0.0 - 211.2 (15.3)

Figure S175. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #1: 'Time to Death'

'amp_xp11.21' versus 'YEARS_TO_BIRTH'

P value = 3.21e-06 (Wilcoxon-test), Q value = 1.7e-05

Table S176. Gene #32: 'amp_xp11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
AMP PEAK 32(XP11.21) MUTATED	104	43.9 (15.7)
AMP PEAK 32(XP11.21) WILD-TYPE	978	51.5 (15.6)

Figure S176. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp11.21' versus 'TUMOR_TISSUE_SITE'

P value = 1.89e-05 (Fisher's exact test), Q value = 7.2e-05

Table S177. Gene #32: 'amp_xp11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
AMP PEAK 32(XP11.21) MUTATED	34	70
AMP PEAK 32(XP11.21) WILD-TYPE	537	442

Figure S177. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_xp11.21' versus 'GENDER'

P value = 0.0284 (Fisher's exact test), Q value = 0.061

Table S178. Gene #32: 'amp_xp11.21' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
AMP PEAK 32(XP11.21) MUTATED	54	50
AMP PEAK 32(XP11.21) WILD-TYPE	398	581

Figure S178. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #4: 'GENDER'

'amp_xp11.21' versus 'RADIATION_THERAPY'

P value = 0.00971 (Fisher's exact test), Q value = 0.024

Table S179. Gene #32: 'amp_xp11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
AMP PEAK 32(XP11.21) MUTATED	14	84
AMP PEAK 32(XP11.21) WILD-TYPE	244	683

Figure S179. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_xp11.21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0254 (Wilcoxon-test), Q value = 0.056

Table S180. Gene #32: 'amp_xp11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
AMP PEAK 32(XP11.21) MUTATED	67	84.3 (15.1)
AMP PEAK 32(XP11.21) WILD-TYPE	663	81.0 (14.6)

Figure S180. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xp11.21' versus 'HISTOLOGICAL_TYPE'

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

Table S181. Gene #32: 'amp_xp11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
AMP PEAK 32(XP11.21) MUTATED	44	3	17	9	2	29
AMP PEAK 32(XP11.21) WILD-TYPE	150	25	112	180	16	496

Figure S181. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'amp_xp11.21' versus 'ETHNICITY'

P value = 0.0304 (Fisher's exact test), Q value = 0.065

Table S182. Gene #32: 'amp_xp11.21' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
AMP PEAK 32(XP11.21) MUTATED	9	84
AMP PEAK 32(XP11.21) WILD-TYPE	35	835

Figure S182. Get High-res Image Gene #32: 'amp_xp11.21' versus Clinical Feature #9: 'ETHNICITY'

'del_1p36.32' versus 'Time to Death'

P value = 5.51e-09 (logrank test), Q value = 3.5e-08

Table S183. Gene #33: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 1(1P36.32) MUTATED	312	127	0.1 - 182.3 (17.2)
DEL PEAK 1(1P36.32) WILD-TYPE	767	464	0.0 - 211.2 (14.9)

Figure S183. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'TUMOR_TISSUE_SITE'

P value = 1.26e-14 (Fisher's exact test), Q value = 1.4e-13

Table S184. Gene #33: 'del_1p36.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 1(1P36.32) MUTATED	108	206
DEL PEAK 1(1P36.32) WILD-TYPE	463	306

Figure S184. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p36.32' versus 'RADIATION_THERAPY'

P value = 5.48e-08 (Fisher's exact test), Q value = 3.3e-07

Table S185. Gene #33: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 1(1P36.32) MUTATED	110	187
DEL PEAK 1(1P36.32) WILD-TYPE	148	580

Figure S185. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p36.32' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0215 (Wilcoxon-test), Q value = 0.048

Table S186. Gene #33: 'del_1p36.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 1(1P36.32) MUTATED	215	82.7 (15.9)
DEL PEAK 1(1P36.32) WILD-TYPE	515	80.7 (14.2)

Figure S186. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.32' versus 'HISTOLOGICAL_TYPE'

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

Table S187. Gene #33: 'del_1p36.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 1(1P36.32) MUTATED	22	1	46	138	4	103
DEL PEAK 1(1P36.32) WILD-TYPE	172	27	83	51	14	422

Figure S187. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p36.32' versus 'RACE'

P value = 0.022 (Fisher's exact test), Q value = 0.049

Table S188. Gene #33: 'del_1p36.32' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 1(1P36.32) MUTATED	1	10	14	281
DEL PEAK 1(1P36.32) WILD-TYPE	0	11	57	676

Figure S188. Get High-res Image Gene #33: 'del_1p36.32' versus Clinical Feature #8: 'RACE'

'del_1p36.23' versus 'Time to Death'

P value = 1.37e-05 (logrank test), Q value = 5.3e-05

Table S189. Gene #34: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 2(1P36.23) MUTATED	342	154	0.1 - 182.3 (16.5)
DEL PEAK 2(1P36.23) WILD-TYPE	737	437	0.0 - 211.2 (15.0)

Figure S189. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

'del_1p36.23' versus 'TUMOR_TISSUE_SITE'

P value = 1.23e-10 (Fisher's exact test), Q value = 9.7e-10

Table S190. Gene #34: 'del_1p36.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 2(1P36.23) MUTATED	132	212
DEL PEAK 2(1P36.23) WILD-TYPE	439	300

Figure S190. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p36.23' versus 'RADIATION_THERAPY'

P value = 4.42e-07 (Fisher's exact test), Q value = 2.6e-06

Table S191. Gene #34: 'del_1p36.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 2(1P36.23) MUTATED	116	211
DEL PEAK 2(1P36.23) WILD-TYPE	142	556

Figure S191. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p36.23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00254 (Wilcoxon-test), Q value = 0.0073

Table S192. Gene #34: 'del_1p36.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 2(1P36.23) MUTATED	234	83.1 (16.0)
DEL PEAK 2(1P36.23) WILD-TYPE	496	80.4 (14.0)

Figure S192. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.23' versus 'HISTOLOGICAL_TYPE'

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

Table S193. Gene #34: 'del_1p36.23' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 2(1P36.23) MUTATED	24	4	48	140	3	125
DEL PEAK 2(1P36.23) WILD-TYPE	170	24	81	49	15	400

Figure S193. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p36.23' versus 'RACE'

P value = 0.046 (Fisher's exact test), Q value = 0.093

Table S194. Gene #34: 'del_1p36.23' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 2(1P36.23) MUTATED	1	11	18	304
DEL PEAK 2(1P36.23) WILD-TYPE	0	10	53	653

Figure S194. Get High-res Image Gene #34: 'del_1p36.23' versus Clinical Feature #8: 'RACE'

'del_1p32.3' versus 'Time to Death'

P value = 9.31e-14 (logrank test), Q value = 9.2e-13

Table S195. Gene #35: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 3(1P32.3) MUTATED	254	81	0.1 - 182.3 (17.1)
DEL PEAK 3(1P32.3) WILD-TYPE	825	510	0.0 - 211.2 (15.1)

Figure S195. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #1: 'Time to Death'

'del_1p32.3' versus 'TUMOR_TISSUE_SITE'

P value = 1.69e-27 (Fisher's exact test), Q value = 2.7e-26

Table S196. Gene #35: 'del_1p32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 3(1P32.3) MUTATED	60	196
DEL PEAK 3(1P32.3) WILD-TYPE	511	316

Figure S196. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p32.3' versus 'RADIATION_THERAPY'

P value = 3.12e-13 (Fisher's exact test), Q value = 3e-12

Table S197. Gene #35: 'del_1p32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 3(1P32.3) MUTATED	105	134
DEL PEAK 3(1P32.3) WILD-TYPE	153	633

Figure S197. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p32.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00142 (Wilcoxon-test), Q value = 0.0042

Table S198. Gene #35: 'del_1p32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 3(1P32.3) MUTATED	161	84.5 (13.4)
DEL PEAK 3(1P32.3) WILD-TYPE	569	80.4 (14.9)

Figure S198. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p32.3' versus 'HISTOLOGICAL_TYPE'

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

Table S199. Gene #35: 'del_1p32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 3(1P32.3) MUTATED	16	1	42	138	2	57
DEL PEAK 3(1P32.3) WILD-TYPE	178	27	87	51	16	468

Figure S199. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p32.3' versus 'RACE'

P value = 0.0379 (Fisher's exact test), Q value = 0.078

Table S200. Gene #35: 'del_1p32.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 3(1P32.3) MUTATED	1	7	10	230
DEL PEAK 3(1P32.3) WILD-TYPE	0	14	61	727

Figure S200. Get High-res Image Gene #35: 'del_1p32.3' versus Clinical Feature #8: 'RACE'

'del_1p22.1' versus 'Time to Death'

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

Table S201. Gene #36: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 4(1P22.1) MUTATED	231	66	0.1 - 182.3 (20.1)
DEL PEAK 4(1P22.1) WILD-TYPE	848	525	0.0 - 211.2 (14.9)

Figure S201. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #1: 'Time to Death'

'del_1p22.1' versus 'YEARS_TO_BIRTH'

P value = 0.00387 (Wilcoxon-test), Q value = 0.011

Table S202. Gene #36: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 4(1P22.1) MUTATED	232	48.3 (13.9)
DEL PEAK 4(1P22.1) WILD-TYPE	850	51.5 (16.2)

Figure S202. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p22.1' versus 'TUMOR_TISSUE_SITE'

P value = 2.27e-30 (Fisher's exact test), Q value = 3.8e-29

Table S203. Gene #36: 'del_1p22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 4(1P22.1) MUTATED	47	186
DEL PEAK 4(1P22.1) WILD-TYPE	524	326

Figure S203. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1p22.1' versus 'RADIATION_THERAPY'

P value = 2.08e-14 (Fisher's exact test), Q value = 2.3e-13

Table S204. Gene #36: 'del_1p22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 4(1P22.1) MUTATED	100	117
DEL PEAK 4(1P22.1) WILD-TYPE	158	650

Figure S204. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000136 (Wilcoxon-test), Q value = 0.00047

Table S205. Gene #36: 'del_1p22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 4(1P22.1) MUTATED	148	84.9 (14.5)
DEL PEAK 4(1P22.1) WILD-TYPE	582	80.4 (14.6)

Figure S205. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p22.1' versus 'HISTOLOGICAL_TYPE'

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

Table S206. Gene #36: 'del_1p22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 4(1P22.1) MUTATED	11	1	39	136	4	42
DEL PEAK 4(1P22.1) WILD-TYPE	183	27	90	53	14	483

Figure S206. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_1p22.1' versus 'ETHNICITY'

P value = 0.139 (Fisher's exact test), Q value = 0.24

Table S207. Gene #36: 'del_1p22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 4(1P22.1) MUTATED	14	202
DEL PEAK 4(1P22.1) WILD-TYPE	30	717

Figure S207. Get High-res Image Gene #36: 'del_1p22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_1q42.11' versus 'Time to Death'

P value = 0.0283 (logrank test), Q value = 0.061

Table S208. Gene #37: 'del_1q42.11' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 5(1Q42.11) MUTATED	77	50	0.1 - 146.1 (12.6)
DEL PEAK 5(1Q42.11) WILD-TYPE	1002	541	0.0 - 211.2 (16.0)

Figure S208. Get High-res Image Gene #37: 'del_1q42.11' versus Clinical Feature #1: 'Time to Death'

'del_1q42.11' versus 'YEARS_TO_BIRTH'

P value = 0.0334 (Wilcoxon-test), Q value = 0.071

Table S209. Gene #37: 'del_1q42.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 5(1Q42.11) MUTATED	77	54.6 (15.0)
DEL PEAK 5(1Q42.11) WILD-TYPE	1005	50.5 (15.8)

Figure S209. Get High-res Image Gene #37: 'del_1q42.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q42.11' versus 'TUMOR_TISSUE_SITE'

P value = 0.0576 (Fisher's exact test), Q value = 0.11

Table S210. Gene #37: 'del_1q42.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 5(1Q42.11) MUTATED	49	28
DEL PEAK 5(1Q42.11) WILD-TYPE	522	484

Figure S210. Get High-res Image Gene #37: 'del_1q42.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_1q42.11' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0152 (Wilcoxon-test), Q value = 0.035

Table S211. Gene #37: 'del_1q42.11' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 5(1Q42.11) MUTATED	61	75.9 (18.0)
DEL PEAK 5(1Q42.11) WILD-TYPE	669	81.8 (14.3)

Figure S211. Get High-res Image Gene #37: 'del_1q42.11' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q22.1' versus 'Time to Death'

P value = 0.00412 (logrank test), Q value = 0.011

Table S212. Gene #39: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 7(2Q22.1) MUTATED	68	51	1.3 - 117.4 (15.2)
DEL PEAK 7(2Q22.1) WILD-TYPE	1011	540	0.0 - 211.2 (15.8)

Figure S212. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.0169 (Wilcoxon-test), Q value = 0.039

Table S213. Gene #39: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 7(2Q22.1) MUTATED	68	55.0 (16.8)
DEL PEAK 7(2Q22.1) WILD-TYPE	1014	50.5 (15.7)

Figure S213. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00558 (Fisher's exact test), Q value = 0.015

Table S214. Gene #39: 'del_2q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 7(2Q22.1) MUTATED	47	21
DEL PEAK 7(2Q22.1) WILD-TYPE	524	491

Figure S214. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0771 (Wilcoxon-test), Q value = 0.14

Table S215. Gene #39: 'del_2q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 7(2Q22.1) MUTATED	48	78.3 (13.1)
DEL PEAK 7(2Q22.1) WILD-TYPE	682	81.5 (14.8)

Figure S215. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00396 (Fisher's exact test), Q value = 0.011

Table S216. Gene #39: 'del_2q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 7(2Q22.1) MUTATED	13	5	3	5	2	40
DEL PEAK 7(2Q22.1) WILD-TYPE	181	23	126	184	16	485

Figure S216. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_2q22.1' versus 'ETHNICITY'

P value = 0.105 (Fisher's exact test), Q value = 0.19

Table S217. Gene #39: 'del_2q22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 7(2Q22.1) MUTATED	0	60
DEL PEAK 7(2Q22.1) WILD-TYPE	44	859

Figure S217. Get High-res Image Gene #39: 'del_2q22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_2q37.1' versus 'YEARS_TO_BIRTH'

P value = 0.0283 (Wilcoxon-test), Q value = 0.061

Table S218. Gene #40: 'del_2q37.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 8(2Q37.1) MUTATED	121	47.9 (17.0)
DEL PEAK 8(2Q37.1) WILD-TYPE	961	51.1 (15.6)

Figure S218. Get High-res Image Gene #40: 'del_2q37.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.1 (Fisher's exact test), Q value = 0.18

Table S219. Gene #40: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 8(2Q37.1) MUTATED	55	66
DEL PEAK 8(2Q37.1) WILD-TYPE	516	446

Figure S219. Get High-res Image Gene #40: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00613 (Fisher's exact test), Q value = 0.016

Table S220. Gene #40: 'del_2q37.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 8(2Q37.1) MUTATED	34	3	20	12	1	51
DEL PEAK 8(2Q37.1) WILD-TYPE	160	25	109	177	17	474

Figure S220. Get High-res Image Gene #40: 'del_2q37.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.0012 (Fisher's exact test), Q value = 0.0037

Table S221. Gene #41: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 9(3P21.31) MUTATED	13	91
DEL PEAK 9(3P21.31) WILD-TYPE	245	676

Figure S221. Get High-res Image Gene #41: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3q13.31' versus 'Time to Death'

P value = 0.114 (logrank test), Q value = 0.2

Table S222. Gene #42: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 10(3Q13.31) MUTATED	95	63	0.1 - 117.4 (15.9)
DEL PEAK 10(3Q13.31) WILD-TYPE	984	528	0.0 - 211.2 (15.4)

Figure S222. Get High-res Image Gene #42: 'del_3q13.31' versus Clinical Feature #1: 'Time to Death'

'del_3q13.31' versus 'RADIATION_THERAPY'

P value = 0.0722 (Fisher's exact test), Q value = 0.14

Table S223. Gene #42: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 10(3Q13.31) MUTATED	15	73
DEL PEAK 10(3Q13.31) WILD-TYPE	243	694

Figure S223. Get High-res Image Gene #42: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q34.3' versus 'Time to Death'

P value = 3.46e-05 (logrank test), Q value = 0.00013

Table S224. Gene #44: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 12(4Q34.3) MUTATED	230	101	0.1 - 156.2 (19.8)
DEL PEAK 12(4Q34.3) WILD-TYPE	849	490	0.0 - 211.2 (14.9)

Figure S224. Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0122 (Wilcoxon-test), Q value = 0.029

Table S225. Gene #44: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 12(4Q34.3) MUTATED	230	48.5 (14.5)
DEL PEAK 12(4Q34.3) WILD-TYPE	852	51.4 (16.1)

Figure S225. Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'TUMOR_TISSUE_SITE'

P value = 1.5e-05 (Fisher's exact test), Q value = 5.8e-05

Table S226. Gene #44: 'del_4q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 12(4Q34.3) MUTATED	92	138
DEL PEAK 12(4Q34.3) WILD-TYPE	479	374

Figure S226. Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_4q34.3' versus 'GENDER'

P value = 0.114 (Fisher's exact test), Q value = 0.2

Table S227. Gene #44: 'del_4q34.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 12(4Q34.3) MUTATED	85	145
DEL PEAK 12(4Q34.3) WILD-TYPE	367	486

Figure S227. Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #4: 'GENDER'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00123 (Fisher's exact test), Q value = 0.0037

Table S228. Gene #44: 'del_4q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 12(4Q34.3) MUTATED	49	5	36	53	2	85
DEL PEAK 12(4Q34.3) WILD-TYPE	145	23	93	136	16	440

Figure S228. Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.000375 (Fisher's exact test), Q value = 0.0012

Table S229. Gene #45: 'del_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 13(5P15.33) MUTATED	11	88
DEL PEAK 13(5P15.33) WILD-TYPE	247	679

Figure S229. Get High-res Image Gene #45: 'del_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0255 (Fisher's exact test), Q value = 0.056

Table S230. Gene #45: 'del_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 13(5P15.33) MUTATED	23	3	19	8	1	52
DEL PEAK 13(5P15.33) WILD-TYPE	171	25	110	181	17	473

Figure S230. Get High-res Image Gene #45: 'del_5p15.33' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_5q34' versus 'YEARS_TO_BIRTH'

P value = 0.0929 (Wilcoxon-test), Q value = 0.17

Table S231. Gene #46: 'del_5q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 14(5Q34) MUTATED	132	48.5 (17.7)
DEL PEAK 14(5Q34) WILD-TYPE	950	51.1 (15.5)

Figure S231. Get High-res Image Gene #46: 'del_5q34' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q34' versus 'RADIATION_THERAPY'

P value = 0.00179 (Fisher's exact test), Q value = 0.0053

Table S232. Gene #46: 'del_5q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 14(5Q34) MUTATED	17	106
DEL PEAK 14(5Q34) WILD-TYPE	241	661

Figure S232. Get High-res Image Gene #46: 'del_5q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_5q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.00054

Table S233. Gene #46: 'del_5q34' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 14(5Q34) MUTATED	40	6	13	10	1	62
DEL PEAK 14(5Q34) WILD-TYPE	154	22	116	179	17	463

Figure S233. Get High-res Image Gene #46: 'del_5q34' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 1.65e-07 (logrank test), Q value = 9.8e-07

Table S234. Gene #47: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 15(6P25.3) MUTATED	137	95	0.1 - 145.1 (10.8)
DEL PEAK 15(6P25.3) WILD-TYPE	942	496	0.0 - 211.2 (16.3)

Figure S234. Get High-res Image Gene #47: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0347 (Wilcoxon-test), Q value = 0.073

Table S235. Gene #47: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 15(6P25.3) MUTATED	138	53.3 (15.9)
DEL PEAK 15(6P25.3) WILD-TYPE	944	50.4 (15.7)

Figure S235. Get High-res Image Gene #47: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00607 (Fisher's exact test), Q value = 0.016

Table S236. Gene #47: 'del_6p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 15(6P25.3) MUTATED	88	50
DEL PEAK 15(6P25.3) WILD-TYPE	483	462

Figure S236. Get High-res Image Gene #47: 'del_6p25.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6p25.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.131 (Wilcoxon-test), Q value = 0.23

Table S237. Gene #47: 'del_6p25.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 15(6P25.3) MUTATED	99	79.7 (13.9)
DEL PEAK 15(6P25.3) WILD-TYPE	631	81.5 (14.8)

Figure S237. Get High-res Image Gene #47: 'del_6p25.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0577 (Fisher's exact test), Q value = 0.11

Table S238. Gene #47: 'del_6p25.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 15(6P25.3) MUTATED	24	3	10	16	2	83
DEL PEAK 15(6P25.3) WILD-TYPE	170	25	119	173	16	442

Figure S238. Get High-res Image Gene #47: 'del_6p25.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'Time to Death'

P value = 9.96e-12 (logrank test), Q value = 8.6e-11

Table S239. Gene #48: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 16(6Q22.31) MUTATED	233	161	0.1 - 117.4 (12.6)
DEL PEAK 16(6Q22.31) WILD-TYPE	846	430	0.0 - 211.2 (16.8)

Figure S239. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'YEARS_TO_BIRTH'

P value = 4.01e-05 (Wilcoxon-test), Q value = 0.00015

Table S240. Gene #48: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 16(6Q22.31) MUTATED	234	54.6 (15.4)
DEL PEAK 16(6Q22.31) WILD-TYPE	848	49.7 (15.7)

Figure S240. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q22.31' versus 'TUMOR_TISSUE_SITE'

P value = 6.44e-07 (Fisher's exact test), Q value = 3.6e-06

Table S241. Gene #48: 'del_6q22.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 16(6Q22.31) MUTATED	157	77
DEL PEAK 16(6Q22.31) WILD-TYPE	414	435

Figure S241. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q22.31' versus 'GENDER'

P value = 0.0995 (Fisher's exact test), Q value = 0.18

Table S242. Gene #48: 'del_6q22.31' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 16(6Q22.31) MUTATED	109	125
DEL PEAK 16(6Q22.31) WILD-TYPE	343	506

Figure S242. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #4: 'GENDER'

'del_6q22.31' versus 'RADIATION_THERAPY'

P value = 0.0351 (Fisher's exact test), Q value = 0.074

Table S243. Gene #48: 'del_6q22.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 16(6Q22.31) MUTATED	43	176
DEL PEAK 16(6Q22.31) WILD-TYPE	215	591

Figure S243. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00692 (Wilcoxon-test), Q value = 0.018

Table S244. Gene #48: 'del_6q22.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 16(6Q22.31) MUTATED	169	78.9 (14.8)
DEL PEAK 16(6Q22.31) WILD-TYPE	561	82.0 (14.6)

Figure S244. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

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

Table S245. Gene #48: 'del_6q22.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 16(6Q22.31) MUTATED	47	6	11	19	7	144
DEL PEAK 16(6Q22.31) WILD-TYPE	147	22	118	170	11	381

Figure S245. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'RACE'

P value = 0.0988 (Fisher's exact test), Q value = 0.18

Table S246. Gene #48: 'del_6q22.31' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 16(6Q22.31) MUTATED	1	6	20	200
DEL PEAK 16(6Q22.31) WILD-TYPE	0	15	51	757

Figure S246. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #8: 'RACE'

'del_6q22.31' versus 'ETHNICITY'

P value = 0.13 (Fisher's exact test), Q value = 0.22

Table S247. Gene #48: 'del_6q22.31' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 16(6Q22.31) MUTATED	5	199
DEL PEAK 16(6Q22.31) WILD-TYPE	39	720

Figure S247. Get High-res Image Gene #48: 'del_6q22.31' versus Clinical Feature #9: 'ETHNICITY'

'del_6q26' versus 'Time to Death'

P value = 1.63e-11 (logrank test), Q value = 1.4e-10

Table S248. Gene #49: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 17(6Q26) MUTATED	258	178	0.0 - 145.1 (13.2)
DEL PEAK 17(6Q26) WILD-TYPE	821	413	0.1 - 211.2 (16.8)

Figure S248. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

'del_6q26' versus 'YEARS_TO_BIRTH'

P value = 0.000142 (Wilcoxon-test), Q value = 0.00049

Table S249. Gene #49: 'del_6q26' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 17(6Q26) MUTATED	259	53.9 (14.9)
DEL PEAK 17(6Q26) WILD-TYPE	823	49.8 (15.9)

Figure S249. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q26' versus 'TUMOR_TISSUE_SITE'

P value = 2.65e-09 (Fisher's exact test), Q value = 1.8e-08

Table S250. Gene #49: 'del_6q26' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 17(6Q26) MUTATED	178	81
DEL PEAK 17(6Q26) WILD-TYPE	393	431

Figure S250. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q26' versus 'RADIATION_THERAPY'

P value = 0.00225 (Fisher's exact test), Q value = 0.0065

Table S251. Gene #49: 'del_6q26' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 17(6Q26) MUTATED	43	199
DEL PEAK 17(6Q26) WILD-TYPE	215	568

Figure S251. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_6q26' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00312 (Wilcoxon-test), Q value = 0.0087

Table S252. Gene #49: 'del_6q26' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 17(6Q26) MUTATED	186	79.0 (14.4)
DEL PEAK 17(6Q26) WILD-TYPE	544	82.1 (14.7)

Figure S252. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

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

Table S253. Gene #49: 'del_6q26' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 17(6Q26) MUTATED	48	7	12	21	9	162
DEL PEAK 17(6Q26) WILD-TYPE	146	21	117	168	9	363

Figure S253. Get High-res Image Gene #49: 'del_6q26' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'Time to Death'

P value = 0.000161 (logrank test), Q value = 0.00054

Table S254. Gene #50: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 18(8P23.2) MUTATED	87	59	0.1 - 120.6 (12.7)
DEL PEAK 18(8P23.2) WILD-TYPE	992	532	0.0 - 211.2 (16.0)

Figure S254. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'YEARS_TO_BIRTH'

P value = 6.13e-05 (Wilcoxon-test), Q value = 0.00022

Table S255. Gene #50: 'del_8p23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 18(8P23.2) MUTATED	88	57.1 (14.5)
DEL PEAK 18(8P23.2) WILD-TYPE	994	50.2 (15.8)

Figure S255. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_8p23.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.07e-05 (Fisher's exact test), Q value = 4.2e-05

Table S256. Gene #50: 'del_8p23.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 18(8P23.2) MUTATED	66	22
DEL PEAK 18(8P23.2) WILD-TYPE	505	490

Figure S256. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_8p23.2' versus 'RADIATION_THERAPY'

P value = 0.0111 (Fisher's exact test), Q value = 0.027

Table S257. Gene #50: 'del_8p23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 18(8P23.2) MUTATED	11	71
DEL PEAK 18(8P23.2) WILD-TYPE	247	696

Figure S257. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.00041

Table S258. Gene #50: 'del_8p23.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 18(8P23.2) MUTATED	13	3	5	4	1	62
DEL PEAK 18(8P23.2) WILD-TYPE	181	25	124	185	17	463

Figure S258. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.0141 (Fisher's exact test), Q value = 0.033

Table S259. Gene #50: 'del_8p23.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 18(8P23.2) MUTATED	0	6	6	72
DEL PEAK 18(8P23.2) WILD-TYPE	1	15	65	885

Figure S259. Get High-res Image Gene #50: 'del_8p23.2' versus Clinical Feature #8: 'RACE'

'del_8q24.3' versus 'Time to Death'

P value = 0.0126 (logrank test), Q value = 0.03

Table S260. Gene #51: 'del_8q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 19(8Q24.3) MUTATED	78	49	0.2 - 82.6 (14.3)
DEL PEAK 19(8Q24.3) WILD-TYPE	1001	542	0.0 - 211.2 (15.9)

Figure S260. Get High-res Image Gene #51: 'del_8q24.3' versus Clinical Feature #1: 'Time to Death'

'del_8q24.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0248 (Fisher's exact test), Q value = 0.055

Table S261. Gene #51: 'del_8q24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 19(8Q24.3) MUTATED	51	27
DEL PEAK 19(8Q24.3) WILD-TYPE	520	485

Figure S261. Get High-res Image Gene #51: 'del_8q24.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_8q24.3' versus 'RADIATION_THERAPY'

P value = 0.0127 (Fisher's exact test), Q value = 0.03

Table S262. Gene #51: 'del_8q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 19(8Q24.3) MUTATED	10	65
DEL PEAK 19(8Q24.3) WILD-TYPE	248	702

Figure S262. Get High-res Image Gene #51: 'del_8q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0845 (Fisher's exact test), Q value = 0.16

Table S263. Gene #51: 'del_8q24.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 19(8Q24.3) MUTATED	12	1	9	6	2	48
DEL PEAK 19(8Q24.3) WILD-TYPE	182	27	120	183	16	477

Figure S263. Get High-res Image Gene #51: 'del_8q24.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'Time to Death'

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

Table S264. Gene #52: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 20(9P21.3) MUTATED	587	409	0.1 - 169.8 (13.3)
DEL PEAK 20(9P21.3) WILD-TYPE	492	182	0.0 - 211.2 (18.7)

Figure S264. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 3.58e-30 (Wilcoxon-test), Q value = 5.9e-29

Table S265. Gene #52: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 20(9P21.3) MUTATED	588	55.6 (14.8)
DEL PEAK 20(9P21.3) WILD-TYPE	494	45.0 (14.9)

Figure S265. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'TUMOR_TISSUE_SITE'

P value = 5.89e-38 (Fisher's exact test), Q value = 1.1e-36

Table S266. Gene #52: 'del_9p21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 20(9P21.3) MUTATED	415	174
DEL PEAK 20(9P21.3) WILD-TYPE	156	338

Figure S266. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_9p21.3' versus 'RADIATION_THERAPY'

P value = 4.11e-10 (Fisher's exact test), Q value = 3e-09

Table S267. Gene #52: 'del_9p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 20(9P21.3) MUTATED	96	458
DEL PEAK 20(9P21.3) WILD-TYPE	162	309

Figure S267. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 4.66e-13 (Wilcoxon-test), Q value = 4.4e-12

Table S268. Gene #52: 'del_9p21.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 20(9P21.3) MUTATED	409	77.9 (15.5)
DEL PEAK 20(9P21.3) WILD-TYPE	321	85.6 (12.4)

Figure S268. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

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

Table S269. Gene #52: 'del_9p21.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 20(9P21.3) MUTATED	85	21	36	53	15	379
DEL PEAK 20(9P21.3) WILD-TYPE	109	7	93	136	3	146

Figure S269. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RACE'

P value = 0.015 (Fisher's exact test), Q value = 0.035

Table S270. Gene #52: 'del_9p21.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 20(9P21.3) MUTATED	0	12	50	508
DEL PEAK 20(9P21.3) WILD-TYPE	1	9	21	449

Figure S270. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #8: 'RACE'

'del_9p21.3' versus 'ETHNICITY'

P value = 0.0636 (Fisher's exact test), Q value = 0.12

Table S271. Gene #52: 'del_9p21.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 20(9P21.3) MUTATED	17	491
DEL PEAK 20(9P21.3) WILD-TYPE	27	428

Figure S271. Get High-res Image Gene #52: 'del_9p21.3' versus Clinical Feature #9: 'ETHNICITY'

'del_10p15.3' versus 'Time to Death'

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

Table S272. Gene #53: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 21(10P15.3) MUTATED	546	437	0.1 - 134.3 (12.2)
DEL PEAK 21(10P15.3) WILD-TYPE	533	154	0.0 - 211.2 (21.0)

Figure S272. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 2.28e-71 (Wilcoxon-test), Q value = 6e-70

Table S273. Gene #53: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 21(10P15.3) MUTATED	547	59.1 (12.4)
DEL PEAK 21(10P15.3) WILD-TYPE	535	42.2 (14.2)

Figure S273. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'TUMOR_TISSUE_SITE'

P value = 1.4e-109 (Fisher's exact test), Q value = 5e-108

Table S274. Gene #53: 'del_10p15.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 21(10P15.3) MUTATED	464	83
DEL PEAK 21(10P15.3) WILD-TYPE	107	429

Figure S274. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10p15.3' versus 'GENDER'

P value = 0.0645 (Fisher's exact test), Q value = 0.12

Table S275. Gene #53: 'del_10p15.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 21(10P15.3) MUTATED	213	334
DEL PEAK 21(10P15.3) WILD-TYPE	239	297

Figure S275. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #4: 'GENDER'

'del_10p15.3' versus 'RADIATION_THERAPY'

P value = 1.12e-15 (Fisher's exact test), Q value = 1.3e-14

Table S276. Gene #53: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 21(10P15.3) MUTATED	75	443
DEL PEAK 21(10P15.3) WILD-TYPE	183	324

Figure S276. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p15.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 6.84e-18 (Wilcoxon-test), Q value = 9.9e-17

Table S277. Gene #53: 'del_10p15.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 21(10P15.3) MUTATED	398	77.4 (15.3)
DEL PEAK 21(10P15.3) WILD-TYPE	332	86.0 (12.5)

Figure S277. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10p15.3' versus 'HISTOLOGICAL_TYPE'

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

Table S278. Gene #53: 'del_10p15.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 21(10P15.3) MUTATED	50	20	15	18	11	433
DEL PEAK 21(10P15.3) WILD-TYPE	144	8	114	171	7	92

Figure S278. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10p15.3' versus 'RACE'

P value = 0.00766 (Fisher's exact test), Q value = 0.019

Table S279. Gene #53: 'del_10p15.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 21(10P15.3) MUTATED	1	9	48	468
DEL PEAK 21(10P15.3) WILD-TYPE	0	12	23	489

Figure S279. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #8: 'RACE'

'del_10p15.3' versus 'ETHNICITY'

P value = 0.00501 (Fisher's exact test), Q value = 0.013

Table S280. Gene #53: 'del_10p15.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 21(10P15.3) MUTATED	12	453
DEL PEAK 21(10P15.3) WILD-TYPE	32	466

Figure S280. Get High-res Image Gene #53: 'del_10p15.3' versus Clinical Feature #9: 'ETHNICITY'

'del_10p13' versus 'Time to Death'

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

Table S281. Gene #54: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 22(10P13) MUTATED	546	439	0.1 - 134.3 (12.3)
DEL PEAK 22(10P13) WILD-TYPE	533	152	0.0 - 211.2 (21.1)

Figure S281. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'YEARS_TO_BIRTH'

P value = 1.44e-71 (Wilcoxon-test), Q value = 3.9e-70

Table S282. Gene #54: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 22(10P13) MUTATED	547	59.1 (12.2)
DEL PEAK 22(10P13) WILD-TYPE	535	42.2 (14.4)

Figure S282. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'TUMOR_TISSUE_SITE'

P value = 6.21e-111 (Fisher's exact test), Q value = 2.3e-109

Table S283. Gene #54: 'del_10p13' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 22(10P13) MUTATED	465	82
DEL PEAK 22(10P13) WILD-TYPE	106	430

Figure S283. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10p13' versus 'GENDER'

P value = 0.0265 (Fisher's exact test), Q value = 0.058

Table S284. Gene #54: 'del_10p13' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 22(10P13) MUTATED	210	337
DEL PEAK 22(10P13) WILD-TYPE	242	294

Figure S284. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #4: 'GENDER'

'del_10p13' versus 'RADIATION_THERAPY'

P value = 9.39e-17 (Fisher's exact test), Q value = 1.3e-15

Table S285. Gene #54: 'del_10p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 22(10P13) MUTATED	73	445
DEL PEAK 22(10P13) WILD-TYPE	185	322

Figure S285. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p13' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.63e-16 (Wilcoxon-test), Q value = 3.5e-15

Table S286. Gene #54: 'del_10p13' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 22(10P13) MUTATED	399	77.6 (15.3)
DEL PEAK 22(10P13) WILD-TYPE	331	85.8 (12.5)

Figure S286. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10p13' versus 'HISTOLOGICAL_TYPE'

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

Table S287. Gene #54: 'del_10p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 22(10P13) MUTATED	50	19	15	17	11	435
DEL PEAK 22(10P13) WILD-TYPE	144	9	114	172	7	90

Figure S287. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10p13' versus 'RACE'

P value = 0.016 (Fisher's exact test), Q value = 0.037

Table S288. Gene #54: 'del_10p13' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 22(10P13) MUTATED	1	9	47	469
DEL PEAK 22(10P13) WILD-TYPE	0	12	24	488

Figure S288. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #8: 'RACE'

'del_10p13' versus 'ETHNICITY'

P value = 0.00501 (Fisher's exact test), Q value = 0.013

Table S289. Gene #54: 'del_10p13' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 22(10P13) MUTATED	12	453
DEL PEAK 22(10P13) WILD-TYPE	32	466

Figure S289. Get High-res Image Gene #54: 'del_10p13' versus Clinical Feature #9: 'ETHNICITY'

'del_10p11.23' versus 'Time to Death'

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

Table S290. Gene #55: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 23(10P11.23) MUTATED	551	443	0.1 - 134.3 (12.2)
DEL PEAK 23(10P11.23) WILD-TYPE	528	148	0.0 - 211.2 (21.4)

Figure S290. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'YEARS_TO_BIRTH'

P value = 3.67e-75 (Wilcoxon-test), Q value = 1.1e-73

Table S291. Gene #55: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 23(10P11.23) MUTATED	552	59.3 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE	530	41.9 (14.1)

Figure S291. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p11.23' versus 'TUMOR_TISSUE_SITE'

P value = 4.92e-114 (Fisher's exact test), Q value = 1.9e-112

Table S292. Gene #55: 'del_10p11.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 23(10P11.23) MUTATED	470	82
DEL PEAK 23(10P11.23) WILD-TYPE	101	430

Figure S292. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10p11.23' versus 'GENDER'

P value = 0.0485 (Fisher's exact test), Q value = 0.097

Table S293. Gene #55: 'del_10p11.23' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 23(10P11.23) MUTATED	214	338
DEL PEAK 23(10P11.23) WILD-TYPE	238	293

Figure S293. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #4: 'GENDER'

'del_10p11.23' versus 'RADIATION_THERAPY'

P value = 6.1e-16 (Fisher's exact test), Q value = 7.6e-15

Table S294. Gene #55: 'del_10p11.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 23(10P11.23) MUTATED	76	448
DEL PEAK 23(10P11.23) WILD-TYPE	182	319

Figure S294. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p11.23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.49e-19 (Wilcoxon-test), Q value = 3.8e-18

Table S295. Gene #55: 'del_10p11.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 23(10P11.23) MUTATED	404	77.3 (15.3)
DEL PEAK 23(10P11.23) WILD-TYPE	326	86.3 (12.3)

Figure S295. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10p11.23' versus 'HISTOLOGICAL_TYPE'

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

Table S296. Gene #55: 'del_10p11.23' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 23(10P11.23) MUTATED	50	20	14	18	10	440
DEL PEAK 23(10P11.23) WILD-TYPE	144	8	115	171	8	85

Figure S296. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10p11.23' versus 'RACE'

P value = 0.00155 (Fisher's exact test), Q value = 0.0046

Table S297. Gene #55: 'del_10p11.23' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 23(10P11.23) MUTATED	1	9	50	470
DEL PEAK 23(10P11.23) WILD-TYPE	0	12	21	487

Figure S297. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #8: 'RACE'

'del_10p11.23' versus 'ETHNICITY'

P value = 0.00325 (Fisher's exact test), Q value = 0.009

Table S298. Gene #55: 'del_10p11.23' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 23(10P11.23) MUTATED	12	459
DEL PEAK 23(10P11.23) WILD-TYPE	32	460

Figure S298. Get High-res Image Gene #55: 'del_10p11.23' versus Clinical Feature #9: 'ETHNICITY'

'del_10q23.31' versus 'Time to Death'

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

Table S299. Gene #56: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 24(10Q23.31) MUTATED	621	484	0.1 - 156.2 (12.6)
DEL PEAK 24(10Q23.31) WILD-TYPE	458	107	0.0 - 211.2 (22.9)

Figure S299. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 8.17e-64 (Wilcoxon-test), Q value = 2e-62

Table S300. Gene #56: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 24(10Q23.31) MUTATED	622	57.6 (13.6)
DEL PEAK 24(10Q23.31) WILD-TYPE	460	41.5 (13.7)

Figure S300. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'TUMOR_TISSUE_SITE'

P value = 2.51e-118 (Fisher's exact test), Q value = 1e-116

Table S301. Gene #56: 'del_10q23.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 24(10Q23.31) MUTATED	508	114
DEL PEAK 24(10Q23.31) WILD-TYPE	63	398

Figure S301. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 3.55e-19 (Fisher's exact test), Q value = 5.4e-18

Table S302. Gene #56: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 24(10Q23.31) MUTATED	87	504
DEL PEAK 24(10Q23.31) WILD-TYPE	171	263

Figure S302. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q23.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 2.2e-18 (Wilcoxon-test), Q value = 3.3e-17

Table S303. Gene #56: 'del_10q23.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 24(10Q23.31) MUTATED	444	77.7 (15.2)
DEL PEAK 24(10Q23.31) WILD-TYPE	286	86.8 (11.9)

Figure S303. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

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

Table S304. Gene #56: 'del_10q23.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 24(10Q23.31) MUTATED	68	23	19	27	13	472
DEL PEAK 24(10Q23.31) WILD-TYPE	126	5	110	162	5	53

Figure S304. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'RACE'

P value = 0.00702 (Fisher's exact test), Q value = 0.018

Table S305. Gene #56: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 24(10Q23.31) MUTATED	1	11	53	535
DEL PEAK 24(10Q23.31) WILD-TYPE	0	10	18	422

Figure S305. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

'del_10q23.31' versus 'ETHNICITY'

P value = 0.00831 (Fisher's exact test), Q value = 0.021

Table S306. Gene #56: 'del_10q23.31' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 24(10Q23.31) MUTATED	16	522
DEL PEAK 24(10Q23.31) WILD-TYPE	28	397

Figure S306. Get High-res Image Gene #56: 'del_10q23.31' versus Clinical Feature #9: 'ETHNICITY'

'del_10q26.3' versus 'Time to Death'

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

Table S307. Gene #57: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 25(10Q26.3) MUTATED	657	490	0.1 - 172.8 (13.3)
DEL PEAK 25(10Q26.3) WILD-TYPE	422	101	0.0 - 211.2 (22.2)

Figure S307. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 4.8e-50 (Wilcoxon-test), Q value = 1e-48

Table S308. Gene #57: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 25(10Q26.3) MUTATED	659	56.4 (14.3)
DEL PEAK 25(10Q26.3) WILD-TYPE	423	42.0 (13.9)

Figure S308. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'TUMOR_TISSUE_SITE'

P value = 7.75e-97 (Fisher's exact test), Q value = 2.5e-95

Table S309. Gene #57: 'del_10q26.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 25(10Q26.3) MUTATED	509	150
DEL PEAK 25(10Q26.3) WILD-TYPE	62	362

Figure S309. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_10q26.3' versus 'RADIATION_THERAPY'

P value = 8.23e-17 (Fisher's exact test), Q value = 1.2e-15

Table S310. Gene #57: 'del_10q26.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 25(10Q26.3) MUTATED	101	528
DEL PEAK 25(10Q26.3) WILD-TYPE	157	239

Figure S310. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q26.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 3.22e-16 (Wilcoxon-test), Q value = 4.2e-15

Table S311. Gene #57: 'del_10q26.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 25(10Q26.3) MUTATED	469	78.1 (15.4)
DEL PEAK 25(10Q26.3) WILD-TYPE	261	86.9 (11.3)

Figure S311. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

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

Table S312. Gene #57: 'del_10q26.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 25(10Q26.3) MUTATED	81	23	32	37	14	472
DEL PEAK 25(10Q26.3) WILD-TYPE	113	5	97	152	4	53

Figure S312. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'RACE'

P value = 0.00837 (Fisher's exact test), Q value = 0.021

Table S313. Gene #57: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 25(10Q26.3) MUTATED	1	11	55	570
DEL PEAK 25(10Q26.3) WILD-TYPE	0	10	16	387

Figure S313. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

'del_10q26.3' versus 'ETHNICITY'

P value = 0.0271 (Fisher's exact test), Q value = 0.059

Table S314. Gene #57: 'del_10q26.3' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 25(10Q26.3) MUTATED	19	556
DEL PEAK 25(10Q26.3) WILD-TYPE	25	363

Figure S314. Get High-res Image Gene #57: 'del_10q26.3' versus Clinical Feature #9: 'ETHNICITY'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.000747 (Wilcoxon-test), Q value = 0.0023

Table S315. Gene #58: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 26(11P15.5) MUTATED	234	47.8 (15.9)
DEL PEAK 26(11P15.5) WILD-TYPE	848	51.6 (15.7)

Figure S315. Get High-res Image Gene #58: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'GENDER'

P value = 0.0515 (Fisher's exact test), Q value = 0.1

Table S316. Gene #58: 'del_11p15.5' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 26(11P15.5) MUTATED	111	123
DEL PEAK 26(11P15.5) WILD-TYPE	341	508

Figure S316. Get High-res Image Gene #58: 'del_11p15.5' versus Clinical Feature #4: 'GENDER'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.0146 (Fisher's exact test), Q value = 0.034

Table S317. Gene #58: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 26(11P15.5) MUTATED	42	180
DEL PEAK 26(11P15.5) WILD-TYPE	216	587

Figure S317. Get High-res Image Gene #58: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S318. Gene #58: 'del_11p15.5' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 26(11P15.5) MUTATED	58	6	29	18	6	117
DEL PEAK 26(11P15.5) WILD-TYPE	136	22	100	171	12	408

Figure S318. Get High-res Image Gene #58: 'del_11p15.5' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_11p15.1' versus 'Time to Death'

P value = 0.0903 (logrank test), Q value = 0.16

Table S319. Gene #59: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 27(11P15.1) MUTATED	175	112	0.2 - 156.2 (16.5)
DEL PEAK 27(11P15.1) WILD-TYPE	904	479	0.0 - 211.2 (15.4)

Figure S319. Get High-res Image Gene #59: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

'del_11p15.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0697 (Fisher's exact test), Q value = 0.13

Table S320. Gene #59: 'del_11p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 27(11P15.1) MUTATED	104	72
DEL PEAK 27(11P15.1) WILD-TYPE	467	440

Figure S320. Get High-res Image Gene #59: 'del_11p15.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_11p15.1' versus 'GENDER'

P value = 0.0372 (Fisher's exact test), Q value = 0.077

Table S321. Gene #59: 'del_11p15.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 27(11P15.1) MUTATED	86	90
DEL PEAK 27(11P15.1) WILD-TYPE	366	541

Figure S321. Get High-res Image Gene #59: 'del_11p15.1' versus Clinical Feature #4: 'GENDER'

'del_11p15.1' versus 'RADIATION_THERAPY'

P value = 0.0243 (Fisher's exact test), Q value = 0.054

Table S322. Gene #59: 'del_11p15.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 27(11P15.1) MUTATED	30	136
DEL PEAK 27(11P15.1) WILD-TYPE	228	631

Figure S322. Get High-res Image Gene #59: 'del_11p15.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p15.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00023 (Fisher's exact test), Q value = 0.00076

Table S323. Gene #59: 'del_11p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 27(11P15.1) MUTATED	43	5	15	14	5	94
DEL PEAK 27(11P15.1) WILD-TYPE	151	23	114	175	13	431

Figure S323. Get High-res Image Gene #59: 'del_11p15.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_11p11.2' versus 'Time to Death'

P value = 0.00283 (logrank test), Q value = 0.0081

Table S324. Gene #60: 'del_11p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 28(11P11.2) MUTATED	159	111	0.2 - 117.4 (15.9)
DEL PEAK 28(11P11.2) WILD-TYPE	920	480	0.0 - 211.2 (15.5)

Figure S324. Get High-res Image Gene #60: 'del_11p11.2' versus Clinical Feature #1: 'Time to Death'

'del_11p11.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.000289 (Fisher's exact test), Q value = 0.00095

Table S325. Gene #60: 'del_11p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 28(11P11.2) MUTATED	105	54
DEL PEAK 28(11P11.2) WILD-TYPE	466	458

Figure S325. Get High-res Image Gene #60: 'del_11p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_11p11.2' versus 'RADIATION_THERAPY'

P value = 0.00293 (Fisher's exact test), Q value = 0.0083

Table S326. Gene #60: 'del_11p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 28(11P11.2) MUTATED	23	126
DEL PEAK 28(11P11.2) WILD-TYPE	235	641

Figure S326. Get High-res Image Gene #60: 'del_11p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.00041

Table S327. Gene #60: 'del_11p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 28(11P11.2) MUTATED	30	5	13	11	6	94
DEL PEAK 28(11P11.2) WILD-TYPE	164	23	116	178	12	431

Figure S327. Get High-res Image Gene #60: 'del_11p11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'Time to Death'

P value = 0.0581 (logrank test), Q value = 0.11

Table S328. Gene #61: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 29(12P13.1) MUTATED	108	68	0.1 - 95.1 (15.5)
DEL PEAK 29(12P13.1) WILD-TYPE	971	523	0.0 - 211.2 (15.7)

Figure S328. Get High-res Image Gene #61: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

'del_12p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00631 (Fisher's exact test), Q value = 0.016

Table S329. Gene #61: 'del_12p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 29(12P13.1) MUTATED	71	38
DEL PEAK 29(12P13.1) WILD-TYPE	500	474

Figure S329. Get High-res Image Gene #61: 'del_12p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0114 (Fisher's exact test), Q value = 0.027

Table S330. Gene #61: 'del_12p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 29(12P13.1) MUTATED	20	1	9	9	1	69
DEL PEAK 29(12P13.1) WILD-TYPE	174	27	120	180	17	456

Figure S330. Get High-res Image Gene #61: 'del_12p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12p13.1' versus 'ETHNICITY'

P value = 0.115 (Fisher's exact test), Q value = 0.2

Table S331. Gene #61: 'del_12p13.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 29(12P13.1) MUTATED	1	94
DEL PEAK 29(12P13.1) WILD-TYPE	43	825

Figure S331. Get High-res Image Gene #61: 'del_12p13.1' versus Clinical Feature #9: 'ETHNICITY'

'del_12q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00116 (Fisher's exact test), Q value = 0.0036

Table S332. Gene #62: 'del_12q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 30(12Q12) MUTATED	42	3	16	12	2	71
DEL PEAK 30(12Q12) WILD-TYPE	152	25	113	177	16	454

Figure S332. Get High-res Image Gene #62: 'del_12q12' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 0.00702 (Fisher's exact test), Q value = 0.018

Table S333. Gene #63: 'del_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 31(12Q15) MUTATED	37	4	14	12	3	71
DEL PEAK 31(12Q15) WILD-TYPE	157	24	115	177	15	454

Figure S333. Get High-res Image Gene #63: 'del_12q15' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'Time to Death'

P value = 3.31e-05 (logrank test), Q value = 0.00012

Table S334. Gene #64: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 32(13Q14.2) MUTATED	380	247	0.1 - 211.2 (15.0)
DEL PEAK 32(13Q14.2) WILD-TYPE	699	344	0.0 - 182.3 (16.2)

Figure S334. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.0605 (Wilcoxon-test), Q value = 0.12

Table S335. Gene #64: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 32(13Q14.2) MUTATED	381	52.0 (16.2)
DEL PEAK 32(13Q14.2) WILD-TYPE	701	50.1 (15.5)

Figure S335. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'TUMOR_TISSUE_SITE'

P value = 1.23e-06 (Fisher's exact test), Q value = 6.7e-06

Table S336. Gene #64: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 32(13Q14.2) MUTATED	239	142
DEL PEAK 32(13Q14.2) WILD-TYPE	332	370

Figure S336. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q14.2' versus 'GENDER'

P value = 0.122 (Fisher's exact test), Q value = 0.21

Table S337. Gene #64: 'del_13q14.2' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 32(13Q14.2) MUTATED	147	234
DEL PEAK 32(13Q14.2) WILD-TYPE	305	397

Figure S337. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #4: 'GENDER'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.00263 (Fisher's exact test), Q value = 0.0076

Table S338. Gene #64: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 32(13Q14.2) MUTATED	72	294
DEL PEAK 32(13Q14.2) WILD-TYPE	186	473

Figure S338. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q14.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00468 (Wilcoxon-test), Q value = 0.013

Table S339. Gene #64: 'del_13q14.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 32(13Q14.2) MUTATED	269	79.4 (14.7)
DEL PEAK 32(13Q14.2) WILD-TYPE	461	82.4 (14.6)

Figure S339. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

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

Table S340. Gene #64: 'del_13q14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 32(13Q14.2) MUTATED	63	9	36	43	6	224
DEL PEAK 32(13Q14.2) WILD-TYPE	131	19	93	146	12	301

Figure S340. Get High-res Image Gene #64: 'del_13q14.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q22.1' versus 'Time to Death'

P value = 1.74e-05 (logrank test), Q value = 6.6e-05

Table S341. Gene #65: 'del_13q22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 33(13Q22.1) MUTATED	363	235	0.1 - 211.2 (15.0)
DEL PEAK 33(13Q22.1) WILD-TYPE	716	356	0.0 - 182.3 (16.2)

Figure S341. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #1: 'Time to Death'

'del_13q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.031

Table S342. Gene #65: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 33(13Q22.1) MUTATED	364	52.4 (15.5)
DEL PEAK 33(13Q22.1) WILD-TYPE	718	49.9 (15.8)

Figure S342. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q22.1' versus 'TUMOR_TISSUE_SITE'

P value = 6.34e-06 (Fisher's exact test), Q value = 3.2e-05

Table S343. Gene #65: 'del_13q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 33(13Q22.1) MUTATED	227	137
DEL PEAK 33(13Q22.1) WILD-TYPE	344	375

Figure S343. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q22.1' versus 'RADIATION_THERAPY'

P value = 0.0151 (Fisher's exact test), Q value = 0.035

Table S344. Gene #65: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 33(13Q22.1) MUTATED	72	279
DEL PEAK 33(13Q22.1) WILD-TYPE	186	488

Figure S344. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00209 (Wilcoxon-test), Q value = 0.0061

Table S345. Gene #65: 'del_13q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 33(13Q22.1) MUTATED	255	79.2 (14.6)
DEL PEAK 33(13Q22.1) WILD-TYPE	475	82.4 (14.6)

Figure S345. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.00035

Table S346. Gene #65: 'del_13q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 33(13Q22.1) MUTATED	59	9	34	44	5	213
DEL PEAK 33(13Q22.1) WILD-TYPE	135	19	95	145	13	312

Figure S346. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_13q22.1' versus 'ETHNICITY'

P value = 0.142 (Fisher's exact test), Q value = 0.24

Table S347. Gene #65: 'del_13q22.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 33(13Q22.1) MUTATED	10	313
DEL PEAK 33(13Q22.1) WILD-TYPE	34	606

Figure S347. Get High-res Image Gene #65: 'del_13q22.1' versus Clinical Feature #9: 'ETHNICITY'

'del_14q13.1' versus 'Time to Death'

P value = 1.86e-10 (logrank test), Q value = 1.4e-09

Table S348. Gene #66: 'del_14q13.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 34(14Q13.1) MUTATED	244	169	0.1 - 130.8 (13.8)
DEL PEAK 34(14Q13.1) WILD-TYPE	835	422	0.0 - 211.2 (16.5)

Figure S348. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #1: 'Time to Death'

'del_14q13.1' versus 'YEARS_TO_BIRTH'

P value = 1.2e-09 (Wilcoxon-test), Q value = 8.5e-09

Table S349. Gene #66: 'del_14q13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 34(14Q13.1) MUTATED	244	56.1 (14.3)
DEL PEAK 34(14Q13.1) WILD-TYPE	838	49.2 (15.9)

Figure S349. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q13.1' versus 'TUMOR_TISSUE_SITE'

P value = 2.96e-12 (Fisher's exact test), Q value = 2.7e-11

Table S350. Gene #66: 'del_14q13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 34(14Q13.1) MUTATED	176	68
DEL PEAK 34(14Q13.1) WILD-TYPE	395	444

Figure S350. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q13.1' versus 'RADIATION_THERAPY'

P value = 0.0203 (Fisher's exact test), Q value = 0.046

Table S351. Gene #66: 'del_14q13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 34(14Q13.1) MUTATED	45	188
DEL PEAK 34(14Q13.1) WILD-TYPE	213	579

Figure S351. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_14q13.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00597 (Wilcoxon-test), Q value = 0.016

Table S352. Gene #66: 'del_14q13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 34(14Q13.1) MUTATED	178	79.6 (13.1)
DEL PEAK 34(14Q13.1) WILD-TYPE	552	81.8 (15.1)

Figure S352. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q13.1' versus 'HISTOLOGICAL_TYPE'

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

Table S353. Gene #66: 'del_14q13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 34(14Q13.1) MUTATED	31	6	15	22	6	164
DEL PEAK 34(14Q13.1) WILD-TYPE	163	22	114	167	12	361

Figure S353. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q13.1' versus 'RACE'

P value = 0.0466 (Fisher's exact test), Q value = 0.094

Table S354. Gene #66: 'del_14q13.1' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 34(14Q13.1) MUTATED	1	4	23	205
DEL PEAK 34(14Q13.1) WILD-TYPE	0	17	48	752

Figure S354. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #8: 'RACE'

'del_14q13.1' versus 'ETHNICITY'

P value = 0.0569 (Fisher's exact test), Q value = 0.11

Table S355. Gene #66: 'del_14q13.1' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 34(14Q13.1) MUTATED	4	201
DEL PEAK 34(14Q13.1) WILD-TYPE	40	718

Figure S355. Get High-res Image Gene #66: 'del_14q13.1' versus Clinical Feature #9: 'ETHNICITY'

'del_14q24.2' versus 'Time to Death'

P value = 0.00176 (logrank test), Q value = 0.0052

Table S356. Gene #67: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 35(14Q24.2) MUTATED	289	182	0.1 - 130.8 (15.1)
DEL PEAK 35(14Q24.2) WILD-TYPE	790	409	0.0 - 211.2 (15.9)

Figure S356. Get High-res Image Gene #67: 'del_14q24.2' versus Clinical Feature #1: 'Time to Death'

'del_14q24.2' versus 'YEARS_TO_BIRTH'

P value = 0.0667 (Wilcoxon-test), Q value = 0.13

Table S357. Gene #67: 'del_14q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 35(14Q24.2) MUTATED	290	52.2 (15.7)
DEL PEAK 35(14Q24.2) WILD-TYPE	792	50.2 (15.8)

Figure S357. Get High-res Image Gene #67: 'del_14q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q24.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.0134 (Fisher's exact test), Q value = 0.031

Table S358. Gene #67: 'del_14q24.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 35(14Q24.2) MUTATED	171	119
DEL PEAK 35(14Q24.2) WILD-TYPE	400	393

Figure S358. Get High-res Image Gene #67: 'del_14q24.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q24.2' versus 'GENDER'

P value = 0.0602 (Fisher's exact test), Q value = 0.12

Table S359. Gene #67: 'del_14q24.2' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 35(14Q24.2) MUTATED	135	155
DEL PEAK 35(14Q24.2) WILD-TYPE	317	476

Figure S359. Get High-res Image Gene #67: 'del_14q24.2' versus Clinical Feature #4: 'GENDER'

'del_14q24.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0504 (Fisher's exact test), Q value = 0.1

Table S360. Gene #67: 'del_14q24.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 35(14Q24.2) MUTATED	52	5	28	39	7	159
DEL PEAK 35(14Q24.2) WILD-TYPE	142	23	101	150	11	366

Figure S360. Get High-res Image Gene #67: 'del_14q24.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q31.3' versus 'Time to Death'

P value = 0.00337 (logrank test), Q value = 0.0092

Table S361. Gene #68: 'del_14q31.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 36(14Q31.3) MUTATED	273	170	0.1 - 130.8 (15.3)
DEL PEAK 36(14Q31.3) WILD-TYPE	806	421	0.0 - 211.2 (15.8)

Figure S361. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #1: 'Time to Death'

'del_14q31.3' versus 'YEARS_TO_BIRTH'

P value = 0.0713 (Wilcoxon-test), Q value = 0.13

Table S362. Gene #68: 'del_14q31.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 36(14Q31.3) MUTATED	274	52.2 (15.6)
DEL PEAK 36(14Q31.3) WILD-TYPE	808	50.3 (15.8)

Figure S362. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q31.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0427 (Fisher's exact test), Q value = 0.087

Table S363. Gene #68: 'del_14q31.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 36(14Q31.3) MUTATED	159	115
DEL PEAK 36(14Q31.3) WILD-TYPE	412	397

Figure S363. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_14q31.3' versus 'GENDER'

P value = 0.0559 (Fisher's exact test), Q value = 0.11

Table S364. Gene #68: 'del_14q31.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	452	631
DEL PEAK 36(14Q31.3) MUTATED	128	146
DEL PEAK 36(14Q31.3) WILD-TYPE	324	485

Figure S364. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #4: 'GENDER'

'del_14q31.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0872 (Fisher's exact test), Q value = 0.16

Table S365. Gene #68: 'del_14q31.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 36(14Q31.3) MUTATED	50	6	29	36	8	145
DEL PEAK 36(14Q31.3) WILD-TYPE	144	22	100	153	10	380

Figure S365. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_14q31.3' versus 'RACE'

P value = 0.0921 (Fisher's exact test), Q value = 0.17

Table S366. Gene #68: 'del_14q31.3' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 36(14Q31.3) MUTATED	1	6	24	234
DEL PEAK 36(14Q31.3) WILD-TYPE	0	15	47	723

Figure S366. Get High-res Image Gene #68: 'del_14q31.3' versus Clinical Feature #8: 'RACE'

'del_15q14' versus 'Time to Death'

P value = 2.76e-07 (logrank test), Q value = 1.6e-06

Table S367. Gene #69: 'del_15q14' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 37(15Q14) MUTATED	210	148	0.2 - 134.3 (14.2)
DEL PEAK 37(15Q14) WILD-TYPE	869	443	0.0 - 211.2 (16.2)

Figure S367. Get High-res Image Gene #69: 'del_15q14' versus Clinical Feature #1: 'Time to Death'

'del_15q14' versus 'YEARS_TO_BIRTH'

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

Table S368. Gene #69: 'del_15q14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 37(15Q14) MUTATED	211	55.6 (16.0)
DEL PEAK 37(15Q14) WILD-TYPE	871	49.6 (15.5)

Figure S368. Get High-res Image Gene #69: 'del_15q14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q14' versus 'TUMOR_TISSUE_SITE'

P value = 4.08e-09 (Fisher's exact test), Q value = 2.7e-08

Table S369. Gene #69: 'del_15q14' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 37(15Q14) MUTATED	150	62
DEL PEAK 37(15Q14) WILD-TYPE	421	450

Figure S369. Get High-res Image Gene #69: 'del_15q14' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_15q14' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0318 (Wilcoxon-test), Q value = 0.068

Table S370. Gene #69: 'del_15q14' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 37(15Q14) MUTATED	132	79.5 (13.7)
DEL PEAK 37(15Q14) WILD-TYPE	598	81.7 (14.9)

Figure S370. Get High-res Image Gene #69: 'del_15q14' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_15q14' versus 'HISTOLOGICAL_TYPE'

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

Table S371. Gene #69: 'del_15q14' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 37(15Q14) MUTATED	26	8	14	22	4	138
DEL PEAK 37(15Q14) WILD-TYPE	168	20	115	167	14	387

Figure S371. Get High-res Image Gene #69: 'del_15q14' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16p12.2' versus 'Time to Death'

P value = 1.53e-10 (logrank test), Q value = 1.2e-09

Table S372. Gene #70: 'del_16p12.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 38(16P12.2) MUTATED	114	92	0.4 - 78.3 (14.6)
DEL PEAK 38(16P12.2) WILD-TYPE	965	499	0.0 - 211.2 (15.9)

Figure S372. Get High-res Image Gene #70: 'del_16p12.2' versus Clinical Feature #1: 'Time to Death'

'del_16p12.2' versus 'YEARS_TO_BIRTH'

P value = 1.07e-07 (Wilcoxon-test), Q value = 6.4e-07

Table S373. Gene #70: 'del_16p12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 38(16P12.2) MUTATED	114	58.3 (14.3)
DEL PEAK 38(16P12.2) WILD-TYPE	968	49.9 (15.7)

Figure S373. Get High-res Image Gene #70: 'del_16p12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16p12.2' versus 'TUMOR_TISSUE_SITE'

P value = 8.05e-11 (Fisher's exact test), Q value = 6.4e-10

Table S374. Gene #70: 'del_16p12.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 38(16P12.2) MUTATED	92	22
DEL PEAK 38(16P12.2) WILD-TYPE	479	490

Figure S374. Get High-res Image Gene #70: 'del_16p12.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16p12.2' versus 'RADIATION_THERAPY'

P value = 0.0611 (Fisher's exact test), Q value = 0.12

Table S375. Gene #70: 'del_16p12.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 38(16P12.2) MUTATED	19	90
DEL PEAK 38(16P12.2) WILD-TYPE	239	677

Figure S375. Get High-res Image Gene #70: 'del_16p12.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_16p12.2' versus 'HISTOLOGICAL_TYPE'

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

Table S376. Gene #70: 'del_16p12.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 38(16P12.2) MUTATED	14	3	3	5	1	88
DEL PEAK 38(16P12.2) WILD-TYPE	180	25	126	184	17	437

Figure S376. Get High-res Image Gene #70: 'del_16p12.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_16q23.1' versus 'Time to Death'

P value = 1.29e-09 (logrank test), Q value = 9e-09

Table S377. Gene #71: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 39(16Q23.1) MUTATED	127	100	0.1 - 127.6 (13.0)
DEL PEAK 39(16Q23.1) WILD-TYPE	952	491	0.0 - 211.2 (16.2)

Figure S377. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 5.91e-05 (Wilcoxon-test), Q value = 0.00021

Table S378. Gene #71: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 39(16Q23.1) MUTATED	127	55.9 (14.9)
DEL PEAK 39(16Q23.1) WILD-TYPE	955	50.1 (15.8)

Figure S378. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'TUMOR_TISSUE_SITE'

P value = 6.77e-10 (Fisher's exact test), Q value = 4.9e-09

Table S379. Gene #71: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 39(16Q23.1) MUTATED	99	28
DEL PEAK 39(16Q23.1) WILD-TYPE	472	484

Figure S379. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16q23.1' versus 'RADIATION_THERAPY'

P value = 0.0909 (Fisher's exact test), Q value = 0.16

Table S380. Gene #71: 'del_16q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 39(16Q23.1) MUTATED	22	96
DEL PEAK 39(16Q23.1) WILD-TYPE	236	671

Figure S380. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_16q23.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0112 (Wilcoxon-test), Q value = 0.027

Table S381. Gene #71: 'del_16q23.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 39(16Q23.1) MUTATED	88	77.4 (16.4)
DEL PEAK 39(16Q23.1) WILD-TYPE	642	81.8 (14.4)

Figure S381. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

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

Table S382. Gene #71: 'del_16q23.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 39(16Q23.1) MUTATED	15	3	6	7	2	94
DEL PEAK 39(16Q23.1) WILD-TYPE	179	25	123	182	16	431

Figure S382. Get High-res Image Gene #71: 'del_16q23.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17p13.1' versus 'Time to Death'

P value = 1.88e-09 (logrank test), Q value = 1.3e-08

Table S383. Gene #72: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 40(17P13.1) MUTATED	114	84	0.1 - 92.7 (11.8)
DEL PEAK 40(17P13.1) WILD-TYPE	965	507	0.0 - 211.2 (16.3)

Figure S383. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

'del_17p13.1' versus 'YEARS_TO_BIRTH'

P value = 4.99e-07 (Wilcoxon-test), Q value = 2.8e-06

Table S384. Gene #72: 'del_17p13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 40(17P13.1) MUTATED	114	57.7 (15.0)
DEL PEAK 40(17P13.1) WILD-TYPE	968	50.0 (15.7)

Figure S384. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 1.57e-13 (Fisher's exact test), Q value = 1.5e-12

Table S385. Gene #72: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 40(17P13.1) MUTATED	96	18
DEL PEAK 40(17P13.1) WILD-TYPE	475	494

Figure S385. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0344 (Fisher's exact test), Q value = 0.073

Table S386. Gene #72: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 40(17P13.1) MUTATED	18	90
DEL PEAK 40(17P13.1) WILD-TYPE	240	677

Figure S386. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17p13.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0134 (Wilcoxon-test), Q value = 0.031

Table S387. Gene #72: 'del_17p13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 40(17P13.1) MUTATED	79	78.4 (13.2)
DEL PEAK 40(17P13.1) WILD-TYPE	651	81.6 (14.8)

Figure S387. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_17p13.1' versus 'HISTOLOGICAL_TYPE'

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

Table S388. Gene #72: 'del_17p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 40(17P13.1) MUTATED	6	4	4	8	3	89
DEL PEAK 40(17P13.1) WILD-TYPE	188	24	125	181	15	436

Figure S388. Get High-res Image Gene #72: 'del_17p13.1' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'Time to Death'

P value = 3.78e-08 (logrank test), Q value = 2.3e-07

Table S389. Gene #73: 'del_17q11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 41(17Q11.2) MUTATED	91	66	0.1 - 92.7 (12.2)
DEL PEAK 41(17Q11.2) WILD-TYPE	988	525	0.0 - 211.2 (16.2)

Figure S389. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #1: 'Time to Death'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.000205 (Wilcoxon-test), Q value = 0.00068

Table S390. Gene #73: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 41(17Q11.2) MUTATED	91	56.4 (13.5)
DEL PEAK 41(17Q11.2) WILD-TYPE	991	50.3 (15.9)

Figure S390. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 9.35e-07 (Fisher's exact test), Q value = 5.2e-06

Table S391. Gene #73: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 41(17Q11.2) MUTATED	70	21
DEL PEAK 41(17Q11.2) WILD-TYPE	501	491

Figure S391. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17q11.2' versus 'RADIATION_THERAPY'

P value = 0.116 (Fisher's exact test), Q value = 0.2

Table S392. Gene #73: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 41(17Q11.2) MUTATED	15	69
DEL PEAK 41(17Q11.2) WILD-TYPE	243	698

Figure S392. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17q11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0111 (Wilcoxon-test), Q value = 0.027

Table S393. Gene #73: 'del_17q11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 41(17Q11.2) MUTATED	67	76.3 (17.7)
DEL PEAK 41(17Q11.2) WILD-TYPE	663	81.8 (14.3)

Figure S393. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_17q11.2' versus 'HISTOLOGICAL_TYPE'

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

Table S394. Gene #73: 'del_17q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 41(17Q11.2) MUTATED	11	3	4	6	2	65
DEL PEAK 41(17Q11.2) WILD-TYPE	183	25	125	183	16	460

Figure S394. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'RACE'

P value = 0.0845 (Fisher's exact test), Q value = 0.16

Table S395. Gene #73: 'del_17q11.2' versus Clinical Feature #8: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	21	71	957
DEL PEAK 41(17Q11.2) MUTATED	1	2	8	78
DEL PEAK 41(17Q11.2) WILD-TYPE	0	19	63	879

Figure S395. Get High-res Image Gene #73: 'del_17q11.2' versus Clinical Feature #8: 'RACE'

'del_18q23' versus 'YEARS_TO_BIRTH'

P value = 0.0625 (Wilcoxon-test), Q value = 0.12

Table S396. Gene #74: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 42(18Q23) MUTATED	151	53.0 (16.1)
DEL PEAK 42(18Q23) WILD-TYPE	931	50.4 (15.7)

Figure S396. Get High-res Image Gene #74: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'Time to Death'

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

Table S397. Gene #75: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 43(19Q13.41) MUTATED	363	131	0.0 - 182.3 (18.7)
DEL PEAK 43(19Q13.41) WILD-TYPE	716	460	0.1 - 211.2 (14.3)

Figure S397. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

'del_19q13.41' versus 'YEARS_TO_BIRTH'

P value = 4.16e-08 (Wilcoxon-test), Q value = 2.5e-07

Table S398. Gene #75: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 43(19Q13.41) MUTATED	365	47.3 (14.6)
DEL PEAK 43(19Q13.41) WILD-TYPE	717	52.6 (16.1)

Figure S398. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'TUMOR_TISSUE_SITE'

P value = 3.95e-34 (Fisher's exact test), Q value = 7e-33

Table S399. Gene #75: 'del_19q13.41' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 43(19Q13.41) MUTATED	99	267
DEL PEAK 43(19Q13.41) WILD-TYPE	472	245

Figure S399. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_19q13.41' versus 'RADIATION_THERAPY'

P value = 1.35e-08 (Fisher's exact test), Q value = 8.5e-08

Table S400. Gene #75: 'del_19q13.41' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 43(19Q13.41) MUTATED	124	218
DEL PEAK 43(19Q13.41) WILD-TYPE	134	549

Figure S400. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.41' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 5.97e-05 (Wilcoxon-test), Q value = 0.00021

Table S401. Gene #75: 'del_19q13.41' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 43(19Q13.41) MUTATED	238	84.3 (13.2)
DEL PEAK 43(19Q13.41) WILD-TYPE	492	79.8 (15.2)

Figure S401. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.41' versus 'HISTOLOGICAL_TYPE'

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

Table S402. Gene #75: 'del_19q13.41' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 43(19Q13.41) MUTATED	54	3	60	153	4	92
DEL PEAK 43(19Q13.41) WILD-TYPE	140	25	69	36	14	433

Figure S402. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_19q13.41' versus 'ETHNICITY'

P value = 0.146 (Fisher's exact test), Q value = 0.25

Table S403. Gene #75: 'del_19q13.41' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 43(19Q13.41) MUTATED	20	316
DEL PEAK 43(19Q13.41) WILD-TYPE	24	603

Figure S403. Get High-res Image Gene #75: 'del_19q13.41' versus Clinical Feature #9: 'ETHNICITY'

'del_19q13.43' versus 'Time to Death'

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

Table S404. Gene #76: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 44(19Q13.43) MUTATED	351	116	0.0 - 182.3 (20.0)
DEL PEAK 44(19Q13.43) WILD-TYPE	728	475	0.1 - 211.2 (14.2)

Figure S404. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

'del_19q13.43' versus 'YEARS_TO_BIRTH'

P value = 4.72e-14 (Wilcoxon-test), Q value = 5e-13

Table S405. Gene #76: 'del_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 44(19Q13.43) MUTATED	353	45.7 (14.5)
DEL PEAK 44(19Q13.43) WILD-TYPE	729	53.2 (15.8)

Figure S405. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.43' versus 'TUMOR_TISSUE_SITE'

P value = 2.06e-41 (Fisher's exact test), Q value = 4.2e-40

Table S406. Gene #76: 'del_19q13.43' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 44(19Q13.43) MUTATED	84	270
DEL PEAK 44(19Q13.43) WILD-TYPE	487	242

Figure S406. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_19q13.43' versus 'RADIATION_THERAPY'

P value = 1.43e-09 (Fisher's exact test), Q value = 9.9e-09

Table S407. Gene #76: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 44(19Q13.43) MUTATED	124	208
DEL PEAK 44(19Q13.43) WILD-TYPE	134	559

Figure S407. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.43' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 4.12e-06 (Wilcoxon-test), Q value = 2.2e-05

Table S408. Gene #76: 'del_19q13.43' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 44(19Q13.43) MUTATED	234	84.7 (13.4)
DEL PEAK 44(19Q13.43) WILD-TYPE	496	79.7 (15.0)

Figure S408. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19q13.43' versus 'HISTOLOGICAL_TYPE'

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

Table S409. Gene #76: 'del_19q13.43' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 44(19Q13.43) MUTATED	58	4	62	150	4	76
DEL PEAK 44(19Q13.43) WILD-TYPE	136	24	67	39	14	449

Figure S409. Get High-res Image Gene #76: 'del_19q13.43' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'Time to Death'

P value = 1.61e-11 (logrank test), Q value = 1.4e-10

Table S410. Gene #77: 'del_22q13.32' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	1079	591	0.0 - 211.2 (15.7)
DEL PEAK 45(22Q13.32) MUTATED	289	213	0.1 - 156.2 (15.1)
DEL PEAK 45(22Q13.32) WILD-TYPE	790	378	0.0 - 211.2 (16.0)

Figure S410. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #1: 'Time to Death'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 1.31e-10 (Wilcoxon-test), Q value = 1e-09

Table S411. Gene #77: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 45(22Q13.32) MUTATED	289	55.7 (15.6)
DEL PEAK 45(22Q13.32) WILD-TYPE	793	49.0 (15.5)

Figure S411. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'TUMOR_TISSUE_SITE'

P value = 1.22e-16 (Fisher's exact test), Q value = 1.7e-15

Table S412. Gene #77: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	BRAIN	CENTRAL NERVOUS SYSTEM
ALL	571	512
DEL PEAK 45(22Q13.32) MUTATED	212	77
DEL PEAK 45(22Q13.32) WILD-TYPE	359	435

Figure S412. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_22q13.32' versus 'RADIATION_THERAPY'

P value = 0.000173 (Fisher's exact test), Q value = 0.00058

Table S413. Gene #77: 'del_22q13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	258	767
DEL PEAK 45(22Q13.32) MUTATED	46	228
DEL PEAK 45(22Q13.32) WILD-TYPE	212	539

Figure S413. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_22q13.32' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00307 (Wilcoxon-test), Q value = 0.0086

Table S414. Gene #77: 'del_22q13.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 45(22Q13.32) MUTATED	205	79.2 (14.9)
DEL PEAK 45(22Q13.32) WILD-TYPE	525	82.1 (14.5)

Figure S414. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

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

Table S415. Gene #77: 'del_22q13.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	GLIOBLASTOMA MULTIFORME (GBM)	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	194	28	129	189	18	525
DEL PEAK 45(22Q13.32) MUTATED	43	10	16	18	6	196
DEL PEAK 45(22Q13.32) WILD-TYPE	151	18	113	171	12	329

Figure S415. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #7: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'ETHNICITY'

P value = 0.117 (Fisher's exact test), Q value = 0.2

Table S416. Gene #77: 'del_22q13.32' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	44	919
DEL PEAK 45(22Q13.32) MUTATED	7	247
DEL PEAK 45(22Q13.32) WILD-TYPE	37	672

Figure S416. Get High-res Image Gene #77: 'del_22q13.32' versus Clinical Feature #9: 'ETHNICITY'

'del_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0388 (Wilcoxon-test), Q value = 0.08

Table S417. Gene #79: 'del_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	1082	50.8 (15.8)
DEL PEAK 47(XQ21.1) MUTATED	183	52.8 (15.9)
DEL PEAK 47(XQ21.1) WILD-TYPE	899	50.4 (15.7)

Figure S417. Get High-res Image Gene #79: 'del_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xq21.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0989 (Wilcoxon-test), Q value = 0.18

Table S418. Gene #79: 'del_xq21.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	730	81.3 (14.7)
DEL PEAK 47(XQ21.1) MUTATED	128	78.9 (16.1)
DEL PEAK 47(XQ21.1) WILD-TYPE	602	81.8 (14.3)

Figure S418. Get High-res Image Gene #79: 'del_xq21.1' versus Clinical Feature #6: 'KARNOFSKY_PERFORMANCE_SCORE'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/19791525/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBMLGG-TP/19775190/GBMLGG-TP.merged_data.txt
Number of patients = 1083
Number of significantly focal cnvs = 79
Number of selected clinical features = 9
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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