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

Brain Lower Grade Glioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1N29VPC

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 50 focal events and 8 clinical features across 400 patients, 28 significant findings detected with Q value < 0.25.

amp_1q22 cnv correlated to 'AGE'.
amp_1q32.1 cnv correlated to 'AGE'.
amp_3q26.33 cnv correlated to 'Time to Death'.
amp_7p11.2 cnv correlated to 'Time to Death' and 'AGE'.
amp_7q31.2 cnv correlated to 'AGE'.
amp_7q32.3 cnv correlated to 'AGE'.
amp_12q14.1 cnv correlated to 'Time to Death'.
amp_19p13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
amp_19p13.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_1p36.32 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_1p32.3 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_5q34 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_6p25.3 cnv correlated to 'Time to Death'.
del_6q22.31 cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.
del_6q24.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_9p23 cnv correlated to 'Time to Death'.
del_9p21.3 cnv correlated to 'Time to Death' and 'AGE'.
del_10q26.3 cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
del_11p15.5 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_14q24.3 cnv correlated to 'Time to Death'.
del_19q13.42 cnv correlated to 'HISTOLOGICAL.TYPE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 50 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 10q26 3	116 (29%)	284	1.17e-09 (4.68e-07)	5.34e-06 (0.00209)	0.149 (1.00)	0.162 (1.00)	0.00011 (0.0414)	1 (1.00)	0.153 (1.00)	0.776 (1.00)
amp 7p11 2	101 (25%)	299	1.74e-06 (0.000682)	4.85e-08 (1.92e-05)	0.204 (1.00)	0.0922 (1.00)	0.0316 (1.00)	0.491 (1.00)	0.0628 (1.00)	1 (1.00)
del 1p36 32	166 (42%)	234	0.234 (1.00)	5.49e-06 (0.00214)	0.474 (1.00)	0.743 (1.00)	1e-05 (0.00389)	0.0377 (1.00)	0.171 (1.00)	1 (1.00)
del 1p32 3	157 (39%)	243	0.0236 (1.00)	3.3e-05 (0.0126)	0.606 (1.00)	0.626 (1.00)	1e-05 (0.00389)	0.00317 (1.00)	0.541 (1.00)	1 (1.00)
del 6q22 31	58 (14%)	342	5.26e-05 (0.0199)	0.13 (1.00)	0.887 (1.00)	0.164 (1.00)	1e-05 (0.00389)	0.307 (1.00)	0.16 (1.00)	1 (1.00)
del 9p21 3	132 (33%)	268	1.52e-11 (6.07e-09)	5.02e-07 (0.000199)	0.915 (1.00)	0.00499 (1.00)	0.00148 (0.543)	0.0102 (1.00)	1 (1.00)	0.781 (1.00)
amp 1q22	35 (9%)	365	0.0277 (1.00)	0.000658 (0.246)	0.86 (1.00)	0.248 (1.00)	0.402 (1.00)	0.394 (1.00)	0.26 (1.00)	0.38 (1.00)
amp 1q32 1	34 (8%)	366	0.00324 (1.00)	9.91e-07 (0.000392)	1 (1.00)	0.0334 (1.00)	0.191 (1.00)	0.287 (1.00)	0.155 (1.00)	0.628 (1.00)
amp 3q26 33	17 (4%)	383	0.000369 (0.139)	0.132 (1.00)	0.465 (1.00)	0.212 (1.00)	0.00082 (0.303)	0.229 (1.00)	0.0482 (1.00)	1 (1.00)
amp 7q31 2	138 (34%)	262	0.00147 (0.54)	3.53e-06 (0.00138)	0.0902 (1.00)	0.458 (1.00)	0.0408 (1.00)	0.613 (1.00)	0.0877 (1.00)	1 (1.00)
amp 7q32 3	144 (36%)	256	0.00403 (1.00)	1.1e-06 (0.000433)	0.0467 (1.00)	0.592 (1.00)	0.0422 (1.00)	0.456 (1.00)	0.124 (1.00)	1 (1.00)
amp 12q14 1	29 (7%)	371	4.27e-08 (1.7e-05)	0.00175 (0.64)	0.699 (1.00)	0.408 (1.00)	0.0126 (1.00)	0.354 (1.00)	0.123 (1.00)	1 (1.00)
amp 19p13 3	103 (26%)	297	0.729 (1.00)	0.0306 (1.00)	0.818 (1.00)	0.486 (1.00)	1e-05 (0.00389)	0.681 (1.00)	0.667 (1.00)	0.552 (1.00)
amp 19p13 2	98 (24%)	302	0.739 (1.00)	0.0118 (1.00)	0.351 (1.00)	0.324 (1.00)	1e-05 (0.00389)	0.889 (1.00)	0.644 (1.00)	0.541 (1.00)
del 5q34	51 (13%)	349	0.0289 (1.00)	0.48 (1.00)	1 (1.00)	0.331 (1.00)	5e-05 (0.0189)	0.105 (1.00)	0.495 (1.00)	0.704 (1.00)
del 6p25 3	39 (10%)	361	2.29e-05 (0.00878)	0.152 (1.00)	0.737 (1.00)	0.0674 (1.00)	0.0522 (1.00)	0.842 (1.00)	0.086 (1.00)	0.646 (1.00)
del 6q24 3	61 (15%)	339	0.000794 (0.295)	0.423 (1.00)	0.577 (1.00)	0.164 (1.00)	4e-05 (0.0152)	0.247 (1.00)	0.199 (1.00)	1 (1.00)
del 9p23	110 (28%)	290	4.16e-05 (0.0158)	0.0038 (1.00)	1 (1.00)	0.0553 (1.00)	0.00773 (1.00)	0.0149 (1.00)	0.521 (1.00)	0.768 (1.00)
del 11p15 5	78 (20%)	322	0.337 (1.00)	0.0505 (1.00)	0.0309 (1.00)	0.0829 (1.00)	0.00067 (0.25)	0.449 (1.00)	1 (1.00)	1 (1.00)
del 14q24 3	94 (24%)	306	6.59e-05 (0.0249)	0.0393 (1.00)	0.287 (1.00)	0.316 (1.00)	0.104 (1.00)	0.777 (1.00)	0.213 (1.00)	0.535 (1.00)
del 19q13 42	216 (54%)	184	0.00652 (1.00)	0.166 (1.00)	0.841 (1.00)	0.788 (1.00)	1e-05 (0.00389)	1 (1.00)	0.843 (1.00)	0.609 (1.00)
amp 2p24 3	16 (4%)	384	0.163 (1.00)	0.498 (1.00)	1 (1.00)	0.767 (1.00)	0.102 (1.00)	1 (1.00)	1 (1.00)	0.0907 (1.00)
amp 4q12	21 (5%)	379	0.0329 (1.00)	0.37 (1.00)	1 (1.00)	0.58 (1.00)	0.0144 (1.00)	1 (1.00)	0.616 (1.00)	0.569 (1.00)
amp 8q24 13	77 (19%)	323	0.758 (1.00)	0.258 (1.00)	0.25 (1.00)	0.206 (1.00)	0.00151 (0.553)	0.763 (1.00)	0.863 (1.00)	1 (1.00)
amp 9q34 3	39 (10%)	361	0.537 (1.00)	0.925 (1.00)	0.126 (1.00)	0.113 (1.00)	0.0374 (1.00)	0.55 (1.00)	0.147 (1.00)	0.177 (1.00)
amp 10p15 3	52 (13%)	348	0.813 (1.00)	0.000875 (0.323)	0.295 (1.00)	0.143 (1.00)	0.00068 (0.253)	0.0308 (1.00)	1 (1.00)	0.119 (1.00)
amp 11q24 1	71 (18%)	329	0.801 (1.00)	0.18 (1.00)	0.357 (1.00)	0.832 (1.00)	0.396 (1.00)	0.434 (1.00)	0.844 (1.00)	0.324 (1.00)
amp 12p13 32	56 (14%)	344	0.394 (1.00)	0.0611 (1.00)	0.0598 (1.00)	0.456 (1.00)	0.133 (1.00)	0.0589 (1.00)	0.449 (1.00)	0.706 (1.00)
amp 13q34	20 (5%)	380	0.384 (1.00)	0.834 (1.00)	0.492 (1.00)	0.0866 (1.00)	0.679 (1.00)	1 (1.00)	0.576 (1.00)	0.55 (1.00)
amp 15q26 3	14 (4%)	386	0.00178 (0.649)	0.77 (1.00)	1 (1.00)	0.103 (1.00)	0.0646 (1.00)	0.523 (1.00)	1 (1.00)	0.418 (1.00)
amp 17q25 1	33 (8%)	367	0.00892 (1.00)	0.192 (1.00)	1 (1.00)	0.632 (1.00)	0.282 (1.00)	0.666 (1.00)	0.183 (1.00)	0.342 (1.00)
amp xp11 22	32 (8%)	368	0.842 (1.00)	0.147 (1.00)	0.715 (1.00)	0.994 (1.00)	0.104 (1.00)	0.118 (1.00)	0.242 (1.00)	1 (1.00)
amp xp11 22	47 (12%)	353	0.528 (1.00)	0.659 (1.00)	0.211 (1.00)	0.643 (1.00)	0.00253 (0.913)	0.353 (1.00)	0.372 (1.00)	1 (1.00)
del 1q43	20 (5%)	380	0.746 (1.00)	0.65 (1.00)	0.359 (1.00)	0.559 (1.00)	0.0943 (1.00)	0.784 (1.00)	0.279 (1.00)	0.569 (1.00)
del 2q37 3	59 (15%)	341	0.651 (1.00)	0.0344 (1.00)	0.32 (1.00)	0.975 (1.00)	0.0165 (1.00)	0.503 (1.00)	0.536 (1.00)	0.713 (1.00)
del 3p21 31	33 (8%)	367	0.151 (1.00)	0.78 (1.00)	0.857 (1.00)	0.00219 (0.794)	0.848 (1.00)	0.126 (1.00)	0.708 (1.00)	0.128 (1.00)
del 3q29	34 (8%)	366	0.0285 (1.00)	0.636 (1.00)	0.367 (1.00)	0.192 (1.00)	0.192 (1.00)	0.522 (1.00)	0.488 (1.00)	0.373 (1.00)
del 4q34 3	109 (27%)	291	0.611 (1.00)	0.131 (1.00)	0.734 (1.00)	0.676 (1.00)	0.713 (1.00)	0.225 (1.00)	0.624 (1.00)	1 (1.00)
del 5p15 33	37 (9%)	363	0.793 (1.00)	0.157 (1.00)	0.299 (1.00)	0.0665 (1.00)	0.00307 (1.00)	0.0111 (1.00)	0.54 (1.00)	1 (1.00)
del 7p22 3	16 (4%)	384	0.233 (1.00)	0.892 (1.00)	0.319 (1.00)	0.617 (1.00)	0.77 (1.00)	0.762 (1.00)	1 (1.00)	1 (1.00)
del 8q24 3	21 (5%)	379	0.445 (1.00)	0.514 (1.00)	0.823 (1.00)	0.642 (1.00)	0.17 (1.00)	0.431 (1.00)	0.18 (1.00)	0.0395 (1.00)
del 12p13 1	31 (8%)	369	0.00472 (1.00)	0.469 (1.00)	0.577 (1.00)	0.51 (1.00)	0.0521 (1.00)	0.369 (1.00)	0.694 (1.00)	0.615 (1.00)
del 12q12	51 (13%)	349	0.986 (1.00)	0.33 (1.00)	0.454 (1.00)	0.583 (1.00)	0.00541 (1.00)	0.721 (1.00)	0.484 (1.00)	0.234 (1.00)
del 13q14 2	112 (28%)	288	0.0103 (1.00)	0.749 (1.00)	0.179 (1.00)	0.0157 (1.00)	0.153 (1.00)	0.11 (1.00)	0.278 (1.00)	0.569 (1.00)
del 13q14 2	114 (28%)	286	0.0151 (1.00)	0.766 (1.00)	0.182 (1.00)	0.0159 (1.00)	0.118 (1.00)	0.144 (1.00)	0.284 (1.00)	0.568 (1.00)
del 13q34	86 (22%)	314	0.0236 (1.00)	0.714 (1.00)	0.391 (1.00)	0.332 (1.00)	0.94 (1.00)	0.305 (1.00)	0.208 (1.00)	1 (1.00)
del 15q21 3	48 (12%)	352	0.272 (1.00)	0.231 (1.00)	1 (1.00)	0.905 (1.00)	1 (1.00)	0.585 (1.00)	1 (1.00)	0.233 (1.00)
del 18q23	64 (16%)	336	0.761 (1.00)	0.0292 (1.00)	0.412 (1.00)	0.962 (1.00)	0.466 (1.00)	0.87 (1.00)	0.236 (1.00)	0.713 (1.00)
del 22q13 31	59 (15%)	341	0.00198 (0.719)	0.00562 (1.00)	0.67 (1.00)	0.105 (1.00)	0.00535 (1.00)	0.737 (1.00)	0.217 (1.00)	0.706 (1.00)
del xq21 1	55 (14%)	345	0.114 (1.00)	0.0507 (1.00)	0.884 (1.00)	0.898 (1.00)	0.521 (1.00)	1 (1.00)	0.511 (1.00)	0.704 (1.00)

'amp_1q22' versus 'AGE'

P value = 0.000658 (Wilcoxon-test), Q value = 0.25

Table S1. Gene #1: 'amp_1q22' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
AMP PEAK 1(1Q22) MUTATED	35	50.6 (13.1)
AMP PEAK 1(1Q22) WILD-TYPE	365	42.5 (13.2)

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #2: 'AGE'

'amp_1q32.1' versus 'AGE'

P value = 9.91e-07 (Wilcoxon-test), Q value = 0.00039

Table S2. Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
AMP PEAK 2(1Q32.1) MUTATED	34	54.2 (12.1)
AMP PEAK 2(1Q32.1) WILD-TYPE	366	42.2 (13.0)

Figure S2. Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

'amp_3q26.33' versus 'Time to Death'

P value = 0.000369 (logrank test), Q value = 0.14

Table S3. Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
AMP PEAK 4(3Q26.33) MUTATED	16	6	0.2 - 47.8 (11.3)
AMP PEAK 4(3Q26.33) WILD-TYPE	379	65	0.0 - 211.2 (15.1)

Figure S3. Get High-res Image Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'Time to Death'

P value = 1.74e-06 (logrank test), Q value = 0.00068

Table S4. Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
AMP PEAK 6(7P11.2) MUTATED	100	34	0.1 - 211.2 (13.6)
AMP PEAK 6(7P11.2) WILD-TYPE	295	37	0.0 - 182.3 (15.1)

Figure S4. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 4.85e-08 (Wilcoxon-test), Q value = 1.9e-05

Table S5. Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
AMP PEAK 6(7P11.2) MUTATED	101	49.7 (13.5)
AMP PEAK 6(7P11.2) WILD-TYPE	299	41.1 (12.6)

Figure S5. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q31.2' versus 'AGE'

P value = 3.53e-06 (Wilcoxon-test), Q value = 0.0014

Table S6. Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
AMP PEAK 7(7Q31.2) MUTATED	138	47.6 (13.4)
AMP PEAK 7(7Q31.2) WILD-TYPE	262	41.0 (12.8)

Figure S6. Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

'amp_7q32.3' versus 'AGE'

P value = 1.1e-06 (Wilcoxon-test), Q value = 0.00043

Table S7. Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
AMP PEAK 8(7Q32.3) MUTATED	144	47.6 (13.2)
AMP PEAK 8(7Q32.3) WILD-TYPE	256	40.8 (12.8)

Figure S7. Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

'amp_12q14.1' versus 'Time to Death'

P value = 4.27e-08 (logrank test), Q value = 1.7e-05

Table S8. Gene #14: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
AMP PEAK 14(12Q14.1) MUTATED	29	13	1.2 - 80.0 (12.0)
AMP PEAK 14(12Q14.1) WILD-TYPE	366	58	0.0 - 211.2 (15.1)

Figure S8. Get High-res Image Gene #14: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_19p13.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S9. Gene #18: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
AMP PEAK 18(19P13.3) MUTATED	19	25	59
AMP PEAK 18(19P13.3) WILD-TYPE	124	79	94

Figure S9. Get High-res Image Gene #18: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'amp_19p13.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S10. Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
AMP PEAK 19(19P13.2) MUTATED	18	21	59
AMP PEAK 19(19P13.2) WILD-TYPE	125	83	94

Figure S10. Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_1p36.32' versus 'AGE'

P value = 5.49e-06 (Wilcoxon-test), Q value = 0.0021

Table S11. Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
DEL PEAK 1(1P36.32) MUTATED	166	46.6 (12.6)
DEL PEAK 1(1P36.32) WILD-TYPE	234	40.9 (13.4)

Figure S11. Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #2: 'AGE'

'del_1p36.32' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S12. Gene #22: 'del_1p36.32' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 1(1P36.32) MUTATED	18	36	112
DEL PEAK 1(1P36.32) WILD-TYPE	125	68	41

Figure S12. Get High-res Image Gene #22: 'del_1p36.32' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_1p32.3' versus 'AGE'

P value = 3.3e-05 (Wilcoxon-test), Q value = 0.013

Table S13. Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
DEL PEAK 2(1P32.3) MUTATED	157	46.6 (13.0)
DEL PEAK 2(1P32.3) WILD-TYPE	243	41.1 (13.1)

Figure S13. Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

'del_1p32.3' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S14. Gene #23: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 2(1P32.3) MUTATED	11	33	113
DEL PEAK 2(1P32.3) WILD-TYPE	132	71	40

Figure S14. Get High-res Image Gene #23: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_5q34' versus 'HISTOLOGICAL.TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.019

Table S15. Gene #30: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 9(5Q34) MUTATED	31	12	8
DEL PEAK 9(5Q34) WILD-TYPE	112	92	145

Figure S15. Get High-res Image Gene #30: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 2.29e-05 (logrank test), Q value = 0.0088

Table S16. Gene #31: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 10(6P25.3) MUTATED	37	13	0.2 - 94.5 (17.8)
DEL PEAK 10(6P25.3) WILD-TYPE	358	58	0.0 - 211.2 (14.8)

Figure S16. Get High-res Image Gene #31: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'Time to Death'

P value = 5.26e-05 (logrank test), Q value = 0.02

Table S17. Gene #32: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 11(6Q22.31) MUTATED	56	18	0.1 - 117.4 (15.9)
DEL PEAK 11(6Q22.31) WILD-TYPE	339	53	0.0 - 211.2 (14.7)

Figure S17. Get High-res Image Gene #32: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S18. Gene #32: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 11(6Q22.31) MUTATED	38	10	10
DEL PEAK 11(6Q22.31) WILD-TYPE	105	94	143

Figure S18. Get High-res Image Gene #32: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.015

Table S19. Gene #33: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 12(6Q24.3) MUTATED	38	11	12
DEL PEAK 12(6Q24.3) WILD-TYPE	105	93	141

Figure S19. Get High-res Image Gene #33: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'Time to Death'

P value = 4.16e-05 (logrank test), Q value = 0.016

Table S20. Gene #36: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 15(9P23) MUTATED	108	29	0.1 - 117.4 (14.5)
DEL PEAK 15(9P23) WILD-TYPE	287	42	0.0 - 211.2 (15.1)

Figure S20. Get High-res Image Gene #36: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'Time to Death'

P value = 1.52e-11 (logrank test), Q value = 6.1e-09

Table S21. Gene #37: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 16(9P21.3) MUTATED	130	41	0.1 - 117.4 (14.2)
DEL PEAK 16(9P21.3) WILD-TYPE	265	30	0.0 - 211.2 (15.3)

Figure S21. Get High-res Image Gene #37: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'AGE'

P value = 5.02e-07 (Wilcoxon-test), Q value = 2e-04

Table S22. Gene #37: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
DEL PEAK 16(9P21.3) MUTATED	132	48.1 (13.6)
DEL PEAK 16(9P21.3) WILD-TYPE	268	40.9 (12.6)

Figure S22. Get High-res Image Gene #37: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'Time to Death'

P value = 1.17e-09 (logrank test), Q value = 4.7e-07

Table S23. Gene #38: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 17(10Q26.3) MUTATED	114	43	0.1 - 156.2 (15.0)
DEL PEAK 17(10Q26.3) WILD-TYPE	281	28	0.0 - 211.2 (15.0)

Figure S23. Get High-res Image Gene #38: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'AGE'

P value = 5.34e-06 (Wilcoxon-test), Q value = 0.0021

Table S24. Gene #38: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
DEL PEAK 17(10Q26.3) MUTATED	116	48.2 (13.9)
DEL PEAK 17(10Q26.3) WILD-TYPE	284	41.2 (12.6)

Figure S24. Get High-res Image Gene #38: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.041

Table S25. Gene #38: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 17(10Q26.3) MUTATED	60	26	30
DEL PEAK 17(10Q26.3) WILD-TYPE	83	78	123

Figure S25. Get High-res Image Gene #38: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_11p15.5' versus 'HISTOLOGICAL.TYPE'

P value = 0.00067 (Fisher's exact test), Q value = 0.25

Table S26. Gene #39: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 18(11P15.5) MUTATED	39	23	16
DEL PEAK 18(11P15.5) WILD-TYPE	104	81	137

Figure S26. Get High-res Image Gene #39: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_14q24.3' versus 'Time to Death'

P value = 6.59e-05 (logrank test), Q value = 0.025

Table S27. Gene #45: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
DEL PEAK 24(14Q24.3) MUTATED	92	30	0.1 - 130.8 (15.9)
DEL PEAK 24(14Q24.3) WILD-TYPE	303	41	0.0 - 211.2 (14.7)

Figure S27. Get High-res Image Gene #45: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0039

Table S28. Gene #48: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
DEL PEAK 27(19Q13.42) MUTATED	43	49	124
DEL PEAK 27(19Q13.42) WILD-TYPE	100	55	29

Figure S28. Get High-res Image Gene #48: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LGG-TP.merged_data.txt
Number of patients = 400
Number of significantly focal cnvs = 50
Number of selected clinical features = 8
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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