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

Brain Lower Grade Glioma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1HQ3XSK

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 52 focal events and 8 clinical features across 430 patients, 31 significant findings detected with Q value < 0.25.

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_10p15.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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 'Time to Death' and '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_19q13.41 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_19q13.42 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_22q13.31 cnv correlated to 'Time to Death'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 52 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 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	123 (29%)	307	2.57e-11 (1.07e-08)	8.01e-06 (0.00323)	0.0416 (1.00)	0.158 (1.00)	4e-05 (0.0157)	0.896 (1.00)	0.223 (1.00)	0.787 (1.00)
amp 7p11 2	104 (24%)	326	1.73e-08 (7.14e-06)	1.62e-08 (6.71e-06)	0.259 (1.00)	0.115 (1.00)	0.0212 (1.00)	0.334 (1.00)	0.111 (1.00)	1 (1.00)
del 1p36 32	177 (41%)	253	0.0987 (1.00)	2.33e-06 (0.000955)	0.622 (1.00)	0.691 (1.00)	1e-05 (0.00402)	0.0401 (1.00)	0.3 (1.00)	1 (1.00)
del 1p32 3	168 (39%)	262	0.00802 (1.00)	6.32e-06 (0.00256)	0.766 (1.00)	0.559 (1.00)	1e-05 (0.00402)	0.00484 (1.00)	0.491 (1.00)	1 (1.00)
del 6q22 31	62 (14%)	368	2.97e-06 (0.00121)	0.138 (1.00)	0.68 (1.00)	0.0681 (1.00)	1e-05 (0.00402)	0.309 (1.00)	0.141 (1.00)	1 (1.00)
del 6q24 3	66 (15%)	364	6.9e-05 (0.027)	0.461 (1.00)	0.346 (1.00)	0.0681 (1.00)	2e-05 (0.0079)	0.321 (1.00)	0.146 (1.00)	0.719 (1.00)
del 9p21 3	145 (34%)	285	3.99e-10 (1.65e-07)	2.82e-06 (0.00115)	0.355 (1.00)	0.00322 (1.00)	0.0026 (0.972)	0.0164 (1.00)	0.727 (1.00)	1 (1.00)
amp 1q32 1	36 (8%)	394	0.00395 (1.00)	4.22e-06 (0.00172)	1 (1.00)	0.0561 (1.00)	0.226 (1.00)	0.284 (1.00)	0.312 (1.00)	0.381 (1.00)
amp 3q26 33	18 (4%)	412	0.0004 (0.155)	0.141 (1.00)	0.342 (1.00)	0.157 (1.00)	0.00817 (1.00)	0.229 (1.00)	0.0645 (1.00)	1 (1.00)
amp 7q31 2	148 (34%)	282	0.00151 (0.572)	7.85e-06 (0.00317)	0.0832 (1.00)	0.469 (1.00)	0.0377 (1.00)	0.616 (1.00)	0.0967 (1.00)	0.796 (1.00)
amp 7q32 3	153 (36%)	277	0.00395 (1.00)	1.51e-06 (0.000621)	0.0678 (1.00)	0.608 (1.00)	0.0476 (1.00)	0.456 (1.00)	0.133 (1.00)	0.794 (1.00)
amp 10p15 3	57 (13%)	373	0.819 (1.00)	0.00144 (0.548)	0.153 (1.00)	0.111 (1.00)	0.00045 (0.175)	0.0354 (1.00)	1 (1.00)	0.249 (1.00)
amp 12q14 1	29 (7%)	401	4.72e-08 (1.94e-05)	0.00123 (0.472)	0.701 (1.00)	0.49 (1.00)	0.0211 (1.00)	0.477 (1.00)	0.228 (1.00)	1 (1.00)
amp 19p13 3	111 (26%)	319	0.572 (1.00)	0.0434 (1.00)	0.825 (1.00)	0.677 (1.00)	1e-05 (0.00402)	0.684 (1.00)	0.826 (1.00)	0.772 (1.00)
amp 19p13 2	104 (24%)	326	0.947 (1.00)	0.0115 (1.00)	0.428 (1.00)	0.476 (1.00)	1e-05 (0.00402)	1 (1.00)	0.762 (1.00)	0.555 (1.00)
del 5q34	53 (12%)	377	0.033 (1.00)	0.462 (1.00)	0.883 (1.00)	0.316 (1.00)	3e-05 (0.0118)	0.0727 (1.00)	0.442 (1.00)	0.706 (1.00)
del 6p25 3	41 (10%)	389	6.13e-06 (0.00249)	0.24 (1.00)	1 (1.00)	0.046 (1.00)	0.159 (1.00)	0.84 (1.00)	0.0933 (1.00)	0.655 (1.00)
del 9p23	122 (28%)	308	0.000463 (0.179)	0.00476 (1.00)	0.668 (1.00)	0.035 (1.00)	0.014 (1.00)	0.0248 (1.00)	0.675 (1.00)	1 (1.00)
del 11p15 5	84 (20%)	346	0.25 (1.00)	0.0627 (1.00)	0.0659 (1.00)	0.104 (1.00)	0.0001 (0.039)	0.454 (1.00)	0.729 (1.00)	1 (1.00)
del 14q24 3	100 (23%)	330	4.79e-05 (0.0188)	0.0269 (1.00)	0.206 (1.00)	0.222 (1.00)	0.105 (1.00)	0.778 (1.00)	0.241 (1.00)	1 (1.00)
del 19q13 41	227 (53%)	203	0.029 (1.00)	0.0186 (1.00)	0.771 (1.00)	0.66 (1.00)	1e-05 (0.00402)	0.721 (1.00)	0.79 (1.00)	0.611 (1.00)
del 19q13 42	234 (54%)	196	0.00143 (0.547)	0.114 (1.00)	1 (1.00)	0.786 (1.00)	1e-05 (0.00402)	1 (1.00)	0.759 (1.00)	0.449 (1.00)
del 22q13 31	61 (14%)	369	0.000612 (0.236)	0.00351 (1.00)	0.487 (1.00)	0.0985 (1.00)	0.00347 (1.00)	0.612 (1.00)	0.176 (1.00)	0.71 (1.00)
amp 1q22	37 (9%)	393	0.133 (1.00)	0.00149 (0.564)	0.864 (1.00)	0.328 (1.00)	0.438 (1.00)	0.394 (1.00)	0.527 (1.00)	0.38 (1.00)
amp 2p24 3	19 (4%)	411	0.393 (1.00)	0.508 (1.00)	0.485 (1.00)	0.632 (1.00)	0.0868 (1.00)	0.775 (1.00)	1 (1.00)	0.128 (1.00)
amp 4q12	25 (6%)	405	0.0682 (1.00)	0.427 (1.00)	1 (1.00)	0.515 (1.00)	0.00222 (0.832)	0.799 (1.00)	0.731 (1.00)	1 (1.00)
amp 8q24 13	83 (19%)	347	0.707 (1.00)	0.111 (1.00)	0.391 (1.00)	0.301 (1.00)	0.00154 (0.582)	0.88 (1.00)	0.779 (1.00)	1 (1.00)
amp 9q34 3	40 (9%)	390	0.61 (1.00)	0.894 (1.00)	0.0941 (1.00)	0.149 (1.00)	0.0382 (1.00)	0.538 (1.00)	0.0757 (1.00)	0.184 (1.00)
amp 11q24 1	73 (17%)	357	0.791 (1.00)	0.2 (1.00)	0.366 (1.00)	0.989 (1.00)	0.495 (1.00)	0.634 (1.00)	0.677 (1.00)	0.326 (1.00)
amp 12p13 32	57 (13%)	373	0.371 (1.00)	0.0659 (1.00)	0.0863 (1.00)	0.557 (1.00)	0.236 (1.00)	0.0354 (1.00)	0.893 (1.00)	0.708 (1.00)
amp 13q34	21 (5%)	409	0.396 (1.00)	0.748 (1.00)	0.656 (1.00)	0.113 (1.00)	0.557 (1.00)	1 (1.00)	0.651 (1.00)	0.564 (1.00)
amp 15q26 3	14 (3%)	416	0.0043 (1.00)	0.827 (1.00)	1 (1.00)	0.119 (1.00)	0.0743 (1.00)	0.501 (1.00)	1 (1.00)	0.414 (1.00)
amp 17q25 1	35 (8%)	395	0.0161 (1.00)	0.0926 (1.00)	1 (1.00)	0.699 (1.00)	0.189 (1.00)	0.67 (1.00)	0.158 (1.00)	0.368 (1.00)
amp xp11 22	35 (8%)	395	0.853 (1.00)	0.216 (1.00)	1 (1.00)	0.905 (1.00)	0.0352 (1.00)	0.126 (1.00)	0.201 (1.00)	1 (1.00)
amp xp11 22	50 (12%)	380	0.543 (1.00)	0.526 (1.00)	0.289 (1.00)	0.601 (1.00)	0.00091 (0.35)	0.353 (1.00)	0.752 (1.00)	1 (1.00)
del 1q43	23 (5%)	407	0.964 (1.00)	0.544 (1.00)	0.519 (1.00)	0.964 (1.00)	0.302 (1.00)	1 (1.00)	0.339 (1.00)	1 (1.00)
del 2q37 3	61 (14%)	369	0.693 (1.00)	0.0823 (1.00)	0.33 (1.00)	0.834 (1.00)	0.026 (1.00)	0.399 (1.00)	0.485 (1.00)	0.717 (1.00)
del 3p21 31	36 (8%)	394	0.214 (1.00)	0.992 (1.00)	1 (1.00)	0.00207 (0.779)	0.599 (1.00)	0.135 (1.00)	0.799 (1.00)	0.153 (1.00)
del 3q13 31	29 (7%)	401	0.00317 (1.00)	0.58 (1.00)	0.0319 (1.00)	0.452 (1.00)	0.693 (1.00)	0.159 (1.00)	1 (1.00)	0.307 (1.00)
del 3q29	35 (8%)	395	0.0204 (1.00)	0.542 (1.00)	0.287 (1.00)	0.247 (1.00)	0.188 (1.00)	0.513 (1.00)	0.63 (1.00)	0.631 (1.00)
del 4q34 3	114 (27%)	316	0.701 (1.00)	0.127 (1.00)	0.51 (1.00)	0.512 (1.00)	0.841 (1.00)	0.177 (1.00)	0.662 (1.00)	1 (1.00)
del 5p15 33	39 (9%)	391	0.925 (1.00)	0.202 (1.00)	0.313 (1.00)	0.0446 (1.00)	0.00464 (1.00)	0.00675 (1.00)	0.69 (1.00)	1 (1.00)
del 7p22 3	19 (4%)	411	0.192 (1.00)	0.943 (1.00)	1 (1.00)	0.751 (1.00)	0.916 (1.00)	1 (1.00)	0.37 (1.00)	1 (1.00)
del 8q24 3	23 (5%)	407	0.597 (1.00)	0.695 (1.00)	0.83 (1.00)	0.732 (1.00)	0.229 (1.00)	0.595 (1.00)	0.447 (1.00)	0.0498 (1.00)
del 11p15 1	60 (14%)	370	0.0671 (1.00)	0.305 (1.00)	0.161 (1.00)	0.0249 (1.00)	0.00106 (0.407)	0.392 (1.00)	0.708 (1.00)	1 (1.00)
del 12p13 1	33 (8%)	397	0.0148 (1.00)	0.71 (1.00)	0.858 (1.00)	0.469 (1.00)	0.0596 (1.00)	0.37 (1.00)	0.777 (1.00)	0.621 (1.00)
del 12q12	59 (14%)	371	0.787 (1.00)	0.683 (1.00)	0.323 (1.00)	0.539 (1.00)	0.00194 (0.731)	1 (1.00)	0.467 (1.00)	0.143 (1.00)
del 13q14 2	120 (28%)	310	0.0135 (1.00)	0.74 (1.00)	0.196 (1.00)	0.0092 (1.00)	0.0967 (1.00)	0.112 (1.00)	0.378 (1.00)	0.573 (1.00)
del 13q14 2	122 (28%)	308	0.0193 (1.00)	0.751 (1.00)	0.236 (1.00)	0.00949 (1.00)	0.0763 (1.00)	0.147 (1.00)	0.385 (1.00)	0.574 (1.00)
del 13q34	90 (21%)	340	0.0222 (1.00)	0.379 (1.00)	0.404 (1.00)	0.207 (1.00)	0.942 (1.00)	0.241 (1.00)	0.4 (1.00)	1 (1.00)
del 18q23	66 (15%)	364	0.725 (1.00)	0.0255 (1.00)	0.283 (1.00)	0.899 (1.00)	0.545 (1.00)	0.624 (1.00)	0.181 (1.00)	0.717 (1.00)
del xq21 1	58 (13%)	372	0.0625 (1.00)	0.0541 (1.00)	1 (1.00)	0.928 (1.00)	0.656 (1.00)	1 (1.00)	0.42 (1.00)	0.707 (1.00)

'amp_1q32.1' versus 'AGE'

P value = 4.22e-06 (Wilcoxon-test), Q value = 0.0017

Table S1. Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
AMP PEAK 2(1Q32.1) MUTATED	36	53.1 (12.7)
AMP PEAK 2(1Q32.1) WILD-TYPE	393	42.1 (12.9)

Figure S1. Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

'amp_3q26.33' versus 'Time to Death'

P value = 4e-04 (logrank test), Q value = 0.16

Table S2. Gene #4: 'amp_3q26.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
AMP PEAK 4(3Q26.33) MUTATED	17	6	0.1 - 47.8 (12.0)
AMP PEAK 4(3Q26.33) WILD-TYPE	410	69	0.0 - 211.2 (16.0)

Figure S2. 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 = 1.73e-08 (logrank test), Q value = 7.1e-06

Table S3. Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
AMP PEAK 6(7P11.2) MUTATED	104	37	0.1 - 211.2 (14.0)
AMP PEAK 6(7P11.2) WILD-TYPE	323	38	0.0 - 182.3 (16.4)

Figure S3. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 1.62e-08 (Wilcoxon-test), Q value = 6.7e-06

Table S4. Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
AMP PEAK 6(7P11.2) MUTATED	104	49.6 (13.5)
AMP PEAK 6(7P11.2) WILD-TYPE	325	40.9 (12.5)

Figure S4. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q31.2' versus 'AGE'

P value = 7.85e-06 (Wilcoxon-test), Q value = 0.0032

Table S5. Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
AMP PEAK 7(7Q31.2) MUTATED	148	47.0 (13.3)
AMP PEAK 7(7Q31.2) WILD-TYPE	281	40.9 (12.8)

Figure S5. Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

'amp_7q32.3' versus 'AGE'

P value = 1.51e-06 (Wilcoxon-test), Q value = 0.00062

Table S6. Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
AMP PEAK 8(7Q32.3) MUTATED	153	47.1 (13.1)
AMP PEAK 8(7Q32.3) WILD-TYPE	276	40.7 (12.8)

Figure S6. Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

'amp_10p15.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S7. Gene #11: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
AMP PEAK 11(10P15.3) MUTATED	29	19	9
AMP PEAK 11(10P15.3) WILD-TYPE	130	88	155

Figure S7. Get High-res Image Gene #11: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'amp_12q14.1' versus 'Time to Death'

P value = 4.72e-08 (logrank test), Q value = 1.9e-05

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
AMP PEAK 14(12Q14.1) MUTATED	29	13	1.2 - 80.0 (12.2)
AMP PEAK 14(12Q14.1) WILD-TYPE	398	62	0.0 - 211.2 (16.2)

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 = 0.004

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
AMP PEAK 18(19P13.3) MUTATED	22	25	64
AMP PEAK 18(19P13.3) WILD-TYPE	137	82	100

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 = 0.004

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
AMP PEAK 19(19P13.2) MUTATED	20	21	63
AMP PEAK 19(19P13.2) WILD-TYPE	139	86	101

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

'del_1p36.32' versus 'AGE'

P value = 2.33e-06 (Wilcoxon-test), Q value = 0.00095

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

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
DEL PEAK 1(1P36.32) MUTATED	176	46.4 (12.5)
DEL PEAK 1(1P36.32) WILD-TYPE	253	40.6 (13.3)

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 = 0.004

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 1(1P36.32) MUTATED	18	38	121
DEL PEAK 1(1P36.32) WILD-TYPE	141	69	43

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

'del_1p32.3' versus 'AGE'

P value = 6.32e-06 (Wilcoxon-test), Q value = 0.0026

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

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
DEL PEAK 2(1P32.3) MUTATED	167	46.5 (12.9)
DEL PEAK 2(1P32.3) WILD-TYPE	262	40.7 (13.0)

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 = 0.004

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 2(1P32.3) MUTATED	12	35	121
DEL PEAK 2(1P32.3) WILD-TYPE	147	72	43

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

'del_5q34' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S15. Gene #31: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 10(5Q34) MUTATED	34	11	8
DEL PEAK 10(5Q34) WILD-TYPE	125	96	156

Figure S15. Get High-res Image Gene #31: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 6.13e-06 (logrank test), Q value = 0.0025

Table S16. Gene #32: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 11(6P25.3) MUTATED	40	14	0.2 - 94.5 (17.5)
DEL PEAK 11(6P25.3) WILD-TYPE	387	61	0.0 - 211.2 (15.5)

Figure S16. Get High-res Image Gene #32: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'Time to Death'

P value = 2.97e-06 (logrank test), Q value = 0.0012

Table S17. Gene #33: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 12(6Q22.31) MUTATED	61	20	0.1 - 117.4 (15.0)
DEL PEAK 12(6Q22.31) WILD-TYPE	366	55	0.0 - 211.2 (16.1)

Figure S17. Get High-res Image Gene #33: '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 = 0.004

Table S18. Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 12(6Q22.31) MUTATED	40	11	11
DEL PEAK 12(6Q22.31) WILD-TYPE	119	96	153

Figure S18. Get High-res Image Gene #33: 'del_6q22.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6q24.3' versus 'Time to Death'

P value = 6.9e-05 (logrank test), Q value = 0.027

Table S19. Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 13(6Q24.3) MUTATED	65	20	0.0 - 130.8 (15.0)
DEL PEAK 13(6Q24.3) WILD-TYPE	362	55	0.1 - 211.2 (16.2)

Figure S19. Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #1: 'Time to Death'

'del_6q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0079

Table S20. Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 13(6Q24.3) MUTATED	41	12	13
DEL PEAK 13(6Q24.3) WILD-TYPE	118	95	151

Figure S20. Get High-res Image Gene #34: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'Time to Death'

P value = 0.000463 (logrank test), Q value = 0.18

Table S21. Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 16(9P23) MUTATED	121	31	0.1 - 164.4 (17.3)
DEL PEAK 16(9P23) WILD-TYPE	306	44	0.0 - 211.2 (15.8)

Figure S21. Get High-res Image Gene #37: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'Time to Death'

P value = 3.99e-10 (logrank test), Q value = 1.7e-07

Table S22. Gene #38: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 17(9P21.3) MUTATED	144	44	0.1 - 164.4 (14.8)
DEL PEAK 17(9P21.3) WILD-TYPE	283	31	0.0 - 211.2 (16.0)

Figure S22. Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'AGE'

P value = 2.82e-06 (Wilcoxon-test), Q value = 0.0012

Table S23. Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
DEL PEAK 17(9P21.3) MUTATED	144	47.3 (13.7)
DEL PEAK 17(9P21.3) WILD-TYPE	285	40.8 (12.5)

Figure S23. Get High-res Image Gene #38: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'Time to Death'

P value = 2.57e-11 (logrank test), Q value = 1.1e-08

Table S24. Gene #39: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 18(10Q26.3) MUTATED	122	46	0.1 - 156.2 (14.6)
DEL PEAK 18(10Q26.3) WILD-TYPE	305	29	0.0 - 211.2 (16.4)

Figure S24. Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'AGE'

P value = 8.01e-06 (Wilcoxon-test), Q value = 0.0032

Table S25. Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
DEL PEAK 18(10Q26.3) MUTATED	123	47.7 (13.8)
DEL PEAK 18(10Q26.3) WILD-TYPE	306	41.1 (12.5)

Figure S25. Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.016

Table S26. Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 18(10Q26.3) MUTATED	66	26	31
DEL PEAK 18(10Q26.3) WILD-TYPE	93	81	133

Figure S26. Get High-res Image Gene #39: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_11p15.5' versus 'HISTOLOGICAL.TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.039

Table S27. Gene #40: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 19(11P15.5) MUTATED	45	23	16
DEL PEAK 19(11P15.5) WILD-TYPE	114	84	148

Figure S27. Get High-res Image Gene #40: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_14q24.3' versus 'Time to Death'

P value = 4.79e-05 (logrank test), Q value = 0.019

Table S28. Gene #47: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 26(14Q24.3) MUTATED	98	31	0.1 - 130.8 (16.7)
DEL PEAK 26(14Q24.3) WILD-TYPE	329	44	0.0 - 211.2 (15.4)

Figure S28. Get High-res Image Gene #47: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

'del_19q13.41' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S29. Gene #49: 'del_19q13.41' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 28(19Q13.41) MUTATED	46	49	132
DEL PEAK 28(19Q13.41) WILD-TYPE	113	58	32

Figure S29. Get High-res Image Gene #49: 'del_19q13.41' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_19q13.42' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S30. Gene #50: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
DEL PEAK 29(19Q13.42) MUTATED	49	52	133
DEL PEAK 29(19Q13.42) WILD-TYPE	110	55	31

Figure S30. Get High-res Image Gene #50: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_22q13.31' versus 'Time to Death'

P value = 0.000612 (logrank test), Q value = 0.24

Table S31. Gene #51: 'del_22q13.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
DEL PEAK 30(22Q13.31) MUTATED	61	23	0.1 - 156.2 (18.0)
DEL PEAK 30(22Q13.31) WILD-TYPE	366	52	0.0 - 211.2 (15.4)

Figure S31. Get High-res Image Gene #51: 'del_22q13.31' versus Clinical Feature #1: 'Time to Death'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LGG-TP.merged_data.txt
Number of patients = 430
Number of significantly focal cnvs = 52
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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