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

Glioblastoma Multiforme (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/C1C53JQC

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 71 focal events and 8 clinical features across 565 patients, 15 significant findings detected with Q value < 0.25.

amp_7p11.2 cnv correlated to 'Time to Death' and 'AGE'.
amp_7q11.21 cnv correlated to 'Time to Death' and 'AGE'.
amp_7q21.2 cnv correlated to 'AGE'.
del_9p21.3 cnv correlated to 'AGE'.
del_10p15.3 cnv correlated to 'Time to Death' and 'AGE'.
del_10p13 cnv correlated to 'Time to Death' and 'AGE'.
del_10p11.23 cnv correlated to 'Time to Death' and 'AGE'.
del_10q23.31 cnv correlated to 'Time to Death' and 'AGE'.
del_10q26.3 cnv correlated to 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 71 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 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
amp 7p11 2	496 (88%)	69	4.56e-07 (0.000256)	2.67e-12 (1.52e-09)	0.357 (1.00)	0.0692 (1.00)	0.0557 (1.00)	0.0992 (1.00)	0.44 (1.00)	0.0595 (1.00)
amp 7q11 21	454 (80%)	111	3.98e-05 (0.0221)	2.11e-07 (0.000119)	0.278 (1.00)	0.503 (1.00)	0.00869 (1.00)	0.115 (1.00)	0.269 (1.00)	0.14 (1.00)
del 10p15 3	459 (81%)	106	3.74e-06 (0.00209)	2.35e-08 (1.33e-05)	0.185 (1.00)	0.512 (1.00)	0.0179 (1.00)	0.646 (1.00)	0.176 (1.00)	0.274 (1.00)
del 10p13	460 (81%)	105	2.36e-06 (0.00132)	4.88e-08 (2.76e-05)	0.0599 (1.00)	0.847 (1.00)	0.00668 (1.00)	0.908 (1.00)	0.119 (1.00)	0.27 (1.00)
del 10p11 23	465 (82%)	100	1.07e-07 (6.05e-05)	1.79e-10 (1.02e-07)	0.143 (1.00)	0.128 (1.00)	0.00255 (1.00)	0.814 (1.00)	0.152 (1.00)	0.251 (1.00)
del 10q23 31	502 (89%)	63	1.69e-05 (0.00941)	2.12e-07 (0.000119)	0.785 (1.00)	0.0807 (1.00)	0.0099 (1.00)	1 (1.00)	0.345 (1.00)	0.637 (1.00)
amp 7q21 2	469 (83%)	96	0.000455 (0.252)	7.5e-06 (0.00418)	0.492 (1.00)	0.4 (1.00)	0.0992 (1.00)	0.152 (1.00)	0.0389 (1.00)	0.0442 (1.00)
del 9p21 3	412 (73%)	153	0.0175 (1.00)	5.87e-05 (0.0325)	0.44 (1.00)	0.15 (1.00)	0.584 (1.00)	0.364 (1.00)	0.784 (1.00)	0.746 (1.00)
del 10q26 3	503 (89%)	62	0.0011 (0.605)	8.56e-06 (0.00477)	0.68 (1.00)	0.082 (1.00)	0.0337 (1.00)	1 (1.00)	0.095 (1.00)	0.634 (1.00)
amp 1p36 21	91 (16%)	474	0.0549 (1.00)	0.275 (1.00)	0.483 (1.00)	0.193 (1.00)	0.0314 (1.00)	0.716 (1.00)	0.125 (1.00)	0.402 (1.00)
amp 1q32 1	156 (28%)	409	0.415 (1.00)	0.187 (1.00)	0.923 (1.00)	0.382 (1.00)	0.923 (1.00)	0.764 (1.00)	0.934 (1.00)	0.527 (1.00)
amp 1q44	98 (17%)	467	0.331 (1.00)	0.958 (1.00)	0.213 (1.00)	0.535 (1.00)	0.262 (1.00)	0.554 (1.00)	0.784 (1.00)	0.428 (1.00)
amp 2p24 3	49 (9%)	516	0.207 (1.00)	0.271 (1.00)	0.445 (1.00)	0.934 (1.00)	1 (1.00)	0.874 (1.00)	0.397 (1.00)	0.612 (1.00)
amp 3q26 33	108 (19%)	457	0.254 (1.00)	0.0324 (1.00)	0.662 (1.00)	0.728 (1.00)	0.00208 (1.00)	1 (1.00)	0.206 (1.00)	0.701 (1.00)
amp 4p16 3	48 (8%)	517	0.817 (1.00)	0.843 (1.00)	0.356 (1.00)	0.368 (1.00)	0.902 (1.00)	0.748 (1.00)	0.835 (1.00)	1 (1.00)
amp 4q12	106 (19%)	459	0.391 (1.00)	0.186 (1.00)	0.323 (1.00)	0.815 (1.00)	0.399 (1.00)	0.303 (1.00)	0.667 (1.00)	1 (1.00)
amp 7q31 2	462 (82%)	103	0.00727 (1.00)	0.00159 (0.878)	0.318 (1.00)	0.999 (1.00)	0.249 (1.00)	0.0487 (1.00)	0.0489 (1.00)	0.0552 (1.00)
amp 8q24 21	70 (12%)	495	0.278 (1.00)	0.434 (1.00)	0.516 (1.00)	0.948 (1.00)	1 (1.00)	0.786 (1.00)	0.119 (1.00)	1 (1.00)
amp 11p13	30 (5%)	535	0.963 (1.00)	0.274 (1.00)	1 (1.00)	0.583 (1.00)	0.496 (1.00)	1 (1.00)	0.762 (1.00)	0.519 (1.00)
amp 12p13 32	83 (15%)	482	0.878 (1.00)	0.232 (1.00)	0.904 (1.00)	0.697 (1.00)	0.877 (1.00)	0.526 (1.00)	0.506 (1.00)	0.687 (1.00)
amp 12q14 1	132 (23%)	433	0.303 (1.00)	0.662 (1.00)	0.417 (1.00)	0.93 (1.00)	0.506 (1.00)	0.75 (1.00)	0.762 (1.00)	0.31 (1.00)
amp 12q15	92 (16%)	473	0.76 (1.00)	0.57 (1.00)	0.353 (1.00)	0.993 (1.00)	0.942 (1.00)	0.467 (1.00)	0.632 (1.00)	0.23 (1.00)
amp 13q34	32 (6%)	533	0.854 (1.00)	0.682 (1.00)	0.36 (1.00)	0.545 (1.00)	0.36 (1.00)	0.699 (1.00)	0.885 (1.00)	1 (1.00)
amp 13q34	30 (5%)	535	0.852 (1.00)	0.409 (1.00)	0.568 (1.00)	0.399 (1.00)	0.5 (1.00)	0.843 (1.00)	0.39 (1.00)	1 (1.00)
amp 14q32 33	36 (6%)	529	0.451 (1.00)	0.00547 (1.00)	0.486 (1.00)	0.316 (1.00)	0.351 (1.00)	0.856 (1.00)	0.902 (1.00)	1 (1.00)
amp 17p13 2	50 (9%)	515	0.552 (1.00)	0.61 (1.00)	0.175 (1.00)	0.939 (1.00)	0.656 (1.00)	0.636 (1.00)	0.769 (1.00)	1 (1.00)
amp 17q25 1	82 (15%)	483	0.0314 (1.00)	0.0122 (1.00)	0.143 (1.00)	0.46 (1.00)	0.821 (1.00)	0.61 (1.00)	0.159 (1.00)	0.691 (1.00)
amp 19p13 3	238 (42%)	327	0.215 (1.00)	0.61 (1.00)	0.931 (1.00)	0.151 (1.00)	0.531 (1.00)	1 (1.00)	0.393 (1.00)	0.571 (1.00)
amp 19p13 2	243 (43%)	322	0.143 (1.00)	0.948 (1.00)	1 (1.00)	0.516 (1.00)	0.464 (1.00)	0.928 (1.00)	0.737 (1.00)	0.77 (1.00)
amp 19q12	210 (37%)	355	0.428 (1.00)	0.612 (1.00)	0.534 (1.00)	0.939 (1.00)	0.757 (1.00)	0.853 (1.00)	0.791 (1.00)	0.383 (1.00)
amp 21q21 1	68 (12%)	497	0.674 (1.00)	0.0136 (1.00)	1 (1.00)	0.368 (1.00)	0.24 (1.00)	0.49 (1.00)	0.0776 (1.00)	0.377 (1.00)
del 1p36 32	96 (17%)	469	0.977 (1.00)	0.625 (1.00)	0.0292 (1.00)	0.64 (1.00)	0.223 (1.00)	0.812 (1.00)	0.116 (1.00)	0.7 (1.00)
del 1p36 23	129 (23%)	436	0.507 (1.00)	0.173 (1.00)	0.0102 (1.00)	0.0601 (1.00)	0.077 (1.00)	0.336 (1.00)	0.126 (1.00)	0.313 (1.00)
del 1p32 3	60 (11%)	505	0.557 (1.00)	0.0559 (1.00)	0.126 (1.00)	0.62 (1.00)	0.711 (1.00)	0.144 (1.00)	0.296 (1.00)	1 (1.00)
del 1p22 1	47 (8%)	518	0.542 (1.00)	0.362 (1.00)	1 (1.00)	0.353 (1.00)	0.0909 (1.00)	0.518 (1.00)	0.912 (1.00)	1 (1.00)
del 1q42 11	48 (8%)	517	0.1 (1.00)	0.372 (1.00)	0.878 (1.00)	0.0457 (1.00)	1 (1.00)	0.197 (1.00)	0.508 (1.00)	0.245 (1.00)
del 1q44	34 (6%)	531	0.5 (1.00)	0.324 (1.00)	1 (1.00)	0.309 (1.00)	0.746 (1.00)	0.71 (1.00)	0.872 (1.00)	0.478 (1.00)
del 2q22 1	46 (8%)	519	0.352 (1.00)	0.0953 (1.00)	0.431 (1.00)	0.593 (1.00)	0.118 (1.00)	0.0696 (1.00)	0.284 (1.00)	0.611 (1.00)
del 2q37 1	54 (10%)	511	0.988 (1.00)	0.743 (1.00)	0.187 (1.00)	0.632 (1.00)	1 (1.00)	0.29 (1.00)	0.535 (1.00)	1 (1.00)
del 3p21 1	52 (9%)	513	0.0205 (1.00)	0.025 (1.00)	0.882 (1.00)	0.78 (1.00)	0.18 (1.00)	0.0305 (1.00)	0.613 (1.00)	0.333 (1.00)
del 3q13 31	56 (10%)	509	0.654 (1.00)	0.394 (1.00)	0.567 (1.00)	0.239 (1.00)	0.625 (1.00)	0.231 (1.00)	0.431 (1.00)	0.352 (1.00)
del 3q22 1	58 (10%)	507	0.657 (1.00)	0.382 (1.00)	1 (1.00)	0.439 (1.00)	0.637 (1.00)	0.658 (1.00)	0.252 (1.00)	0.371 (1.00)
del 3q29	65 (12%)	500	0.343 (1.00)	0.563 (1.00)	1 (1.00)	0.325 (1.00)	0.854 (1.00)	0.263 (1.00)	1 (1.00)	1 (1.00)
del 4p16 3	76 (13%)	489	0.489 (1.00)	0.0892 (1.00)	0.256 (1.00)	0.358 (1.00)	0.365 (1.00)	0.0872 (1.00)	0.573 (1.00)	0.66 (1.00)
del 4q34 3	91 (16%)	474	0.183 (1.00)	0.112 (1.00)	0.0462 (1.00)	0.714 (1.00)	0.835 (1.00)	0.181 (1.00)	0.167 (1.00)	1 (1.00)
del 5q34	66 (12%)	499	0.0433 (1.00)	0.386 (1.00)	0.182 (1.00)	0.727 (1.00)	0.787 (1.00)	0.577 (1.00)	0.15 (1.00)	0.155 (1.00)
del 6q22 31	157 (28%)	408	0.0561 (1.00)	0.223 (1.00)	0.0835 (1.00)	0.546 (1.00)	0.503 (1.00)	1 (1.00)	0.365 (1.00)	0.193 (1.00)
del 6q26	178 (32%)	387	0.101 (1.00)	0.898 (1.00)	0.196 (1.00)	0.982 (1.00)	0.23 (1.00)	0.772 (1.00)	0.749 (1.00)	0.354 (1.00)
del 8p23 2	66 (12%)	499	0.231 (1.00)	0.0416 (1.00)	0.286 (1.00)	0.312 (1.00)	0.785 (1.00)	0.78 (1.00)	0.0248 (1.00)	0.376 (1.00)
del 9q34 2	76 (13%)	489	0.998 (1.00)	0.953 (1.00)	1 (1.00)	0.7 (1.00)	0.315 (1.00)	0.793 (1.00)	0.623 (1.00)	0.231 (1.00)
del 11p15 5	128 (23%)	437	0.0222 (1.00)	0.00886 (1.00)	0.258 (1.00)	0.204 (1.00)	0.498 (1.00)	0.749 (1.00)	1 (1.00)	1 (1.00)
del 11p11 2	104 (18%)	461	0.0789 (1.00)	0.794 (1.00)	0.268 (1.00)	0.624 (1.00)	0.264 (1.00)	0.817 (1.00)	0.696 (1.00)	1 (1.00)
del 11q14 1	96 (17%)	469	0.97 (1.00)	0.539 (1.00)	0.359 (1.00)	0.785 (1.00)	0.44 (1.00)	0.12 (1.00)	1 (1.00)	0.7 (1.00)
del 12p13 1	71 (13%)	494	0.111 (1.00)	0.991 (1.00)	0.437 (1.00)	0.405 (1.00)	0.469 (1.00)	0.282 (1.00)	0.188 (1.00)	1 (1.00)
del 12q12	74 (13%)	491	0.475 (1.00)	0.621 (1.00)	0.8 (1.00)	0.999 (1.00)	0.595 (1.00)	0.598 (1.00)	0.308 (1.00)	0.653 (1.00)
del 12q15	77 (14%)	488	0.648 (1.00)	0.521 (1.00)	0.531 (1.00)	0.292 (1.00)	0.867 (1.00)	0.299 (1.00)	0.309 (1.00)	0.207 (1.00)
del 13q14 2	237 (42%)	328	0.936 (1.00)	0.667 (1.00)	0.601 (1.00)	0.783 (1.00)	0.514 (1.00)	0.649 (1.00)	0.461 (1.00)	1 (1.00)
del 13q22 1	225 (40%)	340	0.898 (1.00)	0.873 (1.00)	1 (1.00)	0.252 (1.00)	0.443 (1.00)	0.41 (1.00)	0.869 (1.00)	0.378 (1.00)
del 14q13 1	174 (31%)	391	0.563 (1.00)	0.481 (1.00)	0.113 (1.00)	0.528 (1.00)	0.449 (1.00)	0.497 (1.00)	0.265 (1.00)	0.119 (1.00)
del 14q24 2	170 (30%)	395	0.787 (1.00)	0.597 (1.00)	0.26 (1.00)	0.834 (1.00)	0.334 (1.00)	0.434 (1.00)	0.632 (1.00)	1 (1.00)
del 15q14	148 (26%)	417	0.287 (1.00)	0.0242 (1.00)	0.696 (1.00)	0.969 (1.00)	0.686 (1.00)	0.475 (1.00)	0.165 (1.00)	0.323 (1.00)
del 16p12 2	92 (16%)	473	0.0534 (1.00)	0.211 (1.00)	0.353 (1.00)	0.527 (1.00)	0.517 (1.00)	0.333 (1.00)	0.668 (1.00)	1 (1.00)
del 16q23 1	99 (18%)	466	0.0103 (1.00)	0.746 (1.00)	0.821 (1.00)	0.151 (1.00)	0.844 (1.00)	0.0248 (1.00)	0.421 (1.00)	0.703 (1.00)
del 17p13 2	84 (15%)	481	0.831 (1.00)	0.656 (1.00)	0.229 (1.00)	0.309 (1.00)	1 (1.00)	0.706 (1.00)	0.766 (1.00)	1 (1.00)
del 17p13 1	94 (17%)	471	0.373 (1.00)	0.128 (1.00)	0.0652 (1.00)	0.995 (1.00)	0.744 (1.00)	0.228 (1.00)	0.952 (1.00)	1 (1.00)
del 17q11 2	69 (12%)	496	0.322 (1.00)	0.616 (1.00)	0.794 (1.00)	0.388 (1.00)	1 (1.00)	0.0764 (1.00)	0.77 (1.00)	1 (1.00)
del 18q22 3	81 (14%)	484	0.587 (1.00)	0.59 (1.00)	0.902 (1.00)	0.17 (1.00)	0.818 (1.00)	0.702 (1.00)	0.405 (1.00)	0.399 (1.00)
del 19q13 41	99 (18%)	466	0.0399 (1.00)	0.469 (1.00)	0.821 (1.00)	0.574 (1.00)	0.757 (1.00)	0.723 (1.00)	0.383 (1.00)	1 (1.00)
del 21q21 1	55 (10%)	510	0.92 (1.00)	0.537 (1.00)	1 (1.00)	0.573 (1.00)	1 (1.00)	0.228 (1.00)	0.854 (1.00)	0.362 (1.00)
del 22q13 32	211 (37%)	354	0.971 (1.00)	0.185 (1.00)	0.859 (1.00)	0.466 (1.00)	0.903 (1.00)	0.711 (1.00)	0.294 (1.00)	1 (1.00)
del xp22 2	116 (21%)	449	0.32 (1.00)	0.591 (1.00)	0.916 (1.00)	0.372 (1.00)	0.952 (1.00)	0.912 (1.00)	0.605 (1.00)	0.474 (1.00)

'amp_7p11.2' versus 'Time to Death'

P value = 4.56e-07 (logrank test), Q value = 0.00026

Table S1. Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
AMP PEAK 8(7P11.2) MUTATED	496	414	0.1 - 127.6 (9.5)
AMP PEAK 8(7P11.2) WILD-TYPE	69	48	0.2 - 108.8 (14.9)

Figure S1. Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 2.67e-12 (Wilcoxon-test), Q value = 1.5e-09

Table S2. Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
AMP PEAK 8(7P11.2) MUTATED	496	59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE	69	43.2 (18.9)

Figure S2. Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q11.21' versus 'Time to Death'

P value = 3.98e-05 (logrank test), Q value = 0.022

Table S3. Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
AMP PEAK 9(7Q11.21) MUTATED	454	376	0.1 - 127.6 (9.4)
AMP PEAK 9(7Q11.21) WILD-TYPE	111	86	0.2 - 108.8 (13.6)

Figure S3. Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

'amp_7q11.21' versus 'AGE'

P value = 2.11e-07 (Wilcoxon-test), Q value = 0.00012

Table S4. Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
AMP PEAK 9(7Q11.21) MUTATED	454	59.8 (12.5)
AMP PEAK 9(7Q11.21) WILD-TYPE	111	49.3 (18.7)

Figure S4. Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'AGE'

'amp_7q21.2' versus 'AGE'

P value = 7.5e-06 (Wilcoxon-test), Q value = 0.0042

Table S5. Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
AMP PEAK 10(7Q21.2) MUTATED	469	59.5 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE	96	49.4 (19.9)

Figure S5. Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

'del_9p21.3' versus 'AGE'

P value = 5.87e-05 (Wilcoxon-test), Q value = 0.033

Table S6. Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 19(9P21.3) MUTATED	412	59.2 (13.8)
DEL PEAK 19(9P21.3) WILD-TYPE	153	53.9 (15.7)

Figure S6. Get High-res Image Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10p15.3' versus 'Time to Death'

P value = 3.74e-06 (logrank test), Q value = 0.0021

Table S7. Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
DEL PEAK 21(10P15.3) MUTATED	459	383	0.1 - 92.7 (9.9)
DEL PEAK 21(10P15.3) WILD-TYPE	106	79	0.1 - 127.6 (11.7)

Figure S7. Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'AGE'

P value = 2.35e-08 (Wilcoxon-test), Q value = 1.3e-05

Table S8. Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 21(10P15.3) MUTATED	459	59.8 (12.6)
DEL PEAK 21(10P15.3) WILD-TYPE	106	49.0 (18.5)

Figure S8. Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

'del_10p13' versus 'Time to Death'

P value = 2.36e-06 (logrank test), Q value = 0.0013

Table S9. Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
DEL PEAK 22(10P13) MUTATED	460	384	0.1 - 92.7 (9.9)
DEL PEAK 22(10P13) WILD-TYPE	105	78	0.1 - 127.6 (11.5)

Figure S9. Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'AGE'

P value = 4.88e-08 (Wilcoxon-test), Q value = 2.8e-05

Table S10. Gene #47: 'del_10p13' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 22(10P13) MUTATED	460	59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE	105	48.9 (19.1)

Figure S10. Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #2: 'AGE'

'del_10p11.23' versus 'Time to Death'

P value = 1.07e-07 (logrank test), Q value = 6.1e-05

Table S11. Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
DEL PEAK 23(10P11.23) MUTATED	465	388	0.1 - 92.7 (9.7)
DEL PEAK 23(10P11.23) WILD-TYPE	100	74	0.1 - 127.6 (12.8)

Figure S11. Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'AGE'

P value = 1.79e-10 (Wilcoxon-test), Q value = 1e-07

Table S12. Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 23(10P11.23) MUTATED	465	60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE	100	47.5 (18.8)

Figure S12. Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

'del_10q23.31' versus 'Time to Death'

P value = 1.69e-05 (logrank test), Q value = 0.0094

Table S13. Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
DEL PEAK 24(10Q23.31) MUTATED	502	416	0.1 - 127.6 (9.9)
DEL PEAK 24(10Q23.31) WILD-TYPE	63	46	0.2 - 108.8 (12.7)

Figure S13. Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'AGE'

P value = 2.12e-07 (Wilcoxon-test), Q value = 0.00012

Table S14. Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 24(10Q23.31) MUTATED	502	59.1 (13.3)
DEL PEAK 24(10Q23.31) WILD-TYPE	63	47.2 (18.6)

Figure S14. Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'AGE'

P value = 8.56e-06 (Wilcoxon-test), Q value = 0.0048

Table S15. Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
DEL PEAK 25(10Q26.3) MUTATED	503	58.9 (13.5)
DEL PEAK 25(10Q26.3) WILD-TYPE	62	48.3 (18.7)

Figure S15. Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = GBM-TP.merged_data.txt
Number of patients = 565
Number of significantly focal cnvs = 71
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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