Correlation between copy number variations of arm-level result 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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1GX49FS

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 80 arm-level events and 8 clinical features across 565 patients, 11 significant findings detected with Q value < 0.25.

7p gain cnv correlated to 'Time to Death' and 'AGE'.
7q gain cnv correlated to 'Time to Death' and 'AGE'.
10p gain cnv correlated to 'AGE'.
20p gain cnv correlated to 'AGE'.
20q gain cnv correlated to 'AGE'.
10p loss cnv correlated to 'Time to Death' and 'AGE'.
10q loss cnv correlated to 'Time to Death' and 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 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
7p gain	458 (81%)	107	0.000108 (0.0682)	4.34e-06 (0.00276)	0.827 (1.00)	0.853 (1.00)	0.0205 (1.00)	0.136 (1.00)	0.0536 (1.00)	0.27 (1.00)
7q gain	463 (82%)	102	0.000282 (0.177)	1.48e-05 (0.00942)	0.314 (1.00)	0.96 (1.00)	0.0301 (1.00)	0.103 (1.00)	0.0335 (1.00)	0.249 (1.00)
10p loss	472 (84%)	93	2.98e-05 (0.0189)	6.98e-09 (4.46e-06)	0.245 (1.00)	0.165 (1.00)	0.00488 (1.00)	0.629 (1.00)	0.105 (1.00)	0.132 (1.00)
10q loss	483 (85%)	82	7.54e-05 (0.0477)	5.06e-08 (3.23e-05)	0.541 (1.00)	0.0142 (1.00)	0.0411 (1.00)	0.799 (1.00)	0.0661 (1.00)	0.0902 (1.00)
10p gain	12 (2%)	553	0.00415 (1.00)	0.000204 (0.129)	0.0707 (1.00)	0.633 (1.00)	0.379 (1.00)	1 (1.00)	0.0292 (1.00)	0.265 (1.00)
20p gain	217 (38%)	348	0.486 (1.00)	4.6e-05 (0.0292)	0.33 (1.00)	0.54 (1.00)	0.353 (1.00)	0.407 (1.00)	0.025 (1.00)	1 (1.00)
20q gain	215 (38%)	350	0.669 (1.00)	0.00023 (0.145)	0.25 (1.00)	0.722 (1.00)	0.35 (1.00)	0.518 (1.00)	0.0376 (1.00)	1 (1.00)
1p gain	81 (14%)	484	0.219 (1.00)	0.469 (1.00)	0.624 (1.00)	0.24 (1.00)	0.0627 (1.00)	0.306 (1.00)	0.947 (1.00)	0.667 (1.00)
1q gain	88 (16%)	477	0.57 (1.00)	0.618 (1.00)	0.342 (1.00)	0.335 (1.00)	0.387 (1.00)	0.389 (1.00)	0.584 (1.00)	0.691 (1.00)
2p gain	37 (7%)	528	0.595 (1.00)	0.788 (1.00)	0.163 (1.00)	0.544 (1.00)	1 (1.00)	0.72 (1.00)	0.24 (1.00)	1 (1.00)
2q gain	36 (6%)	529	0.486 (1.00)	0.313 (1.00)	0.378 (1.00)	0.383 (1.00)	1 (1.00)	1 (1.00)	0.23 (1.00)	1 (1.00)
3p gain	56 (10%)	509	0.981 (1.00)	0.0251 (1.00)	0.391 (1.00)	0.888 (1.00)	0.264 (1.00)	1 (1.00)	0.922 (1.00)	1 (1.00)
3q gain	62 (11%)	503	0.734 (1.00)	0.0702 (1.00)	0.492 (1.00)	0.811 (1.00)	0.211 (1.00)	0.569 (1.00)	0.928 (1.00)	1 (1.00)
4p gain	36 (6%)	529	0.899 (1.00)	0.49 (1.00)	0.86 (1.00)	0.0747 (1.00)	1 (1.00)	0.586 (1.00)	0.549 (1.00)	0.58 (1.00)
4q gain	33 (6%)	532	0.968 (1.00)	0.561 (1.00)	0.467 (1.00)	0.0712 (1.00)	1 (1.00)	0.343 (1.00)	0.385 (1.00)	1 (1.00)
5p gain	49 (9%)	516	0.822 (1.00)	0.681 (1.00)	0.169 (1.00)	0.207 (1.00)	0.0568 (1.00)	0.751 (1.00)	1 (1.00)	0.303 (1.00)
5q gain	41 (7%)	524	0.657 (1.00)	0.529 (1.00)	0.134 (1.00)	0.736 (1.00)	0.0813 (1.00)	0.605 (1.00)	0.741 (1.00)	0.612 (1.00)
6p gain	24 (4%)	541	0.413 (1.00)	0.494 (1.00)	0.671 (1.00)	0.766 (1.00)	1 (1.00)	0.268 (1.00)	0.572 (1.00)	1 (1.00)
6q gain	23 (4%)	542	0.359 (1.00)	0.248 (1.00)	1 (1.00)	0.73 (1.00)	1 (1.00)	0.651 (1.00)	0.461 (1.00)	1 (1.00)
8p gain	52 (9%)	513	0.826 (1.00)	0.808 (1.00)	0.657 (1.00)	0.595 (1.00)	0.74 (1.00)	0.757 (1.00)	0.229 (1.00)	1 (1.00)
8q gain	59 (10%)	506	0.478 (1.00)	0.368 (1.00)	0.482 (1.00)	0.699 (1.00)	0.642 (1.00)	1 (1.00)	0.484 (1.00)	1 (1.00)
9p gain	47 (8%)	518	0.626 (1.00)	0.646 (1.00)	0.164 (1.00)	0.875 (1.00)	0.221 (1.00)	0.871 (1.00)	0.386 (1.00)	0.245 (1.00)
9q gain	70 (12%)	495	0.867 (1.00)	0.931 (1.00)	0.153 (1.00)	0.814 (1.00)	0.503 (1.00)	0.892 (1.00)	0.479 (1.00)	0.646 (1.00)
10q gain	3 (1%)	562	0.472 (1.00)	0.66 (1.00)	0.565 (1.00)		1 (1.00)	0.249 (1.00)	1 (1.00)	0.0734 (1.00)
11p gain	17 (3%)	548	0.6 (1.00)	0.955 (1.00)	0.806 (1.00)	0.374 (1.00)	1 (1.00)	0.6 (1.00)	0.595 (1.00)	0.338 (1.00)
11q gain	14 (2%)	551	0.147 (1.00)	0.116 (1.00)	0.267 (1.00)	0.164 (1.00)	0.435 (1.00)	0.162 (1.00)	1 (1.00)	0.302 (1.00)
12p gain	58 (10%)	507	0.635 (1.00)	0.416 (1.00)	0.571 (1.00)	0.789 (1.00)	0.767 (1.00)	0.461 (1.00)	0.853 (1.00)	1 (1.00)
12q gain	47 (8%)	518	0.981 (1.00)	0.786 (1.00)	0.279 (1.00)	0.936 (1.00)	0.522 (1.00)	0.518 (1.00)	0.0955 (1.00)	1 (1.00)
13q gain	10 (2%)	555	0.537 (1.00)	0.011 (1.00)	0.202 (1.00)	0.072 (1.00)	0.52 (1.00)	0.0859 (1.00)	0.675 (1.00)	1 (1.00)
14q gain	22 (4%)	543	0.256 (1.00)	0.0587 (1.00)	0.513 (1.00)	0.471 (1.00)	0.0737 (1.00)	0.817 (1.00)	1 (1.00)	1 (1.00)
15q gain	24 (4%)	541	0.495 (1.00)	0.883 (1.00)	0.527 (1.00)	0.0921 (1.00)	0.66 (1.00)	0.182 (1.00)	0.84 (1.00)	1 (1.00)
16p gain	38 (7%)	527	0.0323 (1.00)	0.851 (1.00)	0.306 (1.00)	0.957 (1.00)	1 (1.00)	0.0716 (1.00)	0.315 (1.00)	1 (1.00)
16q gain	37 (7%)	528	0.121 (1.00)	0.872 (1.00)	0.606 (1.00)	0.848 (1.00)	1 (1.00)	0.0714 (1.00)	0.266 (1.00)	1 (1.00)
17p gain	47 (8%)	518	0.227 (1.00)	0.0379 (1.00)	0.212 (1.00)	0.387 (1.00)	0.639 (1.00)	0.417 (1.00)	0.521 (1.00)	1 (1.00)
17q gain	58 (10%)	507	0.0362 (1.00)	0.0202 (1.00)	0.48 (1.00)	0.473 (1.00)	0.638 (1.00)	0.376 (1.00)	0.593 (1.00)	0.371 (1.00)
18p gain	57 (10%)	508	0.757 (1.00)	0.394 (1.00)	0.669 (1.00)	0.237 (1.00)	0.086 (1.00)	0.766 (1.00)	0.292 (1.00)	0.352 (1.00)
18q gain	57 (10%)	508	0.909 (1.00)	0.229 (1.00)	0.2 (1.00)	0.24 (1.00)	0.0864 (1.00)	0.551 (1.00)	0.498 (1.00)	1 (1.00)
19p gain	219 (39%)	346	0.383 (1.00)	0.806 (1.00)	0.791 (1.00)	0.979 (1.00)	0.619 (1.00)	0.854 (1.00)	0.578 (1.00)	0.55 (1.00)
19q gain	193 (34%)	372	0.446 (1.00)	0.588 (1.00)	0.586 (1.00)	0.884 (1.00)	0.929 (1.00)	0.571 (1.00)	0.33 (1.00)	0.355 (1.00)
21q gain	62 (11%)	503	0.598 (1.00)	0.106 (1.00)	1 (1.00)	0.125 (1.00)	0.141 (1.00)	1 (1.00)	0.106 (1.00)	0.376 (1.00)
22q gain	34 (6%)	531	0.419 (1.00)	0.576 (1.00)	1 (1.00)	0.322 (1.00)	0.399 (1.00)	1 (1.00)	0.686 (1.00)	0.151 (1.00)
xq gain	16 (3%)	549	0.846 (1.00)	0.557 (1.00)	1 (1.00)	0.619 (1.00)	0.313 (1.00)	0.174 (1.00)	0.733 (1.00)	0.246 (1.00)
1p loss	15 (3%)	550	0.281 (1.00)	0.0518 (1.00)	0.425 (1.00)	0.819 (1.00)	0.464 (1.00)	0.58 (1.00)	0.732 (1.00)	1 (1.00)
1q loss	14 (2%)	551	0.519 (1.00)	0.0265 (1.00)	1 (1.00)	0.17 (1.00)	1 (1.00)	0.4 (1.00)	0.712 (1.00)	1 (1.00)
2p loss	31 (5%)	534	0.819 (1.00)	0.0829 (1.00)	0.0877 (1.00)	0.844 (1.00)	1 (1.00)	0.324 (1.00)	0.671 (1.00)	1 (1.00)
2q loss	31 (5%)	534	0.996 (1.00)	0.111 (1.00)	0.185 (1.00)	0.572 (1.00)	0.52 (1.00)	0.166 (1.00)	0.673 (1.00)	1 (1.00)
3p loss	40 (7%)	525	0.291 (1.00)	0.0681 (1.00)	1 (1.00)	0.998 (1.00)	0.464 (1.00)	0.0827 (1.00)	0.583 (1.00)	0.207 (1.00)
3q loss	34 (6%)	531	0.766 (1.00)	0.652 (1.00)	0.589 (1.00)	0.636 (1.00)	0.745 (1.00)	0.572 (1.00)	0.697 (1.00)	0.519 (1.00)
4p loss	53 (9%)	512	0.752 (1.00)	0.733 (1.00)	0.184 (1.00)	0.258 (1.00)	0.416 (1.00)	0.541 (1.00)	0.577 (1.00)	0.303 (1.00)
4q loss	54 (10%)	511	0.214 (1.00)	0.122 (1.00)	0.771 (1.00)	0.305 (1.00)	1 (1.00)	0.76 (1.00)	0.587 (1.00)	0.284 (1.00)
5p loss	42 (7%)	523	0.056 (1.00)	0.518 (1.00)	1 (1.00)	0.567 (1.00)	0.48 (1.00)	0.0252 (1.00)	0.109 (1.00)	0.207 (1.00)
5q loss	43 (8%)	522	0.108 (1.00)	0.568 (1.00)	1 (1.00)	0.757 (1.00)	0.254 (1.00)	0.126 (1.00)	0.404 (1.00)	0.0499 (1.00)
6p loss	86 (15%)	479	0.00482 (1.00)	0.388 (1.00)	0.811 (1.00)	0.496 (1.00)	0.677 (1.00)	0.619 (1.00)	0.239 (1.00)	0.701 (1.00)
6q loss	124 (22%)	441	0.369 (1.00)	0.761 (1.00)	0.298 (1.00)	0.691 (1.00)	0.789 (1.00)	1 (1.00)	0.18 (1.00)	0.478 (1.00)
7p loss	8 (1%)	557	0.355 (1.00)	0.0522 (1.00)	1 (1.00)	0.741 (1.00)	1 (1.00)	0.448 (1.00)	0.592 (1.00)	1 (1.00)
7q loss	6 (1%)	559	0.528 (1.00)	0.0236 (1.00)	1 (1.00)	0.303 (1.00)	1 (1.00)	0.669 (1.00)	0.488 (1.00)	1 (1.00)
8p loss	58 (10%)	507	0.602 (1.00)	0.175 (1.00)	0.156 (1.00)	0.39 (1.00)	0.768 (1.00)	0.461 (1.00)	0.00535 (1.00)	0.62 (1.00)
8q loss	42 (7%)	523	0.201 (1.00)	0.211 (1.00)	0.416 (1.00)	0.245 (1.00)	1 (1.00)	0.866 (1.00)	0.304 (1.00)	1 (1.00)
9p loss	197 (35%)	368	0.71 (1.00)	0.547 (1.00)	0.652 (1.00)	0.525 (1.00)	0.81 (1.00)	0.707 (1.00)	0.437 (1.00)	0.064 (1.00)
9q loss	92 (16%)	473	0.578 (1.00)	0.741 (1.00)	0.414 (1.00)	0.77 (1.00)	0.211 (1.00)	0.716 (1.00)	0.226 (1.00)	0.234 (1.00)
11p loss	98 (17%)	467	0.184 (1.00)	0.948 (1.00)	0.111 (1.00)	0.759 (1.00)	0.449 (1.00)	0.636 (1.00)	0.652 (1.00)	0.7 (1.00)
11q loss	93 (16%)	472	0.904 (1.00)	0.361 (1.00)	0.419 (1.00)	0.773 (1.00)	1 (1.00)	0.276 (1.00)	1 (1.00)	0.229 (1.00)
12p loss	58 (10%)	507	0.999 (1.00)	0.62 (1.00)	0.48 (1.00)	0.778 (1.00)	0.835 (1.00)	0.461 (1.00)	0.298 (1.00)	1 (1.00)
12q loss	57 (10%)	508	0.96 (1.00)	0.667 (1.00)	0.568 (1.00)	0.611 (1.00)	0.518 (1.00)	1 (1.00)	0.291 (1.00)	0.333 (1.00)
13q loss	183 (32%)	382	0.75 (1.00)	0.715 (1.00)	1 (1.00)	0.76 (1.00)	0.594 (1.00)	0.701 (1.00)	0.5 (1.00)	0.759 (1.00)
14q loss	144 (25%)	421	0.976 (1.00)	0.689 (1.00)	0.429 (1.00)	0.881 (1.00)	0.546 (1.00)	0.758 (1.00)	0.199 (1.00)	0.311 (1.00)
15q loss	102 (18%)	463	0.712 (1.00)	0.0527 (1.00)	0.576 (1.00)	0.982 (1.00)	0.719 (1.00)	0.0799 (1.00)	0.516 (1.00)	0.249 (1.00)
16p loss	63 (11%)	502	0.042 (1.00)	0.312 (1.00)	0.683 (1.00)	0.862 (1.00)	0.279 (1.00)	0.045 (1.00)	1 (1.00)	1 (1.00)
16q loss	82 (15%)	483	0.015 (1.00)	0.83 (1.00)	1 (1.00)	0.599 (1.00)	0.59 (1.00)	0.0216 (1.00)	0.481 (1.00)	0.699 (1.00)
17p loss	62 (11%)	503	0.658 (1.00)	0.579 (1.00)	0.336 (1.00)	0.947 (1.00)	0.919 (1.00)	0.196 (1.00)	0.933 (1.00)	1 (1.00)
17q loss	40 (7%)	525	0.978 (1.00)	0.472 (1.00)	0.503 (1.00)	0.69 (1.00)	1 (1.00)	0.0527 (1.00)	0.591 (1.00)	0.591 (1.00)
18p loss	69 (12%)	496	0.129 (1.00)	0.73 (1.00)	0.602 (1.00)	0.601 (1.00)	0.682 (1.00)	1 (1.00)	0.325 (1.00)	0.646 (1.00)
18q loss	61 (11%)	504	0.3 (1.00)	0.682 (1.00)	0.89 (1.00)	0.278 (1.00)	0.777 (1.00)	0.248 (1.00)	0.199 (1.00)	0.143 (1.00)
19p loss	27 (5%)	538	0.548 (1.00)	0.948 (1.00)	1 (1.00)	0.749 (1.00)	0.843 (1.00)	0.835 (1.00)	1 (1.00)	1 (1.00)
19q loss	35 (6%)	530	0.661 (1.00)	0.877 (1.00)	1 (1.00)	0.766 (1.00)	0.335 (1.00)	1 (1.00)	0.794 (1.00)	1 (1.00)
20p loss	18 (3%)	547	0.857 (1.00)	0.382 (1.00)	0.219 (1.00)	0.92 (1.00)	1 (1.00)	1 (1.00)	0.287 (1.00)	0.338 (1.00)
20q loss	16 (3%)	549	0.765 (1.00)	0.715 (1.00)	0.196 (1.00)	0.988 (1.00)	1 (1.00)	0.787 (1.00)	0.754 (1.00)	1 (1.00)
21q loss	41 (7%)	524	0.968 (1.00)	0.852 (1.00)	0.619 (1.00)	0.321 (1.00)	1 (1.00)	0.388 (1.00)	0.821 (1.00)	0.235 (1.00)
22q loss	180 (32%)	385	0.482 (1.00)	0.11 (1.00)	0.926 (1.00)	0.437 (1.00)	0.569 (1.00)	0.847 (1.00)	0.78 (1.00)	1 (1.00)
xq loss	104 (18%)	461	0.364 (1.00)	0.729 (1.00)	0.375 (1.00)	0.394 (1.00)	0.852 (1.00)	0.729 (1.00)	0.193 (1.00)	0.468 (1.00)

'7p gain' versus 'Time to Death'

P value = 0.000108 (logrank test), Q value = 0.068

Table S1. Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
7P GAIN MUTATED	458	382	0.1 - 127.6 (9.7)
7P GAIN WILD-TYPE	107	80	0.2 - 108.8 (12.4)

Figure S1. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'AGE'

P value = 4.34e-06 (Wilcoxon-test), Q value = 0.0028

Table S2. Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
7P GAIN MUTATED	458	59.6 (12.4)
7P GAIN WILD-TYPE	107	49.8 (19.4)

Figure S2. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

'7q gain' versus 'Time to Death'

P value = 0.000282 (logrank test), Q value = 0.18

Table S3. Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
7Q GAIN MUTATED	463	383	0.1 - 127.6 (9.6)
7Q GAIN WILD-TYPE	102	79	0.2 - 108.8 (13.8)

Figure S3. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'AGE'

P value = 1.48e-05 (Wilcoxon-test), Q value = 0.0094

Table S4. Gene #14: '7q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
7Q GAIN MUTATED	463	59.6 (12.3)
7Q GAIN WILD-TYPE	102	49.6 (20.1)

Figure S4. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'AGE'

'10p gain' versus 'AGE'

P value = 0.000204 (Wilcoxon-test), Q value = 0.13

Table S5. Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
10P GAIN MUTATED	12	38.1 (18.1)
10P GAIN WILD-TYPE	553	58.2 (14.1)

Figure S5. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'AGE'

P value = 4.6e-05 (Wilcoxon-test), Q value = 0.029

Table S6. Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
20P GAIN MUTATED	217	60.9 (13.0)
20P GAIN WILD-TYPE	348	55.8 (15.0)

Figure S6. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'AGE'

P value = 0.00023 (Wilcoxon-test), Q value = 0.14

Table S7. Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
20Q GAIN MUTATED	215	60.7 (13.3)
20Q GAIN WILD-TYPE	350	56.0 (14.9)

Figure S7. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'10p loss' versus 'Time to Death'

P value = 2.98e-05 (logrank test), Q value = 0.019

Table S8. Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
10P LOSS MUTATED	472	391	0.1 - 127.6 (9.8)
10P LOSS WILD-TYPE	93	71	0.2 - 108.8 (12.7)

Figure S8. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'AGE'

P value = 6.98e-09 (Wilcoxon-test), Q value = 4.5e-06

Table S9. Gene #59: '10p loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
10P LOSS MUTATED	472	59.6 (12.7)
10P LOSS WILD-TYPE	93	48.1 (18.8)

Figure S9. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'AGE'

'10q loss' versus 'Time to Death'

P value = 7.54e-05 (logrank test), Q value = 0.048

Table S10. Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	565	462	0.1 - 127.6 (10.0)
10Q LOSS MUTATED	483	400	0.1 - 127.6 (9.9)
10Q LOSS WILD-TYPE	82	62	0.2 - 108.8 (12.2)

Figure S10. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'AGE'

P value = 5.06e-08 (Wilcoxon-test), Q value = 3.2e-05

Table S11. Gene #60: '10q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	565	57.8 (14.5)
10Q LOSS MUTATED	483	59.4 (13.0)
10Q LOSS WILD-TYPE	82	48.1 (18.5)

Figure S11. Get High-res Image Gene #60: '10q loss' 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 arm-level cnvs = 80
Number of selected clinical features = 8
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

References

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

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

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

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