Correlation between copy number variations of arm-level result and selected clinical features

Glioblastoma Multiforme (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1CR5SRB

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 82 arm-level events and 8 clinical features across 573 patients, 15 significant findings detected with Q value < 0.25.

7p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
7q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
10p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
17q gain cnv correlated to 'YEARS_TO_BIRTH'.
20p gain cnv correlated to 'YEARS_TO_BIRTH'.
20q gain cnv correlated to 'YEARS_TO_BIRTH'.
6p loss cnv correlated to 'Time to Death'.
8p loss cnv correlated to 'RACE'.
10p loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
10q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level 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	YEARS TO BIRTH	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	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test
7p gain	465 (81%)	108	3.71e-05 (0.00347)	1.91e-06 (0.000418)	0.744 (1.00)	0.207 (1.00)	0.995 (1.00)	0.0404 (0.822)	0.0534 (0.822)	0.268 (1.00)
7q gain	471 (82%)	102	3.7e-05 (0.00347)	3.81e-06 (0.000626)	0.219 (1.00)	0.331 (1.00)	0.688 (1.00)	0.0401 (0.822)	0.0358 (0.822)	0.248 (1.00)
10p gain	13 (2%)	560	0.00173 (0.0945)	6.04e-05 (0.00495)	0.0404 (0.822)	0.375 (1.00)	0.336 (1.00)	0.298 (1.00)	0.0123 (0.393)	0.28 (1.00)
10p loss	476 (83%)	97	0.000102 (0.00741)	3.55e-09 (2.33e-06)	0.209 (1.00)	0.505 (1.00)	0.0479 (0.822)	0.00669 (0.274)	0.128 (0.992)	0.239 (1.00)
10q loss	488 (85%)	85	0.000333 (0.0198)	1.81e-07 (5.92e-05)	0.549 (1.00)	0.861 (1.00)	0.0084 (0.324)	0.085 (0.887)	0.0589 (0.84)	0.0971 (0.91)
17q gain	61 (11%)	512	0.0126 (0.393)	0.00564 (0.247)	0.488 (1.00)	0.216 (1.00)	0.51 (1.00)	0.439 (1.00)	0.541 (1.00)	0.632 (1.00)
20p gain	221 (39%)	352	0.322 (1.00)	2.45e-05 (0.00322)	0.292 (1.00)	0.898 (1.00)	0.827 (1.00)	0.489 (1.00)	0.0385 (0.822)	1 (1.00)
20q gain	219 (38%)	354	0.53 (1.00)	0.000126 (0.00829)	0.219 (1.00)	1 (1.00)	0.75 (1.00)	0.501 (1.00)	0.0526 (0.822)	1 (1.00)
6p loss	87 (15%)	486	0.00191 (0.0966)	0.345 (1.00)	0.721 (1.00)	0.22 (1.00)	0.638 (1.00)	0.515 (1.00)	0.257 (1.00)	0.702 (1.00)
8p loss	58 (10%)	515	0.743 (1.00)	0.183 (1.00)	0.157 (1.00)	0.68 (1.00)	0.389 (1.00)	0.496 (1.00)	0.00421 (0.197)	0.618 (1.00)
1p gain	82 (14%)	491	0.281 (1.00)	0.413 (1.00)	0.542 (1.00)	0.155 (1.00)	0.0837 (0.887)	0.118 (0.992)	0.9 (1.00)	0.667 (1.00)
1q gain	89 (16%)	484	0.795 (1.00)	0.553 (1.00)	0.24 (1.00)	0.228 (1.00)	0.205 (1.00)	0.355 (1.00)	0.779 (1.00)	0.69 (1.00)
2p gain	37 (6%)	536	0.661 (1.00)	0.798 (1.00)	0.163 (1.00)	0.451 (1.00)	0.379 (1.00)	0.89 (1.00)	0.336 (1.00)	1 (1.00)
2q gain	35 (6%)	538	0.577 (1.00)	0.391 (1.00)	0.476 (1.00)	0.792 (1.00)	0.238 (1.00)	1 (1.00)	0.309 (1.00)	1 (1.00)
3p gain	57 (10%)	516	0.811 (1.00)	0.0478 (0.822)	0.319 (1.00)	0.537 (1.00)	0.567 (1.00)	0.572 (1.00)	0.927 (1.00)	1 (1.00)
3q gain	63 (11%)	510	0.669 (1.00)	0.118 (0.992)	0.413 (1.00)	0.843 (1.00)	0.512 (1.00)	0.409 (1.00)	0.932 (1.00)	1 (1.00)
4p gain	35 (6%)	538	0.518 (1.00)	0.653 (1.00)	1 (1.00)	0.792 (1.00)	0.043 (0.822)	1 (1.00)	0.723 (1.00)	0.562 (1.00)
4q gain	34 (6%)	539	0.879 (1.00)	0.768 (1.00)	0.368 (1.00)	1 (1.00)	0.086 (0.887)	1 (1.00)	0.545 (1.00)	1 (1.00)
5p gain	49 (9%)	524	0.714 (1.00)	0.671 (1.00)	0.169 (1.00)	0.375 (1.00)	0.191 (1.00)	0.0964 (0.91)	1 (1.00)	0.296 (1.00)
5q gain	41 (7%)	532	0.372 (1.00)	0.54 (1.00)	0.134 (0.996)	0.213 (1.00)	0.686 (1.00)	0.126 (0.992)	0.832 (1.00)	0.613 (1.00)
6p gain	24 (4%)	549	0.248 (1.00)	0.487 (1.00)	0.671 (1.00)	1 (1.00)	0.816 (1.00)	1 (1.00)	0.48 (1.00)	1 (1.00)
6q gain	23 (4%)	550	0.189 (1.00)	0.244 (1.00)	1 (1.00)	1 (1.00)	0.779 (1.00)	1 (1.00)	0.563 (1.00)	1 (1.00)
8p gain	52 (9%)	521	0.839 (1.00)	0.788 (1.00)	0.657 (1.00)	0.375 (1.00)	0.785 (1.00)	0.594 (1.00)	0.322 (1.00)	1 (1.00)
8q gain	59 (10%)	514	0.502 (1.00)	0.356 (1.00)	0.482 (1.00)	0.675 (1.00)	0.894 (1.00)	0.499 (1.00)	0.758 (1.00)	1 (1.00)
9p gain	47 (8%)	526	0.347 (1.00)	0.663 (1.00)	0.164 (1.00)	0.356 (1.00)	0.944 (1.00)	0.11 (0.988)	0.296 (1.00)	0.239 (1.00)
9q gain	70 (12%)	503	0.929 (1.00)	0.738 (1.00)	0.243 (1.00)	0.124 (0.992)	0.647 (1.00)	0.584 (1.00)	0.292 (1.00)	0.643 (1.00)
10q gain	3 (1%)	570	0.346 (1.00)	0.665 (1.00)	0.564 (1.00)	1 (1.00)		1 (1.00)	1 (1.00)	0.0723 (0.862)
11p gain	18 (3%)	555	0.681 (1.00)	0.667 (1.00)	0.807 (1.00)	0.491 (1.00)	0.223 (1.00)	0.787 (1.00)	0.611 (1.00)	0.35 (1.00)
11q gain	15 (3%)	558	0.33 (1.00)	0.0537 (0.822)	0.18 (1.00)	0.706 (1.00)	0.0692 (0.856)	0.502 (1.00)	1 (1.00)	0.316 (1.00)
12p gain	60 (10%)	513	0.597 (1.00)	0.38 (1.00)	0.489 (1.00)	0.0637 (0.84)	0.594 (1.00)	0.929 (1.00)	0.93 (1.00)	1 (1.00)
12q gain	49 (9%)	524	0.993 (1.00)	0.727 (1.00)	0.285 (1.00)	0.18 (1.00)	0.858 (1.00)	0.48 (1.00)	0.149 (1.00)	0.612 (1.00)
13q gain	10 (2%)	563	0.442 (1.00)	0.0112 (0.388)	0.202 (1.00)	0.294 (1.00)	0.091 (0.896)	0.59 (1.00)	1 (1.00)	1 (1.00)
14q gain	22 (4%)	551	0.277 (1.00)	0.0607 (0.84)	0.513 (1.00)	0.742 (1.00)	0.521 (1.00)	0.0833 (0.887)	0.831 (1.00)	1 (1.00)
15q gain	25 (4%)	548	0.269 (1.00)	0.903 (1.00)	0.677 (1.00)	0.13 (0.992)	0.256 (1.00)	0.839 (1.00)	0.726 (1.00)	1 (1.00)
16p gain	38 (7%)	535	0.0444 (0.822)	0.84 (1.00)	0.306 (1.00)	0.456 (1.00)	0.971 (1.00)	0.889 (1.00)	0.464 (1.00)	1 (1.00)
16q gain	37 (6%)	536	0.172 (1.00)	0.862 (1.00)	0.606 (1.00)	0.455 (1.00)	0.919 (1.00)	0.889 (1.00)	0.449 (1.00)	1 (1.00)
17p gain	49 (9%)	524	0.0865 (0.887)	0.0158 (0.451)	0.223 (1.00)	0.256 (1.00)	0.638 (1.00)	0.529 (1.00)	0.421 (1.00)	1 (1.00)
18p gain	58 (10%)	515	0.445 (1.00)	0.332 (1.00)	0.571 (1.00)	0.835 (1.00)	0.336 (1.00)	0.248 (1.00)	0.192 (1.00)	0.354 (1.00)
18q gain	58 (10%)	515	0.554 (1.00)	0.188 (1.00)	0.157 (1.00)	0.835 (1.00)	0.257 (1.00)	0.249 (1.00)	0.404 (1.00)	1 (1.00)
19p gain	224 (39%)	349	0.463 (1.00)	0.963 (1.00)	0.861 (1.00)	0.0959 (0.91)	0.832 (1.00)	0.524 (1.00)	0.494 (1.00)	0.552 (1.00)
19q gain	196 (34%)	377	0.584 (1.00)	0.445 (1.00)	0.719 (1.00)	0.692 (1.00)	0.832 (1.00)	0.832 (1.00)	0.241 (1.00)	0.356 (1.00)
21q gain	64 (11%)	509	0.772 (1.00)	0.0663 (0.852)	1 (1.00)	0.842 (1.00)	0.655 (1.00)	0.101 (0.924)	0.117 (0.992)	0.376 (1.00)
22q gain	34 (6%)	539	0.199 (1.00)	0.584 (1.00)	1 (1.00)	0.603 (1.00)	0.373 (1.00)	0.284 (1.00)	0.795 (1.00)	0.147 (1.00)
xp gain	15 (3%)	558	0.844 (1.00)	0.433 (1.00)	0.598 (1.00)	0.705 (1.00)	0.564 (1.00)	0.737 (1.00)	0.723 (1.00)	0.203 (1.00)
xq gain	17 (3%)	556	0.507 (1.00)	0.545 (1.00)	0.806 (1.00)	0.706 (1.00)	0.694 (1.00)	0.424 (1.00)	0.571 (1.00)	0.261 (1.00)
1p loss	16 (3%)	557	0.565 (1.00)	0.0299 (0.754)	0.304 (1.00)	0.439 (1.00)	0.144 (1.00)	0.394 (1.00)	0.57 (1.00)	1 (1.00)
1q loss	15 (3%)	558	0.203 (1.00)	0.0146 (0.436)	0.791 (1.00)	0.417 (1.00)	0.01 (0.365)	0.733 (1.00)	0.725 (1.00)	1 (1.00)
2p loss	32 (6%)	541	0.697 (1.00)	0.0835 (0.887)	0.135 (0.996)	0.0537 (0.822)	0.897 (1.00)	0.768 (1.00)	0.89 (1.00)	1 (1.00)
2q loss	33 (6%)	540	0.759 (1.00)	0.0849 (0.887)	0.146 (1.00)	0.0606 (0.84)	0.658 (1.00)	0.447 (1.00)	0.893 (1.00)	1 (1.00)
3p loss	41 (7%)	532	0.52 (1.00)	0.0714 (0.862)	0.868 (1.00)	0.0461 (0.822)	0.94 (1.00)	0.655 (1.00)	0.75 (1.00)	0.211 (1.00)
3q loss	36 (6%)	537	0.96 (1.00)	0.724 (1.00)	0.597 (1.00)	0.292 (1.00)	0.583 (1.00)	1 (1.00)	0.903 (1.00)	0.538 (1.00)
4p loss	56 (10%)	517	0.176 (1.00)	0.695 (1.00)	0.313 (1.00)	0.402 (1.00)	0.311 (1.00)	0.446 (1.00)	0.247 (1.00)	0.325 (1.00)
4q loss	55 (10%)	518	0.0193 (0.526)	0.115 (0.992)	0.886 (1.00)	0.394 (1.00)	0.297 (1.00)	0.71 (1.00)	0.477 (1.00)	0.287 (1.00)
5p loss	43 (8%)	530	0.123 (0.992)	0.534 (1.00)	0.871 (1.00)	0.34 (1.00)	0.568 (1.00)	0.898 (1.00)	0.0898 (0.896)	0.211 (1.00)
5q loss	45 (8%)	528	0.0839 (0.887)	0.442 (1.00)	1 (1.00)	0.344 (1.00)	0.772 (1.00)	0.446 (1.00)	0.326 (1.00)	0.0551 (0.822)
6q loss	126 (22%)	447	0.172 (1.00)	0.633 (1.00)	0.258 (1.00)	0.451 (1.00)	0.954 (1.00)	0.816 (1.00)	0.254 (1.00)	0.478 (1.00)
7p loss	8 (1%)	565	0.464 (1.00)	0.0523 (0.822)	1 (1.00)	1 (1.00)	0.72 (1.00)	1 (1.00)	0.623 (1.00)	1 (1.00)
7q loss	6 (1%)	567	0.62 (1.00)	0.0237 (0.623)	1 (1.00)	0.582 (1.00)	0.303 (1.00)	1 (1.00)	0.522 (1.00)	1 (1.00)
8q loss	42 (7%)	531	0.064 (0.84)	0.219 (1.00)	0.416 (1.00)	0.635 (1.00)	0.257 (1.00)	0.896 (1.00)	0.285 (1.00)	1 (1.00)
9p loss	201 (35%)	372	0.403 (1.00)	0.482 (1.00)	0.858 (1.00)	0.603 (1.00)	0.766 (1.00)	0.835 (1.00)	0.518 (1.00)	0.0638 (0.84)
9q loss	94 (16%)	479	0.872 (1.00)	0.714 (1.00)	0.357 (1.00)	0.396 (1.00)	0.572 (1.00)	0.201 (1.00)	0.13 (0.992)	0.235 (1.00)
11p loss	98 (17%)	475	0.263 (1.00)	0.922 (1.00)	0.0546 (0.822)	0.869 (1.00)	0.498 (1.00)	0.387 (1.00)	0.665 (1.00)	0.7 (1.00)
11q loss	92 (16%)	481	0.863 (1.00)	0.291 (1.00)	0.415 (1.00)	0.503 (1.00)	0.752 (1.00)	0.732 (1.00)	0.952 (1.00)	0.228 (1.00)
12p loss	59 (10%)	514	0.556 (1.00)	0.431 (1.00)	0.401 (1.00)	0.537 (1.00)	0.851 (1.00)	0.503 (1.00)	0.167 (1.00)	1 (1.00)
12q loss	57 (10%)	516	0.82 (1.00)	0.603 (1.00)	0.568 (1.00)	0.287 (1.00)	0.99 (1.00)	0.535 (1.00)	0.194 (1.00)	0.335 (1.00)
13q loss	185 (32%)	388	0.658 (1.00)	0.947 (1.00)	1 (1.00)	0.0836 (0.887)	0.971 (1.00)	0.557 (1.00)	0.55 (1.00)	0.759 (1.00)
14q loss	146 (25%)	427	0.747 (1.00)	0.765 (1.00)	0.378 (1.00)	0.2 (1.00)	0.938 (1.00)	0.439 (1.00)	0.312 (1.00)	0.311 (1.00)
15q loss	104 (18%)	469	0.909 (1.00)	0.0374 (0.822)	0.506 (1.00)	0.255 (1.00)	0.871 (1.00)	0.616 (1.00)	1 (1.00)	0.476 (1.00)
16p loss	63 (11%)	510	0.0915 (0.896)	0.325 (1.00)	0.683 (1.00)	0.414 (1.00)	0.4 (1.00)	0.158 (1.00)	1 (1.00)	1 (1.00)
16q loss	83 (14%)	490	0.127 (0.992)	0.917 (1.00)	0.904 (1.00)	0.368 (1.00)	0.777 (1.00)	0.568 (1.00)	0.691 (1.00)	0.698 (1.00)
17p loss	65 (11%)	508	0.912 (1.00)	0.348 (1.00)	0.349 (1.00)	0.557 (1.00)	0.622 (1.00)	0.487 (1.00)	0.938 (1.00)	1 (1.00)
17q loss	41 (7%)	532	0.619 (1.00)	0.389 (1.00)	0.407 (1.00)	0.809 (1.00)	0.965 (1.00)	1 (1.00)	0.495 (1.00)	0.596 (1.00)
18p loss	71 (12%)	502	0.211 (1.00)	0.833 (1.00)	0.517 (1.00)	0.182 (1.00)	0.385 (1.00)	0.476 (1.00)	0.232 (1.00)	0.65 (1.00)
18q loss	62 (11%)	511	0.52 (1.00)	0.767 (1.00)	0.784 (1.00)	0.0686 (0.856)	0.338 (1.00)	0.689 (1.00)	0.19 (1.00)	0.144 (1.00)
19p loss	26 (5%)	547	0.575 (1.00)	0.712 (1.00)	0.838 (1.00)	0.339 (1.00)	0.72 (1.00)	0.849 (1.00)	1 (1.00)	1 (1.00)
19q loss	35 (6%)	538	0.576 (1.00)	0.507 (1.00)	0.722 (1.00)	0.412 (1.00)	0.98 (1.00)	0.466 (1.00)	0.711 (1.00)	1 (1.00)
20p loss	19 (3%)	554	0.977 (1.00)	0.414 (1.00)	0.24 (1.00)	0.732 (1.00)	0.637 (1.00)	1 (1.00)	0.197 (1.00)	0.35 (1.00)
20q loss	17 (3%)	556	0.755 (1.00)	0.751 (1.00)	0.314 (1.00)	0.49 (1.00)	0.697 (1.00)	1 (1.00)	0.375 (1.00)	1 (1.00)
21q loss	42 (7%)	531	0.559 (1.00)	0.652 (1.00)	0.416 (1.00)	1 (1.00)	0.101 (0.924)	1 (1.00)	1 (1.00)	0.239 (1.00)
22q loss	181 (32%)	392	0.887 (1.00)	0.112 (0.991)	1 (1.00)	0.506 (1.00)	0.256 (1.00)	0.908 (1.00)	0.657 (1.00)	1 (1.00)
xp loss	116 (20%)	457	0.136 (0.996)	0.642 (1.00)	0.459 (1.00)	0.349 (1.00)	0.532 (1.00)	0.957 (1.00)	0.119 (0.992)	0.718 (1.00)
xq loss	106 (18%)	467	0.162 (1.00)	0.821 (1.00)	0.509 (1.00)	0.196 (1.00)	0.365 (1.00)	0.755 (1.00)	0.137 (0.996)	0.471 (1.00)

'7p gain' versus 'Time to Death'

P value = 3.71e-05 (logrank test), Q value = 0.0035

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
7P GAIN MUTATED	462	392	0.1 - 127.6 (11.8)
7P GAIN WILD-TYPE	108	81	0.2 - 120.6 (15.3)

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

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 1.91e-06 (Wilcoxon-test), Q value = 0.00042

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

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
7P GAIN MUTATED	465	59.7 (12.4)
7P GAIN WILD-TYPE	108	49.6 (19.4)

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

'7q gain' versus 'Time to Death'

P value = 3.7e-05 (logrank test), Q value = 0.0035

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
7Q GAIN MUTATED	468	395	0.1 - 127.6 (11.8)
7Q GAIN WILD-TYPE	102	78	0.2 - 120.6 (16.2)

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

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 3.81e-06 (Wilcoxon-test), Q value = 0.00063

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

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
7Q GAIN MUTATED	471	59.6 (12.2)
7Q GAIN WILD-TYPE	102	49.2 (20.1)

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

'10p gain' versus 'Time to Death'

P value = 0.00173 (logrank test), Q value = 0.094

Table S5. Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
10P GAIN MUTATED	13	8	0.4 - 100.0 (28.7)
10P GAIN WILD-TYPE	557	465	0.1 - 127.6 (12.2)

Figure S5. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 6.04e-05 (Wilcoxon-test), Q value = 0.005

Table S6. Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
10P GAIN MUTATED	13	37.5 (17.4)
10P GAIN WILD-TYPE	560	58.3 (14.1)

Figure S6. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00564 (Wilcoxon-test), Q value = 0.25

Table S7. Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
17Q GAIN MUTATED	61	62.2 (13.6)
17Q GAIN WILD-TYPE	512	57.3 (14.5)

Figure S7. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 2.45e-05 (Wilcoxon-test), Q value = 0.0032

Table S8. Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
20P GAIN MUTATED	221	61.0 (13.0)
20P GAIN WILD-TYPE	352	55.8 (15.0)

Figure S8. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000126 (Wilcoxon-test), Q value = 0.0083

Table S9. Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
20Q GAIN MUTATED	219	60.8 (13.2)
20Q GAIN WILD-TYPE	354	55.9 (14.9)

Figure S9. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'Time to Death'

P value = 0.00191 (logrank test), Q value = 0.097

Table S10. Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
6P LOSS MUTATED	87	78	0.2 - 92.7 (9.2)
6P LOSS WILD-TYPE	483	395	0.1 - 127.6 (12.6)

Figure S10. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'RACE'

P value = 0.00421 (Fisher's exact test), Q value = 0.2

Table S11. Gene #56: '8p loss' versus Clinical Feature #7: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	13	50	487
8P LOSS MUTATED	5	2	46
8P LOSS WILD-TYPE	8	48	441

Figure S11. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'RACE'

'10p loss' versus 'Time to Death'

P value = 0.000102 (logrank test), Q value = 0.0074

Table S12. Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
10P LOSS MUTATED	474	401	0.1 - 127.6 (12.1)
10P LOSS WILD-TYPE	96	72	0.4 - 115.9 (14.6)

Figure S12. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 3.55e-09 (Wilcoxon-test), Q value = 2.3e-06

Table S13. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
10P LOSS MUTATED	476	59.8 (12.6)
10P LOSS WILD-TYPE	97	48.2 (18.9)

Figure S13. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'Time to Death'

P value = 0.000333 (logrank test), Q value = 0.02

Table S14. Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	473	0.1 - 127.6 (12.2)
10Q LOSS MUTATED	486	408	0.1 - 127.6 (12.1)
10Q LOSS WILD-TYPE	84	65	0.4 - 115.9 (14.3)

Figure S14. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 1.81e-07 (Wilcoxon-test), Q value = 5.9e-05

Table S15. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	573	57.8 (14.5)
10Q LOSS MUTATED	488	59.4 (13.1)
10Q LOSS WILD-TYPE	85	48.6 (18.5)

Figure S15. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/22538152/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/22506586/GBM-TP.merged_data.txt
Number of patients = 573
Number of significantly arm-level cnvs = 82
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)

Made with Nozzle