Glioblastoma Multiforme: Correlation between copy number variations of arm-level result and selected clinical features<BR>(primary solid tumor cohort)

Glioblastoma Multiforme: Correlation between copy number variations of arm-level result and selected clinical features
(primary solid tumor cohort)

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

- Overview

+ Introduction

- Summary

Testing the association between copy number variation 79 arm-level results and 5 clinical features across 544 patients, 10 significant findings detected with Q value < 0.25.

6p gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
6q gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
7p gain cnv correlated to 'AGE'.
7q gain cnv correlated to 'AGE'.
10p gain cnv correlated to 'AGE' and 'KARNOFSKY.PERFORMANCE.SCORE'.
20p gain cnv correlated to 'AGE'.
10p loss cnv correlated to 'Time to Death' and 'AGE'.
10q loss cnv correlated to 'AGE'.

- Results

- Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 10 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	RADIATIONS RADIATION REGIMENINDICATION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test
10p gain	11 (2%)	533	0.00302 (1.00)	9.55e-05 (0.0371)	0.0296 (1.00)	0.000254 (0.098)	1 (1.00)
10p loss	426 (78%)	118	0.000152 (0.0586)	1.26e-09 (4.92e-07)	0.395 (1.00)	0.358 (1.00)	0.316 (1.00)
6p gain	7 (1%)	537	0.1 (1.00)	0.0989 (1.00)	1 (1.00)	0.000254 (0.098)	0.438 (1.00)
6q gain	9 (2%)	535	0.134 (1.00)	0.0449 (1.00)	0.745 (1.00)	0.000254 (0.098)	0.725 (1.00)
7p gain	423 (78%)	121	0.00488 (1.00)	5.79e-06 (0.00226)	1 (1.00)	0.53 (1.00)	0.0976 (1.00)
7q gain	427 (78%)	117	0.00601 (1.00)	7.78e-06 (0.00303)	0.594 (1.00)	0.584 (1.00)	0.148 (1.00)
20p gain	174 (32%)	370	0.888 (1.00)	0.000315 (0.121)	0.707 (1.00)	0.371 (1.00)	0.279 (1.00)
10q loss	439 (81%)	105	0.00068 (0.259)	2.4e-07 (9.39e-05)	0.58 (1.00)	0.0968 (1.00)	0.562 (1.00)
1p gain	38 (7%)	506	0.607 (1.00)	0.617 (1.00)	0.606 (1.00)	0.868 (1.00)	0.476 (1.00)
1q gain	43 (8%)	501	0.987 (1.00)	0.503 (1.00)	1 (1.00)	0.979 (1.00)	0.612 (1.00)
2p gain	18 (3%)	526	0.577 (1.00)	0.196 (1.00)	0.219 (1.00)	0.301 (1.00)	0.448 (1.00)
2q gain	16 (3%)	528	0.772 (1.00)	0.501 (1.00)	0.44 (1.00)	0.737 (1.00)	0.29 (1.00)
3p gain	30 (6%)	514	0.124 (1.00)	0.532 (1.00)	1 (1.00)	0.837 (1.00)	0.322 (1.00)
3q gain	30 (6%)	514	0.126 (1.00)	0.437 (1.00)	1 (1.00)	0.892 (1.00)	0.322 (1.00)
4p gain	15 (3%)	529	0.0811 (1.00)	0.0695 (1.00)	0.791 (1.00)	0.127 (1.00)	0.407 (1.00)
4q gain	14 (3%)	530	0.031 (1.00)	0.342 (1.00)	0.789 (1.00)	0.146 (1.00)	0.245 (1.00)
5p gain	28 (5%)	516	0.916 (1.00)	0.206 (1.00)	0.697 (1.00)	0.0435 (1.00)	0.144 (1.00)
5q gain	21 (4%)	523	0.711 (1.00)	0.52 (1.00)	0.497 (1.00)	0.301 (1.00)	0.238 (1.00)
8p gain	26 (5%)	518	0.765 (1.00)	0.553 (1.00)	0.539 (1.00)	0.402 (1.00)	0.831 (1.00)
8q gain	31 (6%)	513	0.833 (1.00)	0.205 (1.00)	0.345 (1.00)	0.389 (1.00)	1 (1.00)
9p gain	17 (3%)	527	0.24 (1.00)	0.0378 (1.00)	0.314 (1.00)	0.00622 (1.00)	0.6 (1.00)
9q gain	32 (6%)	512	0.0339 (1.00)	0.0482 (1.00)	0.0612 (1.00)	0.0256 (1.00)	0.439 (1.00)
11p gain	4 (1%)	540	0.568 (1.00)	0.383 (1.00)	0.65 (1.00)	0.841 (1.00)	1 (1.00)
11q gain	7 (1%)	537	0.152 (1.00)	0.211 (1.00)	0.254 (1.00)	0.0913 (1.00)	0.438 (1.00)
12p gain	40 (7%)	504	0.928 (1.00)	0.15 (1.00)	1 (1.00)	0.93 (1.00)	0.6 (1.00)
12q gain	30 (6%)	514	0.498 (1.00)	0.667 (1.00)	0.445 (1.00)	0.554 (1.00)	0.322 (1.00)
13q gain	3 (1%)	541	0.991 (1.00)	0.104 (1.00)	0.0612 (1.00)		0.0329 (1.00)
14q gain	6 (1%)	538	0.0771 (1.00)	0.816 (1.00)	0.685 (1.00)	0.514 (1.00)	1 (1.00)
15q gain	5 (1%)	539	0.427 (1.00)	0.19 (1.00)	1 (1.00)	0.292 (1.00)	0.659 (1.00)
16p gain	17 (3%)	527	0.044 (1.00)	0.0244 (1.00)	0.13 (1.00)	0.71 (1.00)	0.11 (1.00)
16q gain	17 (3%)	527	0.0449 (1.00)	0.0676 (1.00)	0.0422 (1.00)	0.971 (1.00)	0.291 (1.00)
17p gain	10 (2%)	534	0.0168 (1.00)	0.0354 (1.00)	0.747 (1.00)	0.0913 (1.00)	1 (1.00)
17q gain	18 (3%)	526	0.0339 (1.00)	0.123 (1.00)	1 (1.00)	0.0318 (1.00)	0.801 (1.00)
18p gain	26 (5%)	518	0.848 (1.00)	0.929 (1.00)	1 (1.00)	0.0964 (1.00)	0.831 (1.00)
18q gain	28 (5%)	516	0.82 (1.00)	0.938 (1.00)	0.697 (1.00)	0.301 (1.00)	0.836 (1.00)
19p gain	170 (31%)	374	0.197 (1.00)	0.452 (1.00)	0.85 (1.00)	0.795 (1.00)	0.277 (1.00)
19q gain	147 (27%)	397	0.141 (1.00)	0.246 (1.00)	0.694 (1.00)	0.773 (1.00)	0.837 (1.00)
20q gain	172 (32%)	372	0.651 (1.00)	0.000657 (0.251)	0.573 (1.00)	0.406 (1.00)	0.167 (1.00)
21q gain	32 (6%)	512	0.137 (1.00)	0.856 (1.00)	1 (1.00)	0.634 (1.00)	0.439 (1.00)
22q gain	11 (2%)	533	0.97 (1.00)	0.391 (1.00)	1 (1.00)	0.968 (1.00)	0.516 (1.00)
Xq gain	3 (1%)	541	0.128 (1.00)	0.593 (1.00)	1 (1.00)		1 (1.00)
1p loss	5 (1%)	539	0.0316 (1.00)	0.707 (1.00)	0.653 (1.00)	0.868 (1.00)	1 (1.00)
1q loss	4 (1%)	540	0.721 (1.00)	0.0658 (1.00)	0.65 (1.00)	0.0873 (1.00)	1 (1.00)
2p loss	10 (2%)	534	0.179 (1.00)	0.516 (1.00)	0.204 (1.00)	0.76 (1.00)	1 (1.00)
2q loss	9 (2%)	535	0.235 (1.00)	0.743 (1.00)	0.328 (1.00)	0.76 (1.00)	0.725 (1.00)
3p loss	22 (4%)	522	0.293 (1.00)	0.0224 (1.00)	1 (1.00)	0.846 (1.00)	0.0184 (1.00)
3q loss	16 (3%)	528	0.774 (1.00)	0.231 (1.00)	0.44 (1.00)	0.708 (1.00)	0.29 (1.00)
4p loss	25 (5%)	519	0.14 (1.00)	0.297 (1.00)	0.142 (1.00)	0.825 (1.00)	0.083 (1.00)
4q loss	24 (4%)	520	0.21 (1.00)	0.229 (1.00)	0.67 (1.00)	0.167 (1.00)	0.51 (1.00)
5p loss	21 (4%)	523	0.0545 (1.00)	0.277 (1.00)	0.821 (1.00)	0.503 (1.00)	0.238 (1.00)
5q loss	20 (4%)	524	0.0597 (1.00)	0.294 (1.00)	0.645 (1.00)	0.786 (1.00)	0.33 (1.00)
6p loss	47 (9%)	497	0.008 (1.00)	0.761 (1.00)	0.878 (1.00)	0.711 (1.00)	0.747 (1.00)
6q loss	79 (15%)	465	0.277 (1.00)	0.656 (1.00)	0.534 (1.00)	0.581 (1.00)	0.897 (1.00)
7p loss	5 (1%)	539	0.514 (1.00)	0.658 (1.00)	1 (1.00)	0.61 (1.00)	1 (1.00)
7q loss	4 (1%)	540	0.617 (1.00)	0.362 (1.00)	1 (1.00)		1 (1.00)
8p loss	34 (6%)	510	0.972 (1.00)	0.422 (1.00)	0.209 (1.00)	0.541 (1.00)	0.0233 (1.00)
8q loss	21 (4%)	523	0.995 (1.00)	0.435 (1.00)	0.497 (1.00)	0.133 (1.00)	0.00375 (1.00)
9p loss	160 (29%)	384	0.748 (1.00)	0.41 (1.00)	0.773 (1.00)	0.427 (1.00)	0.42 (1.00)
9q loss	63 (12%)	481	0.396 (1.00)	0.575 (1.00)	0.0139 (1.00)	0.384 (1.00)	0.776 (1.00)
11p loss	64 (12%)	480	0.312 (1.00)	0.222 (1.00)	0.221 (1.00)	0.89 (1.00)	0.254 (1.00)
11q loss	55 (10%)	489	0.96 (1.00)	0.814 (1.00)	0.772 (1.00)	0.934 (1.00)	0.0146 (1.00)
12p loss	37 (7%)	507	0.598 (1.00)	0.913 (1.00)	0.864 (1.00)	0.89 (1.00)	0.586 (1.00)
12q loss	34 (6%)	510	0.578 (1.00)	0.992 (1.00)	1 (1.00)	0.61 (1.00)	0.706 (1.00)
13q loss	134 (25%)	410	0.978 (1.00)	0.39 (1.00)	0.417 (1.00)	0.538 (1.00)	0.749 (1.00)
14q loss	120 (22%)	424	0.995 (1.00)	0.891 (1.00)	0.752 (1.00)	0.769 (1.00)	1 (1.00)
15q loss	62 (11%)	482	0.433 (1.00)	0.181 (1.00)	0.132 (1.00)	0.486 (1.00)	0.25 (1.00)
16p loss	23 (4%)	521	0.155 (1.00)	0.119 (1.00)	0.514 (1.00)	0.0929 (1.00)	1 (1.00)
16q loss	40 (7%)	504	0.0807 (1.00)	0.927 (1.00)	1 (1.00)	0.204 (1.00)	1 (1.00)
17p loss	35 (6%)	509	0.466 (1.00)	0.285 (1.00)	0.722 (1.00)	0.643 (1.00)	1 (1.00)
17q loss	19 (3%)	525	0.936 (1.00)	0.315 (1.00)	0.815 (1.00)	0.62 (1.00)	0.626 (1.00)
18p loss	43 (8%)	501	0.302 (1.00)	0.768 (1.00)	0.871 (1.00)	0.625 (1.00)	0.612 (1.00)
18q loss	38 (7%)	506	0.384 (1.00)	0.432 (1.00)	0.497 (1.00)	0.349 (1.00)	0.589 (1.00)
19p loss	13 (2%)	531	0.635 (1.00)	0.187 (1.00)	0.775 (1.00)	0.58 (1.00)	1 (1.00)
19q loss	18 (3%)	526	0.194 (1.00)	0.667 (1.00)	1 (1.00)	0.276 (1.00)	0.801 (1.00)
20p loss	11 (2%)	533	0.456 (1.00)	0.14 (1.00)	0.357 (1.00)	0.7 (1.00)	0.752 (1.00)
20q loss	10 (2%)	534	0.473 (1.00)	0.468 (1.00)	0.527 (1.00)	0.612 (1.00)	0.304 (1.00)
21q loss	25 (5%)	519	0.849 (1.00)	0.235 (1.00)	0.212 (1.00)	0.629 (1.00)	0.666 (1.00)
22q loss	138 (25%)	406	0.647 (1.00)	0.0288 (1.00)	0.764 (1.00)	0.613 (1.00)	1 (1.00)
Xq loss	11 (2%)	533	0.23 (1.00)	0.0255 (1.00)	0.759 (1.00)	0.914 (1.00)	0.516 (1.00)

	nPatients	Mean (Std.Dev)
ALL	409	77.3 (14.7)
6P GAIN MUTATED	4	80.0 (0.0)
6P GAIN WILD-TYPE	405	77.3 (14.8)

	nPatients	Mean (Std.Dev)
ALL	409	77.3 (14.7)
6Q GAIN MUTATED	5	80.0 (0.0)
6Q GAIN WILD-TYPE	404	77.3 (14.8)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
7P GAIN MUTATED	423	59.7 (12.2)
7P GAIN WILD-TYPE	121	51.3 (18.5)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
7Q GAIN MUTATED	427	59.7 (12.1)
7Q GAIN WILD-TYPE	117	51.1 (19.1)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
10P GAIN MUTATED	11	34.3 (12.9)
10P GAIN WILD-TYPE	533	58.3 (13.9)

	nPatients	Mean (Std.Dev)
ALL	409	77.3 (14.7)
10P GAIN MUTATED	11	80.0 (0.0)
10P GAIN WILD-TYPE	398	77.2 (14.9)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
20P GAIN MUTATED	174	60.9 (13.1)
20P GAIN WILD-TYPE	370	56.4 (14.6)

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
10P LOSS MUTATED	426	323	0.1 - 127.6 (9.3)
10P LOSS WILD-TYPE	118	88	0.2 - 108.8 (10.8)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
10P LOSS MUTATED	426	60.3 (11.8)
10P LOSS WILD-TYPE	118	48.8 (18.3)

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
10Q LOSS MUTATED	439	59.8 (12.4)
10Q LOSS WILD-TYPE	105	49.6 (18.2)

+ Methods & Data

+ Input

+ Survival analysis

+ Student's t-test analysis

+ Fisher's exact test

+ Q value calculation

+ Download Results

+ References

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