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

Glioblastoma Multiforme (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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/C1WH2ND9

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 68 focal events and 6 clinical features across 553 patients, 18 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 'Time to Death' and 'AGE'.
amp_7q31.2 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', 'AGE', and 'HISTOLOGICAL.TYPE'.
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 68 focal events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 18 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test
del 10p11 23	455 (82%)	98	9.13e-08 (3.69e-05)	1.06e-08 (4.33e-06)	0.171 (1.00)	0.244 (1.00)	0.000576 (0.225)	0.81 (1.00)
amp 7p11 2	485 (88%)	68	3.9e-07 (0.000157)	1.4e-09 (5.72e-07)	0.428 (1.00)	0.0373 (1.00)	0.0194 (1.00)	0.0949 (1.00)
amp 7q11 21	444 (80%)	109	2.87e-05 (0.0114)	5.93e-08 (2.4e-05)	0.276 (1.00)	0.679 (1.00)	0.00207 (0.804)	0.133 (1.00)
amp 7q21 2	458 (83%)	95	0.000303 (0.119)	9.4e-06 (0.00374)	0.566 (1.00)	0.491 (1.00)	0.0207 (1.00)	0.223 (1.00)
del 10p15 3	449 (81%)	104	1.91e-06 (0.000765)	3.76e-08 (1.53e-05)	0.121 (1.00)	0.617 (1.00)	0.00306 (1.00)	0.64 (1.00)
del 10p13	451 (82%)	102	1.27e-06 (0.000508)	1.82e-07 (7.33e-05)	0.0564 (1.00)	0.86 (1.00)	0.00228 (0.883)	0.906 (1.00)
del 10q23 31	491 (89%)	62	1.08e-05 (0.00429)	6.33e-06 (0.00253)	0.681 (1.00)	0.0789 (1.00)	0.00239 (0.922)	1 (1.00)
amp 7q31 2	451 (82%)	102	0.0039 (1.00)	0.000444 (0.174)	0.433 (1.00)	0.721 (1.00)	0.0222 (1.00)	0.0764 (1.00)
del 9p21 3	402 (73%)	151	0.023 (1.00)	0.000304 (0.119)	0.558 (1.00)	0.096 (1.00)	0.176 (1.00)	0.471 (1.00)
del 10q26 3	492 (89%)	61	0.00133 (0.517)	5.9e-05 (0.0233)	0.582 (1.00)	0.0647 (1.00)	0.006 (1.00)	1 (1.00)
amp 1p36 21	91 (16%)	462	0.0364 (1.00)	0.226 (1.00)	0.483 (1.00)	0.423 (1.00)	0.208 (1.00)	1 (1.00)
amp 1q32 1	152 (27%)	401	0.506 (1.00)	0.202 (1.00)	0.846 (1.00)	0.273 (1.00)	0.554 (1.00)	0.757 (1.00)
amp 1q44	97 (18%)	456	0.298 (1.00)	0.939 (1.00)	0.304 (1.00)	0.598 (1.00)	0.447 (1.00)	0.717 (1.00)
amp 2p24 3	48 (9%)	505	0.308 (1.00)	0.24 (1.00)	0.357 (1.00)	0.929 (1.00)	0.867 (1.00)	0.871 (1.00)
amp 3q26 33	108 (20%)	445	0.16 (1.00)	0.0116 (1.00)	0.585 (1.00)	0.888 (1.00)	0.0184 (1.00)	0.728 (1.00)
amp 4p16 3	47 (8%)	506	0.981 (1.00)	0.723 (1.00)	0.28 (1.00)	0.439 (1.00)	1 (1.00)	0.742 (1.00)
amp 4q12	104 (19%)	449	0.338 (1.00)	0.342 (1.00)	0.436 (1.00)	0.737 (1.00)	0.281 (1.00)	0.289 (1.00)
amp 8q24 21	68 (12%)	485	0.414 (1.00)	0.183 (1.00)	0.428 (1.00)	0.895 (1.00)	0.719 (1.00)	0.781 (1.00)
amp 11p13	29 (5%)	524	0.971 (1.00)	0.435 (1.00)	0.847 (1.00)	0.691 (1.00)	0.564 (1.00)	1 (1.00)
amp 12p13 32	82 (15%)	471	0.811 (1.00)	0.0917 (1.00)	1 (1.00)	0.99 (1.00)	1 (1.00)	0.606 (1.00)
amp 12q14 1	131 (24%)	422	0.423 (1.00)	0.521 (1.00)	0.413 (1.00)	0.687 (1.00)	0.878 (1.00)	1 (1.00)
amp 12q15	91 (16%)	462	0.807 (1.00)	0.664 (1.00)	0.412 (1.00)	0.762 (1.00)	0.769 (1.00)	0.385 (1.00)
amp 13q34	31 (6%)	522	0.803 (1.00)	0.639 (1.00)	0.454 (1.00)	0.858 (1.00)	0.345 (1.00)	0.69 (1.00)
amp 14q32 33	36 (7%)	517	0.401 (1.00)	0.0205 (1.00)	0.485 (1.00)	0.276 (1.00)	0.0782 (1.00)	1 (1.00)
amp 17p13 2	48 (9%)	505	0.802 (1.00)	0.951 (1.00)	0.164 (1.00)	0.631 (1.00)	0.867 (1.00)	0.744 (1.00)
amp 17q25 1	79 (14%)	474	0.0355 (1.00)	0.0251 (1.00)	0.137 (1.00)	0.739 (1.00)	1 (1.00)	0.694 (1.00)
amp 19p13 2	239 (43%)	314	0.166 (1.00)	0.486 (1.00)	1 (1.00)	0.47 (1.00)	0.588 (1.00)	0.853 (1.00)
amp 19q12	205 (37%)	348	0.463 (1.00)	0.298 (1.00)	0.472 (1.00)	0.881 (1.00)	0.815 (1.00)	0.703 (1.00)
amp 21q21 1	66 (12%)	487	0.478 (1.00)	0.00861 (1.00)	0.79 (1.00)	0.419 (1.00)	0.128 (1.00)	0.479 (1.00)
del 1p36 32	95 (17%)	458	0.906 (1.00)	0.72 (1.00)	0.0374 (1.00)	0.979 (1.00)	0.272 (1.00)	1 (1.00)
del 1p36 23	131 (24%)	422	0.494 (1.00)	0.0207 (1.00)	0.0105 (1.00)	0.203 (1.00)	0.185 (1.00)	0.516 (1.00)
del 1p32 3	59 (11%)	494	0.712 (1.00)	0.0493 (1.00)	0.159 (1.00)	0.528 (1.00)	0.776 (1.00)	0.101 (1.00)
del 1p22 1	46 (8%)	507	0.45 (1.00)	0.337 (1.00)	0.755 (1.00)	0.576 (1.00)	0.0948 (1.00)	0.509 (1.00)
del 1q42 11	46 (8%)	507	0.0446 (1.00)	0.0388 (1.00)	1 (1.00)	0.0106 (1.00)	1 (1.00)	0.243 (1.00)
del 1q44	32 (6%)	521	0.303 (1.00)	0.207 (1.00)	1 (1.00)	0.0693 (1.00)	1 (1.00)	1 (1.00)
del 2q22 1	43 (8%)	510	0.526 (1.00)	0.324 (1.00)	0.333 (1.00)	0.673 (1.00)	0.495 (1.00)	0.122 (1.00)
del 2q37 1	53 (10%)	500	0.836 (1.00)	0.342 (1.00)	0.141 (1.00)	0.51 (1.00)	1 (1.00)	0.275 (1.00)
del 3p21 1	52 (9%)	501	0.0252 (1.00)	0.012 (1.00)	0.883 (1.00)	0.714 (1.00)	0.419 (1.00)	0.0593 (1.00)
del 3q13 31	55 (10%)	498	0.447 (1.00)	0.0636 (1.00)	0.383 (1.00)	0.316 (1.00)	0.665 (1.00)	0.166 (1.00)
del 3q22 1	55 (10%)	498	0.547 (1.00)	0.137 (1.00)	1 (1.00)	0.503 (1.00)	0.665 (1.00)	0.442 (1.00)
del 3q29	63 (11%)	490	0.214 (1.00)	0.25 (1.00)	1 (1.00)	0.473 (1.00)	1 (1.00)	0.246 (1.00)
del 4p16 3	75 (14%)	478	0.412 (1.00)	0.0342 (1.00)	0.256 (1.00)	0.169 (1.00)	0.385 (1.00)	0.107 (1.00)
del 4q34 3	87 (16%)	466	0.183 (1.00)	0.142 (1.00)	0.0556 (1.00)	0.606 (1.00)	0.444 (1.00)	0.1 (1.00)
del 5q35 3	52 (9%)	501	0.0478 (1.00)	0.11 (1.00)	1 (1.00)	0.606 (1.00)	1 (1.00)	0.431 (1.00)
del 6q22 31	151 (27%)	402	0.0664 (1.00)	0.252 (1.00)	0.118 (1.00)	0.399 (1.00)	0.0636 (1.00)	0.758 (1.00)
del 6q26	172 (31%)	381	0.138 (1.00)	0.971 (1.00)	0.26 (1.00)	0.732 (1.00)	0.0986 (1.00)	0.552 (1.00)
del 8p23 2	64 (12%)	489	0.234 (1.00)	0.0468 (1.00)	0.497 (1.00)	0.55 (1.00)	0.888 (1.00)	0.668 (1.00)
del 9q34 2	72 (13%)	481	0.522 (1.00)	0.691 (1.00)	1 (1.00)	0.493 (1.00)	0.895 (1.00)	1 (1.00)
del 11p15 5	125 (23%)	428	0.0148 (1.00)	0.00238 (0.922)	0.177 (1.00)	0.141 (1.00)	0.5 (1.00)	0.743 (1.00)
del 11p11 2	101 (18%)	452	0.0531 (1.00)	0.474 (1.00)	0.177 (1.00)	0.551 (1.00)	0.226 (1.00)	0.905 (1.00)
del 11q14 1	94 (17%)	459	0.991 (1.00)	0.776 (1.00)	0.297 (1.00)	0.757 (1.00)	0.399 (1.00)	0.111 (1.00)
del 12p13 1	71 (13%)	482	0.135 (1.00)	0.631 (1.00)	0.438 (1.00)	0.448 (1.00)	0.809 (1.00)	0.492 (1.00)
del 12q12	74 (13%)	479	0.459 (1.00)	0.81 (1.00)	0.898 (1.00)	0.89 (1.00)	1 (1.00)	0.419 (1.00)
del 13q14 2	233 (42%)	320	0.709 (1.00)	0.593 (1.00)	0.792 (1.00)	0.789 (1.00)	0.584 (1.00)	0.514 (1.00)
del 14q13 1	170 (31%)	383	0.749 (1.00)	0.643 (1.00)	0.157 (1.00)	0.175 (1.00)	0.0875 (1.00)	0.487 (1.00)
del 14q24 2	166 (30%)	387	0.581 (1.00)	0.24 (1.00)	0.298 (1.00)	0.466 (1.00)	0.0624 (1.00)	0.422 (1.00)
del 15q14	145 (26%)	408	0.31 (1.00)	0.047 (1.00)	0.693 (1.00)	0.491 (1.00)	0.577 (1.00)	0.403 (1.00)
del 16p12 2	89 (16%)	464	0.135 (1.00)	0.312 (1.00)	0.239 (1.00)	0.826 (1.00)	0.224 (1.00)	0.534 (1.00)
del 16q23 3	92 (17%)	461	0.0674 (1.00)	0.964 (1.00)	0.56 (1.00)	0.181 (1.00)	0.391 (1.00)	0.0256 (1.00)
del 17p13 2	82 (15%)	471	0.579 (1.00)	0.469 (1.00)	0.272 (1.00)	0.199 (1.00)	1 (1.00)	0.698 (1.00)
del 17p13 1	92 (17%)	461	0.327 (1.00)	0.148 (1.00)	0.0798 (1.00)	0.819 (1.00)	1 (1.00)	0.11 (1.00)
del 17q11 2	68 (12%)	485	0.19 (1.00)	0.484 (1.00)	0.895 (1.00)	0.238 (1.00)	1 (1.00)	0.0677 (1.00)
del 18q22 3	78 (14%)	475	0.649 (1.00)	0.606 (1.00)	0.709 (1.00)	0.117 (1.00)	1 (1.00)	0.793 (1.00)
del 19q13 41	97 (18%)	456	0.0367 (1.00)	0.265 (1.00)	1 (1.00)	0.253 (1.00)	0.718 (1.00)	1 (1.00)
del 21q22 3	57 (10%)	496	0.449 (1.00)	0.062 (1.00)	0.32 (1.00)	0.0503 (1.00)	0.886 (1.00)	0.881 (1.00)
del 22q13 32	205 (37%)	348	0.863 (1.00)	0.434 (1.00)	0.857 (1.00)	0.477 (1.00)	0.86 (1.00)	0.776 (1.00)
del xp22 2	113 (20%)	440	0.151 (1.00)	0.276 (1.00)	0.829 (1.00)	0.516 (1.00)	0.804 (1.00)	0.909 (1.00)
del xq23	103 (19%)	450	0.0875 (1.00)	0.999 (1.00)	0.823 (1.00)	0.361 (1.00)	0.277 (1.00)	0.288 (1.00)

'amp_7p11.2' versus 'Time to Death'

P value = 3.9e-07 (logrank test), Q value = 0.00016

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
AMP PEAK 8(7P11.2) MUTATED	485	398	0.1 - 127.6 (9.4)
AMP PEAK 8(7P11.2) WILD-TYPE	68	47	0.2 - 108.8 (15.1)

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 = 1.4e-09 (t-test), Q value = 5.7e-07

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

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 8(7P11.2) MUTATED	485	59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE	68	43.6 (18.8)

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 = 2.87e-05 (logrank test), Q value = 0.011

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
AMP PEAK 9(7Q11.21) MUTATED	444	361	0.1 - 127.6 (9.4)
AMP PEAK 9(7Q11.21) WILD-TYPE	109	84	0.2 - 108.8 (14.0)

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 = 5.93e-08 (t-test), Q value = 2.4e-05

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

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 9(7Q11.21) MUTATED	444	59.9 (12.4)
AMP PEAK 9(7Q11.21) WILD-TYPE	109	49.2 (18.4)

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

'amp_7q21.2' versus 'Time to Death'

P value = 0.000303 (logrank test), Q value = 0.12

Table S5. Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
AMP PEAK 10(7Q21.2) MUTATED	458	375	0.1 - 127.6 (9.7)
AMP PEAK 10(7Q21.2) WILD-TYPE	95	70	0.1 - 108.8 (12.4)

Figure S5. Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.2' versus 'AGE'

P value = 9.4e-06 (t-test), Q value = 0.0037

Table S6. Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 10(7Q21.2) MUTATED	458	59.5 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE	95	49.7 (19.8)

Figure S6. Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'AGE'

'amp_7q31.2' versus 'AGE'

P value = 0.000444 (t-test), Q value = 0.17

Table S7. Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 11(7Q31.2) MUTATED	451	59.2 (12.7)
AMP PEAK 11(7Q31.2) WILD-TYPE	102	51.9 (19.5)

Figure S7. Get High-res Image Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

'del_9p21.3' versus 'AGE'

P value = 0.000304 (t-test), Q value = 0.12

Table S8. Gene #42: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 19(9P21.3) MUTATED	402	59.3 (13.7)
DEL PEAK 19(9P21.3) WILD-TYPE	151	54.0 (15.7)

Figure S8. Get High-res Image Gene #42: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10p15.3' versus 'Time to Death'

P value = 1.91e-06 (logrank test), Q value = 0.00077

Table S9. Gene #44: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
DEL PEAK 21(10P15.3) MUTATED	449	369	0.1 - 92.6 (9.8)
DEL PEAK 21(10P15.3) WILD-TYPE	104	76	0.1 - 127.6 (11.7)

Figure S9. Get High-res Image Gene #44: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'AGE'

P value = 3.76e-08 (t-test), Q value = 1.5e-05

Table S10. Gene #44: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 21(10P15.3) MUTATED	449	59.9 (12.5)
DEL PEAK 21(10P15.3) WILD-TYPE	104	48.8 (18.5)

Figure S10. Get High-res Image Gene #44: 'del_10p15.3' versus Clinical Feature #2: 'AGE'

'del_10p13' versus 'Time to Death'

P value = 1.27e-06 (logrank test), Q value = 0.00051

Table S11. Gene #45: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
DEL PEAK 22(10P13) MUTATED	451	370	0.1 - 92.6 (9.9)
DEL PEAK 22(10P13) WILD-TYPE	102	75	0.1 - 127.6 (11.5)

Figure S11. Get High-res Image Gene #45: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'AGE'

P value = 1.82e-07 (t-test), Q value = 7.3e-05

Table S12. Gene #45: 'del_10p13' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 22(10P13) MUTATED	451	59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE	102	48.9 (19.0)

Figure S12. Get High-res Image Gene #45: 'del_10p13' versus Clinical Feature #2: 'AGE'

'del_10p11.23' versus 'Time to Death'

P value = 9.13e-08 (logrank test), Q value = 3.7e-05

Table S13. Gene #46: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
DEL PEAK 23(10P11.23) MUTATED	455	373	0.1 - 92.6 (9.7)
DEL PEAK 23(10P11.23) WILD-TYPE	98	72	0.1 - 127.6 (12.8)

Figure S13. Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'AGE'

P value = 1.06e-08 (t-test), Q value = 4.3e-06

Table S14. Gene #46: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 23(10P11.23) MUTATED	455	60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE	98	47.7 (18.9)

Figure S14. Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #2: 'AGE'

'del_10p11.23' versus 'HISTOLOGICAL.TYPE'

P value = 0.000576 (Fisher's exact test), Q value = 0.23

Table S15. Gene #46: 'del_10p11.23' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	GLIOBLASTOMA MULTIFORME (GBM)	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	10	18	525
DEL PEAK 23(10P11.23) MUTATED	5	10	440
DEL PEAK 23(10P11.23) WILD-TYPE	5	8	85

Figure S15. Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_10q23.31' versus 'Time to Death'

P value = 1.08e-05 (logrank test), Q value = 0.0043

Table S16. Gene #47: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	553	445	0.1 - 127.6 (9.9)
DEL PEAK 24(10Q23.31) MUTATED	491	401	0.1 - 127.6 (9.9)
DEL PEAK 24(10Q23.31) WILD-TYPE	62	44	0.2 - 108.8 (12.5)

Figure S16. Get High-res Image Gene #47: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'AGE'

P value = 6.33e-06 (t-test), Q value = 0.0025

Table S17. Gene #47: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 24(10Q23.31) MUTATED	491	59.2 (13.2)
DEL PEAK 24(10Q23.31) WILD-TYPE	62	47.2 (18.7)

Figure S17. Get High-res Image Gene #47: 'del_10q23.31' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'AGE'

P value = 5.9e-05 (t-test), Q value = 0.023

Table S18. Gene #48: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 25(10Q26.3) MUTATED	492	59.0 (13.4)
DEL PEAK 25(10Q26.3) WILD-TYPE	61	48.3 (18.9)

Figure S18. Get High-res Image Gene #48: '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 = 553
Number of significantly focal cnvs = 68
Number of selected clinical features = 6
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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

[4] 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