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

Glioblastoma Multiforme (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

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 (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1MP51KG

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 70 focal events and 6 clinical features across 553 patients, 17 significant findings detected with Q value < 0.25.

AMP PEAK 8(7P11.2) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
AMP PEAK 9(7Q11.21) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
AMP PEAK 10(7Q21.2) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 19(9P21.3) MUTATION ANALYSIS cnv correlated to 'AGE'.
DEL PEAK 21(10P15.3) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 22(10P13) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 23(10P11.23) MUTATION ANALYSIS cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
DEL PEAK 24(10Q23.31) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 25(10Q26.3) MUTATION ANALYSIS cnv correlated to 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 focal events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 17 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 PEAK 23(10P11 23) MUTATION ANALYSIS	455 (82%)	98	9.13e-08 (3.8e-05)	1.06e-08 (4.46e-06)	0.171 (1.00)	0.244 (1.00)	0.000576 (0.233)	0.81 (1.00)
AMP PEAK 8(7P11 2) MUTATION ANALYSIS	484 (88%)	69	2.4e-07 (9.94e-05)	1.84e-09 (7.74e-07)	0.511 (1.00)	0.0373 (1.00)	0.0246 (1.00)	0.0943 (1.00)
AMP PEAK 9(7Q11 21) MUTATION ANALYSIS	443 (80%)	110	1.83e-05 (0.00749)	6.97e-08 (2.91e-05)	0.328 (1.00)	0.679 (1.00)	0.00222 (0.89)	0.134 (1.00)
AMP PEAK 10(7Q21 2) MUTATION ANALYSIS	458 (83%)	95	0.000339 (0.138)	1.8e-05 (0.00738)	0.566 (1.00)	0.507 (1.00)	0.0207 (1.00)	0.223 (1.00)
DEL PEAK 21(10P15 3) MUTATION ANALYSIS	449 (81%)	104	1.91e-06 (0.000788)	3.76e-08 (1.57e-05)	0.121 (1.00)	0.617 (1.00)	0.00306 (1.00)	0.64 (1.00)
DEL PEAK 22(10P13) MUTATION ANALYSIS	451 (82%)	102	1.27e-06 (0.000523)	1.82e-07 (7.54e-05)	0.0564 (1.00)	0.86 (1.00)	0.00228 (0.908)	0.906 (1.00)
DEL PEAK 24(10Q23 31) MUTATION ANALYSIS	491 (89%)	62	1.08e-05 (0.00443)	6.33e-06 (0.0026)	0.681 (1.00)	0.0789 (1.00)	0.00239 (0.95)	1 (1.00)
DEL PEAK 19(9P21 3) MUTATION ANALYSIS	403 (73%)	150	0.0242 (1.00)	0.00047 (0.19)	0.435 (1.00)	0.1 (1.00)	0.175 (1.00)	0.535 (1.00)
DEL PEAK 25(10Q26 3) MUTATION ANALYSIS	492 (89%)	61	0.00133 (0.533)	5.9e-05 (0.024)	0.582 (1.00)	0.0647 (1.00)	0.006 (1.00)	1 (1.00)
AMP PEAK 1(1P36 21) MUTATION ANALYSIS	87 (16%)	466	0.043 (1.00)	0.318 (1.00)	0.283 (1.00)	0.636 (1.00)	0.269 (1.00)	1 (1.00)
AMP PEAK 2(1Q32 1) MUTATION ANALYSIS	149 (27%)	404	0.362 (1.00)	0.266 (1.00)	0.695 (1.00)	0.265 (1.00)	0.549 (1.00)	0.756 (1.00)
AMP PEAK 3(1Q44) MUTATION ANALYSIS	94 (17%)	459	0.171 (1.00)	0.903 (1.00)	0.297 (1.00)	0.582 (1.00)	0.512 (1.00)	0.903 (1.00)
AMP PEAK 4(2P24 3) MUTATION ANALYSIS	45 (8%)	508	0.212 (1.00)	0.186 (1.00)	0.34 (1.00)	0.594 (1.00)	0.853 (1.00)	0.867 (1.00)
AMP PEAK 5(3Q26 33) MUTATION ANALYSIS	105 (19%)	448	0.18 (1.00)	0.0302 (1.00)	0.825 (1.00)	0.711 (1.00)	0.0205 (1.00)	0.907 (1.00)
AMP PEAK 6(4P16 3) MUTATION ANALYSIS	45 (8%)	508	0.787 (1.00)	0.54 (1.00)	0.525 (1.00)	0.439 (1.00)	1 (1.00)	0.401 (1.00)
AMP PEAK 7(4Q12) MUTATION ANALYSIS	103 (19%)	450	0.508 (1.00)	0.534 (1.00)	0.221 (1.00)	0.615 (1.00)	0.277 (1.00)	0.479 (1.00)
AMP PEAK 11(7Q31 2) MUTATION ANALYSIS	450 (81%)	103	0.00598 (1.00)	0.00115 (0.463)	0.503 (1.00)	0.496 (1.00)	0.0234 (1.00)	0.124 (1.00)
AMP PEAK 12(7Q36 1) MUTATION ANALYSIS	455 (82%)	98	0.0171 (1.00)	0.00177 (0.709)	0.649 (1.00)	0.753 (1.00)	0.0143 (1.00)	0.471 (1.00)
AMP PEAK 13(8Q24 21) MUTATION ANALYSIS	63 (11%)	490	0.47 (1.00)	0.141 (1.00)	0.275 (1.00)	0.788 (1.00)	0.786 (1.00)	0.666 (1.00)
AMP PEAK 14(11P13) MUTATION ANALYSIS	25 (5%)	528	0.898 (1.00)	0.228 (1.00)	0.406 (1.00)	0.321 (1.00)	0.365 (1.00)	0.828 (1.00)
AMP PEAK 15(12P13 32) MUTATION ANALYSIS	79 (14%)	474	0.885 (1.00)	0.103 (1.00)	1 (1.00)	0.679 (1.00)	1 (1.00)	0.793 (1.00)
AMP PEAK 16(12Q14 1) MUTATION ANALYSIS	129 (23%)	424	0.384 (1.00)	0.565 (1.00)	0.411 (1.00)	0.83 (1.00)	0.934 (1.00)	1 (1.00)
AMP PEAK 17(12Q15) MUTATION ANALYSIS	89 (16%)	464	0.75 (1.00)	0.723 (1.00)	0.346 (1.00)	0.931 (1.00)	0.766 (1.00)	0.263 (1.00)
AMP PEAK 18(13Q34) MUTATION ANALYSIS	30 (5%)	523	0.749 (1.00)	0.848 (1.00)	0.339 (1.00)	0.827 (1.00)	0.329 (1.00)	0.688 (1.00)
AMP PEAK 19(14Q32 33) MUTATION ANALYSIS	32 (6%)	521	0.344 (1.00)	0.0207 (1.00)	0.582 (1.00)	0.249 (1.00)	0.249 (1.00)	1 (1.00)
AMP PEAK 20(17P13 2) MUTATION ANALYSIS	44 (8%)	509	0.875 (1.00)	0.565 (1.00)	0.336 (1.00)	0.113 (1.00)	0.848 (1.00)	0.614 (1.00)
AMP PEAK 21(17Q25 1) MUTATION ANALYSIS	75 (14%)	478	0.03 (1.00)	0.078 (1.00)	0.256 (1.00)	0.855 (1.00)	1 (1.00)	0.687 (1.00)
AMP PEAK 22(19P13 2) MUTATION ANALYSIS	234 (42%)	319	0.123 (1.00)	0.733 (1.00)	1 (1.00)	0.47 (1.00)	0.379 (1.00)	0.852 (1.00)
AMP PEAK 23(19Q12) MUTATION ANALYSIS	199 (36%)	354	0.361 (1.00)	0.465 (1.00)	0.527 (1.00)	0.962 (1.00)	0.735 (1.00)	0.565 (1.00)
AMP PEAK 24(21Q21 1) MUTATION ANALYSIS	64 (12%)	489	0.504 (1.00)	0.0175 (1.00)	0.684 (1.00)	0.564 (1.00)	0.428 (1.00)	0.566 (1.00)
DEL PEAK 1(1P36 32) MUTATION ANALYSIS	95 (17%)	458	0.699 (1.00)	0.818 (1.00)	0.0645 (1.00)	0.979 (1.00)	0.272 (1.00)	1 (1.00)
DEL PEAK 2(1P36 23) MUTATION ANALYSIS	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 PEAK 3(1P32 3) MUTATION ANALYSIS	58 (10%)	495	0.812 (1.00)	0.0716 (1.00)	0.201 (1.00)	0.549 (1.00)	0.774 (1.00)	0.073 (1.00)
DEL PEAK 4(1P22 1) MUTATION ANALYSIS	46 (8%)	507	0.447 (1.00)	0.322 (1.00)	1 (1.00)	0.595 (1.00)	0.0948 (1.00)	0.742 (1.00)
DEL PEAK 5(1Q42 11) MUTATION ANALYSIS	45 (8%)	508	0.0641 (1.00)	0.0611 (1.00)	1 (1.00)	0.00983 (1.00)	1 (1.00)	0.18 (1.00)
DEL PEAK 6(1Q44) MUTATION ANALYSIS	31 (6%)	522	0.398 (1.00)	0.287 (1.00)	0.85 (1.00)	0.0652 (1.00)	1 (1.00)	0.844 (1.00)
DEL PEAK 7(2Q22 1) MUTATION ANALYSIS	44 (8%)	509	0.445 (1.00)	0.244 (1.00)	0.262 (1.00)	0.673 (1.00)	0.599 (1.00)	0.0878 (1.00)
DEL PEAK 8(2Q37 1) MUTATION ANALYSIS	56 (10%)	497	0.766 (1.00)	0.227 (1.00)	0.194 (1.00)	0.672 (1.00)	1 (1.00)	0.286 (1.00)
DEL PEAK 9(3P21 1) MUTATION ANALYSIS	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 PEAK 10(3Q13 31) MUTATION ANALYSIS	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 PEAK 11(3Q22 1) MUTATION ANALYSIS	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 PEAK 12(3Q29) MUTATION ANALYSIS	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 PEAK 13(4P16 3) MUTATION ANALYSIS	76 (14%)	477	0.44 (1.00)	0.0317 (1.00)	0.255 (1.00)	0.161 (1.00)	0.389 (1.00)	0.0844 (1.00)
DEL PEAK 14(4Q34 3) MUTATION ANALYSIS	89 (16%)	464	0.135 (1.00)	0.0957 (1.00)	0.0588 (1.00)	0.64 (1.00)	0.453 (1.00)	0.0615 (1.00)
DEL PEAK 15(5Q35 2) MUTATION ANALYSIS	54 (10%)	499	0.0617 (1.00)	0.124 (1.00)	0.661 (1.00)	0.796 (1.00)	0.88 (1.00)	0.165 (1.00)
DEL PEAK 16(6Q22 31) MUTATION ANALYSIS	152 (27%)	401	0.07 (1.00)	0.313 (1.00)	0.0802 (1.00)	0.476 (1.00)	0.0647 (1.00)	0.757 (1.00)
DEL PEAK 17(6Q26) MUTATION ANALYSIS	172 (31%)	381	0.168 (1.00)	0.782 (1.00)	0.189 (1.00)	0.732 (1.00)	0.0986 (1.00)	0.552 (1.00)
DEL PEAK 18(8P23 2) MUTATION ANALYSIS	66 (12%)	487	0.21 (1.00)	0.0314 (1.00)	0.594 (1.00)	0.648 (1.00)	0.889 (1.00)	0.571 (1.00)
DEL PEAK 20(9Q34 2) MUTATION ANALYSIS	71 (13%)	482	0.452 (1.00)	0.586 (1.00)	1 (1.00)	0.513 (1.00)	0.894 (1.00)	1 (1.00)
DEL PEAK 26(11P15 5) MUTATION ANALYSIS	126 (23%)	427	0.0194 (1.00)	0.0036 (1.00)	0.213 (1.00)	0.256 (1.00)	0.503 (1.00)	0.913 (1.00)
DEL PEAK 27(11P11 2) MUTATION ANALYSIS	100 (18%)	453	0.0555 (1.00)	0.684 (1.00)	0.143 (1.00)	0.818 (1.00)	0.222 (1.00)	0.812 (1.00)
DEL PEAK 28(11Q14 1) MUTATION ANALYSIS	94 (17%)	459	0.98 (1.00)	0.77 (1.00)	0.297 (1.00)	0.521 (1.00)	0.399 (1.00)	0.0656 (1.00)
DEL PEAK 29(12P13 1) MUTATION ANALYSIS	73 (13%)	480	0.208 (1.00)	0.852 (1.00)	0.441 (1.00)	0.729 (1.00)	0.811 (1.00)	0.786 (1.00)
DEL PEAK 30(12Q12) MUTATION ANALYSIS	75 (14%)	478	0.54 (1.00)	0.7 (1.00)	0.9 (1.00)	0.792 (1.00)	1 (1.00)	0.347 (1.00)
DEL PEAK 31(12Q15) MUTATION ANALYSIS	76 (14%)	477	0.572 (1.00)	0.681 (1.00)	0.451 (1.00)	0.178 (1.00)	0.669 (1.00)	0.144 (1.00)
DEL PEAK 32(13Q14 2) MUTATION ANALYSIS	233 (42%)	320	0.748 (1.00)	0.577 (1.00)	0.792 (1.00)	0.789 (1.00)	0.584 (1.00)	0.514 (1.00)
DEL PEAK 33(14Q13 1) MUTATION ANALYSIS	172 (31%)	381	0.691 (1.00)	0.562 (1.00)	0.189 (1.00)	0.224 (1.00)	0.0839 (1.00)	0.552 (1.00)
DEL PEAK 34(14Q24 2) MUTATION ANALYSIS	167 (30%)	386	0.645 (1.00)	0.421 (1.00)	0.344 (1.00)	0.545 (1.00)	0.0593 (1.00)	0.369 (1.00)
DEL PEAK 35(14Q31 3) MUTATION ANALYSIS	154 (28%)	399	0.874 (1.00)	0.689 (1.00)	0.561 (1.00)	0.581 (1.00)	0.0336 (1.00)	0.474 (1.00)
DEL PEAK 36(15Q14) MUTATION ANALYSIS	146 (26%)	407	0.314 (1.00)	0.064 (1.00)	0.768 (1.00)	0.723 (1.00)	0.546 (1.00)	0.348 (1.00)
DEL PEAK 37(16P12 2) MUTATION ANALYSIS	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 PEAK 38(16Q23 3) MUTATION ANALYSIS	93 (17%)	460	0.0572 (1.00)	0.956 (1.00)	0.485 (1.00)	0.256 (1.00)	0.395 (1.00)	0.0268 (1.00)
DEL PEAK 39(17P13 2) MUTATION ANALYSIS	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 PEAK 40(17P13 1) MUTATION ANALYSIS	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 PEAK 41(17Q11 2) MUTATION ANALYSIS	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 PEAK 42(18Q22 3) MUTATION ANALYSIS	79 (14%)	474	0.537 (1.00)	0.594 (1.00)	0.805 (1.00)	0.122 (1.00)	1 (1.00)	0.896 (1.00)
DEL PEAK 43(19Q13 41) MUTATION ANALYSIS	99 (18%)	454	0.0311 (1.00)	0.314 (1.00)	1 (1.00)	0.278 (1.00)	0.725 (1.00)	1 (1.00)
DEL PEAK 44(21Q22 3) MUTATION ANALYSIS	59 (11%)	494	0.534 (1.00)	0.0624 (1.00)	0.325 (1.00)	0.205 (1.00)	1 (1.00)	0.655 (1.00)
DEL PEAK 45(22Q13 32) MUTATION ANALYSIS	207 (37%)	346	0.922 (1.00)	0.373 (1.00)	1 (1.00)	0.547 (1.00)	0.86 (1.00)	0.705 (1.00)
DEL PEAK 46(XP22 2) MUTATION ANALYSIS	123 (22%)	430	0.0913 (1.00)	0.34 (1.00)	0.676 (1.00)	0.8 (1.00)	0.618 (1.00)	0.58 (1.00)

'AMP PEAK 8(7P11.2) MUTATION STATUS' versus 'Time to Death'

P value = 2.4e-07 (logrank test), Q value = 9.9e-05

Table S1. Gene #8: 'AMP PEAK 8(7P11.2) MUTATION STATUS' 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	484	397	0.1 - 127.6 (9.4)
AMP PEAK 8(7P11.2) WILD-TYPE	69	48	0.2 - 108.8 (15.3)

Figure S1. Get High-res Image Gene #8: 'AMP PEAK 8(7P11.2) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 8(7P11.2) MUTATION STATUS' versus 'AGE'

P value = 1.84e-09 (t-test), Q value = 7.7e-07

Table S2. Gene #8: 'AMP PEAK 8(7P11.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 8(7P11.2) MUTATED	484	59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE	69	43.9 (18.8)

Figure S2. Get High-res Image Gene #8: 'AMP PEAK 8(7P11.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 9(7Q11.21) MUTATION STATUS' versus 'Time to Death'

P value = 1.83e-05 (logrank test), Q value = 0.0075

Table S3. Gene #9: 'AMP PEAK 9(7Q11.21) MUTATION STATUS' 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	443	360	0.1 - 127.6 (9.4)
AMP PEAK 9(7Q11.21) WILD-TYPE	110	85	0.2 - 108.8 (14.3)

Figure S3. Get High-res Image Gene #9: 'AMP PEAK 9(7Q11.21) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 9(7Q11.21) MUTATION STATUS' versus 'AGE'

P value = 6.97e-08 (t-test), Q value = 2.9e-05

Table S4. Gene #9: 'AMP PEAK 9(7Q11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 9(7Q11.21) MUTATED	443	59.9 (12.5)
AMP PEAK 9(7Q11.21) WILD-TYPE	110	49.4 (18.4)

Figure S4. Get High-res Image Gene #9: 'AMP PEAK 9(7Q11.21) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 10(7Q21.2) MUTATION STATUS' versus 'Time to Death'

P value = 0.000339 (logrank test), Q value = 0.14

Table S5. Gene #10: 'AMP PEAK 10(7Q21.2) MUTATION STATUS' 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 PEAK 10(7Q21.2) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 10(7Q21.2) MUTATION STATUS' versus 'AGE'

P value = 1.8e-05 (t-test), Q value = 0.0074

Table S6. Gene #10: 'AMP PEAK 10(7Q21.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
AMP PEAK 10(7Q21.2) MUTATED	458	59.4 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE	95	50.0 (19.8)

Figure S6. Get High-res Image Gene #10: 'AMP PEAK 10(7Q21.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 19(9P21.3) MUTATION STATUS' versus 'AGE'

P value = 0.00047 (t-test), Q value = 0.19

Table S7. Gene #43: 'DEL PEAK 19(9P21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	553	57.8 (14.4)
DEL PEAK 19(9P21.3) MUTATED	403	59.2 (13.7)
DEL PEAK 19(9P21.3) WILD-TYPE	150	54.1 (15.7)

Figure S7. Get High-res Image Gene #43: 'DEL PEAK 19(9P21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 21(10P15.3) MUTATION STATUS' versus 'Time to Death'

P value = 1.91e-06 (logrank test), Q value = 0.00079

Table S8. Gene #45: 'DEL PEAK 21(10P15.3) MUTATION STATUS' 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 S8. Get High-res Image Gene #45: 'DEL PEAK 21(10P15.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 21(10P15.3) MUTATION STATUS' versus 'AGE'

P value = 3.76e-08 (t-test), Q value = 1.6e-05

Table S9. Gene #45: 'DEL PEAK 21(10P15.3) MUTATION STATUS' 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 S9. Get High-res Image Gene #45: 'DEL PEAK 21(10P15.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 22(10P13) MUTATION STATUS' versus 'Time to Death'

P value = 1.27e-06 (logrank test), Q value = 0.00052

Table S10. Gene #46: 'DEL PEAK 22(10P13) MUTATION STATUS' 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 S10. Get High-res Image Gene #46: 'DEL PEAK 22(10P13) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 22(10P13) MUTATION STATUS' versus 'AGE'

P value = 1.82e-07 (t-test), Q value = 7.5e-05

Table S11. Gene #46: 'DEL PEAK 22(10P13) MUTATION STATUS' 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 S11. Get High-res Image Gene #46: 'DEL PEAK 22(10P13) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 23(10P11.23) MUTATION STATUS' versus 'Time to Death'

P value = 9.13e-08 (logrank test), Q value = 3.8e-05

Table S12. Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' 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 S12. Get High-res Image Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 23(10P11.23) MUTATION STATUS' versus 'AGE'

P value = 1.06e-08 (t-test), Q value = 4.5e-06

Table S13. Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' 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 S13. Get High-res Image Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 23(10P11.23) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

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

Table S14. Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' 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 S14. Get High-res Image Gene #47: 'DEL PEAK 23(10P11.23) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'DEL PEAK 24(10Q23.31) MUTATION STATUS' versus 'Time to Death'

P value = 1.08e-05 (logrank test), Q value = 0.0044

Table S15. Gene #48: 'DEL PEAK 24(10Q23.31) MUTATION STATUS' 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 S15. Get High-res Image Gene #48: 'DEL PEAK 24(10Q23.31) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 24(10Q23.31) MUTATION STATUS' versus 'AGE'

P value = 6.33e-06 (t-test), Q value = 0.0026

Table S16. Gene #48: 'DEL PEAK 24(10Q23.31) MUTATION STATUS' 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 S16. Get High-res Image Gene #48: 'DEL PEAK 24(10Q23.31) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 25(10Q26.3) MUTATION STATUS' versus 'AGE'

P value = 5.9e-05 (t-test), Q value = 0.024

Table S17. Gene #49: 'DEL PEAK 25(10Q26.3) MUTATION STATUS' 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 S17. Get High-res Image Gene #49: 'DEL PEAK 25(10Q26.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = GBM-TP.clin.merged.picked.txt
Number of patients = 553
Number of significantly focal cnvs = 70
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)

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