Correlation between copy number variation genes and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

22 February 2013 | analyses__2013_02_22

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 and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1125QVV

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 51 peak regions and 8 molecular subtypes across 236 patients, 34 significant findings detected with Q value < 0.25.

Amp Peak 1(1p12) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 8(6p25.1) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 10(7p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(7q34) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 20(17q25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(20q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.31) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 3(2q37.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
Del Peak 7(5q31.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 8(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 9(7q31.1) cnvs correlated to 'CN_CNMF'.
Del Peak 11(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 12(9p21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 13(10p15.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 14(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 15(10q26.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(11q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(14q32.2) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 51 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 8(6p25 1)	136 (58%)	100	7.76e-08 (3.14e-05)	0.000731 (0.273)	0.0141 (1.00)	0.47 (1.00)	0.146 (1.00)	0.0155 (1.00)	0.000201 (0.0772)	2.81e-05 (0.011)
Amp Peak 7(5q35 3)	37 (16%)	199	0.000636 (0.238)	0.000359 (0.137)	0.176 (1.00)	0.0836 (1.00)	0.108 (1.00)	0.0273 (1.00)	0.049 (1.00)	0.02 (1.00)
Del Peak 1(1p36 31)	56 (24%)	180	0.0041 (1.00)	7.52e-05 (0.0289)	0.467 (1.00)	0.431 (1.00)	0.0883 (1.00)	0.000446 (0.168)	0.153 (1.00)	0.214 (1.00)
Del Peak 2(1p22 1)	62 (26%)	174	0.00233 (0.841)	0.000432 (0.164)	0.171 (1.00)	0.145 (1.00)	0.00062 (0.233)	0.00449 (1.00)	0.591 (1.00)	0.902 (1.00)
Del Peak 12(9p21 3)	181 (77%)	55	4.76e-10 (1.93e-07)	0.00129 (0.475)	0.41 (1.00)	0.279 (1.00)	2.72e-05 (0.0107)	0.00114 (0.422)	0.631 (1.00)	0.561 (1.00)
Del Peak 13(10p15 3)	130 (55%)	106	1.76e-06 (0.000701)	0.00935 (1.00)	0.715 (1.00)	0.405 (1.00)	1.66e-05 (0.00653)	0.00181 (0.657)	0.144 (1.00)	0.374 (1.00)
Del Peak 14(10q23 31)	145 (61%)	91	3.06e-06 (0.00122)	0.0258 (1.00)	0.496 (1.00)	0.87 (1.00)	0.000246 (0.0941)	0.00594 (1.00)	0.514 (1.00)	0.607 (1.00)
Del Peak 15(10q26 3)	147 (62%)	89	3.29e-05 (0.0128)	0.195 (1.00)	0.629 (1.00)	0.98 (1.00)	2.9e-05 (0.0113)	0.00132 (0.482)	0.409 (1.00)	0.845 (1.00)
Amp Peak 1(1p12)	70 (30%)	166	3.43e-05 (0.0133)	0.434 (1.00)	0.727 (1.00)	0.121 (1.00)	0.102 (1.00)	0.0412 (1.00)	0.659 (1.00)	0.539 (1.00)
Amp Peak 2(1q21 3)	120 (51%)	116	6.22e-06 (0.00246)	0.116 (1.00)	0.836 (1.00)	0.199 (1.00)	0.0507 (1.00)	0.219 (1.00)	0.424 (1.00)	0.53 (1.00)
Amp Peak 3(1q44)	125 (53%)	111	2.94e-06 (0.00117)	0.0119 (1.00)	0.866 (1.00)	0.986 (1.00)	0.172 (1.00)	0.252 (1.00)	0.156 (1.00)	0.119 (1.00)
Amp Peak 6(5p15 33)	71 (30%)	165	0.000371 (0.141)	0.25 (1.00)	0.434 (1.00)	0.505 (1.00)	0.269 (1.00)	0.14 (1.00)	0.014 (1.00)	0.0888 (1.00)
Amp Peak 10(7p22 3)	126 (53%)	110	2.28e-11 (9.28e-09)	0.276 (1.00)	0.777 (1.00)	0.906 (1.00)	0.0405 (1.00)	0.0415 (1.00)	0.636 (1.00)	0.509 (1.00)
Amp Peak 11(7q34)	140 (59%)	96	5.52e-15 (2.25e-12)	0.615 (1.00)	0.675 (1.00)	0.433 (1.00)	0.128 (1.00)	0.672 (1.00)	0.581 (1.00)	0.31 (1.00)
Amp Peak 12(8q11 21)	98 (42%)	138	2.78e-05 (0.0109)	0.00437 (1.00)	0.31 (1.00)	0.343 (1.00)	0.0386 (1.00)	0.0395 (1.00)	0.412 (1.00)	0.832 (1.00)
Amp Peak 13(8q24 21)	115 (49%)	121	1.1e-07 (4.43e-05)	0.00346 (1.00)	0.772 (1.00)	0.72 (1.00)	0.0298 (1.00)	0.118 (1.00)	0.667 (1.00)	0.268 (1.00)
Amp Peak 20(17q25 3)	87 (37%)	149	0.000204 (0.0782)	0.0049 (1.00)	0.248 (1.00)	0.135 (1.00)	0.0787 (1.00)	0.166 (1.00)	0.0871 (1.00)	0.0301 (1.00)
Amp Peak 22(20q13 2)	125 (53%)	111	5.89e-07 (0.000236)	0.00952 (1.00)	0.372 (1.00)	0.995 (1.00)	0.00857 (1.00)	0.042 (1.00)	0.873 (1.00)	0.621 (1.00)
Del Peak 3(2q37 3)	61 (26%)	175	0.386 (1.00)	0.0618 (1.00)	0.334 (1.00)	0.121 (1.00)	0.0378 (1.00)	4.17e-05 (0.0161)	0.0434 (1.00)	0.0174 (1.00)
Del Peak 7(5q31 3)	88 (37%)	148	0.215 (1.00)	8.64e-06 (0.00341)	0.121 (1.00)	0.672 (1.00)	0.785 (1.00)	0.699 (1.00)	0.535 (1.00)	0.362 (1.00)
Del Peak 8(6q26)	149 (63%)	87	5.79e-07 (0.000233)	0.0171 (1.00)	0.493 (1.00)	0.464 (1.00)	0.00186 (0.677)	0.224 (1.00)	0.492 (1.00)	0.899 (1.00)
Del Peak 9(7q31 1)	18 (8%)	218	0.000433 (0.164)	0.0339 (1.00)	0.293 (1.00)	0.487 (1.00)	0.395 (1.00)	0.205 (1.00)	0.213 (1.00)	0.181 (1.00)
Del Peak 11(9p23)	160 (68%)	76	4.39e-07 (0.000177)	0.0437 (1.00)	0.27 (1.00)	0.648 (1.00)	0.00116 (0.428)	0.00557 (1.00)	0.487 (1.00)	0.233 (1.00)
Del Peak 16(11q23 3)	132 (56%)	104	7.12e-07 (0.000285)	0.0714 (1.00)	0.662 (1.00)	0.388 (1.00)	0.292 (1.00)	0.158 (1.00)	0.249 (1.00)	0.0608 (1.00)
Del Peak 21(14q32 2)	78 (33%)	158	2.94e-05 (0.0114)	0.579 (1.00)	0.0207 (1.00)	0.572 (1.00)	0.02 (1.00)	0.437 (1.00)	0.581 (1.00)	0.598 (1.00)
Amp Peak 4(3p13)	60 (25%)	176	0.63 (1.00)	0.676 (1.00)	0.982 (1.00)	0.0468 (1.00)	1 (1.00)	0.98 (1.00)	0.806 (1.00)	0.446 (1.00)
Amp Peak 5(4q12)	45 (19%)	191	0.000815 (0.303)	0.309 (1.00)	0.338 (1.00)	0.124 (1.00)	0.703 (1.00)	0.266 (1.00)	0.0705 (1.00)	0.00818 (1.00)
Amp Peak 9(6q12)	55 (23%)	181	0.000796 (0.297)	0.609 (1.00)	0.441 (1.00)	0.606 (1.00)	0.0486 (1.00)	0.679 (1.00)	0.267 (1.00)	0.256 (1.00)
Amp Peak 14(9p24 1)	21 (9%)	215	0.654 (1.00)	0.385 (1.00)	0.463 (1.00)	0.827 (1.00)	0.562 (1.00)	0.953 (1.00)	0.401 (1.00)	0.836 (1.00)
Amp Peak 15(11q13 3)	44 (19%)	192	0.198 (1.00)	0.199 (1.00)	0.763 (1.00)	0.96 (1.00)	0.734 (1.00)	0.926 (1.00)	0.323 (1.00)	0.302 (1.00)
Amp Peak 16(11q13 4)	41 (17%)	195	0.0827 (1.00)	0.0865 (1.00)	0.888 (1.00)	0.794 (1.00)	0.344 (1.00)	0.439 (1.00)	0.171 (1.00)	0.153 (1.00)
Amp Peak 17(12q14 1)	41 (17%)	195	0.029 (1.00)	0.392 (1.00)	0.419 (1.00)	0.425 (1.00)	0.207 (1.00)	0.0646 (1.00)	0.792 (1.00)	0.814 (1.00)
Amp Peak 18(12q15)	39 (17%)	197	0.026 (1.00)	0.904 (1.00)	0.651 (1.00)	0.305 (1.00)	0.773 (1.00)	0.695 (1.00)	0.851 (1.00)	0.606 (1.00)
Amp Peak 19(15q24 3)	76 (32%)	160	0.00156 (0.569)	0.458 (1.00)	0.462 (1.00)	0.713 (1.00)	0.463 (1.00)	0.754 (1.00)	0.871 (1.00)	0.744 (1.00)
Amp Peak 21(19p13 2)	49 (21%)	187	0.0105 (1.00)	0.177 (1.00)	0.622 (1.00)	0.253 (1.00)	0.0504 (1.00)	0.0431 (1.00)	0.478 (1.00)	0.0505 (1.00)
Amp Peak 23(22q13 2)	100 (42%)	136	0.0158 (1.00)	0.0455 (1.00)	0.65 (1.00)	0.813 (1.00)	0.584 (1.00)	0.501 (1.00)	0.213 (1.00)	0.481 (1.00)
Del Peak 4(3q23)	37 (16%)	199	0.153 (1.00)	0.011 (1.00)	0.622 (1.00)	0.736 (1.00)	0.517 (1.00)	0.691 (1.00)	0.709 (1.00)	0.71 (1.00)
Del Peak 5(4q34 3)	66 (28%)	170	0.0041 (1.00)	0.129 (1.00)	0.143 (1.00)	0.643 (1.00)	0.0315 (1.00)	0.000947 (0.351)	0.0365 (1.00)	0.00104 (0.384)
Del Peak 6(5q11 2)	65 (28%)	171	0.226 (1.00)	0.027 (1.00)	0.383 (1.00)	0.163 (1.00)	0.428 (1.00)	0.123 (1.00)	0.727 (1.00)	0.582 (1.00)
Del Peak 10(8p23 3)	60 (25%)	176	0.0298 (1.00)	0.0827 (1.00)	0.00836 (1.00)	0.106 (1.00)	0.133 (1.00)	0.726 (1.00)	0.175 (1.00)	0.432 (1.00)
Del Peak 17(12p13 31)	36 (15%)	200	0.408 (1.00)	0.142 (1.00)	0.197 (1.00)	0.275 (1.00)	0.198 (1.00)	1 (1.00)	0.403 (1.00)	0.926 (1.00)
Del Peak 18(12q23 3)	55 (23%)	181	0.0116 (1.00)	0.0175 (1.00)	0.481 (1.00)	0.486 (1.00)	0.807 (1.00)	0.446 (1.00)	0.938 (1.00)	0.541 (1.00)
Del Peak 19(12q24 33)	54 (23%)	182	0.00784 (1.00)	0.0306 (1.00)	0.491 (1.00)	0.586 (1.00)	0.686 (1.00)	0.405 (1.00)	0.881 (1.00)	0.442 (1.00)
Del Peak 20(13q34)	57 (24%)	179	0.0111 (1.00)	0.00335 (1.00)	0.451 (1.00)	0.978 (1.00)	0.502 (1.00)	0.455 (1.00)	0.446 (1.00)	0.0854 (1.00)
Del Peak 22(15q13 3)	54 (23%)	182	0.00836 (1.00)	0.166 (1.00)	0.747 (1.00)	0.897 (1.00)	0.451 (1.00)	0.0576 (1.00)	0.451 (1.00)	0.381 (1.00)
Del Peak 23(15q15 3)	56 (24%)	180	0.038 (1.00)	0.198 (1.00)	0.616 (1.00)	0.921 (1.00)	0.822 (1.00)	0.11 (1.00)	0.329 (1.00)	0.0774 (1.00)
Del Peak 24(16p13 3)	46 (19%)	190	0.765 (1.00)	0.0284 (1.00)	0.472 (1.00)	0.619 (1.00)	0.319 (1.00)	0.29 (1.00)	0.0932 (1.00)	0.853 (1.00)
Del Peak 25(16q12 1)	79 (33%)	157	0.229 (1.00)	0.297 (1.00)	0.812 (1.00)	0.284 (1.00)	0.269 (1.00)	0.857 (1.00)	0.107 (1.00)	0.15 (1.00)
Del Peak 26(16q24 3)	87 (37%)	149	0.213 (1.00)	0.4 (1.00)	0.759 (1.00)	0.166 (1.00)	0.0367 (1.00)	0.26 (1.00)	0.0243 (1.00)	0.0671 (1.00)
Del Peak 27(19p13 3)	70 (30%)	166	0.0349 (1.00)	0.298 (1.00)	0.184 (1.00)	0.265 (1.00)	0.00187 (0.678)	0.0833 (1.00)	0.524 (1.00)	0.493 (1.00)
Del Peak 28(22q13 31)	31 (13%)	205	0.437 (1.00)	0.759 (1.00)	0.418 (1.00)	0.162 (1.00)	1 (1.00)	0.822 (1.00)	0.0604 (1.00)	0.652 (1.00)

'Amp Peak 1(1p12) mutation analysis' versus 'CN_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.013

Table S1. Gene #1: 'Amp Peak 1(1p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 1(1P12) MUTATED	39	19	12
AMP PEAK 1(1P12) WILD-TYPE	41	71	54

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q21.3) mutation analysis' versus 'CN_CNMF'

P value = 6.22e-06 (Fisher's exact test), Q value = 0.0025

Table S2. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 2(1Q21.3) MUTATED	58	33	29
AMP PEAK 2(1Q21.3) WILD-TYPE	22	57	37

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(1q44) mutation analysis' versus 'CN_CNMF'

P value = 2.94e-06 (Fisher's exact test), Q value = 0.0012

Table S3. Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 3(1Q44) MUTATED	60	34	31
AMP PEAK 3(1Q44) WILD-TYPE	20	56	35

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 0.000371 (Fisher's exact test), Q value = 0.14

Table S4. Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 6(5P15.33) MUTATED	33	14	24
AMP PEAK 6(5P15.33) WILD-TYPE	47	76	42

Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(5q35.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000636 (Fisher's exact test), Q value = 0.24

Table S5. Gene #7: 'Amp Peak 7(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 7(5Q35.3) MUTATED	21	5	11
AMP PEAK 7(5Q35.3) WILD-TYPE	59	85	55

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(5q35.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.14

Table S6. Gene #7: 'Amp Peak 7(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	84	91
AMP PEAK 7(5Q35.3) MUTATED	19	12	6
AMP PEAK 7(5Q35.3) WILD-TYPE	42	72	85

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 8(6p25.1) mutation analysis' versus 'CN_CNMF'

P value = 7.76e-08 (Fisher's exact test), Q value = 3.1e-05

Table S7. Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 8(6P25.1) MUTATED	66	39	31
AMP PEAK 8(6P25.1) WILD-TYPE	14	51	35

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 8(6p25.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.077

Table S8. Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	98	90
AMP PEAK 8(6P25.1) MUTATED	25	71	39
AMP PEAK 8(6P25.1) WILD-TYPE	22	27	51

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Amp Peak 8(6p25.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.011

Table S9. Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	62	147
AMP PEAK 8(6P25.1) MUTATED	14	21	100
AMP PEAK 8(6P25.1) WILD-TYPE	12	41	47

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 10(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.28e-11 (Fisher's exact test), Q value = 9.3e-09

Table S10. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 10(7P22.3) MUTATED	40	29	57
AMP PEAK 10(7P22.3) WILD-TYPE	40	61	9

Figure S10. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(7q34) mutation analysis' versus 'CN_CNMF'

P value = 5.52e-15 (Fisher's exact test), Q value = 2.3e-12

Table S11. Gene #11: 'Amp Peak 11(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 11(7Q34) MUTATED	35	41	64
AMP PEAK 11(7Q34) WILD-TYPE	45	49	2

Figure S11. Get High-res Image Gene #11: 'Amp Peak 11(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 12(8q11.21) mutation analysis' versus 'CN_CNMF'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.011

Table S12. Gene #12: 'Amp Peak 12(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 12(8Q11.21) MUTATED	40	21	37
AMP PEAK 12(8Q11.21) WILD-TYPE	40	69	29

Figure S12. Get High-res Image Gene #12: 'Amp Peak 12(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 13(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 1.1e-07 (Fisher's exact test), Q value = 4.4e-05

Table S13. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 13(8Q24.21) MUTATED	50	23	42
AMP PEAK 13(8Q24.21) WILD-TYPE	30	67	24

Figure S13. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 20(17q25.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.078

Table S14. Gene #20: 'Amp Peak 20(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 20(17Q25.3) MUTATED	43	21	23
AMP PEAK 20(17Q25.3) WILD-TYPE	37	69	43

Figure S14. Get High-res Image Gene #20: 'Amp Peak 20(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 22(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.89e-07 (Fisher's exact test), Q value = 0.00024

Table S15. Gene #22: 'Amp Peak 22(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
AMP PEAK 22(20Q13.2) MUTATED	51	28	46
AMP PEAK 22(20Q13.2) WILD-TYPE	29	62	20

Figure S15. Get High-res Image Gene #22: 'Amp Peak 22(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.029

Table S16. Gene #24: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	84	91
DEL PEAK 1(1P36.31) MUTATED	27	17	12
DEL PEAK 1(1P36.31) WILD-TYPE	34	67	79

Figure S16. Get High-res Image Gene #24: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000446 (Fisher's exact test), Q value = 0.17

Table S17. Gene #24: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	116	57
DEL PEAK 1(1P36.31) MUTATED	15	17	24
DEL PEAK 1(1P36.31) WILD-TYPE	44	99	33

Figure S17. Get High-res Image Gene #24: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 2(1p22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000432 (Fisher's exact test), Q value = 0.16

Table S18. Gene #25: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	84	91
DEL PEAK 2(1P22.1) MUTATED	28	15	19
DEL PEAK 2(1P22.1) WILD-TYPE	33	69	72

Figure S18. Get High-res Image Gene #25: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.23

Table S19. Gene #25: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	67	84
DEL PEAK 2(1P22.1) MUTATED	33	9	19
DEL PEAK 2(1P22.1) WILD-TYPE	48	58	65

Figure S19. Get High-res Image Gene #25: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 3(2q37.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.016

Table S20. Gene #26: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	59	116	57
DEL PEAK 3(2Q37.3) MUTATED	9	23	28
DEL PEAK 3(2Q37.3) WILD-TYPE	50	93	29

Figure S20. Get High-res Image Gene #26: 'Del Peak 3(2q37.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 7(5q31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 8.64e-06 (Fisher's exact test), Q value = 0.0034

Table S21. Gene #30: 'Del Peak 7(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	84	91
DEL PEAK 7(5Q31.3) MUTATED	11	47	30
DEL PEAK 7(5Q31.3) WILD-TYPE	50	37	61

Figure S21. Get High-res Image Gene #30: 'Del Peak 7(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(6q26) mutation analysis' versus 'CN_CNMF'

P value = 5.79e-07 (Fisher's exact test), Q value = 0.00023

Table S22. Gene #31: 'Del Peak 8(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 8(6Q26) MUTATED	64	38	47
DEL PEAK 8(6Q26) WILD-TYPE	16	52	19

Figure S22. Get High-res Image Gene #31: 'Del Peak 8(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(7q31.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000433 (Fisher's exact test), Q value = 0.16

Table S23. Gene #32: 'Del Peak 9(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 9(7Q31.1) MUTATED	13	5	0
DEL PEAK 9(7Q31.1) WILD-TYPE	67	85	66

Figure S23. Get High-res Image Gene #32: 'Del Peak 9(7q31.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(9p23) mutation analysis' versus 'CN_CNMF'

P value = 4.39e-07 (Fisher's exact test), Q value = 0.00018

Table S24. Gene #34: 'Del Peak 11(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 11(9P23) MUTATED	64	42	54
DEL PEAK 11(9P23) WILD-TYPE	16	48	12

Figure S24. Get High-res Image Gene #34: 'Del Peak 11(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 4.76e-10 (Fisher's exact test), Q value = 1.9e-07

Table S25. Gene #35: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 12(9P21.3) MUTATED	69	49	63
DEL PEAK 12(9P21.3) WILD-TYPE	11	41	3

Figure S25. Get High-res Image Gene #35: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.011

Table S26. Gene #35: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	67	84
DEL PEAK 12(9P21.3) MUTATED	75	42	62
DEL PEAK 12(9P21.3) WILD-TYPE	6	25	22

Figure S26. Get High-res Image Gene #35: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 13(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 1.76e-06 (Fisher's exact test), Q value = 7e-04

Table S27. Gene #36: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 13(10P15.3) MUTATED	46	33	51
DEL PEAK 13(10P15.3) WILD-TYPE	34	57	15

Figure S27. Get High-res Image Gene #36: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(10p15.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0065

Table S28. Gene #36: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	67	84
DEL PEAK 13(10P15.3) MUTATED	61	28	38
DEL PEAK 13(10P15.3) WILD-TYPE	20	39	46

Figure S28. Get High-res Image Gene #36: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 14(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.0012

Table S29. Gene #37: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 14(10Q23.31) MUTATED	50	40	55
DEL PEAK 14(10Q23.31) WILD-TYPE	30	50	11

Figure S29. Get High-res Image Gene #37: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000246 (Fisher's exact test), Q value = 0.094

Table S30. Gene #37: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	67	84
DEL PEAK 14(10Q23.31) MUTATED	64	34	45
DEL PEAK 14(10Q23.31) WILD-TYPE	17	33	39

Figure S30. Get High-res Image Gene #37: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 15(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 3.29e-05 (Fisher's exact test), Q value = 0.013

Table S31. Gene #38: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 15(10Q26.3) MUTATED	48	44	55
DEL PEAK 15(10Q26.3) WILD-TYPE	32	46	11

Figure S31. Get High-res Image Gene #38: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(10q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.9e-05 (Fisher's exact test), Q value = 0.011

Table S32. Gene #38: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	67	84
DEL PEAK 15(10Q26.3) MUTATED	66	35	43
DEL PEAK 15(10Q26.3) WILD-TYPE	15	32	41

Figure S32. Get High-res Image Gene #38: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 16(11q23.3) mutation analysis' versus 'CN_CNMF'

P value = 7.12e-07 (Fisher's exact test), Q value = 0.00028

Table S33. Gene #39: 'Del Peak 16(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 16(11Q23.3) MUTATED	63	36	33
DEL PEAK 16(11Q23.3) WILD-TYPE	17	54	33

Figure S33. Get High-res Image Gene #39: 'Del Peak 16(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(14q32.2) mutation analysis' versus 'CN_CNMF'

P value = 2.94e-05 (Fisher's exact test), Q value = 0.011

Table S34. Gene #44: 'Del Peak 21(14q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	90	66
DEL PEAK 21(14Q32.2) MUTATED	30	15	33
DEL PEAK 21(14Q32.2) WILD-TYPE	50	75	33

Figure S34. Get High-res Image Gene #44: 'Del Peak 21(14q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = SKCM-TM.transferedmergedcluster.txt
Number of patients = 236
Number of copy number variation regions = 51
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] 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)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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)

[4] GISTIC_version2

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