Correlation between copy number variation genes and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

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 and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C18S4N9W

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 55 peak regions and 10 molecular subtypes across 267 patients, 34 significant findings detected with Q value < 0.25.

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' and 'MIRSEQ_MATURE_CNMF'.
Amp Peak 7(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 8(6p25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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 15(11q13.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(11q13.4) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(20q13.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 23(22q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 9(5q31.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 10(6q22.31) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 14(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(10p15.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 18(10q26.3) cnvs correlated to 'MRNASEQ_CNMF'.
Del Peak 19(11q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 24(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 55 regions and 10 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	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact 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)	0 (0%)	116	3.31e-05 (0.0175)	0.000379 (0.196)	0.224 (1.00)	0.00992 (1.00)	0.0527 (1.00)	0.00583 (1.00)	0.00122 (0.624)	1.03e-05 (0.00553)	0.0123 (1.00)	2.5e-05 (0.0133)
Amp Peak 6(5p15 33)	0 (0%)	182	1.27e-09 (6.92e-07)	0.29 (1.00)	0.846 (1.00)	0.421 (1.00)	0.301 (1.00)	0.149 (1.00)	0.000584 (0.301)	0.0333 (1.00)	9.59e-05 (0.0502)	0.0072 (1.00)
Amp Peak 7(5q35 3)	0 (0%)	225	2.8e-05 (0.0148)	0.000302 (0.157)	0.1 (1.00)	0.0263 (1.00)	0.0881 (1.00)	0.0186 (1.00)	0.0245 (1.00)	0.0383 (1.00)	0.134 (1.00)	0.101 (1.00)
Del Peak 2(1p22 1)	0 (0%)	199	0.0633 (1.00)	0.000127 (0.0662)	0.615 (1.00)	0.0886 (1.00)	0.000117 (0.0611)	0.126 (1.00)	0.497 (1.00)	0.343 (1.00)	0.186 (1.00)	0.289 (1.00)
Del Peak 15(9p21 3)	0 (0%)	61	1.09e-09 (5.95e-07)	0.00226 (1.00)	0.605 (1.00)	0.6 (1.00)	0.000114 (0.0594)	0.0236 (1.00)	0.896 (1.00)	0.698 (1.00)	0.882 (1.00)	0.851 (1.00)
Del Peak 16(10p15 3)	0 (0%)	122	1.88e-05 (0.01)	0.0271 (1.00)	0.685 (1.00)	0.598 (1.00)	8.7e-05 (0.0457)	0.00157 (0.801)	0.548 (1.00)	0.506 (1.00)	0.492 (1.00)	0.469 (1.00)
Del Peak 17(10q23 31)	0 (0%)	103	3.27e-05 (0.0173)	0.0976 (1.00)	0.911 (1.00)	0.076 (1.00)	8.53e-05 (0.0448)	0.00778 (1.00)	0.496 (1.00)	0.539 (1.00)	0.772 (1.00)	0.239 (1.00)
Amp Peak 2(1q21 3)	0 (0%)	132	3.14e-10 (1.72e-07)	0.032 (1.00)	0.285 (1.00)	1 (1.00)	0.027 (1.00)	0.478 (1.00)	0.268 (1.00)	0.0177 (1.00)	0.49 (1.00)	0.211 (1.00)
Amp Peak 3(1q44)	0 (0%)	125	2.22e-10 (1.22e-07)	0.00678 (1.00)	0.109 (1.00)	0.489 (1.00)	0.0985 (1.00)	0.545 (1.00)	0.135 (1.00)	0.00209 (1.00)	0.401 (1.00)	0.0413 (1.00)
Amp Peak 10(7p22 3)	0 (0%)	124	1.15e-05 (0.00616)	0.492 (1.00)	0.528 (1.00)	0.87 (1.00)	0.0229 (1.00)	0.404 (1.00)	0.876 (1.00)	0.812 (1.00)	0.695 (1.00)	0.365 (1.00)
Amp Peak 11(7q34)	0 (0%)	109	0.000344 (0.178)	0.267 (1.00)	0.331 (1.00)	0.526 (1.00)	0.0966 (1.00)	0.128 (1.00)	0.0756 (1.00)	0.189 (1.00)	0.171 (1.00)	0.289 (1.00)
Amp Peak 12(8q11 21)	0 (0%)	150	1.54e-05 (0.00821)	0.00353 (1.00)	0.442 (1.00)	0.226 (1.00)	0.026 (1.00)	0.301 (1.00)	0.676 (1.00)	0.966 (1.00)	0.559 (1.00)	0.713 (1.00)
Amp Peak 13(8q24 21)	0 (0%)	132	3.17e-08 (1.72e-05)	0.00273 (1.00)	0.525 (1.00)	0.532 (1.00)	0.00933 (1.00)	0.546 (1.00)	0.831 (1.00)	0.585 (1.00)	0.802 (1.00)	0.616 (1.00)
Amp Peak 15(11q13 3)	0 (0%)	217	7.05e-06 (0.0038)	0.0868 (1.00)	0.874 (1.00)	0.541 (1.00)	0.44 (1.00)	1 (1.00)	0.803 (1.00)	0.237 (1.00)	0.492 (1.00)	0.576 (1.00)
Amp Peak 16(11q13 4)	0 (0%)	221	3.58e-06 (0.00193)	0.017 (1.00)	0.903 (1.00)	0.655 (1.00)	0.121 (1.00)	0.545 (1.00)	0.463 (1.00)	0.124 (1.00)	0.255 (1.00)	0.838 (1.00)
Amp Peak 22(20q13 33)	0 (0%)	131	0.000106 (0.0553)	0.0172 (1.00)	0.737 (1.00)	0.871 (1.00)	0.00475 (1.00)	0.218 (1.00)	0.573 (1.00)	0.141 (1.00)	0.123 (1.00)	0.0305 (1.00)
Amp Peak 23(22q13 2)	0 (0%)	156	3.43e-07 (0.000185)	0.0422 (1.00)	0.904 (1.00)	0.904 (1.00)	0.532 (1.00)	0.748 (1.00)	0.354 (1.00)	0.726 (1.00)	0.578 (1.00)	0.321 (1.00)
Del Peak 9(5q31 3)	0 (0%)	168	0.0769 (1.00)	7.76e-05 (0.0409)	0.602 (1.00)	0.978 (1.00)	0.706 (1.00)	0.488 (1.00)	0.786 (1.00)	0.295 (1.00)	0.214 (1.00)	0.125 (1.00)
Del Peak 10(6q22 31)	0 (0%)	108	1.4e-14 (7.69e-12)	0.136 (1.00)	0.861 (1.00)	0.14 (1.00)	0.00412 (1.00)	0.342 (1.00)	0.487 (1.00)	0.562 (1.00)	0.935 (1.00)	0.771 (1.00)
Del Peak 11(6q25 3)	0 (0%)	98	4.82e-13 (2.64e-10)	0.237 (1.00)	0.535 (1.00)	0.531 (1.00)	0.00446 (1.00)	0.457 (1.00)	0.615 (1.00)	0.895 (1.00)	0.973 (1.00)	0.807 (1.00)
Del Peak 12(6q26)	0 (0%)	101	8.58e-15 (4.72e-12)	0.146 (1.00)	0.61 (1.00)	0.549 (1.00)	0.0047 (1.00)	0.417 (1.00)	0.344 (1.00)	0.642 (1.00)	0.79 (1.00)	0.932 (1.00)
Del Peak 14(9p23)	0 (0%)	85	1.2e-05 (0.0064)	0.0535 (1.00)	0.409 (1.00)	0.782 (1.00)	0.0027 (1.00)	0.0658 (1.00)	0.708 (1.00)	0.247 (1.00)	0.293 (1.00)	0.303 (1.00)
Del Peak 18(10q26 3)	0 (0%)	100	0.00114 (0.585)	0.274 (1.00)	0.677 (1.00)	0.443 (1.00)	1.91e-05 (0.0101)	0.000579 (0.299)	0.764 (1.00)	0.946 (1.00)	0.543 (1.00)	0.808 (1.00)
Del Peak 19(11q23 3)	0 (0%)	122	1.43e-07 (7.76e-05)	0.12 (1.00)	0.989 (1.00)	0.299 (1.00)	0.242 (1.00)	0.657 (1.00)	0.198 (1.00)	0.0827 (1.00)	0.0942 (1.00)	0.216 (1.00)
Del Peak 24(14q32 2)	0 (0%)	176	7.99e-06 (0.0043)	0.799 (1.00)	0.311 (1.00)	0.24 (1.00)	0.00356 (1.00)	0.64 (1.00)	0.699 (1.00)	0.69 (1.00)	0.664 (1.00)	0.478 (1.00)
Amp Peak 1(1p12)	0 (0%)	186	0.00179 (0.91)	0.357 (1.00)	0.488 (1.00)	1 (1.00)	0.118 (1.00)	0.491 (1.00)	0.49 (1.00)	0.56 (1.00)	0.452 (1.00)	0.961 (1.00)
Amp Peak 4(3p13)	0 (0%)	198	0.444 (1.00)	0.696 (1.00)	0.0978 (1.00)	0.0104 (1.00)	0.907 (1.00)	0.681 (1.00)	0.827 (1.00)	0.148 (1.00)	1 (1.00)	0.177 (1.00)
Amp Peak 5(4q12)	0 (0%)	217	0.0263 (1.00)	0.386 (1.00)	0.0894 (1.00)	0.0641 (1.00)	0.469 (1.00)	0.299 (1.00)	0.021 (1.00)	0.013 (1.00)	0.0185 (1.00)	0.00611 (1.00)
Amp Peak 9(6q12)	0 (0%)	207	0.618 (1.00)	0.521 (1.00)	0.839 (1.00)	0.00495 (1.00)	0.0939 (1.00)	0.0757 (1.00)	0.211 (1.00)	0.278 (1.00)	0.817 (1.00)	0.527 (1.00)
Amp Peak 14(9p24 1)	0 (0%)	244	1 (1.00)	0.511 (1.00)	0.72 (1.00)	0.786 (1.00)	0.491 (1.00)	0.491 (1.00)	0.219 (1.00)	0.531 (1.00)	0.0989 (1.00)	0.462 (1.00)
Amp Peak 17(12q14 1)	0 (0%)	221	0.00121 (0.618)	0.564 (1.00)	0.71 (1.00)	0.296 (1.00)	0.121 (1.00)	0.159 (1.00)	0.712 (1.00)	0.397 (1.00)	0.857 (1.00)	0.819 (1.00)
Amp Peak 18(12q15)	0 (0%)	223	0.0152 (1.00)	0.647 (1.00)	0.497 (1.00)	0.391 (1.00)	0.557 (1.00)	0.617 (1.00)	0.89 (1.00)	0.422 (1.00)	0.833 (1.00)	0.943 (1.00)
Amp Peak 19(15q26 2)	0 (0%)	178	0.0441 (1.00)	0.712 (1.00)	0.93 (1.00)	0.534 (1.00)	0.629 (1.00)	0.343 (1.00)	0.753 (1.00)	0.557 (1.00)	0.803 (1.00)	0.673 (1.00)
Amp Peak 20(17q25 3)	0 (0%)	175	0.00327 (1.00)	0.00229 (1.00)	0.0165 (1.00)	0.0318 (1.00)	0.2 (1.00)	0.365 (1.00)	0.302 (1.00)	0.0109 (1.00)	0.0159 (1.00)	0.0451 (1.00)
Amp Peak 21(19p13 2)	0 (0%)	214	0.0554 (1.00)	0.119 (1.00)	0.301 (1.00)	0.702 (1.00)	0.0105 (1.00)	0.00394 (1.00)	0.715 (1.00)	0.0475 (1.00)	0.114 (1.00)	0.0135 (1.00)
Del Peak 1(1p36 31)	0 (0%)	203	0.21 (1.00)	0.000694 (0.357)	0.677 (1.00)	0.135 (1.00)	0.0717 (1.00)	0.0208 (1.00)	0.491 (1.00)	0.468 (1.00)	0.868 (1.00)	0.54 (1.00)
Del Peak 3(2q37 3)	0 (0%)	200	0.49 (1.00)	0.0252 (1.00)	0.0371 (1.00)	0.00703 (1.00)	0.00713 (1.00)	0.0241 (1.00)	0.0309 (1.00)	0.0447 (1.00)	0.112 (1.00)	0.0629 (1.00)
Del Peak 4(3p21 2)	0 (0%)	217	0.8 (1.00)	0.902 (1.00)	0.721 (1.00)	0.756 (1.00)	0.406 (1.00)	0.311 (1.00)	0.554 (1.00)	0.67 (1.00)	0.46 (1.00)	0.759 (1.00)
Del Peak 5(3q23)	0 (0%)	226	0.275 (1.00)	0.0183 (1.00)	0.276 (1.00)	0.404 (1.00)	0.316 (1.00)	0.599 (1.00)	1 (1.00)	0.649 (1.00)	0.928 (1.00)	0.6 (1.00)
Del Peak 6(4q34 3)	0 (0%)	197	0.419 (1.00)	0.091 (1.00)	0.943 (1.00)	0.468 (1.00)	0.0568 (1.00)	0.00942 (1.00)	0.00905 (1.00)	0.00244 (1.00)	0.00213 (1.00)	0.0041 (1.00)
Del Peak 7(5p15 31)	0 (0%)	212	0.268 (1.00)	0.296 (1.00)	0.446 (1.00)	0.449 (1.00)	0.252 (1.00)	0.799 (1.00)	0.601 (1.00)	0.27 (1.00)	0.355 (1.00)	0.465 (1.00)
Del Peak 8(5q11 2)	0 (0%)	194	0.00554 (1.00)	0.109 (1.00)	0.306 (1.00)	0.417 (1.00)	0.719 (1.00)	0.555 (1.00)	0.951 (1.00)	0.406 (1.00)	0.205 (1.00)	0.477 (1.00)
Del Peak 13(8p23 3)	0 (0%)	202	0.518 (1.00)	0.0762 (1.00)	0.192 (1.00)	0.058 (1.00)	0.101 (1.00)	0.749 (1.00)	0.257 (1.00)	0.386 (1.00)	0.238 (1.00)	0.558 (1.00)
Del Peak 20(12p13 31)	0 (0%)	224	0.759 (1.00)	0.252 (1.00)	0.471 (1.00)	0.0454 (1.00)	0.0546 (1.00)	0.527 (1.00)	0.975 (1.00)	0.967 (1.00)	0.952 (1.00)	1 (1.00)
Del Peak 21(12q23 3)	0 (0%)	203	0.0781 (1.00)	0.013 (1.00)	0.791 (1.00)	0.441 (1.00)	0.423 (1.00)	0.547 (1.00)	0.713 (1.00)	0.306 (1.00)	0.534 (1.00)	0.478 (1.00)
Del Peak 22(13q12 11)	0 (0%)	206	0.004 (1.00)	0.266 (1.00)	0.167 (1.00)	0.664 (1.00)	1 (1.00)	0.981 (1.00)	0.166 (1.00)	0.107 (1.00)	0.219 (1.00)	0.543 (1.00)
Del Peak 23(13q34)	0 (0%)	205	0.246 (1.00)	0.00347 (1.00)	0.0674 (1.00)	0.357 (1.00)	0.916 (1.00)	0.279 (1.00)	0.91 (1.00)	0.298 (1.00)	0.801 (1.00)	0.435 (1.00)
Del Peak 25(15q13 3)	0 (0%)	204	0.0473 (1.00)	0.0774 (1.00)	0.133 (1.00)	0.39 (1.00)	0.435 (1.00)	0.183 (1.00)	0.525 (1.00)	0.734 (1.00)	0.504 (1.00)	0.89 (1.00)
Del Peak 26(15q15 1)	0 (0%)	200	0.0459 (1.00)	0.0295 (1.00)	0.383 (1.00)	0.0595 (1.00)	0.661 (1.00)	0.396 (1.00)	0.839 (1.00)	0.693 (1.00)	0.966 (1.00)	1 (1.00)
Del Peak 27(16p13 3)	0 (0%)	218	0.4 (1.00)	0.176 (1.00)	0.00834 (1.00)	0.103 (1.00)	0.165 (1.00)	0.267 (1.00)	0.14 (1.00)	0.308 (1.00)	0.211 (1.00)	0.529 (1.00)
Del Peak 28(16q12 1)	0 (0%)	182	0.286 (1.00)	0.685 (1.00)	0.0151 (1.00)	0.37 (1.00)	0.101 (1.00)	0.206 (1.00)	0.194 (1.00)	0.132 (1.00)	0.238 (1.00)	0.0445 (1.00)
Del Peak 29(16q24 3)	0 (0%)	174	0.00563 (1.00)	0.566 (1.00)	0.0934 (1.00)	0.61 (1.00)	0.0139 (1.00)	0.0551 (1.00)	0.0935 (1.00)	0.0519 (1.00)	0.0889 (1.00)	0.0329 (1.00)
Del Peak 30(17q21 31)	0 (0%)	209	0.913 (1.00)	0.744 (1.00)	0.325 (1.00)	0.773 (1.00)	0.479 (1.00)	0.612 (1.00)	0.804 (1.00)	0.355 (1.00)	0.498 (1.00)	0.386 (1.00)
Del Peak 31(19p13 3)	0 (0%)	190	0.0212 (1.00)	0.621 (1.00)	0.00261 (1.00)	0.0275 (1.00)	0.00838 (1.00)	0.091 (1.00)	0.726 (1.00)	0.272 (1.00)	0.606 (1.00)	0.223 (1.00)
Del Peak 32(22q13 1)	0 (0%)	240	0.371 (1.00)	0.343 (1.00)	0.848 (1.00)	0.904 (1.00)	0.874 (1.00)	0.56 (1.00)	0.135 (1.00)	0.821 (1.00)	0.667 (1.00)	0.869 (1.00)

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

P value = 3.14e-10 (Fisher's exact test), Q value = 1.7e-07

Table S1. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 2(1Q21.3) CNV	67	41	27
AMP PEAK 2(1Q21.3) WILD-TYPE	17	65	50

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 2.22e-10 (Fisher's exact test), Q value = 1.2e-07

Table S2. Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 3(1Q44) CNV	69	45	28
AMP PEAK 3(1Q44) WILD-TYPE	15	61	49

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.27e-09 (Fisher's exact test), Q value = 6.9e-07

Table S3. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 6(5P15.33) CNV	39	11	35
AMP PEAK 6(5P15.33) WILD-TYPE	45	95	42

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(5p15.33)' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.59e-05 (Fisher's exact test), Q value = 0.05

Table S4. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	109	69
AMP PEAK 6(5P15.33) CNV	32	41	8
AMP PEAK 6(5P15.33) WILD-TYPE	50	68	61

Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

P value = 2.8e-05 (Fisher's exact test), Q value = 0.015

Table S5. Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 7(5Q35.3) CNV	15	5	22
AMP PEAK 7(5Q35.3) WILD-TYPE	69	101	55

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000302 (Fisher's exact test), Q value = 0.16

Table S6. Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	98	102
AMP PEAK 7(5Q35.3) CNV	21	13	8
AMP PEAK 7(5Q35.3) WILD-TYPE	46	85	94

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 3.31e-05 (Fisher's exact test), Q value = 0.017

Table S7. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 8(6P25.1) CNV	58	42	51
AMP PEAK 8(6P25.1) WILD-TYPE	26	64	26

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(6p25.1)' versus 'METHLYATION_CNMF'

P value = 0.000379 (Fisher's exact test), Q value = 0.2

Table S8. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	98	102
AMP PEAK 8(6P25.1) CNV	48	60	43
AMP PEAK 8(6P25.1) WILD-TYPE	19	38	59

Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0055

Table S9. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	28	83	149
AMP PEAK 8(6P25.1) CNV	15	30	102
AMP PEAK 8(6P25.1) WILD-TYPE	13	53	47

Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 8(6p25.1)' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.5e-05 (Fisher's exact test), Q value = 0.013

Table S10. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	151	32
AMP PEAK 8(6P25.1) CNV	27	101	19
AMP PEAK 8(6P25.1) WILD-TYPE	50	50	13

Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0062

Table S11. Gene #10: 'Amp Peak 10(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 10(7P22.3) CNV	57	38	48
AMP PEAK 10(7P22.3) WILD-TYPE	27	68	29

Figure S11. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000344 (Fisher's exact test), Q value = 0.18

Table S12. Gene #11: 'Amp Peak 11(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 11(7Q34) CNV	51	49	58
AMP PEAK 11(7Q34) WILD-TYPE	33	57	19

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0082

Table S13. Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 12(8Q11.21) CNV	46	28	43
AMP PEAK 12(8Q11.21) WILD-TYPE	38	78	34

Figure S13. Get High-res Image Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 3.17e-08 (Fisher's exact test), Q value = 1.7e-05

Table S14. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 13(8Q24.21) CNV	50	31	54
AMP PEAK 13(8Q24.21) WILD-TYPE	34	75	23

Figure S14. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 15(11q13.3)' versus 'CN_CNMF'

P value = 7.05e-06 (Fisher's exact test), Q value = 0.0038

Table S15. Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 15(11Q13.3) CNV	8	13	29
AMP PEAK 15(11Q13.3) WILD-TYPE	76	93	48

Figure S15. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 16(11q13.4)' versus 'CN_CNMF'

P value = 3.58e-06 (Fisher's exact test), Q value = 0.0019

Table S16. Gene #16: 'Amp Peak 16(11q13.4)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 16(11Q13.4) CNV	8	10	28
AMP PEAK 16(11Q13.4) WILD-TYPE	76	96	49

Figure S16. Get High-res Image Gene #16: 'Amp Peak 16(11q13.4)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 22(20q13.33)' versus 'CN_CNMF'

P value = 0.000106 (Fisher's exact test), Q value = 0.055

Table S17. Gene #22: 'Amp Peak 22(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 22(20Q13.33) CNV	53	37	46
AMP PEAK 22(20Q13.33) WILD-TYPE	31	69	31

Figure S17. Get High-res Image Gene #22: 'Amp Peak 22(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 23(22q13.2)' versus 'CN_CNMF'

P value = 3.43e-07 (Fisher's exact test), Q value = 0.00019

Table S18. Gene #23: 'Amp Peak 23(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
AMP PEAK 23(22Q13.2) CNV	55	29	27
AMP PEAK 23(22Q13.2) WILD-TYPE	29	77	50

Figure S18. Get High-res Image Gene #23: 'Amp Peak 23(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.000127 (Fisher's exact test), Q value = 0.066

Table S19. Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	98	102
DEL PEAK 2(1P22.1) CNV	30	15	23
DEL PEAK 2(1P22.1) WILD-TYPE	37	83	79

Figure S19. Get High-res Image Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.000117 (Fisher's exact test), Q value = 0.061

Table S20. Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	72	103
DEL PEAK 2(1P22.1) CNV	37	9	22
DEL PEAK 2(1P22.1) WILD-TYPE	54	63	81

Figure S20. Get High-res Image Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 9(5q31.3)' versus 'METHLYATION_CNMF'

P value = 7.76e-05 (Fisher's exact test), Q value = 0.041

Table S21. Gene #32: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	98	102
DEL PEAK 9(5Q31.3) CNV	13	51	35
DEL PEAK 9(5Q31.3) WILD-TYPE	54	47	67

Figure S21. Get High-res Image Gene #32: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 10(6q22.31)' versus 'CN_CNMF'

P value = 1.4e-14 (Fisher's exact test), Q value = 7.7e-12

Table S22. Gene #33: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 10(6Q22.31) CNV	52	37	70
DEL PEAK 10(6Q22.31) WILD-TYPE	32	69	7

Figure S22. Get High-res Image Gene #33: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(6q25.3)' versus 'CN_CNMF'

P value = 4.82e-13 (Fisher's exact test), Q value = 2.6e-10

Table S23. Gene #34: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 11(6Q25.3) CNV	55	43	71
DEL PEAK 11(6Q25.3) WILD-TYPE	29	63	6

Figure S23. Get High-res Image Gene #34: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(6q26)' versus 'CN_CNMF'

P value = 8.58e-15 (Fisher's exact test), Q value = 4.7e-12

Table S24. Gene #35: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 12(6Q26) CNV	56	39	71
DEL PEAK 12(6Q26) WILD-TYPE	28	67	6

Figure S24. Get High-res Image Gene #35: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(9p23)' versus 'CN_CNMF'

P value = 1.2e-05 (Fisher's exact test), Q value = 0.0064

Table S25. Gene #37: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 14(9P23) CNV	63	55	64
DEL PEAK 14(9P23) WILD-TYPE	21	51	13

Figure S25. Get High-res Image Gene #37: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(9p21.3)' versus 'CN_CNMF'

P value = 1.09e-09 (Fisher's exact test), Q value = 5.9e-07

Table S26. Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 15(9P21.3) CNV	70	62	74
DEL PEAK 15(9P21.3) WILD-TYPE	14	44	3

Figure S26. Get High-res Image Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 15(9p21.3)' versus 'MRNASEQ_CNMF'

P value = 0.000114 (Fisher's exact test), Q value = 0.059

Table S27. Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	72	103
DEL PEAK 15(9P21.3) CNV	83	47	76
DEL PEAK 15(9P21.3) WILD-TYPE	8	25	27

Figure S27. Get High-res Image Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 16(10p15.3)' versus 'CN_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.01

Table S28. Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 16(10P15.3) CNV	56	39	50
DEL PEAK 16(10P15.3) WILD-TYPE	28	67	27

Figure S28. Get High-res Image Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 16(10p15.3)' versus 'MRNASEQ_CNMF'

P value = 8.7e-05 (Fisher's exact test), Q value = 0.046

Table S29. Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	72	103
DEL PEAK 16(10P15.3) CNV	66	34	45
DEL PEAK 16(10P15.3) WILD-TYPE	25	38	58

Figure S29. Get High-res Image Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 17(10q23.31)' versus 'CN_CNMF'

P value = 3.27e-05 (Fisher's exact test), Q value = 0.017

Table S30. Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 17(10Q23.31) CNV	64	48	52
DEL PEAK 17(10Q23.31) WILD-TYPE	20	58	25

Figure S30. Get High-res Image Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 8.53e-05 (Fisher's exact test), Q value = 0.045

Table S31. Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	72	103
DEL PEAK 17(10Q23.31) CNV	72	39	53
DEL PEAK 17(10Q23.31) WILD-TYPE	19	33	50

Figure S31. Get High-res Image Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 18(10q26.3)' versus 'MRNASEQ_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.01

Table S32. Gene #41: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	72	103
DEL PEAK 18(10Q26.3) CNV	74	40	53
DEL PEAK 18(10Q26.3) WILD-TYPE	17	32	50

Figure S32. Get High-res Image Gene #41: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 19(11q23.3)' versus 'CN_CNMF'

P value = 1.43e-07 (Fisher's exact test), Q value = 7.8e-05

Table S33. Gene #42: 'Del Peak 19(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 19(11Q23.3) CNV	66	42	37
DEL PEAK 19(11Q23.3) WILD-TYPE	18	64	40

Figure S33. Get High-res Image Gene #42: 'Del Peak 19(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 24(14q32.2)' versus 'CN_CNMF'

P value = 7.99e-06 (Fisher's exact test), Q value = 0.0043

Table S34. Gene #47: 'Del Peak 24(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	106	77
DEL PEAK 24(14Q32.2) CNV	33	19	39
DEL PEAK 24(14Q32.2) WILD-TYPE	51	87	38

Figure S34. Get High-res Image Gene #47: 'Del Peak 24(14q32.2)' versus Molecular Subtype #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 = 267
Number of copy number variation regions = 55
Number of molecular subtypes = 10
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

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] 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] 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)

[3] GISTIC_version2

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