Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes<BR>(All

Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes
(All_Metastatic cohort)

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

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 244 patients, 32 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' 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 19(15q24.3) 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'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 8(5q31.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 9(6q26) 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', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 14(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 15(10q26.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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, 32 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	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 13(10p15 3)	133 (55%)	111	6.73e-07 (0.000268)	0.0123 (1.00)	0.481 (1.00)	0.787 (1.00)	2.76e-06 (0.00109)	0.000289 (0.11)	0.116 (1.00)	0.259 (1.00)
Del Peak 15(10q26 3)	151 (62%)	93	4.59e-07 (0.000184)	0.348 (1.00)	0.4 (1.00)	0.83 (1.00)	3.59e-06 (0.00141)	0.000195 (0.0745)	0.207 (1.00)	0.852 (1.00)
Amp Peak 7(5q35 3)	38 (16%)	206	2.6e-05 (0.0101)	0.000528 (0.199)	0.564 (1.00)	0.342 (1.00)	0.253 (1.00)	0.0985 (1.00)	0.104 (1.00)	0.195 (1.00)
Amp Peak 8(6p25 1)	139 (57%)	105	1.65e-10 (6.73e-08)	0.000692 (0.26)	0.00798 (1.00)	0.542 (1.00)	0.0856 (1.00)	0.00485 (1.00)	0.00153 (0.563)	1.05e-05 (0.00408)
Del Peak 12(9p21 3)	189 (77%)	55	4.59e-09 (1.87e-06)	0.00143 (0.531)	0.749 (1.00)	0.127 (1.00)	0.000146 (0.0563)	0.0102 (1.00)	0.961 (1.00)	0.602 (1.00)
Del Peak 14(10q23 31)	149 (61%)	95	5.89e-08 (2.37e-05)	0.0721 (1.00)	0.214 (1.00)	0.732 (1.00)	0.000165 (0.0632)	0.00158 (0.578)	0.739 (1.00)	0.713 (1.00)
Amp Peak 1(1p12)	73 (30%)	171	0.000382 (0.145)	0.485 (1.00)	0.379 (1.00)	0.404 (1.00)	0.109 (1.00)	0.396 (1.00)	0.72 (1.00)	0.744 (1.00)
Amp Peak 2(1q21 3)	123 (50%)	121	1.14e-08 (4.64e-06)	0.101 (1.00)	0.662 (1.00)	0.303 (1.00)	0.0556 (1.00)	0.788 (1.00)	0.383 (1.00)	0.291 (1.00)
Amp Peak 3(1q44)	130 (53%)	114	1.8e-08 (7.26e-06)	0.0145 (1.00)	0.943 (1.00)	0.95 (1.00)	0.209 (1.00)	0.566 (1.00)	0.153 (1.00)	0.0745 (1.00)
Amp Peak 6(5p15 33)	73 (30%)	171	0.000333 (0.126)	0.366 (1.00)	0.0961 (1.00)	0.603 (1.00)	0.522 (1.00)	0.158 (1.00)	0.0187 (1.00)	0.11 (1.00)
Amp Peak 10(7p22 3)	131 (54%)	113	4.71e-08 (1.9e-05)	0.434 (1.00)	0.65 (1.00)	0.924 (1.00)	0.0979 (1.00)	0.25 (1.00)	0.958 (1.00)	0.468 (1.00)
Amp Peak 11(7q34)	145 (59%)	99	8.16e-09 (3.31e-06)	0.58 (1.00)	0.249 (1.00)	0.546 (1.00)	0.217 (1.00)	0.359 (1.00)	0.343 (1.00)	0.302 (1.00)
Amp Peak 12(8q11 21)	101 (41%)	143	3.28e-06 (0.00129)	0.00931 (1.00)	0.687 (1.00)	0.645 (1.00)	0.0367 (1.00)	0.32 (1.00)	0.35 (1.00)	0.872 (1.00)
Amp Peak 13(8q24 21)	118 (48%)	126	6.12e-07 (0.000245)	0.00788 (1.00)	0.529 (1.00)	0.89 (1.00)	0.0357 (1.00)	0.678 (1.00)	0.476 (1.00)	0.386 (1.00)
Amp Peak 19(15q24 3)	81 (33%)	163	0.000102 (0.0395)	0.657 (1.00)	0.955 (1.00)	0.653 (1.00)	0.474 (1.00)	0.321 (1.00)	0.952 (1.00)	0.387 (1.00)
Amp Peak 20(17q25 3)	87 (36%)	157	6.98e-05 (0.027)	0.00367 (1.00)	0.0204 (1.00)	0.149 (1.00)	0.257 (1.00)	0.233 (1.00)	0.088 (1.00)	0.033 (1.00)
Amp Peak 22(20q13 2)	129 (53%)	115	5.31e-06 (0.00208)	0.0111 (1.00)	0.753 (1.00)	0.993 (1.00)	0.0147 (1.00)	0.315 (1.00)	0.83 (1.00)	0.576 (1.00)
Del Peak 1(1p36 31)	59 (24%)	185	0.00648 (1.00)	0.000106 (0.0409)	0.134 (1.00)	0.419 (1.00)	0.206 (1.00)	0.00631 (1.00)	0.442 (1.00)	0.338 (1.00)
Del Peak 2(1p22 1)	63 (26%)	181	0.0343 (1.00)	0.000333 (0.126)	0.76 (1.00)	0.301 (1.00)	0.00151 (0.56)	0.0525 (1.00)	0.512 (1.00)	0.709 (1.00)
Del Peak 8(5q31 3)	90 (37%)	154	0.224 (1.00)	2.41e-05 (0.00937)	0.125 (1.00)	0.823 (1.00)	0.916 (1.00)	0.751 (1.00)	0.511 (1.00)	0.334 (1.00)
Del Peak 9(6q26)	153 (63%)	91	9.37e-06 (0.00366)	0.0268 (1.00)	0.367 (1.00)	0.782 (1.00)	0.000949 (0.355)	0.726 (1.00)	0.703 (1.00)	0.941 (1.00)
Del Peak 11(9p23)	168 (69%)	76	2.5e-06 (0.00099)	0.0422 (1.00)	0.842 (1.00)	0.555 (1.00)	0.00592 (1.00)	0.0364 (1.00)	0.877 (1.00)	0.398 (1.00)
Del Peak 16(11q23 3)	134 (55%)	110	2.05e-06 (0.000814)	0.0989 (1.00)	0.227 (1.00)	0.464 (1.00)	0.282 (1.00)	0.599 (1.00)	0.145 (1.00)	0.13 (1.00)
Del Peak 21(14q32 2)	83 (34%)	161	1.75e-06 (0.000697)	0.566 (1.00)	0.162 (1.00)	0.419 (1.00)	0.0184 (1.00)	0.662 (1.00)	0.786 (1.00)	0.682 (1.00)
Amp Peak 4(3p13)	64 (26%)	180	0.177 (1.00)	0.455 (1.00)	0.376 (1.00)	0.123 (1.00)	0.821 (1.00)	0.546 (1.00)	1 (1.00)	0.49 (1.00)
Amp Peak 5(4q12)	46 (19%)	198	0.00119 (0.443)	0.417 (1.00)	0.293 (1.00)	0.313 (1.00)	0.816 (1.00)	0.358 (1.00)	0.0688 (1.00)	0.0136 (1.00)
Amp Peak 9(6q12)	56 (23%)	188	0.00288 (1.00)	0.614 (1.00)	0.587 (1.00)	0.427 (1.00)	0.0688 (1.00)	0.428 (1.00)	0.327 (1.00)	0.238 (1.00)
Amp Peak 14(9p24 1)	21 (9%)	223	0.81 (1.00)	0.337 (1.00)	0.711 (1.00)	0.815 (1.00)	0.613 (1.00)	0.56 (1.00)	0.262 (1.00)	0.841 (1.00)
Amp Peak 15(11q13 3)	47 (19%)	197	0.184 (1.00)	0.14 (1.00)	0.733 (1.00)	0.956 (1.00)	0.896 (1.00)	1 (1.00)	0.499 (1.00)	0.326 (1.00)
Amp Peak 16(11q13 4)	44 (18%)	200	0.0807 (1.00)	0.0561 (1.00)	0.968 (1.00)	0.968 (1.00)	0.532 (1.00)	0.602 (1.00)	0.263 (1.00)	0.137 (1.00)
Amp Peak 17(12q14 1)	41 (17%)	203	0.0186 (1.00)	0.298 (1.00)	0.62 (1.00)	0.508 (1.00)	0.4 (1.00)	0.0473 (1.00)	0.905 (1.00)	0.695 (1.00)
Amp Peak 18(12q15)	39 (16%)	205	0.00998 (1.00)	0.927 (1.00)	0.408 (1.00)	0.52 (1.00)	0.716 (1.00)	0.588 (1.00)	0.95 (1.00)	0.615 (1.00)
Amp Peak 21(19p13 2)	50 (20%)	194	0.00153 (0.563)	0.191 (1.00)	0.758 (1.00)	0.33 (1.00)	0.0265 (1.00)	0.0109 (1.00)	0.351 (1.00)	0.09 (1.00)
Amp Peak 23(22q13 2)	102 (42%)	142	0.00669 (1.00)	0.0656 (1.00)	0.745 (1.00)	0.789 (1.00)	0.809 (1.00)	0.884 (1.00)	0.419 (1.00)	0.536 (1.00)
Amp Peak 24(Xq28)	42 (17%)	202	0.0445 (1.00)	0.0111 (1.00)	0.455 (1.00)	0.715 (1.00)	0.203 (1.00)	0.447 (1.00)	0.568 (1.00)	0.226 (1.00)
Del Peak 3(2q37 3)	63 (26%)	181	0.0401 (1.00)	0.0771 (1.00)	0.433 (1.00)	0.246 (1.00)	0.0448 (1.00)	0.0271 (1.00)	0.0717 (1.00)	0.0346 (1.00)
Del Peak 4(3q23)	37 (15%)	207	0.125 (1.00)	0.0143 (1.00)	0.845 (1.00)	0.903 (1.00)	0.576 (1.00)	0.519 (1.00)	0.607 (1.00)	0.692 (1.00)
Del Peak 5(4q22 1)	56 (23%)	188	0.0263 (1.00)	0.304 (1.00)	0.641 (1.00)	0.648 (1.00)	0.000715 (0.268)	0.0031 (1.00)	0.00467 (1.00)	0.00243 (0.887)
Del Peak 6(4q34 3)	67 (27%)	177	0.0194 (1.00)	0.185 (1.00)	0.658 (1.00)	0.769 (1.00)	0.0124 (1.00)	0.00771 (1.00)	0.0142 (1.00)	0.00324 (1.00)
Del Peak 7(5q11 2)	67 (27%)	177	0.411 (1.00)	0.0392 (1.00)	0.0465 (1.00)	0.227 (1.00)	0.687 (1.00)	0.703 (1.00)	0.777 (1.00)	0.524 (1.00)
Del Peak 10(8p23 3)	61 (25%)	183	0.0421 (1.00)	0.0528 (1.00)	0.00918 (1.00)	0.21 (1.00)	0.0775 (1.00)	0.624 (1.00)	0.32 (1.00)	0.336 (1.00)
Del Peak 17(12p13 31)	37 (15%)	207	0.591 (1.00)	0.194 (1.00)	0.363 (1.00)	0.787 (1.00)	0.197 (1.00)	0.481 (1.00)	0.716 (1.00)	0.864 (1.00)
Del Peak 18(12q23 3)	58 (24%)	186	0.12 (1.00)	0.00876 (1.00)	0.589 (1.00)	0.492 (1.00)	0.845 (1.00)	0.353 (1.00)	0.669 (1.00)	0.499 (1.00)
Del Peak 19(12q24 33)	57 (23%)	187	0.0696 (1.00)	0.0128 (1.00)	0.581 (1.00)	0.541 (1.00)	0.766 (1.00)	0.128 (1.00)	0.771 (1.00)	0.587 (1.00)
Del Peak 20(13q34)	58 (24%)	186	0.0941 (1.00)	0.00483 (1.00)	0.078 (1.00)	0.785 (1.00)	0.963 (1.00)	0.215 (1.00)	0.82 (1.00)	0.106 (1.00)
Del Peak 22(15q13 3)	54 (22%)	190	0.00153 (0.563)	0.184 (1.00)	0.393 (1.00)	0.656 (1.00)	0.623 (1.00)	0.218 (1.00)	0.41 (1.00)	0.405 (1.00)
Del Peak 23(15q15 3)	56 (23%)	188	0.00113 (0.42)	0.214 (1.00)	0.382 (1.00)	0.501 (1.00)	0.872 (1.00)	0.615 (1.00)	0.309 (1.00)	0.0819 (1.00)
Del Peak 24(16p13 3)	46 (19%)	198	0.718 (1.00)	0.028 (1.00)	0.199 (1.00)	0.408 (1.00)	0.329 (1.00)	0.681 (1.00)	0.373 (1.00)	0.555 (1.00)
Del Peak 25(16q12 1)	81 (33%)	163	0.217 (1.00)	0.346 (1.00)	0.0151 (1.00)	0.547 (1.00)	0.179 (1.00)	0.348 (1.00)	0.147 (1.00)	0.143 (1.00)
Del Peak 26(16q24 3)	89 (36%)	155	0.269 (1.00)	0.482 (1.00)	0.331 (1.00)	0.828 (1.00)	0.0122 (1.00)	0.18 (1.00)	0.0713 (1.00)	0.0543 (1.00)
Del Peak 27(19p13 3)	71 (29%)	173	0.039 (1.00)	0.471 (1.00)	0.00607 (1.00)	0.0213 (1.00)	0.00451 (1.00)	0.156 (1.00)	0.856 (1.00)	0.401 (1.00)

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

P value = 0.000382 (Fisher's exact test), Q value = 0.14

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	69	95
AMP PEAK 1(1P12) MUTATED	37	18	18
AMP PEAK 1(1P12) WILD-TYPE	43	51	77

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 = 1.14e-08 (Fisher's exact test), Q value = 4.6e-06

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	69	95
AMP PEAK 2(1Q21.3) MUTATED	62	28	33
AMP PEAK 2(1Q21.3) WILD-TYPE	18	41	62

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 = 1.8e-08 (Fisher's exact test), Q value = 7.3e-06

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	69	95
AMP PEAK 3(1Q44) MUTATED	64	29	37
AMP PEAK 3(1Q44) WILD-TYPE	16	40	58

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 = 0.000333 (Fisher's exact test), Q value = 0.13

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	69	95
AMP PEAK 6(5P15.33) MUTATED	33	25	15
AMP PEAK 6(5P15.33) WILD-TYPE	47	44	80

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 = 2.6e-05 (Fisher's exact test), Q value = 0.01

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	69	95
AMP PEAK 7(5Q35.3) MUTATED	23	11	4
AMP PEAK 7(5Q35.3) WILD-TYPE	57	58	91

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 = 0.000528 (Fisher's exact test), Q value = 0.2

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	89	94
AMP PEAK 7(5Q35.3) MUTATED	19	12	7
AMP PEAK 7(5Q35.3) WILD-TYPE	42	77	87

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 = 1.65e-10 (Fisher's exact test), Q value = 6.7e-08

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	69	95
AMP PEAK 8(6P25.1) MUTATED	69	29	41
AMP PEAK 8(6P25.1) WILD-TYPE	11	40	54

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_CHIERARCHICAL'

P value = 1.05e-05 (Fisher's exact test), Q value = 0.0041

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	141	72
AMP PEAK 8(6P25.1) MUTATED	14	97	25
AMP PEAK 8(6P25.1) WILD-TYPE	12	44	47

Figure S8. 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 = 4.71e-08 (Fisher's exact test), Q value = 1.9e-05

Table S9. Gene #10: 'Amp Peak 10(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
AMP PEAK 10(7P22.3) MUTATED	43	55	33
AMP PEAK 10(7P22.3) WILD-TYPE	37	14	62

Figure S9. 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 = 8.16e-09 (Fisher's exact test), Q value = 3.3e-06

Table S10. Gene #11: 'Amp Peak 11(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
AMP PEAK 11(7Q34) MUTATED	40	61	44
AMP PEAK 11(7Q34) WILD-TYPE	40	8	51

Figure S10. 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 = 3.28e-06 (Fisher's exact test), Q value = 0.0013

Table S11. Gene #12: 'Amp Peak 12(8q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
AMP PEAK 12(8Q11.21) MUTATED	37	42	22
AMP PEAK 12(8Q11.21) WILD-TYPE	43	27	73

Figure S11. 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 = 6.12e-07 (Fisher's exact test), Q value = 0.00024

Table S12. Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
AMP PEAK 13(8Q24.21) MUTATED	47	45	26
AMP PEAK 13(8Q24.21) WILD-TYPE	33	24	69

Figure S12. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 19(15q24.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.04

Table S13. Gene #19: 'Amp Peak 19(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
AMP PEAK 19(15Q24.3) MUTATED	23	37	21
AMP PEAK 19(15Q24.3) WILD-TYPE	57	32	74

Figure S13. Get High-res Image Gene #19: 'Amp Peak 19(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 6.98e-05 (Fisher's exact test), Q value = 0.027

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	69	95
AMP PEAK 20(17Q25.3) MUTATED	43	23	21
AMP PEAK 20(17Q25.3) WILD-TYPE	37	46	74

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 = 5.31e-06 (Fisher's exact test), Q value = 0.0021

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	69	95
AMP PEAK 22(20Q13.2) MUTATED	49	48	32
AMP PEAK 22(20Q13.2) WILD-TYPE	31	21	63

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 = 0.000106 (Fisher's exact test), Q value = 0.041

Table S16. Gene #25: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	89	94
DEL PEAK 1(1P36.31) MUTATED	27	19	13
DEL PEAK 1(1P36.31) WILD-TYPE	34	70	81

Figure S16. Get High-res Image Gene #25: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 0.000333 (Fisher's exact test), Q value = 0.13

Table S17. Gene #26: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	89	94
DEL PEAK 2(1P22.1) MUTATED	28	16	19
DEL PEAK 2(1P22.1) WILD-TYPE	33	73	75

Figure S17. Get High-res Image Gene #26: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 8(5q31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.0094

Table S18. Gene #32: 'Del Peak 8(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	61	89	94
DEL PEAK 8(5Q31.3) MUTATED	11	48	31
DEL PEAK 8(5Q31.3) WILD-TYPE	50	41	63

Figure S18. Get High-res Image Gene #32: 'Del Peak 8(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 9(6q26) mutation analysis' versus 'CN_CNMF'

P value = 9.37e-06 (Fisher's exact test), Q value = 0.0037

Table S19. Gene #33: 'Del Peak 9(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 9(6Q26) MUTATED	62	49	42
DEL PEAK 9(6Q26) WILD-TYPE	18	20	53

Figure S19. Get High-res Image Gene #33: 'Del Peak 9(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 2.5e-06 (Fisher's exact test), Q value = 0.00099

Table S20. Gene #35: 'Del Peak 11(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 11(9P23) MUTATED	61	59	48
DEL PEAK 11(9P23) WILD-TYPE	19	10	47

Figure S20. Get High-res Image Gene #35: 'Del Peak 11(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 4.59e-09 (Fisher's exact test), Q value = 1.9e-06

Table S21. Gene #36: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 12(9P21.3) MUTATED	66	67	56
DEL PEAK 12(9P21.3) WILD-TYPE	14	2	39

Figure S21. Get High-res Image Gene #36: '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 = 0.000146 (Fisher's exact test), Q value = 0.056

Table S22. Gene #36: 'Del Peak 12(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 12(9P21.3) MUTATED	73	46	69
DEL PEAK 12(9P21.3) WILD-TYPE	6	24	23

Figure S22. Get High-res Image Gene #36: '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 = 6.73e-07 (Fisher's exact test), Q value = 0.00027

Table S23. Gene #37: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 13(10P15.3) MUTATED	44	54	35
DEL PEAK 13(10P15.3) WILD-TYPE	36	15	60

Figure S23. Get High-res Image Gene #37: '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 = 2.76e-06 (Fisher's exact test), Q value = 0.0011

Table S24. Gene #37: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 13(10P15.3) MUTATED	61	30	40
DEL PEAK 13(10P15.3) WILD-TYPE	18	40	52

Figure S24. Get High-res Image Gene #37: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 0.000289 (Fisher's exact test), Q value = 0.11

Table S25. Gene #37: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	57	122
DEL PEAK 13(10P15.3) MUTATED	30	44	57
DEL PEAK 13(10P15.3) WILD-TYPE	32	13	65

Figure S25. Get High-res Image Gene #37: 'Del Peak 13(10p15.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 5.89e-08 (Fisher's exact test), Q value = 2.4e-05

Table S26. Gene #38: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 14(10Q23.31) MUTATED	47	60	42
DEL PEAK 14(10Q23.31) WILD-TYPE	33	9	53

Figure S26. Get High-res Image Gene #38: '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 = 0.000165 (Fisher's exact test), Q value = 0.063

Table S27. Gene #38: 'Del Peak 14(10q23.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 14(10Q23.31) MUTATED	63	37	48
DEL PEAK 14(10Q23.31) WILD-TYPE	16	33	44

Figure S27. Get High-res Image Gene #38: '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 = 4.59e-07 (Fisher's exact test), Q value = 0.00018

Table S28. Gene #39: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 15(10Q26.3) MUTATED	45	60	46
DEL PEAK 15(10Q26.3) WILD-TYPE	35	9	49

Figure S28. Get High-res Image Gene #39: '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 = 3.59e-06 (Fisher's exact test), Q value = 0.0014

Table S29. Gene #39: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	70	92
DEL PEAK 15(10Q26.3) MUTATED	66	37	46
DEL PEAK 15(10Q26.3) WILD-TYPE	13	33	46

Figure S29. Get High-res Image Gene #39: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

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

P value = 0.000195 (Fisher's exact test), Q value = 0.075

Table S30. Gene #39: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	57	122
DEL PEAK 15(10Q26.3) MUTATED	29	47	73
DEL PEAK 15(10Q26.3) WILD-TYPE	33	10	49

Figure S30. Get High-res Image Gene #39: 'Del Peak 15(10q26.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 2.05e-06 (Fisher's exact test), Q value = 0.00081

Table S31. Gene #40: 'Del Peak 16(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 16(11Q23.3) MUTATED	62	33	39
DEL PEAK 16(11Q23.3) WILD-TYPE	18	36	56

Figure S31. Get High-res Image Gene #40: '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 = 1.75e-06 (Fisher's exact test), Q value = 7e-04

Table S32. Gene #45: 'Del Peak 21(14q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	80	69	95
DEL PEAK 21(14Q32.2) MUTATED	27	39	17
DEL PEAK 21(14Q32.2) WILD-TYPE	53	30	78

Figure S32. Get High-res Image Gene #45: '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-All_Metastatic.transferedmergedcluster.txt
Number of patients = 244
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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